33 research outputs found
Simit language extensions with applications to lattice QCD
No full textThesis: M. Eng. in Computer Science and Engineering, Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2016.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 155-160).This thesis presents language extensions to Simit, a language for linear algebra on graphs. Currently, Simit doesn't efficiently handle lattice graphs (regular grids). This thesis defines a stencil assembly construct to capture linear algebra on these graphs. A prototype compiler with a Halide backend demonstrates that these extensions capture the full structure of linear algebra applications operating on lattices, are easily schedulable, and achieve comparable performance to existing methods. Many physical simulations take the form of linear algebra on lattices. This thesis reviews Lattice QCD as a representative example of such a class of applications and identifies the structure of the linear algebra involved. In this application, iterative inversion of the Dirac matrix dominates the runtime, and time-intensive hand-optimization of inverters for specific forms of the matrix limit further research. This thesis implements this computation using the language extensions, while demonstrating competitive performance to existing methods.by Gurtej Kanwar.M. Eng. in Computer Science and Engineerin
Local adaptation in the land snail, Cepaea nemoralis : exploratory genetic analysis with AFLP markers
No full textThe polymorphic land snail, Cepaea nemoralis (L.) shows a higher prevalence of yellow, banded shells in open habitats and non-yellow (Pink and brown), unbanded shells in woodland. Shell characters are genetically controlled and this pattern of local adaptation is geographically repeated, implying selection is operating. However, no molecular evidence exists to support this claim. An FSI-outlier approach revealed six AFLP loci with elevated levels of differentiation compared to neutral expectations - three in one open-woodland population pair and another three in another pair - providing evidence of positive selection operating between open and woodland habitats. The non-repeated nature of outliers suggests tlie two sites are adapting to habitats by different strategies. Pairwise F SI and a neighbour-joining tree show the two study sites to be genetically divergent from each other, probably because they are geographically isolated (~60km apart) and there are low levels of differentiation between habitats within each pair. An attempt was made at creating a preliminary AFLP linkage map for C. nemoralis using a pseudo-testcross design. A mapping population segregating for shell colour and mid-banding was established but only three, small AFLP linkage groups were identified in one of the parental maps and none in the other. This was largely due to a small proportion of loci being in testcross configuration. In addition, morph frequency data were compared to historic records to look for changes in morph/allele frequency over time. All open populations showed significant differences in colour or banding, whereas no significant differences were found in any woodland populations. This could be an adaptive response to differences in habitat stability between open and woodland, the latter being more stable. Alternatively, balancing selection could be operating in woodlands and open populations fluctuate randomly. The difference in morph frequency stability between habitats was not reflected in allele frequency changes (assuming Hardy-Weinberg equilibrium). 1.EThOS - Electronic Theses Online ServiceGBUnited Kingdo
Data from: Characterising a hybrid zone between a cryptic species pair of freshwater snails
No full textCharacterising hybrid zones and their dynamics is a central goal in evolutionary biology, but this is particularly challenging for morphologically cryptic species. The lack of conspicuous divergence between parental types means intermediate hybrid forms often go undetected. We aimed to detect and characterise a suspected hybrid zone between a pair of morphologically cryptic lineages of the freshwater snail, Radix. We sampled Radix from across a contact zone between two mitochondrial lineages (Radix balthica and an undescribed lineage termed MOTU3) and detected admixture between two nuclear genotype clusters, which were significantly but not categorically associated with the mitochondrial lineages. In a model selection approach, we show that the admixture cline is best explained by an interaction between precipitation and temperature gradients over the area, rather than geographic distance. We thus hypothesise that the correlation with climatic gradients suggests environmental selection has played a role in maintaining the hybrid zone. In a 2050 climate change scenario, we furthermore predict an expansion of one of the nuclear clusters and a widening of the hybrid zone as the climate warms and dries
Performance and Emission Improvements of 4 - Stroke Multi- Cylinder CI- Engine by Use of DMCEGM-Diesel Blends
No full textABSTRACT Dimethyl carbonate (DMC) and ethylene glycol monoacetate (EGM) are two hopeful alternative fuels as well as fuel additives to improve performance and emissions in CI engine, due to their high oxygen content. This paper presents an experimental study on their effects on the performance and emissions characteristics of CI engine. Test results show that brake thermal efficiency for the DMCEGM05 blends is higher than that of diesel blend while in the case of DMCEGM10 and DMCEGM15 blends it is lower. BSEC of DMCEGM-diesel blends show decreasing trend for increasing brake power or load. As engine load raises the values of EGT increase. Maximum EGT is measured at full load conditions for all blends. CO emissions can be remarkably reduced with the addition of DMC and EGM to diesel. Minimum CO is found for DMCEGM10 fuel. The blends of diesel with 10% DMC and EGM by volume is the best fraction for reduction of smoke and CO emissions. The obtained results show that the fuel which effectively reduces the CO emissions is less effective in reducing the NO x emissions. All these results indicate the potential of the DMC-EGM-diesel blends for clean combustion in diesel engine. The blends of diesel with 15% DMC and EGM by volume is the best fraction for reduction of smoke and CO emissions
POPS_predictionfile
No full textThis file contains climate prediction data for each of the individuals/sample sites in the core population set, in the year 2050. This file was used as input for the POPS prediction utility
co1_outgroups_aln
No full textThis is a mega file (for use with the program MEGA: http://www.megasoftware.net/) containing aligned cytochrome c oxidase subunit 1 (COI) sequence data from Radix (and other) snails
act1a_aln
No full textThis is a fasta file containing aligned Actin-1a (act1a) sequence data from Radix snails
Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (<i>Poecilia mexicana</i>)
No full textReplicated ecological gradients are prime systems to study processes of molecularevolution underlying ecological divergence. Here, we investigated the repeated adaptation of the neotropical fish Poecilia mexicana to habitats containing toxic hydrogen sulphide (H2S) and compared two population pairs of sulphide-adapted and ancestral fishby sequencing population pools of >200 individuals (Pool-Seq). We inferred the evolutionary processes shaping divergence and tested the hypothesis of increase of parallelismfrom SNPs to molecular pathways. Coalescence analyses showed that the divergenceoccurred in the face of substantial bidirectional gene flow. Population divergenceinvolved many short, widely dispersed regions across the genome. Analyses of allele frequency spectra suggest that differentiation at most loci was driven by divergent selection, followed by a selection-mediated reduction of gene flow. Reconstructing allelicstate changes suggested that selection acted mainly upon de novo mutations in the sulphide-adapted populations. Using a corrected Jaccard index to quantify parallel evolution, we found a negligible proportion of statistically significant parallel evolution ofJcorr = 0.0032 at the level of SNPs, divergent genome regions (Jcorr = 0.0061) and genestherein (Jcorr = 0.0091). At the level of metabolic pathways, the overlap was Jcorr = 0.2545,indicating increasing parallelism with increasing level of biological integration. Themajority of pathways contained positively selected genes in both sulphide populations.Hence, adaptation to sulphidic habitats necessitated adjustments throughout the genome. The largely unique evolutionary trajectories may be explained by a high proportionof de novo mutations driving the divergence. Our findings favour Gould’s view that evolution is often the unrepeatable result of stochastic events with highly contingent effects. </p
POPS_geo_dist_circle
No full textThis is a file containing pairwise distances between each individual/sample site calculated using the greater circles algorithm in POPS
