Molecular Dynamics of Monomeric Water Dissolved in Very Hydrophobic Solvents:  the Current State of the Art of Vibrational Spectroscopy Analyzed from Analytical Model and MD Simulations

2000 ◽  
Vol 104 (42) ◽  
pp. 9415-9427 ◽  
Author(s):  
Y. Danten ◽  
T. Tassaing ◽  
M. Besnard
Keyword(s):  
Molecular Dynamics ◽  
Analytical Model ◽  
Vibrational Spectroscopy ◽  
State Of The Art ◽  
Md Simulations ◽  
Current State

Nanotribological Simulations With Molecular Dynamics

2008 ◽  
Author(s):  
Michael Chandross
Keyword(s):  
Molecular Dynamics ◽  
State Of The Art ◽  
Md Simulations ◽  
Shear Rates ◽  
The Past ◽  
Current State ◽  
Exciting Current ◽  
Basic Concepts

The use of molecular dynamics (MD) simulations in nanotribology has made many advances in the past twenty years. While early simulations were limited to hundreds or thousands of atoms undergoing shear at 100 m/s, the current state of the art simulations in nanotribology approach millions of atoms with shear rates that can, in certain cases, match experiment. However, many of the exciting current simulations involve techniques that can be difficult for non-experts to understand. In this tutorial we hope to alleviate some of this confusion by reviewing the basic concepts that form the foundations of molecular dynamics (MD) simulations. This will include both a discussion of the method in general, was well as a focus on the use of MD in nanotribological simulations.

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.

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.

Current State-of-the-Art Molecular Dynamics Methods and Applications

2014 ◽  
pp. 269-313 ◽  
Author(s):  
Dimitrios Vlachakis ◽  
Elena Bencurova ◽  
Nikitas Papangelopoulos ◽  
Sophia Kossida
Keyword(s):  
Molecular Dynamics ◽  
State Of The Art ◽  
Current State ◽  
Molecular Dynamics Methods

scholarly journals A Review of Recent Developments in Molecular Dynamics Simulations of the Photoelectrochemical Water Splitting Process

Catalysts ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 807
Author(s):  
Nicolae Goga ◽  
Leonhard Mayrhofer ◽  
Ionut Tranca ◽  
Silvia Nedea ◽  
Koen Heijmans ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water Splitting ◽  
State Of The Art ◽  
Special Focus ◽  
Semiconductor Interfaces ◽  
Current State ◽  
Recent Developments ◽  
Dynamics Simulations ◽  
Photoelectrochemical Hydrogen Production ◽  
Splitting Process

In this review, we provide a short overview of the Molecular Dynamics (MD) method and how it can be used to model the water splitting process in photoelectrochemical hydrogen production. We cover classical non-reactive and reactive MD techniques as well as multiscale extensions combining classical MD with quantum chemical and continuum methods. Selected examples of MD investigations of various aqueous semiconductor interfaces with a special focus on TiO2 are discussed. Finally, we identify gaps in the current state-of-the-art where further developments will be needed for better utilization of MD techniques in the field of water splitting.

scholarly journals Developing a molecular dynamics force field for both folded and disordered protein states

2018 ◽  
Vol 115 (21) ◽  
pp. E4758-E4766 ◽  
Author(s):  
Paul Robustelli ◽  
Stefano Piana ◽  
David E. Shaw
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Md Simulation ◽  
State Of The Art ◽  
Force Fields ◽  
Md Simulations ◽  
Disordered Proteins ◽  
Disordered Protein ◽  
Data Points ◽  
Folded Proteins

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB-disp, should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields.

Pressure Suppression Containment Design—Current State of the Art

1969 ◽  
Vol 91 (1) ◽  
pp. 13-20 ◽  
Author(s):  
D. R. Miller
Keyword(s):  
Analytical Model ◽  
Test Data ◽  
State Of The Art ◽  
Nuclear Reactors ◽  
Current State ◽  
Graphical Technique ◽  
Containment Pressure

A summary of the thermodynamic design limits for pressure suppression containments for nuclear reactors is presented. Those parameters which must adhere to tested values are tabulated and discussed. An analytical model is described and is shown to accurately predict the existing test data. A graphical technique for predicting the transient peak containment pressure, based on the model, is presented for use in containment design.

scholarly journals Fine-tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

2020 ◽  
Author(s):  
Vojtěch Mlýnský ◽  
Petra Kührová ◽  
Tomáš Kühr ◽  
Michal Otyepka ◽  
Giovanni Bussi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
State Of The Art ◽  
Dynamic Properties ◽  
Md Simulations ◽  
Experimental Methods ◽  
Fine Tuning ◽  
Enhanced Sampling ◽  
Structural Dynamic ◽  
Nmr Data

ABSTRACTDetermination of RNA structural-dynamic properties is challenging for experimental methods. Thus atomistic molecular dynamics (MD) simulations represent a helpful technique complementary to experiments. However, contemporary MD methods still suffer from limitations of force fields (ffs), including imbalances in the non-bonded ff terms. We have recently demonstrated that some improvement of state-of-the-art AMBER RNA ff can be achieved by adding a new term for H-bonding called gHBfix, which increases tuning flexibility and reduces the risk of side-effects. Still, the first gHBfix version did not fully correct simulations of short RNA tetranucleotides (TNs). TNs are key benchmark systems due to availability of unique NMR data, although giving too much weight on improving TN simulations can easily lead to over-fitting to A-form RNA. Here we combine the gHBfix version with another term called tHBfix, which separately treats H-bond interactions formed by terminal nucleotides. This allows to refine simulations of RNA TNs without affecting simulations of other RNAs. The approach is in line with adopted strategy of current RNA ffs, where the terminal nucleotides possess different parameters for the terminal atoms than the internal nucleotides. The combination of gHBfix with tHBfix significantly improves the behavior of RNA TNs during well-converged enhanced-sampling simulations. TNs mostly populate canonical A-form like states while spurious intercalated structures are largely suppressed. Still, simulations of r(AAAA) and r(UUUU) TNs show some residual discrepancies with the primary NMR data which suggests that future tuning of some other ff terms might be useful.

scholarly journals On the Use of Molecular Dynamics Simulations for Elucidating Fine Structural, Physico-Chemical and Thermomechanical Properties of Lignocellulosic Systems: Historical and Future Perspectives

2021 ◽  
Vol 5 (2) ◽  
pp. 55
Author(s):  
Krishnamurthy Prasad ◽  
Mostafa Nikzad ◽  
Shammi Sultana Nisha ◽  
Igor Sbarski
Keyword(s):  
Molecular Dynamics ◽  
High Performance ◽  
Molecular Mechanisms ◽  
Md Simulations ◽  
Thermomechanical Properties ◽  
Current State ◽  
Physico Chemical ◽  
Carbohydrate Complex ◽  
Dynamics Simulations

The use of Molecular Dynamics (MD) simulations for predicting subtle structural, thermomechanical and related characteristics of lignocellulosic systems is studied. A historical perspective and the current state of the art are discussed. The use of parameterised MD force fields, scaling up simulations via high performance computing and intrinsic molecular mechanisms influencing the mechanical, thermal and chemical characteristics of lignocellulosic systems and how these can be predicted and modelled using MD is shown. Individual discussions on the MD simulations of the lignin, cellulose, lignin-carbohydrate complex (LCC) and how MD can elucidate the role of water on the surface and microstructural characteristics of these lignocellulosic systems is shown. In addition, the use of MD for unearthing molecular mechanisms behind lignin-enzyme interactions during precipitation processes and the deforming/structure weakening brought about by cellulosic interactions in some lignocellulosic systems is both predicted and quantified. MD results from relatively smaller systems comprised of several hundred to a few thousand atoms and massive multi-million atom systems are both discussed. The versatility and effectiveness of MD based on its ability to provide viable predictions from both smaller and massive starting systems is presented in detail.

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.

Sign in / Sign up

Export Citation Format

Share Document