Related papers: Crowding-Regulated Binding of Divalent Biomolecule…
Cells sense environmental signals and transmit information intracellularly through changes in the abundance of molecular components. Such molecular abundances can be measured in single cells and exhibit significant heterogeneity in clonal…
Bimolecular binding rate constants are often used to describe the association of large molecules, such as proteins. In this paper, we analyze a model for such binding rates that includes the fact that pairs of molecules can bind only in…
The dispersal of cells from an initially constrained location is a crucial aspect of many physiological phenomena ranging from morphogenesis to tumour spreading. In such processes, the way cell-cell interactions impact the motion of single…
We study the effect of confinement on diffusion limited bimolecular reactions within a lattice model where a small number of reactants diffuse amongst a much larger number of inert particles. When the number of inert particles is held…
Multivalent particles have the ability to form multiple bonds to a substrate. Hence, a multivalent interaction can be strong, even if the individual bonds are weak. However, much more interestingly, multivalency greatly increases the…
In crowded systems, particle currents can be mediated by propagating collective excitations which are generated as rare events, are localized and have a finite lifetime. The theoretical description of such excitations is hampered by the…
Multiple phenotypic protein expressions arising from one genome represent variations in the protein relative abundance and their stoichiometry. A lack of definite compositional parts challenges the modeling of protein megacomplexes and…
Self-propelled particles undergoing persistent motion can accumulate either through excluded-volume interactions or through quorum sensing, where self-propulsion decreases at high local density. Using kinetic balance theory and simulations,…
Plant and animal cells are commonly understood as acquiring specialized functions through differentiation and asymmetric division. However, unique capabilities are also acquired when two or more cells fuse together, mixing cytoplasmic and…
We examine theoretically how dipole-dipole interactions arising from multiple photon scattering lead to a modified distribution of ground state populations in a driven, ordered 1D array of multilevel atoms. Specifically, we devise a level…
Many real-world network are multilayer, with nontrivial correlations across layers. Here we show that these correlations amplify geometry in networks. We focus on mutual clustering--a measure of the amount of triangles that are present in…
We consider a binary system of small and large objects in the continuous space interacting via a non-negative potential. By integrating over the small objects, the effective interaction between the large ones becomes multi-body. We prove…
Macromolecular diffusion in dense colloidal suspensions is an intriguing topic of interdisciplinary relevance in Science and Engineering. While significant efforts have been undertaken to establish the impact of crowding on the dynamics of…
A numerical model with broad applications to complex (dusty) plasmas is presented. The self-consistent N-body code allows simulation of the coagulation of fractal aggregates, including the charge-dipole interaction of the clusters due to…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Nonlinear responses in crystalline solids are attracting a great deal of attention because of exciting phenomena, such as the bulk photovoltaic effect in noncentrosymmetric crystals and the third harmonic generation related to Higgs modes…
We study the impact of an environment on the electromagnetic responses of a molecule in the presence of a dielectric medium. By applying the dipole-dipole coupling between the molecule's and the environment's degrees of freedom, we can…
The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected for by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a…
The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…
We consider a biopolymer bundle consisting of filaments that are crosslinked together. The crosslinks are reversible: they can dynamically bind and unbind adjacent filament pairs as controlled by a binding enthalpy. The bundle is subjected…