DNA Spools under Tension

DNA-spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core are ubiquitous in nature. We develop a general theory describing the non-equilibrium behavior of DNA-spools under linear tension. Two puzzling and seemingly unrelated recent experimental findings, the sudden quantized unwrapping of nucleosomes and that of DNA toroidal condensates under tension are theoretically explained and shown to be of the same origin. The study provides new insights into nucleosome and chromatin fiber stability and dynamics

Quantum bistability and spin current shot noise of a single quantum dot coupled to an optical microcavity

Here we explore spin dependent quantum transport through a single quantum dot coupled to an optical microcavity. The spin current is generated by electron tunneling between a single doped reservoir and the dot combined with intradot spin flip transitions induced by a quantized cavity mode. In the limit of strong Coulomb blockade, this model is analogous to the Jaynes-Cummings model in quantum optics and generates a pure spin current in the absence of any charge current. Earlier research has shown that in the classical limit where a large number of such dots interact with the cavity field, the spin current exhibits bistability as a function of the laser amplitude that drives the cavity. We show that in the limit of a single quantum dot this bistability continues to be present in the intracavity photon statistics. Signatures of the bistable photon statistics manifest themselves in the frequency dependent shot noise of the spin current despite the fact that the quantum mechanical average spin current no longer exhibits bistability. Besides having significance for future quantum dot based optoelectronic devices, our results shed light on the relation between bistability, which is traditionally viewed as a classical effect, and quantum mechanics

Statistical Mechanics of Torque Induced Denaturation of DNA

A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular structure. We show that denaturation corresponds to a first-order phase transition from B-DNA to d-DNA phases and that the coexistence region is naturally parametrized by the degree of supercoiling sigma. The denaturation free energy, the temperature dependence of the twist angle, the phase diagram in the T,Gamma plane and isotherms in the sigma, Gamma plane are calculated and show a good agreement with experimental data.Comment: 5 pages, 3 figures, model improve

Gravity induced over a smooth soliton

I consider gravity induced over a smooth (finite thickness) soliton. Graviton kinetic term is coupled to bulk scalar that develops solitonic vacuum expectation value. Couplings of Kaluza-Klein modes to soliton-localized matter are suppressed, giving rise to crossover distance $r_c=M_{P}^2/M_{*}^3$ between 4D and 5D behavior. This system can be viewed as a finite thickness brane regularization of the model of Dvali, Gabadadze and Porrati.Comment: 12 pages, 2 figure

Twirling and Whirling: Viscous Dynamics of Rotating Elastica

Motivated by diverse phenomena in cellular biophysics, including bacterial flagellar motion and DNA transcription and replication, we study the overdamped nonlinear dynamics of a rotationally forced filament with twist and bend elasticity. Competition between twist injection, twist diffusion, and writhing instabilities is described by a novel pair of coupled PDEs for twist and bend evolution. Analytical and numerical methods elucidate the twist/bend coupling and reveal two dynamical regimes separated by a Hopf bifurcation: (i) diffusion-dominated axial rotation, or twirling, and (ii) steady-state crankshafting motion, or whirling. The consequences of these phenomena for self-propulsion are investigated, and experimental tests proposed.Comment: To be published in Physical Review Letter

Automated control system for a mashing process

The goal of this paper is to describe a system for a mashing process, which is the first part of brewing beer. The mashing is a procedure where the fermentable (and some non-fermentable) sugars are extracted from malts. The program part based on LabVIEW, which is used to control NI CompactRIO. The main target of the project is to reach a predefined levels of the temperatures and maintain it during the pauses. When the necessary break time is ended the system is ready to go to the new value. The precise control of the temperatures during the breaks is one of the critical factors that define the texture and alcohol content of the beer. The system has two tanks with resistors PT100 in both of them, heat exchanger (coil), heater and pump. The first tank has heating element in order to rise the temperature in the other one. This project has practical solution with all explanations and graphs which are proven working ability of this control system

An amperometric biosensor based on laccase immobilized in polymer matrices for determining phenolic compounds

An amperometric enzyme electrode based on laccase for determining phenolic compounds is proposed. The following three types of polymer materials were used for enzyme immobilization on the surface of a glassy-carbon electrode: positively charged cetyl ethyl poly (ethyleneimine) (CEPEI) and negatively charged commercial Nafion and Eastman AQ 29D polymers. The advantages and disadvantages of each of the above polymers for enzyme immobilization are discussed. The detection limits of the model phenolic compounds hydroquinone and pyrocatechol in a buffer solution on laccase immobilization in a Nation membrane were 3.5 x 10(-8) and 5.0 x 10(-8) M, respectively, at a signal-to-noise ratio of 3. Electrodes with laccase immobilized in Nation and Eastman AQ 29D membranes exhibited the shortest response time. The operating stability and the stability in storage can be significantly improved by the additional incorporation of gelatin in the polymer matrices. Gelatin prevents enzyme inactivation as a result of enzyme modification by the free-radical oxidation products of phenolic compounds

On the Green function of linear evolution equations for a region with a boundary

We derive a closed-form expression for the Green function of linear evolution equations with the Dirichlet boundary condition for an arbitrary region, based on the singular perturbation approach to boundary problems.Comment: 9 page

The Power of Brane-Induced Gravity

We study the role of the brane-induced graviton kinetic term in theories with large extra dimensions. In five dimensions we construct a model with a TeV-scale fundamental Planck mass and a {\it flat} extra dimension the size of which can be astronomically large. 4D gravity on the brane is mediated by a massless zero-mode, whereas the couplings of the heavy Kaluza-Klein modes to ordinary matter are suppressed. The model can manifest itself through the predicted deviations from Einstein theory in long distance precision measurements of the planetary orbits. The bulk states can be a rather exotic form of dark matter, which at sub-solar distances interact via strong 5D gravitational force. We show that the induced term changes dramatically the phenomenology of sub-millimeter extra dimensions. For instance, high-energy constraints from star cooling or cosmology can be substantially relaxed.Comment: 24 pages, 4 eps figures; v2 typos corrected; v3 1 ref. added; PRD versio