We have recently completed a full re-architecturing of the ROSETTA molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid prototyping of novel protocols by providing easy-to-use interfaces to powerful tools for molecular modeling. The source code of this rearchitecturing has been released as ROSETTA3 and is freely available for ...

A continuum-based elastic micromechanics model is developed for silica nanoparticle/polyimide composites with various nanoparticle/polyimide interfacial treatments. The model incorporates the molecular structures of the nanoparticle, polyimide, and interfacial regions, which are determined using a molecular modeling method that involves coarse-grained and reversemapping techniques. The micromec...

Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is o...

Drug designing and molecular dynamic studies were an intense, lengthy and an inter-disciplinary venture. At present, a new approach towards the use of computational chemistry and molecular modeling for in-silico drug design. Computational in-silico drug design skills are used in bioinformatics, computational biology and molecular biology. Drug designing using in-silico methods is cost effective...

A group of regioisomeric 5-oxo-1,4,5,6,7,8 hexahydroquinoline derivatives possessing a COX-2 SO2Me pharmacophore at the para position of the C-2 or C-4 phenyl ring, in conjunction with a C-4 or C-2 phenyl (4-H) or substituted-phenyl ring (4-F,4-Cl,4-Br,4-OMe,4-Me, 4-NO2), were designed for evaluation as selective cyclooxygenase-2 (COX-2) inhibitors. These target 5-oxo-1,4,5,6,7,8 hexahydroquino...

Implicit solvent-based methods play an increasingly important role in molecular modeling of biomolecular structure and dynamics. Recent methodological developments have mainly focused on the extension of the generalized Born (GB) formalism for variable dielectric environments and accurate treatment of nonpolar solvation. Extensive efforts in parameterization of GB models and implicit solvent fo...

We employ fully atomistic molecular modeling to investigate the concentration dependence of the electro-optic coefficient of two guest-host polymer composites. Using classical molecular dynamics, we record the time-evolution of the guest-host system under the application of an external electric field. Through analysis of the orientation of the nonlinear optical chromophores in the guest-host co...

In this paper, a rational Bézier surface is proposed as a uniform approach to modeling all three types of molecular surfaces (MS): the van der Waals surface (vdWS), solvent accessible surface (SAS) and solvent excluded surface (SES). Each molecular surface can be divided into molecular patches, which can be defined by their boundary arcs. The solution consists of three steps: topology modeling,...