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This chapter describes a protocol to establish a three-dimensional (3D) model of a protein and to explore its conformational landscape. It combines predictions from up-to-date bioinformatics methods with low-resolution experimental data. It also proposes to examine rapidly the dynamics of the protein using molecular dynamics simulations with a coarse-grained force field. Tools for analyzing these trajectories are suggested as well as those for constructing all-atoms models. Thus, starting from a protein sequence and using free software, the user can get important conformational information, which might improve the knowledge about the protein function.

The dynamics of short-lived mRNA results in bursts of protein production in gene regulatory networks. We investigate the propagation of bursting noise between different levels of mathematical modelling and demonstrate that conventional approaches based on diffusion approximations can fail to capture bursting noise. An alternative coarse-grained model, the so-called piecewise deterministic Markov process (PDMP), is seen to outperform the diffusion approximation in biologically relevant parameter regimes. We provide a systematic embedding of the PDMP model into the landscape of existing approaches, and we present analytical methods to calculate its stationary distribution and switching frequencies., (© 2016 The Authors.)

Back Cover: Polymer molecules (represented by the yellow lines) are coarse‐grained into chains of fluctuating soft spheres (represented by the red blobs). They correspond to density clouds representing the spatial distribution of segments of the underlying microscopic sub‐chains. Thus the nonbonded interactions can be efficiently calculated from the cloud overlap via a grid (the grey mesh). Further details can be found in the article by G. Zhang, K. C. Daoulas, and K. Kremer* on page 214. [ABSTRACT FROM AUTHOR]

Polystyrene is abundant in marine debris. Like most synthetic polymers, it degrades very slowly, producing smaller and smaller particles easily ingested by wildlife. The presence of plastic microscopic particles in fish and marine wildlife is massive and well documented, but its impact on cellular activity is not understood. Biological activity generally requires interaction with biological membranes, but this is difficult to study at the molecular scale in vivo. Here we use coarse-grained molecular simulations to determine the effect of nanosized polystyrene (PS) particles on the properties of model biological membranes. We find that PS nanoparticles permeate easily into lipid membranes. Dissolved in the membrane core, PS chains alter membrane structure, significantly reduce molecular diffusion, and soften the membrane. Moreover, PS severely affects membrane lateral organization by stabilizing raft-like domains. Changes in membrane properties and lateral organization can severely affect the activity of membrane proteins and thereby cellular function.

In this chapter, we summarize recent theoretical efforts to address a variety of issues in Golgi morphogenesis: de novo biogenesis of compartments with precise chemical identity, the transport of proteins through the Golgi, the maintenance of chemical identity, and the morphology of Golgi compartments, from the perspective of nonequilibrium physics., (Copyright © 2013 Elsevier Inc. All rights reserved.)