Macroscopic tunneling, decoherence and noise-induced activation

We study the effects of the environment at zero temperature on tunneling in an open system described by a static double-well potential. We show that the evolution of the system in an initial Schrodinger cat state, can be summarized in terms of three main physical phenomena, namely decoherence, quantum tunneling and noise-induced activation. Using large-scale numerical simulations, we obtain a detailed picture of the main stages of the evolution and of the relevant dynamical processesComment: Contribution to the Proceedings of DICE'0

Temperature-fermion number correlations in finite paired systems

We investigate finite systems of N paired fermions, common in atomic nuclei, for example. These systems exhibit quantum mechanical features akin to those of superconductors. We discover, however, some specific N dependent effects that can not be attained in the thermodynamics limit of ordinary superconductivity. In particular, an important fact is uncovered: there is a strong correlation between the temperature T and the number of fermions N. A certain temperature increase ∆T produces, in thermal quantifiers (such as the entropy), quite different effects if N = 4 or N = 25. In fact, whether a given temperature value should be regarded as high or low can not be ascertained independent of the N value.Fil: Plastino, Ángelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Monteoliva, Diana. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; Argentina. Universidad Nacional de La Plata; ArgentinaFil: Plastino, Ángel Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires. Centro de Bioinvestigaciones (Sede Pergamino); Argentin

Quasi-Magical Fermion Numbers and Thermal Many-Body Dynamics

This work scrutinizes, using statistical mechanics indicators, important traits displayed by quantum many-body systems. Our statistical mechanics quantifiers are employed, in the context of Gibbs’ canonical ensemble at temperature T. A new quantifier of this sort is also presented here. The present discussion focuses attention on the role played by the fermion number N in many-fermion dynamics, that is, N is our protagonist. We have discovered discovers particular values of N for which the thermal indicators exhibit unexpected abrupt variations. Such a fact reflects an unanticipated characteristic of fermionic dynamics.Fil: Plastino, Ángel Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Monteoliva, Diana. Universidad Nacional de La Plata; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; ArgentinaFil: Plastino, Ángel Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires. Centro de Bioinvestigaciones (Sede Junín); Argentin

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.Instituto de Física La PlataFacultad de Ciencias Exacta

Role of cooperative binding on noise expression

The origin of stochastic fluctuations in gene expression has received considerable attention recently. Fluctuations in gene expression are particularly pronounced in cellular systems because of the small copy number of species undergoing transitions between discrete chemical states and the small size of biological compartments. In this paper, we propose a stochastic model for gene expression regulation including several binding sites, considering elementary reactions only. The model is used to investigate the role of cooperativity on the intrinsic fluctuations of gene expression by means of master-equation formalism. We found that the Hill coefficient and the level of noise increase as the interaction energy between activators increases. Additionally, we show that the model allows one to distinguish between two cooperative binding mechanisms.Centro Regional de Estudios GenómicosInstituto de Física La Plat

Promoters architecture-based mechanism for noise-induced oscillations in a single-gene circuit

It is well known that single-gene circuits with negative feedback loop can lead to oscillatory gene expression when they operate with time delay. In order to generate these oscillations many processes can contribute to properly timing such delay. Here we show that the time delay coming from the transitions between internal states of the cis-regulatory system (CRS) can drive sustained oscillations in an auto-repressive single-gene circuit operating in a small volume like a cell. We found that the cooperative binding of repressor molecules is not mandatory for a oscillatory behavior if there are enough binding sites in the CRS. These oscillations depend on an adequate balance between the CRS kinetic, and the synthesis/ degradation rates of repressor molecules. This finding suggest that the multi-site CRS architecture can play a key role for oscillatory behavior of gene expression. Finally, our results can also help to synthetic biologists on the design of the promoters architecture for new genetic oscillatory circuits.Instituto de Física de Líquidos y Sistemas BiológicosFacultad de Ciencias ExactasCentro Regional de Estudios Genómico

Mesoscopic oscillations in a single-gene circuit without delay

It is well known that single-gene circuits with negative feedback loop can lead to oscillatory gene expression when they operate with time delay. In order to generate these oscillations many processes can contribute to properly timing such delay. Here we show that the time delay coming from the transitions between internal states of the cis-regulatory system (CRS) can drive sustained oscillations in an auto-repressive single-gene circuit operating in a small volume like a cell. We found that the cooperative binding of repressor molecules is not mandatory for a oscillatory behavior if there are enough binding sites in the CRS. These oscillations depend on an adequate balance between the CRS kinetic, and the synthesis/degradation rates of repressor molecules. This finding suggest that the multi-site CRS architecture plays a key role for oscillatory behavior of gene expression.Instituto de Física de Líquidos y Sistemas BiológicosCentro Regional de Estudios Genómico

Statistical quantifiers resolve a nuclear theory controversy

We deal here with an exactly solvable N-nucleon system that has been used to mimic typical features of quantum many-body systems. There is in the literature some controversy regarding the possible existence of a quantum phase transition in the model. We show here that an appeal to a suitable statistical quantifier called thermal efficiency puts an end to the controversy.Instituto de Física La Plat

Role of cooperative binding on noise expression

The origin of stochastic fluctuations in gene expression has received considerable attention recently. Fluctuations in gene expression are particularly pronounced in cellular systems because of the small copy number of species undergoing transitions between discrete chemical states and the small size of biological compartments. In this paper, we propose a stochastic model for gene expression regulation including several binding sites, considering elementary reactions only. The model is used to investigate the role of cooperativity on the intrinsic fluctuations of gene expression by means of master-equation formalism. We found that the Hill coefficient and the level of noise increase as the interaction energy between activators increases. Additionally, we show that the model allows one to distinguish between two cooperative binding mechanisms.Centro Regional de Estudios GenómicosInstituto de Física La Plat