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1. QCD on the BlueGene/L Supercomputer

Author

Bhanot, G., Chen, D., Gara, A., Sexton, J., and Vranas, P.

Subjects
High Energy Physics - Lattice
Abstract

In June 2004 QCD was simulated for the first time at sustained speed exceeding 1 TeraFlops in the BlueGene/L supercomputer at the IBM T.J. Watson Research Lab. The implementation and performance of QCD in the BlueGene/L is presented., Comment: Talk presented at Lattice2004(machines), Fermilab, 21-26 June 2004, 3 pages, 5 figures

Published
2004
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2. Study of a New Neuron

Author

Adler, S. L., Bhanot, G. V., and Weckel, J. D.

Subjects
Nonlinear Sciences - Adaptation and Self-Organizing Systems, Quantitative Biology
Abstract

We study a modular neuron alternative to the McCulloch-Pitts neuron that arises naturally in analog devices in which the neuron inputs are represented as coherent oscillatory wave signals. Although the modular neuron can compute $XOR$ at the one neuron level, it is still characterized by the same Vapnik-Chervonenkis dimension as the standard neuron. We give the formulas needed for constructing networks using the new neuron and training them using back-propagation. A numerical study of the modular neuron on two data sets is presented, which demonstrates that the new neuron performs at least as well as the standard neuron., Comment: 19 pages, 7 figures(not included) available upon request, postscript file

Published
1994

3. Specific Heat Exponent for the 3-d Ising Model from a 24-th Order High Temperature Series

Author

Bhanot, G., Creutz, M., Glaessner, U., and Schilling, K.

Subjects
High Energy Physics - Lattice
Abstract

We compute high temperature expansions of the 3-d Ising model using a recursive transfer-matrix algorithm and extend the expansion of the free energy to 24th order. Using ID-Pade and ratio methods, we extract the critical exponent of the specific heat to be alpha=0.104(4)., Comment: 10 pages, LaTeX with 5 eps-figures using epsf.sty, IASSNS-93/83 and WUB-93-40

Published
1993
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4. Proof of Jacobi identity in generalized quantum dynamics

Author

Adler, S. L., Bhanot, G. V., and Weckel, J. D.

Subjects
High Energy Physics - Theory
Abstract

We prove that the Jacobi identity for the generalized Poisson bracket is satisfied in the generalization of Heisenberg picture quantum mechanics recently proposed by one of us (SLA). The identity holds for any combination of fermionic and bosonic fields, and requires no assumptions about their mutual commutativity., Comment: 9 pages, plain tex file, IASSNS-HEP-93/46

Published
1993
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5. $1+1$-Dimensional Large $N$ QCD coupled to Adjoint Fermions

Author

Bhanot, G., Demeterfi, K., and Klebanov, I.

Subjects
High Energy Physics - Theory, High Energy Physics - Lattice
Abstract

We consider 1+1-dimensional QCD coupled to Majorana fermions in the adjoint representation of the gauge group $SU(N)$. Pair creation of partons (fermion quanta) is not suppressed in the large-$N$ limit, where the glueball-like bound states become free. In this limit the spectrum is given by a linear \lc\ Schr\" odinger equation, which we study numerically using the discretized \lcq. We find a discrete spectrum of bound states, with the logarithm of the level density growing approximately linearly with the mass. The wave function of a typical excited state is a complicated mixture of components with different parton numbers. A few low-lying states, however, are surprisingly close to being eigenstates of the parton number, and their masses can be accurately calculated by truncated diagonalizations., Comment: 22 pages + 9 figures (available by request from kresimir@puhep1.princeton.edu), uses phyzzx.tex + tables.tex PUPT-1413, IASSNS-HEP-93/42

Published
1993
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6. Low Temperature Expansions for Potts Models

Author

Bhanot, G., Creutz, M., Glassner, U., Horvath, I., Lacki, J., Schilling, K., and Weckel, J.

Subjects
High Energy Physics - Lattice, High Energy Physics - Theory
Abstract

On simple cubic lattices, we compute low temperature series expansions for the energy, magnetization and susceptibility of the three-state Potts model in D=2 and D=3 to 45 and 39 excited bonds respectively, and the eight-state Potts model in D=2 to 25 excited bonds. We use a recursive procedure which enumerates states explicitly. We analyze the series using Dlog Pade analysis and inhomogeneous differential approximants., Comment: (17 pages + 8 figures)

Published
1993
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7. Measuring the Decorrelation Times of Fourier Modes in Simulations

Author

Ben-Av, R. and Bhanot, G.

Subjects
High Energy Physics - Lattice, High Energy Physics - Theory
Abstract

We describe a method to study the rate at which modes decorrelate in numerical simulations. We study the XY model updated with the Metropolis and Wolff dynamics respectively and compute the rate at which each eigenvector of the dynamics decorrelates. Our method allows us to identify the decorrelation time for each mode separately. We find that the autocorrelation function of the various modes is markedly different for the `local' Metropolis compared to the `non-local' Wolff dynamics. Equipped with this new insight, it may be possible to devise highly efficient algorithms., Comment: 16 pp (LaTeX), PUPT-1378 , IASSNS-HEP-93/2

Published
1993
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13. Massively parallel quantum chromodynamics

Author

Vranas, P., Blumrich, M.A., Chen, D., Gara, A., Giampapa, M.E., Heidelberger, P., Salapura, V., Sexton, J.C., Soltz, R., and Bhanot, G.

Subjects
Multiprocessing, Multiprocessing -- Methods, Quantum chromodynamics -- Analysis, Nuclear forces (Physics) -- Analysis
Abstract

Quantum chromodynamics (QCD), the theory of the strong nuclear force, can be numerically simulated on massively parallel supercomputers using the method of lattice gauge theory. We describe the special programming requirements of lattice QCD (LQCD) as well as the optimal supercomputer hardware architectures for which LQCD suggests a need. We demonstrate these methods on the IBM Blue Gene/[TM] (BG/L) massively parallel supercomputer and argue that the BG/L architecture is very well suited for LQCD studies. This suitability arises from the fact that LQCD is a regular lattice discretization of space into lattice sites, while the BG/L supercomputer is a discretization of space into compute nodes. Both LQCD and the BG/L architecture are constrained by the requirement of short-distance exchanges. This simple relation is technologically important and theoretically intriguing. We demonstrate a computational speedup of LQCD using up to 131,072 CPUs on the largest BG/L supercomputer available in 2007. As the number of CPUs is increased, the speedup increases linearly with sustained performance of about 20% of the maximum possible hardware speed. This corresponds to a maximum of 70.5 sustained teraflops. At these speeds, LQCD and the BG/L supercomputer are able to produce theoretical results for the next generation of strong-interaction physics.

Published
2008

14. Optimizing task layout on the Blue Gene/L supercomputer

Author

Bhanot, G., Gara, A., Heidelberger, P., Lawless, E., Sexton, J.C., and Walkup, R.

Subjects
Supercomputer, Technology application, Supercomputers -- Research, Supercomputers -- Design and construction, Monte Carlo method -- Research, Monte Carlo method -- Technology application
Abstract

A general method for optimizing problem layout on the Blue Gene[R]/L (BG/L) supercomputer is described. The method takes as input the communication matrix of an arbitrary problem as an array with entries C(i, j), which represents the data communicated from domain i to domain j. Given C(i, j), we implement a heuristic map that attempts to sequentially map a domain and its communication neighbors either to the same BG/L node or to near-neighbor nodes on the BG/L torus, while keeping the number of domains mapped to a BG/L node constant. We then generate a Markov chain of maps using Monte Carlo simulation with free energy F=[[SIGMA].sub.i,j] C(i,j)H(i,j), where H(i,j) is the smallest number of hops on the BG/L torus between domain i and domain j. For two large parallel applications, SAGE and UMT2000, the method was tested against the default Message Passing Interface rank order layout on up to 2,048 BG/L nodes. It produced maps that improved communication efficiency by up to 45%.

Published
2005

15. Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma

Author

Serody, J.S., Smith, C.C., Kim, W.Y., Bixby, L.M., Bortone, D.S., Swanstrom, R., Beckermann, K.E., Bhanot, G., Vincent, B.G., Selitsky, S.R., Lee, S.J., Parker, J.S., Milowsky, M.I., Ganesan, S., Cubas, A.A., Wallen, E.M., Rathmell, K., and Panda, A.

Abstract

Human endogenous retroviruses (hERVs) are remnants of exogenous retroviruses that have integrated into the genome throughout evolution. We developed a computational workflow, hervQuant, which identified more than 3,000 transcriptionally active hERVs within The Cancer Genome Atlas (TCGA) pan-cancer RNA-Seq database. hERV expression was associated with clinical prognosis in several tumor types, most significantly clear cell renal cell carcinoma (ccRCC). We explored two mechanisms by which hERV expression may influence the tumor immune microenvironment in ccRCC: (i) RIG-I-like signaling and (ii) retroviral antigen activation of adaptive immunity. We demonstrated the ability of hERV signatures associated with these immune mechanisms to predict patient survival in ccRCC, independent of clinical staging and molecular subtyping. We identified potential tumor-specific hERV epitopes with evidence of translational activity through the use of a ccRCC ribosome profiling (Ribo-Seq) dataset, validated their ability to bind HLA in vitro, and identified the presence of MHC tetramer-positive T cells against predicted epitopes. hERV sequences identified through this screening approach were significantly more highly expressed in ccRCC tumors responsive to treatment with programmed death receptor 1 (PD-1) inhibition. hervQuant provides insights into the role of hERVs within the tumor immune microenvironment, as well as evidence that hERV expression could serve as a biomarker for patient prognosis and response to immunotherapy. © 2018 American Society for Clinical Investigation. All rights reserved.

Published
2018
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17. ErbB2, EphrinB1, Src kinase and PTPN13 signaling complex regulates MAP kinase signaling in human cancers.

Author

Vermeer, P.D., Bell, M., Lee, K., Vermeer, D.W., Wieking, B.G., Bilal, E., Bhanot, G., Drapkin, R.I., Ganesan, S., Klingelhutz, A.J., Hendriks, W.J.A.J., Lee, J.H., Vermeer, P.D., Bell, M., Lee, K., Vermeer, D.W., Wieking, B.G., Bilal, E., Bhanot, G., Drapkin, R.I., Ganesan, S., Klingelhutz, A.J., Hendriks, W.J.A.J., and Lee, J.H.

Abstract

Contains fulltext : 107772.pdf (publisher's version ) (Open Access), In non-cancerous cells, phosphorylated proteins exist transiently, becoming de-phosphorylated by specific phosphatases that terminate propagation of signaling pathways. In cancers, compromised phosphatase activity and/or expression occur and contribute to tumor phenotype. The non-receptor phosphatase, PTPN13, has recently been dubbed a putative tumor suppressor. It decreased expression in breast cancer correlates with decreased overall survival. Here we show that PTPN13 regulates a new signaling complex in breast cancer consisting of ErbB2, Src, and EphrinB1. To our knowledge, this signaling complex has not been previously described. Co-immunoprecipitation and localization studies demonstrate that EphrinB1, a PTPN13 substrate, interacts with ErbB2. In addition, the oncogenic V660E ErbB2 mutation enhances this interaction, while Src kinase mediates EphrinB1 phosphorylation and subsequent MAP Kinase signaling. Decreased PTPN13 function further enhances signaling. The association of oncogene kinases (ErbB2, Src), a signaling transmembrane ligand (EphrinB1) and a phosphatase tumor suppressor (PTPN13) suggest that EphrinB1 may be a relevant therapeutic target in breast cancers harboring ErbB2-activating mutations and decreased PTPN13 expression.

Published
2012

20. Neurite Sprouting and Synapse Deterioration in the Aging Caenorhabditis elegans Nervous System

Author

Toth, M. L., primary, Melentijevic, I., additional, Shah, L., additional, Bhatia, A., additional, Lu, K., additional, Talwar, A., additional, Naji, H., additional, Ibanez-Ventoso, C., additional, Ghose, P., additional, Jevince, A., additional, Xue, J., additional, Herndon, L. A., additional, Bhanot, G., additional, Rongo, C., additional, Hall, D. H., additional, and Driscoll, M., additional

Published
2012
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22. Autophagy Suppresses Tumorigenesis through Elimination of p62

Author

Mathew, R., primary, Karp, C.M., additional, Beaudoin, B., additional, Vuong, N., additional, Chen, G., additional, Chen, H.-Y., additional, Bray, K., additional, Reddy, A., additional, Bhanot, G., additional, Gelinas, C., additional, DiPaola, R.S., additional, Karantza-Wadsworth, V., additional, and White, E., additional

Published
2011
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24. Molecular Stratification of Clear Cell Renal Cell Carcinoma by Consensus Clustering Reveals Distinct Subtypes and Survival Patterns

Author

Brannon, A. R., primary, Reddy, A., additional, Seiler, M., additional, Arreola, A., additional, Moore, D. T., additional, Pruthi, R. S., additional, Wallen, E. M., additional, Nielsen, M. E., additional, Liu, H., additional, Nathanson, K. L., additional, Ljungberg, B., additional, Zhao, H., additional, Brooks, J. D., additional, Ganesan, S., additional, Bhanot, G., additional, and Rathmell, W. K., additional

Published
2010
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29. EARLY EXPERIENCES WITH THE 360TF IBM BLUE GENE/L PLATFORM

Author

BHANOT, G., primary, DENNIS, J. M., additional, EDWARDS, J., additional, GRABOWSKI, W., additional, GUPTA, M., additional, JORDAN, K., additional, LOFT, R. D., additional, SEXTON, J., additional, ST-CYR, A., additional, THOMAS, S. J., additional, TUFO, H. M., additional, VORAN, T., additional, WALKUP, R., additional, and WYSZOGRODSKI, A. A., additional

Published
2008
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33. An Overview of the BlueGene/L Supercomputer

Author

Adiga, N.R., primary, Almasi, G., additional, Almasi, G.S., additional, Aridor, Y., additional, Barik, R., additional, Beece, D., additional, Bellofatto, R., additional, Bhanot, G., additional, Bickford, R., additional, Blumrich, M., additional, Bright, A.A., additional, Brunheroto, J., additional, Cascaval, C., additional, Castanos, J., additional, Chan, W., additional, Ceze, L., additional, Coteus, P., additional, Chatterjee, S., additional, Chen, D., additional, Chiu, G., additional, Cipolla, T.M., additional, Crumley, P., additional, Desai, K.M., additional, Deutsch, A., additional, Domany, T., additional, Dombrowa, M.B., additional, Donath, W., additional, Eleftheriou, M., additional, Erway, C., additional, Esch, J., additional, Fitch, B., additional, Gagliano, J., additional, Gara, A., additional, Garg, R., additional, Germain, R., additional, Giampapa, M.E., additional, Gopalsamy, B., additional, Gunnels, J., additional, Gupta, M., additional, Gustavson, F., additional, Hall, S., additional, Haring, R.A., additional, Heidel, D., additional, Heidelberger, P., additional, Herger, L.M., additional, Hoenicke, D., additional, Jackson, R.D., additional, Jamal-Eddine, T., additional, Kopcsay, G.V., additional, Krevat, E., additional, Kurhekar, M.P., additional, Lanzetta, A.P., additional, Lieber, D., additional, Liu, L.K., additional, Lu, M., additional, Mendell, M., additional, Misra, A., additional, Moatti, Y., additional, Mok, L., additional, Moreira, J.E., additional, Nathanson, B.J., additional, Newton, M., additional, Ohmacht, M., additional, Oliner, A., additional, Pandit, V., additional, Pudota, R.B., additional, Rand, R., additional, Regan, R., additional, Rubin, B., additional, Ruehli, A., additional, Rus, S., additional, Sahoo, R.K., additional, Sanomiya, A., additional, Schenfeld, E., additional, Sharma, M., additional, Shmueli, E., additional, Singh, S., additional, Song, P., additional, Srinivasan, V., additional, Steinmacher-Burow, B.D., additional, Strauss, K., additional, Surovic, C., additional, Swetz, R., additional, Takken, T., additional, Tremaine, R.B., additional, Tsao, M., additional, Umamaheshwaran, A.R., additional, Verma, P., additional, Vranas, P., additional, Ward, T.J.C., additional, Wazlowski, M., additional, Barrett, W., additional, Engel, C., additional, Drehmel, B., additional, Hilgart, B., additional, Hill, D., additional, Kasemkhani, F., additional, Krolak, D., additional, Li, C.T., additional, Liebsch, T., additional, Marcella, J., additional, Muff, A., additional, Okomo, A., additional, Rouse, M., additional, Schram, A., additional, Tubbs, M., additional, Ulsh, G., additional, Wait, C., additional, Wittrup, J., additional, Bae, M., additional, Dockser, K., additional, Kissel, L., additional, Seager, M.K., additional, Vetter, J.S., additional, and Yates, K., additional

Published
2002
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34. An overview of the BlueGene/L Supercomputer.

Author

Adiga, NR, Almasi, G, Almasi, GS, Aridor, Y, Barik, R, Beece, D, Bellofatto, R, Bhanot, G, Bickford, R, Blumrich, M, Bright, AA, Brunheroto, J, Caşcaval, C, Castaños, J, Chan, W, Ceze, L, Coteus, P, Chatterjee, S, Chen, D, and Chiu, G

Published
2002

37. TEXAS: a calorimeter-based high-rate detector for the SSC

Author

Alverson, G., primary, Ayer, F., additional, Bhanot, G., additional, Dautat, H., additional, Dunn, W.L., additional, Dye, S., additional, Elder, C., additional, Faissler, W., additional, Glaubman, M., additional, von Goeler, E., additional, Grimes, A., additional, Hecht, M., additional, Hofteizer, J., additional, Hurlbut, C., additional, Jaquet, P., additional, Jones, G., additional, Kamon, T., additional, Klein, S., additional, Lane, C., additional, Leedom, I., additional, McIntyre, R.J., additional, Miller, J.P., additional, Moromisato, J., additional, Mucci, J., additional, Murray, J., additional, Myers, S.K., additional, O'Foghlundha, F., additional, Oh, C., additional, Orr, D., additional, Perlman, D., additional, Pothier, E., additional, Rahman, M.A., additional, Reardon, J., additional, Reucroft, S., additional, Roberts, B.L., additional, Saletan, E., additional, Saupp, S.L., additional, Schulte, T., additional, Simpkins, J.D., additional, Stapleton, J.W., additional, Stone, J., additional, Sulak, L., additional, Sullivan, D., additional, Thurston, T., additional, Webb, R., additional, Winn, D., additional, Womble, E., additional, Woosley, J.K., additional, Worstell, W., additional, and Yacout, A.M., additional

Published
1991
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46. Special issue on computational science and engineering

Author

Johnson, C., Keyes, D., Ulrich Ruede, Bhanot, G., Biswas, R., Chow, E., Deng, Y., Diachin, L. F., Ghattas, O., Halpern, L., Harrison, R., Hendrickson, B., Jordan, K., Kolda, T., Komzsik, L., Langer, U., Langtangen, H. P., Lee, S., Nakajima, K., Nakano, A., Ng, E. G., Turek, S., Wathen, A., Wright, M., and Young, D. P.

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