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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
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