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Summary: Macromolecular assembly vertebrates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential increase of the number of configurational states with the number of components. CplexA is a Mathematica package that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the energetics of the interactions. The package is particularly suited to study gene expression at complex promoters controlled by multiple, local and distal, DNA binding sites for transcription factors. Availability: CplexA is freely available together with documentation at http://sourceforge.net/projects/cplexa/., Comment: 28 pages. Includes Mathematica, Matlab, and Python implementation tutorials. Software can be downloaded at http://cplexa.sourceforge.net/

We show that the Comment [arXiv:0808.1224] by Horowitz and Jarzynski obtains as a main result a general free energy change for a harmonic system that in the macroscopic limit does not recover the textbook expression for the energy change of a Hookean spring. The reason is that Horowitz and Jarzynski improperly identify work with parametric changes of the Hamiltonian instead of with the standard quantity, force times displacement., Comment: To appear in Physical Review Letters

We show that Peliti's Comment [arXiv:0808.2855] fails to appreciate basic physical principles and consequently misrepresents both our work as well as the classical work of Gibbs and Tolman., Comment: To appear in Physical Review Letters

The behavior of interacting populations typically displays irregular temporal and spatial patterns that are difficult to reconcile with an underlying deterministic dynamics. A classical example is the heterogeneous distribution of plankton communities, which has been observed to be patchy over a wide range of spatial and temporal scales. Here, we use plankton communities as prototype systems to present theoretical approaches for the analysis of the combined effects of turbulent advection and stochastic growth in the spatiotemporal dynamics of the population. Incorporation of these two factors into mathematical models brings an extra level of realism to the description and leads to better agreement with experimental data than that of previously proposed models based on reaction-diffusion equations., Comment: 11 pages, 9 figures. Submitted to EPJ Special Topics

Concepts of everyday use like energy, heat, and temperature have acquired a precise meaning after the development of thermodynamics. Thermodynamics provides the basis for understanding how heat and work are related and with the general rules that the macroscopic properties of systems at equilibrium follow. Outside equilibrium and away from macroscopic regimes most of those rules cannot be applied directly. Here we present recent developments that extend the applicability of thermodynamic concepts deep into mesoscopic and irreversible regimes. We show how the probabilistic interpretation of thermodynamics together with probability conservation laws can be used to obtain Fokker-Planck equations for the relevant degrees of freedom. This approach provides a systematic method to obtain the stochastic dynamics of a system directly from its equilibrium properties. A wide variety of situations can be studied in this way, including many that were thought to be out of reach of thermodynamic theories, such as non-linear transport in the presence of potential barriers, activated processes, slow relaxation phenomena, and basic processes in biomolecules, like translocation and stretching., Comment: Feature Article, 32 pages, 5 figures

We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We integrate three different levels of description -molecular, cellular, and that of cell population- into a single model, which seems to capture many experimental aspects of the system.

Plankton is the productive base of aquatic ecosystems and plays a major role in the global control of atmospheric carbon dioxide. Nevertheless, after intensive study, the factors that drive its spatial distribution are still far from being clear. The models proposed so far show very limited agreement with actual data as many of their results are not consistent with field observations. Here we show that fluctuations and turbulent diffusion in standard prey-predator models are able to accurately and consistently explain plankton field observations at mesoscales (1-100 km). This includes not only the spatial pattern but also its temporal evolution. We explicitly elucidate the interplay between physical and biological factors, suggesting that the form in which small scale biotic fluctuations are transferred to larger scales may constitute one of the key elements in determining the spatial distribution of plankton in the sea., Comment: 16 pages, 3 figures

We have analyzed the interplay between an externally added noise and the intrinsic noise of systems that relax fast towards a stationary state, and found that increasing the intensity of the external noise can reduce the total noise of the system. We have established a general criterion for the appearance of this phenomenon and discussed two examples in detail., Comment: 4 pages, 4 figures

Nonequilibrium thermodynamics has shown its applicability in a wide variety of different situations pertaining to fields such as physics, chemistry, biology, and engineering. As successful as it is, however, its current formulation considers only systems close to equilibrium --those satisfying the so-called local equilibrium hypothesis. Here we show that diffusion processes that occur far away from equilibrium can be viewed as at local equilibrium in a space that includes all the relevant variables in addition to the spatial coordinate. In this way, nonequilibrium thermodynamics can be used and the difficulties and ambiguities associated with the lack of a thermodynamic description disappear. We analyze explicitly the inertial effects in diffusion and outline how the main ideas can be applied to other situations., Comment: 11 pages, 1 figure

We present some aspects of the rheology of field-responsive suspensions, a class of field-responsive liquid matter systems possessing the ability to undergo significant changes in their strength upon application of an external field. Both the single-particle and the many-particle domains are discussed. In the former, consideration of the full nonlinear dynamics of the particles leads to an anomalous behavior of the viscosity whereas in the latter the most salient feature is the formation of chains and fractal structures. We indicate how to deal with the rheology at moderately concentrations leaving open the problem at higher concentrations for which the complexity of the emergent structures strongly limits the knowledge of their dynamics., Comment: 10 pages, to appear in J. Phys. : Condens. Matter, Plenary talk presented at the 4th Liquid Matter Conference (Granada 1999)

In a recent paper, Diaz-Guilera et al. [Phys. Rev. E 57, 3820 (1998)] analyze the mechanisms of synchronization and pattern formation in a lattice of pulse-coupled oscillators. In essence, their analysis consists in the study of the stability of the fixed points of several linear return maps which are obtained from the original system by means of matrix manipulations. We show that although the model they consider is very specific and actually unable to account even for a linear phase response curve, their method does not give correct information on the original system since many of the assumptions involved are in general not correct. To clarify these aspects, several issues concerning the real dynamics are also discussed., Comment: 4 pages, 3 figures, Revtex

We explore systems of pulse-coupled oscillators beyond the mean-field limit [R.E. Mirollo and S.H. Strogatz, {SIAM J. Appl. Math.} {\bf 50}, 1645 (1990)] by means of a manageable description which leads to a great simplification of the dynamics. Sufficient conditions for synchronization are exactly obtained for a ring with nearest-neighbor directed interactions, turning out to be the same as in the all-to-all case. Our analysis shows new synchronization mechanisms occurring when the interactions are local., Comment: 4 pages, 2 figures

We present a mesoscopic approach to analyze the dynamics of a single magnetic dipole under the influence of an oscillating magnetic field, based on the formulation of a Fokker-Planck equation. The dissipated power and the viscosity of a suspension of such magnetic dipoles are calculated from non-equilibrium thermodynamics of magnetized systems. By means of this method we have found a non-monotonous behaviour of the viscosity as a function of the frequency of the field which has been referred to as the ``negative'' viscosity effect. Moreover, we have shown that the viscosity depends on the vorticity field thus exhibiting non-Newtonian behaviour. Our analysis is complemented with numerical simulations which reproduce the behaviour of the viscosity we have found and extend the scope of our analytical approach to higher values of the magnetic field., Comment: 9 pages, 2 eps figures, simulations have been added

We have analyzed the interplay between noise and periodic modulations in a classical Lotka-Volterra model of two-species competition. We have found that the consideration of noise changes drastically the behavior of the system and leads to new situations which have no counterpart in the deterministic case. Among others, noise is responsible for temporal oscillations, spatial patterns, and the enhancement of the response of the system via stochastic resonance., Comment: 4 pages, RevTex, 4 PostScript figures

We have analyzed the interplay between noise and periodic modulations in a mean field model of a neural excitable medium. To this purpose, we have considered two types of modulations; namely, variations of the resistance and oscillations of the threshold. In both cases, stochastic resonance is present, irrespective of if the system is monostable or bistable., Comment: 13 pages, RevTex, 5 PostScript figures

We have analyzed the interplay between noise and periodic spatial modulations in bistable systems outside equilibrium and found that noise is able to increase the spatial order of the system, giving rise to periodic patterns which otherwise look random. This new phenomenon, which may be viewed as the spatial counterpart of stochastic resonance, then shows a constructive role of noise in spatially extended systems, not considered up to now., Comment: 4 pages, RevTex, 5 PostScript figures

We show that scaling arguments are very useful to analyze the dynamics of periodically modulated noisy systems. Information about the behavior of the relevant quantities, such as the signal-to-noise ratio, upon variations of the noise level, can be obtained by analyzing the symmetries and invariances of the system. In this way, it is possible to predict diverse physical manifestations of the cooperative behavior between noise and input signal, as for instance stochastic resonance, spatiotemporal stochastic resonance, and stochastic multiresonance., Comment: 8 pages, RevTex

We have analyzed the effects of the addition of external noise to non-dynamical systems displaying intrinsic noise, and established general conditions under which stochastic resonance appears. The criterion we have found may be applied to a wide class of non-dynamical systems, covering situations of different nature. Some particular examples are discussed in detail., Comment: 4 pages, RevTex, 3 PostScript figures available upon request

We present a class of systems for which the signal-to-noise ratio as a function of the noise level may display a multiplicity of maxima. This phenomenon, referred to as stochastic multiresonance, indicates the possibility that periodic signals may be enhanced at multiple values of the noise level, instead of at a single value which has occurred in systems considered up to now in the framework of stochastic resonance., Comment: 4 pages, RevTex, 3 PostScript figures

We analyze the consequences that the choice of the output of the system has in the efficiency of signal detection. It is shown that the signal and the signal-to-noise ratio (SNR), used to characterize the phenomenon of stochastic resonance, strongly depend on the form of the output. In particular, the SNR may be enhanced for an adequate output., Comment: 4 pages, RevTex, 6 PostScript figures

We show the appearance of spatiotemporal stochastic resonance in the Swift-Hohenberg equation. This phenomenon emerges when a control parameter varies periodically in time around the bifurcation point. By using general scaling arguments and by taking into account the common features occurring in a bifurcation, we outline possible manifestations of the phenomenon in other pattern-forming systems., Comment: 4 pages, RevTex, 4 PostScript figures

We show that the dipole, a system usually proposed to model relaxation phenomena, exhibits a maximum in the signal-to-noise ratio at a non-zero noise level, thus indicating the appearance of stochastic resonance. The phenomenon occurs in two different situations, i.e. when the minimum of the potential of the dipole remains fixed in time and when it switches periodically between two equilibrium points. We have also found that the signal-to-noise ratio has a maximum for a certain value of the amplitude of the oscillating field., Comment: 4 pages, RevTex, 6 PostScript figures available upon request; to appear in Phys. Rev. E

We present a class of systems for which the signal-to-noise ratio always increases when increasing the noise and diverges at infinite noise level. This new phenomenon is a direct consequence of the existence of a scaling law for the signal-to-noise ratio and implies the appearance of stochastic resonance in some monostable systems. We outline applications of our results to a wide variety of systems pertaining to different scientific areas. Two particular examples are discussed in detail., Comment: 4 pages, RevTex, 3 PostScript figures available upon request; to appear in Phys. Rev. Lett