scholarly journals Reversible electrowetting transitions on superhydrophobic surfaces

2021 ◽  
Author(s):  
Davide Vanzo ◽  
Alenka Luzar ◽  
Dusan Bratko
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Md Simulations ◽  
Superhydrophobic Surfaces ◽  
Wenzel State

Electric field applied across the interface has been shown to enable transitions from Cassie to Wenzel state on superhydrophobic surfaces with miniature corrugations. Molecular Dynamics (MD) simulations manifest the possibility...

Molecular Dynamics Study of Confined Fluid in Graphene Nanopores

2014 ◽  
Vol 1061-1062 ◽  
pp. 205-208
Author(s):  
Kun Li ◽  
Jing Jie Sha ◽  
Lei Liu ◽  
Gen Sheng Wu ◽  
Wei Si ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Field Strength ◽  
Electric Field ◽  
Electric Field Strength ◽  
Ionic Currents ◽  
Md Simulations ◽  
Solution Concentration ◽  
Main Peak ◽  
Ion Distributions ◽  
Solvent Molecules

With the miniaturization of the NEMS/MEMS, the size effect becomes significant in the nanochannels/nanopores through which fluid flows as well as the interface effect. By all-atom molecular dynamics (MD) simulations, the ion transportation is investigated in nanopores as well as the physical properties at solid-liquid interface. To describe the anion and cation distributions of NaCl solution in vicinity of graphene nanopores, a new MD model was developed, taking thermal vibration of wall atoms, the structure of solvent molecules and ion sizes into consideration. The main peak locations of ion distributions stayed unchanged by changing the nanopore size, the solution concentration and the electric field strength. The ionic currents increased linearly with the diameter and the electric field strength, while it increased non-linearly with the solution concentration.

Influence of an external electric field on the deprotonation reactions of an Fe3+-solvated molecule: a reactive molecular dynamics study

2020 ◽  
Vol 22 (11) ◽  
pp. 6291-6299 ◽  
Author(s):  
Qiaofeng Gao ◽  
Yong Han ◽  
Pengyuan Liang ◽  
Jie Meng
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
External Electric Field ◽  
Md Simulations ◽  
Reactive Molecular Dynamics

An EEF can promote deprotonation reactions of Fe3+ using associated methods of MD simulations and experiments.

scholarly journals Polyelectrolytes polarization in nonuniform electric fields

2014 ◽  
Vol 25 (12) ◽  
pp. 1441010 ◽  
Author(s):  
Farnoush Farahpour ◽  
Mohammad Reza Ejtehadi ◽  
Fathollah Varnik
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
External Electric Field ◽  
Electric Fields ◽  
Lattice Boltzmann ◽  
Driving Force ◽  
Equilibrium Configuration ◽  
Md Simulations ◽  
Extended Chain ◽  
Entropic Traps

Stretching dynamics of polymers in microfluidics is of particular interest for polymer scientists. As a charged polymer, a polyelectrolyte (PE) can be deformed from its coiled equilibrium configuration to an extended chain by applying uniform or nonuniform electric fields. By means of hybrid lattice Boltzmann (LB)-molecular dynamics (MD) simulations, we investigate how the condensed counterions (CIs) around the PE contribute to the polymer stretching in inhomogeneous fields. As an application, we discuss the translocation phenomena and entropic traps, when the driving force is an applied external electric field.

Electric field triggered release of gas from a quasi-one-dimensional hydrate in the carbon nanotube

Nanoscale ◽  
2020 ◽  
Vol 12 (24) ◽  
pp. 12801-12808
Author(s):  
Jiaxian Li ◽  
Hangjun Lu ◽  
Xiaoyan Zhou
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Electric Field ◽  
Gas Hydrates ◽  
Md Simulations ◽  
Triggered Release ◽  
Nitrogen Gas ◽  
Single Walled Carbon Nanotube ◽  
One Dimensional ◽  
Single Walled Carbon

We systematically investigate the effects of an axial electric field on the formation and decomposition of quasi-one-dimensional nitrogen gas hydrates within a single-walled carbon nanotube (SWNT) by using molecular dynamics (MD) simulations.

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

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 The Impact of the Electric Field on Surface Condensation of Water Vapor: Insight from Molecular Dynamics Simulation

Nanomaterials ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 64 ◽  
Author(s):  
Qin Wang ◽  
Hui Xie ◽  
Zhiming Hu ◽  
Chao Liu
Keyword(s):  
Molecular Dynamics ◽  
Water Vapor ◽  
Electric Field ◽  
Intermolecular Forces ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Attraction Force ◽  
Condensation Rate ◽  
Shape Transformation ◽  
The Impact

In this study, molecular dynamics simulations were carried out to study the coupling effect of electric field strength and surface wettability on the condensation process of water vapor. Our results show that an electric field can rotate water molecules upward and restrict condensation. Formed clusters are stretched to become columns above the threshold strength of the field, causing the condensation rate to drop quickly. The enhancement of surface attraction force boosts the rearrangement of water molecules adjacent to the surface and exaggerates the threshold value for shape transformation. In addition, the contact area between clusters and the surface increases with increasing amounts of surface attraction force, which raises the condensation efficiency. Thus, the condensation rate of water vapor on a surface under an electric field is determined by competition between intermolecular forces from the electric field and the surface.

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

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