Information-Theoretic Features of Many Fermion Systems: An Exploration Based on Exactly Solvable Models.

Finite quantum many fermion systems are essential for our current understanding of Nature. They are at the core of molecular, atomic, and nuclear physics. In recent years, the application of information and complexity measures to the study of diverse types of many-fermion systems has opened a line of research that elucidates new aspects of the structure and behavior of this class of physical systems. In this work we explore the main features of information and information-based complexity indicators in exactly soluble many-fermion models of the Lipkin kind. Models of this kind have been extremely useful in shedding light on the intricacies of quantum many body physics. Models of the Lipkin kind play, for finite systems, a role similar to the one played by the celebrated Hubbard model of solid state physics. We consider two many fermion systems and show how their differences can be best appreciated by recourse to information theoretic tools. We appeal to information measures as tools to compare the structural details of different fermion systems. We will discover that few fermion systems are endowed by a much larger complexity-degree than many fermion ones. The same happens with the coupling-constants strengths. Complexity augments as they decrease, without reaching zero. Also, the behavior of the two lowest lying energy states are crucial in evaluating the system's complexity.

Noise minimisation in gene expression switches.

Gene expression is subject to stochastic variation which leads to fluctuations in the rate of protein production. Recently, a study in yeast at a genomic scale showed that, in some cases, gene expression variability alters phenotypes while, in other cases, these remain unchanged despite fluctuations in the expression of other genes. These studies suggested that noise in gene expression is a physiologically relevant trait and, to prevent harmful stochastic variation in the expression levels of some genes, it can be subject to minimisation. However, the mechanisms for noise minimisation are still unclear. In the present work, we analysed how noise expression depends on the architecture of the cis-regulatory system, in particular on the number of regulatory binding sites. Using analytical calculations and stochastic simulations, we found that the fluctuation level in noise expression decreased with the number of regulatory sites when regulatory transcription factors interacted with only one other bound transcription factor. In contrast, we observed that there was an optimal number of binding sites when transcription factors interacted with many bound transcription factors. This finding suggested a new mechanism for preventing large fluctuations in the expression of genes which are sensitive to the concentration of regulators.

Cooperative binding of transcription factors promotes bimodal gene expression response.

In the present work we extend and analyze the scope of our recently proposed stochastic model for transcriptional regulation, which considers an arbitrarily complex cis-regulatory system using only elementary reactions. Previously, we determined the role of cooperativity on the intrinsic fluctuations of gene expression for activating transcriptional switches, by means of master equation formalism and computer simulation. This model allowed us to distinguish between two cooperative binding mechanisms and, even though the mean expression levels were not affected differently by the acting mechanism, we showed that the associated fluctuations were different. In the present generalized model we include other regulatory functions in addition to those associated to an activator switch. Namely, we introduce repressive regulatory functions and two theoretical mechanisms that account for the biphasic response that some cis-regulatory systems show to the transcription factor concentration. We have also extended our previous master equation formalism in order to include protein production by stochastic translation of mRNA. Furthermore, we examine the graded/binary scenarios in the context of the interaction energy between transcription factors. In this sense, this is the first report to show that the cooperative binding of transcription factors to DNA promotes the "all-or-none" phenomenon observed in eukaryotic systems. In addition, we confirm that gene expression fluctuation levels associated with one of two cooperative binding mechanism never exceed the fluctuation levels of the other.

Decoherence, tunneling, and noise-induced activation in a double-potential well at high and zero temperature.

We study the effects of the environment on tunneling in an open system described by a static double-well potential. We describe the evolution of a quantum state localized in one of the minima of the potential at t = 0, in both the limits of high and zero environment temperature. We show that the evolution of the system can be summarized in terms of three main physical phenomena--namely, decoherence, quantum tunneling, and noise-induced activation--and we obtain analytical estimates for the corresponding time scales. These analytical predictions are confirmed by large-scale numerical simulations, providing a detailed picture of the main stages of the evolution and of the relevant dynamical processes.