Related papers: Interactive molecular dynamics in virtual reality …
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
The ability to perform ab initio molecular dynamics simulations using potential energies calculated on quantum computers would allow virtually exact dynamics for chemical and biochemical systems, with substantial impacts on the fields of…
Examination of thermal expansion of two-dimensional (2D) nanomaterials is a challenging theoretical task with either ab-initio or classical molecular dynamics simulations. In this regard, while ab-initio molecular dynamics (AIMD)…
This preprint presents a web app (essentially a web page-based program) with which two or more users (peers) can view and handle 3D molecular structures in a concurrent, interactive way through their web browsers. This means they can share…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…
We contribute MolecuSense, a virtual version of a physical molecule construction kit, based on visualization in Virtual Reality (VR) and interaction with force-feedback gloves. Targeting at chemistry education, our goal is to make virtual…
The Collective Variables Dashboard is a software tool for real-time, seamless exploration of molecular structures and trajectories in a customizable space of collective variables. The Dashboard arises from the integration of the Collective…
Neural network potentials (NNPs) enable large-scale molecular dynamics (MD) simulations of systems containing >10,000 atoms with the accuracy comparable to ab initio methods and play a crucial role in material studies. Although NNPs are…
We introduce VR-Doh, an open-source, hands-on 3D modeling system that enables intuitive creation and manipulation of elastoplastic objects in Virtual Reality (VR). By customizing the Material Point Method (MPM) for real-time simulation of…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
Computational Grids are emerging as a popular paradigm for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application composition, resource management and scheduling in these…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
Mixed Reality (MR) increasingly explores how virtual elements can shape physical behavior, yet how MR objects guide group movement remains underexplored. We address this gap by examining how virtual objects can nudge collective, co-located…
A novel approach to simulate simple protein-ligand systems at large time- and length-scales is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction-diffusion (RD) simulations, MSM/RD. Currently, MSM/RD…
Deep learning is transforming many areas in science, and it has great potential in modeling molecular systems. However, unlike the mature deployment of deep learning in computer vision and natural language processing, its development in…