Low-Frequency Collective Motions in Proteins

2003 ◽  
Vol 02 (02) ◽  
pp. 163-169 ◽  
Author(s):  
Dimitri Antoniou ◽  
Steven D. Schwartz
Keyword(s):  
Molecular Dynamics ◽  
Linear Response ◽  
Collective Motion ◽  
Interatomic Potential ◽  
Low Frequency ◽  
Linear Response Theory ◽  
Density Fluctuations ◽  
Dynamics Simulation ◽  
Collective Motions ◽  
Theoretical Predictions

There are several kinds of low-frequency collective motions in proteins, which are believed to have a significant effect on their properties. We propose that a new kind of global collective motion in proteins are density fluctuations, which are slowly-varying, long-lived, propagating disturbances. These can be studied using the linear response formalism, which is a dynamical approximation that uses the full anharmonic interatomic potential. We have performed a molecular dynamics simulation of a realistic protein and have found results that are consistent with the theoretical predictions of linear response theory.

Momentum Removal to Obtain the Position-Dependent Diffusion Constant in Constrained Molecular Dynamics Simulation

2021 ◽  
Author(s):  
Kazushi Fujimoto ◽  
Tetsuro Nagai ◽  
Tsuyoshi Yamaguchi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Mass Velocity ◽  
Center Of Mass ◽  
Heterogeneous Systems ◽  
Diffusion Constant ◽  
Dynamics Simulation ◽  
Coulombic Interaction ◽  
Ewald Method ◽  
Theoretical Predictions

<div>The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink-Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate the period of the removal of the center-of-mass velocity in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf-Roux method.</div>

scholarly journals Molecular Dynamics Simulation of Zener Pinning by Differently Shaped and Oriented Particles

2021 ◽  
Vol 8 ◽  
Author(s):  
Yi Li ◽  
Jian Zhou ◽  
Runjie Li ◽  
Qingyu Zhang
Keyword(s):  
Molecular Dynamics ◽  
Dynamics Simulation ◽  
Pinning Force ◽  
Theoretical Studies ◽  
Constant Energy ◽  
Zener Pinning ◽  
Interaction Processes ◽  
Interface Characteristics ◽  
Theoretical Predictions ◽  
Ag Particle

Zener pinning between a curved Cu grain boundary (GB) and a differently shaped and oriented Ag particle has been simulated via molecular dynamics. The computed magnitudes of the maximum pinning force agreed with theoretical predictions only when the force was small. As the force increased, discrepancy became obvious. Through careful inspection of the structures of the Cu–Ag interfaces, detailed interaction processes, and variation of the Cu GB during the interaction, the discrepancy is found to correlate with GB faceting, which very likely reduces the maximum pinning force and facilitates boundary passage. GB anisotropy and/or interface characteristics are also found to slightly contribute to the discrepancy. These findings suggest that the assumption of an isotropic GB with constant energy utilized in previous theoretical studies for deriving the maximum pinning force might be inappropriate and that an accurate maximum pinning force could not be predicted without knowing the effects of GB evolution together with detailed properties of both GBs and interfaces.

scholarly journals Optical Diagnostics of Supercritical CO2 and CO2-Ethanol Mixture in the Widom Delta

Molecules ◽  
2020 ◽  
Vol 25 (22) ◽  
pp. 5424
Author(s):  
Evgenii Mareev ◽  
Timur Semenov ◽  
Alexander Lazarev ◽  
Nikita Minaev ◽  
Alexander Sviridov ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Optical Properties ◽  
Supercritical Co2 ◽  
Cluster Formation ◽  
Mie Scattering ◽  
Density Fluctuations ◽  
Optical Measurements ◽  
Dynamics Simulation ◽  
Ethanol Mixture ◽  
Wide Range

The supercritical CO2 (scCO2) is widely used as solvent and transport media in different technologies. The technological aspects of scCO2 fluid applications strongly depend on spatial–temporal fluctuations of its thermodynamic parameters. The region of these parameters’ maximal fluctuations on the p-T (pressure-temperature) diagram is called Widom delta. It has significant practical and fundamental interest. We offer an approach that combines optical measurements and molecular dynamics simulation in a wide range of pressures and temperatures. We studied the microstructure of supercritical CO2 fluid and its binary mixture with ethanol in a wide range of temperatures and pressures using molecular dynamics (MD) simulation. MD is used to retrieve a set of optical characteristics such as Raman spectra, refractive indexes and molecular refraction and was verified by appropriate experimental measurements. We demonstrated that in the Widom delta the monotonic dependence of the optical properties on the CO2 density is violated. It is caused by the rapid increase of density fluctuations and medium-sized (20–30 molecules) cluster formation. We identified the correlation between cluster parameters and optical properties of the media; in particular, it is established that the clusters in the Widom delta acts as a seed for clustering in molecular jets. MD demonstrates that the cluster formation is stronger in the supercritical CO2-ethanol mixture, where the extended binary clusters are formed; that is, the nonlinear refractive index significantly increased. The influence of the supercritical state in the cell on the formation of supersonic cluster jets is studied using the Mie scattering technique.

COMPUTER SIMULATION OF EPITAXIAL GROWTH OF SILICON ON Si (001) SURFACE

2002 ◽  
Vol 16 (01n02) ◽  
pp. 227-232 ◽  
Author(s):  
M. H. LIANG ◽  
X. XIE ◽  
S. LI
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Epitaxial Growth ◽  
Interatomic Potential ◽  
Simulation Method ◽  
Growth Direction ◽  
Dynamics Simulation ◽  
Interatomic Potentials ◽  
Weber Potential ◽  
Deposition Conditions

Epitaxial growth of silicon on Si (001) surface has been studied with interatomic potential based molecular dynamics simulation method. Three silicon interatomic potentials developed separately by Stillinger-Weber, Tersoff, and Bazant-Kaxiras were used. Energetic beam of 8 eV, substrate temperature of 500K and deposition rate of 1.15 ps/atom were used as the deposition conditions. Morphologies of the growth were obtained and densities in the growth direction analyzed. Epitaxial growth under the deposition conditions imposed was found possible only using the Stillinger-Weber potential. Disordered growths of differing degree were obtained using the Bazant-Kaxiras and Tersoff potentials. The disordered growth may be attributed to the existence of an epitaxial transition temperature higher than 500K that these potentials might have.

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