Related papers: Molcontroller: a VMD Graphical User Interface for …
How to effectively represent molecules is a long-standing challenge for molecular property prediction and drug discovery. This paper studies this problem and proposes to incorporate chemical domain knowledge, specifically related to…
Medical vision-and-language models (MVLMs) have attracted substantial interest due to their capability to offer a natural language interface for interpreting complex medical data. Their applications are versatile and have the potential to…
A fluid flow in a simple dense liquid, passing an obstacle in a two-dimensional thin film geometry, is simulated by Molecular Dynamics (MD) computer simulation and compared to results of Lattice Boltzmann (LB) simulations. By the…
Prediction of solubility has been a complex and challenging physiochemical problem that has tremendous implications in the chemical and pharmaceutical industry. Recent advancements in machine learning methods have provided great scope for…
Magnetic Resonance Imaging (MRI) is a well-established modality for pre-operative planning and is also explored for intra-operative guidance of procedures such as intravascular interventions. Among the experimental robot-assisted…
Progress in hardware, algorithms, and force fields are pushing the scope of molecular dynamics (MD) simulations towards the length- and time scales of complex biochemical processes. This creates a need for developing advanced analysis…
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of…
Molecular language modeling tasks such as molecule captioning have been recognized for their potential to further understand molecular properties that can aid drug discovery or material synthesis based on chemical reactions. Unlike the…
We previously introduced a conformational sampling method, a multi-dimensional virtual-system coupled molecular dynamics (mD-VcMD), to enhance conformational sampling of a biomolecular system by computer simulations. Here, we present a new…
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…
Direct manipulation interfaces provide intuitive and interactive features to a broad range of users, but they often exhibit two limitations: the built-in features cannot possibly cover all use cases, and the internal representation of the…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
This paper presents the design and implementation of a modular multi-document interface (MDI) framework for scientific visualization and simulation in the Java Virtual Machine (JVM) ecosystem. The framework emphasizes architectural…
Molecular Relational Learning (MRL), aiming to understand interactions between molecular pairs, plays a pivotal role in advancing biochemical research. Recently, the adoption of large language models (LLMs), known for their vast knowledge…
Multiscale magnetic simulations, including micromagnetic and atomistic spin dynamics simulations, are widely used in the study of complex magnetic systems over a wide range of spatial and temporal scales. The advances in these simulation…
Graphics design is important for various applications, including movie production and game design. To create a high-quality scene, designers usually need to spend hours in software like Blender, in which they might need to interleave and…
In this work, we propose a simple transformer-based baseline for multimodal molecular representation learning, integrating three distinct modalities: SMILES strings, 2D graph representations, and 3D conformers of molecules. A key aspect of…
We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral…
Neural network potentials (NNPs) are rapidly changing the landscape of state-of-the-art molecular dynamics (MD) simulations. To make full use of this development, the community needs flexible, easy-to-use interfaces firmly integrated with…
Software development of modern, data-driven applications still relies on tools that use interaction paradigms that have remained mostly unchanged for decades. While rich forms of interactions exist as an alternative to textual command…