Thermodynamic uncertainty relations in a linear system

We consider a Brownian particle in harmonic confinement of stiffness $k$, in one dimension in the underdamped regime. The whole setup is immersed in a heat bath at temperature $T$. The center of harmonic trap is dragged under any arbitrary protocol. The thermodynamic uncertainty relations for both position of the particle and current at time $t$ are obtained using the second law of thermodynamics as well as the positive semi-definite property of the correlation matrix of work and degrees of freedom of the system for both underdamped and overdamped cases.Comment: Minor revision, Accepted in EPJ

A high gain antenna system for airborne satellite communication applications

A high gain antenna for commercial aviation satellites communication is discussed. Electromagnetic and practical design considerations as well as candidate systems implementation are presented. An evaluation of these implementation schemes is given, resulting in the selection of a simple top mounted aerodynamic phased array antenna with a remotely located beam steering unit. This concept has been developed into a popular product known as the Canadian Marconi Company CMA-2100. A description of the technical details is followed by a summary of results from the first production antennas

Growth or Reproduction: Emergence of an Evolutionary Optimal Strategy

Modern ecology has re-emphasized the need for a quantitative understanding of the original 'survival of the fittest theme' based on analyzis of the intricate trade-offs between competing evolutionary strategies that characterize the evolution of life. This is key to the understanding of species coexistence and ecosystem diversity under the omnipresent constraint of limited resources. In this work we propose an agent based model replicating a community of interacting individuals, e.g. plants in a forest, where all are competing for the same finite amount of resources and each competitor is characterized by a specific growth-reproduction strategy. We show that such an evolution dynamics drives the system towards a stationary state characterized by an emergent optimal strategy, which in turn depends on the amount of available resources the ecosystem can rely on. We find that the share of resources used by individuals is power-law distributed with an exponent directly related to the optimal strategy. The model can be further generalized to devise optimal strategies in social and economical interacting systems dynamics.Comment: 10 pages, 5 figure

A novel iterative strategy for protein design

We propose and discuss a novel strategy for protein design. The method is based on recent theoretical advancements which showed the importance to treat carefully the conformational free energy of designed sequences. In this work we show how computational cost can be kept to a minimum by encompassing negative design features, i.e. isolating a small number of structures that compete significantly with the target one for being occupied at low temperature. The method is succesfully tested on minimalist protein models and using a variety of amino acid interaction potentials.Comment: 9 pages, 8 figure

Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models

Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a time-scale currently not accessible by all-atom potential based molecular dynamics. To avoid the massive computational effort required by this approach several simplified schemes have been introduced. One of the most satisfactory is the Gaussian Network approach based on the energy expansion in terms of the deviation of the protein backbone from its native configuration. Here we consider an extension of this model which captures in a more realistic way the distribution of native interactions due to the introduction of effective sidechain centroids. Since their location is entirely determined by the protein backbone, the model is amenable to the same exact and computationally efficient treatment as previous simpler models. The ability of the model to describe the correlated motion of protein residues in thermodynamic equilibrium is established through a series of successful comparisons with an extensive (14 ns) MD simulation based on the AMBER potential of HIV-1 protease in complex with a peptide substrate. Thus, the model presented here emerges as a powerful tool to provide preliminary, fast yet accurate characterizations of proteins near-native motion.Comment: 14 pages 7 figure

A Stochastic Model for the Species Abundance Problem in an Ecological Community

We propose a model based on coupled multiplicative stochastic processes to understand the dynamics of competing species in an ecosystem. This process can be conveniently described by a Fokker-Planck equation. We provide an analytical expression for the marginalized stationary distribution. Our solution is found in excellent agreement with numerical simulations and compares rather well with observational data from tropical forests.Comment: 4 pages, 3 figures, submitted to PR

Phase diagram of force-induced DNA unzipping in exactly solvable models

The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of interacting pairs of directed walks in the (1,1,...,1) direction on the hypercubic lattice, and the phase diagram in the force-temperature plane is studied for a variety of cases. The scaling behaviour is determined at both the unzipping and the melting transition. We confirm the existence of a cold denaturation transition recently observed in numerical simulations: for a finite range of forces the system gets unzipped by {\it decreasing} the temperature. The existence of this transition is rigorously established for generic lattice and continuum space models.Comment: 19 pages, 5 eps figures; revised version with minor changes, presentation simplified in the text with details in appendix. Accepted for publication in Phys. Rev.

On entropy production in nonequilibrium systems

In this paper we discuss the meaning of the Schnakenberg formula for entropy production in non-equilibrium systems. To this end we consider a non-equilibrium system as part of a larger isolated system which includes the environment. We prove that the Schnakenberg formula provides only a lower bound to the actual entropy production in the environment. This is also demonstrated in the simplest example of a three-state clock model.Comment: PDFLaTeX, 16 pages, 5 figure

Swollen-Collapsed Transition in Random Hetero-Polymers

A lattice model of a hetero-polymer with random hydrophilic-hydrophobic charges interacting with the solvent is introduced, whose continnuum counterpart has been proposed by T. Garel, L. Leibler and H. Orland {J. Phys. II France 4, 2139 (1994)]. The transfer matrix technique is used to study various constrained annealed systems which approximate at various degrees of accuracy the original quenched model. For highly hydrophobic chains an ordinary $\theta$-point transition is found from a high temperature swollen phase to a low temperature compact phase. Depending on the type of constrained averages, at very low temperatures a swollen phase or a coexistence between compact and swollen phases are found. The results are carefully compared with the corresponding ones obtained in the continuum limit, and various improvements in the original calculations are discussed.Comment: 13 pages, 8 figures; revised version with minor changes, accepted for publication in European Physical Journal