Molecular Dynamics Study of Microscopic Mechanism of Diffusion in Li2SiO3 System

1991 ◽  
Vol 46 (7) ◽  
pp. 616-620 ◽  
Author(s):  
Junko Habasaki
Keyword(s):  
Molecular Dynamics ◽  
Coordination Number ◽  
Md Simulation ◽  
Mean Square Displacement ◽  
Mean Square ◽  
Lithium Ions ◽  
Microscopic Mechanism ◽  
Trapping Model ◽  
The Mean

MD simulation has been performed to learn the microscopic mechanism of diffusion of ions in the Li2SiO3 system. The motion of lithium ions can be explained by the trapping model, where lithium is trapped in the polyhedron and moves with fluctuation of the coordination number. The mean square displacement of lithium was found to correlate well with the net changes in coordination number.

scholarly journals Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations

Entropy ◽  
2020 ◽  
Vol 22 (4) ◽  
pp. 405
Author(s):  
Piotr Weber ◽  
Piotr Bełdowski ◽  
Krzysztof Domino ◽  
Damian Ledziński ◽  
Adam Gadomski
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Root Mean Square ◽  
Mean Square Displacement ◽  
Conformational Space ◽  
Global Dynamics ◽  
Mean Square ◽  
Conformational Entropy ◽  
The Mean ◽  
Dynamics Simulations

This work presents the analysis of the conformation of albumin in the temperature range of 300 K – 312 K , i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from two angles that reflect global dynamics in the conformational space. A thorough rationalization, based on the scaling theory, for the subdiffusion Flory–De Gennes type exponent of 0 . 4 unfolds in conjunction with picking up the most appreciable fluctuations of the corresponding statistical-test parameter. These fluctuations coincide adequately with entropy fluctuations, namely the oscillations out of thermodynamic equilibrium. Using Fisher’s test, we investigate the conformational entropy over time and suggest its oscillatory properties in the corresponding time domain. Using the Kruscal–Wallis test, we also analyze differences between the mean root mean square displacement of a molecule at various temperatures. Here we show that its values in the range of 306 K – 309 K are different than in another temperature. Using the Kullback–Leibler theory, we investigate differences between the distribution of the mean root mean square displacement for each temperature and time window.

Tight-Binding Quantum Chemical Molecular Dynamics of Oxygen Migration of Rh-supporting CeO2 Surfaces

2014 ◽  
Vol 1704 ◽  
Author(s):  
Ai Suzuki ◽  
Ryuji Miura ◽  
Nozomu Hatakeyama ◽  
Akira Miyamoto
Keyword(s):  
Molecular Dynamics ◽  
Quantum Chemical ◽  
Oxygen Vacancies ◽  
Tight Binding ◽  
Mean Square Displacement ◽  
Mean Square ◽  
Oxygen Mobility ◽  
Oxygen Migration ◽  
The Mean ◽  
Quantum Chemical Molecular Dynamics

ABSTRACTThe electronic properties of the interface between Rh clusters and CeO2 (111), (110) and (100) surfaces were studied using an isothermal-isobaric (NPT) ensemble at 773 K and 101.343 kPa using the tight binding-quantum chemical molecular dynamics (TB-QCMD) method. The amount of electronic exchange by interaction at the interface between the supported Rh55 clusters and each CeO2 surface was investigated quantitatively. A comparison of the mean square displacement (MSD) showed that the topmost oxygens on the Rh-supporting CeO2 surface exhibited higher mobility than those of the bare CeO2 surface. Although the mobility of the topmost oxygens on the bare CeO2 surface was in the order (100) > (110) > (111), this sequence was altered by the presence of Rh, so that the oxygen mobility for the more open (110) surface was the largest. The amount of electron exchange that occurred between Rh and the CeO2 (110) surface was also larger than for the (111) or (100) surface. The Ce 4f orbitals on the CeO2 (110) surface exhibited the strongest mixing with Rh 4d orbitals, which simultaneously caused restructuring and instability of the topmost Ce-O bonds. This enhancement of oxygen migration in the presence of Rh was occurred together with an increase in the number of oxygen vacancies on the ceria surface. This was because the topmost oxygens was shifted to have a stronger affinity with Rh and thus formed stronger bonds with Rh than with Ce.

The Influence of Graphene Sheet on the Dynamics of Cholesterol Molecules in the Lodgment Located near a Transmembrane Protein – MD Study

2008 ◽  
Vol 140 ◽  
pp. 141-146
Author(s):  
P. Raczynski ◽  
A. Dawid ◽  
Z. Gburski
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Graphene Sheet ◽  
Transmembrane Protein ◽  
Mean Square Displacement ◽  
Md Simulations ◽  
Mean Square ◽  
Velocity Autocorrelation ◽  
The Mean ◽  
Velocity Autocorrelation Functions

Molecular dynamics (MD) simulations have been made for a cluster of cholesterols localized near the transmembrane protein at the physiological temperature of 310 K. It was observed that the cholesterol molecules form a lodgment on the surface of protein. Additional studies were made of the influence of graphene sheet on several physical observables of cholesterol molecules including: the radial distribution function, the mean square displacement, diffusion coefficient and the linear and angular velocity autocorrelation functions.

scholarly journals Reconstruction of Diffusion Coefficients and Power Exponents from Single Lagrangian Trajectories

Fluids ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 111
Author(s):  
Leonid M. Ivanov ◽  
Collins A. Collins ◽  
Tetyana Margolina
Keyword(s):  
Black Sea ◽  
Diffusion Coefficients ◽  
Current System ◽  
Mean Square Displacement ◽  
California Current ◽  
The Black Sea ◽  
Mean Square ◽  
California Current System ◽  
The Mean ◽  
Non Gaussian

Using discrete wavelets, a novel technique is developed to estimate turbulent diffusion coefficients and power exponents from single Lagrangian particle trajectories. The technique differs from the classical approach (Davis (1991)’s technique) because averaging over a statistical ensemble of the mean square displacement (<X2>) is replaced by averaging along a single Lagrangian trajectory X(t) = {X(t), Y(t)}. Metzler et al. (2014) have demonstrated that for an ergodic (for example, normal diffusion) flow, the mean square displacement is <X2> = limT→∞τX2(T,s), where τX2 (T, s) = 1/(T − s) ∫0T−s(X(t+Δt) − X(t))2 dt, T and s are observational and lag times but for weak non-ergodic (such as super-diffusion and sub-diffusion) flows <X2> = limT→∞≪τX2(T,s)≫, where ≪…≫ is some additional averaging. Numerical calculations for surface drifters in the Black Sea and isobaric RAFOS floats deployed at mid depths in the California Current system demonstrated that the reconstructed diffusion coefficients were smaller than those calculated by Davis (1991)’s technique. This difference is caused by the choice of the Lagrangian mean. The technique proposed here is applied to the analysis of Lagrangian motions in the Black Sea (horizontal diffusion coefficients varied from 105 to 106 cm2/s) and for the sub-diffusion of two RAFOS floats in the California Current system where power exponents varied from 0.65 to 0.72. RAFOS float motions were found to be strongly non-ergodic and non-Gaussian.

THE EFFECT OF PREMELTING: STUDY FOR SEMI-INFINITE CRYSTALS AND NANO-SYSTEMS

1994 ◽  
Vol 08 (24) ◽  
pp. 3411-3422 ◽  
Author(s):  
W. SCHOMMERS
Keyword(s):  
Pair Correlation ◽  
Mean Square Displacement ◽  
Phonon Density ◽  
Mean Square ◽  
Phonon Density Of States ◽  
Molecular Dynamics Calculations ◽  
Theory Of Melting ◽  
The Mean ◽  
Dynamical Properties ◽  
Reliable Interaction

The effect of premelting is of particular interest in connection with the theory of melting. In this paper, we discuss the structural and dynamical properties of the surfaces of semi-infinite crystals as well as of nano-clusters, which show the effect of premelting. The investigations are based on molecular-dynamics calculations: different models are used for the systematic study of the effect of premelting. In particular, the behaviour of the following functions have been studied: pair correlation function, generalized phonon density of states, and the mean-square displacement as a function of time. The calculations have been done for krypton since for this substance a reliable interaction potential is available.

Non-Markovian effect of the fractional damping environment and Newton’s second law of motion

2018 ◽  
Vol 32 (19) ◽  
pp. 1850210
Author(s):  
Chun-Yang Wang ◽  
Zhao-Peng Sun ◽  
Ming Qin ◽  
Yu-Qing Xu ◽  
Shu-Qin Lv ◽  
...  
Keyword(s):  
Diffusion Process ◽  
Mean Square Displacement ◽  
Dynamical Analysis ◽  
Second Law ◽  
Mean Square ◽  
Fractional Damping ◽  
Dynamical Mechanism ◽  
Brownian Particles ◽  
The Mean ◽  
Dissipative Environments

We report, in this paper, a recent study on the dynamical mechanism of Brownian particles diffusing in the fractional damping environment, where several important quantities such as the mean square displacement (MSD) and mean square velocity are calculated for dynamical analysis. A particular type of backward motion is found in the diffusion process. The reason of it is analyzed intrinsically by comparing with the diffusion in various dissipative environments. Results show that the diffusion in the fractional damping environment obeys the Langevin dynamics which is quite different form what is expected.

Transient Response of a Shear Beam to Correlated Random Boundary Excitation

1977 ◽  
Vol 44 (3) ◽  
pp. 487-491 ◽  
Author(s):  
S. F. Masri ◽  
F. Udwadia
Keyword(s):  
Time Delays ◽  
Spectral Characteristics ◽  
Mean Square Displacement ◽  
Dimensionless Time ◽  
Mean Square ◽  
Random Boundary ◽  
Mean Square Response ◽  
Shear Beam ◽  
The Mean ◽  
Support Motion

The transient mean-square displacement, slope, and relative motion of a viscously damped shear beam subjected to correlated random boundary excitation is presented. The effects of various system parameters including the spectral characteristics of the excitation, the delay time between the beam support motion, and the beam damping have been investigated. Marked amplifications in the mean-square response are shown to occur for certain dimensionless time delays.

scholarly journals Generalized Diffusion Equation Associated with a Power-Law Correlated Continuous Time Random Walk

2019 ◽  
Vol 2019 ◽  
pp. 1-5
Author(s):  
Long Shi
Keyword(s):  
Random Walk ◽  
Diffusion Equation ◽  
Power Law ◽  
Continuous Time ◽  
Continuum Limit ◽  
Waiting Times ◽  
Mean Square Displacement ◽  
Continuous Time Random Walk ◽  
Mean Square ◽  
The Mean

In this work, a generalization of continuous time random walk is considered, where the waiting times among the subsequent jumps are power-law correlated with kernel function M(t)=tρ(ρ>-1). In a continuum limit, the correlated continuous time random walk converges in distribution a subordinated process. The mean square displacement of the proposed process is computed, which is of the form 〈x2(t)〉∝tH=t1/(1+ρ+1/α). The anomy exponent H varies from α to α/(1+α) when -1<ρ<0 and from α/(1+α) to 0 when ρ>0. The generalized diffusion equation of the process is also derived, which has a unified form for the above two cases.

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