Complementary approaches to understanding the plant circadian clock

Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24-hour day/night cycle. The clock of the green alga Ostreococcus tauri is the simplest plant clock discovered so far. Its many advantages as an experimental system facilitate the testing of computational predictions. We present a model of the Ostreococcus clock in the stochastic process algebra Bio-PEPA and exploit its mapping to different analysis techniques, such as ordinary differential equations, stochastic simulation algorithms and model-checking. The small number of molecules reported for this system tests the limits of the continuous approximation underlying differential equations. We investigate the difference between continuous-deterministic and discrete-stochastic approaches. Stochastic simulation and model-checking allow us to formulate new hypotheses on the system behaviour, such as the presence of self-sustained oscillations in single cells under constant light conditions. We investigate how to model the timing of dawn and dusk in the context of model-checking, which we use to compute how the probability distributions of key biochemical species change over time. These show that the relative variation in expression level is smallest at the time of peak expression, making peak time an optimal experimental phase marker. Building on these analyses, we use approaches from evolutionary systems biology to investigate how changes in the rate of mRNA degradation impacts the phase of a key protein likely to affect fitness. We explore how robust this circadian clock is towards such potential mutational changes in its underlying biochemistry. Our work shows that multiple approaches lead to a more complete understanding of the clock

A Genetic Algorithm for Power-Aware Virtual Machine Allocation in Private Cloud

Energy efficiency has become an important measurement of scheduling algorithm for private cloud. The challenge is trade-off between minimizing of energy consumption and satisfying Quality of Service (QoS) (e.g. performance or resource availability on time for reservation request). We consider resource needs in context of a private cloud system to provide resources for applications in teaching and researching. In which users request computing resources for laboratory classes at start times and non-interrupted duration in some hours in prior. Many previous works are based on migrating techniques to move online virtual machines (VMs) from low utilization hosts and turn these hosts off to reduce energy consumption. However, the techniques for migration of VMs could not use in our case. In this paper, a genetic algorithm for power-aware in scheduling of resource allocation (GAPA) has been proposed to solve the static virtual machine allocation problem (SVMAP). Due to limited resources (i.e. memory) for executing simulation, we created a workload that contains a sample of one-day timetable of lab hours in our university. We evaluate the GAPA and a baseline scheduling algorithm (BFD), which sorts list of virtual machines in start time (i.e. earliest start time first) and using best-fit decreasing (i.e. least increased power consumption) algorithm, for solving the same SVMAP. As a result, the GAPA algorithm obtains total energy consumption is lower than the baseline algorithm on simulated experimentation.Comment: 10 page

Phase transitions in Pareto optimal complex networks

The organization of interactions in complex systems can be described by networks connecting different units. These graphs are useful representations of the local and global complexity of the underlying systems. The origin of their topological structure can be diverse, resulting from different mechanisms including multiplicative processes and optimization. In spatial networks or in graphs where cost constraints are at work, as it occurs in a plethora of situations from power grids to the wiring of neurons in the brain, optimization plays an important part in shaping their organization. In this paper we study network designs resulting from a Pareto optimization process, where different simultaneous constraints are the targets of selection. We analyze three variations on a problem finding phase transitions of different kinds. Distinct phases are associated to different arrangements of the connections; but the need of drastic topological changes does not determine the presence, nor the nature of the phase transitions encountered. Instead, the functions under optimization do play a determinant role. This reinforces the view that phase transitions do not arise from intrinsic properties of a system alone, but from the interplay of that system with its external constraints.Comment: 14 pages, 7 figure