Focus on soft mesoscopics: physics for biology at a mesoscopic scale

Modern biology is, to a large extent, a mescoscale science. That the genome is encoded in a single giant macromolecule does not imply that knowledge of the molecular content of an organism is synonymous with its complete understanding and control. There remains the huge challenge to explain how biological function emerges via a vast network of molecular interactions, on the (multi-)cellular level. This is an attractive area for experimental soft matter physicists who have experience with wet supramolecular systems, and for theorists working with coarse-grained models. When moving from a molecular to a mesoscale description, molecular information becomes evaluated. Some aspects are emphasized as important, others dismissed as contingent or accidental details. As a rule, coarse graining wipes out most molecular details and gives way to simplicity, universality, and redundancy. Concomitantly, novel collective qualities, with their own scope for biological function, specificity, and evolutionary selection, emerge on the mesoscale. Think of DNA supercoils, histons, chromosomes, the proteome, the supramolecular assemblies of the cytoskeleton, swirls and topological defects in active polymer solutions or bacterial colonies, etc. Even the notion of biological function itself may be addressed as a mesoscale concept. Among other things, an approach focusing on mesoscale mechanisms therefore promises to improve also our conceptual understanding of malfunction and disease.

Many of the contributions to the issue can be grouped according to the physical mesoscale phenomenon they aim to elucidate in the biological world. This can be exemplified by the broad field of active matter, and in particular for the phenomenon of autonomous locomotion of living organisms. This focus issue comprises studies of artificial swimming mechanisms [1], specific studies and models of the migration of amoebea [2–4], kinetoplastea [5], and algae [6, 7]. Beyond the specific properties of individual swimmers, these studies address generic theoretical aspects, for example synchronisation in the last-mentioned chlamydomonas papers, or the emergence of collective effects such as aggregation and pattern formation in systems of self-propelled particles [8, 9], or their continuum modeling [10].

The focus issue also gathers contributions that consider closely related (or identical) soft-matter phenomenona in animate and inanimate systems, for example anomalous diffusion [11, 12] or elastic shape deformations of elastic membranes [13–15]. Next to membranes, the cytoskeleton is the crucial meso-scale structure where mechanical self-organization takes place. A number of studies therefore address the formation or relaxation of forces and spatial patterns in the cytoskeleton, as well as in cells and tissues under geometric constraints [16–23]. Finally, the interaction and orchestration of various organelles or functional modules, such as the cytoskeleton and the cell membrane are considered [24–27].

Sometimes experimental methods commonly used to study soft matter systems need to be adapted or redesigned to target mesoscopic phenomena in biology. Therefore, the issue also includes a few such methodologically oriented studies that feature a diverse toolbox of techniques ranging from x-ray diffraction [28] over image correlation spectroscopy that directly targets protein transport in live cells [29] to microrheometric probes of the active cytoskeleton [30, 31] and of the thermorheology of reconstituted networks [32] and living cells [33].

It may be needless to say that a wide variety of theoretical methods from statistical mechanics and soft matter physics is brought to bear on mesoscale phenomena in biology. Thermodynamic concepts are applied to viral assembly [34] and protein mechanics [35]. Graph and network theory are used analyse neural networks [36] or very general interaction networks and their mesoscale symmetries, which can reveal striking structural similarities across diverse scales and systems [37–39]. This is why minimalistic mathematical models dictated by conservation laws and topological constraints, such as the so-called exclusion processes, can provide valuable predictions for complex biological functions such as cytoskeletal transport along biopolymers [40] and in networks thereof [41]. Theory also elucidates the different role of defects in active (excitable) versus passive media [42].

Altogether, the studies gathered in this focus issue thus provide a snapshot of current activities in the emerging field of 'soft mesoscopics', the quest for the physical principles at work at the mesoscopic scale in soft and biological matter.