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.

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 Impulse response function for Brownian motion

Soft Matter ◽  
2021 ◽  
Author(s):  
Nicos Makris
Keyword(s):  
Brownian Motion ◽  
Time Derivative ◽  
Mean Square Displacement ◽  
Impulse Response Function ◽  
Velocity Autocorrelation Function ◽  
Mean Square ◽  
Velocity Autocorrelation ◽  
The Mean ◽  
First Time

Motivated from the central role of the mean-square displacement and its second time-derivative – that is the velocity autocorrelation function in the description of Brownian motion, we revisit the physical meaning of its first time-derivative.

scholarly journals A molecular dynamics study on the diffusion and imprint ability of spectinomycin under different sizes of aniline oligomers

2022 ◽  
Author(s):  
Chanadan Douykhumklaw ◽  
Thana Sutthibutpong
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Mean Square Displacement ◽  
Md Simulations ◽  
Template Molecule ◽  
Aniline Oligomers ◽  
The Mean ◽  
The Stability ◽  
Further Development ◽  
Aniline Oligomer

Abstract Molecularly imprinted polymers (MIP) are the polymers created by molecular imprinting techniques that leave cavities for the specific interactions with a template molecule, and have been applied in molecular selectivity tasks. In this study, the molecular dynamics (MD) simulation technique was used to demonstrate that aniline oligomer could be developed as a potential MIP for detection and separation of the spectinomycin drug molecule for gonorrhoea treatment. MD simulations were performed for the systems of a spectinomycin within aniline oligomers of different sizes. The mean square displacement (MSD) and the diffusivity calculated from MD simulations showed that the diffusion coefficient was significantly dropped when the length of aniline oligomer was greater than two. The diffusion coefficient of spectinomycin became the lowest within aniline trimers, corresponded to the highest atomic distribution of MIP around the template. Then, the specific cavity in MIP systems with and without spectinomycin were calculated to assess the stability of the cavity created by the template. The volume of a cavity created within the trimer system was closest to the spectinomycin volume, and therefore became the optimal oligomer size for further development of MIP.

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.

scholarly journals Resolution Effects on the Mean Square Displacement as Obtained by the Self-Distribution-Function Procedure

2012 ◽  
Vol 340 ◽  
pp. 012093 ◽  
Author(s):  
A Benedetto ◽  
S Magazù ◽  
F Migliardo ◽  
C Mondelli ◽  
M A Gonzalez
Keyword(s):  
Distribution Function ◽  
Mean Square Displacement ◽  
The Self ◽  
Mean Square ◽  
The Mean

Phonon dispersion in Co0.92Fe0.08

1979 ◽  
Vol 57 (2) ◽  
pp. 253-262 ◽  
Author(s):  
E. C. Svensson ◽  
B. M. Powell ◽  
A. D. B. Woods ◽  
W. -D. Teuchert
Keyword(s):  
Distribution Function ◽  
Dispersion Relation ◽  
Electronic Structures ◽  
Phonon Dispersion ◽  
Characteristic Temperature ◽  
Mean Square Displacement ◽  
Mean Square ◽  
Neutron Inelastic Scattering ◽  
Atomic Force ◽  
The Mean

The dispersion relation for phonons propagating along the [00ζ], [ζζ0], and [ζζζ] directions in face-centred-cubic Co0.92Fe0.08 at T = 296 K has been determined by means of neutron inelastic scattering. The results have been analysed to obtain atomic force constants, the frequency distribution function, and the temperature dependence of the Debye characteristic temperature and the mean square displacement of the atoms. On average, the frequencies for Co0.92Fe0.08 scale approximately as expected with those for Ni and Cu but there are definite wave-vector-dependent variations in the scaling which presumably reflect the different electronic structures of the three materials.

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.

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