Molecular Distributions in Gene Regulatory Dynamics

We show how one may analytically compute the stationary density of the distribution of molecular constituents in populations of cells in the presence of noise arising from either bursting transcription or translation, or noise in degradation rates arising from low numbers of molecules. We have compared our results with an analysis of the same model systems (either inducible or repressible operons) in the absence of any stochastic effects, and shown the correspondence between behaviour in the deterministic system and the stochastic analogs. We have identified key dimensionless parameters that control the appearance of one or two steady states in the deterministic case, or unimodal and bimodal densities in the stochastic systems, and detailed the analytic requirements for the occurrence of different behaviours. This approach provides, in some situations, an alternative to computationally intensive stochastic simulations. Our results indicate that, within the context of the simple models we have examined, bursting and degradation noise cannot be distinguished analytically when present alone.Comment: 14 pages, 12 figures. Conferences: "2010 Annual Meeting of The Society of Mathematical Biology", Rio de Janeiro (Brazil), 24-29/07/2010. "First International workshop on Differential and Integral Equations with Applications in Biology and Medicine", Aegean University, Karlovassi, Samos island (Greece), 6-10/09/201

Models of Dictyostelium discoideum aggregation

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Quantum-assisted finite-element design optimization

Quantum annealing devices such as the ones produced by D-Wave systems are typically used for solving optimization and sampling tasks, and in both academia and industry the characterization of their usefulness is subject to active research. Any problem that can naturally be described as a weighted, undirected graph may be a particularly interesting candidate, since such a problem may be formulated a as quadratic unconstrained binary optimization (QUBO) instance, which is solvable on D-Wave's Chimera graph architecture. In this paper, we introduce a quantum-assisted finite-element method for design optimization. We show that we can minimize a shape-specific quantity, in our case a ray approximation of sound pressure at a specific position around an object, by manipulating the shape of this object. Our algorithm belongs to the class of quantum-assisted algorithms, as the optimization task runs iteratively on a D-Wave 2000Q quantum processing unit (QPU), whereby the evaluation and interpretation of the results happens classically. Our first and foremost aim is to explain how to represent and solve parts of these problems with the help of a QPU, and not to prove supremacy over existing classical finite-element algorithms for design optimization.Algorithms and the Foundations of Software technolog

Mathematical description of bacterial traveling pulses

The Keller-Segel system has been widely proposed as a model for bacterial waves driven by chemotactic processes. Current experiments on {\em E. coli} have shown precise structure of traveling pulses. We present here an alternative mathematical description of traveling pulses at a macroscopic scale. This modeling task is complemented with numerical simulations in accordance with the experimental observations. Our model is derived from an accurate kinetic description of the mesoscopic run-and-tumble process performed by bacteria. This model can account for recent experimental observations with {\em E. coli}. Qualitative agreements include the asymmetry of the pulse and transition in the collective behaviour (clustered motion versus dispersion). In addition we can capture quantitatively the main characteristics of the pulse such as the speed and the relative size of tails. This work opens several experimental and theoretical perspectives. Coefficients at the macroscopic level are derived from considerations at the cellular scale. For instance the stiffness of the signal integration process turns out to have a strong effect on collective motion. Furthermore the bottom-up scaling allows to perform preliminary mathematical analysis and write efficient numerical schemes. This model is intended as a predictive tool for the investigation of bacterial collective motion

Trail formation based on directed pheromone deposition

We propose an Individual-Based Model of ant-trail formation. The ants are modeled as self-propelled particles which deposit directed pheromones and interact with them through alignment interaction. The directed pheromones intend to model pieces of trails, while the alignment interaction translates the tendency for an ant to follow a trail when it meets it. Thanks to adequate quantitative descriptors of the trail patterns, the existence of a phase transition as the ant-pheromone interaction frequency is increased can be evidenced. Finally, we propose both kinetic and fluid descriptions of this model and analyze the capabilities of the fluid model to develop trail patterns. We observe that the development of patterns by fluid models require extra trail amplification mechanisms that are not needed at the Individual-Based Model level

Survey of coherent ∼1 Hz waves in Mercury's inner magnetosphere from MESSENGER observations

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95559/1/jgra22073.pd