In eukaryotic proteins, intrinsically disordered regions (IDRs) are ubiquitous and often exist in linker regions that flank the functional domains of modular proteins, regulating their functions. For detailed structural ensemble modeling of IDRs, we propose a multiscale method for IDRs that possess significant long-range order in modular proteins and apply it to the eukaryotic transcription fac...

Background: Human serum albumin (HSA) is one of the most prominent protein in human blood. Trimethoprim (TMP) is an efficient antibiotic drug for treatment of pneumocystis pneumonia (PCP). Patients with HIV/AIDS and cancer are extremely affected by the disease due to immune system deficiency. Objective: The aim of this study is to evaluate the molecular dynamics simulation (MD) of HSA with TMP...

We show that arbitrary phase space vector fields can be used to generate phase functions whose ensemble averages give the thermodynamic temperature. We describe conditions for the validity of these functions in periodic boundary systems and the Molecular Dynamics (MD) ensemble, and test them with a short-ranged potential MD simulation. 05.20.-y 05.20.Gd Typeset using REVTEX 1

Molecular dynamics (MD) simulation is used to study effects from moisture at cellulose nanofibril (CNF)–graphene oxide (GO) interfaces adhering in the wet state.

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studie...

To enable a simulation of the growth of crystalline fibers at a cluster of workstations, I developed a parallel molecular-dynamics (MD) algorithm. The structure of the MD algorithm is described briefly, together with its parallelization. Some specific features of our application will be discussed and an illustration of the program performance will be given.

membrane distillation has the potential to concentrate solutions to their saturation level, thus offering the possibility to recover valuable salts from the solutions. the process performance and stability, however, is strongly dependent upon the features of membranes applied. in addition, several other parameters, membrane thickness and thermal conductivity significantly affect the process per...

Replica exchange methods (REMs) are increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. However, despite having been shown to be very effective on model systems, the application of REM in complex systems such as for the simulation of protein and peptide folding in explicit solvent has not been objectively tested in detail. Here we present a comp...

Canonical molecular dynamics MD and Monte Carlo MC simulations for liquid/vapor equilibrium in truncated Lennard-Jones fluid have been carried out. Different results for coexistence properties orthobaric densities, normal and tangential pressure profiles, and surface tension have been reported in each method. These differences are attributed in literature to different set up conditions, e.g., s...

Computational modeling has a potential of making an important contribution to the advancement of laser-driven methods in nanotechnology. In this paper we discuss two computational schemes developed for simulation of laser coupling to organic materials and metals and present a multiscale model for laser ablation and cluster deposition of nanostructured materials. In the multiscale model the init...