Substantial clinical and experimental evidence supports the hypothesis that amyloid β-protein (Aβ) forms assemblies with potent neurotoxic properties that cause Alzheimer’s disease (AD). Therapeutic targeting of these assemblies would be facilitated by the elucidation of the structural dynamics of Aβ aggregation at atomic resolution. We apply the ab initio discrete molecular dynamics approach c...

We present a model for the molecular traffic of ligands, substrates, and products through the active site of cholinesterases (ChEs). First, we describe a common treatment of the diffusion to a buried active site of cationic and neutral species. We then explain the specificity of ChEs for cationic ligands and substrates by introducing two additional components to this common treatment. The first...

We study models of two sequential enzyme-catalyzed reactions as a basic functional building block for coupled biochemical networks. We investigate the influence of enzyme distributions and long-range molecular interactions on reaction kinetics, which have been exploited in biological systems to maximize metabolic efficiency and signaling effects. Specifically, we examine how the maximal rate of...

Functional graphenic material (FGM) scaffolds instruct bacterial attachment through electrostatic interactions with the cell wall.

The Problem: A number of powerful optimization techniques have been developed to deal with different aspects of molecular design problems that arise in biology and biological engineering, including the design of protein folds and protein binding interfaces. The two key examples are algorithms for optimizing packing interactions and a separate approach for optimizing electrostatic interactions. ...