Related papers: Crowding-Regulated Binding of Divalent Biomolecule…
Inspired by recent experiments on the effects of cytosolic crowders on the organization of bacterial chromosomes, we consider a "feather-boa" type model chromosome in the presence of non-additive crowders, encapsulated within a cylindrical…
Clustering is one of the mayor collective phenomena observed in active matter. We study the overdamped motion of interacting active Brownian particles in two dimensions. An instability in the pair correlation function causes the onset of…
Multivalent binding employs multiple simultaneous supramolecular interactions, increasing avidity and selectivity compared with monovalent binding. While equilibrium aspects of multivalency are well characterized, non-equilibrium behavior…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
This paper proposes the simulation of structured behaviors in a crowd of virtual agents by extending the BioCrowds simulation model. Three behaviors were simulated and evaluated, a queue as a generic case and two specific behaviors observed…
Decades of research suggest that information exchange in groups and organizations can reliably improve judgment accuracy in tasks such as financial forecasting, market research, and medical decision-making. However, we show that improving…
Intermolecular interactions are pivotal for aggregation, solvation, and crystallization. We demonstrate that the collective strong coupling of several molecules to a single optical mode results in notable changes in the molecular…
The spread of one disease, in some cases, can stimulate the spreading of another infectious disease. Here, we treat analytically a symmetric coinfection model for spreading of two diseases on a two-layer multiplex network. We allow layer…
In dynamic force spectroscopy, a (bio-)molecular complex is subjected to a steadily increasing force until the chemical bond breaks. Repeating the same experiment many times results in a broad distribution of rupture forces, whose…
Traditionally, the evolution of cooperation has been studied on single, isolated networks. Yet a player, especially in human societies, will typically be a member of many different networks, and those networks will play a different role in…
The role of macromolecular crowding in living systems is widely appreciated, but artificial crowders used to model these effects in vitro are often inadequately characterized. In this work, we examine density, viscosity, polymer…
A mixture of solvent particles with short-range, directional interactions and solute particles with short-range, isotropic interactions that can bond multiple times is of fundamental interest in understanding liquids and colloidal mixtures.…
Enzymatic ligation is essential for the synthesis of long DNA. However, the number of ligated products exponentially decays as the DNA synthesis proceeds in a random manner. The controlling of ligation randomness is of importance to…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
Motivation: Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base construction and protein structure determination all benefit from human input. In…
In systems as diverse as migrating mammals to road traffic, crowding acts to inhibit efficient collective movement. Bacteria, however, are observed to move in very dense groups containing billions of individuals without causing the gridlock…
Biomolecules, such as proteins and RNAs, can phase separate in the cytoplasm of cells to form biomolecular condensates. Such condensates are liquid-like droplets that can wet biological surfaces such as membranes. Many molecules that…
The interplay between static and dynamic disorder and collective optical response in molecular ensembles is an important characteristic of nanoplasmonic and nanophotonic molecular systems. Here we investigate the cooperative superradiant…
Collective cell motility plays central roles in various biological phenomena such as inflammatory response, wound healing, cancer metastasis and embryogenesis. These are biological demonstrations of the unjamming transition. However,…
Protein aggregation is of particular interest due to its connection with many diseases and disorders. Many factors can alter the dynamics and result of this process, one of them being the diffusivity of the monomers and aggregates in the…