相关论文: Evolutionary advantage of directional symmetry bre…
Asymmetric segregation of key proteins at cell division -- be it a beneficial or deleterious protein -- is ubiquitous in unicellular organisms and often considered as an evolved trait to increase fitness in a stressed environment. Here, we…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby…
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As…
In this paper we study the structure of specific linear codes called DNA codes. The first attempts on studying such codes have been proposed over four element rings which are naturally matched with DNA four letters. Later, double (pair) DNA…
Eukaryotic cells are often exposed to fluctuations in growth conditions as well as endogenous and exogenous stress-related agents. In addition, during development global patterns of gene transcription change dramatically, and these changes…
The rate of recombination affects the mode of molecular evolution. In high-recombining sequence, the targets of selection are individual genetic loci; under low recombination, selection collectively acts on large, genetically linked genomic…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
Synthetic bio-molecular spiders with "legs" made of single-stranded segments of DNA can move on a surface which is also covered by single-stranded segments of DNA complementary to the leg DNA. In experimental realizations, when a leg…
In bacteria, regulatory proteins search for a specific DNA binding target via "facilitated diffusion": a series of rounds of 3D diffusion in the cytoplasm, and 1D linear diffusion along the DNA contour. Using large scale Brownian dynamics…
Locally broken symmetries are used across fields to transport matter, particles and information in preferential directions. Beyond local mechanisms, spatially distributed nonlinearities in crystalline media have enabled non-reciprocal…
From self-assembly and protein folding to combinatorial metamaterials, a key challenge in material design is finding the right combination of interacting building blocks that yield targeted properties. Such structures are fiendishly…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
A mystery about the origins of life is which molecular structures $-$ and what spontaneous processes $-$ drove the autocatalytic transition from simple chemistry to biology? Using the HP lattice model of polymer sequence spaces leads to the…
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…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
The statistical theory of polymers tethered around the inner surface of a cylindrical channel has traditionally employed the assumption that the equilibrium density of the polymers is independent of the azimuthal coordinate. However,…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Synthetic microswimmers show great promise in biomedical applications such as drug delivery and microsurgery. Their locomotion, however, is subject to stringent constraints due to the dominance of viscous over inertial forces at low…