On the form of growing strings

Patterns and forms adopted by Nature, such as the shape of living cells, the geometry of shells and the branched structure of plants, are often the result of simple dynamical paradigms. Here we show that a growing self-interacting string attached to a tracking origin, modeled to resemble nascent polypeptides in vivo, develops helical structures which are more pronounced at the growing end. We also show that the dynamic growth ensemble shares several features of an equilibrium ensemble in which the growing end of the polymer is under an effective stretching force. A statistical analysis of native states of proteins shows that the signature of this non-equilibrium phenomenon has been fixed by evolution at the C-terminus, the growing end of a nascent protein. These findings suggest that a generic non-equilibrium growth process might have provided an additional evolutionary advantage for nascent proteins by favoring the preferential selection of helical structures.Comment: 4 pages, 3 figures. Accepted for publication in Phys. Rev. Let

Walks of molecular motors in two and three dimensions

Molecular motors interacting with cytoskeletal filaments undergo peculiar random walks consisting of alternating sequences of directed movements along the filaments and diffusive motion in the surrounding solution. An ensemble of motors is studied which interacts with a single filament in two and three dimensions. The time evolution of the probability distribution for the bound and unbound motors is determined analytically. The diffusion of the motors is strongly enhanced parallel to the filament. The analytical expressions are in excellent agreement with the results of Monte Carlo simulations.Comment: 7 pages, 2 figures, to be published in Europhys. Let

Beeping a Maximal Independent Set

We consider the problem of computing a maximal independent set (MIS) in an extremely harsh broadcast model that relies only on carrier sensing. The model consists of an anonymous broadcast network in which nodes have no knowledge about the topology of the network or even an upper bound on its size. Furthermore, it is assumed that an adversary chooses at which time slot each node wakes up. At each time slot a node can either beep, that is, emit a signal, or be silent. At a particular time slot, beeping nodes receive no feedback, while silent nodes can only differentiate between none of its neighbors beeping, or at least one of its neighbors beeping. We start by proving a lower bound that shows that in this model, it is not possible to locally converge to an MIS in sub-polynomial time. We then study four different relaxations of the model which allow us to circumvent the lower bound and find an MIS in polylogarithmic time. First, we show that if a polynomial upper bound on the network size is known, it is possible to find an MIS in O(log^3 n) time. Second, if we assume sleeping nodes are awoken by neighboring beeps, then we can also find an MIS in O(log^3 n) time. Third, if in addition to this wakeup assumption we allow sender-side collision detection, that is, beeping nodes can distinguish whether at least one neighboring node is beeping concurrently or not, we can find an MIS in O(log^2 n) time. Finally, if instead we endow nodes with synchronous clocks, it is also possible to find an MIS in O(log^2 n) time.Comment: arXiv admin note: substantial text overlap with arXiv:1108.192

Finite size effects and error-free communication in Gaussian channels

The efficacy of a specially constructed Gallager-type error-correcting code to communication in a Gaussian channel is being examined. The construction is based on the introduction of complex matrices, used in both encoding and decoding, which comprise sub-matrices of cascading connection values. The finite size effects are estimated for comparing the results to the bounds set by Shannon. The critical noise level achieved for certain code-rates and infinitely large systems nearly saturates the bounds set by Shannon even when the connectivity used is low

Statistical Physics of Irregular Low-Density Parity-Check Codes

Low-density parity-check codes with irregular constructions have been recently shown to outperform the most advanced error-correcting codes to date. In this paper we apply methods of statistical physics to study the typical properties of simple irregular codes. We use the replica method to find a phase transition which coincides with Shannon's coding bound when appropriate parameters are chosen. The decoding by belief propagation is also studied using statistical physics arguments; the theoretical solutions obtained are in good agreement with simulations. We compare the performance of irregular with that of regular codes and discuss the factors that contribute to the improvement in performance.Comment: 20 pages, 9 figures, revised version submitted to JP

Statistical Mechanics Analysis of LDPC Coding in MIMO Gaussian Channels

Using analytical methods of statistical mechanics, we analyse the typical behaviour of a multiple-input multiple-output (MIMO) Gaussian channel with binary inputs under LDPC network coding and joint decoding. The saddle point equations for the replica symmetric solution are found in particular realizations of this channel, including a small and large number of transmitters and receivers. In particular, we examine the cases of a single transmitter, a single receiver and the symmetric and asymmetric interference channels. Both dynamical and thermodynamical transitions from the ferromagnetic solution of perfect decoding to a non-ferromagnetic solution are identified for the cases considered, marking the practical and theoretical limits of the system under the current coding scheme. Numerical results are provided, showing the typical level of improvement/deterioration achieved with respect to the single transmitter/receiver result, for the various cases.Comment: 25 pages, 7 figure

Quantum Portfolios

Quantum computation holds promise for the solution of many intractable problems. However, since many quantum algorithms are stochastic in nature they can only find the solution of hard problems probabilistically. Thus the efficiency of the algorithms has to be characterized both by the expected time to completion {\it and} the associated variance. In order to minimize both the running time and its uncertainty, we show that portfolios of quantum algorithms analogous to those of finance can outperform single algorithms when applied to the NP-complete problems such as 3-SAT.Comment: revision includes additional data and corrects minor typo

On the Gold Standard for Security of Universal Steganography

While symmetric-key steganography is quite well understood both in the information-theoretic and in the computational setting, many fundamental questions about its public-key counterpart resist persistent attempts to solve them. The computational model for public-key steganography was proposed by von Ahn and Hopper in EUROCRYPT 2004. At TCC 2005, Backes and Cachin gave the first universal public-key stegosystem - i.e. one that works on all channels - achieving security against replayable chosen-covertext attacks (SS-RCCA) and asked whether security against non-replayable chosen-covertext attacks (SS-CCA) is achievable. Later, Hopper (ICALP 2005) provided such a stegosystem for every efficiently sampleable channel, but did not achieve universality. He posed the question whether universality and SS-CCA-security can be achieved simultaneously. No progress on this question has been achieved since more than a decade. In our work we solve Hopper's problem in a somehow complete manner: As our main positive result we design an SS-CCA-secure stegosystem that works for every memoryless channel. On the other hand, we prove that this result is the best possible in the context of universal steganography. We provide a family of 0-memoryless channels - where the already sent documents have only marginal influence on the current distribution - and prove that no SS-CCA-secure steganography for this family exists in the standard non-look-ahead model.Comment: EUROCRYPT 2018, llncs styl

Determining the neurotransmitter concentration profile at active synapses

Establishing the temporal and concentration profiles of neurotransmitters during synaptic release is an essential step towards understanding the basic properties of inter-neuronal communication in the central nervous system. A variety of ingenious attempts has been made to gain insights into this process, but the general inaccessibility of central synapses, intrinsic limitations of the techniques used, and natural variety of different synaptic environments have hindered a comprehensive description of this fundamental phenomenon. Here, we describe a number of experimental and theoretical findings that has been instrumental for advancing our knowledge of various features of neurotransmitter release, as well as newly developed tools that could overcome some limits of traditional pharmacological approaches and bring new impetus to the description of the complex mechanisms of synaptic transmission

On the dynamics of the glass transition on Bethe lattices

The Glauber dynamics of disordered spin models with multi-spin interactions on sparse random graphs (Bethe lattices) is investigated. Such models undergo a dynamical glass transition upon decreasing the temperature or increasing the degree of constrainedness. Our analysis is based upon a detailed study of large scale rearrangements which control the slow dynamics of the system close to the dynamical transition. Particular attention is devoted to the neighborhood of a zero temperature tricritical point. Both the approach and several key results are conjectured to be valid in a considerably more general context.Comment: 56 pages, 38 eps figure