Supercoil formation in DNA denaturation

We generalize the Poland-Scheraga (PS) model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional stress induced by denaturation enforces formation of supercoils whose writhe absorbs the linking number expelled by the loops. Our model predicts that, when the entropy parameter of a loop satisfies $c \le 2$, denaturation transition does not take place. On the other hand for $c>2$ a first-order denaturation transition is consistent with our model and may take place in the actual system, as in the case with no supercoils. These results are in contrast with other treatments of circular DNA melting where denaturation is assumed to be accompanied by an increase in twist rather than writhe on the bound segments.Comment: 4 pages, 3 figures, accepted for publication in PRE Rapid Com

Nonlinear supratransmission and bistability in the Fermi-Pasta-Ulam model

The recently discovered phenomenon of nonlinear supratransmission consists in a sudden increase of the amplitude of a transmitted wave triggered by the excitation of nonlinear localized modes of the medium. We examine this process for the Fermi-Pasta-Ulam chain, sinusoidally driven at one edge and damped at the other. The supratransmission regime occurs for driving frequencies above the upper band-edge and originates from direct moving discrete breather creation. We derive approximate analytical estimates of the supratransmission threshold, which are in excellent agreement with numerics. When analysing the long-time behavior, we discover that, below the supratransmission threshold, a conducting stationary state coexists with the insulating one. We explain the bistable nature of the energy flux in terms of the excitation of quasi-harmonic extended waves. This leads to the analytical calculation of a lower-transmission threshold which is also in reasonable agreement with numerical experiments.Comment: 8 pages, 9 figures. Phys. Rev. E (accepted

The grand canonical ABC model: a reflection asymmetric mean field Potts model

We investigate the phase diagram of a three-component system of particles on a one-dimensional filled lattice, or equivalently of a one-dimensional three-state Potts model, with reflection asymmetric mean field interactions. The three types of particles are designated as $A$, $B$, and $C$. The system is described by a grand canonical ensemble with temperature $T$ and chemical potentials $T\lambda_A$, $T\lambda_B$, and $T\lambda_C$. We find that for $\lambda_A=\lambda_B=\lambda_C$ the system undergoes a phase transition from a uniform density to a continuum of phases at a critical temperature $\hat T_c=(2\pi/\sqrt3)^{-1}$. For other values of the chemical potentials the system has a unique equilibrium state. As is the case for the canonical ensemble for this $ABC$ model, the grand canonical ensemble is the stationary measure satisfying detailed balance for a natural dynamics. We note that $\hat T_c=3T_c$, where $T_c$ is the critical temperature for a similar transition in the canonical ensemble at fixed equal densities $r_A=r_B=r_C=1/3$.Comment: 24 pages, 3 figure

Time-, Frequency-, and Wavevector-Resolved X-Ray Diffraction from Single Molecules

Using a quantum electrodynamic framework, we calculate the off-resonant scattering of a broad-band X-ray pulse from a sample initially prepared in an arbitrary superposition of electronic states. The signal consists of single-particle (incoherent) and two-particle (coherent) contributions that carry different particle form factors that involve different material transitions. Single-molecule experiments involving incoherent scattering are more influenced by inelastic processes compared to bulk measurements. The conditions under which the technique directly measures charge densities (and can be considered as diffraction) as opposed to correlation functions of the charge-density are specified. The results are illustrated with time- and wavevector-resolved signals from a single amino acid molecule (cysteine) following an impulsive excitation by a stimulated X-ray Raman process resonant with the sulfur K-edge. Our theory and simulations can guide future experimental studies on the structures of nano-particles and proteins

Phase diagram of the ABC model with nonconserving processes

The three species ABC model of driven particles on a ring is generalized to include vacancies and particle-nonconserving processes. The model exhibits phase separation at high densities. For equal average densities of the three species, it is shown that although the dynamics is {\it local}, it obeys detailed balance with respect to a Hamiltonian with {\it long-range interactions}, yielding a nonadditive free energy. The phase diagrams of the conserving and nonconserving models, corresponding to the canonical and grand-canonical ensembles, respectively, are calculated in the thermodynamic limit. Both models exhibit a transition from a homogeneous to a phase-separated state, although the phase diagrams are shown to differ from each other. This conforms with the expected inequivalence of ensembles in equilibrium systems with long-range interactions. These results are based on a stability analysis of the homogeneous phase and exact solution of the hydrodynamic equations of the models. They are supported by Monte-Carlo simulations. This study may serve as a useful starting point for analyzing the phase diagram for unequal densities, where detailed balance is not satisfied and thus a Hamiltonian cannot be defined.Comment: 32 page, 7 figures. The paper was presented at Statphys24, held in Cairns, Australia, July 201

Analytical study of an exclusive genetic switch

The nonequilibrium stationary state of an exclusive genetic switch is considered. The model comprises two competing species and a single binding site which, when bound to by a protein of one species, causes the other species to be repressed. The model may be thought of as a minimal model of the power struggle between two competing parties. Exact solutions are given for the limits of vanishing binding/unbinding rates and infinite binding/unbinding rates. A mean field theory is introduced which is exact in the limit of vanishing binding/unbinding rates. The mean field theory and numerical simulations reveal that generically bistability occurs and the system is in a symmetry broken state. An exact perturbative solution which in principle allows the nonequilibrium stationary state to be computed is also developed and computed to first and second order.Comment: 28 pages, 6 figure

A dynamically extending exclusion process

An extension of the totally asymmetric exclusion process, which incorporates a dynamically extending lattice is explored. Although originally inspired as a model for filamentous fungal growth, here the dynamically extending exclusion process (DEEP) is studied in its own right, as a nontrivial addition to the class of nonequilibrium exclusion process models. Here we discuss various mean-field approximation schemes and elucidate the steady state behaviour of the model and its associated phase diagram. Of particular note is that the dynamics of the extending lattice leads to a new region in the phase diagram in which a shock discontinuity in the density travels forward with a velocity that is lower than the velocity of the tip of the lattice. Thus in this region the shock recedes from both boundaries.Comment: 20 pages, 12 figure

Motion of condensates in non-Markovian zero-range dynamics

Condensation transition in a non-Markovian zero-range process is studied in one and higher dimensions. In the mean-field approximation, corresponding to infinite range hopping, the model exhibits condensation with a stationary condensate, as in the Markovian case, but with a modified phase diagram. In the case of nearest-neighbor hopping, the condensate is found to drift by a "slinky" motion from one site to the next. The mechanism of the drift is explored numerically in detail. A modified model with nearest-neighbor hopping which allows exact calculation of the steady state is introduced. The steady state of this model is found to be a product measure, and the condensate is stationary.Comment: 31 pages, 9 figure

Nonlinear optical spectroscopy of single, few, and many molecules; nonequilibrium Green's function QED approach

Nonlinear optical signals from an assembly of N noninteracting particles consist of an incoherent and a coherent component, whose magnitudes scale \sim N and \sim N(N-1), respectively. A unified microscopic description of both types of signals is developed using a quantum electrodynamical (QED) treatment of the optical fields. Closed nonequilibrium Green's function expressions are derived that incorporate both stimulated and spontaneous processes. General (n+1)-wave mixing experiments are discussed as an example of spontaneously generated signals. When performed on a single particle, such signals cannot be expressed in terms of the nth order polarization, as predicted by the semiclassical theory. Stimulated processes are shown to be purely incoherent in nature. Within the QED framework, heterodyne-detected wave mixing signals are simply viewed as incoherent stimulated emission, whereas homodyne signals are generated by coherent spontaneous emission.Comment: article: 33 pages (preprint format!) ''paper.tex'' figures: 17 figures (.eps) in folder ``figures'

Cooperating or Fighting with Decoherence in the Optimal Control of Quantum Dynamics

This paper explores the use of laboratory closed-loop learning control to either fight or cooperate with decoherence in the optimal manipulation of quantum dynamics. Simulations of the processes are performed in a Lindblad formulation on multilevel quantum systems strongly interacting with the environment without spontaneous emission. When seeking a high control yield it is possible to find fields that successfully fight with decoherence while attaining a good quality yield. When seeking modest control yields, fields can be found which are optimally shaped to cooperate with decoherence and thereby drive the dynamics more efficiently. In the latter regime when the control field and the decoherence strength are both weak, a theoretical foundation is established to describe how they cooperate with each other. In general, the results indicate that the population transfer objectives can be effectively met by appropriately either fighting or cooperating with decoherence