In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is ...

Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields, which have been developed and validated using relatively short simulations of small molecules, become apparent. One common artifact is aggregation of water-soluble b...

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide ...

A novel methodology is presented for evaluating a dynamic ensemble of oligosaccharide conformations by lanthanide-assisted NMR spectroscopy combined with molecular dynamics (MD) simulations. The results obtained using the GM3 trisaccharide demonstrated that pseudocontact shift measurements offer a valuable experimental tool for the validation of MD simulations of highly flexible biomolecules.

Communications Correlated motions can be accurately extracted from molecular dynamics (MD) simulations that are compatible with the measured NMR spectroscopic data (NOE and order parameters) for two different proteins (Cov: covariance matrix). B. de Groot and co-workers discuss the results of MD simulations on a fragment of protein G in their Communication on the following pages.

This study aimed to investigate the adsorption of CH4, CO2, H2S at a temperature of 298.15 K and pressurerange of 0.1 to 30 atm, and compare the results with experimental data for MIL-47 using GCMC. Themaximum CH4, CO2 and H2S adsorptions were 3.6, 10.45, and 12.57 mol.kg-1, respectively. In addition, theselectivity for binary mixtures of CH4/CO2 and CH4/H2S was calculated. Th...

Dynamic irregular applications such as molecular dynamics (MD) simulation often suffer considerable performance deterioration during execution. To address this problem, an optimal data-reordering schedule has been developed for runtime memory-access optimization of MD simulations on parallel computers. Analysis of the memory-access penalty during MD simulations shows that the performance improv...

Molecular dynamics (MD) simulation is an established method for studying the conformational changes that are important for protein function. Recent advances in hardware and software have allowed MD simulations over the same timescales as experiment, improving the agreement between theory and experiment to a large extent. However, running such simulations are costly, in terms of resources, stora...

While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD) simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. T...

In this paper, we propose coarse-grained single-site (CGSS), wall-CO(2), and CO(2)-CO(2) interaction potential models to study the structure of carbon dioxide under confinement. The CGSS potentials are used in an empirical potential based quasi-continuum theory, EQT, to compute the center-of-mass density and potential profiles of CO(2) confined inside different size graphite slit pores. Results...