Related papers: Crowding induced entropy-enthalpy compensation in …
Sensitive detection of low-abundance molecular targets is widely assumed to require enzymatic amplification, such as PCR, to achieve low detection limits. In amplification-free platforms, sensitivity is traditionally constrained by…
Entropy is a central concept in physics, but can be challenging to calculate even for systems that are easily simulated. This is exacerbated out of equilibrium, where generally little is known about the distribution characterizing simulated…
Many biological channels perform highly selective transport without direct input of metabolic energy and without transitions from a 'closed' to an 'open' state during transport. Mechanisms of selectivity of such channels serve as an…
We study the dynamics of proliferating cell collectives whose microscopic constituents' growth is inhibited by macroscopic growth-induced stress. Discrete particle simulations of a growing collective show the emergence of concentric-ring…
The increasing number of mass events involving large crowds calls for a better understanding of the dynamics of dense crowds. Inquiring into the possibility of a mechanical description of these dynamics, we experimentally study the crossing…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
The prominent collective character of long-range interacting quantum systems makes them promising candidates for quantum technological applications. Yet, lack of additivity overthrows the traditional picture for entanglement scaling and…
The principle of maximum entropy provides a useful method for inferring statistical mechanics models from observations in correlated systems, and is widely used in a variety of fields where accurate data are available. While the assumptions…
We provide a bird's eye view on developments in analyzing the long time, large crowd behavior of Cucker-Smale alignment dynamics. We consider a class of (fully-)discrete models, paying particular attention to general alignment protocols in…
We elucidate the structural transitions in a helical off-lattice homopolymer induced by crowding agents, as function of the number of monomers ($N$) and volume fraction ($\phi_c$) of crowding particles. At $\phi_c = 0$, the homopolymer…
Mathematical models are important tools to study the excluded volume effects on reaction-diffusion systems, which are known to play an important role inside living cells. Detailed microscopic simulations with off-lattice Brownian dynamics…
The statistical properties of an ecosystem composed of species interacting via pairwise, random interactions and deterministic, concentration limiting self-interaction are studied analytically with tools of equilibrium statistical mechanics…
We study the effect of the choice of embedding geometry on the entropy of random geometric graph ensembles with soft connection functions. First we show that when the connection range is small, the entropy is dependent only on the dimension…
In this work we develop a theory of interaction of randomly patterned surfaces as a generic prototype model of protein-protein interactions. The theory predicts that pairs of randomly superimposed identical (homodimeric) random patterns…
30% of the DNA in E. coli bacteria is covered by proteins. Such high degree of crowding affect the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc.) in ways that are not yet fully…
In this paper we consider a continuous-time anisotropic swarm model with an attraction/repulsion function and study its aggregation properties. It is shown that the swarm members will aggregate and eventually form a cohesive cluster of…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
We investigate the competition between barrier slowing down and proliferation induced superdiffusion in a model of population dynamics in a random force field. Numerical results in $d=1$ suggest that a new intermediate diffusion behaviour…
The effect of crowding on the run-and-tumble dynamics of swimmers such as bacteria is studied using a discrete lattice model of mutually excluding particles that move with constant velocity along a direction that is randomized at a rate…
Finite-size impurities suspended in incompressible flows distribute inhomogeneously, leading to a drastic enhancement of collisions. A description of the dynamics in the full position-velocity phase space is essential to understand the…