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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…
PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts. By harnessing state-of-the-art web technologies…
Accurate simulations of atomistic systems from first principles are limited by computational cost. In high-throughput settings, machine learning can reduce these costs significantly by accurately interpolating between reference…
Given an algorithm the quality of the output largely depends on a proper specification of the input parameters. A lot of work has been done to analyze tasks related to using a fixed model [25] and finding a good set of inputs. In this paper…
Atomic and molecular data for the transitions of a number of astrophysically interesting species are summarized, including energy levels, statistical weights, Einstein A-coefficients and collisional rate coefficients. Available collisional…
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 article presents the "PubChemQC B3LYP/6-31G*//PM6" dataset, containing electronic properties of 85,938,443 molecules. It includes orbitals, orbital energies, total energies, dipole moments, and other relevant properties. The dataset…
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…
ORBKIT is a toolbox for post-processing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary…
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…
Machine learning (ML) can be used to construct surrogate models for the fast prediction of a property of interest. ML can thus be applied to chemical projects, where the usual experimentation or calculation techniques can take hours or days…
Simulating a quantum system is more efficient on a quantum computer than on a classical computer. The time required for solving the Schr\"odinger equation to obtain molecular energies has been demonstrated to scale polynomially with system…
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…
The quantum Hamiltonian is a fundamental property that governs a molecule's electronic structure and behavior, and its calculation and prediction are paramount in computational chemistry and materials science. Accurate prediction is highly…
Molecular-orbital-based machine learning (MOB-ML) enables the prediction of accurate correlation energies at the cost of obtaining molecular orbitals. Here, we present the derivation, implementation, and numerical demonstration of MOB-ML…
Using a realistic flexible molecule model of the fragile glass former orthoterphenyl, we calculate via molecular dynamics simulation the collective dynamic structure factor, recently measured in this system by Inelastic X-ray Scattering.…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Lie-algebraic and quantum-algebraic techniques are used in the analysis of thermodynamic properties of molecules and solids. The local anharmonic effects are described by a Morse-like potential associated with the $su(2)$ algebra. A…
Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware…
A program to calculate the three-particle hyperspherical brackets is presented. Test results are listed and it is seen that the program is well applicable up to very high values of the hypermomentum and orbital momenta. The listed runs show…