Related papers: Diffusive coupling of two well-mixed compartments …
A diffuse-interface model for microstructure with an arbitrary number of components and phases was developed from basic thermodynamic and kinetic principles and formalized within a variational framework. The model includes a composition…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Fluorescence microscopy has led to impressive quantitative models and new insights gained from richer sets of biomedical imagery. However, there is a dearth of rigorous and established bioimaging strategies for modeling spatiotemporal…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
Turing patterns are stationary, wave-like structures that emerge from the nonequilibrium assembly of reactive and diffusive components. While they are foundational in biophysics, their classical formulation relies on a single characteristic…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
We introduce a three-dimensional stochastic reaction-diffusion model to describe MinD/MinE dynamical structures in Escherichia coli. This model spontaneously generates pole-to-pole oscillations of the membrane-associated MinD proteins, MinE…
In eukaryotic cells, mitochondria form networks that range from highly fused interconnected structures to fragmented populations of individual organelles that undergo transient interactions. These structures can be described as temporal…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…
The formation of polarized signaling domains on cell membranes is a fundamental example of biological pattern formation. While such patterns resemble structures from equilibrium phase separation, they are intrinsically non-equilibrium,…
A phase-separation front will leave in its wake a phase-separated morphology that differs markedly from homogeneous phase-separation morphologies. For a purely diffusive system such a front, moving with constant velocity, will generate very…
Recent findings suggest that shell protein distribution and morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. We explore how the morphology and component…
Ordered polarity alignment of a cell population plays a vital role in biology, such as in hair follicle alignment and asymmetric cell division. Here, we propose a theoretical framework for the understanding of generic dynamical properties…
Experimental studies of protein-pattern formation have stimulated new interest in the dynamics of reaction-diffusion systems. However, a comprehensive theoretical understanding of the dynamics of such highly nonlinear, spatially extended…
Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
It is not merely the position of residues that are of utmost importance in protein function and stability, but the interactions between them. We illustrate, by using a network construction on a set of 595 non-homologous proteins, that…