Related papers: Interactive molecular dynamics in virtual reality …

With the rapid advancement of large language models (LLMs) and vision-language models (VLMs), significant progress has been made in developing open-vocabulary robotic manipulation systems. However, many existing approaches overlook the…

Data-driven generation of molecules with desired properties, also known as inverse molecular design (IMD), has attracted significant attention in recent years. Despite the significant progress in the accuracy and diversity of solutions,…

All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…

We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…

3D modeling is becoming a well-developed field of medicine, but its applicability can be limited due to the lack of software allowing for easy utilizations of generated 3D visualizations. By leveraging recent advances in virtual reality, we…

We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus,…

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models…

Advances in manufacturing and characterization of complex molecular systems have created a need for new methods for design at molecular length scales. Emerging approaches are increasingly relying on the use of Artificial Intelligence (AI),…

Throughout computational science, there is a growing need to utilize the continual improvements in raw computational horsepower to achieve greater physical fidelity through scale-bridging over brute-force increases in the number of mesh…

Interaction in virtual reality (VR) environments is essential to achieve a pleasant and immersive experience. Most of the currently existing VR applications, lack of robust object grasping and manipulation, which are the cornerstone of…

Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…

Robotic manipulation requires understanding both the 3D spatial structure of the environment and its temporal evolution, yet most existing policies overlook one or both. They typically rely on 2D visual observations and backbones pretrained…

The atomic-scale response of inhomogeneous fluids at interfaces and surrounding solute particles plays a critical role in governing chemical, electrochemical and biological processes at such interfaces. Classical molecular dynamics…

Interactive volume visualization using a mixed reality (MR) system helps provide users with an intuitive spatial perception of volumetric data. Due to sophisticated requirements of user interaction and vision when using MR head-mounted…

The complexity of the data generated by (magneto)-hydrodynamic (HD/MHD) simulations requires advanced tools for their analysis and visualization. The dramatic improvements in virtual reality (VR) technologies have inspired us to seek the…

As life expectancy is mostly increasing, the incidence of many neurological disorders is also constantly growing. For improving the physical functions affected by a neurological disorder, rehabilitation procedures are mandatory, and they…

Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…

Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…

Tight-binding (TB) molecular dynamics (MD) has emerged as a powerful method for investigating the atomic-scale structure of materials --- in particular the interplay between structural and electronic properties --- bridging the gap between…

The two main thrusts of computational science are more accurate predictions and faster calculations; to this end, the zeitgeist in molecular dynamics (MD) simulations is pursuing machine learned and data driven interatomic models, e.g.…