Coarse-Grained Lattice Model for Molecular Recognition

Coarse-grained lattice model for molecular recognition.

We present a simple model which allows us to investigate the equilibrium aspects of molecular recognition between rigid biomolecules on a generic level. Using a two-stage approach, which consists of a design and a testing step, the role of cooperativity and of varying bond strength in molecular recognition is investigated. Cooperativity is found to enhance selectivity. In complexes which requir...

Coarse Grained Molecular Kinetics

The dynamic behavior of molecules can often be described by Markov processes. From computational molecular simulations one can derive transition rates or transition probabilities between subsets of the discretized conformational space. On the basis of this dynamic information, the spatial subsets are combined into a small number of so-called metastable molecular conformations. This is done by c...

Coarse Grained Molecular Dynamics

A coarse-grained model for a nanometer-scale molecular pump.

A theory for a nanometer-scale pump based on the ratchet concept is presented. A lattice gas model with a set of moves that satisfy hydrodynamic equations is used to describe an asymmetric nanometer channel connecting two reservoirs of fluid. The channel, which is coupled to an external oscillatory (or stochastic) driving force, pumps fluid from one reservoir to the other. The frequency of the ...

A coarse-grained molecular dynamics model for crystalline solids

A general mathematical framework for coarse-graining molecular dynamics (MD) model for solid system is presented. The formulation is based directly on the full MD model. The reduction of the atomic degrees of freedom is accomplished using the Mori–Zwanzig projection method. We also demonstrate how to simplify the model under this framework to make the numerical implementation much easier. Copyr...