Charles Addo-Quaye

Thermal-aware floorplanning using genetic algorithms

In this work, we present a genetic algorithm based thermal-aware floorplanning framework that aims at reducing hot spots and distributing temperature evenly across a chip while optimizing the traditional design metric, chip area. The floorplanning problem is formulated as a genetic algorithm problem, and a tool called HotSpot is used to calculate floorplanning temperature based on the power dissipation, the physical dimension, and the location of modules. Area and/or temperature optimizations guide the genetic algorithm to generate the final fittest solution. The experimental results using MCNC benchmarks and a face detection chip show that our combined area and thermal optimization technique decreases the peak temperature sufficiently while providing floorplans that are as compact as the traditional area-oriented techniques.

Thermal-aware mapping and placement for 3-D NoC designs

Networks on chip (NoC) and 3D integrated circuits have been proposed as solutions to the ever-growing interconnect woes surrounding systems-on-chip. 3D designs however suffer from hotspot creation, due to the increase in the power density of parts of the chip. In this paper, we propose the use of a genetic algorithm for a thermal and communication aware mapping and placement of application tasks on 3D NoC environment. Our results show a significant reduction in system temperature when compared to a random mapping and placement, and provide an encouraging situation for migration to the 3D design space

Thermal-aware IP virtualization and placement for networks-on-chip architecture

Networks-on-chip (NoC), a new SoC paradigm, has been proposed as a solution to mitigate complex on-chip interconnect problems. NoC architecture consists of a collection of IP cores or processing elements (PEs) interconnected by on-chip switching fabrics or routers. Hardware virtualization, which maps logic processing units onto PEs, affects the power consumption of each PE and the communications among PEs. The communication among PEs affects the overall performance and router power consumption, and it depends on the placement of PEs. Therefore, the temperature distribution profile of the chip depends on the IP core virtualization and placement. In this paper, we present an IP virtualization and placement algorithm for generic regular network on chip (NoC) architecture. The algorithm attempts to achieve a thermal balanced design while minimizing the communication cost via placement. Our framework can also realize hardware virtualization which can further accomplish better performance. A case study on low density parity checks (LDPC) decoder is presented to evaluate our algorithm.

Physcomitrella patens DCL3 Is Required for 22–24 nt siRNA Accumulation, Suppression of Retrotransposon-Derived Transcripts, and Normal Development

Endogenous 24 nt short interfering RNAs (siRNAs), derived mostly from intergenic and repetitive genomic regions, constitute a major class of endogenous small RNAs in flowering plants. Accumulation of Arabidopsis thaliana 24 nt siRNAs requires the Dicer family member DCL3, and clear homologs of DCL3 exist in both flowering and non-flowering plants. However, the absence of a conspicuous 24 nt peak in the total RNA populations of several non-flowering plants has raised the question of whether this class of siRNAs might, in contrast to the ancient 21 nt microRNAs (miRNAs) and 21–22 nt trans-acting siRNAs (tasiRNAs), be an angiosperm-specific innovation. Analysis of non-miRNA, non-tasiRNA hotspots of small RNA production within the genome of the moss Physcomitrella patens revealed multiple loci that consistently produced a mixture of 21–24 nt siRNAs with a peak at 23 nt. These Pp23SR loci were significantly enriched in transposon content, depleted in overlap with annotated genes, and typified by dense concentrations of the 5-methyl cytosine (5 mC) DNA modification. Deep sequencing of small RNAs from two independent Ppdcl3 mutants showed that the P. patens DCL3 homolog is required for the accumulation of 22–24 nt siRNAs, but not 21 nt siRNAs, at Pp23SR loci. The 21 nt component of Pp23SR-derived siRNAs was also unaffected by a mutation in the RNA-dependent RNA polymerase mutant Pprdr6. Transcriptome-wide, Ppdcl3 mutants failed to accumulate 22–24 nt small RNAs from repetitive regions while transcripts from two abundant families of long terminal repeat (LTR) retrotransposon-associated reverse transcriptases were up-regulated. Ppdcl3 mutants also displayed an acceleration of leafy gametophore production, suggesting that repetitive siRNAs may play a role in the development of P. patens. We conclude that intergenic/repeat-derived siRNAs are indeed a broadly conserved, distinct class of small regulatory RNAs within land plants.

Expression of Small RNA in Aphis gossypii and Its Potential Role in the Resistance Interaction with Melon

Background The regulatory role of small RNAs (sRNAs) in various biological processes is an active area of investigation; however, there has been limited information available on the role of sRNAs in plant-insect interactions. This study was designed to identify sRNAs in cotton-melon aphid (Aphis gossypii) during the Vat-mediated resistance interaction with melon (Cucumis melo). Methodology/Principal Findings The role of miRNAs was investigated in response to aphid herbivory, during both resistant and susceptible interactions. sRNA libraries made from A. gossypii tissues feeding on Vat+ and Vat− plants revealed an unexpected abundance of 27 nt long sRNA sequences in the aphids feeding on Vat+ plants. Eighty-one conserved microRNAs (miRNAs), twelve aphid-specific miRNAs, and nine novel candidate miRNAs were also identified. Plant miRNAs found in the aphid libraries were most likely ingested during phloem feeding. The presence of novel miRNAs was verified by qPCR experiments in both resistant Vat+ and susceptible Vat− interactions. The comparative analyses revealed that novel miRNAs were differentially regulated during the resistant and susceptible interactions. Gene targets predicted for the miRNAs identified in this study by in silico analyses revealed their involvement in morphogenesis and anatomical structure determination, signal transduction pathways, cell differentiation and catabolic processes. Conclusion/Significance In this study, conserved and novel miRNAs were reported in A. gossypii. Deep sequencing data showed differences in the abundance of miRNAs and piRNA-like sequences in A. gossypii. Quantitative RT-PCR revealed that A. gossypii miRNAs were differentially regulated during resistant and susceptible interactions. Aphids can also ingest plant miRNAs during phloem feeding that are stable in the insect.

Re-Evaluation of Reportedly Metal Tolerant Arabidopsis thaliana Accessions.

Santa Clara, Limeport, and Berkeley are Arabidopsis thaliana accessions previously identified as diversely metal resistant. Yet these same accessions were determined to be genetically indistinguishable from the metal sensitive Col-0. We robustly tested tolerance for Zn, Ni and Cu, and genetic relatedness by growing these accessions under a range of Ni, Zn and Cu concentrations for three durations in multiple replicates. Neither metal resistance nor variance in growth were detected between them and Col-0. We re-sequenced the genomes of these accessions and all stocks available for each accession. In all cases they were nearly indistinguishable from the standard laboratory accession Col-0. As Santa Clara was allegedly collected from the Jasper Ridge serpentine outcrop in California, USA we investigated the possibility of extant A. thaliana populations adapted to serpentine soils. Botanically vouchered Arabidopsis accessions in the Jepson database were overlaid with soil maps of California. This provided no evidence of A. thaliana collections from serpentine sites in California. Thus, our work demonstrates that the Santa Clara, Berkeley and Limeport accessions are not metal tolerant, not genetically distinct from Col-0, and that there are no known serpentine adapted populations or accessions of A. thaliana.