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Mesoscopic simulations at the physics-chemistry-biology interface

Massimo Bernaschi, Simone Melchionna, and Sauro Succi

Massimo Bernaschi

  • IAC-CNR, via dei Taurini 19, 00185, Rome, Italy

Simone Melchionna

  • ISC-CNR, c/o Dipartimento di Fisica, Università La Sapienza, P. le A. Moro 5, 00185, Rome, Italy and IACS-SEAS, Harvard University, Oxford Street 29, Cambridge, Massachusetts 02138, USA

Sauro Succi

  • Center for Life Nano Science@Sapienza, Italian Institute of Technology, Viale Regina Elena, 295, I-00161 Rome, Italy, IAC-CNR, via dei Taurini 19, 00185, Rome, Italy, and IACS-SEAS, Harvard University, Oxford Street 29, Cambridge, Massachusetts 02138, USA

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Rev. Mod. Phys. 91, 025004 – Published 28 May, 2019

DOI: https://doi.org/10.1103/RevModPhys.91.025004

Abstract

This review discusses the lattice Boltzmann–particle dynamics (LBPD) multiscale paradigm for the simulation of complex states of flowing matter at the interface between physics, chemistry, and biology. In particular, current large-scale LBPD simulations of biopolymer translocation across cellular membranes, molecular transport in ion channels, and amyloid aggregation in cells are described. Prospects are provided for future LBPD explorations in the direction of cellular organization, the direct simulation of full biological organelles, all the way up to physiological scales of potential relevance to future precision-medicine applications, such as the accurate description of homeostatic processes. It is argued that, with the advent of Exascale computing, the mesoscale physics approach advocated in this review may come to age in the next decade and open up new exciting perspectives for physics-based computational medicine.

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Rev. Mod. Phys. 91, 025004– Published 28 May, 2019
  • Received 14 February 2018
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