Magic Numbers and Mixing Degree in Many-Fermion Systems.

We consider an N fermion system at low temperature T in which we encounter special particle number values Nm exhibiting special traits. These values arise when focusing attention upon the degree of mixture (DM) of the pertinent quantum states. Given the coupling constant of the Hamiltonian, the DMs stay constant for all N-values but experience sudden jumps at the Nm. For a quantum state described by the matrix ρ, its purity is expressed by Trρ2 and then the degree of mixture is given by 1-Trρ2, a quantity that coincides with the entropy Sq for q=2. Thus, Tsallis entropy of index two faithfully represents the degree of mixing of a state, that is, it measures the extent to which the state departs from maximal purity. Macroscopic manifestations of the degree of mixing can be observed through various physical quantities. Our present study is closely related to properties of many-fermion systems that are usually manipulated at zero temperature. Here, we wish to study the subject at finite temperature. The Gibbs ensemble is appealed to. Some interesting insights are thereby gained.

Information propagation in a noisy gene cascade.

We use information theory to study the information transmission through a simple gene cascade where the product of an unregulated gene regulates the expression activity of a cooperative genetic switch. While the input signal is provided by the upstream gene with two states, we consider that the expression of downstream gene is controlled by a cis-regulatory system with three binding sites for the regulator product, which can bind cooperatively. By computing exactly the associated probability distributions, we estimate information transmission thought the mutual information measure. We found that the mutual information associated with unimodal input signal is lower than the associated with bimodal inputs. We also observe that mutual information presents a maximum in the cooperativity intensity, and the position of this maximum depends on the kinetic rates of the promoter. Furthermore, we found that the bursting dynamics of the input signal can enhance the information transmission capacity.

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.

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.

Decoherence in a classically chaotic quantum system: entropy production and quantum-classical correspondence.

We study the decoherence process for an open quantum system that is classically chaotic (a quartic double well with harmonic driving coupled to a sea of harmonic oscillators). We carefully analyze the time dependence of the rate of entropy production showing that it has two relevant regimes: For short times it is proportional to the diffusion coefficient (fixed by the system-environment coupling strength); for longer times (but before equilibration) it is fixed by dynamical properties of the system (and is related to the Lyapunov exponent). The nature of the transition time between both regimes is investigated and the issue of quantum to classical correspondence is addressed. Finally, the impact of the interaction with the environment on coherent tunneling is analyzed.

Decoherence and the rate of entropy production in chaotic quantum systems

We show that for an open quantum system which is classically chaotic (a quartic double well with harmonic driving coupled to a sea of harmonic oscillators) the rate of entropy production has, as a function of time, two relevant regimes: For short times it is proportional to the diffusion coefficient (fixed by the system-environment coupling strength). For longer times (but before equilibration) there is a regime where the entropy production rate is fixed by the Lyapunov exponent. The nature of the transition time between both regimes is investigated.