Related papers: Phenomenological and microscopic theories for catc…
We study a model for the evolution of chemical species under a combination of population dynamics on a short time scale and a selection mechanism on a longer time scale. Least fit nodes are replaced by new nodes whose links are attached to…
We investigate micro-to-macroscopic derivations in two models of living cells, in presence to cell-cell adhesive interactions. We rigorously address two PDE-based models, one featuring non-local terms and another purely local, as a a result…
Cell-cell adhesion plays a vital role in the development and maintenance of multicellular organisms. One of its functions is regulation of cell migration, such as occurs, e.g. during embryogenesis or in cancer. In this work, we develop a…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
Biological organisms are adaptive, able to function in unpredictably changing environments. Drawing on recent nonequilibrium physics, we show that in adaptation, fitness has two components parameterized by observable coordinates: a static…
Mechanically induced unfolding of passive crosslinkers is a fundamental biological phenomenon encountered across the scales from individual macro-molecules to cytoskeletal actin networks. In this paper we study a conceptual model of…
The dynamics of filaments in flow are central to understanding a wide range of biological and soft-matter systems, yet their behavior under time-dependent forcing remains poorly understood. Here, we investigate the long-time dynamics of…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with…
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in…
Cells sense the geometry and stiffness of their adhesive environment by active contractility. For strong adhesion to flat substrates, two-dimensional contractile network models can be used to understand how force is distributed throughout…
Pairs of free particles cannot form bound states in elastic collision due to momentum and energy conservation. In many ultracold experiments, however, the particles collide in the presence of an external trapping potential which can couple…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
Adhesion-dependent cells actively sense the mechanical properties of their environment through mechanotransductory processes at focal adhesions, which are integrin-based contacts connecting the extracellular matrix to the cytoskeleton. Here…
We address the issue of the compositeness of hadronic states and demonstrate that starting with a genuine state of nonmolecular nature, but which couples to some meson-meson component to be observable in that channel, if that state is…
Force-clamp spectroscopy reveals the unfolding and disulfide bond rupture times of single protein molecules as a function of the stretching force, point mutations and solvent conditions. The statistics of these times reveal whether the…
In granular media, the presence of even small amounts of interparticle cohesion manifests as an increase in the bulk strength and stiffness, effects that are typically associated with an increase in the average number of constraints per…
Fiberboids are active filaments trapped at the interface of two phases, able of harnessing energy (and matter) fluxes across the interface in order to produce a rolling-like self-propulsion. We discuss several table-top examples and develop…