Related papers: Interactive molecular dynamics in virtual reality …
Numerical simulation serves as a cornerstone in scientific modeling, yet the process of fine-tuning simulation parameters poses significant challenges. Conventionally, parameter adjustment relies on extensive numerical simulations, data…
In the modern drug discovery process, medicinal chemists deal with the complexity of analysis of large ensembles of candidate molecules. Computational tools, such as dimensionality reduction (DR) and classification, are commonly used to…
As computer simulations progress to increasingly complex, non-linear, and three-dimensional systems and phenomena, intuitive and immediate visualization of their results is becoming crucial. While Virtual Reality (VR) and Natural User…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
Improving the throughput of molecular docking, a computationally intensive phase of the virtual screening process, is a highly sought area of research since it has a significant weight in the drug designing process. With such improvements,…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…
We present our ongoing work aimed at accelerating a particle-resolved direct numerical simulation model designed to study aerosol-cloud-turbulence interactions. The dynamical model consists of two main components - a set of fluid dynamics…
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the…
Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. With the recent development of large language models (LLMs), a growing number of studies…
In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein-protein interactions. However, many commonly used methods to predict these effects perform poorly in important…
Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular…
Effective data visualization is a key part of the discovery process in the era of big data. It is the bridge between the quantitative content of the data and human intuition, and thus an essential component of the scientific path from data…
Virtual Reality (VR) and Augmented Reality (AR) tools have been applied in all engineering fields in order to avoid the use of physical prototypes, to train in high-risk situations, and to interpret real or simulated results. In order to…
The motion of the three-phase contact line between two immiscible fluids and a solid surface arises in a variety of wetting phenomena and technological applications. One challenge in continuum theory is the effective representation of…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
Plasma physics simulations create complex datasets for which researchers need state-of-the-art visualization tools to gain insights. These datasets are 3D in nature but are commonly depicted and analyzed using 2D idioms displayed on 2D…
Microbiomes are a vital part of the human body, engaging in tasks like food digestion and immune defense. Their structure and function must be understood in order to promote host health and facilitate swift recovery during disease. Due to…