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Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
The selection of a balanced active space is a critical step in multi-reference quantum chemistry calculations, particularly for systems with strong electron correlation. Likewise, active space selection is a key to unlock the potential of…
Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of…
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…
Virtual Lab by Quantum Flytrap explores novel ways to represent quantum phenomena interactively and intuitively. It is a no-code online laboratory with a real-time simulation of an optical table, supporting up to three entangled photons.…
Agent Based Models are very popular in a number of different areas. For example, they have been used in a range of domains ranging from modeling of tumor growth, immune systems, molecules to models of social networks, crowds and computer…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: 1) atomic and molecular absorption spectra,…
This study examines the potential of utilizing Vision Language Models (VLMs) to improve the perceptual capabilities of semi-autonomous prosthetic hands. We introduce a unified benchmark for end-to-end perception and grasp inference,…
Advances in spatial omics and high-resolution imaging enable the creation of three-dimensional (3D) tissue maps that capture cellular organization and interactions in situ. While these data provide critical insights into tissue function and…
Statistical Shape Models of faces and various body parts are heavily used in medical image analysis, computer vision and visualization. Whilst the field is well explored with many existing tools, all of them aim at experts, which limits…
Agent-based modeling and network science have been used extensively to advance our understanding of emergent collective behavior in systems that are composed of a large number of simple interacting individuals or agents. With the increasing…
This paper proposes a unified software architecture for visualization and simulation based on a design targeting an N-dimensional space. The contributions of this study are twofold. First, it presents an architectural configuration that…
Simulating vibronic spectra is a central task in physical chemistry, offering insight into important properties of molecules. Recently, it has been experimentally demonstrated that photonic platforms based on Gaussian boson sampling (GBS)…
We discuss the Lattice Boltzmann-Particle Dynamics (LBPD) multiscale paradigm for the simulation of complex states of flowing matter at the interface between Physics, Chemistry and Biology. In particular, we describe current large-scale…
Realizing scaling laws in embodied AI has become a focus. However, previous work has been scattered across diverse simulation platforms, with assets and models lacking unified interfaces, which has led to inefficiencies in research. To…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
Histological images are critical in the diagnosis and treatment of cancers. Unfortunately, the current method for capturing these microscopy images require resource intensive tissue preparation that delays diagnosis for many days to a few…
Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing…
Polymer-Attenuated Coulombic Self-Assembly (PACS) is a flexible experimental approach for generating crystals from simple colloidal building blocks. The central components are charged spherical particles coated with a polymer brush that…