Related papers: BioVEC: A program for Biomolecule Visualization wi…
Vector fields are one of the fundamental parts of mathematics which are key for modelling many physics phenomena such as electromagnetic fields or fluid and gas flows. Fields found in nature often exhibit complex structures which can be…
In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization. The wave function analysis module can calculate and generate 3D cubes for various types of molecular…
-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…
Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites within molecules, but obtaining an integrated global view…
This paper presents the Visual Place Cell Encoding (VPCE) model, a biologically inspired computational framework for simulating place cell-like activation using visual input. Drawing on evidence that visual landmarks play a central role in…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
We report an implementation of a program for visualizing complex-valued molecular orbitals. The orbital phase information is encoded on each of the vertices of triangle meshes using the standard color wheel. Using this program, we…
Coarse-grained (CG) models parameterized using atomistic reference data, i.e., 'bottom up' CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using the family of CALVADOS models of biomolecules including…
Background: Visualization of multi-channel microscopy data plays a vital role in biological research. With the ever-increasing resolution of modern microscopes the data set size of the scanned specimen grows steadily. On commodity hardware…
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…
Existing methods for visual reasoning attempt to directly map inputs to outputs using black-box architectures without explicitly modeling the underlying reasoning processes. As a result, these black-box models often learn to exploit biases…
Tackling binary program analysis problems has traditionally implied manually defining rules and heuristics, a tedious and time-consuming task for human analysts. In order to improve automation and scalability, we propose an alternative…
This tutorial explains how to use piecewise cubic B\'ezier curves to draw arbitrarily oriented ellipses and elliptical arcs. The geometric principles discussed here result in strikingly simple interfaces for graphics functions that can draw…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
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…
VPIC is a general purpose Particle-in-Cell simulation code for modeling plasma phenomena such as magnetic reconnection, fusion, solar weather, and laser-plasma interaction in three dimensions using large numbers of particles. VPIC's…
Visual representations of data (visualizations) are tools of great importance and widespread use in data analytics as they provide users visual insight to patterns in the observed data in a simple and effective way. However, since…