相关论文: Effect of Sequence-Dependent Rigidity on Plectonem…
The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects.…
A selective sweep describes the reduction of diversity due to strong positive selection. If the mutation rate to a selectively beneficial allele is sufficiently high, Pennings and Hermisson (2006a) have shown, that it becomes likely, that a…
We report spin-selective tunneling of electrons along natural and artificial double-stranded DNA (dsDNA) sandwiched by nonmagnetic leads. The results reveal that the spin polarization strongly depends on the dsDNA sequence and is dominated…
Rigidity percolation provides an important basis for understanding the onset of mechanical stability in disordered materials. While most studies on the triangular lattice have focused on static properties at fixed bond~(site) occupation…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
The buckling and twisting of slender, elastic fibers is a deep and well-studied field. A slender elastic rod that is twisted with respect to a fixed end will spontaneously form a loop, or hockle, to relieve the torsional stress that builds.…
Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
Monte Carlo simulations are employed to investigate the surface growth generated by deposition of particles of different sizes on a substrate, in one and two dimensions. The particles have a linear form, and occupy an integer number of…
Electron localization property of a random chain changing under the influence of a constant electric field has been studied. We have adopted the multifractal scaling formalism to explore the possible localization behavior in the system. We…
All the models of elementary particles and their interactions derived from String Theory involve a compact six-dimensional internal space. Its volume and shape should be fixed or stabilized, since otherwise massless scalar fields (moduli)…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
Cellular adaptation to environmental changes relies on the dynamic remodeling of subcellular structures. Among these, sarcomere structures are fundamental to the organization and function of the cytoskeletal architecture. In muscle-type…
Bacteria evolve in volatile environments and complex spatial structures. Migration, fluctuations and environmental variability therefore have a significant impact on the evolution of microbial populations. Here, we consider a class of…
The effect of a step wise change in the pillar density on the dynamics of droplets is investigated via three-dimensional lattice Boltzmann simulations. For the same pillar density gradient but different pillar arrangements, both motion over…
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
Consider a genetic locus carrying a strongly beneficial allele which has recently fixed in a large population. As strongly beneficial alleles fix quickly, sequence diversity at partially linked neutral loci is reduced. This phenomenon is…
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…