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Wyświetlanie 1-10 z 144
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:
Molecular Dynamics in Cyclic Olefin Copolymer
Autorzy:
Makrocka-Rydzyk, M.
Orozbaev, B.
Nowaczyk, G.
Głowinkowski, S.
Jurga, S.
Powiązania:
https://bibliotekanauki.pl/articles/2043644.pdf
Data publikacji:
2005-08
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
36.20.Ey
76.60.-k
77.22.Gm
83.85.Vb
82.35.Jk
Opis:
Nuclear magnetic resonance, broadband dielectric spectroscopy and dynamic-mechanical thermal analysis were employed to study molecular dynamics of ethylene-norbornene copolymer. The analysis of experimental data indicates existence of three motional processes denoted as αβ, andγ in order of decreasing temperature. Theα relaxation is related to the dynamic glass transition, while the β relaxation, observed only for the untreated sample, is assigned to short range segmental motions involving norbornene units. Theγ relaxation is due to very local motions of ethylene units e.g. trans-gauche isomerization, similar to those responsible forγ relaxation in polyethylene. The rate of motion accountable for γ process, follows the Vogel-Fulcher-Tammann equation, similarly to α transition, indicating cooperative nature of the motion.
Źródło:
Acta Physica Polonica A; 2005, 108, 2; 385-393
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties
Autorzy:
Fojtíková, J.
Kalvoda, L.
Sedlák, P.
Powiązania:
https://bibliotekanauki.pl/articles/1402106.pdf
Data publikacji:
2015-10
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
31.15.xv
61.41.+e
81.05.Lg
Opis:
Models of poly(dimethylsiloxane) (PDMS) oligomers differing in topology are defined and structure and mechanical properties of these analysed by three different theoretical approaches: the Bicerano graph method, atomistic molecular dynamics simulations and mesoscale dissipative particle dynamics. The calculations are performed within the simulation software environment Materials Studio (Accelrys Software Inc.). The obtained values of the Young and bulk modulus are juxtaposed to experimental data available for real PDMS materials and quality of the agreement discussed in relation to the theory level and simulation method applied.
Źródło:
Acta Physica Polonica A; 2015, 128, 4; 637-639
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
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:
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:
Molecular Dynamics of Proteins Investigated by NMR Relaxation Methods
Autorzy:
Wierzuchowska, D.
Blicharska, B.
Powiązania:
https://bibliotekanauki.pl/articles/1360657.pdf
Data publikacji:
2014-04
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
76.60.-k
76.90.+d
Opis:
The nuclear magnetic resonance relaxation times of solvent water nuclei are known to decrease upon addition of diamagnetic solute protein. For this reason NMR relaxation methods are able to provide information on molecular dynamics changes of water protons and their interaction with macromolecules' surfaces. We present results of measurements of relaxation rates $R_1$ = 1/$T_1$, $R_2$ = 1/$T_2$ and $R_{1ρ}$ = 1/$T_{1ρ}$ in the rotating frame for three proteins: chicken egg white lysozyme, egg white albumin, and bovine serum albumin, obtained at proton resonant frequency of 60 MHz. Besides the relaxation rates dependences on concentration in the 4-23% (g/100 g solution) range, the analysis of the Carr-Purcell-Meiboom-Gill CPMG multi-echo $T_2$ experiments with variable pulse rate τ was performed. The dependences of relaxation rates on protein concentration are linear at low concentration. When protein concentration increases the slope of the straight line rapidly changes at so-called "critical" concentration which depends on MW of the diluted protein. Investigated dispersion of $T_2$, obtained using the CPMG method with a variable pulse rate, for concentrations higher and lower than the "critical" one, exhibits unequal behavior. At high concentration one-exponential curves and at low concentration two-exponential curves correspond closely with experimental data. The obtained parameters of exponents allow an estimation of the ratio of the amount of water with the determined motion freedom, that is free and bounded water, in solution. We showed that the CPMG dispersion method applied to aqueous protein solutions may widen the current understanding of the nature of molecular dynamics of hydrated water protons in non-perturbed environment.
Źródło:
Acta Physica Polonica A; 2014, 125, 4; 907-910
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Reconstruction of the (001) Surface of Si from Molecular Dynamics
Autorzy:
Holender, J.
Jędrzejek, Cz.
Powiązania:
https://bibliotekanauki.pl/articles/1877536.pdf
Data publikacji:
1991-01
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
68.35.Md
68.35.Bs
Opis:
The reconstruction of the (001) surface of Si at various temperatures is studied using molecular dynamics with many-body interactions. Two types of potentials were used: the Stillinger-Weber (SW), and Pearson and co-workers Axilrod-Teller type potential (AT). For Stillinger-Weber potential at low temperatures the (2x1) dimer reconstruction is about 0.07 eV per surface atom more preferable than the c(2x2)structure which is in agreement with the experimental reconstruction observed by STM. Contrary, for Axilrod-Teller type potential the c(2x2) structure is lower by 0.2 eV than the (2x1) structure. The silicon surface is stable up to 1500 K, all the dimers remain unbroken but some of them are tilted. The energies of various defects (suggested by STM studies) like single vacancy, two adjacent Si atoms vacancy, dimer vacancy, dimer vacancy with lower layer atoms rebonding and double dimer vacancy are estimated.
Źródło:
Acta Physica Polonica A; 1991, 79, 1; 117-120
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
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 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
Wyświetlanie 1-10 z 144

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