Related papers: Adaptive Resolution Molecular Dynamics Technique: …
Predictive computational modeling of polymer materials is necessary for the efficient design of composite materials and the corresponding processing methods. Molecular dynamics (MD) modeling is especially important for establishing accurate…
In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this work, we show a novel approach where the latest version of the…
The imminent impact of immersive technologies in society urges for active research in real-time and interactive physics simulation for virtual worlds to be realistic. In this context, realistic means to be compliant to the laws of physics.…
Using an adiabatic approximation method, which searches for Tomlinson model-like instabilities for a simple but still realistic model for two crystalline surfaces in the extremely light contact limit, with mobile molecules present at the…
Dynamic mode decomposition (DMD) has proven to be a valuable tool for the analysis of complex flow-fields but the application of this technique to flows with moving boundaries is not straightforward. This is due to the difficulty in…
A modification of the Adaptive Biasing Force method is introduced, in which the free energy is approximated by a sum of tensor products of one-dimensional functions. This enables to handle a larger number of reaction coordinates than the…
Scientific research and engineering practice often require the modeling and decomposition of nonlinear systems. The Dynamic Mode Decomposition (DMD) is a novel Koopman-based technique that effectively dissects high-dimensional nonlinear…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
Refractory body-centered cubic (BCC) metals and alloys are of extraordinary importance in modern technological and structural applications. However, their wider adoption in science and technology is severely restricted by low-temperature…
We study the change in the temperature of maximum density (TMD) of a water-like solvent when small amounts of solute are added to the mixture. The water is modeled as a two length scales potential, which is known to exhibit water-like…
The efficacy of drug treatments depends on how tightly small molecules bind to their target proteins. The rapid and accurate quantification of the strength of these interactions (as measured by binding affinity) is a grand challenge of…
Accurate quantum mechanical treatment of molecular reactions remains a longstanding challenge, especially for reactions involving deep potential wells and long-lived intermediate complexes. Here, we introduce an interaction region…
We present a systematic, top-down, thermodynamic parametrization scheme for dissipative particle dynamics (DPD) using water-octanol partition coefficients, supplemented by water-octanol phase equilibria and pure liquid phase density data.…
Thermodynamic multi-component solution solidification approach to liquid-to-glass transition is proposed and actual mechanisms underlying vitrification, other than viscous slowdown, are identified. Due to polydisperse aggregation in liquid…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…
Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated…
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…
The computational cost of stiff chemical kinetics remains a dominant bottleneck in reacting-flow simulation, yet hybrid integration strategies are typically driven by hand-tuned heuristics or supervised predictors that make myopic decisions…
The recent development of the calculation of specific heat ($C$) of liquids and glasses by first-principles molecular dynamics (MD) simulations is reviewed. Liquid and glass states have common properties in that there is no periodicity and…
The description of fluid mixtures molecular behavior is significant for various industry fields due to the complex composition of fluid found in nature. Statistical mechanics approaches use intermolecular interaction potential to predict…