Related papers: Visualizing biomolecular electrostatics in virtual…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which…
Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of…
We describe a framework for interactive molecular dynamics in a multiuser virtual reality environment, combining rigorous cloud-mounted physical atomistic simulation with commodity virtual reality hardware, which we have made accessible to…
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
A cost-effective augmented reality (AR) system is presented for visualising three-dimensional magnetic field structures and charged-particle trajectories in magnetically confined fusion plasmas. The system presented in this study integrates…
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…
Several visualization schemes have been developed for imaging materials at the atomic level through atom probe tomography. The main shortcoming of these tools is their inability to parallel process data using multi-core computing units to…
Bionic vision uses neuroprostheses to restore useful vision to people living with incurable blindness. However, a major outstanding challenge is predicting what people 'see' when they use their devices. The limited field of view of current…
Accurate molecular property prediction (MPP) is a critical step in modern drug development. However, the scarcity of experimental validation data poses a significant challenge to AI-driven research paradigms. Under few-shot learning…
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…
In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…
Protein-protein interaction networks (PPIN) enable the study of cellular processes in organisms. Visualizing PPINs in extended reality (XR), including virtual reality (VR) and mixed reality (MR), is crucial for exploring subnetworks,…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Virtual screening (VS) is an essential technique for understanding biomolecular interactions, particularly, drug design and discovery. The best-performing VS models depend vitally on three-dimensional (3D) structures, which are not…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
As molecular scientists have made progress in their ability to engineer nano-scale molecular structure, we are facing new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs…
Digital biomarkers (DBMs) are a growing field and increasingly tested in the therapeutic areas of psychiatric and neurodegenerative disorders. Meanwhile, isolated silos of knowledge of audiovisual DBMs use in industry, academia, and clinics…
Pathologists diagnose cancer using gigapixel whole-slide images (WSIs), but the current digital workflow is fragmented. These multiscale datasets often exceed 100,000 x 100,000 pixels, yet standard 2D monitors restrict the field of view.…
Ultrasound-guided drug and gene delivery (usdg) enables controlled and spatially precise delivery of drugs and macromolecules, encapsulated in microbubbles (embs) and submicron gas vesicles (gvs), to target areas such as cancer tumors. It…