ToPoliNano: Nanoarchitectures Design Made Real

Many facts about emerging nanotechnologies are yet to be assessed. There are still major concerns, for instance, about maximum achievable device density, or about which architecture is best fit for a specific application. Growing complexity requires taking into account many aspects of technology, application and architecture at the same time. Researchers face problems that are not new per se, but are now subject to very different constraints, that need to be captured by design tools. Among the emerging nanotechnologies, two-dimensional nanowire based arrays represent promising nanostructures, especially for massively parallel computing architectures. Few attempts have been done, aimed at giving the possibility to explore architectural solutions, deriving information from extensive and reliable nanoarray characterization. Moreover, in the nanotechnology arena there is still not a clear winner, so it is important to be able to target different technologies, not to miss the next big thing. We present a tool, ToPoliNano, that enables such a multi-technological characterization in terms of logic behavior, power and timing performance, area and layout constraints, on the basis of specific technological and topological descriptions. This tool can aid the design process, beside providing a comprehensive simulation framework for DC and timing simulations, and detailed power analysis. Design and simulation results will be shown for nanoarray-based circuits. ToPoliNano is the first real design tool that tackles the top down design of a circuit based on emerging technologie

Performance Evaluation for Hybrid Architectures

In this dissertation we discuss methologies for estimating the performance of applications on hybrid architectures, systems that include various types of computing resources (e.g. traditional general-purpose processors, chip multiprocessors, reconfigurable hardware). A common use of hybrid architectures will be to deploy coarse pipeline stages of application on suitable compute units with communication path for transferring data. The first problem we focus on relates to the sizing the data queues between the different processing elements of an hybrid system. Much of the discussion centers on our analytical models that can be used to derive performance metrics of interest such as, throughput and stalling probability for networks of processing elements with finite data buffering between them. We then discuss to the reliability of performance models. There we start by presenting scenarios where our analytical model is reliable, and introduce tests that can detect their inapplicability. As we transition into the question of reliability of performance models, we access the accuracy and applicability of various evaluation methods. We present results from our experiments to show the need for measuring and accounting for operating system effects in architectural modeling and estimation

The Genome and Methylome of a Subsocial Small Carpenter Bee, Ceratina calcarata

Understanding the evolution of animal societies, considered to be a major transition in evolution, is a key topic in evolutionary biology. Recently, new gateways for understanding social evolution have opened up due to advances in genomics, allowing for unprecedented opportunities in studying social behavior on a molecular level. In particular, highly eusocial insect species (caste-containing societies with nonreproductives that care for siblings) have taken center stage in studies of the molecular evolution of sociality. Despite advances in genomic studies of both solitary and eusocial insects, we still lack genomic resources for early insect societies. To study the genetic basis of social traits requires comparison of genomes from a diversity of organisms ranging from solitary to complex social forms. Here we present the genome of a subsocial bee, Ceratina calcarata. This study begins to address the types of genomic changes associated with the earliest origins of simple sociality using the small carpenter bee. Genes associated with lipid transport and DNA recombination have undergone positive selection in C. calcarata relative to other bee lineages. Furthermore, we provide the first methylome of a noneusocial bee. Ceratina calcarata contains the complete enzymatic toolkit for DNA methylation. As in the honey bee and many other holometabolous insects, DNA methylation is targeted to exons. The addition of this genome allows for new lines of research into the genetic and epigenetic precursors to complex social behaviors

JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions

BACKGROUND: Predicting complete protein-coding genes in human DNA remains a significant challenge. Though a number of promising approaches have been investigated, an ideal suite of tools has yet to emerge that can provide near perfect levels of sensitivity and specificity at the level of whole genes. As an incremental step in this direction, it is hoped that controlled gene finding experiments in the ENCODE regions will provide a more accurate view of the relative benefits of different strategies for modeling and predicting gene structures. RESULTS: Here we describe our general-purpose eukaryotic gene finding pipeline and its major components, as well as the methodological adaptations that we found necessary in accommodating human DNA in our pipeline, noting that a similar level of effort may be necessary by ourselves and others with similar pipelines whenever a new class of genomes is presented to the community for analysis. We also describe a number of controlled experiments involving the differential inclusion of various types of evidence and feature states into our models and the resulting impact these variations have had on predictive accuracy. CONCLUSION: While in the case of the non-comparative gene finders we found that adding model states to represent specific biological features did little to enhance predictive accuracy, for our evidence-based 'combiner' program the incorporation of additional evidence tracks tended to produce significant gains in accuracy for most evidence types, suggesting that improved modeling efforts at the hidden Markov model level are of relatively little value. We relate these findings to our current plans for future research

Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model

The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human–chimp–gorilla–orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human–chimp (4.1 ± 0.4 million years), and fairly large ancestral effective population sizes (65,000 ± 30,000 for the human–chimp ancestor and 45,000 ± 10,000 for the human–chimp–gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient