scholarly journals Casimir force and its effects on pull-in instability modelled using molecular dynamics simulations

2020 ◽  
Vol 476 (2242) ◽  
pp. 20200311
Author(s):  
Avirup Sircar ◽  
Puneet Kumar Patra ◽  
Romesh C. Batra
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Casimir Force ◽  
Casimir Effect ◽  
Md Simulations ◽  
Casimir Forces ◽  
Total Potential ◽  
Continuum Scale ◽  
Casimir Interactions ◽  
Dynamics Simulations

We present a new methodology to incorporate the Casimir forces within the molecular dynamics (MD) framework. At atomistic scales, the potential energy between two particles arising due to the Casimir effect can be represented as U ( r ij ) =  C / r 7 . Incorporating the Casimir effect in MD simulations requires the knowledge of C , a problem hitherto unsolved. We overcome this by equating the total potential energy contributions due to each atomistic pair with the potential energy of continuum scale interacting bodies having similar geometries. After having identified the functional form of C , standard MD simulations are augmented with the potential energy contribution due to pairwise Casimir interactions. The developed framework is used to study effects of the Casimir force on the pull-in instability of rectangular and hollow cylindrical shaped deformable electrodes separated by a small distance from a fixed substrate electrode. Our MD results for pull-instability qualitatively agree with the previously reported analytical results but are quantitatively different. The effect of using longer-ranged Casimir forces in a constant temperature environment on the pull-in behaviour has also been studied.

scholarly journals Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations

2019 ◽  
Vol 1 ◽  
pp. e4 ◽  
Author(s):  
Takuya Shimato ◽  
Kota Kasahara ◽  
Junichi Higo ◽  
Takuya Takahashi
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
High Frequency ◽  
Md Simulations ◽  
Energy Space ◽  
Bias Potential ◽  
Ensemble Approach ◽  
Dynamics Simulations

Background The generalized ensemble approach with the molecular dynamics (MD) method has been widely utilized. This approach usually has two features. (i) A bias potential, whose strength is replaced during a simulation, is applied. (ii) Sampling can be performed by many parallel runs of simulations. Although the frequency of the bias-strength replacement and the number of parallel runs can be adjusted, the effects of these settings on the resultant ensemble remain unclear. Method In this study, we performed multicanonical MD simulations for a foldable mini-protein (Trp-cage) and two unstructured peptides (8- and 20-residue poly-glutamic acids) with various settings. Results As a result, running many short simulations yielded robust results for the Trp-cage model. Regarding the frequency of the bias-potential replacement, although using a high frequency enhanced the traversals in the potential energy space, it did not promote conformational changes in all the systems.

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

scholarly journals Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Hydrodynamic Radius ◽  
Md Simulations ◽  
Molecular Models ◽  
Experimental Values ◽  
Carbon Dioxide Co2 ◽  
Dynamics Simulations ◽  
Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

Mechanism of stacking fault annihilation in 3C-SiC epitaxially grown on Si(001) by molecular dynamics simulations

CrystEngComm ◽  
2021 ◽  
Author(s):  
Andrey Sarikov ◽  
Anna Marzegalli ◽  
Luca Barbisan ◽  
Massimo Zimbone ◽  
Corrado Bongiorno ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Stacking Faults ◽  
Md Simulations ◽  
Stacking Fault ◽  
Dynamics Simulations

In this work, annihilation mechanism of stacking faults (SFs) in epitaxial 3C-SiC layers grown on Si(001) substrates is studied by molecular dynamics (MD) simulations. The evolution of SFs located in...

scholarly journals Molecular Dynamics Simulations of Crystal Nucleation near Interfaces in Incompatible Polymer Blends

Polymers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 347
Author(s):  
Wenlin Zhang ◽  
Lingyi Zou
Keyword(s):  
Molecular Dynamics ◽  
Polymer Blends ◽  
Md Simulations ◽  
Nucleation And Growth ◽  
Crystal Nucleation ◽  
Crystalline Order ◽  
Mobile Species ◽  
Deep Supercooling ◽  
Crystallizable Polymer ◽  
Dynamics Simulations

We apply molecular dynamics (MD) simulations to investigate crystal nucleation in incompatible polymer blends under deep supercooling conditions. Simulations of isothermal nucleation are performed for phase-separated blends with different degrees of incompatibility. In weakly segregated blends, slow and incompatible chains in crystallizable polymer domains can significantly hinder the crystal nucleation and growth. When a crystallizable polymer is blended with a more mobile species in interfacial regions, enhanced molecular mobility leads to the fast growth of crystalline order. However, the incubation time remains the same as that in pure samples. By inducing anisotropic alignment near the interfaces of strongly segregated blends, phase separation also promotes crystalline order to grow near interfaces between different polymer domains.

scholarly journals Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

2016 ◽  
Vol 18 (37) ◽  
pp. 25806-25816 ◽  
Author(s):  
Carlos Navarro-Retamal ◽  
Anne Bremer ◽  
Jans Alzate-Morales ◽  
Julio Caballero ◽  
Dirk K. Hincha ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Arabidopsis Thaliana ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Cd Spectroscopy ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Dynamics Simulations ◽  
Crowded Environment

Unfolding of intrinsically unstructured full-length LEA proteins in a differentially crowded environment can be modeled by 30 ns MD simulations in accordance with experimental data.

scholarly journals Simulated Breathing: Application of Molecular Dynamics Simulations to Pulmonary Lung Surfactant

Symmetry ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1259
Author(s):  
Maksymilian Dziura ◽  
Basel Mansour ◽  
Mitchell DiPasquale ◽  
P. Charukeshi Chandrasekera ◽  
James W. Gauld ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Pulmonary Surfactant ◽  
Lung Surfactant ◽  
Protein Composition ◽  
Md Simulations ◽  
Building Blocks ◽  
Future Research ◽  
Total Composition ◽  
Protein Components ◽  
Dynamics Simulations

In this review, we delve into the topic of the pulmonary surfactant (PS) system, which is present in the respiratory system. The total composition of the PS has been presented and explored, from the types of cells involved in its synthesis and secretion, down to the specific building blocks used, such as the various lipid and protein components. The lipid and protein composition varies across species and between individuals, but ultimately produces a PS monolayer with the same role. As such, the composition has been investigated for the ways in which it imposes function and confers peculiar biophysical characteristics to the system as a whole. Moreover, a couple of theories/models that are associated with the functions of PS have been addressed. Finally, molecular dynamic (MD) simulations of pulmonary surfactant have been emphasized to not only showcase various group’s findings, but also to demonstrate the validity and importance that MD simulations can have in future research exploring the PS monolayer system.

Structural stability of CmTin microclusters and nanoparticles: Molecular–dynamics simulations

2005 ◽  
Vol 1 (4) ◽  
pp. 204-209
Author(s):  
O.B. Malcıoğlu ◽  
Ş. Erkoç
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binary Systems ◽  
Minimum Energy ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Atomic Interactions ◽  
Dynamics Simulations ◽  
Three Body ◽  
Initial Geometry

The minimum energy structures of CmTin microclusters and nanoparticles have been investigated theoretically by performing molecular–dynamics (MD) simulations. Selected crystalline and completely random initial geometries are considered. The potential energy function (PEF) used in the calculations includes two– and three–body atomic interactions for C-Ti binary systems. Molecular–dynamics simulations have been performed at 1 K and 300 K. It has been found that initial geometry has a very strong influence on relaxed geometry

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