Mechanics of a Graphene Flake Driven by the Stiffness Jump on a Graphene Substrate

2017 ◽  
Vol 84 (8) ◽  
Author(s):  
Hong Gao ◽  
Hongwei Zhang ◽  
Zhengrong Guo ◽  
Tienchong Chang ◽  
Li-Qun Chen
Keyword(s):  
Molecular Dynamics ◽  
Analytical Model ◽  
Driving Force ◽  
Md Simulations ◽  
Driving Mechanism ◽  
Graphene Flake ◽  
Working Temperature ◽  
Directional Motion ◽  
Edge Force ◽  
Motion Behavior

Intrinsic driving mechanism is of particular significance to nanoscale mass delivery and device design. Stiffness gradient-driven directional motion, i.e., nanodurotaxis, provides an intrinsic driving mechanism, but an in-depth understanding of the driving force is still required. Based on molecular dynamics (MD) simulations, here we investigate the motion behavior of a graphene flake on a graphene substrate with a stiffness jump. The effects of the temperature and the stiffness configuration on the driving force are discussed in detail. We show that the driving force is almost totally contributed by the unbalanced edge force and increases with the temperature and the stiffness difference but decreases with the stiffness level. We demonstrate in particular that the shuttle behavior of the flake between two stiffness jumps on the substrate can be controlled by the working temperature and stiffness configuration of the system, and the shuttle frequency can be well predicted by an analytical model. These findings may have general implications for the design of nanodevices driven by stiffness jumps.

Unusually high flexibility of graphene–Cu nanolayered composites under bending

2019 ◽  
Vol 21 (31) ◽  
pp. 17393-17399 ◽  
Author(s):  
Yuxin Zhao ◽  
Xiaoyi Liu ◽  
Jun Zhu ◽  
Sheng-Nian Luo
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Analytical Model ◽  
Md Simulations ◽  
High Flexibility

The mechanical properties of graphene–Cu nanolayered (GCuNL) composites under bend loading are investigated via an energy-based analytical model and molecular dynamics (MD) simulations.

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.

Edge Forces in Contacting Graphene Layers

2015 ◽  
Vol 82 (10) ◽  
Author(s):  
Jianxin Li ◽  
Hongwei Zhang ◽  
Zhengrong Guo ◽  
Tienchong Chang ◽  
Huajian Gao
Keyword(s):  
Molecular Dynamics ◽  
Plane Deformation ◽  
Md Simulations ◽  
Graphene Layers ◽  
Out Of Plane ◽  
Edge Force ◽  
Edge Damage

Temperature- and stiffness-dependent edge forces offer new mechanisms of designing nanodevices driven by temperature and stiffness gradients. Here, we investigate the edge forces in a graphene nanolayer on a spring supported graphene substrate based on molecular dynamics (MD) simulations. The dependences of the edge forces on the temperature and stiffness of the substrate are discussed in detail. Special attention is paid to the effect of the out-of-plane deformation of the substrate on the constituent edge forces and the resultant edge force. The results show that the deformation may lead to a significant redistribution of the constituent edge forces but does not change the resultant edge force, suggesting that particular caution should be exercised in designing nanodevices based on sliding graphene layers to avoid potential edge damage.

Mechanosensing of a Graphene Flake on a Bent Beam

2020 ◽  
Vol 88 (4) ◽  
Author(s):  
Yue Hu ◽  
Jiantao Leng ◽  
Tienchong Chang
Keyword(s):  
Driving Force ◽  
Intelligent Systems ◽  
Md Simulations ◽  
Two Dimensional ◽  
Graphene Flake ◽  
Two Dimensional Materials ◽  
Potential Applications ◽  
Beam Bending ◽  
Intelligent Devices ◽  
Simulation Results

Abstract The ability of mechanosensing is essential for intelligent systems. Here we show by molecular dynamics (MD) simulations that a graphene flake on a bent beam exhibits amazing mechanosensing behavior, termed flexotaxis. The graphene flake can perceive the beam bending gradient which indeed leads to a gradient of atomic density that produces a driving force on the flake toward the direction of increasing density. An analytical model is developed to further confirm the mechanism, and the simulation results can be well reproduced by the model. Our findings may have general implications not only for the potential applications of graphene as sensing elements in nanoscale intelligent devices but also for the exploration of mechanosensing capability of other two-dimensional materials.

Crack propagation in graphene monolayer under tear loading

2019 ◽  
Vol 21 (5) ◽  
pp. 2659-2664
Author(s):  
Shijia Ye ◽  
Yang Cai ◽  
Xiaoyi Liu ◽  
Xiaohu Yao ◽  
Sheng-Nian Luo
Keyword(s):  
Molecular Dynamics ◽  
Crack Propagation ◽  
Analytical Model ◽  
Md Simulations ◽  
Graphene Monolayer

Crack propagation in graphene monolayer under tear loading is investigated via an energy-based analytical model and 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 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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