Putting reaction-diffusion systems into port-Hamiltonian framework

Reaction-diffusion systems model the evolution of the constituents distributed in space under the influence of chemical reactions and diffusion [6], [10]. These systems arise naturally in chemistry [5], but can also be used to model dynamical processes beyond the realm of chemistry such as biology, ecology, geology, and physics. In this paper, by adopting the viewpoint of port-controlled Hamiltonian systems [7] we cast reaction-diffusion systems into the portHamiltonian framework. Aside from offering conceptually a clear geometric interpretation formalized by a Stokes-Dirac structure [8], a port-Hamiltonian perspective allows to treat these dissipative systems as interconnected and thus makes their analysis, both quantitative and qualitative, more accessible from a modern dynamical systems and control theory point of view. This modeling approach permits us to draw immediately some conclusions regarding passivity and stability of reaction-diffusion systems. It is well-known that adding diffusion to the reaction system can generate behaviors absent in the ode case. This primarily pertains to the problem of diffusion-driven instability which constitutes the basis of Turing’s mechanism for pattern formation [11], [5]. Here the treatment of reaction-diffusion systems as dissipative distributed portHamiltonian systems could prove to be instrumental in supply of the results on absorbing sets, the existence of the maximal attractor and stability analysis. Furthermore, by adopting a discrete differential geometrybased approach [9] and discretizing the reaction-diffusion system in port-Hamiltonian form, apart from preserving a geometric structure, a compartmental model analogous to the standard one [1], [2] is obtaine

Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. 155-181).This thesis describes the development and application of a new tool for profiling marine microbial communities. Chapter 1 places the tool in the context of the range of methods used currently. Chapter 2 describes the development and validation of the "genome proxy" microarray, which targeted marine microbial genomes and genome fragments using sets of 70-mer oligonucleotide probes. In a natural community background, array signal was highly linearly correlated to target cell abundance (R² of 1.0), with a dynamic range from 10²-10⁶ cells/ml. Genotypes with >/=~80% average nucleotide identity to those targeted crosshybridized to target probesets but produced distinct, diagnostic patterns of hybridization. Chapter 3 describes the development an expanded array, targeting 268 microbial genotypes, and its use in profiling 57 samples from Monterey Bay. Comparison of array and pyrosequence data for three samples showed a strong linear correlation between target abundance using the two methods (R²=0.85- 0.91). Array profiles clustered into shallow versus deep, and the majority of targets showed depth-specific distributions consistent with previous observations. Although no correlation was observed to oceanographic season, bloom signatures were evident. Array-based insights into population structure suggested the existence of ecotypes among uncultured clades. Chapter 4 summarizes the work and discusses future directions.by Virginia Rich.Ph.D

Anales del XIII Congreso Argentino de Ciencias de la Computación (CACIC)

Contenido: Arquitecturas de computadoras Sistemas embebidos Arquitecturas orientadas a servicios (SOA) Redes de comunicaciones Redes heterogéneas Redes de Avanzada Redes inalámbricas Redes móviles Redes activas Administración y monitoreo de redes y servicios Calidad de Servicio (QoS, SLAs) Seguridad informática y autenticación, privacidad Infraestructura para firma digital y certificados digitales Análisis y detección de vulnerabilidades Sistemas operativos Sistemas P2P Middleware Infraestructura para grid Servicios de integración (Web Services o .Net)Red de Universidades con Carreras en Informática (RedUNCI

Anales del XIII Congreso Argentino de Ciencias de la Computación (CACIC)

Contenido: Arquitecturas de computadoras Sistemas embebidos Arquitecturas orientadas a servicios (SOA) Redes de comunicaciones Redes heterogéneas Redes de Avanzada Redes inalámbricas Redes móviles Redes activas Administración y monitoreo de redes y servicios Calidad de Servicio (QoS, SLAs) Seguridad informática y autenticación, privacidad Infraestructura para firma digital y certificados digitales Análisis y detección de vulnerabilidades Sistemas operativos Sistemas P2P Middleware Infraestructura para grid Servicios de integración (Web Services o .Net)Red de Universidades con Carreras en Informática (RedUNCI

Microbial metatranscriptomics : towards understanding microbial gene expression and regulation in natural habitats

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 195-212).Metagenomic research has paved the way for a comprehensive understanding of the microbial gene parts list in nature, but a full understanding of microbial gene expression, regulation, and ecology remains a challenge. In this thesis, I present the methodological foundations and applications of deep sequencing-based metatranscriptomics, for profiling community transcriptomes on spatial and temporal scales. Several findings and relevant hypotheses have emerged from this work. I show that transcripts of house-keeping genes necessary for the maintenance of basic cellular machinery are abundant and readily detectable. Habitat-specific transcripts are also discernible when comparing community transcriptomes along distinct geochemical conditions. Normalization of detected transcripts to their corresponding gene abundance suggests that numerically less abundant microorganisms may nevertheless contribute actively to ecologically relevant processes. Along the same lines, it is a recurrent observation that many transcripts are of unknown function or phylogenetic origin, and have not been detected in genomic/metagenomic data sets. These novel sequences may be derived from less abundant species or variable genomic regions that are not represented in sequenced genomes. Furthermore, I applied metatranscriptomics in a microcosm experiment, where a deep water mixing event was simulated and community transcriptomes were monitored over the course of 27 hours. Relative to the control, the treatment sample showed signals of stimulated photosynthesis and carbon fixation by phytoplankton cells, enhanced chemotactic, motility, and growth responses of heterotrophic bacteria, as well as possibly altered phage-host interactions. Such experimental metatranscriptomic studies are well suited to reveal how microorganisms respond during the early stages of environmental perturbations. Finally, I show that metatranscriptomic data sets contain a wealth of highly expressed small RNAs (sRNAs), transcripts that are not translated to proteins but instead function as regulators. I propose a bioinformatics pipeline for identifying these sRNA elements, characterizing their structures and genomic contexts, and predicting possible regulatory targets. The extraordinary abundance of some of the identified sRNAs raises questions about their ecological function, which warrants further biochemical and genetic studies. Overall, this work has extended our knowledge of functional potentials and in situ gene expression of natural microbial communities.by Yanmei Shi.Ph.D