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.

scholarly journals Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins

2016 ◽  
Author(s):  
Yuan-Ping Pang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Root Mean Square ◽  
A Priori ◽  
Model Systems ◽  
Dynamics Simulation ◽  
High Mass ◽  
Mean Square ◽  
Dynamics Simulations

ABSTRACTPredicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2–9 ± 1 Å2for Cα and 7.3 ± 0.9–9.6 ± 0.2 Å2for Cγ, when the sampling was done, for each of these proteins, over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations using AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive toa prioriprediction of crystallographic B-factors of a folded globular protein.

scholarly journals Ballistic Heat Transport in Nanocomposite: The Role of the Shape and Interconnection of Nanoinclusions

Nanomaterials ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1982
Author(s):  
Paul Desmarchelier ◽  
Alice Carré ◽  
Konstantinos Termentzidis ◽  
Anne Tanguy
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Free Path ◽  
Mean Free Path ◽  
Strong Increase ◽  
Moderate Increase ◽  
Energy Propagation ◽  
The Mean ◽  
Dynamics Simulations

In this article, the effect on the vibrational and thermal properties of gradually interconnected nanoinclusions embedded in an amorphous silicon matrix is studied using molecular dynamics simulations. The nanoinclusion arrangement ranges from an aligned sphere array to an interconnected mesh of nanowires. Wave-packet simulations scanning different polarizations and frequencies reveal that the interconnection of the nanoinclusions at constant volume fraction induces a strong increase of the mean free path of high frequency phonons, but does not affect the energy diffusivity. The mean free path and energy diffusivity are then used to estimate the thermal conductivity, showing an enhancement of the effective thermal conductivity due to the existence of crystalline structural interconnections. This enhancement is dominated by the ballistic transport of phonons. Equilibrium molecular dynamics simulations confirm the tendency, although less markedly. This leads to the observation that coherent energy propagation with a moderate increase of the thermal conductivity is possible. These findings could be useful for energy harvesting applications, thermal management or for mechanical information processing.

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 From the Potential of the Mean Force to a Quasiparticle’s Effective Potential in Narrow Ion Channels

2019 ◽  
Vol 18 (02) ◽  
pp. 1940006 ◽  
Author(s):  
M. L. Barabash ◽  
W. A. T. Gibby ◽  
C. Guardiani ◽  
D. G. Luchinsky ◽  
P. V. E. McClintock
Keyword(s):  
Molecular Dynamics ◽  
Ion Channels ◽  
Molecular Dynamics Simulations ◽  
Strong Interaction ◽  
Effective Potential ◽  
Current Voltage ◽  
Ionic Motion ◽  
The Mean ◽  
Highly Correlated ◽  
Dynamics Simulations

We consider the selective permeation of ions through narrow water-filled channels in the presence of strong interaction between the ions. These interactions lead to highly correlated ionic motion, which can conveniently be described via the concept of a quasiparticle. Here, we connect the quasiparticle’s effective potential and the multi-ion potential of the mean force, found through molecular dynamics simulations, and we validate the method on an analytical toy model of the KcsA channel. Possible future applications of the method to the connection between molecular dynamical calculations and the experimentally measured current-voltage and current-concentration characteristics of the channel are discussed.

Molecular dynamics simulation of aggregation of monocrystal and polycrystal copper nanoparticles

2019 ◽  
Vol 33 (16) ◽  
pp. 1950168
Author(s):  
Linxing Zhang ◽  
Guang Hong ◽  
Shouyin Cai
Keyword(s):  
Molecular Dynamics ◽  
Lattice Structure ◽  
Displacement Vector ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Gyration Radius ◽  
Mean Square ◽  
Shrinkage Ratio ◽  
Lower Temperature ◽  
Dynamics Simulations

Molecular dynamics simulations were employed to investigate the aggregation of monocrystal and polycrystal nanoparticles. The lattice structure, displacement vector, potential energy, shrinkage ratio, relative gyration radius and mean square displacement of the two systems are compared. The results indicate that the aggregation of polycrystal nanoparticles is more drastic than that of monocrystal nanoparticles. Besides, the polycrystal nanoparticles are found contacted and melted at lower-temperature than that of monocrystal nanoparticles. The reason for all these phenomena is that there is additional surface energy in the grain boundary of polycrystal nanoparticles.

scholarly journals Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Thomas R. Caulfield ◽  
Batsal Devkota ◽  
Geoffrey C. Rollins
Keyword(s):  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Range Of Motion ◽  
Molecular Dynamics Simulations ◽  
Conformational Space ◽  
X Ray ◽  
Maxwell’S Demon ◽  
Density Maps ◽  
Maxwell's Demon ◽  
Dynamics Simulations

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

scholarly journals Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations

2016 ◽  
Vol 18 (8) ◽  
pp. 5743-5752 ◽  
Author(s):  
Witold Andrałojć ◽  
Enrico Ravera ◽  
Loïc Salmon ◽  
Giacomo Parigi ◽  
Hashim M. Al-Hashimi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Space ◽  
Nmr Data ◽  
Conformational Preferences ◽  
Tar Rna ◽  
Dynamics Simulations ◽  
Maximum Occurrence ◽  
Hiv 1

Molecular dynamics simulations and maximum occurrence distribution identify the same most likely sampled conformations over the available conformational space.

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