High Performance Algorithms for Counting Collisions and Pairwise Interactions

The problem of counting collisions or interactions is common in areas as computer graphics and scientific simulations. Since it is a major bottleneck in applications of these areas, a lot of research has been carried out on such subject, mainly focused on techniques that allow calculations to be performed within pruned sets of objects. This paper focuses on how interaction calculation (such as collisions) within these sets can be done more efficiently than existing approaches. Two algorithms are proposed: a sequential algorithm that has linear complexity at the cost of high memory usage; and a parallel algorithm, mathematically proved to be correct, that manages to use GPU resources more efficiently than existing approaches. The proposed and existing algorithms were implemented, and experiments show a speedup of 21.7 for the sequential algorithm (on small problem size), and 1.12 for the parallel proposal (large problem size). By improving interaction calculation, this work contributes to research areas that promote interconnection in the modern world, such as computer graphics and robotics.Comment: Accepted in ICCS 2019 and published in Springer's LNCS series. Supplementary content at https://mjsaldanha.com/articles/1-hpc-ssp

Dewetting of Glassy Polymer Films

Dynamics and morphology of hole growth in a film of power hardening viscoplastic solid (yield stress ~ [strain-rate]^n) is investigated. At short-times the growth is exponential and depends on the initial hole size. At long-times, for n > 1/3, the growth is exponential with a different exponent. However, for n < 1/3, the hole growth slows; the hole radius approaches an asymptotic value as time tends to infinity. The rim shape is highly asymmetric, the height of which has a power law dependence on the hole radius (exponent close to unity for 0.25 < n < 0.4). The above results explain recent intriguing experiments of Reiter, Phys. Rev. Lett, 87, 186101 (2001).Comment: 4 pages, 5 figures, RevTe

Protein-RNA and protein-protein interactions mediate association of human EST1A/SMG6 with telomerase

The human EST1A/SMG6 polypeptide physically interacts with the chromosome end replication enzyme telomerase. In an attempt to better understand hEST1A function, we have started to dissect the molecular interactions between hEST1A and telomerase. Here, we demonstrate that the interaction between hEST1A and telomerase is mediated by protein-RNA and protein-protein contacts. We identify a domain within hEST1A that binds the telomerase RNA moiety hTR while full-length hEST1A establishes in addition RNase-resistant and hTR-independent protein-protein contacts with the human telomerase reverse transcriptase polypeptide (TERT). Conversely, within hTERT, we identify a hEST1A interaction domain, which comprises hTR-binding activity and RNA-independent hEST1A-binding activity. Purified, recombinant hEST1A binds the telomerase RNA moiety (hTR) with high affinity (apparent overall K(d) = 25 nM) but low specificity. We propose that hEST1A assembles specifically with telomerase in the context of the hTR-hTERT ribonucleoprotein, through the high affinity of hEST1A for hTR and specific protein-protein contacts with hTERT

Evolution of shell structure in neutron-rich calcium isotopes

We employ interactions from chiral effective field theory and compute the binding energies and low-lying excitations of calcium isotopes with the coupled-cluster method. Effects of three-nucleon forces are included phenomenologically as in-medium two-nucleon interactions, and the coupling to the particle continuum is taken into account using a Berggren basis. The computed ground-state energies and the low-lying 2+ states for the isotopes 42,48,50,52Ca are in good agreement with data, and we predict the excitation energy of the first 2+ state in 54Ca at 1.9 MeV, displaying only a weak sub-shell closure. In the odd-mass nuclei 53,55,61Ca we find that the positive parity states deviate strongly from the naive shell model.Comment: 5 pages, 4 figures; small correction of effective 3NF and slight change of the corresponding parameters; updated figures and tables; main results and conclusions unchange

Large Deformation Effects in the N = Z 44Ti Compound Nucleus

The N = Z 44Ti* nucleus has been populated in Fusion Evaporation process at very high excitation energies and angular momenta using two entrance channels with different mass-asymmetry. The deformation effects in the rapidly rotating nuclei have been investigated through the energy distribution of the alpha-particle combined to statistical-model calculations. In the case of low-multiplicity events, the ratio between first particle emitted has been measured and shows significant disagreement with the predictions of the statistical-model. This may explain The large discrepancies observed in proton energy spectra measured in previous experiments performed in the same mass region.Comment: Proceeding of the 10th International Conference on Nuclear Reaction Mechanisms, Varenna Italy, June 9-13 2003. 10 pages, 6 figures, 1 tabl

Does Collocation Inform the Impact of Collaboration?

Background It has been shown that large interdisciplinary teams working across geography are more likely to be impactful. We asked whether the physical proximity of collaborators remained a strong predictor of the scientific impact of their research as measured by citations of the resulting publications. Methodology/Principal Findings Articles published by Harvard investigators from 1993 to 2003 with at least two authors were identified in the domain of biomedical science. Each collaboration was geocoded to the precise three-dimensional location of its authors. Physical distances between any two coauthors were calculated and associated with corresponding citations. Relationship between distance of coauthors and citations for four author relationships (first-last, first-middle, last-middle, and middle-middle) were investigated at different spatial scales. At all sizes of collaborations (from two authors to dozens of authors), geographical proximity between first and last author is highly informative of impact at the microscale (i.e. within building) and beyond. The mean citation for first-last author relationship decreased as the distance between them increased in less than one km range as well as in the three categorized ranges (in the same building, same city, or different city). Such a trend was not seen in other three author relationships. Conclusions/Significance Despite the positive impact of emerging communication technologies on scientific research, our results provide striking evidence for the role of physical proximity as a predictor of the impact of collaborations.Ewing Marion Kauffman FoundationHarvard University. Office of the Provost (1992-

Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME†

Summary: Analysing large amounts of data generated by next-generation sequencing (NGS) technologies is difficult for researchers or clinicians without computational skills. They are often compelled to delegate this task to computer biologists working with command line utilities. The availability of easy-to-use tools will become essential with the generalization of NGS in research and diagnosis. It will enable investigators to handle much more of the analysis. Here, we describe Knime4Bio, a set of custom nodes for the KNIME (The Konstanz Information Miner) interactive graphical workbench, for the interpretation of large biological datasets. We demonstrate that this tool can be utilized to quickly retrieve previously published scientific findings

Large scale variation in DNA copy number in chicken breeds

Background Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. Here we describe a genome-wide CNV study using array comparative genomic hybridization (aCGH) in a wide variety of chicken breeds. Results We identified 3,154 CNVs, grouped into 1,556 CNV regions (CNVRs). Thirty percent of the CNVs were detected in at least 2 individuals. The average size of the CNVs detected was 46.3 kb with the largest CNV, located on GGAZ, being 4.3 Mb. Approximately 75% of the CNVs are copy number losses relatively to the Red Jungle Fowl reference genome. The genome coverage of CNVRs in this study is 60 Mb, which represents almost 5.4% of the chicken genome. In particular large gene families such as the keratin gene family and the MHC show extensive CNV. Conclusions A relative large group of the CNVs are line-specific, several of which were previously shown to be related to the causative mutation for a number of phenotypic variants. The chance that inter-specific CNVs fall into CNVRs detected in chicken is related to the evolutionary distance between the species. Our results provide a valuable resource for the study of genetic and phenotypic variation in this phenotypically diverse species