Selected Publications

Articles In Academic Journals

Year Title
2017 An effective computational method incorporating multiple secondary structure predictions in topology determination for cryo-EM imagesIEEE/ACM transactions on computational biology and bioinformatics. 578-586.
2017 GPU-accelerated high-fidelity simulation of beam-beam effects in particle collidersSimulation Series.
2017 Long-Term Simulations of Beam-Beam Dynamics on GPUs
2017 Near Real-Time Probabilistic Damage Diagnosis Using Surrogate Modeling and High Performance Computing
2016 A Memory-Efficient Parallel Simulation of Electron Beam Dynamics Using GPUs23th Annual IEEE International Conference on High Performance Computing.
2015 A dynamic programming algorithm for finding the optimal placement of a secondary structure topology in Cryo-EM dataJournal of Computational Biology. 837-843.
2015 ISQuest: Finding insertion sequences in prokaryotic sequence fragment dataBioinformatics. btv388.
2014 Simultaneous optimization of the cavity heat load and trip rates in linacs using a genetic algorithmPhysical Review Special Topics-Accelerators and Beams. 101003.
2014 Solving the Secondary Structure Matching Problem in CryoEM De Novo Modeling using a Constrained K-shortest Path Graph AlgorithmIEEE/ACM transactions on computational biology and bioinformatics. 1.
2013 High-performance implementation of planted motif problem on multicore and GPUConcurrency and Computation: Practice and Experience. 1340-1355.
2013 Primary historical sources in the classroom: Discrete mathematics and computer scienceAMC. 12.
2012 Improved efficiency in cryo-EM secondary structure topology determination from inaccurate dataJournal of bioinformatics and computational biology. 1242006.
2012 Upper and lower I/O bounds for pebbling r-pyramidsJournal of Discrete Algorithms. 2-12.
2012 Vertex isoperimetric parameter of a computation graphInternational Journal of Foundations of Computer Science. 941-964.
2011 Designing student projects for teaching and learning discrete mathematics and computer science via primary historical sourcesRecent Developments in Introducing a Historical Dimension in Mathematics Education. 189-201.
2011 Ranking valid topologies of the secondary structure elements using a constraint graphJournal of bioinformatics and computational biology. 415-430.
2009 Counting Triangulations of a Convex PolygonResources for Teaching Discrete Mathematics: Classroom Projects, History Modules, and Articles. 209.
2009 Resources for Teaching Discrete Mathematics: Counting Triangulations of a Convex Polygon
2008 Euclid’s Algorithm for the Greatest Common Divisor, www. cs. nmsu. edu/historical-projects/Projects/EuclidGCD. pdfCiteseer.
2007 Collaborative Research: Learning Discrete Mathematics and Computer Science via Primary Historical Sources
2007 Positive Influence and Negative DependenceCombinatorics, Probability, and Computing. 29-47.
2006 Sequential and Parallel Algorithms for the NCA Problem on Pure Pointer MachinesTheoretical Computer Science. 108-135.
2005 A Simple Optimal Solution for the Temporal Precedence Problem on Pure Pointer MachinesTheory of Computing Systems. 115-130.
2005 Identity Orientation of Complete Bipartite GraphsDiscrete Mathematics. 173-182.
2004 A Comparative Study of 2QBF Algorithms.SAT. 323-328.
2003 Design and implementation of a domain specific language for phylogenetic inferenceJournal of bioinformatics and computational biology. 201-230.
2003 The level-ancestor problem on pure pointer machinesInformation processing letters. 275-283.
2002 An optimal algorithm for finding NCA on pure pointer machinesAlgorithm Theory—SWAT 2002. 428-438.
2002 An optimal data structure to handle dynamic environments in non-deterministic computationsComputer Languages, Systems & Structures. 181-201.
2002 Ancestor problems on pure pointer machinesLecture Notes in Computer Science. 263-277.
2002 Efficient parallel algorithms for solvent accessible surface area of proteinsIEEE Transactions on Parallel and Distributed Systems. 544-555.
2001 Interoperability between bioinformatics tools: A logic programming approachLecture Notes in Computer Science. 153-168.
2000 Data structures for order-sensitive predicates in parallel nondeterministic systemsActa Informatica. 21-43.
2000 The temporal precedence problemAlgorithmica. 288-306.
1999 On the complexity of or-parallelismNew Generation Computing. 285-307.
1999 Session VA: Parallel Applications-Chair: CP Ravikumar, Indian Institute of Technology, Delhi A Parallel Monte Carlo Algorithm for Protein Accessible Surface Area ComputationLecture Notes in Computer Science. 339-348.
1998 Breaking symmetry in complete graphs by orienting edges: asymptotic boundsInformation processing letters. 227-230.
1998 Efficient algorithms for the temporal precedence problemInformation processing letters. 71-78.
1998 On the computational complexity of some classical equivalence relations on Boolean functionsTheory of Computing Systems. 679-693.
1998 The complexity of late-binding in dynamic object-oriented languagesPrinciples of Declarative Programming. 213-229.
1997 Space-filling curves and their use in the design of geometric data structuresTheoretical Computer Science. 3-15.
1996 Balls and bins: A study in negative dependenceBRICS Report Series.
1996 Digital halftoning algorithms based on optimization criteria and their experimental evaluationIEICE TRANSACTIONS on Fundamentals of Electronics, Communications and Computer Sciences. 524-532.
1996 Negative dependence through the FKG inequalityBRICS Report Series.
1995 A simple proof on the decidability of equivalence between recursive and nonrecursive Datalog programsInformation processing letters. 279-282.
1995 Space filling curves and their use in the design of geometric data structuresLATIN’95: Theoretical Informatics. 36-48.
1994 Some correlation inequalities for probabilistic analysis of algorithmsMax-Planck-Institut für Informatik.
1994 Stochastic majorisation: exploding some mythsMax-Planck-Institut für Informatik.
1994 The random oracle hypothesis is falseJournal of Computer and System Sciences. 24-39.
1993 A tool for the analysis of manipulationInformation processing letters. 117-121.
1993 Improving known solutions is hardcomputational complexity. 168-185.
1993 The circuit subfunction relations are $ sum P_2 $-completeMax-Planck-Institut für Informatik.
1993 of Proceedings: Foundations of software technology and theoretical computer science (FSTTCS-93): 13th conferenceSpringer.
1992 Relativization: a revisionistic retrospectiveBulletin of the EATCS. 144-153.
1991 Improving known solutions is hardAutomata, Languages and Programming. 381-392.
1991 Space bounded computations: Review and new separation resultsTheoretical Computer Science. 289-302.
1990 Structural complexity theory: recent surprisesSWAT 90. 1-12.

Books

Year Title
2009 Resources for Teaching Discrete Mathematics: Classroom Projects, History Modules, and Articles

Chapters

Year Title
2009 Designing student projects for teaching and learning discrete mathematics and computer science via primary historical sourcesRecent Developments on Introducting a Historical Dimension in Mathematics Education. Washington, D.C.: Mathematical Association of America.
2002 An Efficient Parallel Pointer Machine Algorithm for the NCA ProblemFoundations of Information Technology in the Era of Network and Mobile Computing. Springer.

Conference Papers

Year Title
2017 A Machine Learning Approach for Efficient Parallel Simulation of Beam Dynamics on GPUs.  462-471.
2017 Simulations of Coherent Synchrotron Radiation on Parallel Hybrid GPU/CPU Platform.  3915-3917.
2016 Challenges in matching secondary structures in cryo-EM: An exploration.  1714-1719.
2016 High-Fidelity Simulations of Long-Term Beam-Beam Dynamics on GPUs.  40-43.
2016 Memory-Efficient Parallel Simulation of Electron Beam Dynamics Using GPUs.  212-221.
2016 Optimizing a multiple right-hand side Dslash kernel for intel knights corner.  390-401.
2015 A novel computational method for deriving protein secondary structure topologies using Cryo-EM density maps and multiple secondary structure predictions.  60-71.
2015 High-Performance Simulations of Coherent Synchrotron Radiation on Multicore GPU and CPU Platforms
2015 High-fidelity simulation of collective effects in electron beams using an innovative parallel method.  1-10.
2014 Big data challenges for estimating genome assembler quality.  653-660.
2014 Maximal clique enumeration for large graphs on hadoop framework.  21-30.
2014 ParK: An efficient algorithm for k-core decomposition on multicore processors.  9-16.
2014 pbitMCE: A bit-based approach for maximal clique enumeration on multicore processors.  478-485.
2013 A constrained k-shortest path algorithm to rank the topologies of the protein secondary structure elements detected in cryoem volume maps.  749.
2013 A memory efficient algorithm for adaptive multidimensional integration with multiple GPUs.  169-175.
2013 An efficient deterministic parallel algorithm for adaptive multidimensional numerical integration on GPUs.  486-491.
2013 Genome Assembly on a Multicore System.  1233-1240.
2013 MACHINE ALGORITHM FOR THE NCA PROBLEM.  157.
2012 Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions.  490-497.
2011 A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors.  160-163.
2011 High performance implementation of planted motif problem using suffix trees.  200-206.
2011 Parallelization of mira whole genome and est sequence assembler
2010 An Efficient Multicore Implementation of Planted Motif Problem
2010 Computational and Biological Approach to Understand the 3 UTR-mediated Posttranscriptional Regulation of Alfalfa Cytosolic Glutamine Synthetase Genes
2010 Enumeration of the Geometrically Constrained Alignments of the Secondary Structures Using Constraint Graph
2010 Solving Planted Motif Problem on GPU
2010 Upper and Lower I/O Bounds for Pebbling r-pyramids
2009 Computational analysis using CisFind of the 3’UTR of cytosolic Glutamine synthetase genes involved in posttranscriptional regulation.  343-343.
2009 Historical Sources as a Teaching Tool
2009 Lower Bounds for Accessing Information on Pure Pointer Machines.  103-107.
2008 Designing student projects for teaching and learning discrete mathematics and computer science via primary historical sources
2008 Historical Projects in Discrete Mathematics and Computer Science
2008 Work in Progress -CS0 Course Implementation in Computer Science
2007 Combination of Computational and Biological Appraoches for Cis-regulatory Element Recognition in Glutamine Synthetase Sequences
2007 Computational Identification of Cis-regulatory Elements Associated with Pungency of Chili Peppers.  1188-1192.
2007 Computational Indentification of Cis-regulatory Elements Associated with Pungency of Chili Peppers.  1188-1192.
2007 Tools for Cis-element Recognition and Phylogenetic Tree Construction Based on Conserved Patterns.  1-6.
2007 Work in Prgoress - Peer-Led Team Learning Implementation in Computer Science
2007 Work in progress-peer-led team learning implementation in computer science.  S4A-7.
2006 A Project in Algorithms based on a Primary Historical Source about Catalan Numbers
2006 Some separation results between classes of pointer algorithms
2005 Computational Issues in Exploiting Dependent And-Parallelism in Logic Programming: Leftness Detection in Dynamic Search Trees.  79-94.
2004 Analysis of search based algorithms for satisfiability of propositional and quantified boolean formulas arising from circuit state space diameter problems.  292-305.
2004 Detecting local symmetry axis in 3-dimensional virus structures.  265-270.
2003 An agent-based domain specific framework for rapid prototyping of applications in evolutionary biology.  76-96.
2003 On the complexity of dependent and-parallelism in logic programming.  361-376.
2002 /spl Phi/LOG: a domain specific language for solving phylogenetic inference problems.  9-20.
2002 Semantics-based filtering
2000 Efficient algorithms for protein solvent accessible surface area.  586-592.
1999 A parallel Monte Carlo algorithm for protein accessible surface area computation.  339-348.
1997 On the complexity of parallel implementation of logic programs.  123-137.
1995 On the Computational Complexity of some Classical Equivalence Relations on...
1993 Searching, sorting and randomised algorithms for central elements and ideal counting in posets.  436-443.
1992 On randomized reductions to sparse sets.  239-242.
1992 On the complexity of incremental computation.  172-180.
1990 Quantifiers and approximation.  446-456.
1989 Space bounded computations: Review and new separation results.  49-66.

Research Overview

  • Dr. Ranjan is primarily interested in the development of efficient algorithms and bioinformatics tools for solving biologically important problems. The scholar's more general research and teaching interests are in efficient data structure and algorithm design and analysis, computational complexity theory, parallel computation, discrete mathematics, and optimization and approximation
  • Grants

  • An Innovative GPU-Optimized Multiscale Code for High-Fidelity Simulation of Collective Effects in Electron Beams  awarded by National Science Foundation 2016 - 2019
  • JSA Physics GRA Support FY 18  awarded by Jefferson Science Associates, LLC (Jefferson Lab) 2017 - 2018
  • ABI Innovation: Advanced Informatics And Effective Algorithms To Enable Cryoem Protein Structure Prediction And Density Analysis  awarded by National Science Foundation 2016 - 2018
  • An Innovative GPU-Optimized Multiscale Code for High-Fidelity Simulation of Collective Eects in Electron Beams  awarded by National Science Foundation 2015 - 2018
  • ABI Innovation: Advanced Informatics and Eective Algorithms for Improved CryoEM Protein Structure Prediction and Density Analysis  awarded by National Science Foundation 2014 - 2017
  • JSA Faculty Support FY16  awarded by Jefferson Science Associates, LLC. (Jefferson Lab) 2016
  • Migration of Larc Codes To Next-Generation Hpc Architectures: GPU  awarded by National Institute of Aerospace Associates 2015 - 2016
  • High-Performance Particle Collider Simulations on Parallel Computing Platforms  awarded by ODU Office of Research 2014 - 2016
  • High-Performance Particle Collider Simulations on Parallel Computing Platforms  awarded by Office of Research (Research Seed Funding Program (RSFP)) 2015
  • Advanced phylogenomics of the human and animal pathogen Mycobacterium marinum  awarded by Jeffress Trust 2014 - 2015
  • AE: Computing Alliance for Hispanic-Serving Insitutions  awarded by NSF (Partnership with UTEP, Florida International, University of Puerto Rico-Mayaguez and several other Hispanic serving institutions 2009 - 2012
  • Collaborative Research: Learning Discrete Mathematics and Computer Science via Primary Historical Sources  awarded by NSF 2008 - 2011
  • IGERT: Computational Molecular Biology Group  awarded by NSF (partnership with Iowa State University) 2005 - 2010
  • Designing an effective real-time methodology to evaluate circadian rhythm in cultured breast cell lines  awarded by NMSU Office of the Vice President for Research 2009
  • CREST: Center for Research Excellence in Bioinformatics and Computational Biology  awarded by NSF 2004 - 2009
  • Frameworks for the Development of Efficient and Scalable Knowledge-based Systems  awarded by NSF 2003 - 2009
  • Bioinformatics Analysis for understanding Nitrogen Assimilation in Plants  awarded by NMSU Office of the Vice President for Research 2007 - 2008
  • Graduate Assistants in Areas of National Need  awarded by Department of Education 2003 - 2008
  • SBIR Phase II: Cheminformatics Teaching Tools for Cheminformatics Virtual Classroom  awarded by NSF 2006 - 2007
  • CRI: Computing Support for the Next Generation Application-driven Delarative Programming Systems  awarded by NSF 2005 - 2007
  • Improving Protein Secondary Structure Prediction using 3-dimensional Spatial Constraints of the Protein  awarded by Los Alamos National Labs 2005 - 2007
  • Phylogenetic predictions of the capabilities of novel biothreat agents  awarded by Los Alamos National Labs 2005 - 2007
  • Collaborative Research: The Impact of Rapid Anthropogenic Land Cover Change in the Chaco and Interior Atlantic Forest in Paraguay on Hantavirus Ecology  awarded by National Institute of Health 2004 - 2007
  • Cellular and Molecular Interactions among Genes in Cerebellar Development over Time and Space  awarded by NSF (Supplement to the CREST grant) 2006
  • Small angle x-ray scattering studies of lipi/cholesterol bilayers, aerogel biosensors, and nanocomposite thermites  awarded by NSF (Supplemented by a CREST grant) 2006
  • Teaching Discrete Mathematics via Original Historical Sources  awarded by NSF 2003 - 2006
  • Algorithms and Software Development for QCD computations on Xeon-Phi Architecture  awarded by Jeerson National Lab 2014 -
  • Doctoral Student support for computational physics  awarded by Jefferson National Lab 2012 -
  • Education And Training

  • Ph.D. in Computer Science, Cornell University 1992
  • M.S. in Computer Science, Cornell University 1990
  • Bachelor of Technology in Computer Science, Indian Institute of Technology Kanpur 1987
  • Full Name

  • Desh Ranjan