Related papers: Resonant helical deformations in nonhomogeneous Ki…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this…
Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of…
We studied the dynamical response of a nanomechanical resonator to biomolecular (e.g. DNA) adsorptions on a resonator's surface by using a theoretical model, which considers the Hamiltonian H such that the potential energy consists of…
Diversity in the properties of exoplanetary systems arises, in part, from dynamical evolution that occurs after planet formation. We use numerical integrations to explore the relative role of secular and resonant dynamics in the long-term…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
Unlike Newtonian fluids, viscoelastic fluids may break time-reversal symmetry at low Reynolds numbers resulting in elastic turbulence. Furthermore, under some conditions, instead of the chaotic turbulence, large-scale regular waves form, as…
We investigate a general system of two coupled harmonic oscillators with cubic nonlinearity. Without damping, the system is Hamiltonian, with the origin as an elliptic equilibrium characterized by two distinct linear frequencies. To…
We blend together continuum elasticity and first principles calculations to measure by a computer experiment the Young modulus of hydrogenated graphene. We provide evidence that hydrogenation generally leads to a much smaller longitudinal…
We have developed a self consistent technique to predict the behavior of plasmon resonances in multi-component systems as a function of wavelength. This approach, based on the tight lower bounds of the Bergman-Milton formulation, is able to…
Dynamics of flexible ferromagnetic filaments in an external magnetic field is considered. We report the existence of a buckling instability of the ferromagnetic filament at the magnetic field reversion, which leads to the formation of a…
The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair…
We use the Discrete Element Method (DEM) to understand the underlying attenuation mechanism in granular media, with special applicability to the measurements of the so-called effective mass developed earlier. We consider that the particles…
Large-scale DNA deformation is ubiquitous in transcriptional regulation in prokaryotes and eukaryotes alike. Though much is known about how transcription factors and constellations of binding sites dictate where and how gene regulation will…
Recently the materials possessing structure of molecular and supramolecular matrix are more and more actively studied. They are relative to many polymeric materials of a technological origin, such as rubber, and living biological tissues.…
Using the generalised nonlinear Schr\"odinger equation, we investigate how the effect of third-order dispersion, self-steepening, and Raman-induced-self-frequency shift have an impact on the higher-order rogue waves. We observe that…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
The effect of optically thin radiative cooling on the Kelvin-Helmholtz instability of three dimensional jets is investigated via linear stability theory and nonlinear hydrodynamical simulation. Two different cooling functions are…