Molecular simulation of diffusion-controlled kinetics in stepwise polymerization

Diffusion-Controlled Reaction Kinetics

Effects of Aluminum Incorporation in Tobermorite Structure on Chloride Diffusion: A Molecular Dynamics Simulation Study

In this paper, the effects of different aluminum to silicon ratios in silicate chains of calcium silicate hydrates (C-S-H) are evaluated on the diffusion coefficient of chloride ions by molecular dynamics method. Tobermorite is a crystalline phase that is used for studying C-S-H properties in nano scale, because of its analogous chemical composition to C-S-H. Aluminum incorporation in C-S-H and...

Modeling kinetics of diffusion-controlled surface wrinkles.

Nonlinear wrinkling of a compressed film on a soft substrate in the presence of inhomogeneous swelling actuation strain caused by solvent diffusion is studied. The simulation relies on a continuum model which integrates phase field microelasticity and Föppl-von Kármán plate theory. We show that the wrinkling morphologies developed in the diffusive domain exceeding a critical compression are con...

Theory and simulation of diffusion-controlled Michaelis-Menten kinetics for a static enzyme in solution.

We develop a uniform theory for the many-particle diffusion-control effects on the Michaelis-Menten scheme in solution, based on the Gopich-Szabo relaxation-time approximation (Gopich, I. V.; Szabo, A. J. Chem. Phys. 2002, 117, 507). We extend the many-particle simulation algorithm to the Michaelis-Menten case by utilizing the Green function previously derived for excited-state reversible gemin...

Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm.

We present a general-purpose model for biomolecular simulations at the molecular level that incorporates stochasticity, spatial dependence, and volume exclusion, using diffusing and reacting particles with physical dimensions. To validate the model, we first established the formal relationship between the microscopic model parameters (timestep, move length, and reaction probabilities) and the m...