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Wyszukujesz frazę "molecular dynamics" wg kryterium: Temat


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

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