Related papers: Computer simulations show that liquid-liquid phase…
I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to…
Condensation is an important aspect of many flow applications due to the universal presence of humidity in the air at ambient conditions. For direct numerical simulations of such flows, simulating the gas phase as a mixture characterized by…
Biomolecules, such as proteins and RNAs, can phase separate in the cytoplasm of cells to form biomolecular condensates. Such condensates are liquid-like droplets that can wet biological surfaces such as membranes. Many molecules that…
Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…
In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually…
Results from molecular dynamics simulations of simple, structured particles capable of self-assembling into polyhedral shells are described. The analysis focuses on the growth histories of individual shells in the presence of an explicit…
Proliferation and motility are ubiquitous drivers of activity in biological systems. Here, we study a dense binary mixture of motile and proliferating particles with exclusively repulsive interactions, where homeostasis in the proliferating…
Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells.…
Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of…
Proteins and nucleic acids can spontaneously self-assemble into membraneless droplet-like compartments, both in vitro and in vivo. A key component of these droplets are multi-valent proteins that possess several adhesive domains with…
We investigate a set of design principles that link specific features of interparticle interactions to predictable structural and dynamic outcomes in two-dimensional self-assembly, a framework relevant to soft matter and biological…
Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
The sustenance of life depends on the high degree of organization that prevails through different levels of living organisms, from subcellular structures such as biomolecular complexes and organelles to tissues and organs. The physical…
Many viruses rely on the self-assembly of their capsids to protect and transport their genomic material. For many viral systems, in particular for human viruses like hepatitis B, adeno or human immunodeficiency virus, that lead to…
The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…
Liquid mixtures of many interacting components often exhibit numerous coexisting types of droplets. An exciting example is the cytosol of biological cells, where diverse droplets, called condensates, are essential for cellular function.…
We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one…
Biomolecular condensates provide distinct chemical environments, which control various cellular processes. The diffusive dynamics and chemical kinetics inside phase-separated condensates can be studied experimentally by fluorescently…