Search results for "Computer simulation"
showing 10 items of 1054 documents
The C-terminal region of the Hot1 transcription factor binds GGGACAAA-related sequences in the promoter of its target genes
2015
Response to hyperosmotic stress in the yeast Saccharomyces cerevisiae involves the participation of the general stress response mediated by Msn2/4 transcription factors and the HOG pathway. One of the transcription factors activated through this pathway is Hot1, which contributes to the control of the expression of several genes involved in glycerol synthesis and flux, or in other functions related to adaptation to adverse conditions. This work provides new data about the interaction mechanism of this transcription factor with DNA. By means of one-hybrid and electrophoretic mobility assays, we demonstrate that the C-terminal region, which corresponds to amino acids 610-719, is the DNA-bindi…
Assessment of Salmonella and Listeria monocytogenes level in ready-to-cook poultry meat: Effect of various high pressure treatments and potassium lac…
2014
International audience; The objective of this study was to develop a probabilistic model in order to determine the contamination level of Salmonella and Listeria monocytogenes in ready-to-cook poultry meat, after a high pressure (HP) treatment. The model included four steps: i) Reception of raw meat materials, mincing and mixing meat, ii) Partitioning and packaging into 200-g modified atmosphere packs, iii) High pressure treatment of the meat, and iv) Storage in chilled conditions until the end of the shelf-life. The model excluded the cooking step and consumption at consumer's home as cooking practices and heating times are highly variable. The initial contamination level of Salmonella and…
Transport of Mobile Particles in an Immobile Environment: Computer Simulations of Sodium Silicates
2007
Molecular dynamics (MD) simulations of various sodium silicate melts, (Na2O)x(SiO2) with x=2, 3, 20, are presented. In these systems, the mobility of sodium ions is much higher, often by orders of magnitude, than that of the silicon and oxygen atoms forming a tetrahedral network structure. We show that the high mobility of sodium is intimately related to the chemical ordering in sodium silicates. A network of percolating sodium-rich channels is formed in the static structure that serve as diffusion channels for the sodium ions. This channel network is revealed in static structure factors by a prepeak at the wavenumber q=0.95 A-1. Inelastic neutron scattering experiments of sodium silicate m…
An adaptive multimeme algorithm for designing HIV multidrug therapies.
2007
This paper proposes a period representation for modeling the multidrug HIV therapies and an Adaptive Multimeme Algorithm (AMmA) for designing the optimal therapy. The period representation offers benefits in terms of flexibility and reduction in dimensionality compared to the binary representation. The AMmA is a memetic algorithm which employs a list of three local searchers adaptively activated by an evolutionary framework. These local searchers, having different features according to the exploration logic and the pivot rule, have the role of exploring the decision space from different and complementary perspectives and, thus, assisting the standard evolutionary operators in the optimizati…
CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding
2014
The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome, even for simulated data. Moreover, even slight improvements in this area are important but challenging, and usually require significantly more computational endeavor. In this paper, we present CUSHAW3, an open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. In this aligner, we have investigated a hybrid seeding approach to improve alignment quality, which incorp…
Self-organization of active particles by quorum sensing rules
2018
Many microorganisms regulate their behaviour according to the density of neighbours. Such quorum sensing is important for the communication and organisation within bacterial populations. In contrast to living systems, where quorum sensing is determined by biochemical processes, the behaviour of synthetic active particles can be controlled by external fields. Accordingly they allow to investigate how variations of a density-dependent particle response affect their self-organisation. Here we experimentally and numerically demonstrate this concept using a suspension of light-activated active particles whose motility is individually controlled by an external feedback-loop, realised by a particl…
Development of a Hybrid Method to Generate Gravito-Inertial Cues for Motion Platforms in Highly Immersive Environments
2021
Motion platforms have been widely used in Virtual Reality (VR) systems for decades to simulate motion in virtual environments, and they have several applications in emerging fields such as driving assistance systems, vehicle automation and road risk management. Currently, the development of new VR immersive systems faces unique challenges to respond to the user’s requirements, such as introducing high-resolution 360° panoramic images and videos. With this type of visual information, it is much more complicated to apply the traditional methods of generating motion cues, since it is generally not possible to calculate the necessary corresponding motion properties that are needed to …
Integration of onshore and offshore seismic arrays to study the seismicity of the Calabrian Region: a two steps automatic procedure for the identific…
2014
Abstract. We plan to deploy in the Taranto Gulf some Ocean Bottom broadband Seismometer with Hydrophones. Our aim is to investigate the offshore seismicity of the Sibari Gulf. The seismographic network optimization consists in the identification of the optimal sites for the installation of the offshore stations, which is a crucial factor for the success of the monitoring campaign. In this paper, we propose a two steps automatic procedure for the identification of the best stations geometry. In the first step, based on the application of a set of a priori criteria, the suitable sites to host the ocean bottom seismic stations are identified. In the second step, the network improvement is eval…
Analysis of motor control and behavior in multi agent systems by means of artificial neural networks
2004
Abstract This article gives a short introduction to Self-Organizing Maps, a particular form of Artificial Neural Networks and shows by some examples, how these approaches can be used in order to analyze and visualize time series data originating from complex systems. The methods shown in this article have originally been developed for the analysis of RoboCup robot soccer games, a special kind of so-called Multi Agent Systems. Although this application has no direct connection to biomechanics, the examples shown here may give an impression of the abilities of Neural Networks in the field of Time Series Analysis in general. Because of the abstractness of the methods, it appears to be very lik…
A Study of the Simulated Evolution of the Spectral Sensitivity of Visual Agent Receptors
2001
In this article we study a model for the evolution of the spectral sensitivity of visual receptors for agents in a continuous virtual environment. The model uses a genetic algorithm (GA) to evolve the agent sensors along with the control of the agents by requiring the agents to solve certain tasks in the simulation environment. The properties of the evolved sensors are analyzed for different scenarios. In particular, it is shown that the GA is able to find a balance between sensor costs and agent performance in such a way that the spectral sensor sensitivity reflects the emission spectrum of the target objects and that the capability of the sensors to evolve can help the agents significantl…