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
The research papers are made available through this page only to ensure easy and timely access to these scholarly works and on a non-commercial basis. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author’s copyright. These works may not be reposited without the explicit permission of the individual copyright holder(s)./span>
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, Physics: Phases,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, CES: The 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, Bioinformatics: PocketMatch: 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, Bioinfomatics: targetTB: 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, Bioinfomatics: Genome 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 Physics: Parallel Implementation of Autodock. J. Appl. Crystallography [appears in J. Appl. Crystallogr, 2007]
      42. Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra, Bioinfomatics: Hallmarks 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, Bioinfomatics: Metabolome 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 Physicsatics: On 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 Physicsatics: The 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 Physicsatics: Impact 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 Physicsatics: Impact 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, SERC: Impact 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]