Related papers: Cellular Griffiths-like phase
We present a hybrid model of a biological filter, a genetic circuit which removes fast fluctuations in the cell's internal representation of the extra cellular environment. The model takes the classic feed-forward loop (FFL) motif and…
We report theoretical and simulation studies of phase coexistence in model globular protein solutions, based on short-range, central, pair potential representations of the interaction among macro-particles. After reviewing our previous…
The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a…
Understanding sub-cellular protein localisation is an essential component to analyse context specific protein function. Recent advances in quantitative mass-spectrometry (MS) have led to high resolution mapping of thousands of proteins to…
Multicomponent systems are ubiquitous in nature and industry. While the physics of few-component liquid mixtures (i.e., binary and ternary ones) is well-understood and routinely taught in undergraduate courses, the thermodynamic and kinetic…
In this paper, we bring together our efforts in identifying and understanding nonequilibrium phase segregation driven by active processes in the living cell, with special focus on the segregation of cell membrane components driven by active…
For point patterns observed in natura, spatial heterogeneity is more the rule than the exception. In numerous applications, this can be mathematically handled by the flexible class of log Gaussian Cox processes (LGCPs); in brief, a LGCP is…
We introduce a simple and predictive model for determining the phase stability of ternary phospholipid-cholesterol mixtures. Assuming that competition between the liquid and gel order of the phospholipids is the main driving force behind…
Disorder is an unavoidable ingredient of real systems. Spatial disorder generates Griffiths phases (GPs) which, in analogy to critical points, are characterized by a slow relaxation of the order parameter and divergences of quantities such…
Biomolecular condensates play essential roles in cellular processes, and recent efforts have focused on understanding their assembly and rational design principles. In this study, we have employed an explicit-solvent minimal statistical…
Liquid cellular compartments spatially segregate from the cytoplasm and can regulate aberrant protein aggregation, a process linked to several medical conditions, including Alzheimer's and Parkinson's diseases. Yet the mechanisms by which…
While proteins have been treated as particles with a spherically symmetric interaction, of course in reality the situation is rather more complex. A simple step towards higher complexity is to treat the proteins as non--spherical particles…
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…
Coagulation and fragmentation (CF) is a fundamental process by which particles attach to each other to form clusters while existing clusters break up into smaller ones. It is a ubiquitous process that plays a key role in many physical and…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
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…
We consider a model of energy minimization arising in the study of the mechanical behavior caused by cell contraction within a fibrous biological medium. The macroscopic model is based on the theory of non rank-one convex nonlinear…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Despite being of vital importance to the immune system, the mechanism by which cells engulf relatively large solid particles during phagocytosis is still poorly understood. From movies of neutrophil phagocytosis of polystyrene beads, we…
The Cahn-Hilliard system has been used to describe a wide number of phase separation processes, from co-polymer systems to lipid membranes. In this work the convergence properties of a closest-point based scheme is investigated. In place of…