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Wyszukujesz frazę "molecular dynamics" wg kryterium: Temat


Wyświetlanie 1-100 z 100
Tytuł:
Molecular Dynamics Study of Vibrational Nonequilibrium in Detonation of Polyatomic Liquids
Autorzy:
Smirnov, A. L.
Dremin, A. N.
Powiązania:
https://bibliotekanauki.pl/articles/358863.pdf
Data publikacji:
2008
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Przemysłu Organicznego
Tematy:
molecular dynamics
detonation
Opis:
Energy transfer mechanisms to internal molecular degrees of freedom in shock and detonation waves in polyatomic liquids are investigated. The proposed approach uses a new version of the method of nonequilibrium molecular dynamics based on the simplest model potential energy surfaces of reacting polyatomic molecules. The main feature is adaptation of some results and approaches of gas theory to liquids. It is shown that vibrational nonequilibrium is produced by shock compression and influences on chemical reactions. So, the structure of shock and detonation waves depends strongly on the peculiarities of vibrational spectra and the structure of normal modes of compounds. Numerical simulations have been carried out for steady state detonation waves and processes of initiation of detonation by shock waves or by local heating. The results demonstrate different shock wave chemistry for substances of almost identical behaviour at static conditions.
Źródło:
Central European Journal of Energetic Materials; 2008, 5, 1; 63-74
1733-7178
Pojawia się w:
Central European Journal of Energetic Materials
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Modelling of the static and dynamic properties of tho-type silicates
Autorzy:
Cauchi, R.
Grima, J. N.
Powiązania:
https://bibliotekanauki.pl/articles/1954447.pdf
Data publikacji:
2014
Wydawca:
Politechnika Gdańska
Tematy:
auxetics
zeolites
thomsonite
molecular dynamics
Opis:
Auxetic materials are materials exhibiting a negative Poisson’s ratio in one of their planes. This phenomenon has been studied in various materials. Zeolites are crystalline substances whose structure is characterised by the framework of linked tetrahedra, each consisting of four oxygen atoms surrounding a cation. The resulting interstitial spaces make them efficient for use as adsorbents and molecular sieves, and many studies have been focused on this aspect. Some of these zeolites may exhibit auxeticity at least in one of their planes. THO (and similar systems, such as NAT and EDI) together with the all-silica equivalent of these have been studied extensively via static simulations for their negative Poisson’s ratio in the (001) plane. In this paper a study of the all-silica equivalent of THO has been carried out via both static and dynamic simulations using the same force-field, where the system was subjected to stress along the x direction. The hypothesised semi-rigid mechanism of deformation, proposed by Grima et al. was then projected over this framework. The results obtained confirmed auxeticity along this plane by means of the COMPASS force-field, in both static and dynamic studies and compared well with the proposed mechanism of semi-rigid rotating polygons. It also showed that as the Young’s modulus of this mechanism increases other mechanisms of deformation increase in importance.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 1; 5-65
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A method of integration of molecular dynamics and continuum mechanics for solids
Autorzy:
Kaczmarek, J.
Powiązania:
https://bibliotekanauki.pl/articles/1963003.pdf
Data publikacji:
2002
Wydawca:
Politechnika Gdańska
Tematy:
continuum mechanics
molecular dynamics
multiscale modelling
Opis:
In this paper a formal system called collection of dynamical systems with dimensional reduction is considered. This is a multiscale method of mathematical description which allows to consider molecular dynamics and continuum mechanics within one theoretical framework. Transition between molecular dynamics and continuum mechanics is realized by means of the dimensional reduction procedure. In order to realize such a procedure the formulation of continuum mechanics is modified. This modification consists in incorporation scale of averaging for properties of processes considered during modelling into this formulation. As a result we introduce finite-dimensional fields on continuum only. All fundamental terms of continuum mechanics are now joined with an elementary dynamical system. In such a case continuum mechanics can be obtained by means of the dimensional reduction procedure applied to the elementary dynamical system. A numerical example of vibrating chain of material points is realized in order to show how in practice the dimensional reduction can be carried out. In this example decomposition of processes into slowly and quickly varying parts is accomplished. To this end a finite element representation of averaged fields is applied. Solutions of equations of the elementary dynamical system and the dimensionally reduced dynamical system are compared.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2002, 6, 2; 253-271
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Stability of finite-size argon thin film coating single wall carbon nanotube
Autorzy:
Kośmider, M.
Dendzik, Z.
Żurek, S.
Górny, K.
Powiązania:
https://bibliotekanauki.pl/articles/1964139.pdf
Data publikacji:
2009
Wydawca:
Politechnika Gdańska
Tematy:
nanotube
molecular dynamics
cluster
thin film
Opis:
The structure and the dynamics of the argon thin film coating (15,4) and (12,12) carbon nanotubes have been studied in a series of molecular dynamic simulations. In the studied temperature regime, the argon atoms in the thin film were well localized. Structural changes and diffusion process inside the argon layers were not been observed. The influence of the chirality and the radius of the nanotube to the cluster properties is also reported.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2009, 13, 3; 187-197
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Synergic Effect of sodium oleate (NaOL) and benzohydroxamic acid (BHA) on flotation of wolframite
Autorzy:
Bu, H.
Cao, M.
Gao, Y.
Huang, H.
Powiązania:
https://bibliotekanauki.pl/articles/110377.pdf
Data publikacji:
2017
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
wolframit
mixed collector
molecular dynamics
synergic effect
Opis:
In this work, two collectors sodium oleate (NaOL) and benzohydroxamic acid (BHA) were used to study the synergic effect in wolframite flotation. The flotation behaviour of these collectors was investigated at various NaOL:BHA ratios. Results show that the mixtures of NaOL with BHA of different ratios result in large improvements in the recovery of wolframite and the 9:1 NaOL:BHA ratio of collector mixture produced the highest wolframite recovery. The amount of NaOL and BHA adsorbed on wolframite was measured for these various reagent mixtures. Compared with pure NaOL, the addition of a certain proportion of BHA is beneficial for NaOL adsorption. Molecular dynamics simulations indicate the formation of HOL–HA (oleic acid–benzohydroxamic acid) complex can take place spontaneously in NaOL–BHA system. Additionally, HOL–HA complex interact with the huebnerite (MnWO4) surface more easily than NaOL–HOL (the highest surface active composition in sodium oleate) and the addition of BHA enable the H of carboxyl group in HOL to generate hydrogen bonds with O atoms of huebnerite surface, resulting in a stronger affinity of mixed surfactants. These results reveal that in a binary NaOL–BHA system, the BHA can encourage greater adsorption of the NaOL.
Źródło:
Physicochemical Problems of Mineral Processing; 2017, 53, 1; 82-93
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Study of icosahedral clusters in close-packed simple liquids
Autorzy:
Kozub, A.
Powiązania:
https://bibliotekanauki.pl/articles/1933986.pdf
Data publikacji:
2012
Wydawca:
Politechnika Gdańska
Tematy:
liquid metals
icosahedral clusters
structure
molecular dynamics
Opis:
The local structure of liquid copper was determined using Steinhardt order parameters, with particular attention paid to icosahedral clusters. The positions of atoms were obtained from three sets of molecular dynamics simulations, with the forces obtained from: the Sutton-Chen (SC) potential, the Naval Research Laboratory total energy tight-binding (NRL-TB) method and the divide-and-conquer learn-on-the-fly (DCLOTF) method, respectively. A broad range of local geometries appeared, which is a typical result for close-packed liquids. Among them a number of icosahedral clusters were detected. The highest density of icosahedral clusters was obtained at the temperature of 1000K for the NRL-TB and DCLOTF simulations and 1200K for the SC simulations. I propose various means of analysing the icosahedral clusters formed in liquid copper. The average number of the clusters, their lifetime and correlations between them at various temperatures were studied as a function of the approach used to generate the trajectories. Finally, I studied the formation and decay of icosahedral clusters.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2012, 16, 1-2; 75-96
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Statistical properties of a polymer chain in the environment with low concentration of nanoparticles
Autorzy:
A. Tsehay, Dessalegne
Luo, Meng-Bo
Powiązania:
https://bibliotekanauki.pl/articles/1050809.pdf
Data publikacji:
2018-05
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
diffusion
conformation
polymer chain
nanoparticles
molecular dynamics
Opis:
We have investigated the statistical properties of polymer in the environment with low concentration of nanoparticles by using large-scale molecular dynamics simulations. The scaling law for the mean square radius of gyration was examined and simulation results for the polymer lengths 64≤N≤144 yielding a reasonably accurate value of the Flory exponent ν=0.58 at weak polymer-nanoparticle interaction ε_{PN}. Within the same range of N, the mean asphericity of the chain is independent of N. We found that the polymer behaves like a self-avoiding walk chain at small ε_{PN} and a compact sphere at large ε_{PN}. The results are attributed to the increase in the contact between polymer and nanoparticles with increasing ε_{PN}. Normal diffusions of polymer are always observed at whatever ε_{PN} and size and concentration of nanoparticles. Our result shows that the normal diffusion behavior of polymer is independent of polymer's state even though there is a phase transition from a desorbed polymer phase at small ε_{PN} to an adsorbed polymer phase at large ε_{PN}.
Źródło:
Acta Physica Polonica A; 2018, 133, 5; 1274-1280
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Water film structure during rupture as revealed by MDS image analysis
Autorzy:
Truong, N. T.
Dang, L. X.
Lin, C.-L.
Wang, X.
Miller, J. D.
Powiązania:
https://bibliotekanauki.pl/articles/110251.pdf
Data publikacji:
2018
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
image processing
molecular dynamics simulation
film stability
molecular porosity
Opis:
The structure of thin water films during the rupture process was investigated by a new approach, which combines molecular dynamics simulation (MDS) with image processing analysis. The analysis procedure was developed to convert MDS trajectories to readable 3D images. The water films were studied at different thicknesses by MDS to determine the critical thickness at which the film ruptures. The potential energy of each specific film thickness during the simulation time was analyzed, and the results showed that the potential energy of stable films remained unchanged while the potential energy kept decreasing for films which ruptured during the simulation time. By applying the new procedure, the molecular porosity, which is defined as the void fraction between the volume of molecular pores in the water film and the total volume of the water film, was calculated. The results of molecular porosity for different film thicknesses during the simulation time suggested a critical molecular porosity as 49%. In other words, stable films have a molecular porosity of less than 49%. If a water film has a molecular porosity greater than 49%, rupture occurs during the simulation.
Źródło:
Physicochemical Problems of Mineral Processing; 2018, 54, 4; 1060-1069
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Effect of antisense peptide binding on the dimerization of human cystatin C - gel electrophoresis and molecular modeling studies.
Autorzy:
Stachowiak, Krystyna
Rodziewicz-Motowidło, Sylwia
Sosnowska, Renata
Kasprzykowski, Franciszek
Łankiewicz, Leszek
Grubb, Anders
Grzonka, Zbigniew
Powiązania:
https://bibliotekanauki.pl/articles/1043334.pdf
Data publikacji:
2004
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
dimerization
antisense peptides
human cystatin C
molecular dynamics
Opis:
Human cystatin C (HCC) shows a tendency to dimerize. This process is particularly easy in the case of the L68Q HCC mutant and might lead to formation of amyloid deposits in brain arteries of young adults. Our purpose was to find ligands of monomeric HCC that can prevent its dimerization. Eleven antisense peptide ligands of monomeric HCC were designed and synthesized. The influence of these ligands on HCC dimerization was studied using gel electrophoresis and molecular modeling methods. The results suggest that all the designed peptides interact with monomeric HCC facilitating its dimerization rather than preventing it.
Źródło:
Acta Biochimica Polonica; 2004, 51, 1; 153-160
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Influence of step errors (truncation errors) on results of molecular dynamics simulations
Autorzy:
Litniewski, M.
Powiązania:
https://bibliotekanauki.pl/articles/1986922.pdf
Data publikacji:
2002
Wydawca:
Politechnika Gdańska
Tematy:
error
molecular dynamics
symplectic
Verlet
Beeman
Cowell-Numerov
Opis:
Step errors (local errors, called also truncation errors) of the algorithms used in molecular dynamics simulations may result in non-physical correlations between particle velocities, as well as in errors of thermodynamic properties of simulated systems (energy, pressure). The simulations of the Lennard-Jones liquid showed, that the influence is especially high for the Verlet velocity algorithm. Beeman's technique decreases the correlations between the velocities, but at high densities the values of the errors of general averages are close to that of the Verlet method. The influence of step errors can be decreased by about two orders of magnitude by applying the Cowell-Numerov 4-th order implicit method (equivalent to the Gear 4-th order method treated as an implicit one). The method is very stable (more stable than the Verlet one), and can be highly optimized by restricting iteration to the closest neighbors of a given particle. As a result, the method becomes more efficient than the higher order explicit symplectic methods.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2002, 6, 3; 461-468
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A molecular dynamics study of the influence of chemical reduction on the structure of amorphous Germania
Autorzy:
Witkowska, A.
Murawski, L.
Bergmański, G.
Powiązania:
https://bibliotekanauki.pl/articles/1963001.pdf
Data publikacji:
2002
Wydawca:
Politechnika Gdańska
Tematy:
oxide glasses
hydrogen reduction
molecular dynamics
structural modelling
Opis:
The contribution is dedicated to the molecular dynamics (MD) study of the structure of reduced germania glass of composition 1Ge 1GeO2. The work is inspired by a recent report on the formation of Ge clusters in hydrogen reduced germanate glasses containing oxides of heavy metals. The MD simulations have been performed in the microcanonical (NVE) ensemble, using a simple two-body Born-Mayer-Huggins interaction potential. A tendency of germanium atoms to agglomeration into clusters, observed in the present calculations, is compared with an analogous tendency of Bi and Pb atoms, observed previously in the xBi (1-x)GeO2 and xPb (1-x)GeO2 systems. The differences in the short and medium-range order in GeO2 system between the 1Ge 1GeO2 and GeO2 glasses are discussed.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2002, 6, 2; 273-281
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The effect of the Glu342Lys mutation in α1-antitrypsin on its structure, studied by molecular modelling methods.
Autorzy:
Jezierski, Grzegorz
Pasenkiewicz-Gierula, Marta
Powiązania:
https://bibliotekanauki.pl/articles/1044164.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
serpins
protein structure
energy minimisation
molecular dynamics simulation
Opis:
The structure of native α1-antitrypsin, the most abundant protease inhibitor in human plasma, is characterised primarily by a reactive loop containing the centre of proteinase inhibition, and a β-sheet composed of five strands. Mobility of the reactive loop is confined as a result of electrostatic interactions between side chains of Glu342 and Lys290, both located at the junction of the reactive loop and the β structure. The most common mutation in the protein, resulting in its inactivation, is Glu342→Lys, named the Z mutation. The main goal of this work was to investigate the influence of the Z mutation on the structure of α1-antitrypsin. Commonly used molecular modelling methods have been applied in a comparative study of two protein models: the wild type and the Z mutant. The results indicate that the Z mutation introduces local instabilities in the region of the reactive loop. Moreover, even parts of the protein located far apart from the mutation region are affected. The Z mutation causes a relative change in the total energy of about 3%. Relatively small root mean square differences between the optimised structures of the wild type and the Z mutant, together with detailed analysis of 'conformational searching' process, lead to the hypothesis that the Z mutation principally induces a change in the dynamics of α1-antitrypsin.
Źródło:
Acta Biochimica Polonica; 2001, 48, 1; 65-75
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A Fluorescence, 1H NMR spectroscopy and molecular dynamics study of the influence of rotamer population on fluorescence decay of tyrosine, phenylalanine and their derivatives
Autorzy:
Ganzynkowicz, R.
Liwo, A.
Wiczk, W.
Powiązania:
https://bibliotekanauki.pl/articles/1965825.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
tyrosine
phenylalanine
rotamers
fluorescence
molecular dynamics
NMR spectroscopy
Opis:
Molecular dynamics simulations were carried out on tyrosine and phenylalanine and their derivatives with various terminal groups to determine the populations of side-chain rotamers. The obtained populations were compared with those calculated from fluorescence-decay lifetime distributions and NMR studies. It was found that theoretically calculated populations do not match the experimental ones, which suggests that the static rotamer model is inadequate to explain the dynamics of tyrosine and phenylalanine side chain in fluorescence and NMR experiments.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 3; 311-316
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Stability of air nucleus in liquid water and cavitation inception on marine engineering
Autorzy:
Fu, Q.
Chen, M.
Wang, X.
Zhu, R.
Zhang, G.
Powiązania:
https://bibliotekanauki.pl/articles/260137.pdf
Data publikacji:
2018
Wydawca:
Politechnika Gdańska. Wydział Inżynierii Mechanicznej i Okrętownictwa
Tematy:
air nuclei
water
molecular dynamics
stability
surface tension
Opis:
The micro air nucleus widely distributed in the ocean is a necessary condition for the cavitation of hydraulic machinery in seawater. In order to study the stability of air nucleus in seawater and cavitation inception, the computational domain of water molecules with air nucleus was studied using the method of molecular dynamics simulation, and the transient characteristics of air nucleus in liquid water were obtained. The key factors influencing nuclei stability were analyzed. The results showed that air nucleus with a certain mass could maintain the dynamic equilibrium in liquid water. The internal density of air nuclei had a critical value that allowed the nuclei to stably exist in water. The air nuclei mass was the decisive factor in its equilibrium volume in water, and the two were positively correlated. The internal density of air nuclei was negatively correlated with the nuclei radius when the nuclei was stable in water. Liquid surface tension was an important factor affecting the stability of the air nuclei. The larger the initial radius of nuclei, the smaller the water pressure, and the more likely the cavitation occurs.
Źródło:
Polish Maritime Research; 2018, S 3; 111-119
1233-2585
Pojawia się w:
Polish Maritime Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Computational repurposing of FDA-approved drugs against specific mastitis-causing pathogens
Obliczeniowa zmiana przeznaczenia leków zatwierdzonych przez FDA przeciwko specyficznym patogenom odpowiedzialnym za mastitis
Autorzy:
Ghafoor, N.A.
Sitkowska, B.
Powiązania:
https://bibliotekanauki.pl/articles/2599141.pdf
Data publikacji:
2021
Wydawca:
Zachodniopomorski Uniwersytet Technologiczny w Szczecinie. Wydawnictwo Uczelniane ZUT w Szczecinie
Tematy:
mastitis
cow milk
Drospirenone
drug repurposing
molecular dynamics
Źródło:
Acta Scientiarum Polonorum. Zootechnica; 2021, 20, 4; 5-13
1644-0714
Pojawia się w:
Acta Scientiarum Polonorum. Zootechnica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Comparison of Wear Resistance in Polycrystalline and Monocrystalline Iron
Autorzy:
Liu, Zhiming
Zhang, Qiang
Liu, Fangying
Zhang, Hezhe
Powiązania:
https://bibliotekanauki.pl/articles/2203723.pdf
Data publikacji:
2023
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
molecular dynamics
polycrystalline
centro symmetric analysis
abrasive wear
Opis:
In the present research, we used molecular dynamics simulation to determine the effect of cutting parameters on micro-grain boundary structures and Burgers vector distribution in single crystal iron and polycrystalline iron materials. The result showed that the destruction of the lattice in polycrystalline iron caused by the cutting tool was restricted to the contact surface area. In addition, in the precision machining process, a higher refining grain was observed on the iron surface. During the cutting process of single crystal iron, large-scale slip occurred along the <111> crystal direction on the {110} crystal plane. And the slip presented an annular shape.
Źródło:
Archives of Metallurgy and Materials; 2023, 68, 1; 15--20
1733-3490
Pojawia się w:
Archives of Metallurgy and Materials
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Analysis of pressure behavior in a temperature controlled molecular dynamic flow
Autorzy:
Najafi, H. R.
Karimian, S. M. H.
Powiązania:
https://bibliotekanauki.pl/articles/280901.pdf
Data publikacji:
2016
Wydawca:
Polskie Towarzystwo Mechaniki Teoretycznej i Stosowanej
Tematy:
nanofluid
molecular dynamics
pressure
bin size
sampling
periodic flow
Opis:
Thermo-fluid properties are required for numerical modeling of nano/micro devices. These properties are mostly obtained from results of molecular dynamics (MD) simulations. Therefore, efforts have been put in developing methods for numerical evaluation of fluid properties, such as pressure. In this paper, the pressure behavior in a controllable nanochannel flow is investigated. The nanoflow field is created by imposing a gradient of a macroscopic property such as temperature. Details of the pressure calculation method in a molecular system and its sensitivity to the approximations made are described first. The effect of temperature rise in a uniform flow on the pressure field is studied next. Then, in the flow under a fixed mean velocity condition, the effect of temperature gradient as a controllable property on the pressure field of nanoflow is studied. Velocity, pressure and molecular density of nanoflows with various temperature gradients and different temperature levels are investigated as well. It has been found that the temperature level at which the temperature gradient is imposed, is important. A fixed temperature gradient will not always lead to the same pressure gradient at different temperature levels. Furthermore, quite interestingly, it is observed that at a fixed temperature gradient, with the variation of mean velocity the pressure field also varies.
Źródło:
Journal of Theoretical and Applied Mechanics; 2016, 54, 3; 881-892
1429-2955
Pojawia się w:
Journal of Theoretical and Applied Mechanics
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Free energy of helix propagation in short polyalanine chains determined from peptide growth simulations of La3+-binding model peptides. Comparison with experimental data
Autorzy:
Maciejczyk, Maciej
Hermans, Jan
Bierzyński, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1041277.pdf
Data publikacji:
2006
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
thermodynamics
peptide
helix-coil equilibrium
thermodynamic integration
molecular dynamics
Opis:
Molecular dynamics (MD) is, at present, a unique tool making it possible to study, at the atomic level, conformational transitions in peptides and proteins. Nevertheless, because MD calculations are always based on a more or less approximate physical model, using a set of approximate parameters, their reliability must be tested by comparison with experimental data. Unfortunately, it is very difficult to find a peptide system in which conformational transitions can be studied both experimentally and using MD simulations so that a direct comparison of the results obtained in both ways could be made. Such a system, containing a rigid α-helix nucleus stabilized by La3+ coordination to a 12-residue sequence taken from an EF-hand protein has recently been used to determine experimentally the helix propagation parameters in very short polyalanine segments (Goch et al. (2003) Biochemistry 42: 6840-6847). The same parameters were calculated here for the same peptide system using the peptide growth simulation method with, alternatively, charmm 22 and cedar potential energy functions. The calculated free energies of the helix-coil transition are about two times too large for cedar and even three times too large for charmm 22, as compared with the experimental values. We suggest that these discrepancies have their origin in the incorrect representation of unfolded peptide backbone in solution by the molecular mechanics force fields.
Źródło:
Acta Biochimica Polonica; 2006, 53, 1; 121-130
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A new program package for structural analysis of computer simulated solids
Autorzy:
Bergmański, G.
Rybicki, J.
Mancini, G.
Powiązania:
https://bibliotekanauki.pl/articles/1954546.pdf
Data publikacji:
2000
Wydawca:
Politechnika Gdańska
Tematy:
ring analysis
structure of matter
molecular dynamics
computer modelling
Opis:
The opportunity to gain detailed information on representative set of rings and chains of atoms is of great importance in the analysis of medium-range order in the computer simulated structures of solids. A new program package (ANELLI) for ring and chain analysis of computer simulated atomic structures is presented. The paper includes detailed description of input and output files. The package presentation is followed by exemplary results obtained using our programs.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2000, 4, 4; 555-573
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A new program package for structural analysis of computer simulated solids
Autorzy:
Bergmański, G.
Rybicki, J.
Mancini, G.
Powiązania:
https://bibliotekanauki.pl/articles/1954549.pdf
Data publikacji:
2000
Wydawca:
Politechnika Gdańska
Tematy:
ring analysis
structure of matter
molecular dynamics
computer modelling
Opis:
The opportunity to gain detailed information on representative set of rings and chains of atoms is of great importance in the analysis of medium-range order in the computer simulated structures of solids. A new program package (ANELLI) for ring and chain analysis of computer simulated atomic structures is presented. The paper includes detailed description of input and output files. The package presentation is followed by exemplary results obtained using our programs.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2000, 4, 4; 555-573
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Polymer Reinforced DNAN/RDX Energetic Composites: Interfacial Interactions and Mechanical Properties
Autorzy:
Qian, W.
Chen, X.
Luo, G.
Powiązania:
https://bibliotekanauki.pl/articles/358170.pdf
Data publikacji:
2017
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Przemysłu Organicznego
Tematy:
energetic composites
dinitroanisole
molecular dynamics
interfacial interactions
mechanical properties
Opis:
2,4-Dinitroanisole (DNAN) has excellent properties as a replacement for 1,3,5-trinitrotoluene (TNT) in melt-cast explosives, and the polymeric modifier used is critical to the mechanical modification of the DNAN/RDX energetic composite. In our research, the typical polymeric modifier acrolein-pentaerythritol resin (APER) was successfully added experimentally to the DNAN/RDX system, and the effects of interfacial interactions on the mechanical properties of these polymers in reinforcing the DNAN/RDX energetic composites were investigated by molecular dynamics simulations, scanning electron microscopy (SEM) and mechanical testing. The results showed that strong attractive interactions exist between the polymer and the explosives, wherein van der Waals forces were found to play the main role. The morphological micro-images also showed tight binding between the polymer/explosive interfaces, which supported the calculated strong interfacial interactions. The mechanical tests confirmed that adding the polymers can obviously reinforce the mechanical strength and toughness of DNAN/RDX systems. The above observations revealed that the cooperative effects of the APER polymer can help to reinforce the interfacial interactions and mechanical properties of DNAN/RDX composites, which is of importance in the formulation and mechanical evaluation of advanced energetic composites.
Źródło:
Central European Journal of Energetic Materials; 2017, 14, 3; 726-741
1733-7178
Pojawia się w:
Central European Journal of Energetic Materials
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Flotation and molecular dynamics simulation of muscovite with mixed anionic/cationic collectors
Autorzy:
Bai, Yang
Li, Caixia
An, Hongyun
Wang, Guoliang
Zhao, Xin
Zhang, Jinqi
Powiązania:
https://bibliotekanauki.pl/articles/110125.pdf
Data publikacji:
2020
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
muscovite
mixed anionic/cationic collectors
flotation
molecular dynamics simulation
Opis:
In this study, three kinds of anionic collectors (sodium oleate (NaOl), sodium dodecyl sulfonate (SDS) and naphthenic acid (NA)) were used in combination with dodecylamine (DDA) to investigate the flotation behavior of muscovite under the action of different mixed anionic/cationic collectors, and their mechanisms for adsorption on the muscovite (001) Surface were clarified using molecular dynamics simulations. The flotation results indicated that different mixed anionic/cationic collectors could improve the recovery of muscovite to varying degrees, but the optimum molar ratio of anionic collectors to DDA and the optimum mixed collector dosage were different. Molecular dynamics simulations showed that the mixed anionic/cationic collectors could significantly increase the hydrophobicity of the muscovite, as evidenced by the decrease in the calculated water molecule density on the muscovite surface and the diffusion coefficient of water molecules at the solid/liquid interface. The interaction between the amino group and the polar group of anionic collectors reduced the electrostatic repulsion between DDA cations and theoretically increased the adsorption capacity of the mixed anionic/cationic collectors on the muscovite surface. Moreover, DDA/NA and DDA/NaOl could improve the calculated carbon atom density on the muscovite surface, which enhanced the hydrophobic association between nonpolar carbon chains, thus further achieving an enhanced flotation performance.
Źródło:
Physicochemical Problems of Mineral Processing; 2020, 56, 2; 313-324
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular dynamics study of the fracture of single layer buckled silicon monosulfide and germanium selenide
Autorzy:
Le, M.-Q
Powiązania:
https://bibliotekanauki.pl/articles/38629974.pdf
Data publikacji:
2022
Wydawca:
Instytut Podstawowych Problemów Techniki PAN
Tematy:
2D materials
fracture
molecular dynamics simulation
mechanical properties
Opis:
Molecular dynamics simulations were conducted with the Stillinger–Weber potential at room temperature to study the mechanical properties and find the mode-I critical stress intensity factor of buckled two-dimensional (2D) hexagonal silicon mono-sulfide (SiS) and germanium selenide (GeSe) sheets. Uniaxial tensile tests were simulated for pristine and pre-cracked sheets. 2D Young’s modulus of SiS and GeSe are estimated at 38.3 and 26.0 N/m, respectively. Their 2D fracture strength is about 3.1–3.5 N/m. By using the initial crack length with the corresponding fracture stress, their mode-I critical stress intensity factor is estimated in the range from 0.19 through 0.22 MPapm. These values differ within 5% from those obtained by the surface energy and are very small compared to the reported fracture toughness of single-crystalline monolayer graphene.
Źródło:
Archives of Mechanics; 2022, 74, 1; 3-12
0373-2029
Pojawia się w:
Archives of Mechanics
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
2D simulations of liquid percolation through model porous media: preliminary MD and DPD results
Autorzy:
Rychcik, M.
Bośko, J.
Rybicki, J.
Alda, W.
Dzwinel, W.
Mancini, G.
Fioretti, L.
Powiązania:
https://bibliotekanauki.pl/articles/1964080.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
2D flow simulations
particle methods
molecular dynamics
dissipative particle dynamics method
Opis:
In the paper we make a short overview of computer models based on particle approach, which can be suitable for the simulation of fluid flow through porous media. We concentrate on Molecular Dynamics (MD) and Dissipative Particle Dynamics (DPD) methods. We describe main features of our simulation programs, and present and discuss preliminary results of MD and DPD simulations of 2D fluid flow through a simple model rigid porous media. The paper aims at the evaluation of the applicability of MD and DPD methods for simulations of liquid flows in media of complicated geometry.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 1; 85-97
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Targets for majority of drugs: G protein-coupled receptors - their structure and interaction with bioligands
Autorzy:
Ciarkowski, J.
Czaplewski, C.
Pasenkiewicz-Gierula, M.
Powiązania:
https://bibliotekanauki.pl/articles/1953953.pdf
Data publikacji:
1998
Wydawca:
Politechnika Gdańska
Tematy:
G protein-coupled receptor
molecular modelling
GPCR/bioligand interaction
molecular dynamics
membrane
Opis:
G protein-coupled receptors (GPCRs) are the most frequent targets for many drugs. They form the largest superfamily of integral membrane proteins, of which more than 1000 members have the following common features: (i) All GPCRs form 7 hydrophobic a-helices of length ~38A (25 amino acids, 7 turns) along a single chain. The consecutive helices alternatively cross the membrane, starting from the extracellular side, so that they form a heptahelical transmembrane domain interwoven with 6 loops, of which the even ones plus the N-terminus create the receptor's extracellular domain while the odd ones plus the C-terminus form its intracellular domain. (ii) All GPCRs are stimulated by diverse extracellular (primary) signals. (iii) Stimulated GPCRs convey the primary signals via their transmembrane and intracellular domains to the cytosolic peripheral heterotrimeric GTP-binding proteins (G proteins), mediating the signal's further transduction to various cellular second messenger systems. A current status of structural studies on GPCRs, consisting of low ~7.5A resolution experimental structures and supplementary molecular modeling, is outlined. Subsequently, some results of authors' own work on studying essential interactions of the V2 vasopressin renal receptor (V2R) with its agonist [Arg8]Vasopressin (AVP) and selected antagonists are presented, as well as their possible impact on the biological signal transduction is discussed. Finally, perspectives for future developments are sketched.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 4; 583-599
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Modelling drug-receptor interactions in an average binding site for NK2
Autorzy:
Alagona, G.
Ghio, C.
Monti, S.
Powiązania:
https://bibliotekanauki.pl/articles/1953954.pdf
Data publikacji:
1998
Wydawca:
Politechnika Gdańska
Tematy:
receptor modelling
docking
non covalent interactions
molecular mechanics
molecular dynamics
substituent effects
Opis:
A tentative procedure applied to the search for a new antagonist of neurokinin A (NKA) is presented. In parallel a tentative 3-D model of the NK2 receptor was created, using bacteriorhodopsin (BRD) as a template. The residue substitutions were performed in BRD to obtain the sequence for NK2R_H and the seven a-helical segments were optimized forcing the a-helical backbone to match the corresponding aligned parts of BRD, while the arrangements of the side chains were model built based on available site-directed mutagenesis studies. Constrained MM and molecular dynamics simulations were carried out H-bonding a low energy conformer of the known drugs to residues in the receptor site, allowing both the receptor site and drugs to relax. The Connolly surface for each ligand allowed to determine an "average" binding site in which all the low energy conformers of known and prospective drugs were docked and classified according to a statistical index. The whole procedure was repeated exploiting the lately published structure of an actual G protein coupled receptor as a better template, thus producing a cavity in the binding site to directly dock the drugs. Corollary validations of the force fields used are also mentioned. In addition intra- and intermolecular interactions suitable to produce more active drugs were evaluated.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 4; 563-581
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular dynamic simulations of large RNA molecules: the yeast tRNA^{Phe}
Autorzy:
Pliszka, B.
Ołodziej, S.
Powiązania:
https://bibliotekanauki.pl/articles/1954518.pdf
Data publikacji:
1999
Wydawca:
Politechnika Gdańska
Tematy:
tRNA Phe
molecular dynamics
modified bases
nucleic acids
electrostatic interaction
Opis:
Molecular dynamics trajectories (700 ps) of the solvated and neutralized 75-residue yeast tRNA Phe were generated using the AMBER 5.0 molecular dynamics software package. The cut-off scheme was used to treat electrostatic interactions; consequently, all long-range interactions beyond 12 angstroms were neglected. The equilibration procedure and conditions during simulations led to a dynamically stable model of the tRNA molecule. During the simulations all base-base interactions (which determine the secondary and the tertiary structure of the molecule) were well preserved. Consequently, the global shape of the molecule was preserved well and the RMS deviation calculated between the starting x-ray structure and the final structure after 700 ps of simulations was 3.25 angstroms. The biggest deviation is observed in the region of the anticodon hairpin loop; this high mobility is associated with the presence of a very unusual Y-base and a binding site of a magnesium ion in this region.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1999, 3, 3; 333-342
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Treatment of disulfide bonds in coarse-grained UNRES force field
Autorzy:
Krupa, P.
Powiązania:
https://bibliotekanauki.pl/articles/1938623.pdf
Data publikacji:
2016
Wydawca:
Politechnika Gdańska
Tematy:
molecular dynamics
protein folding
disulfide bonds
coarse-grained force field
Opis:
Disulfide bonds, despite the advances of the computational methods, are underrepresented in theoretical chemistry and the role of disulfide bonds is of ten diminished in bioinformatical studies. Most of the molecular modeling tools do not allow studying the process of disulfide bond formation and breaking, which is equally important as the sole presence of disulfide bonds in proteins and peptides. The UNRES (UNited RESidue) coarse-grained force field allows treating disulfide bonds in two ways: as static (formed or broken in the simulation) or dynamic (all specified cysteine residues can form and break disulfide bonds during simulation). The comparison between those two approaches of disulfide-bond treatment is presented for protein folding on the example of four small β - and α + β proteins with one, two, three and four disulfide bonds. The results clearly show that proper disulfide bond treatment is important in simulations and significantly enhances the quality of folded structures.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 393-398
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Theoretical Predictions of Lattice Parameters and Mechanical Properties of Pentaerythritol Tetranitrate under the Temperature and Pressure by Molecular Dynamics Simulations
Autorzy:
Tan, J.J.
Hu, C.
Li, Y.
Ge, N.
Chen, T.
Ji, G.
Powiązania:
https://bibliotekanauki.pl/articles/1033453.pdf
Data publikacji:
2017-02
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
molecular dynamics
lattice parameter
equation of state
elasticity
mechanical properties
Opis:
Molecular dynamics simulations with condensed-phase optimized molecular potentials for atomistic simulation studies force field are performed to investigate the structure, equation of state, and mechanical properties of high energetic material pentaerythritol tetranitrate. The equilibrium structural parameters, pressure-volume relationship and elastic constants at ambient conditions agree excellently with experiments. In addition, fitting the pressure-volume data to the Birch-Murnaghan or Murnaghan equation of state, the bulk modulus B₀ and its first pressure derivative B'₀ are obtained. Moreover, the elastic constants are calculated in the pressure range of 0-10 GPa at room temperature and in the temperature range of 200-400 K at the standard pressure, respectively. By the Voigt-Reuss-Hill approximation, the mechanical properties such as bulk modulus B, shear modulus G, and the Young modulus E are also obtained successfully. The predicted physical properties under temperature and pressure can provide powerful guidelines for the engineering application and further experimental investigations.
Źródło:
Acta Physica Polonica A; 2017, 131, 2; 318-323
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular docking-based test for affinities of two ligands toward vasopressin and oxytocin receptors.
Autorzy:
Ślusarz, Rafał
Kaźmierkiewicz, Rajmund
Giełdoń, Artur
Lammek, Bernard
Ciarkowski, Jerzy
Powiązania:
https://bibliotekanauki.pl/articles/1044173.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
simulated annealing
bioligand docking
GPCR receptor/bioligand interaction
molecular dynamics
Opis:
Molecular docking simulations are now fast developing area of research. In this work we describe an effective procedure of preparation of the receptor-ligand complexes. The amino-acid residues involved in ligand binding were identified and described.
Źródło:
Acta Biochimica Polonica; 2001, 48, 1; 131-135
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Preferential solvation of amides by methanol - a comparison of molecular dynamics calculations with the experimental data
Autorzy:
Zielkiewicz, J.
Powiązania:
https://bibliotekanauki.pl/articles/1965827.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
amides
alcohols
preferential solvation
Kirkwood-Buff integrals
molecular dynamics simulations
Opis:
Using the Kirkwood-Buff theory of solutions, the preferential solvation of the N-methylacet-amide (NMA), N-methylformamide, (NMF), and N,N-dimethylformamide, (DMF), molecule has been investigated in the binary {amide+methanol} mixtures at 313.15 K. Moreover, for the {amide+methanol} mixtures, where amide = NMF, DMF, and NMA, the molecular dynamics calculations at xamide=0.518 were performed. From the obtained molecule-molecule radial distribution functions, (rdf), and atom-atom rdf, it was possible to estimate the local mole fractions around the amide molecule, the orientation effects of molecules within the solvation shell, and a possibility of the formation of complexes. The general picture obtained from analysis of the molecular dynamics results is consistent with the deductions derived from thermodynamic data.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 3; 317-329
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Microscopic simulations of non-equilibrium chemical systems
Autorzy:
Górecki, J.
Górecka, J. N.
Powiązania:
https://bibliotekanauki.pl/articles/1965854.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
molecular dynamics
reactive hard spheres
rate constant
chemical wave front
Opis:
In this paper we discuss applications of molecular dynamics in modeling of nonequilibrium effects in chemical systems. We focus our attention on simulations, which use the "reactive" hard spheres technique. It is demonstrated that information on nonequilibrium rate constant in a system with a thermally activated reaction can be easily obtained from such simulations. We also present results for a wavefront propagation in a system with an autocatalitic reaction: A + B --> A + A.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 3; 341-353
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Coarse-graining models for molecular dynamics simulations of FCC metals
Autorzy:
Delafrouz, P.
Pishkenari, H. N.
Powiązania:
https://bibliotekanauki.pl/articles/279591.pdf
Data publikacji:
2018
Wydawca:
Polskie Towarzystwo Mechaniki Teoretycznej i Stosowanej
Tematy:
accelerated molecular dynamics
coarse-grain models
FCC metals
EAM potential
Opis:
In this paper, four coarse-graining (CG) models are proposed to accelerate molecular dynamics simulations of FCC metals. To this aim, at first, a proper map between beads of the CG models and atoms of the all-atom (AA) system is assigned, afterwards mass of the beads and the parameters of the CG models are determined in a manner that the CG models and the original all-atom model have the same physical properties. To evaluate and compare precision of these four CG models, different static and dynamic simulations are conducted. The results show that these CG models are at least 4 times faster than the AA model, while their errors are less than 1 percent.
Źródło:
Journal of Theoretical and Applied Mechanics; 2018, 56, 3; 601-614
1429-2955
Pojawia się w:
Journal of Theoretical and Applied Mechanics
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular modelling in the rational design of some anti-tumor and antifungal agents
Autorzy:
Mazerski, J.
Borowski, E.
Powiązania:
https://bibliotekanauki.pl/articles/1953949.pdf
Data publikacji:
1998
Wydawca:
Politechnika Gdańska
Tematy:
molecular modelling
molecular mechanics
molecular dynamics
semiempirical methods
antifungal agents
anti-tumor agents
rational design
Opis:
In this paper we present our approaches and results concerning application of molecular modelling techniques in the design of new chemotherapeutic agents for the control of eukariotic systems, comprising compounds for the treatment of systemic fungal infections and tumor deseases. In the case of anti-tumor agents we focused our attention on molecular properties of natural and synthetic anthraquinones. In the area of antifungal compounds we adopted two approaches. In one of them we examine molecular nature of undesirable properties of polyene macrolide antifungal antibiotic - amphotericin B using molecular modelling techniques. Another approach was aimed at the development of selective inactivator of glucosamine synthase, a novel target for antifungal compounds. In this problem we have used computational chemistry methods to identify structural features responsible for the selective inactivation of the target enzyme.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 4; 511-550
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The cavitation nuclei transient characteristics of Lennard-Jones fluid in cavitation inception
Autorzy:
Fu, Q.
Zhang, B.
Zhao, Y.
Zhu, R.
Liu, G.
Li, M.
Powiązania:
https://bibliotekanauki.pl/articles/259255.pdf
Data publikacji:
2018
Wydawca:
Politechnika Gdańska. Wydział Inżynierii Mechanicznej i Okrętownictwa
Tematy:
cavitation nuclei
molecular dynamics simulation
Lennard-Jones fluid
cavitation inception
nucleation
Opis:
In the field of ocean engineering, cavitation is widespread, for the study of cavitation nuclei transient characteristics in cavitation inception, we applied theoretical analysis and molecular dynamics (MD) simulation to study Lennard-Jones (L-J) fluid with different initial cavitation nuclei under the NVT-constant ensemble in this manuscript. The results showed that in cavitation inception, due to the decrease of liquid local pressure, the liquid molecules would enter the cavitation nuclei, which contributed to the growth of cavitation nuclei. By using molecular potential energy, it was found that the molecular potential energy was higher in cavitation nuclei part, while the liquid molecular potential energy changes greatly at the beginning of the cavitation nuclei growth. The density of the liquid and the surface layer changes more obvious, but density of vapor in the bubble changes inconspicuously. With the growth of cavitation nuclei, the RDF peak intensity increased, the peak width narrowed and the first valley moved inner. When cavitation nuclei initial size reduced, the peak intensity reduced, the corresponding rbin increased. With the decrease of the initial cavitation nuclei, the system pressure and total energy achieved a balance longer, and correspondingly, they were smaller. In addition, at the beginning of the cavitation nuclei growth, the total energy and system pressure changed greatly.
Źródło:
Polish Maritime Research; 2018, S 2; 75-84
1233-2585
Pojawia się w:
Polish Maritime Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular dynamics simulation studies of lipid bilayer systems.
Autorzy:
Pasenkiewicz-Gierula, Marta
Murzyn, Krzysztof
Róg, Tomasz
Czaplewski, Cezary
Powiązania:
https://bibliotekanauki.pl/articles/1044295.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
phosphatidylethanolamine
cholesterol
vasopressin receptor,molecular dynamics simulations
magainin-2
phosphatidylcholine
phosphatidylglycerol
Opis:
The main structural element of biological membranes is a liquid-crystalline lipid bilayer. Other constituents, i.e. proteins, sterols and peptides, either intercalate into or loosely attach to the bilayer. We applied a molecular dynamics simulation method to study membrane systems at various levels of compositional complexity. The studies were started from simple lipid bilayers containing a single type phosphatidylcholine (PC) and water molecules (PC bilayers). As a next step, cholesterol (Chol) molecules were introduced to the PC bilayers (PC-Chol bilayers). These studies provided detailed information about the structure and dynamics of the membrane/water interface and the hydrocarbon chain region in bilayers built of various types of PCs and Chol. This enabled studies of membrane systems of higher complexity. They included the investigation of an integral membrane protein in its natural environment of a PC bilayer, and the antibacterial activity of magainin-2. The latter study required the construction of a model bacterial membrane which consisted of two types of phospholipids and counter ions. Whenever published experimental data were available, the results of the simulations were compared with them.
Źródło:
Acta Biochimica Polonica; 2000, 47, 3; 601-611
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Preliminary studies of interaction between nanotubes and toll-like receptors
Autorzy:
Mozolewska, M. A.
Krupa, P.
Rasulev, B.
Liwo, A.
Leszczyński, J.
Powiązania:
https://bibliotekanauki.pl/articles/1935817.pdf
Data publikacji:
2014
Wydawca:
Politechnika Gdańska
Tematy:
CNTs
toll-like receptors
molecular dynamics
receptory toll-like
dynamika molekularna
Opis:
Toll-like receptors ( TLR s) are a group of proteins which play a crucial role in the innate immune system. The main function of TLR s is to recognize structurally conserved molecules, which are inserted to the organism of the host by microbes, and then to activate the immune response. Current development of drugs is often connected not only with the drug itself, but also with the way it is delivered into the human body to interact direc tly with the source of the problem. Carbon nanostructures, particularly nanotubes, are one of the car rier molecules of the future. However, there is still no knowledge about the exact mechani sms of toxicity and possible interactions with macromolecules, such as proteins. In our study we tr ied to determine, if the nanotubes could interfere with the innate immune system by interac ting with TLR s. For this purpose, we used the following TLR structures downloaded from the RCSB Protein Data Bank: TLR 2 (3 A 7 C ), TLR 4/ MD (3 FXI ), TLR 5 (3 V 47), TLR 3 (2 A 0 Z ), and the complexes of TLR 1/ TLR 2 (2 Z 7 X ) and TLR 2/ TLR 6 (3 A 79). The preliminary results of our Steered Molecular Dynamics ( SMD ) simulations have shown that nanotubes interact very strongly with the binding pockets of some receptors ( e.g. TLR 2), which results in their binding to these sites without subst antial use of the external force.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 4; 351--355
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Towards mechanisms of nanotoxicity - interaction of gold nanoparticles with proteins and DNA
Autorzy:
Krupa, P.
Mozolewska, M. A.
Rasulev, B.
Czaplewski, C.
Leszczyński, J.
Powiązania:
https://bibliotekanauki.pl/articles/1935819.pdf
Data publikacji:
2014
Wydawca:
Politechnika Gdańska
Tematy:
gold nanoparticles
proteins
DNA
molecular dynamics
nanocząstki złota
białka
dynamika molekularna
Opis:
Even though most of the existing studies of gold nanoparticles indicate that they are safe to use, some researchers show that specific forms of nanoparticles (e.g. nanorods) are able to destroy the cell membrane and very small nanoparticles (below 37nm in diameter) in high concentration have been deadly for mice. We used the Amber12 package to perform a series of molecular dynamics (MD) simulations of gold nanoparticles with various small proteins important for the human body and a DNA molecule to determine the interactions and consequently the possible toxicity of gold clusters. Lennard-Jones interactions were used to simulate the behavior of gold nanoparticles with biomacromolecules in water with an optimal set of parameters (selected based on a comparison of MD structures and structures computed by DFT). Gold nanoparticle structures were obtained as a result of MD simulations from an initial structure, where gold atoms were at a distance of 10 ̊ A from one another. A predicted BDNA structure of a palindromic sequence‘ CGCATGAGTACGC ’ and a 2 JYK molecule were used as representatives of the DNA molecule. The preliminary results show that, in particular small gold nanoparticles, interact strongly with proteins and DNA by creating stable complexes, which can then cause harmful reactions to the human body when present in high concentration.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 4; 337--341
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Structure and dynamics of water adsorbed on the lignite surface: Molecular dynamics simulation
Autorzy:
You, Xiaofang
He, Meng
Cao, Xiaoqiang
Lyu, Xianjun
Li, Lin
Powiązania:
https://bibliotekanauki.pl/articles/109688.pdf
Data publikacji:
2019
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
low rank coal
water molecule
oxygen-containing functional groups
molecular dynamics
Opis:
The effects of oxygen-containing functional groups on the structure and dynamic properties of water molecules near a lignite surface were investigated through molecular dynamics (MD) simulations. Because of its complex composition and structure, a graphite surface containing hydroxyl, carboxyl, and carbonyl groups was used to represent the lignite surface model. According to X-ray photoelectron spectroscopic (XPS) results, the composing proportion of hydroxyl, carbonyl and carboxyl is 21:13:6. The density profiles of oxygen and hydrogen atoms indicate that the brown coal surface characteristics influence the structural and dynamic properties of water molecules. The interfacial water is much more ordered than bulk water. The results of the radial distribution functions, mean square displacements, and local self-diffusion coefficients for the water molecules in the vicinity of three oxygen-containing functional groups confirmed that carboxyl groups are the preferential adsorption sites.
Źródło:
Physicochemical Problems of Mineral Processing; 2019, 55, 1; 10-20
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Effect of oxidation on the wetting of coal surfaces by water: experimental and molecular dynamics simulation studies
Autorzy:
Li, E.
Lu, Y.
Cheng, F.
Wang, X.
Miller, J. D.
Powiązania:
https://bibliotekanauki.pl/articles/109792.pdf
Data publikacji:
2018
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
wettability
oxidation
molecular dynamics simulation
hydrogen bonding
contact angles
coal surfaces
Opis:
The wettability of coal surfaces by water continues to be one of the key factors which determines the success of coal flotation. Consequently, oxidation of coal surfaces is a fundamental issue of interest. In this work, the effect of oxidation on the wetting of coal surfaces and the interaction between water molecules and oxygen-containing sites at the coal surface was investigated based on advancing/receding contact angle measurements and molecular dynamics simulations. For the simulation studies, a flat coal surface was constructed with the assistance of the molecular repulsion between graphite surfaces and the assembly of Wiser coal molecules. Our results indicated that the simulated advancing and receding contact angles were very similar, and both of them decreased, as expected, with an increase of hydroxyl sites at the coal surface. The good agreement between the simulated advancing/receding contact angles and the experimental receding contact angle values suggested that the configuration of the systems and the set of parameters for the simulation were appropriate. The spreading of water is mainly due to the hydrogen bonds formed between the interfacial water molecules and the hydroxyl sites at the coal surface. The hydroxyl groups show stronger hydration capacity than other oxygen-containing groups according to the calculated hydrogen bonds and interaction energies.
Źródło:
Physicochemical Problems of Mineral Processing; 2018, 54, 4; 1039-1051
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular dynamics simulations of thermal conductivity of penta-graphene
Autorzy:
Muna, Isyna
Winczewski, Szymon
Powiązania:
https://bibliotekanauki.pl/articles/1954605.pdf
Data publikacji:
2020
Wydawca:
Politechnika Gdańska
Tematy:
penta-graphene
thermal conductivity
molecular dynamics
grafen
przewodnictwo cieplne
dynamika molekularna
Opis:
The thermal conductivity of penta-graphene (PG), a new two dimensional carbon allotrope and its dependence on temperature, strain, and direction are studied in this paper. The thermal conductivity of PG is investigated using a non-equilibrium molecular dynamics simulation (NEMD) with the Two Region Method by applying the optimized Tersoff interatomic potential. Our study shows that the thermal conductivity of PG (determined for the [100] direction) at the room temperature of 300 K is about 18.7 W/(m K), which is much lower than the thermal conductivity of graphene. As the temperature increases, the thermal conductivity of PG is decreasing because, unlike graphene, PG has lower phonon group velocities and few collective phonon excitations. The obtained dependence of the thermal conductivity on the temperature can be described as κ ∼ T −0.32. For the [110] direction the thermal conductivity at the room temperature of 300 K is very similar: about 17.8 W/(m K). In this case, the temperature dependence follows the κ ∼ T −0.3 relation. Our investigations reveal that the thermal conductivity of PG is isotropic, meaning that heat transport behavior is independent of the heat flow direction. Our results indicate that the thermal conductivity of PG depends in an interesting way on the applied strain: nonmonotonic up-and-down behavior is observed. The thermal conductivity increases between strains from 0% up to 12.5%, and it decreases above a strain of 12.5%. Our investigation highlights the fascinating thermal transport properties of penta-graphene. The ultra-low thermal conductivity, the decreasing thermal conductivity with the increasing temperature, and the ultra-high mechanical strength of PG show that PG possesses a great potential in thermoelectric and nanomechanics applications. We hope that these findings, made by means of simulations, will become a bridge to inspire and encourage the experimental works, especially in the synthesis of PG.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2020, 24, 3; 191-220
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Obtaining ionic forces by the total-energy tight-binding method
Autorzy:
Dziedzic, J.
Powiązania:
https://bibliotekanauki.pl/articles/1933173.pdf
Data publikacji:
2007
Wydawca:
Politechnika Gdańska
Tematy:
total-energy tight-binding
TBMD
Hellmann-Feynman
ionic forces
molecular dynamics
Opis:
Applying a non-orthogonal tight-binding method to calculate ionic forces in a molecular-dynamics simulation vastly improves the transferability the model's transferability to different environments, compared with the tradi-tional empirical potential-driven molecular-dynamics. In this paper we present the details of computing derivatives of Hamiltonian and overlap matrix elements appearing in the Hellmann-Feynman expression for ionic forces in the NRL-TB model of tight-binding. The presented expressions are validated with the results obtained using a tight-binding-driven molecular-dynamics program.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2007, 11, 3; 285-294
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Theoretical studies of binding modes of two covalent inhibitors of cysteine proteases.
Autorzy:
Drabik, Piotr
Politowska, Ewa
Czaplewski, Cezary
Kasprzykowski, Franciszek
Łankiewicz, Leszek
Ciarkowski, Jerzy
Powiązania:
https://bibliotekanauki.pl/articles/1044228.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
cysteine proteases
covalent protease inhibitors
constrained simulated annealing
papain
molecular dynamics
Opis:
Physiological and pathological roles of cysteine proteases make them important targets for inhibitor development. Although highly potent inhibitors of this group of enzymes are known, their major drawback is a lack of sufficient specificity. Two cysteine protease covalent inhibitors, viz. (i) Z-RL-deoxo-V-peptide-epoxysuccinyl hybrid, and (ii) Z-RLVG-methyl-, have been developed and modeled in the catalytic pocket of papain, an archetypal thiol protease. A number of configurations have been generated and relaxed for each system using the AMBER force field. The catalytic pockets S3 and S4 appear rather elusive in view of the observed inhibitors' flexibility. This suggest rather limited chances for the development of selective structure-based inhibitors of thiol proteases, designed to exploit differences in the structure of catalytic pockets of various members of this family.
Źródło:
Acta Biochimica Polonica; 2000, 47, 4; 1061-1066
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Nanovortex evolution in entrance part of the 2D open type long nanocavity
Autorzy:
Kordos, A.
Kucaba-Piętal, A.
Powiązania:
https://bibliotekanauki.pl/articles/200327.pdf
Data publikacji:
2018
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
nanofluidics
molecular dynamics
nanocavity
nanovortices
nanodevices
dynamika molekularna
nanowgłębienia
nanowiry
nanourządzenia
Opis:
Non-equilibrium molecular dynamics method (NEMD) is applied to investigate a formation process of water nanovortex in 7 nm wide nanocavity (aspect ratio of which was equal to 3.6). The flow in the nanocavity was induced by Poiseuille 2D water nanoflow in a main nanochannel, to which the nanocavity is situated perpendicularly. The wall of main channel and the nanocavity is made from quartz. Flow is induced by applying constant force to molecules inside the main channel. Based on NEMD simulation data, the sequence of images representing water velocity vector fields was obtained at constant time intervals equal to 1 ns, which shows vortex formation mechanism. Flow field images analysis indicates that the shape and centre position of the nanovortex vary slightly each nanosecond, nevertheless, the structure remains stable in the flow field at the entrance to the nanocavity.
Źródło:
Bulletin of the Polish Academy of Sciences. Technical Sciences; 2018, 66, 2; 119-125
0239-7528
Pojawia się w:
Bulletin of the Polish Academy of Sciences. Technical Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular dynamics simulations study of nano bubble attachment at hydrophobic surfaces
Autorzy:
Jin, J.
Dang, L. X.
Miller, J. D.
Powiązania:
https://bibliotekanauki.pl/articles/109533.pdf
Data publikacji:
2018
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
molecular dynamics simulations (MDS)
film stability
bubble attachment
interfacial water structure
Opis:
Bubble attachment phenomena are examined using Molecular Dynamics Simulations (MDS) for the first time. The simulation involves a nitrogen nano bubble containing 906 nitrogen molecules in a water phase with 74,000 water molecules at molybdenite surfaces. During a simulation period of 1 ns, film rupture and displacement occurs. The attached nanobubble at the hydrophobic molybdenite face surface results in a contact angle of about 90º. This spontaneous attachment is due to a “water exclusion zone” at the molybdenite face surface and can be explained by a van der Waals (vdW) attractive force, as discussed in the literature. In contrast, the film is stable at the hydrophilic quartz (001) surface and the bubble does not attach. Contact angles determined from MD simulations are reported, and these results agree well with experimental and MDS sessile drop results. In this way, film stability and bubble attachment are described with respect to interfacial water structure for surfaces of different polarity. Interfacial water molecules at the hydrophobic molybdenite face surface have relatively weak interactions with the surface when compared to the hydrophilic quartz (001) surface, as revealed by the presence of a 3 Å “water exclusion zone” at the molybdenite/water interface. The molybdenite armchair-edge and zigzag-edge surfaces show a comparably slow process for film rupture and displacement when compared to the molybdenite face surface, which is consistent with their relatively weak hydrophobic character.
Źródło:
Physicochemical Problems of Mineral Processing; 2018, 54, 1; 89-101
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Thermal Expansion of Explosive Molecular Crystals: Anisotropy and Molecular Stacking
Autorzy:
Qian, W.
Zhang, C.
Xiong, Y.
Zong, H.
Zhang, W.
Shu, Y.
Powiązania:
https://bibliotekanauki.pl/articles/358262.pdf
Data publikacji:
2014
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Przemysłu Organicznego
Tematy:
energetic material
anisotropic thermal expansion
molecular stacking
molecular dynamics simulation
density functional theory method
Opis:
Molecular dynamics simulations of three typical explosive crystals, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), 1,1-diamino-2,2- dinitroethene (FOX-7) and 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), were carried out under NPT ensemble and selected force field. The equilibrium structures at elevated temperatures were obtained, which show that the stacking behaviour of the molecules does not change with temperature. The coefficient of thermal expansion (CTE) values were calculated by linear fitting methods, and the results show that the CTE values are close to the experimental results and are anisotropic. The total energies of the cells expanding along each single crystallographic axis were calculated by the periodic density functional theory method, indicating that the energy change rates are anisotropic, and correlation equations of the energy change vs. CTE values were established. The essence of the anisotropy of the explosive crystal’s thermal expansion was compared and elucidated.
Źródło:
Central European Journal of Energetic Materials; 2014, 11, 1; 59-81
1733-7178
Pojawia się w:
Central European Journal of Energetic Materials
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Analysis of controlled molecular dynamic flow in a channel with non-equal inlet and outlet cross-sectional areas
Autorzy:
Najafi, H. R.
Karimian, S. M. H.
Powiązania:
https://bibliotekanauki.pl/articles/279977.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Mechaniki Teoretycznej i Stosowanej
Tematy:
molecular dynamics
nano-channel
steady flow
non-equal inlet and outlet
pressure
Opis:
Thermo-fluid properties are required for numerical modeling of nano/micro devices. These properties are mostly obtained from the results of molecular dynamics (MD) simulations. Therefore, efforts have been made to develop methods for numerical evaluation of fluid properties such as pressure and velocity. One of the main challenges faced by numerical simulations is to simulate steady molecular flow in channels with non-equal inlet and outlet boundaries. Currently, periodic boundary conditions at the inlet and outlet boundaries are an inevitable condition in many steady flow molecular dynamics simulations. As a result, a nano-channel with different cross sectional areas at the inlet and outlet could not be simulated easily. Here, a method is presented to generate and control steady molecular flow in a nano-channel with different cross sectional areas at the inlet and outlet. The presented method has been applied to a converging-diverging channel, and its performance has been studied through qualitative and quantitative representation of flow properties.
Źródło:
Journal of Theoretical and Applied Mechanics; 2017, 55, 4; 1141-1153
1429-2955
Pojawia się w:
Journal of Theoretical and Applied Mechanics
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Application of the neural networks for developing new parametrization of the Tersoff potential for carbon
Autorzy:
Nwachukwu, Anthony Chukwuemeka
Winczewski, Szymon
Powiązania:
https://bibliotekanauki.pl/articles/1954600.pdf
Data publikacji:
2020
Wydawca:
Politechnika Gdańska
Tematy:
penta-graphene
mechanical properties
molecular dynamics
penta-grafen
właściwości mechaniczne
dynamika molekularna
Opis:
Penta-graphene (PG) is a 2D carbon allotrope composed of a layer of pentagons having sp2- and sp3- bonded carbon atoms. A study carried out in 2018 has shown that the parameterization of the Tersoff potential proposed in 2005 by Ehrhart and Able (T05 potential) performs better than other potentials available for carbon, being able to reproduce structural and mechanical properties of the PG. In this work, we tried to improve the T05 potential by searching for its parameters giving a better reproduction of the structural and mechanical properties of the PG known from the ab initio calculations. We did this using Molecular Statics (MS) simulations and Neural Network (NN). Our test set consisted of the following structural properties: the lattice parameter a; the interlayer spacing h; two lengths of C-C bonds, d1 and d2 respectively; two valence angles, θ1 and θ2, respectively. We also examined the mechanical properties by calculating three elastic constants, C11, C12 and C66, and two elastic moduli, the Young’s modulus E and the Poisson’s ratio v. We used MS technique to compute the structural and mechanical properties of PG at T =0 K. The Neural Network used is composed of 2 hidden layers, with 20 and 10 nodes for the first and second layer, respectively. We used an Adams optimizer for the NN optimization and the Mean Squared Error as the loss function. We obtained inputs (about 80 000 different sets of potential parameters) for the Molecular Statics simulation by using randomly generated numbers. The outputs from these simulations became the inputs to our Neural Network. The Molecular Statics simulations were done with LAMMPS while the Neural Network and other computations were done with Python, Pytorch, Numpy, Pandas, GNUPLOT and Bash scripts. We obtained a parameterization which has a slightly better accuracy (lower relative errors of the calculated structural and mechanical properties) than the original parameterization.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2020, 24, 4; 299-333
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Computational insights into the self-assembly of phenylalanine-based molecules
Autorzy:
German, H. W.
Bhavaraju, M.
Uyaver, S.
Hansmann, U. H. E.
Powiązania:
https://bibliotekanauki.pl/articles/1935816.pdf
Data publikacji:
2014
Wydawca:
Politechnika Gdańska
Tematy:
phenylalanine
diphenylalanine
self-assembly
molecular dynamics
fenyloalanina
difenyloalanina
samodzielny montaż
dynamika molekularna
Opis:
In a recent paper “Self-Assembly of Phenylalanine-Based Molecules”, we have studied the formation and stability of phenylalanine and diphenylalanine constructs. In the case of diphenylalanine we observe nanotubes, however, phenylalanine molecules aggregate in layers of four, not six, molecules. In the preset paper, we extend this previous work and compare the energetics of all experimentally observed structures, simulated structures, and designed structures, by way of single point Density Functional Theory ( DFT) calculations. We take a detailed look at water content, pore size and dipole moments inside our phenylalaninecontaining tubes and analyze stabilizing factors in the nanostructures.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 4; 357--363
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Zinc ion adsorption on carbon nanotubes in an aqueous solution
Autorzy:
Ansari, A.
Mehrabian, M. A.
Hashemipour, H.
Powiązania:
https://bibliotekanauki.pl/articles/779155.pdf
Data publikacji:
2012
Wydawca:
Zachodniopomorski Uniwersytet Technologiczny w Szczecinie. Wydawnictwo Uczelniane ZUT w Szczecinie
Tematy:
adsorption
molecular dynamics simulation
heavy metals
electrostatic force
interaction energy
functional groups
Opis:
The literature devoted to numerical investigation of adsorption of heavy metal ions on carbon nanotubes is scarce. In this paper molecular dynamics is used to simulate the adsorption process and to investigate the effect of the infl uencing parameters on the rate of adsorption. The predictions of the molecular dynamics simulation show that the adsorption process is improved with increasing the temperature, pH of solution, the mass of nanotubes, and surface modifi cation of CNT using hydroxyl and carboxyl functional groups. The results predicted by the model are compared with the experimental results available in the literature; the close agreement validates the accuracy of the predictions. This study reveals that the water layers around the carbon nanotubes and the interaction energies play important roles in the adsorption process. The study also shows that electrostatic force controls the attraction of zinc ions on the nanotube sidewall.
Źródło:
Polish Journal of Chemical Technology; 2012, 14, 3; 29-37
1509-8117
1899-4741
Pojawia się w:
Polish Journal of Chemical Technology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular modelling techniques in environmental research
Autorzy:
Urniaż, R. D.
Rutkowska, E.
Jastrzębski, J. P.
Książek, P.
Rudnicka, K.
Powiązania:
https://bibliotekanauki.pl/articles/363208.pdf
Data publikacji:
2013
Wydawca:
Uniwersytet Warmińsko-Mazurski w Olsztynie
Tematy:
molecular dynamics
molecular modeling
pharmacokinetics
pharmacophore modeling
QSAR
dynamika molekularna
modelowanie molekularne
farmakokinetyka
modelowanie farmakoforowe
Opis:
Over the last few decades significant increase in computational methods (in silico) was annotated. Novel methods have been developed and applied for hypothesis improvement and testing in regions of industrial, pharmaceutical and environmental research. The term in silico methods include variety of approaches. Considerable attention has been attracted to databases, data analysis tools, quantitative structure-activity relationships (QSAR), pharmacophore models, molecular docking and dynamics, pharmacokinetics and other molecular modelling techniques. In silico methods are often accompanied by experimental data, both to create the model and to test it. Such models are frequently used in the discovery and optimization of novel molecules with expected affinity to a target, the estimation of absorption, distribution, metabolism, excretion and toxicity properties as well as physicochemical characterization. The review summarizes briefly the applications of most common molecular modelling techniques and evaluates their application in environmental research. Additionally, this study considers computer aided methods as potential and complex tools that may serve as valuable partnership with wet-lab experiments and may provide a rational aid to minimize the cost and time of research.
Źródło:
Environmental Biotechnology; 2013, 9, 2; 39-51
1734-4964
Pojawia się w:
Environmental Biotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Analysis of elastic deformation of amorphous polyethylene in uniaxial tensile test by using molecular dynamics simulation
Sprężyste odkształcenie amorficznego polietylenu w osiowosymetrycznej próbie rozciągania z zastosowaniem symulacji metodą dynamiki molekularnej
Autorzy:
Le, Tien-Thinh
Powiązania:
https://bibliotekanauki.pl/articles/29520276.pdf
Data publikacji:
2020
Wydawca:
Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie. Wydawnictwo AGH
Tematy:
uniaxial tension
molecular dynamics simulation
amorphous polyethylene
elasticity
symulacja dynamiki molekularnej
elastyczność
Opis:
In this paper, the linear elastic response to uniaxial tension of amorphous polyethylene was investigated by using Molecular Dynamics (MD) simulation. The polymeric system was initiated using a Monte Carlo-based technique and then equilibrated by a relaxation sequence at temperature of 100 K under a NPT control. Uniaxial tension test was carried out by modifying the corresponding component of the pressure tensor, with a loading rate of 0.5 bar/ps. The results showed that at 100 K (which is smaller than the glass transition temperature), the amorphous polymeric material exhibited a linear elastic response to uniaxial tension. The obtained Young’s modulus and Poisson’s ratio were also compared with values reported in the literature. Finally, parametric studies were performed on the stress-strain curve as a function of loading axis, number of chains and number of monomer units, respectively.
W pracy przeprowadzono badania metodą dynamiki molekularnej sprężystej odpowiedzi amorficznego polietylenu w osiowosymetrycznej próbie rozciągania. System polimetryczny został zainicjowany metodą Monte Carlo a następnie zrównoważony poprzez relaksację w temperaturze 100 K ze sterowaniem NPT. Próby rozciągania przeprowadzono poprzez zmodyfikowanie odpowiedniej składowej tensora naprężeń, przyjmując prędkość obciążania 0.5 bar/ps. Wyniki wykazały, że w temperaturze 100 K (która jest niższa od temperatury zeszklenia), amorficzny polimer wykazuje liniową sprężystość w próbie rozciągania. Wyznaczone wartości modułu Younga i współczynnika Poissona zostały porównane z danymi literaturowymi. Wreszcie przeprowadzono parametryczną ocenę krzywych naprężenieodkształcenie w zależności od kierunku obciążenia, liczby łańcuchów oraz liczby jednostek monomeru.
Źródło:
Computer Methods in Materials Science; 2020, 20, 2; 38-44
2720-4081
2720-3948
Pojawia się w:
Computer Methods in Materials Science
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular Dynamics Simulation Studies of the CL-20/DNB Co-crystal
Autorzy:
Sun, T.
Xiao, J. J.
Ji, G. F.
Zhao, F.
Xiao, H. M.
Powiązania:
https://bibliotekanauki.pl/articles/358075.pdf
Data publikacji:
2016
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Przemysłu Organicznego
Tematy:
CL-20/DNB co-crystal
composite
interactions
mechanical properties
molecular dynamics simulation
Opis:
Molecular dynamics (MD) simulation was conducted for a DNB (1,3-dinitrobenzene) crystal, a ε-CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) crystal, a CL-20/DNB co-crystal and a CL-20/DNB composite. From the calculated maximum bond length (Lmax) of the N−NO2 trigger bond, the cohesive energy density (CED) and the binding energy (Ebind), it was found that the CL-20/DNB co-crystal is more insensitive than its composite. Its thermal stability is also better than that of its composite. The pair correlation function (PCF) analysis method was applied to investigate the interfaces between different molecular layers in the CL-20/DNB co-crystal, and in the composite. Additionally, the calculated mechanical data showed that the moduli of the CL-20/DNB co-crystal and its composite are smaller and their elastic elongation and ductility are better than those of the ε-CL-20 and DNB crystals.
Źródło:
Central European Journal of Energetic Materials; 2016, 13, 3; 677-693
1733-7178
Pojawia się w:
Central European Journal of Energetic Materials
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Design, molecular docking, drug-likeness, and molecular dynamics studies of 1,2,4-trioxane derivatives as novel Plasmodium falciparum falcipain-2 (FP-2) inhibitors
Autorzy:
Ghosh, S.
Chetia, D.
Gogoi, N.
Rudrapal, M.
Powiązania:
https://bibliotekanauki.pl/articles/2096418.pdf
Data publikacji:
2021
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
1
2
4-trioxane
Plasmodium falciparum
drug resistance
molecular docking
molecular dynamics
falcipain 2 inhibitors
Opis:
Despite significant progress made in drug discovery and development over the past few decades, malaria remains a life-threatening infectious disease across the globe. Because of the widespread emergence of drug-resistant strains of Plasmodium falciparum, the clinical utility of existing drug therapies including Artemisinin-based Combination Therapies (ACTs) in the treatment of malaria has been increasingly limited. It has become a serious health concern which, therefore, necessitates the development of novel drug molecules and/or alternative therapies to combat, particularly resistant P. falciparum. The objective of the present study was to develop 1,2,4-trioxane derivatives as novel antimalarial agents that would be effective against resistant P. falciparum. In our study, 15 new trioxane derivatives were designed by molecular modification of the 1,2,4-trioxane scaffold as possible antimalarial agents. Molecular modeling studies of trioxane derivatives were performed based on the CADD approach using Biovia Discovery Studio (DS) 2018 software. The protein-ligand docking study was performed against P. falciparum falcipain 2 (FP-2) using the simulation-based docking protocol LibDock by the flexible docking method. The assessment of drug-likeness, ADMET properties, and toxicity was also performed. Furthermore, the compounds CC3 and CC7, which showed the best binding affinity against the target P. falciparum FP-2, were investigated by molecular dynamics (MD) simulation studies followed by the calculation of MM-PBSA binding free energy of protein-ligand complexes using DS 2020. Results of the docking study showed that among the 15 compounds, three trioxane derivatives were found to possess promising binding affinity with LibDock scores ranging from 117.16 to 116.90. Drug-likeness, ADMET, and toxicity properties were found to be satisfactory for all the compounds. Among the 15 compounds, two compounds, namely CC3 and CC7, showed the highest binding affinity against FP-2 with LibDock score of 117.166 and 117.200, respectively. The Libdock score of the co-crystal inhibitor was 114.474. MD studies along with MM-PBSA calculations of binding energies further confirmed the antimalarial potential of the compounds CC3 and CC7, with the formation of well-defined and stable receptor-ligand interactions against the P. falciparum FP-2 enzyme. Additionally, the selectivity of trioxane hits identified as potential inhibitors of P. falciparum cysteine protease FP-2 was determined on human cysteine proteases such as cathepsins (Cat K and Cat L), which are host homologous. Finally, it was concluded that the newly designed 1,2,4-trioxane derivatives can be further studied for in vitro and in vivo antimalarial activities for their possible development as potent antimalarial agents effective against resistant P. falciparum
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2021, 102, 3; 257-275
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Influence of Temperature on the Properties of Cellulose Iβ based on Molecular Dynamics Simulations
Autorzy:
Huang, Shuang
Wu, Xin
Li, Peixing
Powiązania:
https://bibliotekanauki.pl/articles/2056296.pdf
Data publikacji:
2021
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Biopolimerów i Włókien Chemicznych
Tematy:
cellulose Iβ
molecular dynamics simulation
Mulliken population
movement of chain
hydrogen bond
Opis:
Natural plants, such as cotton and linen, are rich in cellulose Iβ. The properties of cellulose Iβ under different temperatures was studied using molecular dynamics simulations. Firstly, the crystal of cellulose Iβ was built. To verify the model, the X-ray fibre diffraction and thermal expansion coefficients were calculated, which were found to agree with experimental results. Then the Mulliken population of the bonds were computed and the movement of the centre chain and hydrogen bonds studied over the range 300-550 K using a PCFF force field. The results of the Mulliken population reveal the three steps of pyrolysis. The higher the temperature is, the more intensely the movement of the centre chain is. However, the impact of temperature on the movement of the centre chain is not obvious. From 300 K to 550 K, the total number of hydrogen bonds decreased by only 20%. Moreocer, the rupture of intrachain hydrogen bonds and the formation of interchain hydrogen bonds at 400 K~450 K temperature occurred.
Źródło:
Fibres & Textiles in Eastern Europe; 2021, 6 (150); 32--36
1230-3666
2300-7354
Pojawia się w:
Fibres & Textiles in Eastern Europe
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Effect of Nanoindentation Rate on Plastic Deformation in Cu Thin Films
Autorzy:
Chocyk, Dariusz
Zientarski, Tomasz
Powiązania:
https://bibliotekanauki.pl/articles/2022488.pdf
Data publikacji:
2022
Wydawca:
Stowarzyszenie Inżynierów i Techników Mechaników Polskich
Tematy:
nanoindentation
stress distribution
dislocation
common neighbor analysis
molecular dynamics simulation
Cu
thin film
Opis:
The paper investigates the nanoindentation process with different rates in the Cu (001) of FCC system. The indentation process was done using molecular dynamics simulation based on the embedded atom method theory and Morse potential. Simulation process of indentation used a rigid spherical indenter with the diamond structure. To structure characterization we applied the adaptive common neighbour and the dislocation extraction analysis. It was found that the range of the linear change of the indentation force depends on the rate of response of the system. The initial range of the linear dependence of stress evolution also depends on the rate of indentation. Moreover, the average total normal stress in the system is only compressive. After linear changes, we observe oscillating changes in stress evolution. During indentation, for the range of linear changes of stress, dislocations aggregated only around the indenter surface. The creation of dislocations is directly connected with the structural changes. The structure analysis revealed the formation of HCP and BCC structure in the Cu (001) of FCC systems and a correlation with the creation of dislocations.
Źródło:
Advances in Science and Technology. Research Journal; 2022, 16, 1; 170-179
2299-8624
Pojawia się w:
Advances in Science and Technology. Research Journal
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Effect of the oxygen-containing functional group on the adsorption of hydrocarbon oily collectors on coal surfaces
Autorzy:
Wan, He
Hu, Xianglin
Luukkanen, Saija
Qu, Juanping
Zhang, Chonghui
Xue, Jiwei
Li, Hui
Yang, Wei
Yang, Shenghong
Bu, Xianzhong
Powiązania:
https://bibliotekanauki.pl/articles/2146920.pdf
Data publikacji:
2022
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
oxygen-containing functional groups
hydrocarbon oily collectors
molecular dynamics simulation
coal surfaces
adsorption
Opis:
The oxygen-containing functional groups (OCFG) on the coal surface affect the adsorption effect of hydrocarbon oily collectors (HOC). An investigation of the interaction between the HOC and OCFG in the absence and presence of water is conducive to understanding the effect of OCFG type on the adsorption of HOC on the coal surface. In this paper, FTIR analysis was used to analyze the OCFG type of coal surface. The adsorption behavior of HOC on different OCFG surfaces was investigated using molecular dynamics simulation. The results indicated the presence of OCFG such as -OH, -COOH, -C=O, and -COCH3 on the coal surface. In conditions without water, the effect of OCFG on HOC adsorption capability follows the order -COOH > -C=O > -OH > -COCH3. In an aqueous solution, the effect of OCFG on HOC adsorption capability follows the order -C=O>-COCH3>-OH>-COOH. Moreover, the hydrophilicity of OCFG is the key factor that affects the adsorption effect of HOC. In other words, the adsorption effect of HOC on the coal surface in an aqueous solution does not depend on the strength of the interaction between the OCFG and HOC in the absence of water, but on the hydrophilicity of the OCFG. The -COOH and -OH on the coal surface are not conducive to the adsorption of HOC onto the coal surface. Masking the -COOH and -OH of the coal surface is beneficial in improving the coal flotation performance with HOC as a collector.
Źródło:
Physicochemical Problems of Mineral Processing; 2022, 58, 4; art. no. 149937
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Nitrosubstituted analogs of isoxazolines and isoxazolidines: a surprising estimation of their biological activity via molecular docking
Autorzy:
Zawadzińska, Karolina
Gostyński, Bartłomiej
Powiązania:
https://bibliotekanauki.pl/articles/35126576.pdf
Data publikacji:
2023
Wydawca:
Radomskie Towarzystwo Naukowe
Tematy:
isoxazolines
isoxazolidines
molecular docking
molecular dynamics
biological activity
izoksazoliny
izoksazolidyny
dokowanie molekularne
dynamika molekularna
aktywność biologiczna
Opis:
The biological activities in the field of antimicrobial application of trihalomethylated isoxazolines and isoxazolidines were investigated by means of molecular docking. In our work, we compared these two groups of heterocyclic compounds due to their strength of non-covalent binding affinity with several exemplary proteins that are known to partake in various biological processes. The obtained results show that the investigated compounds possess higher binding affinities to selected proteins than many hitherto known and applied compounds.
Źródło:
Scientiae Radices; 2023, 2, 1; 25-46
2956-4808
Pojawia się w:
Scientiae Radices
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Conformational studies of tachykinin peptides using NMR spectroscopy
Autorzy:
Rodziewicz, S.
Xiao-Fei, Qi.
Rolka, K.
Powiązania:
https://bibliotekanauki.pl/articles/1954059.pdf
Data publikacji:
1998
Wydawca:
Politechnika Gdańska
Tematy:
conformational analysis
tachykinin peptides
NMR spectroscopy
Scyliorhinin II
molecular dynamics calculation methods
DMSO
Opis:
Conformational analysis of two tachykinin family peptides: Scyliorhinin I (ScyI) and Scyliorhinin II (ScyII) was carried out by 1D- and 2D-NMR (DQF-COSY, TOCSY, HMQC, HMBC, NOESY and ROESY) and molecular dynamics calculation methods in water and DMSO. Scyliorhinin I is an equipotent agonist of NK-1 and NK-2 tachykinin receptors and Scyliorhinin II is a selective agonist of the NK-3 tachykinin receptor. In DMSO, two groups of conformations (major and minor) were obtained for both peptides based on the experimental data. The conformations proposed for ScyI represent a folded structure, which show certain similarities to the structures reported for other NK-1 and NK-2 tachykinin agonists. In water ScyII displays a flexible, extended structure, whereas in DMSO the structure is more compact and in the fragment from the centre to the C-terminus several beta -turns may be present.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 1; 47-53
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The structure of Pb-PbO-SiO2 glass via molecular dynamics simulation
Autorzy:
Rybicki, J.
Witkowska, A.
Bergmański, G.
Mancini, G.
Feliziani, S.
Powiązania:
https://bibliotekanauki.pl/articles/1954650.pdf
Data publikacji:
2022-01-20
Wydawca:
Politechnika Gdańska
Tematy:
lead-silicate glasses
oxide glasses
medium-range order
ring analysis
molecular dynamics simulations
Opis:
The paper is dedicated to a molecular dynamics (MD) study of the structure of partially reduced lead-silicate glass of composition 1Pb 1PbO 1SiO2. The simulations have been performed in the constant volume regime, using a two-body potential (Born-Mayer repulsive forces, and Coulomb forces due to full ionic charges). The system was initially prepared as a well equilibrated hot melt, and then slowly cooled down to 300K. The information on short-range correlations were obtained in a conventional way (from pair and angular distribution functions), while the medium-range order was studied via cation-anion ring analysis. In the paper, the short- and medium-range order in the simulated system is discussed and compared with the structure of a glassy completely reduced system, i.e. 2Pb 1SiO2 and unreduced one, i.e. 2PbO 1SiO2 glass.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2003, 7, 2; 243-256
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
In silico prediction and characterization of three-dimensional structure of actin-1 of Arabidopsis thaliana
Autorzy:
Sahu, M.
Dehury, B.
Sarmah, R.
Sahoo, S.
Sahu, J.
Sarma, K.
Sen, P.
Modi, M.K.
Barooah, M.
Powiązania:
https://bibliotekanauki.pl/articles/80321.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
actin-1
protein sequence
Arabidopsis thaliana
comparative modelling
three-dimensional structure
molecular dynamics simulation
Opis:
Actin-1 is a ubiquitous protein belonging to the reproductive class of Actin family in Arabidopsis thaliana . This protein is involved in the formation of filaments that are major components of the cytoskeleton. Despite the importance of this protein, very little information is available regarding its structure and function in plants. In this study, analysis of the protein sequence was done and comparative model of Actin-1 was constructed (UNIPROT ID: P0CJ46) from Arabidopsis thaliana using the crystal structure of Dictyostelium discoideum actin (PDB ID: 1NLV-A) as template employing Modeller version 9.9. The stable structure was generated by 5 nanosecond molecular dynamics simulation steps using GROMOS43A1 96 force field that characterized its structural and dynamic feature. The biochemical function of the final simulated structure was also investigated using PROFUNC. The molecular simulation study suggested that the modeled Actin-1 protein retain its stable conformation in aqueous solution. The predicted binding sites in the modeled Actin-1 protein are very informative for further protein-ligand interaction study.
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 4
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Comparative stability analysis of D23N mutated Aβ
Autorzy:
Alred, E. J.
Scheele, E. G.
Berhanu, W. M.
Hansmann, U. H. E.
Powiązania:
https://bibliotekanauki.pl/articles/1935815.pdf
Data publikacji:
2014
Wydawca:
Politechnika Gdańska
Tematy:

structural polymorphism
molecular dynamics
parallel and anti-parallel β sheets
Iowa mutant
Opis:
Amyloid β (Aβ) is the subject of numerous studies due to its link to the devastating Alzheimer’s disease and it exists in a parallel structure in fibril aggregate. The Iowa mutant (D 23 N) Aβ posses a unique antiparallel fibril aggregate structure and can also form parallel structure. This structural difference, coupled with the fact that occurrence of the Iowa mutant is correlated with early onset Alzheimer’s, suggests to use these peptides as candidates for computational studies of the structural determinants of the toxicity of Alzheimer’s disease. In order to compare the two observed Aβ structural motifs, we designed a computational study to probe the factors that affect the stability of parallel and antiparallel aggregates. Since the structural changes may occur on a timescale beyond that sampled in traditional molecular dynamics (MD), we employed a techniques of scaling the mass to reduce the solution ’s viscosity and compared the results to regular molecular dynamics. The knowledge gained from this study could provide insight into the mechanism of selection for antiparallel and parallel two fold structures.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 4; 365--371
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Probing of Cu2+ ions binding to A β (5−16) peptide using ITC measurements and MD simulations
Autorzy:
Makowska, J.
Żmudzińska, W.
Wyrzykowski, D.
Brzozowski, K.
Zblewska, H.
Chmurzyński, L.
Powiązania:
https://bibliotekanauki.pl/articles/1938620.pdf
Data publikacji:
2016
Wydawca:
Politechnika Gdańska
Tematy:
A β (5 − 16) fragments
metal-peptide binding
isothermal titration calorimetry
molecular dynamics simulations
Opis:
It is shown that probably three residues: His6, His14 and His16 in the original sequence A β (1−42) serve as metal-binding sites for Cu2+ions. On the other hand, there is a possibility that only one of them plays a crucial role in the formation of the{A β (1-42)-Cu2+} complex. The isothermal titration calorimetry (ITC) measurements supported by molecular dynamic simulation (MD) with the NMR-derived restrains were used to investigate the interactions of Cu2+ with A β(5-16), a fragment of the A β(1-42) protein, with the following sequence: Ac-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-NH2, termed HZ1. The conditional thermodynamic parameters suggest that the formation of the Cu2+-HZ1 complex is both an enthalpy and entropy driven process under the experimental conditions. The studies presented here (after comparison with our previous results) show that the affinity of peptides to copper metal ions depends on two factors: the primary structure (amino acid composition) and the shape of the peptide conformation adopted.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 409-416
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The intercalation of imidazoacridinones into DNA induces conformational changes in their side chain.
Autorzy:
Mazerski, Jan
Muchewicz, Karolina
Powiązania:
https://bibliotekanauki.pl/articles/1044393.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
molecular dynamics simulations
conformational changes
structure of intercalation complex
C-1311
antitumor drugs
imidazoacridinones
Opis:
Imidazoacridinones (IAs) are a new group of highly active antitumor compounds. The intercalation of the IA molecule into DNA is the preliminary step in the mode of action of these compounds. There are no experimental data about the structure of an intercalation complex formed by imidazoacridinones. Therefore the design of new potentially better compounds of this group should employ the molecular modelling techniques. The results of molecular dynamics simulations performed for four IA analogues are presented. Each of the compounds was studied in two systems: i) in water, and ii) in the intercalation complex with dodecamer duplex d(GCGCGCGCGCGC)2. Significant differences in the conformation of the side chain in the two environments were observed for all studied IAs. These changes were induced by electrostatic as well as van der Waals interactions between the intercalator and DNA. Moreover, the results showed that the geometry of the intercalation complex depends on: i) the chemical constitution of the side chain, and ii) the substituent in position 8 of the ring system.
Źródło:
Acta Biochimica Polonica; 2000, 47, 1; 65-78
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Temperature effect on properties of β-galactosidase entrapped in alginate matrix: an experimental research supported by molecular modeling
Wpływ temperatury na właściwości β-galaktozyadazy inkludowanej w matrycy alginianowej: badania eksperymentalne wspomagane molekularnym modelowaniem
Autorzy:
Labus, K.
Radosiński, Ł.
Kuchta, B.
Trusek-Hołownia, A.
Powiązania:
https://bibliotekanauki.pl/articles/2073108.pdf
Data publikacji:
2015
Wydawca:
Stowarzyszenie Inżynierów i Techników Mechaników Polskich
Tematy:
β-galactosidase
alginate
immobilization
temperature
molecular dynamics
β-galaktozydaza
alginian
immobilizacja
temperatura
dynamika molekularna
Opis:
The current study was separated into two parts: experimental study of temperature impact on activity and stability of immobilized β-galactosidase and preliminary modeling of changes generated in alginate-Ca2+ matrix with respect to temperature using molecular dynamics approach. On the basis of obtained results it can be stated that combination of experimental research and computer simulations on molecular level provides an additional insight greatly enhancing capabilities to control and optimize the process using immobilized biocatalyst.
Badania składały się z dwu części: eksperymentalnego wyznaczenia wpływu temperatury na właściwości immobilizowanej β-galaktozydazy oraz wstępnego modelowania dynamiki zmian w strukturze matrycy alginian-Ca2+ w zależności od temperatury na poziomie molekularnym. Na podstawie uzyskanych wyników można stwierdzić, że takie połączenie badań eksperymentalnych z symulacjami komputerowymi na poziomie cząsteczkowym pozwala na uzyskanie bardziej szczegółowej wiedzy na temat dynamiki układu, co w konsekwencji stwarza możliwość lepszej kontroli i optymalizacji procesu prowadzonego z wykorzystaniem immobilizowanego enzymu.
Źródło:
Inżynieria i Aparatura Chemiczna; 2015, 3; 98--100
0368-0827
Pojawia się w:
Inżynieria i Aparatura Chemiczna
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The role of side chains in the interaction of new antitumor pyrimidoacridinetriones with DNA: Molecular dynamics simulations.
Autorzy:
Mazerski, Jan
Antonini, Ippolito
Martelli, Sante
Powiązania:
https://bibliotekanauki.pl/articles/1044390.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
molecular dynamics simulations
structure of intercalation complex
pyrimidoacridinetrione antitumor agents
role of side chain(s)
Opis:
Pyrimidoacridinetriones (PATs) are a new group of highly active antitumor compounds. It seems reasonable to assume that, like for some other acridine derivatives, intercalation into DNA is a necessary, however not a sufficient condition for antitumor activity of these compounds. Rational design of new compounds of this chemotype requires knowledge about the structure of the intercalation complex, as well as about interactions responsible for its stability. Computer simulation techniques such as molecular dynamics (MD) may provide valuable information about these problems. The results of MD simulations performed for three rationally selected PATs are presented in this paper. The compounds differ in the number and position of side chains. Each of the compounds was simulated in two systems: i) in water, and ii) in the intercalation complex with the dodecamer duplex d(GCGCGCGCGCGC)2. The orientation of the side chain in relation to the ring system is determined by the position of its attachment. Orientation of the ring system inside the intercalation cavity depends on the number and position of side chain(s). The conformations of the side chain(s) of all PATs studied in the intercalation complex were found to be very similar to those observed in water.
Źródło:
Acta Biochimica Polonica; 2000, 47, 1; 47-57
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Application of the Lennard-Jones potential in modelling robot motion
Zastosowanie potencjału Lennard-Jonesa do modelowania ruchu robotów
Autorzy:
Wójcicki, Piotr
Zientarski, Tomasz
Powiązania:
https://bibliotekanauki.pl/articles/408380.pdf
Data publikacji:
2019
Wydawca:
Politechnika Lubelska. Wydawnictwo Politechniki Lubelskiej
Tematy:
swarm
Lennard-Jones potential
molecular dynamics simulation
rój
potencjał Lennard-Jones
symulacja metodą dynamiki molekularnej
Opis:
The article proposes a method of controlling the movement of a group of robots with a model used to describe the interatomic interactions. Molecular dynamics simulations were carried out in a system consisting of a moving groups of robots and fixed obstacles. Both the obstacles and the group of robots consisted of uniform spherical objects. Interactions between the objects are described using the Lennard-Jones potential. During the simulation, an ordered group of robots was released at a constant initial velocity towards the obstacles. The objects’ mutual behaviour was modelled only by changing the value of the interaction strength of the potential. The computer simulations showed that it is possible to find the optimal value of the potential impact parameters that enable the implementation of the assumed robotic behaviour scenarios. Three possible variants of behaviour were obtained: stopping, dispersing and avoiding an obstacle by a group of robots.
W artykule zaproponowano metodę kontrolowania ruchu grupy robotów za pomocą modelu stosowanego do opisu oddziaływań międzyatomowych. Przeprowadzono symulacje metodą dynamiki molekularnej w układzie składającym się z ruchomych grup robotów oraz nieruchomych przeszkód. Zarówno przeszkody, jak i roboty składały się z jednolitych sferycznych obiektów. Oddziaływania między obiektami opisano za pomocą potencjału Lennard-Jonesa. Podczas symulacji, początkowo uporządkowana grupa robotów poruszała się ze stałą prędkością w kierunku przeszkód. Wzajemne zachowanie obiektów modelowano tylko poprzez zmianę wartości parametrów potencjału oddziaływań. Symulacje komputerowe wykazały, że możliwe jest znalezienie optymalnych wartości parametrów oddziaływania, które umożliwiają uzyskanie pożądanego zachowania robotów. W trakcie symulacji uzyskano trzy możliwe warianty zachowania: zatrzymywanie, rozpraszanie i omijanie przeszkód przez grupę robotów.
Źródło:
Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska; 2019, 9, 4; 14-17
2083-0157
2391-6761
Pojawia się w:
Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Wpływ benzo[a]pirenu na własności fosfolipidów surfaktantu płucnego: modelowa analiza toksyczności spalin silników Diesla
Influence of benzo[a]pyrene on properties of the lung surfactant phospholipids: model analysis of diesel exhaust gases toxicity
Autorzy:
Sosnowski, T.
Koliński, M.
Gradoń, L.
Powiązania:
https://bibliotekanauki.pl/articles/2070891.pdf
Data publikacji:
2010
Wydawca:
Stowarzyszenie Inżynierów i Techników Mechaników Polskich
Tematy:
spaliny Diesla
toksyczność
surfaktant płucny
dynamika molekularna
diesel exhaust gases
toxicity
lung surfactant
molecular dynamics
Opis:
Doświadczalnie (waga Langmuird) i teoretycznie (dynamika molekularna) badano oddziaływania fizykochemiczne między benzo[a]pirenem (BAP) i głównym składnikiem surfaktantu płucnego, DPPC. Odnotowano zmiany dynamicznego napięcia powierzchniowego i ściśliwości filmu DPPC na powierzchni woda - powietrze, które wyjaśniono w oparciu o mechanizm wbudowywania się molekuł BAP w monowarstwę DPPC. Przyjmując, że podobne zjawiska przebiegają w naturalnym układzie surfaktantu płucnego, wyniki sugerują jedną z możliwych przyczyn toksyczności spalin silników Diesla.
Physicochemical interactions between benzo[a]pyrene (BAP) and a basic constituent of lung surfactant, DPPC, were studied experimentally (Lang-muir balance) and theoretically (molecular dynamic approach). Changes in dynamic surface tension and compressibility of DPPC film at air - water interface were observed and explained by the incorporation of BAP molecules into DPPC monolayer. Similar phenomena can be of importance during oscillations of lung surface during breathing, so the results suggest a potential mechanism of health effects from diesel exhaust gases inhalation.
Źródło:
Inżynieria i Aparatura Chemiczna; 2010, 2; 115-116
0368-0827
Pojawia się w:
Inżynieria i Aparatura Chemiczna
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
From quantity to quality: massive molecular dynamics simulation of nanostructures under plastic deformation in desktop and service grid distributed computing infrastructure
Autorzy:
Gatsenko, O.
Bekenev, L.
Pavlov, E.
Gordienko, Y. G.
Powiązania:
https://bibliotekanauki.pl/articles/305256.pdf
Data publikacji:
2013
Wydawca:
Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie. Wydawnictwo AGH
Tematy:
distributed computing
desktop grid
service grid
speed up
molecular dynamics
materials science
nanocrystal
plastic deformation
Opis:
The distributed computing infrastructure (DCI) on the basis of BOINC and EDGeS-bridge technologies for high-performance distributed computing is used for porting the sequential molecular dynamics (MD) application to its parallel version for DCIwith Desktop Grids (DGs) and Service Grids (SGs). The actual metrics of the working DG-SG DCI were measured, and the normal distribution of host performances, and signs of log-normal distributions of Rother characteristics (CPUs, RAM, and HDD per host) were found. The practical feasibility and high efficiency of the MD simulations on the basis of DG-SG DCI were demonstrated during the experiment with the massive MD simulations for the large quantity of aluminum nanocrystals (Statistical analysis (Kolmogorov-Smirnov test, moment analysis, and bootstrapping analysis) of the defect density distribution over the ensemble of nanocrystals had show that change of plastic deformation mode is followed by the qualitative change of defect density distribution type over ensemble of nanocrystals. Some limitations (fluctuating performance, unpredictable availability of resources, etc.) of the typical DG-SG DCI were outlined, and some advantages (high efficiency, high speedup, and low cost) were demonstrated. Deploying on DG DCI allows to get new scientific quality from the simulated quantity of numerous configurations by harnessing sufficient computational power to undertake MD simulations in a wider range of physical parameters (configurations) in a much shorter timeframe.
Źródło:
Computer Science; 2013, 14 (1); 27-44
1508-2806
2300-7036
Pojawia się w:
Computer Science
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Quantum-inspired evolutionary optimization of SLMoS2 two-phase structures
Autorzy:
Kuś, Wacław
Mrozek, Adam
Powiązania:
https://bibliotekanauki.pl/articles/29520072.pdf
Data publikacji:
2022
Wydawca:
Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie. Wydawnictwo AGH
Tematy:
quantum-inspired evolutionary algorithm
optimization
nanostructure
two-phase SLMoS2
molecular dynamics
molecular statics
atomic potential
ReaxFF
material properties
Opis:
The paper focuses on applying a Quantum Inspired Evolutionary Algorithm to achieve the optimization of 2D material containing two phases, 2H and 1T, of Molybdenum Disulphide (MoS2). The goal of the optimization is to obtain a nanostructure with tailored mechanical properties. The design variables describe the shape of inclusion made from phase 1T in the 2H unit cell. The modification of the size of the inclusions leads to changes in the mechanical properties. The problem is solved with the use of computed mechanical properties on the basis of the Molecular Statics approach with ReaxFF potentials.
Źródło:
Computer Methods in Materials Science; 2022, 22, 2; 67-78
2720-4081
2720-3948
Pojawia się w:
Computer Methods in Materials Science
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Flows in microchannels
Autorzy:
Kucaba-Piętal, A.
Walenta, Z.
Peradzyński, Z.
Powiązania:
https://bibliotekanauki.pl/articles/1955808.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
microchannel flow
microflows
micropolar fluid
molecular dynamics simulations
direct Monte Carlo simulation
direct Monte Carlo methods
Opis:
The aim of this paper is to present a survey of the results for the flows of simple gases and liquids with substructure through narrow channels, obtained with the Direct Monte-Carlo and Molecular Dynamics Simulation methods.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 2; 179-189
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Dyskretne metody symulacji zjawisk przepływowych w gazach i cieczach
Discrete Methods of Simulation of Flow Phenomena in Gases and Liquids
Autorzy:
Wolszakiewicz, T.
Walenta, Z. A.
Powiązania:
https://bibliotekanauki.pl/articles/403663.pdf
Data publikacji:
2013
Wydawca:
Wojskowa Akademia Techniczna im. Jarosława Dąbrowskiego
Tematy:
metody numeryczne
Bezpośrednia Symulacja Monte Carlo
dynamika molekularna
simulation methods
direct simulation Monte Carlo
molecular dynamics
Opis:
W pracy rozpatrzone zostały dwie metody numerycznej symulacji zjawisk przepływowych w ośrodkach gazowych i ciekłych, oparte na molekularnym opisie ośrodka: metoda Bezpośredniej Symulacji Monte Carlo oraz metoda Dynamiki Molekularnej. Metody te pozwalają na modelowanie w sposób bezpośredni przebiegu reakcji chemicznych, oddziaływania ośrodka ze ściankami ich zaletą jest także względna łatwość dostosowania się do skomplikowanej geometrii. Wadą są długie czasy obliczeń, co jednak może być przezwyciężone przez wykorzystanie coraz powszechniej dostępnych komputerów o dużej szybkości obliczeń.
The paper presents two methods of simulation of flow phenomena in gases and liquids based on molecular description of the medium: the Direct Simulation Monte Carlo method and the Molecular Dynamics method. These methods offer the possibility of direct modelling of chemical reactions and interactions of the medium with solid walls. Apart from that they have the advantage of relatively easy adaptation to complex geometries. Their main disadvantage is the long computing time, which, however, may be overcome with the use of the modern, fast computers presently available.
Źródło:
Problemy Mechatroniki : uzbrojenie, lotnictwo, inżynieria bezpieczeństwa; 2013, 4, 4 (14); 67-76
2081-5891
Pojawia się w:
Problemy Mechatroniki : uzbrojenie, lotnictwo, inżynieria bezpieczeństwa
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Grain Boundary Relaxation in Bi-Crystals: Mechanical Spectroscopy and Molecular Dynamics Simulations
Relaksacja granic ziaren w bikryształach: spektroskopia mechaniczna i symulacje metodą dynamiki molekularnej
Autorzy:
Maier, A.-K.
Mari, D.
Tkalcec, I.
Schaller, R.
Powiązania:
https://bibliotekanauki.pl/articles/353074.pdf
Data publikacji:
2015
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
internal friction grain boundaries
gold alloys
molecular dynamics
granice wewnętrzne tarcia ziarna
stop złota
dynamika molekularna
Opis:
Different Au-Ag-Cu samples have been studied by mechanical spectroscopy. Both polycrystals and bi-crystals show a relaxation peak at 800 K, accompanied by an elastic modulus change. Since this peak is absent in single crystals it is related to the presence of grain boundaries. Molecular dynamics simulations reveal two microscopic mechanisms, when a shear stress is applied onto a Σ5 grain boundary: at 700 K, the boundary migrates perpendicularly to the boundary plane under an external stress. At 1000 K, only sliding at the boundary is observed. These two mechanisms acting in different temperature intervals are used to model the mechanic response of a polycrystal under an applied stress. The models yield expressions for the relaxation strength Δ and for the relaxation time τ as a function of the grain size. A comparison with the mechanical spectroscopy measurements of polycrystals and the bi-crystals show that the grain boundary sliding model reproduces correctly the characteristics of the grain boundary peak.
Różne próbki ze stopów Au-Ag-Cu badano metodą spektroskopii mechanicznej. Zarówno w polikryształach, jak i bikryształach występuje pik relaksacyjny w temperaturze 800 K, któremu towarzyszy zmiana modułu sprężystości. Ponieważ pik ten nie występuje w monokryształach to jego występowanie wiązane jest z obecnością granic ziaren. Symulacje dynamiki molekularnej ujawniają dwa mikroskopowe mechanizmy, gdy naprężenie ścinające jest przyłożone do granicy ziarna Σ5: w temperaturze 700 K, granica przemieszcza się prostopadle do płaszczyzny granicznej pod wpływem zewnętrznego naprężenia. W 1000 K, obserwuje się tylko poślizg po granicy. Te dwa mechanizmy działające w różnych zakresach temperatur są używane do modelowania mechanicznej reakcji polikryształu na przyłożone naprężenie. Modele podają wyrażenie na stopień relaksacji Δ i czas relaksacji τ w funkcji wielkości ziaren. Porównanie z wynikami badań polikryształów i bikryształów uzyskanych metodą spektroskopii mechanicznej pokazuje, że model poślizgu granicy ziarna poprawnie odtwarza charakterystykę piku pochodzącego od granic ziaren.
Źródło:
Archives of Metallurgy and Materials; 2015, 60, 1; 377-380
1733-3490
Pojawia się w:
Archives of Metallurgy and Materials
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Study of alkanethiol-based self-assembled monolayers coated with poly(methyl methacrylate) of various tacticity
Badanie samoorganizujących się monowarstw na bazie alkanotioli pokrytych poli(metakrylanem metylu) o różnej taktyczności
Autorzy:
Kozik, Tomasz
Śniechowski, Maciej
Łużny, Wojciech
Powiązania:
https://bibliotekanauki.pl/articles/947598.pdf
Data publikacji:
2020
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Chemii Przemysłowej
Tematy:
self-assembled monolayers
poly(methyl methacrylate)
molecular dynamics
samoorganizujące się monowarstwy
poli(metakrylan metylu)
dynamika molekularna
Opis:
Self-assembled monolayers (SAMs) have a large variety of applications. One particular ap-plication of alkanethiol-based SAMs is tuning the work function of metallic surfaces. In a recent study, it was determined that depositing a poly(methyl methacrylate) layer on selected SAMs further shifts the work function. The effect is sensitive to tacticity and neither the reason behind this nor the exact mechanism of the interaction was determined. The aim of this work is to study the problem by use of molecular dynamics simulations.
Jednym zlicznych zastosowań samoorganizujących się monowarstw (SAMs) jest mody-fikacja pracy wyjścia powierzchni metalicznych. Wliteraturze można znaleźć opracowania dotyczące depozycji cienkich warstw poli(metakrylanu metylu) na wybranych samoorganizujących się monowar-stwach na bazie alkanotioli, prowadzącej do dalszych zmian wartości pracy wyjścia całej struktury. Uzyskany efekt wydaje się być zależny od taktyczności polimeru, jednakże wbadaniach eksperymen-talnych nie udało się określić przyczyn tego zjawiska. Wniniejszej pracy wspomniany efekt zbadano za pomocą symulacji komputerowych metodą dynamiki molekularnej.
Źródło:
Polimery; 2020, 65, 9; 598-604
0032-2725
Pojawia się w:
Polimery
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular dynamics simulation of copolymers
Autorzy:
Banaszak, M.
Powiązania:
https://bibliotekanauki.pl/articles/1964087.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
molecular dynamics
computer simulation
copolymer
diblock
ionic copolymer
diffusion
structure factor
equation of state
thermodynamic properties
Opis:
A series of representative molecular dynamics simulations of model Lennard-Jones copolymer chains is presented. We report measurements of thermodynamic, structural and dynamic properties of our model copolymers. For neutral copolymers we confirm our version of thermodynamic perturbation theory of the first order, while for ionic copolymers we demonstrate microphase formation and the anisotropy of the counterion diffusion.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 1; 17-27
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Fluctuations of kinetic energy at molecular dynamics and the atomic interactions in crystals
Autorzy:
Andriyevsky, B.
Piekarski, J.
Andriyevska, L.
Powiązania:
https://bibliotekanauki.pl/articles/118444.pdf
Data publikacji:
2018
Wydawca:
Politechnika Koszalińska. Wydawnictwo Uczelniane
Tematy:
interatomic interactions
molecular dynamics
silicon
phonon relaxation time
oddziaływania międzyatomowe
dynamika molekularna
krzem
czas relaksacji fononów
Opis:
The calculation method of the molecular dynamics has been applied to study the correlation of the kinetic energy fluctuations and the relaxation time of the velocity autocorrelation function and the phonon relaxation time in a crystal. On the basis of the molecular dynamics data for silicon crystal obtained at different temperatures in the range 200 K – 1000 K the correlation between the kinetic energy fluctuations and the relaxation time of the velocity autocorrelation function has been calculated with the relatively high coefficient of determination R2 = 0.9396. The correlation obtained and the corresponding approach substantiate a use of the kinetic energy fluctuations for the calculation of values related to the heat conductivity in the silicon based semiconductors (coefficients of thermal conductivity and diffusivity).
Obliczeniowa metoda dynamiki molekularnej została zastosowana do badania korelacji fluktuacji energii kinetycznej i czasu relaksacji autokorelacyjnej funkcji prędkości i czasu relaksacji fononów w krysztale. Na bazie danych dynamiki molekularnej kryształu krzemu otrzymanych w różnych temperaturach w zakresie 200 K – 1000 K została obliczona korelacja fluktuacji energii kinetycznej i czasu relaksacji autokorelacyjnej funkcji prędkości, która cechuje się stosunkowo wysokim współczynnikiem determinacji R2 = 0.9396. Otrzymana korelacja uzasadnia zastosowanie fluktuacji energii kinetycznej do badań obliczeniowych wielkości powiązanych z przewodnością cieplną półprzewodników na bazie krzemu (współczynniki przewodności i dyfuzyjności cieplnej).
Źródło:
Zeszyty Naukowe Wydziału Elektroniki i Informatyki Politechniki Koszalińskiej; 2018, 12; 19-24
1897-7421
Pojawia się w:
Zeszyty Naukowe Wydziału Elektroniki i Informatyki Politechniki Koszalińskiej
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Morphological analysis of organo-montmorillonites via MD simulations
Autorzy:
Karataş, Deniz
Tekin, Adem
Can, Muhammed F.
Xu, Zhenghe
Çelik, Mehmet S.
Powiązania:
https://bibliotekanauki.pl/articles/2146936.pdf
Data publikacji:
2022
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
organo-montmorillonite
tetradecyl dimethyl ethyl benzyl ammonium chloride
molecular dynamics simulation
cation exchange capacity
binding energy
Opis:
Adsorption on clay surfaces has been studied intensively in recent years. The most curious subject of these studies, which are generally experimental, is how the surfactants are adsorbed at the atomic level to the surface. In this study, the adsorption of quaternary amine salt (tetradecyl dimethyl ethyl benzyl ammonium chloride–TDEBAC) to sodium montmorillonite (Na-MMT) with various cation exchange capacities (CEC) was investigated by using Molecular Dynamics (MD) simulation. In the simulations, as in the experimental studies, it was revealed that the surfactants were both adsorbed on to basal surfaces and settled between the layers. From the morphological analysis obtained from MD simulations, it was calculated that the inter-molecular interaction between the layers was higher than on the basal surface. For example, for the model with 118 CEC motif, the binding energy of all three surfactants in the models with the hydrophilic heads facing the same direction was calculated as -678.18 kcal/mol at the basal surface, while this value was found to be -688.90 kcal/mol in the interlayer. The more striking result is that in the simulations made by turning the head of the middle one of the three surfactants towards the tails of the right and left ones, only -34.86 kcal/mol binding energy was calculated on the basal surface, while this value was -525.63 kcal/mol in the interlayer. As compared middle reversed surfactant models with the same direction ones, despite increased CEC the intermolecular interaction decreased for the basal surface, but the interaction increased between the layers.
Źródło:
Physicochemical Problems of Mineral Processing; 2022, 58, 5; art. no. 152499
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Theoretical models of catalytic domains of protein phosphatases 1 and 2A with Zn2+ and Mn2+ metal dications and putative bioligands in their catalytic centers.
Autorzy:
Woźniak-Celmer, Edyta
Ołdziej, Stanisław
Ciarkowski, Jerzy
Powiązania:
https://bibliotekanauki.pl/articles/1044161.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
protein phosphatase inhibitors
constrained simulated annealing
protein phosphatase 1A and 2B
molecular dynamics
homology modeling
Opis:
The oligomeric metalloenzymes protein phosphatases dephosphorylate OH groups of Ser/Thr or Tyr residues of proteins whose actions depend on the phosphorus signal. The catalytic units of Ser/Thr protein phosphatases 1, 2A and 2B (PP1c, PP2Ac and PP2Bc, respectively), which exhibit about 45% sequence similarity, have their active centers practically identical. This feature strongly suggests that the unknown structure of PP2Ac could be successfully homology-modeled from the known structures of PP1c and/or PP2Bc. Initially, a theoretical model of PP1c was built, including a phosphate and a metal dication in its catalytic site. The latter was modeled, together with a structural hydroxyl anion, as a triangular pseudo-molecule (Zno or Mno), composed of two metal cations (double Zn2+ or Mn2+, respectively) and the OH- group. To the free PP1c two inhibitor sequences R29RRRPpTPAMLFR40 of DARPP-32 and R30RRRPpTPATLVLT42 of Inhibitor-1, and two putative substrate sequences LRRApSVA and QRRQRKpRRTI were subsequently docked. In the next step, a free PP2Ac model was built via homology re-modeling of the PP1c template and the same four sequences were docked to it. Thus, together, 20 starting model complexes were built, allowing for combination of the Zno and Mno pseudo-molecules, free enzymes and the peptide ligands docked in the catalytic sites of PP1c and PP2Ac. All models were subsequently subjected to 250-300 ps molecular dynamics using the AMBER 5.0 program. The equilibrated trajectories of the final 50 ps were taken for further analyses. The theoretical models of PP1c complexes, irrespective of the dication type, exhibited increased mobilities in the following residue ranges: 195-200, 273-278, 287-209 for the inhibitor sequences and 21-25, 194-200, 222-227, 261, 299-302 for the substrate sequences. Paradoxically, the analogous PP2Ac models appeared much more stable in similar simulations, since only their "prosegment" residues 6-10 and 14-18 exhibited an increased mobility in the inhibitor complexes while no areas of increased mobility were found in the substrate complexes. Another general observation was that the complexes with Mn dications were more stable than those with Zn dications for both PP1c and PP2Ac units.
Źródło:
Acta Biochimica Polonica; 2001, 48, 1; 35-52
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Synergistic mechanism of dodecylamine/octanol mixtures enhancing lepidolite flotation from the self-aggregation behaviors at the air/liquid interface
Autorzy:
Bai, Yang
Xu, Mengxu
Wen, Weixiang
Zhu, Shifei
Mo, Weichen
Yan, Pingke
Powiązania:
https://bibliotekanauki.pl/articles/27323641.pdf
Data publikacji:
2023
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
DDA/OCT mixtures
self-aggregation behaviors
flotation foam
molecular dynamics simulations
surface tension
air interface
liquid interface
Opis:
Surface tension measurements and molecular dynamics (MD) simulations were used to explore the flotation foam properties and self-aggregation behaviors of dodecylamine (DDA)/octanol (OCT) mixtures formed with different mole ratios at the air/liquid interface. Based on the surface and thermodynamic parameters, the DDA/OCT mixtures exhibited greater interfacial activities and adsorption capacities than their individual components. The MD simulations showed that DDA and OCT were aggregated through hydrogen bonding, coulombic forces and hydrophobic association. OCT was inserted into the DDA adsorption layer, causing the alkyl chains of both DDA and OCT to extend from water to air at varying heights and angles. The addition of OCT improved the hydration of the amino groups and reduced the overall number of hydrogen bonds. The stability of the flotation foam decreased, and the high viscosity and difficult defoaming of the DDA flotation foam were significantly improved. When the DDA/OCT mole ratio was 2:1, the included angle formed between the alkyl chains and the interface was maximized, leading to enhanced compatibility among the alkyl chains, and the hydrogen bond energy was relatively large, which showed a strong synergistic effect. The MD simulation findings were consistent with the results obtained from the lepidolite flotation and surface tension experiments conducted in this study; our results could provide a theoretical foundation for the selection of superior mixed collectors and frothers.
Źródło:
Physicochemical Problems of Mineral Processing; 2023, 59, 6; art. no. 176510
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Influence of substitutions of Isu1 residues on binding to Jac1 protein
Autorzy:
Mozolewska, M. A.
Powiązania:
https://bibliotekanauki.pl/articles/1938619.pdf
Data publikacji:
2016
Wydawca:
Politechnika Gdańska
Tematy:
Saccharomyces cerevisiae
Isu1-Jac1 protein complex
alanine scan
molecular dynamics
coarse-grained UNRES force field
Opis:
The iron-sulfur (Fe/S) clusters are the most ancient co-factors of proteins involved in the most essential processes in bacterial systems and yeast, such as Saccharomyces cerevisiae. The main protein involved in the Fe/S cluster transfer is the Iron sulfur cluster assembly protein 1 (Isu1), which interacts with Jac1 during one of the stages of the Fe/S cluster biogenesis cycle forming a binary complex. In this work, the interaction interface of Isu1 was investigated by selective substitutions of amino-acid residues to understand their role in binding to the Jac1 protein. An initial alanine scan was done to limit the number of possible residues subjected to the replacement and to confirm the previously obtained results. Then, MD simulations using the coarse-grained UNRES force field were run for two selected mutants: L63 V72 F94 and L63 V64 G65 D71. The analysis of the dynamics and interaction patterns of the Isu1-Jac1 complexes confirmed that the investigated residues played an important role in their binding.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 417-423
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Estimation of phonon relaxation time for silicon by means of using the velocity autocorrelation function of atoms in molecular dynamics
Autorzy:
Andriyevsky, Bohdan
Maliński, M.
Buryło, Ł.
Stadnyk, V. Y.
Romanuk, M. O.
Piekarski, J.
Andriyevska, L.
Powiązania:
https://bibliotekanauki.pl/articles/201222.pdf
Data publikacji:
2019
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
silicon
molecular dynamics
relaxation time of the velocity autocorrelation function
coefficient of thermal diffusivity
krzem
dynamika molekularna
Opis:
Results of the ab initio molecular dynamics calculations of silicon crystals are presented by means of analysis of the velocity autocorrelation function and determination of mean phonon relaxation time. The mean phonon relaxation time is crucial for prediction of the phonon-associated coefficient of thermal conductivity of materials. A clear correlation between the velocity autocorrelation function relaxation time and the coefficient of thermal diffusivity has been found. The analysis of the results obtained has indicated a decrease of the velocity autocorrelation function relaxation time t with increase of temperature. The method proposed may be used to estimate the coefficient of ther-mal diffusivity and thermal conductivity of the materials based on silicon and of other wide-bandgap semiconductors. The correlation between kinetic energy fluctuations and relaxation time of the velocity autocorrelation function has been calculated with the relatively high coefficient of determination R2 = 0.9396. The correlation obtained and the corresponding approach substantiate the use of kinetic energy fluctuations for the calculation of values related to heat conductivity in silicon-based semiconductors (coefficients of thermal conductivity and diffusivity).
Źródło:
Bulletin of the Polish Academy of Sciences. Technical Sciences; 2019, 67, 3; 651-656
0239-7528
Pojawia się w:
Bulletin of the Polish Academy of Sciences. Technical Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Computational studies of TTR related amyloidosis: exploration of conformational space through petri net-based algorithm
Autorzy:
Jakubowski, R.
Gogolińska, A.
Pepłowski, Ł.
Skrzyniarz, P.
Nowak, W.
Powiązania:
https://bibliotekanauki.pl/articles/1954249.pdf
Data publikacji:
2022-02-01
Wydawca:
Politechnika Gdańska
Tematy:
transthyretin amyloidosis
molecular dynamics
Petri nets
clustering
conformational space
graphs
dynamika molekularna
sieci Petriego grupowanie
konformacyjne miejsca
wykresy
Opis:
Amyloidosis, a serious and widespread disease with a genetic background , manifests itself through the formation of dangerous fibrils in various organs. Apart from the polluted environment and an unhealthy lifestyle, genetic factors may accelerate this process leading in some cases to lethal damages to the body. Recently, a growing interest in amyloidogenic protein research has been observed. Transthyretin (TTR) is a tetrameric protein that transports thyroid hormone thyroxine and retinol binding protein in plasma and the cerebral fluid. Sometimes TTR breaks apart and forms fibrils. Several single point mutations, having de stabilizing impact on the TTR complex, are involved in the amyloidogenic TTR cascade. Problems with the TTR tetramer stability and conformational space characteristics of the protein have not been addressed computationally before. We present selected results of our molecular dynamics (MD, ∼ 2000ns) and steered MD simulations ( SMD ) of three variants of TTR : Wild Type ( WT ), V 30 M and L 55 P . SMD has been used to enforce the dissociation of TTR . Conformational spaces of WT TTR and its amyloidogenic variants have been investigated using a novel “ One Place One Conformation ” ( OPOC ) algorithm based on a graph technique called Petrinet (PN) formalism. While the PN approach alone does not permit a direct identification of protein regions with reduced stability, it gives quite a useful tool for an effective compari son of complex protein energy landscapes explored during classical and/or SMD steered molecular dynamics simulations.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 3; 289--300
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Central-force decomposition of the Tersoff potential
Autorzy:
Tran, H.
Winczewski, Sz.
Powiązania:
https://bibliotekanauki.pl/articles/1940180.pdf
Data publikacji:
2017
Wydawca:
Politechnika Gdańska
Tematy:
central-force decomposition
Tersoff potential
molecular dynamics
empirical potentials
potencjał Tersoffa
dynamika molekularna
potencjały empiryczne
rozkład sił centralnych
Opis:
Central forces play important role in the analysis of results obtained with particle simulation methods, since they allow evaluating stress fields. In this work we derive expressions for a central-force decompositon of the Tersoff potential, which is often used to describe interatomic interactions in covalently bonded materials. We simplify the obtained expressions and discuss their properties.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2017, 21, 3; 261-283
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Surface diffusion and cluster formation of gold on the silicon (111)
Autorzy:
Plechystyy, V.
Shtablavyi, I.
Rybacki, K.
Winczewski, S.
Mudry, S.
Rybicki, J.
Powiązania:
https://bibliotekanauki.pl/articles/952460.pdf
Data publikacji:
2020
Wydawca:
Stowarzyszenie Komputerowej Nauki o Materiałach i Inżynierii Powierzchni w Gliwicach
Tematy:
molecular dynamics
surface diffusion
clusters
atomic monolayer
activation energy
dynamika molekularna
dyfuzja powierzchniowa
klastry
monowarstwa atomowa
energia aktywacji
Opis:
Purpose: Investigation of the gold atoms behaviour on the surface of silicon by molecular dynamics simulation method. The studies were performed for the case of one, two and four atoms, as well as incomplete and complete filling of gold atoms on the silicon surface. Design/methodology/approach: Investigations were performed by the method of molecular dynamics simulation using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). MEAM potential of interatomic interaction was used for modelling. Molecular dynamic simulations were carried out in isothermal-isobaric ensemble (NpT) with a timestep 1.0 fs. Findings: As a result of studies, the preferred interaction between gold atoms and the formation of clusters at temperatures up to 800 K was revealed. Analysis of the temperature dependences of the number of large jumps of atoms made it possible to calculate the activation energy of a single jump. It was found that activation energy of single atomic displacement decreases with increasing number of gold atoms. Research limitations/implications: Only a limited number of sets of atoms were used in the study. It is possible that for another combination of atoms and a larger substrate surface, the formation of gold nanoislands on the silicon surface can be observed, which requires further research. Practical implications: The research results can be used to select the modes of gold sputtering to create gold nanoislands or nanopillars on the silicon surface. Originality/value: Computer modelling of the behaviour of gold atoms on the surface of silicon with the possibility of their self-organization and cluster formation was performed for the first time.
Źródło:
Journal of Achievements in Materials and Manufacturing Engineering; 2020, 101, 2; 49-59
1734-8412
Pojawia się w:
Journal of Achievements in Materials and Manufacturing Engineering
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Quantum-classical calculations of the nanomechanical properties of metals
Autorzy:
Dziedzic, J.
Powiązania:
https://bibliotekanauki.pl/articles/1964138.pdf
Data publikacji:
2009
Wydawca:
Politechnika Gdańska
Tematy:
hybric methods
cross-scaling
tight-binding
learn-on-the-fly
nanoscale
metals
nanoindentation
molecular-dynamics
Sutton-Chen potential
Opis:
Molecular-dynamics (MD) simulations constitute an important tool in the study of nanoscale metallic systems, especially so in the face of the difficulties plaguing their experimental analysis. Main limitations of the MD method stem from the empirical nature of the potentials employed, their functional form which is postulated ad hoc, and its classical nature. The neglect of electronic effects and the unjustified utilization of the potential for system configurations significantly different from those, for which the potential was parametrized makes the results of strictly classical calculations dubious, at least for a certain class of systems. On the other hand, high computational complexity of quantum-based methods, where atomic interactions are described ab initio, prohibits their direct use in the study of systems larger than several tens of atoms. In the last decade, a growing popularity of so-called hybrid (or cross-scaling) methods can be observed, that is, methods which treat the most interesting part of the system with a quantum-based approach, while the remainder is treated classically. Physically sound handshaking between the two methodologies (quantum and classical) within a single simulation constitutes a serious challenge, the majority of difficulties concentrating around the interface between the fragments of the system treated with the two methods. The aforementioned interface is most easily constructed for covalently bonded systems, where the bonds cut by the isolation of the quantum-based region can be saturated by the introduction of specially crafted link-atoms. In metallic systems, however, due to electronic delocalization, this traditional approach cannot be employed. This paper describes a physically sound and adequately efficient computational technique, which allows for the inclusion of results of locally employed quantum-based computations within a molecular-dynamics simulation, for systems described by the many-body Sutton-Chen (SC) potential, used in the study of fcc metals. The proposed technique was developed taking as a point of departure the Learn-on-the-Fly (LOTF) formalism, a recent development itself. The original LOTF approach is only suitable for two- or three-body potentials and is serial in nature, whereas the proposed technique can be used with many-body potentials and is parallel-ready. An implementation of the proposed approach in the form of computer code, which allows for parallel hybrid computations for metallic systems is also described. Finally, results from a set of hybrid simulations of nanoindentation of a copper workmaterial with a hard indenter utilizing the aforementoned technique and computer code is presented, as evidence of its viability.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2009, 13, 3; 207-310
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Właściwości czasowo-rozdzielcze słabych międzycząsteczkowych wiązań wodorowych C-H···F
Time-resolved properties of intermolecular C-H···F hydrogen bonds
Autorzy:
Polańska, Marta
Rodziewicz, Paweł
Powiązania:
https://bibliotekanauki.pl/articles/27310029.pdf
Data publikacji:
2023
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
wiązanie wodorowe
teoria funkcjonału gęstości
dynamika molekularna Cara i Parrinello
hydrogen bond
density functional theory
Car-Parrinello molecular dynamics
Opis:
The hydrogen bond is one of the most important and interesting phenomena in nature. In this publication we will shed light on the discovery of hydrogen bond and a time evolution of its definition in the last 100 years. Both structural and spectroscopic parameters of the hydrogen bond will be discussed. A special focus will be given to the latest IUPAC definition of the hydrogen bond and its consequences to scientific research. The main aim of this study is to highlight theoretical studies based on first principles calculations and molecular dynamics simulations which not only support experimental results but also provide parameters which are crucial to understand the nature of hydrogen bonds. Particular attention will be given to methods and theoretical ideas used in the computational studies of hydrogen bonds. Utilizing static DFT/ab initio calculations and molecular dynamics simulations enables comparison of different binding energies and studying time evolution of the hydrogen-bonded molecular system on the atomistic level. We will discuss time-resolved properties of weak intermolecular hydrogen bonds, using as an example C-H···F containing model systems, namely F3CH*(HF)n molecular complexes and (F3CH)2-4 aggregates.
Źródło:
Wiadomości Chemiczne; 2023, 77, 9-10; 899--919
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Wykorzystanie dynamiki molekularnej w badaniach szkieł
Application of molecular dynamics in examination of glasses
Autorzy:
Goj, P.
Powiązania:
https://bibliotekanauki.pl/articles/169158.pdf
Data publikacji:
2018
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Ceramiki i Materiałów Budowlanych
Tematy:
dynamika molekularna
badania więźby szkieł
symulacje komputerowe
szkła krzemowo-sodowe
molecular dynamics
glass network examination
computer simulations
sodium silicate glasses
Opis:
Klasyczna dynamika molekularna MD jest jedną z technik symulacji komputerowych wieloatomowych lub wielocząsteczkowych układów. Pozwala na badanie struktury oraz właściwości zarówno materiałów krystalicznych, jak i amorficznych. Opiera się na rozwiązywaniu numerycznym klasycznych równań ruchu. Nie tylko uzupełnia badania eksperymentalne, ale jest również narzędziem pozwalającym na badanie budowy materiałów na poziomie nieosiągalnym konwencjonalnymi technikami. W celu przedstawienia klasycznej dynamiki molekularnej wykonano symulacje dwóch szkieł 80SiO2-20Na2O i 85SiO2-15Na2O [%mol]. Otrzymane wyniki dobrze zgadzały się z obecnym stanem wiedzy. Wykonane symulacje świadczą o tym, że technika ta jest niezwykle użyteczna przy poznawaniu struktury szkieł. Wykorzystując tę technikę, można przewidywać wpływ modyfikatorów na więźbę szkła, a przez to możliwe jest wskazywanie kierunku dalszych badań oraz optymalizacja składów chemicznych.
Molecular dynamics MD is one of computer simulation methods of multiatomic or multimolecular systems. It allows to examination of structure and properties both crystalline and amorphous materials. This technique consists of the numerical solution of the classical equation of motion. It complements not only experimental methods but also it is tool make possible examination of material structure on the unavailable level for conventional methods. In order to introduce to molecular dynamics, the simulations of two glasses 80SiO2‑20Na2O and 85SiO2-15Na2O [%mol] were performed. Obtained results corresponds well to the actual state of knowledge. Performed simulation testify that this technique is a very useful to examine glass structure. Using this method, it is possible to predict influence of modifiers on glass network, it’s make possible indication research direction and optimization of chemical composition.
Źródło:
Szkło i Ceramika; 2018, R. 69, nr 1, 1; 12-15
0039-8144
Pojawia się w:
Szkło i Ceramika
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Struktura a nieelastyczne rozpraszanie neutronów przez kryształy molekularne z wiązaniami wodorowymi
Structure and inelastic neutron scattering by the molecular crystals with the hydrogen bonds
Autorzy:
Rok, M.
Bator, G.
Sobczyk, L.
Powiązania:
https://bibliotekanauki.pl/articles/171492.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
kompleksy molekularne
wiązanie wodorowe
struktura krystaliczna
rozpraszanie neutronów
dynamika cząsteczek w fazie stałej
molecular complexes
hydrogen bonds
crystal structure
neutron scattering
molecular dynamics in the solid state
Opis:
The molecular crystals, which are built of organic or organic-inorganic molecules, are characterized by the weak intermolecular interactions. From the viewpoint of the potential applications in electronics or optoelectronics the electric properties of the crystals are essential. In turn these properties are related to their crystal structure as well as the dynamics of the molecules in the solid state. The existence of the hydrogen bonds in the crystal structures, conventional and unconventional, is crucial from the viewpoint of the electric properties of the crystals. The dynamics of methyl groups present in the structure can be a measure of the molecular interactions in the crystals. In this work the dynamical properties, first of all taking into account the research results concerning the neutron scattering, will be discussed. The neutron technique is very effective as regards the methyl group dynamics investigations. The relationship between a formation of the conventional and unconventional hydrogen bonds and a tunneling of the methyl groups at low temperature will be discussed. The method of the interpretation of the INS spectra will be described taking into account the theoretical model, the parameters of which are fitted to the experimental data. The examples will regard the following molecular crystals: p-N,N’-1,10-tetraacethyldiaminodurene (TADD) (Figs. 2 and 4), 2,3,5,6-tetramethylpyrazine with chloranilic acid (TMP·CLA) (Figs. 5, 6 and 7), 2,3,5,6- tetramethylpyrazine with bromanilic acid (TMP·BRA) (Figs. 5 and 6) and the crystal of 3,4,7,8-tetramethylphenantroline (Me4phen) and its complex with picric acid (Me4phen·PIC) (Figs. 8 and 9). In this paper we have shown that the surrounding of the methyl group and its interactions with the adjacent molecules has a stronger effect than the changes in the electronic charge density in the molecule.
Źródło:
Wiadomości Chemiczne; 2017, 71, 7-8; 533-557
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Influence of addition of carbon nanotubes on rheological properties of selected liquid lubricants - a computer simulation study
Autorzy:
Chopra, Anjali
Winczewski, Szymon
Powiązania:
https://bibliotekanauki.pl/articles/1954594.pdf
Data publikacji:
2020
Wydawca:
Politechnika Gdańska
Tematy:
nanotechnology
tribology
lubricants
rheology
propylene glycol
carbon nanotubes
non-equilibrium molecular dynamics
nanotechnologia
tribologia
smary
reologia
glikol propylenowy
nanorurki
nierównowagowa dynamika molekularna
Opis:
This work is motivated by the improvement of anti-friction properties of lubricants by addition of CNTs proved experimentally in literature. In particular, a methodology is developed to compute the shear viscosity of liquid lubricants (Propylene Glycol) based on Molecular Dynamics simulation. Non-Equilibrium molecular dynamics (NEMD) approach is used with a reactive force field ReaxFF implemented in LAMMPS. The simulations are performed using the canonical (NVT) ensemble with the so-called SLLOD algorithm. Couette flow is imposed on the system by using Lees-Edwards periodic boundary conditions. Suitable parameters such as simulation time and imposed shear velocity are obtained. Using these parameters, the influence of addition of 27 wt% CNTs to Propylene Glycol on its viscosity is analyzed. Results show that 3.2 million time-steps with a 0.1 fs time-step size is not sufficient for the system to reach equilibrium state for such calculations. With the available computational resources, a shear velocity of 5 × 10−5 Å/fs was observed to give viscosity value with approximately 43% error as compared to the experimental value. Moreover, the lubricant exhibited a shear thinning behaviour with increasing shear rates. CNTs enhanced the lubricant's viscosity by 100-190% depending upon the averaging method used for calculation.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2020, 24, 4; 345-388
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Modelowanie adsorpcji związków biologicznie czynnych na materiałach węglowych
Modelling of Adsorption of Biologically Active Compounds on Carbonaceous Materials
Autorzy:
Gauden, P. A.
Terzyk, A. P.
Furmaniak, S.
Wiśniewski, M.
Bielicka, A.
Werengowska-Ciećwierz, K
Zieliński, W.
Kruszka, B.
Bieniek, A.
Powiązania:
https://bibliotekanauki.pl/articles/297197.pdf
Data publikacji:
2013
Wydawca:
Politechnika Częstochowska. Wydawnictwo Politechniki Częstochowskiej
Tematy:
benzen
fenol
paracetamol
adsorpcja z fazy ciekłej
materiały węglowe
kinetyka
dynamika molekularna
benzene
phenol
adsorption from solution
carbonaceous materials
kinetics
molecular dynamics simulation
Opis:
Omówiono wpływ porowatości oraz chemicznej natury powierzchni węgla aktywnego na adsorpcję trzech związków organicznych (benzenu, fenolu oraz paracetamolu) z rozcieńczonych roztworów wodnych w oparciu o obliczenia dynamiki molekularnej (pakiet GROMACS). Wykorzystano model porów szczelinopodobnych oraz model tzw. „miękkiego” węgla aktywnego. Charakteryzują się one stopniową zmianą struktury mikroporowatej. Ponadto w strukturę materiałów węglowych wbudowano różną ilość grup funkcyjnych. Wyniki otrzymanych symulacji komputerowych wykazują jakościową zgodność z pomiarami eksperymentalnymi. I tak na przykład zaobserwowano spadek adsorpcji dla paracetamolu w porównaniu z adsorpcją benzenu. Ponadto wyniki obliczeń komputerowych wskazują, że na proces adsorpcji związków organicznych mają wpływ zarówno porowatość, jak i chemiczna natura materiału węglowego (zawartość tlenu). Ten drugi z czynników decyduje o mechanizmie blokowania porów i związany jest ze zwiększeniem gęstości wody w pobliżu grup chemicznych (tworzenie klastrów). Efekt blokowania porów zależy także od rozmiaru porów i przestaje odgrywać rolę dla porów o szerokościach większych niż 0,68 nm. W konsekwencji cząsteczki adsorbowanych związków organicznych nie mogą wnikać w głąb struktury materiału węglowego, ale adsorbują się na powierzchni zewnętrznej porów w pobliżu ich wejść.
MD simulation studies (GROMACS package) showing the influence of porosity and carbon surface oxidation on adsorption of three organic compounds (i.e. benzene, phenol, and paracetamol) from aqueous solutions on carbons were reported. Based on a model of slit-like pores and “soft” activated carbons different adsorbents with gradually changed microporosity were created. Next, different amount of surface oxygen groups was introduced. We observe quantitative agreement between simulation and experiment, i.e. the decrease in adsorption from benzene down to paracetamol. Simulation results clearly demonstrate that the balance between porosity and carbon surface chemical composition in organics adsorption on carbons, and the pore blocking determine adsorption properties of carbons. Pore blocking effect decreases with diameter of slits and practically vanishes for widths larger than c.a. 0.68 nm. Moreover, adsorbed molecules occupy the external surface of the slit pores (the entrances) in the case of oxidized adsorbents.
Źródło:
Inżynieria i Ochrona Środowiska; 2013, 16, 2; 225-234
1505-3695
2391-7253
Pojawia się w:
Inżynieria i Ochrona Środowiska
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Dopant ions size impact on structural properties of ordered poly(3,4-ethylenedioxythiophene) systems
Wpływ wielkości jonów domieszkujących na właściwości strukturalne uporządkowanych układów poli(3,4-etylenodioksytiofenu)
Autorzy:
Śniechowski, Maciej
Kozik, Tomasz A.
Łużny, Wojciech
Powiązania:
https://bibliotekanauki.pl/articles/947384.pdf
Data publikacji:
2020
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Chemii Przemysłowej
Tematy:
self-organization
molecular dynamics simulations
conductive polymers
X-ray diffraction
crystal structure
samoorganizacja
symulacja dynamiki molekularnej
polimery przewodzące
dyfrakcja promieniowania rentgenowskiego
struktura krystaliczna
Opis:
The purpose of this work was to determine whether the structures of ordered part of novel poly(3,4-ethylenedioxythiophene) PEDOT : OTf (doped with trifluoromethanesulfonate anions) and PEDOT : HSulf (doped with hydrogensulfate anions) systems could really be simply the layered structure of PEDOT : Tos (doped with tosylate anions) with the counter ion changed to the appropriate one. Insight into this problem could be provided by molecular dynamics simulations but also by swarm intelligence optimization, developed earlier for the purpose of investigating the other structures.
Zbadano zdolność struktury uporządkowanej części nowych układów domieszkowanych poli(3,4-etylenodioksytiofenu) (PEDOT) [PEDOT : OTf (domieszkowane anionami trifluorometanosulfonianowymi) i PEDOT : HSulf (domieszkowane anionami wodorosiarczanowymi)] do powielania znanej z literatury warstwowej struktury PEDOT : Tos (domieszkowane anionami tosylanowymi) z jonem domieszki zmienionym na odpowiedni. Poszukiwania nowych struktur wspomagano symulacjami dynamiki molekularnej, a także z zastosowaniem optymalizacji opartej na algorytmach inteligencji stadnej.
Źródło:
Polimery; 2020, 65, 9; 639-643
0032-2725
Pojawia się w:
Polimery
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The interaction of poly(L-lactic acid) and the nucleating agent N,N-bis(benzoyl) suberic acid dihydrazide
Interakcje między poli(kwasem L-mlekowym) a czynnikiem zarodkującym —N,N-bis(benzoilo)dihydrazydem kwasu suberynowego
Autorzy:
Cai, Y.-H.
Zhao, L.-S.
Powiązania:
https://bibliotekanauki.pl/articles/947457.pdf
Data publikacji:
2015
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Chemii Przemysłowej
Tematy:
poly(L-lactic acid)
nucleating agent
crystallization
nucleation mechanism
molecular dynamics simulation
poli(kwas L-mlekowy)
czynnik zarodkujący
krystalizacja
mechanizm zarodkowania
symulacja metodą dynamiki molekularnej
Opis:
Since N,N'-bis(benzoyl) suberic acid dihydrazide [NA(S)] acts as a powerful nucleating agent for poly(L-lactic acid) (PLLA), it is necessary to study the nucleation mechanism of NA(S) in the crystallization of PLLA. The interaction between PLLA and NA(S) was investigated by Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA) and temperature-dependent Raman spectroscopy. The results from FT-IR and temperature-dependent Raman spectroscopy showed that a hydrogen bond between the C=O of PLLA and the N-H of NA(S) was formed. The TGA also indicated the existence of an intense interaction between PLLA and NA(S), resulting in the potent nucleation ability of NA(S) for PLLA. Molecular dynamics simulations (MDS) were employed to simulate the interaction of PLLA on the NA(S) surface. The simulation results further confirmed the hydrogen bond between PLLA and NA(S). The MDS study also analyzed the interaction energy between PLLA and NA(S). The MDS results can be used to select the proper nucleating agents and design novel organic nucleating agents.
Zbadano mechanizm zarodkowania przy użyciu N,N'-bis(benzoilo)dihydrazydu kwasu suberynowego [NA(S)] w procesie krystalizacji poli(kwasu L-mlekowego) (PLLA). Interakcje między cząsteczkami PLLA i NA(S) oceniano na podstawie spektroskopii w podczerwieni z transformacją Fouriera, analizy termograwimetrycznej oraz widm Ramana, rejestrowanych w różnej temperaturze. Stwierdzono, że pomiędzy tlenem z grupy C=O w łańcuchu PLLA a wodorem z grupy N-H obecnej w NA(S) tworzą się wiązania wodorowe. Analiza TGA wykazała, że ww. intensywne interakcje są wynikiem dużej zdolności NA(S) do zarodkowania krystalizacji PLLA. Do zbadania oddziaływań na powierzchni NA(S) zastosowano także symulacje metodą dynamiki molekularnej (MDS), które potwierdziły występowanie wiązań wodorowych PLLA/NA(S). Metodą MDS określono też energię interakcji (technika MDS może być wykorzystana przy wyborze środka zarodkującego odpowiedniego dla danego układu).
Źródło:
Polimery; 2015, 60, 11-12; 693-699
0032-2725
Pojawia się w:
Polimery
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Nanopory : budowa, właściwości, modele, zastosowania
Nanopores : structure, properties, models, app lications
Autorzy:
Stachiewicz, A.
Molski, A.
Powiązania:
https://bibliotekanauki.pl/articles/171558.pdf
Data publikacji:
2013
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
nanopory
prąd jonowy
translokacja biopolimerów
równanie Poissona-Boltzmanna
równanie Poissona-Nernsta-Plancka
dynamika molekularna
nanopores
ion current
biopolymer translocation
Poisson-Boltzmann
equation
Poisson-Nernst-Planck equation
molecular dynamics
Opis:
Nanopores are small (1–100 nm diameter) holes/channels formed in biological membranes (Fig. 1) or fabricated in synthetic materials (Fig. 2). Permeation of ions and small molecules through nanopores is common in biological systems. The first experiments where nanopores were used as single-molecule sensors were performed in the 90s [1, 2]. The detection principle is based on a monitoring of an ionic current passing through a nanopore as an electric field is applied across the membrane. Electrically charged particles (e.g. DNA ) move in the electric field and block the ionic current as they pass through the nanopore. A sudden drop of the ionic current signals a single-molecule translocation event (Fig. 3–5). Nanopore sensors can give an information about the analyte: its size, structure and bonds stability. Today, a major topic of interest is the possibility of nanopore DNA sequencing. In this work we present an introduction to nanopore technology and to current research related to potential nanopore applications. First, we describe biological and synthetic nanopores: their structure and methods of fabrication. Next, different modes of nanopore experiments are presented. In the third section, we focus on theoretical models and simulations of nanopores. Finally, we present future perspectives for applications with particular reference to DNA sequencing.
Źródło:
Wiadomości Chemiczne; 2013, 67, 3-4; 277-302
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Application of the molecular dynamics method for modelling of mass transfer on the border of Ni-Al bimetal
Zastosowanie metody dynamiki molekularnej do modelowania transferu masy na granicy bimetalu Ni-Al
Autorzy:
Starostenkov, M.
Demina, I.
Popova, G.
Denisova, N.
Smolarz, A.
Powiązania:
https://bibliotekanauki.pl/articles/408811.pdf
Data publikacji:
2012
Wydawca:
Politechnika Lubelska. Wydawnictwo Politechniki Lubelskiej
Tematy:
modelowanie komputerowe
proces dyfuzji
wakans
metoda dynamiki molekularnej
atom międzywęzłowy
sieć krystaliczna
transport masy
method of computer modelling
diffusion process
vacancy
method of molecular dynamics
internodal atom
crystalline lattice
mass transfer
Opis:
One of the basic issues of examination of process of interaction of two-component alloys is the study of the mass transfer process in the presence of dot flaws: internodal atoms and vacancies. The study of this process in real experiments is impossible; therefore it is reasonable to apply computer modelling. The authors present a model of Ni-Al bimetal diffusion process produced by the method of molecular dynamics.
Jednym z podstawowych zagadnień analizy procesu interakcji stopów dwuskładnikowych jest badanie procesu wymiany masy w obecności defektów punktowych: atomów międzywęzłowych i wakansów. Badania tego procesu w rzeczywistych eksperymentach jest niemożliwe, dlatego uzasadnione jest zastosowanie modelowania komputerowego. Autorzy przedstawiają model procesu dyfuzji w bimetalu Ni-Al stworzony metodą dynamiki molekularnej.
Źródło:
Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska; 2012, 1; 36-38
2083-0157
2391-6761
Pojawia się w:
Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Synthesis, characterization and molecular dynamics simulation of dendronized poly(3,5-diphthalimidoalkylphenyl methacrylate)s
Synteza, charakterystyka i symulacje metodą dynamiki molekularnej dendrymerycznych poli(metakrylanów 3,5-diftalimidoalkilofenylu)
Autorzy:
Alvarado, N.
Alegría, L.
Sandoval, C.
Gargallo, L.
Leiva, A.
Radic, D.
Powiązania:
https://bibliotekanauki.pl/articles/946840.pdf
Data publikacji:
2016
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Chemii Przemysłowej
Tematy:
poly(phtalimidoalkyl methacrylate)
dendronized polymers
spacer groups
molecular dynamics simulation
radius of gyration
end-to-end distance
poli(metakrylan ftalimidoalkylu)
polimery dendrymeryczne
grupy dystansujące
symulacja metodą dynamiki molekularnej
promień bezwładności
odległość między końcami łańcucha
Opis:
Dendronized methacrylates containing 3,5-diphthalimidoalkylphenyl moieties (with ethyl, propyl or butyl spacer groups) were synthesized. These monomers were then polymerized using radical polymerization. Monomers and polymers were characterized using Fourier transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance methods (1H NMR and 13C NMR). Molecular weight was estimated by multi-angle static light scattering (MALS). Molecular dynamics simulation was performed to evaluate the conformational radius of gyration (Rg) and the end-to-end distance (ree). Different spatial arrangements depending on the length of the spacer group are observed.
Zsyntezowano dendrymeryczne metakrylany zawierające ugrupowania 3,5-diftalimidoalkilofenylowe (z etylowymi, propylowymi lub butylowymi grupami dystansującymi), a następnie monomery te poddano polimeryzacji rodnikowej. Do określenia struktury wyjściowych monomerów oraz otrzymanych polimerów zastosowano spektroskopię w podczerwieni z transformacją Fouriera (FT-IR) i metody magnetycznego rezonansu jądrowego (1H NMR i 13C NMR). Oznaczono również masę cząsteczkową polimerów metodą wielokątowego rozpraszania światła (MALS). Symulacje metodą dynamiki molekularnej pozwoliły na wyznaczenie konformacyjnych promieni bezwładności (Rg), a także odległości między końcami łańcucha (ree). Zaobserwowano różne układy przestrzenne, których rodzaj zależał od wielkości grupy dystansującej.
Źródło:
Polimery; 2016, 61, 1; 10-15
0032-2725
Pojawia się w:
Polimery
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Badanie struktury i dynamiki N-terminalnych sekwencji dermorfiny i ich analogów z wykorzystaniem spektroskopii NMR w ciele stałym i rentgenografii
Studies on the structure and dynamics of N-terminal sequences of dermorphin and their analogs by means of solid state NMR spectroscopy and XRD
Autorzy:
Trzeciak-Karlikowska, K.
Powiązania:
https://bibliotekanauki.pl/articles/171648.pdf
Data publikacji:
2012
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
peptydy opioidowe
oddziaływania CH-pi
dynamika molekularna
oddziaływanie peptyd–fosfolipid
spektroskopia NMR
1H Ultra Fast MAS NMR
PISEMA MAS
PILGRIM
XRD
opioid peptides
CH-pi interactions
molecular dynamics
peptide–phospholipid interaction
NMR spectroscopy
Opis:
Deltorphin I (Tyr-d-Ala-Phe-Asp-Val-Val-Gly-NH_2) and dermorphin (Tyr-d-Ala-Phe- -Gly-Tyr-Pro-Ser-NH_2) are natural opioid peptides that have been isolated from the skin of South American frogs [1]. The presence of d-amino acid is crucial for their biological activity. The synthetic analogs of given heptapeptides containing l-alanine are not analgesics [2]. Analysis of the influence of stereochemistry on molecular packing, dynamics and biological functions of neuropeptides is still important for receptor studies and practical applications (e.g. design of new selective pain killers). Presented research is focused on the structure and dynamics of two N-terminal sequences of dermorphin: tripeptide Tyr-d-Ala-Phe 1, tetrapeptide Tyr-D-Ala-Phe-Gly 2, and their analogs with l-alanine: Tyr-Ala-Phe 3 and Tyr-Ala-Phe-Gly 4, using solid state NMR and X-ray diffraction. This study clearly demonstrates that 1 and 2 crystallized under different conditions to form exclusively one structure [3, 4]. In contrast, tripeptide and tetrapeptide with l-Ala in the sequence very easily form different crystal modifications. Tyr-Ala-Phe 3 crystallizes into two forms: 3a and 3b [5], while Tyr-Ala-Phe-Gly 4 gives three modifications: 4a, 4b and 4c [4]. It seems that one of the factors, which can be important in the preorganization mechanism anticipating the formation of crystals, is the intramolecular CH-đ interaction between aromatic rings of tyrosine and/or phenylalanine and the methyl group of alanine. Such interaction is possible only for d-Ala residue. For l-Ala in the peptide sequence, the methyl group is aligned on the opposite side with respect at least to one of the aromatic groups. It can be further speculated that such internal CH-π contacts can also occur during the interaction of ligand–receptor, making the message sequence of opioid peptides more rigid and finally selective. By employing different NMR experiments (e.g. PISEMA MAS and PILGRIM) it was proven that the main skeleton of analyzed peptides is rigid, whereas significant differences in the molecular motion of the aromatic residues were observed [4, 6]. Solid state 2H NMR spectroscopy of samples with deuterium labeled aromatic rings: Tyrd4-d-Ala-Phe 5, Tyr-d-Ala-Phed5 6, Tyrd4-Ala-Phe 7, Tyr-Ala-Phe^d5 8 was used to analyze the geometry and time scale of the molecular motion. At ambient temperature, the tyrosine ring of sample 5 is rigid and in the sample 6 the phenylalanine ring undergoes a "π -flip". The tyrosine rings of form I of 7 and 8 are static, while the phenylalanine rings of form II of 7 and 8 undergo a fast regime exchange [6]. Variable temperature 2H measurements proved that the tyrosine and phenylalanine rings of two forms of compounds 7 and 8 became more mobile with increasing temperature. In contrast, the aromatic rings of samples 5 and 6 preserve their dynamics regime (static tyrosine and "π -flip" phenylalanine) in a large range of temperatures [6]. The analysis of 13C, 15N labeled tetrapeptide Tyr-D-Ala-Phe-Gly 2’-phospholipid membrane interactions suggests that peptide 2’ is aligned on the surface of the membrane (RFDR MAS) and the sandwich-like π -CH_3-π arrangement of the pharmacophore is preserved (DARR) [7].
Źródło:
Wiadomości Chemiczne; 2012, 66, 9-10; 867-891
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Zastosowanie metod dynamiki molekularnej w badaniach nad układami z wiązaniami wodorowymi
An application of molecular dynamics methods in investigations of systems with hydrogen bonds
Autorzy:
Jezierska, A.
Panek, J. J.
Powiązania:
https://bibliotekanauki.pl/articles/172356.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
CPMD
dynamika molekularna Cara-Parrinello
klasyczna dynamika molekularna
wewnątrzcząsteczkowe wiązanie wodorowe
międzycząsteczkowe wiązanie wodorowe
zasada Schiffa
zasada Mannicha
N-tlenki
białka
Car-Parrinello molecular dynamics
classical MD
intramolecular HB
intermolecular HB
Schiff base
Mannich base
N-oxides
proteins
Opis:
Modern computational chemistry offers a wide variety of methods allowing us to investigate very complex systems. In the current study, we would like to focus on ab initio and classical molecular dynamics to show their applications in our research. Car-Parrinello molecular dynamics (CPMD) was carried out to study compounds possessing intra- and intermolecular hydrogen bonds. Our simulations were performed in vacuum, in solvent and in crystalline phase. It is well known that intramolecular hydrogen bonding stabilizes 3D structure of molecules. The strength of the bonding and its features are influenced by inductive and steric effects. Our short overview on CPMD application to systems with intramolecular HB we start from Schiff and Mannich bases -model compounds to investigate intramolecular hydrogen bonding. Other examples reported here derive from the class of N-oxide type compounds. Special attention was devoted to another representative structure in such investigations – picolinic acid N-oxide. In some examples listed above proton transfer phenomena occurred making these compounds interesting objects for future excited state studies. Aliphatic boronic acid was used as a model example to study intermolecular hydrogen bonds based on CPMD method. Further, classical molecular dynamics was applied to investigate proteins. Here, we would like to report our results for two biomolecules. The first one is proteinase K for which the impact of mercury(II) on its catalytic center was studied. The second one is streptavidin. For the latter one its complexes with biotinylated ligands were investigated. We close our review with a paragraph describing further development and perspectives related to CPMD method.
Źródło:
Wiadomości Chemiczne; 2017, 71, 7-8; 473-495
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Właściwości wewnątrzcząsteczkowych wiązań wodorowych w wybranych N-tlenkach pochodnych chinoliny
Intramolecular hydrogen bonds properties in selected N-oxides of quinoline derivatives
Autorzy:
Jezierska, Aneta
Panek, Jarosław J.
Błaziak, Kacper
Powiązania:
https://bibliotekanauki.pl/articles/171511.pdf
Data publikacji:
2019
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
DFT
teoria funkcjonału gęstości
MP2
metoda rachunku zaburzeń drugiego rzędu Møllera-Plesseta
CPMD
dynamika molekularna Cara-Parrinello
wewnątrzcząsteczkowe wiązanie wodorowe
N-tlenki pochodnych chinoliny
density functional theory
Møller-Plesset second order perturbation method
Car-Parrinello molecular dynamics
intramolecular HB
N-oxides of quinoline derivatives
Opis:
In the current article we would like to summarize our research shedding light onto properties of intramolecular hydrogen bonds present in N-oxide quinoline derivatives. The compounds for the current study were chosen to contain diverse types of hydrogen bonds. Therefore, in the current study we analyze three kinds of hydrogen bonding and their properties. It is well known, that the presence of intramolecular hydrogen bonds stabilizes conformations of molecules. Substituent effects (inductive and steric) influence the strength of the H-bonding as well as its features. Moreover, the intramolecular hydrogen bond in the studied N-oxides belongs to the family of resonance assisted hydrogen bonds (RAHB). Our short overview presents the summary of results obtained for twelve N-oxides of quinoline derivatives. Quantum-chemical simulations were performed on the basis of static models (classical DFT and MP2 approaches) as well as ab initio molecular dynamics (Car-Parrinello MD). The metadynamics method was applied to reproduce the maps of free energy for the motion of the bridged proton. The computations were performed in the gas and in the crystalline phases. Electronic ground state is a natural framework in which chemical compounds exist most of the time. However, in many chemical species we observe a spontaneous internal reorganization of their chemical bonds and atoms e.g. proton transfer phenomenon and the appearance of tautomeric forms already in the ground state. Therefore, it was interesting to investigate some N-oxides in the excited electron state knowing that they exhibit excited- state-induced proton transfer (ESIPT effect). At the end of the article we draw some conclusions related to the intramolecular H-bond properties present in the discussed N-oxides of quinoline derivatives.
Źródło:
Wiadomości Chemiczne; 2019, 73, 1-2; 75-95
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Coarse-grained modeling of protein structure, dynamics and protein-protein interactions
Autorzy:
Koliński, A.
Kmiecik, S.
Jamróz, M.
Błaszczyk, M.
Kouza, M.
Kurciński, M.
Powiązania:
https://bibliotekanauki.pl/articles/1954428.pdf
Data publikacji:
2014
Wydawca:
Politechnika Gdańska
Tematy:
coarse-grained modeling
protein folding
protein dynamics
molecular docking
protein docking
Opis:
Theoretical prediction of protein structures and dynamics is essential for understanding the molecular basis of drug action, metabolic and signaling pathways in living cells, designing new technologies in the life science and material sciences . We developed and validated a novel multiscale methodology for the study of protein folding processes including flexible docking of proteins and peptides. The new modeling technique starts from coarse-grained large-scale simulations, followed by selection of the most plausible final structures and intermediates and, finally, by an all-atom rectification of the obtained structures. Except for the most basic bioinformatics tools, the entire computational methodology is based on the models and algorithms developed in our lab. The coarse-grained simulations are based on a high-resolution lattice representation of protein structures, a knowledge based statistical force field and efficient Monte Carlo dynamics schemes, including Replica Exchange algorithms. This paper focuses on the description of the coarse-grained CABS model and its selected applications.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 3; 219--229
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Anisotropic gas transfer through the composite membranes
Autorzy:
Kurchatov, I. M.
Laguntsov, N. I.
Okunev, A. Y.
Pisarev, G. I.
Tronin, V. N.
Uvarov, V. I.
Powiązania:
https://bibliotekanauki.pl/articles/346945.pdf
Data publikacji:
2007
Wydawca:
Politechnika Bydgoska im. Jana i Jędrzeja Śniadeckich. Wydział Technologii i Inżynierii Chemicznej
Tematy:
porous media
permeability
stochastic dynamics
composite membrane
viscous flow
free molecular flow
Opis:
Using of stochastic dynamics methods, the probability distribution function of molecules by their moving directions in arbitrary porous media, where free molecular flow takes place, was determined. It was shown that, in some cases, the molecules in the channel can generally move athwart the channel, while an average velocity of molecules moving along the channel can significantly decrease. The anisotropic phenomenon and the hysteresis of permeability through composite asymmetric membranes were qualitatively explained.
Źródło:
Ars Separatoria Acta; 2007, 5; 45-54
1731-6340
Pojawia się w:
Ars Separatoria Acta
Dostawca treści:
Biblioteka Nauki
Artykuł
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