# Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics.

@article{Vijaykumar2017MultiscaleSO, title={Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics.}, author={Adithya Vijaykumar and Thomas E. Ouldridge and Pieter Rein ten Wolde and Peter G. Bolhuis}, journal={The Journal of chemical physics}, year={2017}, volume={146 11}, pages={ 114106 } }

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we…

## 26 Citations

### Multi-scale simulation of reaction-diffusion systems

- Physics
- 2017

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their…

### An efficient multi-scale Green's function reaction dynamics scheme.

- PhysicsThe Journal of chemical physics
- 2017

It is shown that the choice of the propagation domains has a relevant impact on the computational performance and the algorithm is shown to be more efficient than brute-force Brownian dynamics simulations up to a molar concentration of 103 μM and is up to an order of magnitude more efficient compared with previous MD-GFRD schemes.

### Modeling the Self-Assembly of Protein Complexes through a Rigid-Body Rotational Reaction-Diffusion Algorithm.

- BiologyThe journal of physical chemistry. B
- 2018

This work develops a relatively simple but accurate approach for building rigid structure and rotation into single-particle reaction-diffusion methods, providing a rate-based method for studying protein self-assembly and demonstrates how formation of regular lattices impacts the kinetics of association.

### Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics.

- Computer ScienceThe Journal of chemical physics
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This paper presents a meta-modelling system that automates the very labor-intensive and therefore time-heavy and expensive and therefore expensive and expensive process of inferring Boltzmann's inequality in theorems.

### MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations.

- ChemistryThe Journal of chemical physics
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The first step toward MSM/RD is made by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand and applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported.

### Grand canonical diffusion-influenced reactions: A stochastic theory with applications to multiscale reaction-diffusion simulations.

- MathematicsThe Journal of chemical physics
- 2018

The grand canonical Smoluchowski master equation (GC-SME) is introduced, which consists of a continuous-time Markov chain that models an arbitrary number of B particles, each one of them following Smoluchi's probabilistic dynamics, and is exploited to accurately derive multiscale/hybrid numerical methods that couple particle-based reaction-diffusion simulations with bulk concentration descriptions.

### ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics

- Computer SciencebioRxiv
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The iPRD software ReaDDy 2 is introduced, which provides a Python interface in which the simulation environment, particle interactions and reaction rules can be conveniently defined and the simulation can be run, stored and analyzed.

### Reversible Interacting-Particle Reaction Dynamics.

- PhysicsThe journal of physical chemistry. B
- 2018

It is shown that in dense particle systems, the incorporation of detailed balance is essential to obtain physically realistic solutions and a Monte Carlo algorithm is introduced that ensures detailed balance in the iPRD time-evolution (iPRD-DB).

### An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology

- Biology, ChemistrybioRxiv
- 2019

An algorithm for reversible binding of proteins to continuum surfaces with implicit lipids, providing dramatic speed-ups to many body simulations, and will enable efficient cell-scale simulations involving proteins localizing to realistic membrane models, which is a critical step for predictive modeling and quantification of in vitro and in vivo dynamics.

### Impact of Solution Chemistry and Particle Anisotropy on the Collective Dynamics of Oriented Aggregation.

- Materials ScienceACS nano
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Using Monte Carlo simulations, it is found that a simple geometric parameter, namely, the contact area between two attaching nanoplatelets, presents a useful tool for correlating nanoparticle morphologies to the emerging larger-scale aggregates, hence explaining the unusually high fractal dimensions measured for boehmite aggregates.

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