Related papers: Preferential localization of the bacterial nucleoi…
The problem of RNA genomes packaged inside spherical viruses is studied. The viral capsid is modeled as a hollowed sphere. The attraction between RNA molecules and the inner viral capsid is assumed to be non-specific and occurs at the inner…
The positions of nucleosomes in eukaryotic genomes determine which parts of the DNA sequence are readily accessible for regulatory proteins and which are not. Genome-wide maps of nucleosome positions have revealed a salient pattern around…
Biological membranes are complex, dynamic structures essential for cellular compartmentalization, signaling, and mechanical integrity. The molecular organization of eukaryotic membranes has been extensively studied, including the lipid…
The ability to control the movement and assembly of particles in liquid crystals is not only an important route to design functional materials, but also sheds light on the mechanisms of colloidal interactions. In this study we place…
A short (<150 bp) double-stranded DNA (dsDNA) molecule ligated end-to-end forms a DNA minicircle. Due to sequence-dependent, nonuniform bending energetics, such a minicircle is predicted to adopt a certain inside-out orientation, known as…
We suggest a geometrical mechanism for the ordering of slender filaments inside non-isotropic containers, using cortical microtubules in plant cells and packing of viral genetic material inside capsids as concrete examples. We show…
Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by…
Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly of…
Growing monolayers of rod-shaped bacteria exhibit local alignment similar to extensile active nematics. When confined in a channel or growing inward from a ring, the local nematic order of these monolayers changes to a global ordering with…
Bacteriophages, viruses that infect bacteria, store their micron long DNA inside an icosahedral capsid with a typical diameter of 40 nm to 100 nm. Consistent with experimental observations, such confinement conditions induce an arrangement…
The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat…
During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euchromatin predominantly occupies the…
Eukaryotic cells maintain their inner order by a hectic process of distillation of molecular factors taking place on the surface of their lipid membranes. To understand the properties of this molecular sorting process, a physical model of…
Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic…
The emergence of functional oligonucleotides on early Earth required a molecular selection mechanism to screen for specific sequences with prebiotic functions. Cyclic processes such as daily temperature oscillations were ubiquitous in this…
Nucleosome organization in eukaryotic genomes has a deep impact on gene function. Although progress has been recently made in the identification of various concurring factors influencing nucleosome positioning, it is still unclear whether…
Nuclear pores have an approximately uniform distribution in the nuclear envelope of most living cells. Hence, the morphology of the nuclear envelope is a spherical stomatocyte with a high genus. We have investigated the morphology of…
We introduce a simple physical picture to explain the process of molecular sorting, whereby specific proteins are concentrated and distilled into submicrometric lipid vesicles in eukaryotic cells. To this purpose, we formulate a model based…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
In this letter, we characterize experimentally the diffusiophoretic motion of colloids and lambda- DNA toward higher concentration of solutes, using microfluidic technology to build spatially- and temporally-controlled concentration…