Publications Enabled by SERC Facilities

SERC Facilities Usage and Acknowledgements

This pages lists some research highlights and publications of IISc faculty, achieved utilizing SERC computing resources.

Copyright
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Publications:

      1. Goverdhan Mehta, Saikat Sen, T.N. Guru Row, Deepak Chopra, Sayani Chatttopdhyay, OC: Strength vs. Accessibility: Unraveling the Patterns of Self-Recognition in a Conformationally Locked Amino Alchohol (used GAUSSIAN 98 program package)[appears in www.eurjoc.org,2007.
      2. Goverdhan Mehta, Saikat Sen, Kailasam Venkatesan, OC:Additive induced ploymorphous behavior of a conformationally locked hexol(used GAUSSIAN 98 program package)[appears in The Royal Society of Chemistry 2007]
      3. Jorly Joseph and Eluvathingal D. Jemmis, IPC :Red-, Blue-, or No-Shift in Hydrogen Bonds: A Unified Explanation[appears in J. AM. CHEM. SOC. 9 VOL. 129, NO. 15, 2007]
      4. Kausik Majumdar and Navakanta Bhat, ECE :Bandstructure effects in ultra-thin-body double-gate field effect transistor:A fullband analysis(used high performance computational resources)[appears in JOURNAL OF APPLIED PHYSICS @2008, ,103, 114503]
      5. Vikrant V. Naik and S. Vasudevan, IPC: Conformational Dynamics in Alkyl Chains of an Anchored Bilayer: A Molecular Dynamics Study[appears in J. Phys. Chem. C, 2009, 113 (20), pp 8806-8813]
      6. Ravindra K., Nikhil Vijay Shende, N. Balakrishnan, AE: CFD computations for Common Research Model using the code HIFUN[appears in Fourth AIAA Drag Prediction Workshop, San Antonio, TX June 2122, 2009]
      7. Jain, D K, A Chakraborty and R S Nanjundiah, CES: On the role of cloud adjustment time scale in simulating precipitation with relaxed Arakawa-Schubert Convection scheme.[appears in Meteorology and Atmospheric Physics@2012, 115 (1-2). pp 1-13]
      8. Kumar S V, Nanjundiah R S, Thazhuthaveetil, M J, and Govindrajan R, CES: Impact of Message Compression on the Scalability of an Atmospheric Modelling.Application on Clusters.[appears in Journal of Parallel Computing@2008,doi:10.1016/j.parco-2007.10.0.002, 34, 1-16]
      9. Mishra S., J Srinivasan and R S Nanjundiah, CES: Impact of temporal resolution on ITCZ rainfall.
      10. Sahaney S and R S Nanjundiah, CES:Impact of Convective Downdraft on Rainfall in an Aqua-planet model.[appears in eprints@iisc 2008, Annales Geophysicae, 26 (7). pp. 1877-1887 ]
      11. Chakraborty, A., R S Nanjundiah and J Srinivasan, CES: Impact of African Orography on Somali Jet. Intl. [appears in eprints@iisc 2009,Journal of Climatology, 29, 983-992]
      12. V. Shukla, M. Brachet and R. Pandit, Physics: Turbulence in the two-dimensional Fourier-truncated Gross-Pitaevskii equation
      13. A.R. Nayak and R. Pandit, Physics:Spiral-wave dynamics in ionically realistic mathematical models for human ventricular tissue: The effects of mechanical deformation.
      14. J.M. Kurdestany, R.V. Pai, S. Mukerjee, and R. Pandit, PhysicsPhases,transitions, and boundary conditions in a model of interacting bosons
      15. A. Gupta, P. Perlekar and R. Pandit, Physics: Two-dimensional, homogeneous,isotropic fluid turbulence with polymer additives.
      16. S.S. Ray, D. Mitra and R. Pandit, Physics: The universality of dynamic multiscaling in homogeneous,isotropic navier-stokes and passive-scalar turbulen[appears in New J. Phys. @2008, doi:10.1088/1367-2630/10/3/033003]
      17. U. Frisch, S.S. Ray, G. Sahoo, D. Banerjee, and R. Pandit, Physics: Real-space manifestations of bottlenecks in turbulence spectra[appears in American Physical Society @2013]
      18. R.V. Pai, J.M. Kurdestany, K. Sheshadri, and R. Pandit, Physics: se-hubbard models in confining potentials: Inhomogeneous mean-field theory.
      19. R. Pandit, P. Perlekar, and S.S. Ray, Physics: Statistical properties of turbulence: An overview
      20. G. Sahoo, D. Mitra, and R. Pandit, Physics: Dynamo onset as a first-order transition: Lessons from a shell model formagnetohydrodynamics.
      21. T.K. Shajahan, A.R. Nayak, and R. Pandit, Physics: Spiral-wave turbulence and its control in the presence of inhomogeneities in four mathematical models of cardiac tissue.
      22. R. Majumder, A. R. Nayak, and R. Pandit. Scroll-wave dynamics in human cardiac tissue, Physics: lessons from a mathematical model with inhomogeneties and fiber architecture.
      23. R.V. Pai, K. Sheshadri, and R. Pandit, Physics:  Phases and transitions in the spin-1 bose-hubbard model: Systematics of a mean-field theory
      24. P. Perlekar and R. Pandit, Physics:  Turbulence-induced melting of a nonequilibrium vor-tex crystal in a forced thin fluid film.[appears in New J. Phys.@201012 023033]
      25. R. Pandit, S.S. Ray, and D. Mitra, Physics:  Dynamic multiscaling in turbulence.
      26. U. Frisch, S. Kurien, R. Pandit, W. Pauls, S.S. Ray, A. Wirth, and J-Z. Zhu, Physics:  Hyperviscosity, galerkin truncation and bottlenecks in turbulence.
      27. P. Perlekar, D. Mitra, and R. Pandit, Physics: Direct numerical simulations of statistically steady, homogeneous, isotropic fluid turbulence with polymer additives. [appears in Phys. Rev. E 82, 066313 (2010).
      28. P. Perlekar and R. Pandit, Physics:  Statistically steady turbulence in thin films: Direct nu-merical simulations with ekman friction.
        [appears in New J. Phys. 11 No 7 (July 2009) 073003 (15pp)]
      29. G. Sahoo, P. Perlekar, and R. Pandit, Physics:  Systematics of the magnetic-prandtl-number dependence of homogeneous, isotropic magnetohydrodynamic turbulence. [appears in New J. Phys. 13 01303 (Jan 2011)]
      30. P. Perlekar, S. S. Ray, D. Mitra, and R. Pandit, Physics: The persistence problem in two-dimensional fluid turbulence  [appears in Phys.Rev.Lett.106:054501,2011]
      31. S.S. Ray, D. Mitra, P. Perlekar, and R. Pandit, Physics: Dynamic multiscaling in two-dimensional fluid turbulence.
      32. J.M. Kurdestany, R.V. Pai, and R. Pandit, Physics:The inhomogeneous extended bose-hubbard model: Mean-field theory.
      33. R. Majumder, A.R. Nayak, and R. Pandit , Physics: Nonequilibrium arrhythmic states and transitions in a mathematical model for diffuse fibrosis in human cardiac tissue
      34. Sahany S, V Venugopal and R S Nanjundiah, CESThe Mumbai Heavy Rainfall Event of 26 July 2005, Through the Lens of a Cloud Resolving Model [appears in Meteorology & Atmospheric Physics 2010, 109, pp 115-128].
      35. Praveen Anand, KalidasYeturu and Nagasuma Chandra, Bioinformatics : PocketAnnotate: Towards site-based function annotation. [appears in Nucleic Acids Res. 2012 Jul;40(Web Server issue):W400-8. doi: 10.1093/nar/gks421. Epub 2012 May 22]
      36. Yeturu K, Chandra N, Bioinformatics:PocketAlign a novel algorithm for aligning binding sites in protein structures. J ChemInf Model. [appears in J Chem Inf Model. 2011 Jul 25;51(7):1725-36. doi: 10.1021/ci200132z. Epub 2011 Jun 21]
      37. Nagasuma Chandra, Raghu Bhagavat, Eshita Sharma, Srikanth Reddy, Kumar Somasundaram, Bioinformatics:  Virtual screening, identification and experimental testing of novel inhibitors of PBEF1/Visfatin/NMPRTase for glioma therapy [appears in J Clin Bioinforma. 2011 Jan 20;1(1):5. doi: 10.1186/2043-9113-1-5]
      38. Yeturu K, Chandra N, BioinformaticsPocketMatch: A new algorithm to compare binding sites in protein structures. [appears in BMC Bioinformatics. 2008 Dec 17;9:543. doi: 10.1186/1471-2105-9-543]
      39. Raman K, Yeturu K and Chandra N, BioinfomaticstargetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis [appears in eprints@iisc, 2008]
      40. Poddar P., Chandra N., Ganapathiraju M., Sekar K., Klein-Seetharaman J., Reddy R.& Balakrishnan N, BioinfomaticsGenome sequence analysis using suffix arrays: Application leading to evolutionary insights. [appears in eprits@iisc, 2007]
      41. Khodade P, Prabhu R, Chandra N, Raha S, and Govindarajan R PhysicsParallel Implementation of Autodock. J. Appl. Crystallography [appears in J. Appl. Crystallogr, 2007]
      42. Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra, BioinfomaticsHallmarks of Mycolic Acid Biosynthesis: A Comparative Genomics Study Proteins: Structure, Function and Bioinformatics [appears in eprints@iisc, 2007]
      43. Ketki Verkhedkar, Karthik Raman, Nagasuma Chandra and Saraswathi Vishveshwara, BioinfomaticsMetabolome based reaction graphs of M. tuberculosis and M. leprae: A comparative network analysis
      44. Jain, D K, A Chakraborty and R S Nanjundiah, Meteorology and Atmospheric PhysicsaticsOn the role of cloud adjustment time scale in simulating precipitation with relaxed Arakawa Schubert Convection scheme [appears in eprints@iisc 2012, Meteorology and Atmospheric Physics 115(1-2) pp. 1-13]
      45. Sahany S, V Venugopal and R S Nanjundiah, Meteorology and Atmospheric PhysicsaticsThe Mumbai Heavy Rainfall Event of 26 July 2005, Through the Lens of a Cloud Resolving Model.[appears in eprints@iisc 2007, Meteorology and Atmospheric Physics 109 pp.115-128]
      46. Chakraborty, A., R S Nanjundiah and J Srinivasan, Meteorology and Atmospheric PhysicsaticsImpact of African Orography on Somali Jet. Intl. Journal of Climatology. [appears in eprints@iisc 2009, Meteorology and Atmospheric Physics 29 pp.983-992]
      47. Mishra S., J Srinivasan and R S Nanjundiah, Meteorology and Atmospheric Physicsatics:Impact of temporal resolution on ITCZ rainfall. Monthly Weather Review. [appears in eprints@iisc 2008, Meteorology and Atmospheric Physics 136 pp.4077-4091]
      48. Sahaney S and R S Nanjundiah, Meteorology and Atmospheric PhysicsaticsImpact of Convective Downdraft on Rainfall in an Aqua-planet model. Annales Geophysicae [appears in Annales Geophysicae@2008, 26(7) pp.1877-1887]
      49. Kumar S V, Nanjundiah R S, Thazhuthaveetil, M J, and Govindrajan R, SERCImpact of Message Compression on the Scalability of an Atmospheric Modelling. [appears in Journal of Parallel Computing@2008, vol.34, no.1, pp.1-16]
      50. V. Vadhana and K. G. Ayappa, Department of Chemical Engineering & Centre for Biosystems Science and Engineering : Structure and Dynamics of Octamethylcyclotetrasiloxane Confined between Mica Surfaces. [appears in J. Phys. Chem. B, 2016, 120 (11), pp 2951–2967]
Publication that used SahasraT (Cray XC40):

      1. Thejna Tharammal and Govindasamy Bala ( CAOS ), and David Noone : Impact of deep convection on the isotopic amount effect in tropical precipitation. [appears in Journal of Geophysical Research: Atmospheres 2017.]

 

Publication that used Bluegene:/L

      1. Preeti Malakar, Thomas George, Sameer Kumar, Rashmi Mittal, Vijay Natarajan, Yogish Sabharwal, Vaibhav Saxena, Sathish Vadhiyar,SERC: A Divide and Conquer Strategy for Scaling Weather Simulations with Multiple Regions of Interest [appears in ACM/IEEE Supercomputing (SC 2012), at Salt Lake City, Utah]
      2. Swastibrata Bhattacharyya, Yoshiyuki Kawazoe, and Abhishek K. SinghSERC: Effect of the Edge Type and Strain on the Structural, Electronic and Magnetic Properties of the BNRs [appears in J Nanosci Nanotechnol @2012 12(3) pp 1899-902]
      3. Karthik Raman, Preethi Rajagopalan and Nagasuma ChandraSERC: Hallmarks of Mycolic Acid Biosynthesis: A Comparative Genomics Study Proteins: Structure, Function and Bioinformatics [appears in eprint@iisc 2007 69 (2) pp. 358-368]
      4. Khodade P., Prabhu R, Chandra N., Raha S.& Govindarajan R.,SERC:Parallel Implementation of Autodock. J. Appl. Crystallogr.[appears in J. Appl. Crystallogr. 2007, 40, pp598-599]
      5. Raman K, Yeturu K and Chandra N, SERC: TargetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis BMC Systems. [appears in BMC Systems Biology 2008,doi:10.1186/1752-0509-2-109]
      6. Yeturu K, Chandra N.,SERC: PocketMatch: A new algorithm to compare binding sites in protein structures [appears in BMC Bioinformatics. 2008;9(1):543. PMID 19091072]
      7. Nagasuma Chandra, Raghu Bhagavat, Eshita Sharma, Srikanth Reddy,Kumar Somasundaram, Physics: Virtual screening, identification and experimental testing of novel inhibitors of PBEF1/Visfatin/NMPRTase for glioma therapyClinical Bioinformatics [appears in Journal of Clinical Bioinformatics 2011, 1:5 doi:10.1186/2043-9113-1-5]
      8. Yeturu K, Chandra N., Bioinformatics: PocketAlign a novel algorithm for aligning binding sites in protein structures. J ChemInf Model [appears in J Chem Inf Model. 2011 Jul 25;51(7):1725-36. doi: 10.1021/ci200132z. Epub 2011 Jun 21]
      9. Praveen Anand, KalidasYeturu and Nagasuma Chandra, Biochemistry: PocketAnnotate: Towards site-based function annotation [appears in Nucleic Acids Res. 2012 Jul;40(Web Server issue):W400-8. doi: 10.1093/nar/gks421. Epub 2012 May 22.
      10. V. Shukla, M. Brachet and R. Pandit, Physics: Turbulence in the two-dimensional Fourier-truncated Gross-Pitaevskii equation []
      11. A.R. Nayak and R. Pandit, Physics: Spiral-wave dynamics in ionically realistic mathematical models for human ventricular tissue
      12. J.M. Kurdestany, R.V. Pai, S. Mukerjee, and R. Pandit, Physics: Phases,transitions, and boundary conditions in a model of interacting bosons.
      13. A. Gupta, P. Perlekar, and R. Pandit, Physics: Two-dimensional, homogeneous,isotropic fluid turbulence with polymer additives. [appears in physics arXiv:1207.4774, 2012.
      14. U. Frisch, S.S. Ray, G. Sahoo, D. Banerjee, and R. Pandit., Physics: Real-space manifestations of bottlenecks in turbulence spectra.
      15. R. Majumder, A.R. Nayak, and R. Pandit, Physics: Nonequilibrium arrhythmic states and transitions in a mathematical model for diffuse fibrosis in human cardiac tissue.
      16. R.V. Pai, J.M. Kurdestany, K. Sheshadri, and R. Pandit, Physics: Bose-hubbard models in confining potentials: Inhomogeneous mean-field theory.
      17. J.M. Kurdestany, R.V. Pai, and R. Pandit, Physics: The inhomogeneous extended bose-hubbard model: Mean-field theory.
      18. S.S. Ray, D. Mitra, P. Perlekar, and R. Pandit, Physics: Dynamic multiscaling in two-dimensional fluid turbulence. [appears in Phys. Rev. Lett. 107, 184503 (2011)
      19. R. Majumder, A.R. Nayak, and R. Pandit, Physics: An overview of spiral- and scroll-wave dynamics in mathematical models for cardiac tissue.
      20. R. Majumder, A. R. Nayak, and R. Pandit, Physics: Scroll-wave dynamics in human cardiac tissue: lessons from a mathematical model with inhomogeneties and fiber architecture.
      21. P. Perlekar, S. S. Ray, D. Mitra, and R. Pandit, Physics: The persistence problem in two-dimensional fluid turbulence.[appears in Phys.Rev.Lett.106:054501,2011]
      22. G. Sahoo, P. Perlekar, and R. Pandit, Physics: Systematics of the magnetic-prandtl-number dependence of homogeneous, isotropic magnetohydrodynamic turbulence. [appears in New J. Phys.@2011, Volume 13]
      23. P. Perlekar, D. Mitra, and R. Pandit, Physics: Direct numerical simulations of statistically steady, homogeneous, isotropic fluid turbulence with polymer additives. [appears in Phys. Rev. E 82, 066313 (2010)]
      24. G. Sahoo, D. Mitra, and R. Pandit, Physics: Dynamo onset as a first-order transition: Lessons from a shell model for magnetohydrodynamics. [appears in Physical Review E – Statistical, Nonlinear and Soft Matter Physics@2010, 81 (3, Par)]
      25. P. Perlekar and R. Pandit, Physics: Turbulence-induced melting of a nonequilibrium vor-tex crystal in a forced thin fluid film.
        [appears in New J. Phys.@2010, Volume 12]
      26. R. Pandit, P. Perlekar, and S.S. Ray, Physics: Statistical properties of turbulence: An overview. Pramana.
      27. P. Perlekar and R. Pandit, Physics: Statistically steady turbulence in thin films: Direct nu- merical simulations with ekman friction. [appears in New J. Phys. 11 No 7 (July 2009) 073003 (15pp)]
      28. T.K. Shajahan, A.R. Nayak, and R. Pandit, Physics: Spiral-wave turbulence and its control in the presence of inhomogeneities in four mathematical models of cardiac tissue.
      29. T.K. Shajahan, S. Sinha, and R. Pandit, Physics: The mathematical modelling of inhomogeneities in ventricular tissue
      30. U. Frisch, S. Kurien, R. Pandit, W. Pauls, S.S. Ray, Physics: A. Wirth, and J-Z. Zhu. Hyperviscosity, galerkin truncation and bottlenecks in turbulence.
      31. S.S. Ray, D. Mitra, , and R. Pandit, Physics: The universality of dynamic multiscaling in homogeneous,isotropic navier-stokes and passive-scalar turbulen [appears in New J. Phys.@2008, Volume 10.
      32. R. Pandit, S.S. Ray, and D. Mitra, Physics: Dynamic multiscaling in turbulence.
      33. R.V. Pai, K. Sheshadri, and R. Pandit, Physics: Phases and transitions in the spin-1 bose-hubbard model: Systematics of a mean-field theory.
      34. T.K. Shajahan, S. Sinha, and R. Pandit, Physics: Spiral-wave dynamics depends sensitively on inhomogeneities in mathematical models for ventricular tissue.
      35. R.V. Pai, K. Sheshadri, and R. Pandit, Physics: Mean-field theory for interacting spin-1 bosons on a lattice.
Research highlights:

      1. Govindasamy Bala, CAOS: Warming from decline in “sweating” rate of plants may not abate in the future: Climate Modeling study [appears in the journal Environmental Research Letters,14 November 2011]
      2. Mr. Jorly Joseph and Prof. Eluvathingal D. Jemmis, IPC: An explanation for Red-, and Blue- Shift in X-H Stretching Frequency of X-H…Y Hydrogen Bonds provides the possibility of H-Bonds with no X-H shifts. [appears in Journal of the American Chemical Society, 129 (15). pp. 4620-4632,31 Jul 2007]