相关论文: Biopolymer Elasticity
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…
Cell mechanical properties are fundamental to the organism but remain poorly understood. We report a comprehensive phenomenological framework for the nonlinear rheology of single fibroblast cells: a superposition of elastic stiffening and…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
The presence of nanoparticles in a diblock copolymer leads to changes in the morphology and properties of the matrix and can produce highly organized hybrid materials. The resulting material properties depend not only on the polymer…
We initiate the development of a theory of the elasticity of nanoscale objects based upon new physical concepts which remain properly defined on the nanoscale. This theory provides a powerful way of understanding nanoscale elasticity in…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
Thin bilayers made of elastic sheets with different strain recoveries can be used for dynamic shape morphing through ambient stimuli, such as temperature, mass diffusion, and light. As a fundamentally different approach to designing…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…
A conceptual difficulty in the Hooke's-law description of ideal Gaussian polymer-chain elasticity is sometimes apparent in analyses of experimental data or in physical models designed to simulate the behavior of biopolymers. The problem,…
The elastic properties of semiflexible polymers are of great importance in biology. There are experiments on biopolymers like double stranded DNA, which twist and stretch single molecules to probe their elastic properties. It is known that…
Run-and-tumble motility is widely used by swimming microorganisms including numerous prokaryotic eukaryotic organisms. Here, we experimentally investigate the run-and-tumble dynamics of the bacterium E. coli in polymeric solutions. We find…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…
In recent years, certain molecular crystals have been reported to possess surprising flexibility by undergoing significant elastic or plastic deformation in response to mechanical loads. However, despite this experimental evidence, there…
The polymerization dynamics of double-stranded polymers, such as actin filaments, is investigated theoretically using simple chemical kinetic models that explicitly take into account some microscopic details of the polymer structure and the…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…