Related papers: Preferential localization of the bacterial nucleoi…
We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere…
Biomolecular condensates organize biochemical processes by spatially concentrating molecules while allowing for dynamic exchange with their surroundings. However, transport across their interface can be strongly attenuated, leading to…
Hard-sphere model systems are well-suited in both experiment and simulations to investigate fundamental aspects of the crystallization of fluids. In experiments on colloidal models of hard-sphere fluids, the uid is unavoidably at contact…
We present in this paper an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows to address theoretically the influence of complex position along DNA, as well as…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself…
Crystallization of supersaturated liquids usually starts by heterogeneous nucleation. Mounting evidence shows that even homogeneous nucleation in simple liquids takes place in two steps; first a dense amorphous precursor forms, and the…
While the physics of disordered packing in non-growing systems is well understood, unexplored phenomena can emerge when packing takes place in growing domains. We study the arrangements of pigment cells (chromatophores) on squid skin as a…
Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and…
Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance…
Within the framework of a discrete Gaussian model, we present analytical results for the interaction induced by a lamellar phase between small embedded colloids. We consider the two limits of particles strongly adherent to the adjacent…
Experimental studies of cell motility in culture have shown that under adequate conditions these living organisms possess the ability to organize themselves into complex structures. Such structures may exhibit a synergy that greatly…
The motility of eukaryotic cells is strongly influenced by their environment, with confined cells often developing qualitatively different motility patterns from those migrating on simple two-dimensional substrates. Recent experiments,…
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an intriguing role of topology in…
We showed in our previous studies that just $3\%$ cross-links, at special points along the contour of the bacterial DNA help the DNA-polymer to get organized at micron length scales \cite{jpcm,epl}. In this work, we investigate how does the…
Colloids play an important role in fundamental science as well as in nature and technology. They have had a strong impact on the fundamental understanding of statistical physics. For example, colloids have helped to obtain a better…
Flagellar-driven locomotion plays a critical role in bacterial attachment and colonization of surfaces, contributing to the risks of contamination and infection. Tremendous attempts to uncover the underlying principles governing bacterial…
The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression…
The prevalence of multicellular organisms is due in part to their ability to form complex structures. How cells pack in these structures is a fundamental biophysical issue, underlying their functional properties. However, much remains…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…