相关论文: Bubble Relaxation Dynamics in Double-Stranded DNA
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA…
We study the relaxation process in a two-dimensional lattice gas model, where the interactions come from the excluded volume. In this model particles have three arms with an asymmetrical shape, which results in geometrical frustration that…
We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the…
Genetically engineered bacteria to increase the tumbling frequency of the run-and-tumble motion for the higher local bacterial density form visible stripe pattern composed of successive high and low density regions on an agar plate. We…
Many two-phase materials suffer from grain-growth due to the energy cost which is associated with the interface that separates both phases. While our understanding of the driving forces and the dynamics of grain growth in different…
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively…
We compute the back-reaction of pairs of codimension-two branes within an explicit flux-stabilized compactification, to trace how its properties depend on the parameters that define the brane-bulk couplings. Both brane tension and magnetic…
We consider the formation of finite-size domains in lipid bilayers consisting of saturated and hybrid lipids. First, we describe a monolayer model that includes a coupling between a compositional scalar field and a two-dimensional vectorial…
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
We investigate the shell structure of spherical nuclear bubbles in simple phenomenological shell model potentials. The shell correction energies for doubly magic bubbles may be as large as -40 MeV and probably imply a very long lifetime…
Understanding the structural evolution of granular systems is a long-standing problem. A recently proposed theory for such dynamics in two dimensions predicts that steady states of very dense systems satisfy detailed-balance. We analyse…
Many applications of contemporary science involve multiscale dynamics, which are typically characterized by the time and space scale separation of patterns of motion, with fewer slowly evolving variables and much larger set of faster…
The formation of bubble defects of the double stranded DNA is treated according to the Lifshits theory of disordered chains. A molecule of the DNA is modelled on a harmonic lattice with nearest neighbour interaction, elastic constants being…
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
Within the mode-coupling theory for idealized glass transitions, we study the evolution of structural relaxation in binary mixtures of hard spheres with size ratios $\delta$ of the two components varying between 0.5 and 1.0. We find two…
The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses…
Analysis of single-molecule micromanipulation experiments of DNA unzipping process shows some features of the force-distance curve, namely two consequent plateaus in the area of ${\sim}12-14pN$ dependent on nucleotide sequence structure, as…
Phase separation, the spontaneous segregation of density, is a ubiquitous phenomenon observed across diverse physical and biological systems. Within a crowd of motile elements, active phase separation emerges from the interplay of activity…