相关论文: Evolutionary advantage of directional symmetry bre…

Directed assembly of block polymers is rapidly becoming a viable strategy for lithographic patterning of nanoscopic features. One of the key attributes of directed assembly is that an underlying chemical or topographic substrate pattern…

Predicting adaptive evolutionary trajectories is a primary goal of evolutionary biology. One can differentiate between forward and backward predictability, where forward predictability measures the likelihood of the same adaptive trajectory…

An important issue for the origins of life is ensuring the accurate maintenance of information in replicating polymers in the face of inevitable errors. Here, we investigated how this maintenance depends on reaction kinetics by…

We derive an asymptotic equation for quasi-static, nonlinear surface plasmons propagating on a planar interface between isotropic media. The plasmons are nondispersive with a constant linearized frequency that is independent of their…

DNA Polymerase is an enzyme that participates in the process of DNA replication. In general, forward DNA polymerase moves along the template strand in a 3'-5' direction, and the daughter strand is formed in a 5'-3' direction. This paper…

A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…

Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties in experiments. In free molecular dynamics simulations…

We study theoretically a binary system in which an attraction of unlike particles is combined with a type-independent soft core repulsion. The possible experimental implementation of the system is a mixture of DNA-covered colloids, in which…

We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test charge theory to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for…

We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem…

DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…

The preferred conditions for evolutionary innovation is a fundamental question, but little is known, in part because the question involves rare events. We focused on the potential role of polyploidy in the evolution of novel traits. There…

Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…

We propose that semiflexible polymers in poor solvent collapse in two stages. The first stage is the well known formation of a dense toroidal aggregate. However, if the solvent is sufficiently poor, the condensate will undergo a second…

Left-right axis specification establishes embryonic laterality through asymmetric signaling cascades originating at the cellular scale. We previously reported the presence of a directionality bias in confined pairs of endothelial (and…

The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…

DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very…

A central challenge in the origin of life is understanding how catalytic peptide-like polymers and information-bearing nucleic acid-like polymers emerged as an interde-pendent system. This study constructs a primordial cognitive model…

Molecular clock (MC) is a central concept of molecular evolution according to which each gene evolves at a characteristic, near constant rate. Numerous evolutionary studies have demonstrated the validity of MC but also have shown that MC is…