Qubit thermodynamics far from equilibrium: Two perspectives about the nature of heat and work in the quantum regime.

Considering an entropy-based division of energy transferred into heat and work, we develop an alternative theoretical framework for the thermodynamic analysis of two-level systems. When comparing these results with those obtained using the standard definitions of these quantities, we observe the appearance of a different term of work, which represents the energy cost of rotating the Bloch vector in the presence of the external field that defines the local Hamiltonian. Additionally, we obtain explicit expressions for the temperature, the heat capacity, and the internal entropy production of the system in both paradigms.

Interspecies evolutionary dynamics mediated by public goods in bacterial quorum sensing.

Bacterial quorum sensing is the communication that takes place between bacteria as they secrete certain molecules into the intercellular medium that later get absorbed by the secreting cells themselves and by others. Depending on cell density, this uptake has the potential to alter gene expression and thereby affect global properties of the community. We consider the case of multiple bacterial species coexisting, referring to each one of them as a genotype and adopting the usual denomination of the molecules they collectively secrete as public goods.

Out-of-equilibrium quantum thermodynamics in the Bloch sphere: Temperature and internal entropy production.

An explicit expression for the temperature of an open two-level quantum system is obtained as a function of local properties under the hypothesis of weak interaction with the environment. This temperature is defined for both equilibrium and out-of-equilibrium states and coincides with the environment temperature if the system reaches thermal equilibrium with a heat reservoir. Additionally, we show that within this theoretical framework the total entropy production can be partitioned into two contributions: one due to heat transfer and another, associated to internal irreversibilities, related to the loss of internal coherence by the qubit.

Quasispecies dynamics with network constraints.

A quasispecies is a set of interrelated genotypes that have reached a stationary state while evolving according to the usual Darwinian principles of selection and mutation. Quasispecies studies invariably assume that it is possible for any genotype to mutate into any other, but recent finds indicate that this assumption is not necessarily true. Here we revisit the traditional quasispecies theory by adopting a network structure to constrain the occurrence of mutations.

Early appraisal of the fixation probability in directed networks.

In evolutionary dynamics, the probability that a mutation spreads through the whole population, having arisen from a single individual, is known as the fixation probability. In general, it is not possible to find the fixation probability analytically given the mutant's fitness and the topological constraints that govern the spread of the mutation, so one resorts to simulations instead. Depending on the topology in use, a great number of evolutionary steps may be needed in each of the simulation events, particularly in those that end with the population containing mutants only.

Modeling weight loss and chlorogenic acids content in coffee during roasting.

Roasting is a key step in the production of a high-quality coffee. Roasting degree is directly related to coffee chemical composition and may be determined objectively by weight loss after roasting. Chlorogenic acids (CGA) are thermally labile phenolic compounds that play an important role in the final cup quality and health benefits of coffee.

Network growth for enhanced natural selection.

Natural selection and random drift are competing phenomena for explaining the evolution of populations. Combining a highly fit mutant with a population structure that improves the odds that the mutation spreads through the whole population tips the balance in favor of natural selection. The probability that the spread occurs, known as the fixation probability, depends heavily on how the population is structured.

Generalized memory associativity in a network model for the neuroses.

We review concepts introduced in earlier work, where a neural network mechanism describes some mental processes in neurotic pathology and psychoanalytic working-through, as associative memory functioning, according to the findings of Freud. We developed a complex network model, where modules corresponding to sensorial and symbolic memories interact, representing unconscious and conscious mental processes. The model illustrates Freud's idea that consciousness is related to symbolic and linguistic memory activity in the brain.

Emergence of scale-free networks from local connectivity and communication trade-offs.

We suggest a mechanism of connectivity evolution in networks to account for the emergence of scale-free behavior. The mechanism works on a fixed set of nodes and promotes growth from a minimally connected initial topology by the addition of edges. A new edge is added between two nodes depending on the trade-off between a gain and a cost function of local connectivity and communication properties.