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Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of…
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
We present a percolation model that is inspired by recent works on immiscible two-phase flow in a mixed-wet porous medium made of a mixture of grains with two different wettability properties. The percolation model is constructed on a dual…
Membrane bending is an extensively studied problem from both modeling and experimental perspectives because of the wide implications of curvature generation in cell biology. Many of the curvature generating aspects in membranes can be…
Turing's theory of pattern formation has been used to describe the formation of self-organised periodic patterns in many biological, chemical and physical systems. However, the use of such models is hindered by our inability to predict, in…
Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the…
Spatial heterogeneity is a hallmark of living systems, even at the molecular scale in individual cells. A key example is the partitioning of membrane-bound proteins via lipid domain formation or cytoskeleton-induced corralling. Yet the…
Soft interfaces formed by lipid membranes are fundamental to living cells, synthetic cells, and membrane-based soft materials. However, a quantitative framework linking molecular organization with nonlinear interfacial mechanics remains…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
The cell cortex, a thin film of active material assembled below the cell membrane, plays a key role in cellular symmetry breaking processes such as cell polarity establishment and cell division. Here, we present a minimal model of the…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
In the bacterium Escherichia coli, selection of the division site involves pole-to-pole oscillations of the proteins MinD and MinE. Different oscillation mechanisms based on cooperative effects between Min-proteins and on the exchange of…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
By providing new insights into the distribution of a protein's torsion angles, recent statistical models for this data have pointed the way to more efficient methods for protein structure prediction. Most current approaches have…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by…
A fast and accurate grid-based method with low memory requirement is presented to calculate volume characteristics in molecular systems. The distribution of volume and packing density is characterized in globular proteins, where void space…
Cell polarization underlies many cellular processes, such as differentiation, migration, and budding. Many living cells, such as budding yeast and fission yeast, use cytoskeletal structures to actively transport proteins to one location on…