2016: Year in Review

January 31, 2017

Our 10 top news stories from 2016:

BU Researchers Discover How RNA Editing May Promote Tumor Growth

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A Boston University study utilizing computing resources housed at MGHPCC provides insight on the potential role played by RNA (ribonucleic acid) editing in cancer. MORE

Award Winning Innovation in Analytics​

InTp1kc-767x575@2xIOMICS Corp, a member of the C3DDB Biotech Industry Access Program, is named to Drexel and Analytics 50 for their FUSION Analytics Platform (TM), a cloud-based software system for prescriptive analytics and rapid prototyping of advanced decision models for use in chemical engineering, medical research, and clinical care. MORE

Holyoke Codes

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Holyoke Codes, the collaborative partnership between MGHPCC, Girls Inc. of Holyoke, local graphic design team Sweet and Fizzy, the Commonwealth Alliance for Information Technology Education (CAITE), and New England Regional Developers (NERDs), continues to hold lots of great classes and events geared towards getting more kids involved in coding, robotics, and technology. MORE

New England’s First experimental, Solar Powered Data Center Opens for Business
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The MGHPCC, its member universities and the City of Holyoke launch the Mass Net Zero Data Center (MassNZ) — an experimental, solar-powered, micro data center that is the first of its kind in New England, with a ribbon cutting in February 2016. MORE

Grass to Gas

University of Massachusetts Amherst computational chemist Scott Auerbach uses computers at the MGHPCC in research that helps him understand and optimize the process of producing fuels such as gasoline from plant biomass instead of petroleum. MORE

From Games to Brains

Screen Shot 2017-01-24 at 11.02.46 AMResearchers at Northeastern University are using computers at the MGHPCC to improve the performance of a popular medical imaging tool which estimates 3D light distribution in biological tissue using GPU technology to simultaneously simulate the paths of large numbers of independent photons. MORE

MGHPCC Expands Capacity

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In June 2016 the MGHPCC announces it will be expanding capacity to meet growing demand for computationally intensive scientific research at the state-of-the-art facility, the first of a series of additions anticipated by the data center’s long-term growth plan. MORE

Up in the Air

We report work from researchers at the Massachusetts Institute of Technology developing and using complex computer models housed at the MGHPCC to explore how atmospheric aerosols impact climate. MORE

UMASS Dartmouth hosts second annual state wide HPC day

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In May 2016 we get the chance to meet lots of MGHPCC users at the second annual UMass HPC Day hosted by UMass Dartmouth’s Center for Scientific Computing & Visualization Research. MORE

Teaching Computers to Identify Odors

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The Harvard Gazette reports work using computers housed at the MGHPCC to better understand how brains recognize specific smells. MORE

A Selection of 2016 Publications

Andrey Alekseenko, Olga Kononova, Yaroslav Kholodov, Kenneth A. Marx, Valeri Barsegov (2016), SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies, Journal of Computational Chemistry,  doi: 10.1002/jcc.24368
M.R.M. Assis and L.F. Bittencourt (2016), A survey on cloud federation architectures: Identifying functional and non-functional propertiesJournal of Network and Computer Applications
Volume 72, Pages 51–71, doi: 10.1016/j.jnca.2016.06.014
Shao-Yu Chen, Thomas Goldstein, Dhandapani Venkataraman, Ashwin Ramasubramaniam, and Jun Yan (2016), Activation of New Raman Modes by Inversion Symmetry Breaking in Type II Weyl Semimetal Candidate T′-MoTe2, Nano. Letters, doi: 10.1021/acs.nanolett.6b02666
Moti Fridman, Vlada Artel, Anna Peled, Shir Shahal, Ashwin Ramasubramaniam, Doron Naveh (2016), Realizing Giant Magneto-Optical Effects in 3D Topological Insulators Without Magnetic Fields, arXiv: 1607.04823
Li Guo, Guoyi Zhao, Jin-Rong Xu, H. Corby Kistler, Lixin Gao, Li-Jun Ma (2016), Compartmentalized gene regulatory network of the pathogenic fungusFusarium graminearum, New Phytologist, doi: 10.1111/nph.13912
Julian Gutierrez, Fanny Nina-Paravecino, David Kaeli (2016), A fast level-set segmentation algorithm for image processing designed for parallel architectures, IA^3 ’16 Proceedings of the Sixth Workshop on Irregular Applications: Architectures and Algorithms, pages 66-69, doi: 10.1109/IA3.2016.017
Douglas M. Hall, Isaac R. Bruss, Justin R. Barone & Gregory M. Grason (2016), Morphology selection via geometric frustration in chiral filament bundles, Nature Materials, doi: 10.1038/nmat4598
G.M. Hall and G.M. Grason (2016), How geometric frustration shapes twisted fibers, inside and out: Competing morphologies of chiral filament assembly, arXiv: 1612.02422
Chang-Tsan Lu, Asanka Weerasinghe, Dimitrios Maroudas, and  Ashwin Ramasubramaniam (2016), A Comparison of the Elastic Properties of Graphene- and Fullerene-Reinforced Polymer Composites: The Role of Filler Morphology and SizeScientific Reports 6, Article number: 31735, doi: 10.1038/srep31735
Dimitrios Maroudas, Sophie Blondel, Lin Hu, Karl D Hammond and Brian D Wirth (2016), Helium segregation on surfaces of plasma-exposed tungsten, Journal of Physics: Condensed Matter, Volume 28, Number 6, doi: 10.1088/0953-8984/28/6/064004

Alexander Mathis, Dan Rokni, Vikrant Kapoor, Matthias Bethge, Venkatesh N. Murthy (2016) Reading Out Olfactory Receptors: Feedforward Circuits Detect Odors in Mixtures without Demixing. Neuron, doi: 10.1016/j.neuron.2016.08.007

Kien Nguyen and Paul Whitford (2016), Steric interactions lead to collective tilting motion in the ribosome during mRNA–tRNA translocationNature Communications, 7, Article number: 10586,  doi: 10.1038/ncomms10586

Stella S. R. Offner, Michael M. Dunham, Katherine I. Lee, Hector G. Arce, and Drummond B. Fielding (2016), The Turbulent Origin of Outflow and Spin Misalignment in Multiple Stare Systems, arXiv: 1606.08445

Leela S. Panchakarla, Luc Lajaunie, Ashwin Ramasubramaniam, Raul Arenal, and Reshef Tenne (2016), Nanotubes from Oxide-Based Misfit Family: The Case of Calcium Cobalt Oxide, ACS Nano, doi: 10.1021/acsnano.6b02430
Leela S. Panchakarla, Luc Lajaunie, Ashwin Ramasubramaniam , Raul Arenal , and Reshef Tenne (2016), Strontium Cobalt Oxide Misfit Nanotubes, Chem. Mater., 28 (24), pp 9150–9157,
doi: 10.1021/acs.chemmater.6b04396
Patrick Pegus, Benoy Varghese, Tian Guo, David Irwin, Prashant Shenoy, Anirban Mahanti, James Culbert, John Goodhue, Chris Hill (2016), Analyzing the Efficiency of a Green University Data Center, ICPE’16, March 12–18, 2016, Delft, Netherlands, doi: 10.1145/2851553.2851557
Germań Peŕez-Sańchez, Szu-ChiaChien, JoséR.B.Gomes, M.NataĺiaD.S.Cordeiro, Scott M. Auerbach, Peter A. Monson, and Miguel Jorge (2016), Multiscale Model for the Templated Synthesis of Mesoporous Silica: The Essential Role of Silica OligomersChem. Mater., 28, 2715−2727, doi: 10.1021/acs.chemmater.6b00348
Ishan Prasad, Youngmi Seo, Lisa M. Hall, Gregory M. Grason (2016), Intradomain Textures in Block Copolymers: Multizone Alignment and Biaxiality, Soft Condensed Matter, arXiv: 1612.07994
Lawrence A. Renna, Monojit Bag, Timothy S. Gehan, Xu Han, Paul M. Lahti, Dimitrios Maroudas, and D. Venkataraman (2016), Tunable Percolation in Semiconducting Binary Polymer Nanoparticle Glasses, J. Phys. Chem. B, doi: 10.1021/acs.jpcb.5b11716
Michael J. Rynkiewicz, Stefan Fischer, William Lehman (2016), The propensity for tropomyosin twisting in the presence and absence of F-actinArchives of Biochemistry and Biophysics, Volume 609, pp 51–58, doi: 10.1016/
Florence R. Sullivan, Kevin Keith, Nocholas C. Wilson (2016), Learning from the Periphery in a Collaborative Robotics Workshop for Girls, Universal Journal of Educational Research 4(12): 2814-2825,  doi: 10.13189/ujer.2016.041215
Thomas Goldstein, Shao-Yu Chen, Di Xiao, Ashwin Ramasubramaniam and Jun Yan (2016), Raman scattering and anomalous Stokes–anti-Stokes ratio in MoTe2 atomic layers, arXiv: 1603.03740
Mark J. Veyette, Philip S. Muirhead, Andrew W. Mann, and Frances Allard (2016),The Physical Mechanism Behind M Dwarf Metallicity Indicators and the Role of C and O Abundancies, arXiv:1605.04904v2
Liye Zhang, Chih-Sheng Yang, Xaralabos Varelas, Stefano Monti (2016), Altered RNA editing in 3′ UTR perturbs microRNA-mediated regulation of oncogenes and tumor-suppressors, Nature, Scientific Reports 6, Article Number: 23226, doi: 10.1038/srep23226
We love to hear what people are using their computers at the MGHPCC to do: Email missing citations or pitch your research to Happy New Year!

Research projects

Dusty With a Chance of Star Formation
Checking the Medicine Cabinet to Interrupt COVID-19 at the Molecular Level
Not Too Hot, Not Too Cold But Still, Is It Just Right?​
Smashing Discoveries​
Microbiome Pattern Hunting
Modeling the Air we Breathe
Exploring Phytoplankton Diversity
The Computer Will See You Now
Computing the Toll of Trapped Diamondback Terrapins
Edging Towards a Greener Future
Physics-driven Drug Discovery
Modeling Plasma-Surface Interactions
Sensing Subduction Zones
Neural Networks & Earthquakes
Small Stars, Smaller Planets, Big Computing
Data Visualization using Climate Reanalyzer
Getting to Grips with Glassy Materials
Modeling Molecular Engines
Forest Mapping: When the Budworms come to Dinner
Exploring Thermoelectric Behavior at the Nanoscale
The Trickiness of Talking to Computers
A Genomic Take on Geobiology
From Grass to Gas
Teaching Computers to Identify Odors
From Games to Brains
The Trouble with Turbulence
A New Twist
A Little Bit of This... A Little Bit of That..
Looking Like an Alien!
Locking Up Computing
Modeling Supernovae
Sound Solution
Lessons in a Virtual Test Tube​
Crack Computing
Automated Real-time Medical Imaging Analysis
Towards a Smarter Greener Grid
Heading Off Head Blight
Organic Light-Harvesting Antennae
Art and AI
Excited by Photons
Tapping into an Ocean of Data
Computing Global Change
Star Power
Engineering the Human Microbiome
Computing Social Capital
Computers Diagnosing Disease
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Collaborative projects

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Outreach & Education Projects

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