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Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…

Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial…

Accurate quantum mechanical treatment of molecular reactions remains a longstanding challenge, especially for reactions involving deep potential wells and long-lived intermediate complexes. Here, we introduce an interaction region…

The biological function of proteins is encoded in their structure and expressed through the mediation of their dynamics. Local fluctuations are known to initiate biologically relevant pathways as they cooperatively enhance the dynamics in…

The cornerstone of computational drug design is the calculation of binding affinity between two biological counterparts, especially a chemical compound, i.e., a ligand, and a protein. Predicting the strength of protein-ligand binding with…

Accurate measurements of kinetic rate constants for interacting biomolecules is crucial for understanding the mechanisms underlying intracellular signalling pathways. The magnitude of binding rates plays a very important molecular…

The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…

Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond between the ligand and the target, are particularly valuable due…

We develop a method for simulating colloidal suspensions using multiparticle collision dynamics (MPCD) with a discrete particle model represented as a rigid body. The key steps for incorporating the rigid-body constraints are to thermalize…

We aim to solve the problem of manipulating deformable objects, particularly elastic bands, in real-world scenarios. However, deformable object manipulation (DOM) requires a policy that works on a large state space due to the unlimited…

Virtual reality (VR) offers immersive visualization and intuitive interaction. We leverage VR to enable any biomedical professional to deploy a deep learning (DL) model for image classification. While DL models can be powerful tools for…

Molecular docking is an essential step in the drug discovery process involving the detection of three-dimensional poses of a ligand inside the active site of the protein. In this paper, we address the Molecular Docking search phase by…

Protein-ligand binding complexes are ubiquitous and essential to life. Protein-ligand binding affinity prediction (PLA) quantifies the binding strength between ligands and proteins, providing crucial insights for discovering and designing…

Functional upper-limb prosthetic training can improve users performance in controlling prostheses and has been incorporated into occupational therapy for individuals in need. In recent years, virtual reality (VR) and augmented reality (AR)…

Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…

Finding informative low-dimensional descriptions of high-dimensional simulation data (like the ones arising in molecular dynamics or kinetic Monte Carlo simulations of physical and chemical processes) is crucial to understanding physical…

With the growing need to effectively support workforce upskilling in the manufacturing sector, virtual reality is gaining popularity as a scalable training solution. However, most current systems are designed as static, step-by-step…

Face-to-face conversation in Virtual Reality (VR) is a challenge when participants wear head-mounted displays (HMD). A significant portion of a participant's face is hidden and facial expressions are difficult to perceive. Past research has…

Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…

As consumer Virtual Reality (VR) and Mixed Reality (MR) technologies gain momentum, there's a growing focus on the development of engagements with 3D virtual content. Unfortunately, traditional techniques for content creation, editing, and…