Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten

Thermodynamically Consistent Coarse Graining of Biocatalysts beyond Michaelis--Menten

Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. Œis procedure provides stoichiometries, reaction ƒuxes (rate laws), and reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicabilit...

Effective rates from thermodynamically consistent coarse-graining of models for molecular motors with probe particles.

Many single-molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom representing the motor. We present a coarse-graining method that maps a model comprising two coupled degrees of freedom which represent motor and probe particle to s...

Coarse graining

Multiscale simulations For nearly all systems of interest to us, the most transferrable and fundamental description of matter is one that invokes quantum mechanics. At the highest level of accuracy, this amounts to solving Schrodinger’s equation for all of the subatomic particles in a system. Computationally, many approximations need to be made in order to use ab initio methods, and even these ...

Predictive coarse-graining

Brute-force molecular dynamics simulations are limited by the exuberant number of degrees of freedom and the relatively small time-steps. As a result, only relatively small assemblies of molecules over small time spans are accessible with current and foreseeable computational capabilities. In order to overcome this limitation, coarse-grained models have been proposed which employ a much smaller...

Shape-Based Coarse Graining