RESUMEN

We introduce the Random Walk Approximation (RWA), a new method to approximate the stationary solution of master equations describing stochastic processes taking place on graphs. Our approximation can be used for all processes governed by non-linear master equations without long-range interactions and with a conserved number of entities, which are typical in biological systems, such as gene regulatory or chemical reaction networks, where no exact solution exists. For linear systems, the RWA becomes the exact result obtained from the maximum entropy principle. The RWA allows having a simple analytical, even though approximated, form of the solution, which is global and easier to deal with than the standard System Size Expansion (SSE). Here, we give some theoretically sufficient conditions for the validity of the RWA and estimate the order of error calculated by the approximation with respect to the number of particles. We compare RWA with SSE for two examples, a toy model and the more realistic dual phosphorylation cycle, governed by the same underlying process. Both approximations are compared with the exact integration of the master equation, showing for the RWA good performances of the same order or better than the SSE, even in regions where sufficient conditions are not met.

RESUMEN

Understanding the development of non-linear processes such as economic or population growth is an important prerequisite for informed decisions in those areas. In the function-learning paradigm, people's understanding of the function rule that underlies the to-be predicted process is typically measured by means of extrapolation accuracy. Here we argue, however, that even though accurate extrapolation necessitates rule-learning, the reverse does not necessarily hold: Inaccurate extrapolation does not exclude rule-learning. Experiment 1 shows that more than one third of participants who would be classified as "exemplar-based learners" based on their extrapolation accuracy were able to identify the correct function shape and slope in a rule-selection paradigm, demonstrating accurate understanding of the function rule. Experiment 2 shows that higher proportions of rule learning than ruleapplication in the function-learning paradigm is not due to (i) higher a priori probabilities to guess the correct rule in the rule-selection paradigm; nor is it due to (ii) a lack of simultaneous access to all function values in the function-learning paradigm. We conclude that rule application is not tantamount to rule-learning, and that assessing rule xlearning via extrapolation accuracy underestimates the proportion of rule learners in function-learning experiments.

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RESUMEN

We propose a carbon-nanotube-based neural sensor designed to exploit the electrical sensitivity of an inhomogeneous fractal network of conducting channels. This network forms the active layer of a multi-electrode field effect transistor that in future applications will be gated by the electrical potential associated with neuronal signals. Using a combination of simulated and fabricated networks, we show that thin films of randomly-arranged carbon nanotubes (CNTs) self-assemble into a network featuring statistical fractal characteristics. The extent to which the network's non-linear responses will generate a superior detection of the neuron's signal is expected to depend on both the CNT electrical properties and the geometric properties of the assembled network. We therefore perform exploratory experiments that use metallic gates to mimic the potentials generated by neurons. We demonstrate that the fractal scaling properties of the network, along with their intrinsic asymmetry, generate electrical signatures that depend on the potential's location. We discuss how these properties can be exploited for future neural sensors.

RESUMEN

Heterosis, the superiority of hybrids over their parents for quantitative traits, represents a crucial issue in plant and animal breeding as well as evolutionary biology. Heterosis has given rise to countless genetic, genomic and molecular studies, but has rarely been investigated from the point of view of systems biology. We hypothesized that heterosis is an emergent property of living systems resulting from frequent concave relationships between genotypic variables and phenotypes, or between different phenotypic levels. We chose the enzyme-flux relationship as a model of the concave genotype-phenotype (GP) relationship, and showed that heterosis can be easily created in the laboratory. First, we reconstituted in vitro the upper part of glycolysis. We simulated genetic variability of enzyme activity by varying enzyme concentrations in test tubes. Mixing the content of "parental" tubes resulted in "hybrids," whose fluxes were compared to the parental fluxes. Frequent heterotic fluxes were observed, under conditions that were determined analytically and confirmed by computer simulation. Second, to test this model in a more realistic situation, we modeled the glycolysis/fermentation network in yeast by considering one input flux, glucose, and two output fluxes, glycerol and acetaldehyde. We simulated genetic variability by randomly drawing parental enzyme concentrations under various conditions, and computed the parental and hybrid fluxes using a system of differential equations. Again we found that a majority of hybrids exhibited positive heterosis for metabolic fluxes. Cases of negative heterosis were due to local convexity between certain enzyme concentrations and fluxes. In both approaches, heterosis was maximized when the parents were phenotypically close and when the distributions of parental enzyme concentrations were contrasted and constrained. These conclusions are not restricted to metabolic systems: they only depend on the concavity of the GP relationship, which is commonly observed at various levels of the phenotypic hierarchy, and could account for the pervasiveness of heterosis.

RESUMEN

The propagation within a one-dimensional photonic crystal of a single ultra-short and ultra-intense pulse delivered by an X-ray free-electron laser is analysed with the framework of the time-dependent coupled-wave theory in non-linear media. It is shown that the reflection and the transmission of an ultra-short pulse present a transient period conditioned by the extinction length and also the thickness of the structure for transmission. For ultra-intense pulses, non-linear effects are expected: they could give rise to numerous phenomena, bi-stability, self-induced transparency, gap solitons, switching, etc., which have been previously shown in the optical domain.

RESUMEN

Relapse to alcohol and other substances has generally been described by curves that resemble one another. However, these curves have been generated from the time to first use after a period of abstinence without regard to the movement of individuals into and out of drug use. Instead of measuring continuous abstinence, we considered post-treatment functioning as a more complicated phenomenon, describing how people move in and out of drinking states on a monthly basis over the course of a year. When we looked at time to first drink we observed the ubiquitous relapse curve. When we classified clients (N = 550) according to drinking state however, they frequently moved from one state to another with both abstinent and very heavy drinking states as being rather stable, and light or moderate drinking and heavy drinking being unstable. We found that clients with a family history of alcoholism were less likely to experience these unstable states. When we examined the distribution of cases crossed by the number of times clients switched states we found that a power function explained 83% of that relationship. Some of the remainder of the variance seems to be explained by the stable states of very heavy drinking and abstinence acting as attractors.