1,720,975 research outputs found
Chemically controlled unfolding of a RNA-like polymer model
No full textWe consider a lattice polymer model of the two-tolerant type (i.e., a random walk allowed to visit lattice bonds at most twice), in which doubly visited bonds yield an attractive energy term (pairing energy). Such a model has been previously proposed as a rough, nonspecific description of the RNA folding mechanism. Indeed, the model predicts, besides the usual theta collapse, an extra transition to a low-temperature fully paired state. In the current work, we propose an extension of the model, in which a "micromolecular" chemical species can bind the polymer and locally forbid segment pairing. We investigate equilibrium thermodynamics in the grand-canonical picture, at the level of a Bethe approximation, which is, a refined mean-field technique, equivalent to the exact solution on a random-regular graph. The general trend we observe is that expected from the mechanism implemented in the model (increasing micromolecule concentration favors unfolding and lowers the transition temperature), but the resulting phase diagram turns out to be remarkably interesting and ric
Cluster approximations for the TASEP: stationary state and dynamical transition
No full textWe develop and test cluster approximations, which generalize simple mean-field by taking into account more and more local correlations, for the Totally Asymmetric Simple Exclusion Process with open boundaries. We consider in detail the pair and triplet approximations, discussing the improvements with respect to mean field in various steady state properties. Moreover, we analyze the recently discovered dynamical transition, describing how the spectrum of the relaxation matrix changes at the transition
Design and implementation of a belief-propagation scheduler for multicast traffic in input-queued switches
Full text linkScheduling multicast traffic in input-queued switches to maximize throughput requires solving a hard combinatorial optimization problem in a very short time. This task advocates the design of algorithms that are simple to implement and efficient in terms of performance. We propose a new scheduling algorithm, based on message passing and inspired by the belief propagation paradigm, meant to approximate the provably-optimal scheduling policy for multicast traffic. We design and implement both a software and a hardware version of the algorithm, the latter running on a NetFPGA. We compare the performance and the power consumption of the two versions when integrated in a software router. Our main findings are that our algorithm outperforms other centralized greedy scheduling policies, achieving a better tradeoff between complexity and performance, and it is amenable to practical high-performance implementations
Interaction vs inhomogeneity in a periodic TASEP
Full text linkWe study the non-equilibrium steady states in a totally asymmetric simple exclusion process with periodic boundary conditions, also incorporating (i) an extra (nearest-neighbour) repulsive interaction and (ii) hopping rates characterized by a smooth spatial inhomogeneity. We make use of a generalized mean-field approach (at the level of nearest-neighbour pair clusters), in combination with kinetic Monte Carlo simulations. It turns out that the so-called shock phase can exhibit a lot of qualitatively different subphases, including multiple-shock phases, and a minimal-current shock phase. We argue that the resulting, considerably rich phase diagram should be relatively insensitive to minor details of either interaction or spatial inhomogeneity. As a consequence, we also expect that our results help elucidate the nature of shock subphases detected in previous studies
Partial integration and local mean field approach for a vector lattice model of microemulsions: unbalanced case
No full textWe consider a vector lattice model for mixtures of water, oil and amphiphile, and it extends to the (unbalanced) case of different water and oil volume fractions, an approach previously developed for the balanced case. After an exact summation of the orientational degrees of freedom we get an effective hamiltonian with multi-site couplings, which is then studied in a local mean-field approximation. The phase diagram for several temperatures and strong amphiphilic interactions is mapped out both in terms of the chemical potentials and of the volume fractions of the components. We find several structured phases (lamellar, micellar and cubic) as well as homogeneous phases, and coexistence phenomena
Dynamical Transitions in a One-Dimensional Katz–Lebowitz–Spohn Model
Full text linkDynamical transitions, already found in the high- and low-density phases of the Totally
Asymmetric Simple Exclusion Process and a couple of its generalizations, are singularities in the
rate of relaxation towards the Non-Equilibrium Stationary State (NESS), which do not correspond
to any transition in the NESS itself. We investigate dynamical transitions in the one-dimensional
Katz–Lebowitz–Spohn model, a further generalization of the Totally Asymmetric Simple Exclusion
Process where the hopping rate depends on the occupation state of the 2 nodes adjacent to the nodes
affected by the hop. Following previous work, we choose Glauber rates and bulk-adapted boundary
conditions. In particular, we consider a value of the repulsion which parameterizes the Glauber
rates such that the fundamental diagram of the model exhibits 2 maxima and a minimum, and the
NESS phase diagram is especially rich. We provide evidence, based on pair approximation, domain
wall theory and exact finite size results, that dynamical transitions also occur in the one-dimensional
Katz–Lebowitz–Spohn model, and discuss 2 new phenomena which are peculiar to this model
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