Computer Engineering Commons^™

First-Passage Time Analysis Of A One-Dimensional Diffusion-Reaction Model: Application To Protein Transport Along Dna, Michael L. Mayo, Edward J. Perkins, Preetam Ghosh

Computer Science Publications

Background

Proteins search along the DNA for targets, such as transcription initiation sequences, according to one-dimensional diffusion, which is interrupted by micro- and macro-hopping events and intersegmental transfers that occur under close packing conditions.

Results

A one-dimensional diffusion-reaction model in the form of difference-differential equations is proposed to analyze the nonequilibrium protein sliding kinetics along a segment of bacterial DNA. A renormalization approach is used to derive an expression for the mean first-passage time to arrive at sites downstream of the origin from the occupation probabilities given by the individual transport equations. Monte Carlo simulations are employed to assess the …

A Modified Stokes-Einstein Equation For Aβ Aggregation, Srisairam Achuthan, Bon Jae Chung, Preetam Ghosh, Vijayaraghavan Rangachari, Ashwin Vaidya

Computer Science Publications

Background

In all amyloid diseases, protein aggregates have been implicated fully or partly, in the etiology of the disease. Due to their significance in human pathologies, there have been unprecedented efforts towards physiochemical understanding of aggregation and amyloid formation over the last two decades. An important relation from which hydrodynamic radii of the aggregate is routinely measured is the classic Stokes-Einstein equation. Here, we report a modification in the classical Stokes-Einstein equation using a mixture theory approach, in order to accommodate the changes in viscosity of the solvent due to the changes in solute size and shape, to implement a …