Related papers: Bubble Relaxation Dynamics in Double-Stranded DNA
We investigate the long time behaviour of the one-dimensional ballistic aggregation model that represents a sticky gas of N particles with random initial positions and velocities, moving deterministically, and forming aggregates when they…
Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a…
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an intriguing role of topology in…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
We consider a one-dimensional model consisting of an assembly of two-velocity particles moving freely between collisions. When two particles meet, they instantaneously annihilate each other and disappear from the system. Moreover each…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
We report on quantitative comparisons between simulation results of a bead-spring model and mode-coupling theory calculations for the structural and conformational dynamics of a supercooled, unentangled polymer melt. We find…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
Experiments have not only revealed the remarkably long lifetime of nanobubbles, but also demonstrated the diffusive instability of bubbles above micrometers, thus a full-scale physical understanding on the stability of bubbles is in urgent…
Multiscale dynamics are ubiquitous in applications of modern science. Because of time scale separation between relatively small set of slowly evolving variables and (typically) much larger set of rapidly changing variables, direct numerical…
We experimentally investigate the statistical behaviour of a model two-dimensional granular system undergoing stationary sedimentation. Buoyant cylindrical particles are rotated in liquid-filled drum, thus confined in a harmonic centripetal…
We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded…
A barrier penetration model has been proposed to explain the spontaneous melting of the DNA oligomers into two separate single strands whereas the partially melted intermediate states are shown to be the bound state solution of the same…
We study the dynamics of two air bubbles driven by the motion of a suspending viscous fluid in a Hele-Shaw channel with a small elevation along its centreline via physical experiment and numerical simulation of a depth-averaged model. For a…
The ``Brownian bees'' model describes an ensemble of $N=$~const independent branching Brownian particles. The conservation of $N$ is provided by a modified branching process. When a particle branches into two particles, the particle which…
Conventional phase segregation is controlled by a positive interfacial tension, which implies that the system relaxes towards a state in which the interfacial area (or length) is minimized, typically manifesting as a single droplet that…