Related papers: Can entropy save bacteria?
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of anti-viral immune system in these organisms. We here study the diversity of spacers in CRISPR…
We propose a heuristic explanation for the numerous non-close-packed crystal structures observed in various colloidal systems. By developing an analogy between soap froths and the soft coronas of fuzzy colloids, we provide a geometrical…
Biological mixtures such as the cytosol may consist of thousands of distinct components. There is now a substantial body of evidence showing that, under physiological conditions, intracellular mixtures can phase separate into spatially…
Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework…
We present a theoretical model for predicting the phase behavior of polymer solutions in which phase separation competes with oligomerization. Specifically, we consider scenarios in which the assembly of polymer chains into stoichiometric…
Escherichia coli and other bacteria use rotating helical filaments to swim. Each cell typically has about four filaments, which bundle or disperse depending on the sense of motor rotation. To study the bundling process, we built a…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
Intact-organism imaging of Drosophila larvae reveals and quantifies chromatin-aqueous phase separation. The chromatin can be organized near the lamina layer of the nuclear envelope, conventionally fill the nucleus, be organized centrally,…
In many viruses, hundreds of proteins assemble an outer shell (capsid) around the viral nucleic acid to form an infectious virion. How the assembly process selects the viral genome amidst a vast excess of diverse cellular nucleic acids is…
We present results relevant to the equilibrium organization of DNA strands of arbitrary length interacting with a spherical organizing center, suggestive of DNA-histone complexation in nucleosomes. We obtain a rich phase diagram in which a…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…
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…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
Bacterial cells exhibit a diverse array of shapes and sizes, largely governed by their cell walls in conjunction with cytoskeletal proteins and internal turgor pressure. The present study develops a theoretical framework for modeling the…
We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…
The genomic DNA of bacteria occupies only a fraction of the cell called the nucleoid, although it is not bounded by any membrane and would occupy a volume hundreds of times larger than the cell in the absence of constraints. The two most…
Grafting linkers with open ends of complementary single-stranded DNA makes a flexible tool to tune interactions between colloids,which facilitates the design of complex self-assembly structures. Recently, it has been proposed to coat…
We propose a model of chemostat where the bacterial population is individually-based, each bacterium is explicitly represented and has a mass evolving continuously over time. The substrate concentration is represented as a conventional…
Bacteria, in contrast to eukaryotic cells contain two types of genes: chromosomal genes that are fixed to the cell, and plasmids that are mobile genes, easily shared to other cells. The sharing of plasmid genes between individual bacteria…