Related papers: MDsrv -- visual sharing and analysis of molecular …
Generating molecular dynamics (MD) trajectories using deep generative models has attracted increasing attention, yet remains inherently challenging due to the limited availability of MD data and the complexities involved in modeling…
In recent years, machine learning (ML) has gained significant popularity in the field of chemical informatics and electronic structure theory. These techniques often require researchers to engineer abstract "features" that encode chemical…
ASCRIBE-XR, a novel computational platform designed to facilitate the visualization and exploration of 3D volumetric data and mesh data in the context of synchrotron experiments, is described. Using Godot and PC-VR technologies, the…
Development of applications related to closed-loop control requires either testing on the field or on a realistic simulator, with the latter being more convenient, inexpensive, safe, and leading to shorter development cycles. To address…
The overview-driven visual analysis of large-scale dynamic graphs poses a major challenge. We propose Multiscale Snapshots, a visual analytics approach to analyze temporal summaries of dynamic graphs at multiple temporal scales. First, we…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
We propose a new file format named "H5MD" for storing molecular simulation data, such as trajectories of particle positions and velocities, along with thermodynamic observables that are monitored during the course of the simulation. H5MD…
VTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software when handling massive molecular datasets. VTX employs a meshless molecular graphics…
Recent advances in diffusion models hold significant potential in robotics, enabling the generation of diverse and smooth trajectories directly from raw representations of the environment. Despite this promise, applying diffusion models to…
As with EAST (Experimental Advanced Superconducting Tokamak) experimental data analyzed by more and more collaborators, the experimental videos which directly reflect the real status of vacuum attract more and more researchers' attention.…
In recent years, there has been a significant amount of research on algorithms and control methods for distributed collaborative robots. However, the emergence of collective behavior in a swarm is still difficult to predict and control.…
Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
Masked graph modeling (MGM) is a promising approach for molecular representation learning (MRL).However, extending the success of re-mask decoding from 2D to 3D MGM is non-trivial, primarily due to two conflicting challenges: avoiding 2D…
Recently, researchers in Machine Learning algorithms, Computer Vision scientists, engineers and others, showed a growing interest in 3D simulators as a mean to artificially create experimental settings that are very close to those in the…
Self-supervised learning (SSL) has emerged as a crucial technique in image processing, encoding, and understanding, especially for developing today's vision foundation models that utilize large-scale datasets without annotations to enhance…
The challenge of graphically rendering high frame-rate videos on low compute devices can be addressed through periodic prediction of future frames to enhance the user experience in virtual reality applications. This is studied through the…
The process of screening molecules for desirable properties is a key step in several applications, ranging from drug discovery to material design. During the process of drug discovery specifically, protein-ligand docking, or chemical…
A Molecular Dynamics (MD) parallel to the Control Volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood, J. Chem. Phys. 18, 817 (1950) over a finite cubic volume of molecular dimensions.…
Describing the world behavior through mathematical functions help scientists to achieve a better understanding of the inner mechanisms of different phenomena. Traditionally, this is done by deriving new equations from first principles and…