Related papers: Interactive molecular dynamics in virtual reality …
We introduce VR-Doh, an open-source, hands-on 3D modeling system that enables intuitive creation and manipulation of elastoplastic objects in Virtual Reality (VR). By customizing the Material Point Method (MPM) for real-time simulation of…
Binding processes are difficult to sample with molecular-dynamics (MD) simulations. In particular, the state space exploration is often incomplete. Evaluating the molecular interaction energy on a grid circumvents this problem but is…
Understanding the structure of the protein-ligand complex is crucial to drug development. Existing virtual structure measurement and screening methods are dominated by docking and its derived methods combined with deep learning. However,…
Fully immersive experiences that tightly integrate 6-DoF visual and auditory interaction are essential for virtual and augmented reality. While such experiences can be achieved through computer-generated content, constructing them directly…
User engagement is greatly enhanced by fully immersive multi-modal experiences that combine visual and auditory stimuli. Consequently, the next frontier in VR/AR technologies lies in immersive volumetric videos with complete scene capture,…
The identification of active binding drugs for target proteins (termed as drug-target interaction prediction) is the key challenge in virtual screening, which plays an essential role in drug discovery. Although recent deep learning-based…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational…
Computational approaches to drug discovery can reduce the time and cost associated with experimental assays and enable the screening of novel chemotypes. Structure-based drug design methods rely on scoring functions to rank and predict…
Academic events, such as a doctoral thesis defense, are typically limited to either physical co-location or flat video conferencing, resulting in rigid participation formats and fragmented presence. We present a multimodal framework that…
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 simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Current virtual reality (VR) training simulators of liver punctures often rely on static 3D patient data and use an unrealistic (sinusoidal) periodic animation of the respiratory movement. Existing methods for the animation of breathing…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
Deep learning promises to dramatically improve scoring functions for molecular docking, leading to substantial advances in binding pose prediction and virtual screening. To train scoring functions-and to perform molecular docking-one must…
Aim: Molecular dynamics simulations and normal mode analysis are well-established approaches to generate receptor conformational ensembles (RCEs) for ligand docking and virtual screening. Here, we report new fast molecular dynamics-based…
The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity…
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are…
An accurate treatment of the structures and dynamics that lead to enhanced chemical reactivity in enzymes requires explicit treatment of both electronic and nuclear quantum effects. The former can be captured in ab initio molecular dynamics…