PUBLICATIONS

A selection of research using the Massachusetts Green High Performance Computing Center

2017

Ross Altman (2017), Systematic Phenomenology on the Landscape of Calabi-Yau Hypersurfaces in Toric Varieties, Northeastern University, ProQuest Dissertations Publishing, 10272560

Sophie Blondel, Karl D. Hammond, Lin Hu, Dimitrios Maroudas, Brian D. Wirth (2017), Modeling Helium Segregation to the Surfaces of Plasma-Exposed Tungsten as a Function of Temperature and Surface Orientation, American Nuclear Society, Fusion Science and Technology, Volume 71, Number 1, pp 22-35, doi: 10.13182/FST16-112

Lin Hu, Karl D. Hammond, Brian D. Wirth, Dimitrios Maroudas (2017), Dynamics of Small Mobile Helium Clusters Near a Symmetric Tilt Grain Boundary of Plasma-Exposed Tungsten, American Nuclear Society, Fusion Science and Technology, Volume 71, Number 1 , pp 36-51, doi: 10.13182/FST16-105

Olga Kononova, Rustem I. Litvinov, Dmitry S. Blokhin, Vladimir V. Klochkov, John W. Weisel, Joel S. Bennett, and Valeri Barsegov (2017), Mechanistic Basis for the Binding of RGD- and AGDV-Peptides to the Platelet Integrin αIIbβ3, Biochemistry, 56 (13), pp 1932–1942, doi: 10.1021/acs.biochem.6b01113

Dima Kozakov, David R Hall, Bing Xia, Kathryn A Porter, Dzmitry Padhorny, Christine Yueh, Dmitri Beglov, Sandor Vajda (2017), The ClusPro web server for protein–protein docking, Nature Protocols, 12, pp 255–278, doi: 10.1038/nprot.2016.169

Kien Nguyen , Huan Yang, and Paul C. Whitford (2017),  How the Ribosomal A-Site Finger Can Lead to tRNA Species-Dependent Dynamics, J. Phys. Chem. B, 2017, 121 (13), pp 2767–2775,
doi: 10.1021/acs.jpcb.7b01072

Asanka Weerasinghe, Chang-Tsan Lu, Dimitrios Maroudas, and Ashwin Ramasubramaniam (2017), A Multiscale Shear-Lag Analysis of Stiffness Enhancement in Polymer-Graphene Nanocomposites, Applied Materials & Interfaces, doi: 10.1021/acsami.7b03159

2016 and earlier

A B C D E F G H I J K L M N O P Q R S T U V W Y Z

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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, first published: 26 March 2016,
doi: 10.1002/jcc.24368

Inna Aphasizheva, Liye Zhang, Xiaorong Wang, Robyn M. Kaake, Lan Huang, Stefano Monti and Ruslan Aphasizhev (2014) RNA Binding and Core Complexes Constitute the U-Insertion/Deletion Editosome, Mol. Cell. Biol. December 2014 vol. 34 no. 23 4329-4342, doi: 10.1128/MCB.01075-14

Muhammad Affawn Ashraf, Christopher W. Copeland, Abdulkadir Kocak, Alexandra R. McEnroe and Ricardo B. Metz (2015) Vibrational spectroscopy and theory of Fe2+(CH4)n (n = 1–3), Physical Chemistry Chemical Physics, doi:  10.1039/c5cp01757b

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, September 2016, Pages 51–71, doi: 10.1016/j.jnca.2016.06.014

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Bestavros, A., Krieger, O. (2014) Toward an Open Cloud Marketplace: Vision and First Steps, Internet Computing, IEEE (Volume:18 , Issue: 1 ), IEEE p 72-77, doi: 10.1109/MIC.2014.17

R. Brower, A. Hasenfratz, C. Rebbi, E. Weinberg, O. Witzel (2015) A novel approach to the study of conformality in the SU (3) theory with multiple flavors, Journal of Experimental and Theoretical Physics March 2015, Volume 120, Issue 3, pp 423-427, doi: 10.1134/S1063776115030176

Nilda Roma Burgos, Vijay Singh, Te Ming Tseng, Howard Black, Nelson D. Young, Zhongyun Huang, Katie E. Hyma, David R. Gealy and Ana L. Caicedo (2014) The Impact of Herbicide-Resistant Rice Technology on Phenotypic Diversity and Population Structure of United States Weedy Rice, Plant Physiology November 2014 vol. 166 no. 3 1208-1220, doi: 10.​1104/​pp.​114.​242719

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Jiajun Cao, Gregory Karr, Kapil Arya, and Gene Cooperman (2014), Transparent Checkpoint-restart over Infiniband, HPDC ’14 Proceedings of the 23rd international symposium on High-performance parallel and distributed computing, Pages 13-24, ACM New York, NY, USA ©2014, ISBN: 978-1-4503-2749-7 doi: 10.1145/2600212.2600219

Vitor Cardoso and Gaurav Khanna (2015) Black holes in anti–de Sitter spacetime: Quasinormal modes, tails, and flat spacetime, Phys. Rev. D 91, 024031 – Published 22 January 2015, doi: 10.1103/PhysRevD.91.024031

Chih-Hung Chen, Tristan Cambonie, Veronique Lazarus, Matteo Nicoli, Antonio Pons, and Alain Karma (2015), Crack Front Segmentation and Facet Coarsening in Mixed-Mode Fracture, arXiv:1509.05077

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, online at Nano Letters August 12, 2016, doi: 10.1021/acs.nanolett.6b02666

Jierong Cheng, Wei Li Wang, Hossein Mosallaei, and Efthimios Kaxiras (2014), Surface Plasmon Engineering in Graphene Functionalized with Organic Molecules: A Multiscale Theoretical Investigation, Nano Lett., 2014, 14 (1), pp 50–56, doi: 10.1021/nl403005s

Szu-Chia Chien, Scott M. Auerbach, and Peter A. Monson (2015) Modeling the Self-Assembly of Silica-Templated Nanoparticles in the Initial Stages of Zeolite Formation, Langmuir, 2015, 31 (17), pp 4940–4949, doi: 10.1021/acs.langmuir.5b00382

Kedar C. Chitale, Bart Lipken, Walter Presz Jr. and Olivier Desjardins (2015) Understanding the fluid dynamics associated with macro scale ultrasonic separators, Proceedings of Meetings on Acoustics 23, 045004 (2015), doi: 10.1121/2.0000070

Ekin D. Cubuk, Wei L. Wang, Kejie Zhao, Joost J. Vlassak, Zhigang Suo, and Efthimios Kaxiras (2013) Morphological Evolution of Si Nanowires upon Lithiation: A First-Principles Multiscale Model, Nano Lett., 2013, 13 (5), pp 2011–2015, doi: 10.1021/nl400132q

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Paul A. Dalba, Philip S. Muirhead, Jonathan J. Fortney, Matthew M. Hedman, Philip D. Nicholson, and Mark J. Veyette (2015), The Transit Transmission Spectrum of a Cold Gas Giant PlanetThe Astrophysical Journal, Volume 814, Number 2, doi: 10.1088/0004-637X/814/2/154

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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

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Louis Gagnon, Sava Sakadžić, Fréderic Lesage, Emiri T. Mandeville, Qianqian Fang, Mohammad A. Yaseen, David A. Boas (2015), Multimodal reconstruction of microvascular-flow distributions using combined two-photon microscopy and Doppler optical coherence tomography, Neurophoton. 2(1), 015008 (Mar 12, 2015), doi: 10.1117/1.NPh.2.1.015008

Li Guo, Andrew Breakspear, Guoyi Zhao, Lixin Gao, H. Corby Kistler, Jin-Rong Xu and Li-Jun Ma (2015), Conservation and divergence of the cAMP-PKA pathway in two plant pathogenic fungi, Fusarium graminearum and F. verticillioides, Molecular Plant Pathology (accepted), doi: 10.1111/mpp.12272

Li Guo, Guoyi Zhao, Jin-Rong Xu, H. Corby Kistler, Lixin Gao, Li-Jun Ma (2016), Compartmentalized gene regulatory network of the pathogenic fungus Fusarium graminearum, New Phytologist – published online 14 March 2016, 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/IA3.2016.17

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Douglas M. Hall, Isaac R. Bruss, Justin R. Barone & Gregory M. Grason (2016), Morphology selection via geometric frustration in chiral filament bundles, Nature Materials, published online March 21, 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

David E. Hill and Jason P. Holland (2015) Computational studies on hypervalent iodonium(III) compounds as activated precursors for 18F radiofluorination of electron-rich arenes, Computational and Theoretical Chemistry, Volume 1066, 15 August 2015, Pages 34–46, doi: 10.1016/j.comptc.2015.05.012

David E. Hill, Neil Vasdev, Jason P. Holland (2015) Evaluating the accuracy of density functional theory for calculating 1H and 13C NMR chemical shifts in drug molecules, Computational and Theoretical Chemistry 1051 (2015) 161–172, doi: 10.1016/j.comptc.2014.11.007

Lin Hu, Spencer Wyant, Andre R. Muniz, Ashwin Ramasubramaniam, and Dimitrios Maroudas (2015) Mechanical Behavior and Fracture of Graphene Nanomeshes, J. Appl. Phys. 117, 024302 (2015); doi: 10.1063/1.4905583

Lin Hu, Karl D. Hammond, Brian D. Wirth and Dimitrios Maroudas (2015) Molecular-dynamics analysis of mobile helium cluster reactions near surfaces of plasma-exposed tungstenJ. Appl. Phys. 118, 163301, doi: 10.1063/1.4933393

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Isenstein, E., Wi, S., and Ethan Yang, Y. (2015) Calibration of a Distributed Hydrologic Model Using Streamflow and Remote Sensing Snow Data. World Environmental and Water Resources Congress 2015: pp. 973-982, doi: 10.1061/9780784479162.093

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William Lehman, Greg Medlock, Xiaochuan (Edward) Li, Worawit Suphamungmee, An-Yue Tu, Anja Schmidtmann, Zoltán Ujfalusi, Stefan Fischer, Jeffrey R. Moorea, Michael A. Geeves, Michael Regnier (2015) Phosphorylation of Ser283 enhances the stiffness of the tropomyosin head-to-tail overlap domainArchives of Biochemistry and Biophysics Volume 571, 1 April 2015, Pages 10–15, doi: 10.1016/j.abb.2015.02.026

Boduo Li, Edward Mazur, Yanlei Diao, Andrew McGregor and Prashant Shenoy, SCALLA: A Platform for Scalable One-Pass Analytics Using MapReduceACM Transactions on Database Systems (TODS) , Volume 37 Issue 4, December 2012, doi: 10.1145/2389241.2389246

Xiaochuan Edward Li, Marek Orzechowskia, William Lehman, and Stefan Fischer (2014) Structure and flexibility of the tropomyosin overlap junction, Biochemical and Biophysical Research Communications, Volume 446, Issue 1, 28 March 2014, Pages 304–308, doi: 10.1016/j.bbrc.2014.02.097

Jiaqi Lin and Alfredo Alexander-Katz (2013), Cell Membranes Open “Doors” for Cationic Nanoparticles/Biomolecules: Insights into Uptake Kinetics, ACS Nano, 2013, 7 (12), pp 10799–10808, doi: 10.1021/nn4040553

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 (published online August 2, 2016), doi: 10.1038/srep31735

M

Mahram, A. and Herbordt, M.C. (2012), FMSA: FPGA-Accelerated ClustalW-Based Multiple Sequence Alignment through Pipelined Prefiltering, 2012 IEEE 20th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM), pp. 177 – 183, doi: 10.1109/FCCM.2012.38

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

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 first published September, 7, 2016, doi: 10.1016/j.neuron.2016.08.007

Muhammad Zain Mustafa (2014) Energy Agile Cluster Communication, University of Massachusetts, Amherst, Masters Thesis

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Jeffrey K. Noel and Paul Whitford (2016), How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome, Nature Communications 7, Article number: 13314, doi: 10.1038/ncomms13314

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

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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

Marek Orzechowski, Jeffrey R. Moore, Stefan Fischer, William Lehman (2014) Tropomyosin movement on F-actin during muscle activation explained by energy landscapes, Archives of Biochemistry and Biophysics, Volume 545, 1 March 2014, Pages 63–68, doi: 10.1016/j.abb.2014.01.001

Marek Orzechowski, Stefan Fischer, Jeffrey R. Moore, William Lehman, Gerrie P. Farman (2014) Energy landscapes reveal the myopathic effects of tropomyosin mutations, Archives of Biochemistry and Biophysics, Volume 564, 15 December 2014, Pages 89–99, doi: 10.1016/j.abb.2014.09.007

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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, Article ASAP, doi: 10.1021/acsnano.6b02430, Publication Date (Web): May 24, 2016

Leela S. Panchakarla, Luc Lajaunie, Ashwin Ramasubramaniam , Raul Arenal , and Reshef Tenne (2016), Strontium Cobalt Oxide Misfit Nanotubes, Chem. Mater., 2016, 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. 2016, 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

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Rabassa, Albert O. III (2014) Economic performance of modularized hot-aisle contained datacenter PODs utilizing horizontal airflow cooling, Masters Thesis, Sloan school of Management, MIT

Ashwin Ramasubramaniam and Andre R. Muniz (2014) Ab initio studies of thermodynamic and electronic properties of phosphorene nano ribbons, Phys. Rev. B 90, 085424, doi: 10.1103/PhysRevB.90.085424

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, Article ASAP,
doi: 10.1021/acs.jpcb.5b11716

Michael J. Rynkiewicz, Veronika Schott, Marek Orzechowski, William Lehman , Stefan Fischer (2015) Electrostatic interaction map reveals a new binding position for tropomyosin on F-actin,  Journal of Muscle Research and Cell Motility, doi: 10.1007/s10974-015-9419-z

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, 1 November 2016, Pages 51–58, doi: 10.1016/j.abb.2016.09.008

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Ray M. Sehgal and Dimitrios Maroudas (2015), Equilibrium Shape of Colloidal CrystalsLangmuir, 2015, 31 (42), pp 11428–11437
doi: 10.1021/acs.langmuir.5b02952

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, 2016, doi: 10.13189/ujer.2016.041215

Styers, John M., Gamache Robert (2014), Explicit Parallelization of Robert-Bonamy Formalism, 13th International HITRAN Conference, held 23-25 June 2014 in Cambridge, Massachusetts, USA, doi: 10.5281/zenodo.11186

Latanya Sweeney, Merce Crosas (2015), An Open Science Platform for the Next Generation of Data,  arXiv:1506.05632

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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

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Vetro, R., Farhoodi, R., Kotla, R., Haspel, N., Weisman, D., Rosen, J., Simovici, D. (2014) TIDE: Inter-chromosomal translocation and insertion detection using embeddings, 2014 IEEE International Conference on Big Data, pages 64-70, pub. IEEE, doi: 10.1109/BigData.2014.7004395

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 [astro-ph.SR] 20 May 2016

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Wei L. Wang and Efthimios Kaxiras (2013) Efficient calculation of the effective single-particle potential and its application in electron microscopy, Phys. Rev. B 87, 085103 – Published 5 February 2013, doi: 10.1103/PhysRevB.87.085103

Wei Li Wang, Elton J. G. Santos, Bin Jiang, Ekin Dogus Cubuk, Colin Ophus, Alba Centeno, Amaia Pesquera, Amaia Zurutuza, Jim Ciston, Robert Westervelt, and Efthimios Kaxiras (2014) Direct Observation of a Long-Lived Single-Atom Catalyst Chiseling Atomic Structures in Graphene, Nano Lett., 2014, 14 (2), pp 450–455, doi: 10.1021/nl403327u

Wi, S., Yang, Y. C. E., Steinschneider, S., Khalil, A., and Brown, C. M.: Calibration approaches for distributed hydrologic models in poorly gaged basins: implication for streamflow projections under climate change, Hydrol. Earth Syst. Sci., 19, 857-876, doi: 10.5194/hess-19-857-2015, 2015.

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Zapater, Marina, Ata Turk, Jose M. Moya, Jose L. Ayala, and Ayse K. Coskun (2015), Dynamic Workload and Cooling Management in High-Efficiency Data Centers, The sixth International Green and Sustainable Computing Conference, IEEE, December 14 – 16, 2015

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