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Wyświetlanie 1-15 z 43
Tytuł:
Molecular dynamics simulation of copolymers
Autorzy:
Banaszak, M.
Powiązania:
https://bibliotekanauki.pl/articles/1964087.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
molecular dynamics
computer simulation
copolymer
diblock
ionic copolymer
diffusion
structure factor
equation of state
thermodynamic properties
Opis:
A series of representative molecular dynamics simulations of model Lennard-Jones copolymer chains is presented. We report measurements of thermodynamic, structural and dynamic properties of our model copolymers. For neutral copolymers we confirm our version of thermodynamic perturbation theory of the first order, while for ionic copolymers we demonstrate microphase formation and the anisotropy of the counterion diffusion.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 1; 17-27
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Protein-protein docking refinement using restraint molecular dynamics simulations
Autorzy:
Zacharias, M.
Powiązania:
https://bibliotekanauki.pl/articles/1938618.pdf
Data publikacji:
2016
Wydawca:
Politechnika Gdańska
Tematy:
protein-protein complex
docking prediction
force field modeling
implicit solvent modeling
Opis:
A realistic prediction of the structure of protein-protein complexes is of major importance to obtain three-dimensional models for the interaction of proteins to form complexes and assemblies. In addition to the systematic search for putative binding sites on the surface of two binding partners, the second step of a docking effort, the refinement of docked complexes, is a major bottleneck to obtain realistic interaction geometries. Typically, the first initial systematic search employs rigid partner structures or few flexible degrees of freedom, whereas the refinement step involves fully flexible partner structures. The possibility to refine docked complexes using restraint MD simulations combined with an implicit solvent (Generalized Born) mode l was explored on three example test complexes starting from unbound partner structures. Significant improvement, both in scoring and agreement with the native complex structure after refinement was observed for two test cases. No improvement was found for a test case of a complex with lower binding affinity. The method can be easily applied to any docked protein-protein complex, however, more general applicability requires further improvements in the scoring function.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 353-360
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
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:
Prediction of binding affinities for DNA intercalators by molecular dynamics simulations
Autorzy:
Mazerski, J.
Powiązania:
https://bibliotekanauki.pl/articles/1965824.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
molecular modelling
free energy of binding
intercalation into DNA
linear responce method
free energy perturbation method
Opis:
The computer modelling and simulation methods are widely used in rational drug design to obtain information necessary for understanding interactions between a ligand (drug molecule) and its cellular macromolecular target on molecular level. The determination of free energies of binding for ligand-target complexes is one of the crucial points in those studies. In recent years several methods have been proposed to solve this problem. The majority of them use molecular dynamics (MD) simulations. Two, most popular methods: (i) a free energy perturbation method (FEP), and (ii) a linear response (LR) method, are shortly presented in this paper together with their limitations and advantages. In this work I presented the first attempt to use LR approach to 10 anti-tumour agents able to intercalate into DNA. The LR relationship obtained in the present study indicated that in the system studied the electrostatic term has no influence on the free energy of binding. The relationship is now successfully used in our research group in further molecular modelling studies concerning DNA intercalators with similar structure.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 3; 301-310
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:
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:
The structure of Pb-PbO-SiO2 glass via molecular dynamics simulation
Autorzy:
Rybicki, J.
Witkowska, A.
Bergmański, G.
Mancini, G.
Feliziani, S.
Powiązania:
https://bibliotekanauki.pl/articles/1954650.pdf
Data publikacji:
2022-01-20
Wydawca:
Politechnika Gdańska
Tematy:
lead-silicate glasses
oxide glasses
medium-range order
ring analysis
molecular dynamics simulations
Opis:
The paper is dedicated to a molecular dynamics (MD) study of the structure of partially reduced lead-silicate glass of composition 1Pb 1PbO 1SiO2. The simulations have been performed in the constant volume regime, using a two-body potential (Born-Mayer repulsive forces, and Coulomb forces due to full ionic charges). The system was initially prepared as a well equilibrated hot melt, and then slowly cooled down to 300K. The information on short-range correlations were obtained in a conventional way (from pair and angular distribution functions), while the medium-range order was studied via cation-anion ring analysis. In the paper, the short- and medium-range order in the simulated system is discussed and compared with the structure of a glassy completely reduced system, i.e. 2Pb 1SiO2 and unreduced one, i.e. 2PbO 1SiO2 glass.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2003, 7, 2; 243-256
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The structure of rarefied and densified PbSiO3 glass: a molecular dynamics study
Autorzy:
Bergmański, G.
Białoskórski, M.
Rychcik-Leyk, M.
Witkowska, A.
Rybicki, J.
Mancini, G.
Frigio, S.
Feliziani, S.
Powiązania:
https://bibliotekanauki.pl/articles/1954073.pdf
Data publikacji:
2004
Wydawca:
Politechnika Gdańska
Tematy:
oxide glasses
structure of glasses
ring analysis
MD simulations
Opis:
The paper is a molecular dynamics (MD) study of the structure of rarefied and densified lead-silicate glass of the PbSiO3 composition. Simulations have been performed in the constant volume regime for systems with densities of 3000, 4000, 5000, 5970 (normal density), 7000 and 8000kg/m3, using a two-body potential (Born-Mayer repulsive forces and Coulomb forces due to full ionic charges). All the systems were initially prepared as well equilibrated hot melts, and then slowly cooled down to 300K. The information on short-range correlations was obtained in a conventional way (from radial and angular distribution functions), while the middle-range order was studied via cation-anion ring analysis, using our new programme for basal ring determination. The structure of rarefied and densified glasses is compared with the structure of the same glasses under normal conditions. Moreover, the present results on PbSiO3 glass are compared with the corresponding data previously obtained for rarefied and densified PbGeO3 glass (Rybicki et al. 2001 Comput. Met. Sci. Technol. 7 91-112).
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2004, 8, 3; 393-412
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular dynamics and structural comparison approach to understanding the role of knots in proteins
Autorzy:
Perlinska, A. P.
Macnar, J. M.
Sulkowska, J. I.
Powiązania:
https://bibliotekanauki.pl/articles/1938625.pdf
Data publikacji:
2016
Wydawca:
Politechnika Gdańska
Tematy:
knotted proteins
methyltransferases
TrmD
Trm5
TrmJ
Trm7
Opis:
The role of knots in proteins is still unclear. In this short review, we summarize the current knowledge about structural and dynamical differences between knotted and unknotted proteins. We show how the topological difference helps to distinguish the physical properties, characterize the biological activity or identify the biological function of knotted proteins. This knowledge can be used to correctly annotate protein family members and to identify new members.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 373-381
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Particle agglomeration in flow modelled with molecular dynamics coupled to a thermal Lattice Boltzmann code
Autorzy:
Jiménez, J. F. C.
Powiązania:
https://bibliotekanauki.pl/articles/1955294.pdf
Data publikacji:
2013
Wydawca:
Politechnika Gdańska
Tematy:
particle agglomeration
agglomerate structure
lattice Boltzmann method
Langevin kinetics
Opis:
Particle agglomeration can arise naturally (e.g. dust, salt) or as a result of industrial activities and/or combustion processes (e.g. spray drying, particle flame synthesis). The process itself and its mechanisms are important for many applications since the physical properties of the final structures are mainly determined by the composition, number, diameter and geometric arrangement of their constituent primary particles. Thus, knowing and controlling the extent of agglomeration meets a growing interest in environmental and industrial concerns. The objective of the paper is to develop a simulation model of particles suspended in a flowing fluid using MD simulations coupled to a Lattice Boltzmann (LB) solver. These simulations allowed determining the agglomerate transport and deposition rates depending on the flow conditions and agglomerate structure and understanding the relationship between agglomerate characteristics (i.e. growth kinetics and morphology) and their behavior in a flow field. Two systems of 2000 and 1000 particles were simulated at 300 K and 600 K both of them in a known fluid. Simulations using a Langevin thermostat were also performed to compare with the LB thermostat. This allowed quantifying the influence of the fluid flow on the agglomeration process and agglomerate properties. In further applications, this will help to a priori tailor the flow conditions to achieve a desired aggregate morphology. As a result, reasonable aggregate morphologies were achieved. One of the main conclusions is that taking into account the fluid flow (LB solver) the agglomeration process of the particles is notably accelerated in comparison to the Langevin simulations. One of the main implications of this work could be the possibility of using a known fluid to accelerate an aglomeration process given a suitable fluid and to find a desirable configuration of agglomerates. Another conclusion is that the agglomeration process is sensitive to the temperature variation and that the number of particles in the system influences the final configuration of agglomerates in LB simulations.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2013, 17, 3-4; 181--213
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
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:
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:
Molecular dynamics study of temperature-induced structural changes in YBa2Cu3O7 crystal
Autorzy:
Bośko, J.
Sadowski, W.
Powiązania:
https://bibliotekanauki.pl/articles/1954521.pdf
Data publikacji:
1999
Wydawca:
Politechnika Gdańska
Tematy:
MD simulations
structure
phase transition
oxygen diffusion
trajectory
Opis:
The structure of YBa2Cu3O7 crystal has been studied with the aid of molecular-dynamics (MD) technique. A two-body model potentials proposed by Zhang and Catlow have been used in MD simulations performed in wide range of temperature. The temperature-induced orthorhombic-to-tetragonal phase transition is observed. The distruction of the arrangement of atoms in the CuO chains due to diffusion of oxygen atoms is observed. The diffusion coefficients are calculated, and their variation as a function of temperature is analysed. The activation energy is estimated.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1999, 3, 3; 293-302
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
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:
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
Wyświetlanie 1-15 z 43

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