Multi-resolution dimer models in heat baths with short-range and long-range interactions

Abstract

This work investigates multi-resolution methodologies for simulating dimer models. The solvent particles which make up the heat bath interact with the monomers of the dimer either through direct collisions (short-range) or through harmonic springs (long-range). Two types of multi-resolution methodologies are considered in detail: (a) describing parts of the solvent far away from the dimer by a coarser approach; (b) describing each monomer of the dimer by using a model with different level of resolution. These methodologies are then used to investigate the effect of a shared heat bath versus two uncoupled heat baths, one for each monomer. Furthermore, the validity of the multi-resolution methods is discussed by comparison to dynamics of macroscopic Langevin equations.

Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions

“…The advantage of the presented approach is that we can directly replace the linear model by equations (2)-(5) in multiscale methods which use all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. Coupling MD and BD models is a possible approach to incorporate atomic-level information into models of intracellular processses which include transport of molecules between different parts of the cell (Erban, 2014(Erban, , 2016Gunaratne et al, 2019). The nonlinear SCG model (2)-(5) is studied in Section 4 for N = 1.…”

On Stretching, Bending, Shearing and Twisting of Actin Filaments II: Multi-Resolution Modelling

“…24,25 Multi-resolution modelling has also been used in the literature to coarsegrain the description of the solvent in the parts of computational domain, which is relatively far from the biological structure of interest, [26][27][28] and for replacing the explicit solvent representation in parts of the domain by a stochastic coarse-grained model, which describes the solvent implicitly. [29][30][31] To obtain multi-resolution methods with mutually consistent microscopic and macroscopic models, the parameters of such stochastic coarse-grained models can be inferred from all-atom MD simulations, 31,32 by estimating effective force distributions on coarse-grained sites. [33][34][35] In this way, both microscopic and macroscopic models consistently provide quantitatively the same information at the macroscopic level, while the monomer-based model provides an additional level of detail in the parts of the simulated system which is of interest to a modeller.…”

Multi-resolution simulations of intracellular processes

“…Zavadlav et al [3] consider methods for coupling atomistic and supramolecular water models with applications to solvated proteins. Gunaratne et al [4] analyse this approach using two theoretical heat baths, for which one can prove the convergence of the detailed molecular dynamics model to a coarser stochastic modelling approach. They model a biomolecule at a much coarser bead-spring approach.…”