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A central problem in developmental and synthetic biology is understanding the mechanisms by which cells in a tissue or a Petri dish process external cues and transform such information into a coherent response, e.g., a terminal differentiation state. It was long believed that this type of positional information could be entirely attributed to a gradient of concentration of a specific signaling molecule (i.e., a morphogen). However, advances in experimental methodologies and computer modeling have demonstrated the crucial role of the dynamics of a cell's gene regulatory network (GRN) in decoding the information carried by the morphogen, which is eventually translated into a spatial pattern. This morphogen interpretation mechanism has gained much attention in systems biology as a tractable system to investigate the emergent properties of complex genotype-phenotype maps. In this study, we apply a Markov chain Monte Carlo (MCMC)-like algorithm to probe the design space of three-node GRNs with the ability to generate a band-like expression pattern (target phenotype) in the middle of an arrangement of 30 cells, which resemble a simple (1-D) morphogenetic field in a developing embryo. Unlike most modeling studies published so far, here we explore the space of GRN topologies with nodes having the potential to perceive the same input signal differently. This allows for a lot more flexibility during the search space process, and thus enables us to identify a larger set of potentially interesting and realizable morphogen interpretation mechanisms. Out of 2061 GRNs selected using the search space algorithm, we found 714 classes of network topologies that could correctly interpret the morphogen. Notably, the main network motif that generated the target phenotype in response to the input signal was the type 3 Incoherent Feed-Forward Loop (I3-FFL), which agrees with previous theoretical expectations and experimental observations. Particularly, compared to a previously reported pattern forming GRN topologies, we have uncovered a great variety of novel network designs, some of which might be worth inquiring through synthetic biology methodologies to test for the ability of network design with minimal regulatory complexity to interpret a developmental cue robustly.

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ABSTRACT The understanding of the relationships between the planktonic communities in a reservoir allows us to infer possible changes in the redistribution of matter and energy flows in these systems. This work proposes a dynamic model for the trophic network of the Riogrande II tropical reservoir, which integrates the planktonic trophic chains of detritus and grazing, limiting the prey-predator interactions by introducing the prey meeting factor (pmf). We built a dynamic model of mass balance supported by an extensive bibliographic search. The limitations of consumers and resources were represented simultaneously by means of the pmf. The data used to validate the model were compiled from previous investigations carried out in this reservoir from 2010 to 2013. The values of pmf that we found in each simulation suggest that the top predator can access its main prey in certain concentrations of total phosphorus, with a probability of encounter ranging from 9.3 % to 17.7 %. Our simulations indicate that most of the primary production is poorly used by the primary consumers in the photic zone, however, it enters in the flows of the detrital chain and supports the production of zooplankton almost entirely. According to this finding, the biomass densities obtained in the previous studies can be better explained by the causal relationships assumed in this model.

RESUMEN Entender las relaciones entre las comunidades planctónicas en un embalse nos permite inferir posibles cambios en la redistribución de los flujos de materia y energía en este sistema. Este trabajo propone un modelo dinámico para representar la red trófica del embalse tropical Riogrande II, donde se integran las cadenas tróficas de pastoreo y detritus y se limitan las interacciones entre predadores, presas y recursos al introducir un factor limitante de encuentro con la presa (pmf). El modelo dinámico se enfoca en el balance de masas sustentado en una amplia búsqueda bibliográfica. Los datos usados para validar el modelo se colectaron de datos previamente reportados para el embalse durante los años 2010 y 2013. Los valores de pmf obtenidos en cada simulación, sugieren que el predador dominante puede acceder a su presa principal a ciertas concentraciones de fósforo total, con una probabilidad de encuentro que va desde 9,3 % hasta 17,7 %. Nuestros resultados indican que la mayor parte de la producción primaria es poco aprovechada por los consumidores en la zona fótica, sin embargo, ingresa en el flujo de la cadena detrítica de manera que soporta la producción de zooplancton casi por completo. Las relaciones causales asumidas en este modelo explican en gran medida las densidades de biomasa reportadas en estudios previos.

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Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by providing 3D density maps of biomolecules at near-atomic resolution. However, map validation is still an open issue. Despite several efforts from the community, it is possible to overfit 3D maps to noisy data. Here, we develop a novel methodology that uses a small independent particle set (not used during the 3D refinement) to validate the maps. The main idea is to monitor how the map probability evolves over the control set during the 3D refinement. The method is complementary to the gold-standard procedure, which generates two reconstructions at each iteration. We low-pass filter the two reconstructions for different frequency cutoffs, and we calculate the probability of each filtered map given the control set. For high-quality maps, the probability should increase as a function of the frequency cutoff and the refinement iteration. We also compute the similarity between the densities of probability distributions of the two reconstructions. As higher frequencies are included, the distributions become more dissimilar. We optimized the BioEM package to perform these calculations, and tested it over systems ranging from quality data to pure noise. Our results show that with our methodology, it possible to discriminate datasets that are constructed from noise particles. We conclude that validation against a control particle set provides a powerful tool to assess the quality of cryo-EM maps.

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We present a study of the strong coupling between radiation and matter, considering a system of two quantum dots, which are in mutual interaction and interact with a single mode of light confined in a semiconductor nanocavity. We take into account dissipative mechanisms such as the escape of the cavity photons, decay of the quantum dot excitons by spontaneous emission, and independent exciton pumping. It is shown that the mutual interaction between the dots can be measured off-resonance only if the strong coupling condition is reached. Using the quantum regression theorem, a reasonable definition of the dynamical coupling regimes is introduced in terms of the complex Rabi frequency. Finally, the emission spectrum for relevant conditions is presented and compared with the above definition, demonstrating that the interaction between the excitons does not affect the strong coupling.

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We investigate the effects of considering two different incoherent excitation mechanisms on microcavity quantum dot systems modeled using the Jaynes-Cummings Hamiltonian. When the system is incoherently pumped with polaritons it is able to sustain a large number of photons inside the cavity with Poisson-like statistics in the stationary limit, and it also leads to a separable exciton-photon state. We also investigate the effects of both types of pumpings (excitonic and polaritonic) in the emission spectrum of the cavity. We show that the polaritonic pumping considered here is unable to modify the dynamical regimes of the system at variance with the excitonic pumping. Finally, we obtain a closed form expression for the negativity of the density matrices that the quantum master equation considered here generates.

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The relation between the dynamical regimes (weak and strong coupling) and entanglement for a dissipative quantum dot microcavity system is studied. In the framework of a phenomenological temperature model an analysis in both temporal (population dynamics) and frequency domain (photoluminescence) is carried out in order to identify the associated dynamical behavior. The Wigner function and concurrence are employed to quantify the entanglement in each regime. We find that sudden death of entanglement is a typical characteristic of the strong coupling regime.

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We show that the combined effect of photon emission and Coulomb interactions may drive an exciton-polariton system towards a dynamical coherent state, even without phonon thermalization or any other relaxation mechanism. Exact diagonalization results for a finite system (a multilevel quantum dot interacting with the lowest-energy photon mode of a microcavity) are presented in support of this statement.