Liquid, soft, alive: identifying the biological questions in the physics of cells
CECAM-HQ-EPFL, Lausanne, Switzerland
During the past decade there has been a shift in the way equilibrium con- cepts in soft matter and statistical physics have been employed to understand diverse problems in biology based on liquid-liquid phase separation (LLPS), macromolecular crowding, or formation of equilibrium clusters and aggregates (condensates). A common aspect of all such processes is the likely existence of phase diagrams with multiple stable or metastable polymorphic disordered liq- uid states . However, unlike the passive phase behaviour that is observed in natural and man-made phase separation processes (well understood since long ago), cellular LLPS processes at work in living systems are intrinsically non- equilibrium as a result of the intricate array of internal and external chemostats and mass/charge currents. On the one hand, understanding the fundamental mechanism of such non-equilibrium phase separation is crucial for better under- standing the functioning (and malfunctioning) of the cell. On the other hand, the better the inner workings of the cell are understood at a fundamental level, the more researchers can get inspiration for creating soft matter physics analogs pointing to new strategies for novel functional materials design.
This workshop aims at establishing an environment for fertile cross-talk be- tween cell biologists and soft-matter physicists  who are interested to run experiments and model the non-equilibrium processes that govern key cellular processes. The primary deliverable of such cross-fertilization will be to clearly identify the main biological questions for physicists to address. The second strong objective of the proposed workshop is to discuss state-of-the-art com- putational approaches bridging length- and time-scales to study these complex soft matter and bio-molecular systems.
Liquid-liquid phase separation in biology
The living cells are organized in a highly compartmentalized fashion. Besides membrane-bound organelles, such as lysosomes and mitochondria, there is a plethora of membraneless structures formed through liquid-liquid phase separa- tion (LLPS) act as dynamical cellular organelles . Many aggregation-related processes conducive to neurodegenerative diseases could be regarded and better understood as LLPS-driven mechanisms . Moreover, some vital regulative processes and kinetic mechanisms in cell biology, such as RNA-based regula- tion of gene expression and certain enzymatic kinetics, could be viewed anew as epiphenomena of LLPS-modulated activity. Consequently, during the past decade, there has been an explosive growth in the study of controlled, nano-scale liquid-liquid phase separation (LLPS) inside living cells. It should be stressed that, unlike the passive LLPS that takes place in many man-made separation processes, cellular LLPS is intrinsically non-equilibrium and strongly confined (e.g., in the cell nucleus). The vigorous research activity – involving biolo- gists, chemists and physicists – is revolving around the central question on how complex dynamic environment can organize and control multiple (bio)chemical processes in parallel. Understanding the functioning of such complex micro- reactors is also intimately connected with formation of the protocells . The role of LLPS in basic processes at the core of life has contributed to bringing soft matter physics closer to fundamental questions that arise in cell biology and prebiotic chemistry.
The cell is a nanoporous, active, viscoelastic, compartmentalized open reac- tor . Many molecular species, whose sizes span two to three orders of mag- nitude, diffuse passively or are actively transported from one place to another. However, the available space for mass transport across the cell is small: up to 40 % of the overall volume is occupied by biomolecules, complexes, organelles or cytoskeletal structures . Collectively, this condition is referred to in the litera- ture as macromolecular crowding (MC) . Although rooted in excluded-volume effects, researchers have long realized that the role played by MC is subtle and indissolubly connected to other closely related facets of crowded places. For ex- ample, while excluded-volume effects obviously may exert entropic forces that could stabilize polymers such as proteins within the cell, the presence of modest anisotropic weak non-specific (i.e. occurring among non-specific portions of the partners’ surfaces) interactions may have the opposite effect, namely lead to a destabilization of the folded conformation . Moreover, crucial kinetic processes such as enzymatic catalysis, turned out to be influenced by volume exclusion and related accompanying factors, such as non-specific interactions  and space segmentation [11, 12] (not only it is important how much space is available, but also how that is structured).
Clusters, aggregates, protocells
Biomacromolecules can aggregate to form clusters and networks in various ways – with broad biological implications. A wide variety of proteins form fibrillar aggregates (amyloids), which are implicated in a number of human diseases : Alzheimer’s, Creutzfeldt-Jakob and Huntingdon’s diseases (in the brain), Parkinson’s disease (in nerve cells), type-II diabetes (in the pancreas) , and also autoimmune disorders . Assemblies of protein capsids are vital for functioning of viruses and packing of genetic materials. Coacervates are clusters or droplets (the distinction is sometimes unclear, experimentally ) that are formed due to a combination of electrostatic interactions between poly- electrolytes and hydrophobic interactions. The formation of such microscopic clusters in relatively dilute solutions seems to be crucial for origin of life models – in this context they are called protocells [18, 19].
Aggregation of biomolecules is a complex problem that lends itself well to soft matter studies. Visualization of dynamic biomolecular clusters is challenging and techinques such as small-angle neutron scattering , NMR , neutron spin echo , or similar have to be used. Elucidating mechanisms of clus- ter formation is thus much easier in colloidal model systems where qualitative insights can be gleaned from direct optical techniques  coupled with multi- scale simulations . A general prerequisite for aggregation is some form of inter-particle attraction, generated by physical (e.g., van der Waals or deple- tion interactions), or chemical means. The aggregation process can be diffusion limited (in the absence of a repulsive barrier), or reaction-limited  (with a barrier). Depending on the interaction profile, aggregation can therefore either be irreversible (slowly growing static clusters) or thermodynamic and reversible (dynamic  clusters). The size and structure of the aggregates are delicately connected to their biological function: disordered medium-sized aggregates of proteins are usually toxic – unlike individual proteins, or their large native (or- dered) aggregates. A recent review  suggests that the toxicity is related either to their larger diffusivity, or higher degree of hydrophobicity. Another study  reports that the size and geometry of the crystalline clusters of an- timicrobial peptides crucially affect the activation of immune receptors and that multivalent binding  plays an important role in understanding such effects.
Soft and bio-inspired materials
Biological systems can achieve remarkable efficiency and selectivity, but thus far, the concept of driven LLPS has barely been exploited in man-made devices, and protein aggregation remains a challenge for drug formulations. Better un- derstanding of the interplay between equilibrium thermodynamic driving forces and non-equilibrium activity can open new strategies to design biomimetic sep- aration processes and new materials utilizing such mechanisms.
Anand Yethiraj (Memorial University) - Organiser
Jure Dobnikar (Chinese Academy of Sciences) - Organiser
Francesco Piazza (University of Florence) - Organiser