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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 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:
Multidimensional NQR Spectroscopy - A New Tool in Studies of Molecular Dynamics
Autorzy:
Maćkowiak, M.
Powiązania:
https://bibliotekanauki.pl/articles/2043390.pdf
Data publikacji:
2005-07
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
76.60.Gv
82.56.Fk
82.20.Pm
Opis:
Two-dimensional exchange $\text{}^{35}$Cl nuclear quadrupole resonance spectroscopy for studies of the CCl$\text{}_{3}$-group reorientation processes in hexachloroethane and chloral hydrate has been applied. Experimental results were interpreted on the basis of the 2D exchange nuclear quadrupole resonance theory, which takes into account the off-resonance irradiation. It has been demonstrated that 2D nuclear quadrupole resonance exchange spectroscopy is appropriate for quantitative studies of exchange processes in molecular crystals containing quadrupolar nuclei. The method is of particular value for the detection of exchange networks in systems with many sites. Thus, detailed information on the exchange pathways within a network of structural isomers can be deduced and a proper assignment of the nuclear quadrupole resonance lines can be made. Temperature dependence of the exchange rate was studied. The mixing dynamics by exchange and the expected cross-peak intensities have been derived.
Źródło:
Acta Physica Polonica A; 2005, 108, 1; 61-72
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular Dynamics Simulations of Energetic Ar Cluster Bombardment of Ag(111)
Autorzy:
Palka, G.
Rzeznik, L.
Paruch, R.
Postawa, Z.
Powiązania:
https://bibliotekanauki.pl/articles/1400436.pdf
Data publikacji:
2013-05
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
68.49.Sf
82.80.Ms
83.10.Rs
79.20.Rf
Opis:
Large-scale molecular dynamics computer simulations are used to investigate the dynamics of material ejection during high-energy $Ar_n$ cluster bombardment of Ag(111) at normal incidence. The silver sample containing 7 million atoms is bombarded with $Ar_n$ projectiles (n=45-30000) with kinetic energy spanning from a few keV up to 1 MeV. Such a wide range of projectile parameters allows probing processes taking place during low-density collision cascade as well as during high-density events characteristic of micrometeorite bombardment in space. The material modifications and total sputtering yield of ejected particles are investigated. While at low-energy impacts, ejection of individual silver atoms is the main emission channel, the ejection of large clusters from the corona of the created crater dominates for the high-energy impacts.
Źródło:
Acta Physica Polonica A; 2013, 123, 5; 831-833
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Proton and Deuteron Relaxation Study of Molecular Dynamics in Lysozyme Solutions
Autorzy:
Kakule, J. F.
Węglarz, W. P.
Shenoy, R. K.
Sharp, A. R.
Peemoeller, H.
Powiązania:
https://bibliotekanauki.pl/articles/2014096.pdf
Data publikacji:
2000-07
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
76.60.-k
87.15.-v
Opis:
A nuclear magnetic resonance spin-lattice relaxation dispersion study of the relaxation of several magnetization components in both natural and deuterated lysozyme solutions was undertaken at 20°C. Proton and deuteron resonances were employed. The two-dimensional time evolution of the magnetization and the spin-spin relaxation were analyzed. In addition, an isotopic dilution study was performed at 5 and 30.6MHz. The results indicate that the water proton spin-lattice relaxation rate which arises from intermolecular relaxation between the water protons and the lysozyme protons represents a relatively strong relaxation mechanism. A model for the dynamics of the water molecules, consistent with the proton and deuteron dispersions as well as with the isotopic dilution results, is presented.
Źródło:
Acta Physica Polonica A; 2000, 98, 1-2; 131-152
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
AFM Force Spectroscopy and Steered Molecular Dynamics Simulation of Protein Contactin 4
Autorzy:
Strzelecki, J.
Powiązania:
https://bibliotekanauki.pl/articles/1807636.pdf
Data publikacji:
2009-12
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
82.37.Rs
87.10.Tf
Opis:
We use a single molecule atomic force spectroscopy combined with the steered molecular dynamics simulation to determine a mechanical behavior of neural cell adhesion protein contactin during its unfolding. Force curves typical for modular proteins were observed, showing at most four unfolding peaks. The analysis of force spectra performed within worm-like chain model of polymer elasticity showed the presence of three unfolding lengths. Small plateaus, most likely resulting from forced transitions within domains were observed for the first time. Steered molecular dynamics simulations help to determine atomistic picture of domain unfolding.
Źródło:
Acta Physica Polonica A; 2009, 116, S; S-156-S-159
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Thermodynamic Properties of Potassium Oxide (K₂O) Nanoparticles by Molecular Dynamics Simulations
Autorzy:
Guder, V.
Senturk Dalgic, S.
Powiązania:
https://bibliotekanauki.pl/articles/1032027.pdf
Data publikacji:
2017-03
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
65.80.-g
Opis:
Potassium oxide (K₂O) is a reagent for testing the presence of other compounds in chemical reactions. It is also used in compounding cement and in glass making. However properties of K₂O in nanoscale are still unclear. In this work, thermodynamic properties of spherical K₂O nanoparticles have been investigated. Size dependent cohesive energy, melting point and glass transition temperature have been computed for different sizes of K₂O nanoparticles by molecular dynamics simulations. Thermal expansion coefficients of nanoparticles at zero pressure and various temperatures have been also calculated. Melting point depression for K₂O nanoparticles was determined. The significant change in cohesive energy was obtained for particles smaller than 5.4 nm. The presented model is successful in understanding the size-dependent thermodynamics of spherical K₂O nanoparticles. Theoretical investigations of the thermal properties of K₂O nanoparticles have not been presented previously.
Źródło:
Acta Physica Polonica A; 2017, 131, 3; 490-494
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
In Quest of Optimal Algorithms for Molecular Dynamics Simulation of Surface Phenomena
Autorzy:
Mościński, J.
Alda, W.
Bargiel, M.
Bubak, M.
Dzwinel, W.
Kitowski, J.
Mościńska, E.
Skotniczny, Z.
Powiązania:
https://bibliotekanauki.pl/articles/1891747.pdf
Data publikacji:
1991-11
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
02.70.+d
64.70.Fx
68.10.La
Opis:
In this paper we present short-range molecular dynamics algorithms and programs elaborated for sequential and vector computer architectures. They are suitable for investigations of surface and subsurface layer properties which require of about 10$\text{}^{5}$ molecules in a computational box.
Źródło:
Acta Physica Polonica A; 1991, 80, 5; 649-652
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular Dynamics in Biological Systems Observed by NMR Relaxation in a Rotating Frame
Autorzy:
Wierzuchowska, D.
Skórski, L.
Blicharska, B.
Powiązania:
https://bibliotekanauki.pl/articles/1490095.pdf
Data publikacji:
2012-02
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
76.60.-k
76.90.+d
Opis:
NMR relaxation provides powerful tools for obtaining information on three-dimensional structures, dynamic properties and intermolecular interactions of biological macromolecules. One of these methods, called dispersion profile, is based on measuring the field dependence of spin-relaxation rates in the rotating frame, $R_{1ρ} = 1//T_{1ρ}$, in the presence of a low magnetic field $B_1$. In the presented study we use this method for investigation of molecular dynamics in protein samples. Dispersion profiles can be predicted theoretically and using two models, assuming either dipolar interaction between protons or power law dispersion, we have evaluated some molecular dynamic parameters of water adsorbed on protein surface. Our researches are focused on the connections of obtained parameters of molecular dynamics with conformation changes of protein. We have calculated the correlation times and power parameters for samples of lyophilized powder of albumins (egg white and bovine and rabbit blood serum) and lysozyme, as well as its aqueous solutions. Analysis of these parameters yields valuable information on the molecular nature of investigated biological systems. We also used this method to analyze experimental data of $T_{1ρ}$ obtained by other authors for bovine serum albumin and we have found good accordance with their conclusions concerning molecular dynamics of proteins.
Źródło:
Acta Physica Polonica A; 2012, 121, 2; 434-438
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
High Resolution Density Map as the Visualization of a Larger Time Scale Molecular Dynamics
Autorzy:
Karbowniczek, P.
Powiązania:
https://bibliotekanauki.pl/articles/1189870.pdf
Data publikacji:
2015-06
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
61.20.-p
64.70.dm
61.20.Ja
Opis:
A method of visualization of two-dimensional systems of particles in a large time scale molecular dynamics with application to the domain reorientation process in 2D Lennard-Jones system is presented. The described processing is general and can be used in comparing experimental results of atomic force microscopy with the results calculated using a computer as well as for predicting new phenomena. Domain reorientation process in 2D Lennard-Jones system approaching equilibrium is presented and confronted with the Fourier analysis of the data obtained for different initial parameters and at different states of aggregation. New border domain features accompanying this process are discussed.
Źródło:
Acta Physica Polonica A; 2015, 127, 6; 1644-1647
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular Dynamics of 4-(trans-4-n-Heptylcyclohexyl)- Isothiocyanatobenzene Studied with Dielectric Relaxation Spectroscopy
Autorzy:
Bauman, D.
Czechowski, G.
Jadżyn, J.
Legrand, C.
Douali, R.
Powiązania:
https://bibliotekanauki.pl/articles/2014055.pdf
Data publikacji:
2000-07
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
64.70.Md
77.84.Nh
77.22.Gm
Opis:
Dielectric relaxation study was carried out for the nematic and isotropic phases of 4-(trans-4'-n- heptylcyclohexyl)isothiocyanatobenzene in the frequency range from 100 kHz to 1 GHz. In the nematic phase two relaxation processes were recorded for the electric permittivity component measured parallel to the molecular orientation (director n) and three relaxation processes - for the perpendicular permittivity component. The strength of the nematic potential and the nematic order parameter were estimated.
Źródło:
Acta Physica Polonica A; 2000, 98, 1-2; 71-81
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular Dynamics of Tert-butyl Chloride Confined to CPG (7.4, 15.6 nm)
Autorzy:
Szutkowska, L.
Peplińska, B.
Jurga, S.
Powiązania:
https://bibliotekanauki.pl/articles/2043639.pdf
Data publikacji:
2005-08
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
76.60.Es
81.05.Rm
33.15.Vb
33.20.Bx
68.35.Rh
Opis:
The paper complements our earlier NMR investigation of molecular dynamics of tert-butyl chloride restricted by geometries of the type MCM-41 and CPG by the new sizes of CPG and by differential scanning calorimetry method. We report proton and deuteron NMR lineshapes and the spin-lattice relaxation results of tert-butyl chloride in CPG of the 15.6 nm and 7.4 nm pore diameter in the temperature range 70 K≤ T≤ 292 K. The bulk-like component of the confined tert-butyl chloride, in temperatures corresponding to phase III, is interpreted as a composition of two dynamically different subphases. The parameters of motions of both subphases are derived. The tert-butyl group motion in both subphases is more restricted than in the bulk tert-butyl chloride, although the activation energies are lower. Differential scanning calorimetry was used to determine temperatures of the phase transitions (140 K≤T≤292 K). The results show that the depression of the phase transition temperature is pore size dependent and that the confinement has less influence on transition to the plastic phase than on the freezing and on the solid II - solid III transition.
Źródło:
Acta Physica Polonica A; 2005, 108, 2; 357-370
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Numerical Modelling of Adsorption of Metallic Particles on Graphite Substrate Via Molecular Dynamics Simulation
Autorzy:
Rafii-Tabar, H.
Powiązania:
https://bibliotekanauki.pl/articles/1968758.pdf
Data publikacji:
1998-02
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
02.60.Cb
07.05.Tp
68.55.-a
81.05.Tp
Opis:
A computer-based numerical modelling of the adsorption process of gas phase metallic particles on the surface of a graphite substrate has been performed via the application of molecular dynamics simulation method. The simulation relates to an extensive STM-based experiment performed in this field, and reproduces part of the experimental results. Both two-body and many-body inter-atomic potentials have been employed. A Morse-type potential describing the metal-carbon interactions at the interface was specifically formulated for this modelling. Intercalation of silver in graphite has been observed as well as the correct alignments of monomers, dimers and two-dimensional islands on the surface.
Źródło:
Acta Physica Polonica A; 1998, 93, 2; 343-354
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-15 z 25

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