Professor & Chair
Computer Science

Desh Ranjan

3303 Engr & Comp Sci Bldg
Norfolk, 23529

Ph.D. in Computer Science, Cornell University, (1992)

M.S. in Computer Science, Cornell University, (1990)

Other in Computer Science, Indian Institute of Technology Kanpur, (1987)

Contracts, Grants and Sponsored Research

Ranjan, D. "An Innovative GPU-Optimized Multiscale Code for High-Fidelity Simulation of Collective Eects in Electron Beams" $473315. . , 2015 - , 2018
Ranjan, D. "ABI Innovation: Advanced Informatics and Eective Algorithms for Improved CryoEM Protein Structure Prediction and Density Analysis" $589703. . , 2014 - , 2017
Ranjan, D. "Advanced Phylogenomics of the Human and Animal Pathogen Mycobac- terium Marinum" $100000. . , 2014 - , 2016
Ranjan, D. "High-Performance Particle Collider Simulations on Parallel Computing Platforms" $40000. Old Dominion University. , 2014 - , 2016
Ranjan, D. "Migration of Larc Codes To Next-Generation Hpc Architectures: GPU" $23660.00 . Other. December, 2015 - November, 2016
Ranjan, D. "Doctoral Student support for computational physics" $65000. . , 2012 - ,
Ranjan, D. "AE: Computing Alliance for Hispanic-Serving Insitutions" $2000000. Federal. , 2009 - , 2012
Ranjan, D. "Collaborative Research: Learning Discrete Mathematics and Computer Science via Primary Historical Sources" $500000. Federal. , 2008 - , 2011
Ranjan, D. "IGERT: Computational Molecular Biology Group" $2963687. Federal. , 2005 - , 2010
Ranjan, D. "Designing an effective real-time methodology to evaluate circadian rhythm in cultured breast cell lines" $50000. State. , 2009 - , 2009
Ranjan, D. "CREST: Center for Research Excellence in Bioinformatics and Computational Biology" $4500000. Federal. , 2004 - , 2009
Ranjan, D. "Frameworks for the Development of Efficient and Scalable Knowledge-based Systems" $1500000. Federal. , 2003 - , 2009
Ranjan, D. "Bioinformatics Analysis for understanding Nitrogen Assimilation in Plants" $50000. State. , 2007 - , 2008
Ranjan, D. "Graduate Assistants in Areas of National Need" $495840. Federal. , 2003 - , 2008
Ranjan, D. "SBIR Phase II: Cheminformatics Teaching Tools for Cheminformatics Virtual Classroom" $105000. Federal. , 2006 - , 2007
Ranjan, D. "CRI: Computing Support for the Next Generation Application-driven Delarative Programming Systems" $102879. Federal. , 2005 - , 2007
Ranjan, D. "Improving Protein Secondary Structure Prediction using 3-dimensional Spatial Constraints of the Protein" $122000. Federal. , 2005 - , 2007
Ranjan, D. "Phylogenetic predictions of the capabilities of novel biothreat agents" $135000. Federal. , 2005 - , 2007
Ranjan, D. "Collaborative Research: The Impact of Rapid Anthropogenic Land Cover Change in the Chaco and Interior Atlantic Forest in Paraguay on Hantavirus Ecology" $186000. Federal. , 2004 - , 2007
Ranjan, D. "Teaching Discrete Mathematics via Original Historical Sources" $74432. Federal. , 2003 - , 2006
Ranjan, D. "Cellular and Molecular Interactions among Genes in Cerebellar Development over Time and Space" $22000. Federal. June, 2006 - August, 2006
Ranjan, D. "Small angle x-ray scattering studies of lipi/cholesterol bilayers, aerogel biosensors, and nanocomposite thermites" $26000. Federal. June, 2006 - August, 2006

Research Interests

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

Articles

Biswas, A. (2017). An effective computational method incorporating multiple secondary structure predictions in topology determination for cryo-EM images. IEEE/ACM transactions on computational biology and bioinformatics 14 (3) , pp. 578–586.
Terzic, B. (2017). Long-Term Simulations of Beam-Beam Dynamics on GPUs.
Warner, J. E. (2017). Near Real-Time Probabilistic Damage Diagnosis Using Surrogate Modeling and High Performance Computing.
Biswas, A. (2015). A dynamic programming algorithm for finding the optimal placement of a secondary structure topology in Cryo-EM data. Journal of Computational Biology 22 (9) , pp. 837–843.
Biswas, A. (2015). ISQuest: finding insertion sequences in prokaryotic sequence fragment data. Bioinformatics 31 (21) , pp. 3406–3412.
Terzic, B. (2014). Simultaneous optimization of the cavity heat load and trip rates in linacs using a genetic algorithm. Physical Review Special Topics-Accelerators and Beams 17 (10) , pp. 101003.
Ranjan, D. (2014). Solving the Secondary Structure Matching Problem in CryoEM De Novo Modeling using a Constrained K-shortest Path Graph Algorithm. IEEE/ACM Transactions on Computational Biology and Bioinformatics (1) , pp. 1.
Dasari, N. Shailaja. (2013). High-performance implementation of planted motif problem on multicore and GPU. Concurrency and Computation: Practice and Experience 25 (10) , pp. 1340–1355.
Barnett, J. (2013). Primary historical sources in the classroom: Discrete mathematics and computer science. AMC 10 , pp. 12.
Biswas, A. (2012). Improved efficiency in cryo-EM secondary structure topology determination from inaccurate data. Journal of bioinformatics and computational biology 10 (03) , pp. 1242006.
Ranjan, D. (2012). Upper and lower I/O bounds for pebbling r-pyramids. Journal of Discrete Algorithms 14 , pp. 2–12.
Ranjan, D. (2012). Vertex isoperimetric parameter of a computation graph. International Journal of Foundations of Computer Science 23 (04) , pp. 941–964.
Barnett, J. (2011). Designing student projects for teaching and learning discrete mathematics and computer science via primary historical sources. Recent Developments in Introducing a Historical Dimension in Mathematics Education , pp. 189–201.
Al Nasr, K. (2011). Ranking valid topologies of the secondary structure elements using a constraint graph. Journal of bioinformatics and computational biology 9 (03) , pp. 415–430.
Ranjan, D. (2009). Counting Triangulations of a Convex Polygon. Resources for Teaching Discrete Mathematics: Classroom Projects, History Modules, and Articles (74) , pp. 209.
Ranjan, D. (2009). Resources for Teaching Discrete Mathematics: Counting Triangulations of a Convex Polygon.
Ranjan, D. (2008). Euclid’s Algorithm for the Greatest Common Divisor, www. cs. nmsu. edu/historical-projects/Projects/EuclidGCD. pdf. Citeseer.
Barnett, J. (2007). Collaborative Research: Learning Discrete Mathematics and Computer Science via Primary Historical Sources.
Dubhashi, D. (2007). Positive Influence and Negative Dependence. Combinatorics, Probability, and Computing 16 (1) , pp. 29-47.
Dal Palu, A. (2006). Sequential and Parallel Algorithms for the NCA Problem on Pure Pointer Machines. Theoretical Computer Science 352 (1-3) , pp. 108-135.
Pontelli, E. (2005). A Simple Optimal Solution for the Temporal Precedence Problem on Pure Pointer Machines. Theory of Computing Systems 38 (1) , pp. 115-130.
Harary, F. (2005). Identity Orientation of Complete Bipartite Graphs. Discrete Mathematics 290 (2/3) , pp. 173-182.
Ranjan, D. (2004). A Comparative Study of 2QBF Algorithms.. SAT 4 , pp. 323–328.
Pontelli, E. (2003). Design and implementation of a domain specific language for phylogenetic inference. Journal of bioinformatics and computational biology 1 (02) , pp. 201–230.
Ranjan, D. (2003). The level-ancestor problem on pure pointer machines. Information processing letters 85 (5) , pp. 275–283.
Dal Palú, A. (2002). An optimal algorithm for finding NCA on pure pointer machines. Algorithm Theory—SWAT 2002 , pp. 428–438.
Pontelli, E. (2002). An optimal data structure to handle dynamic environments in non-deterministic computations. Computer Languages, Systems & Structures 28 (2) , pp. 181–201.
Pontelli, E. (2002). Ancestor problems on pure pointer machines. Lecture notes in computer science , pp. 263–277.
Futamura, N. (2002). Efficient parallel algorithms for solvent accessible surface area of proteins. IEEE Transactions on Parallel and Distributed Systems 13 (6) , pp. 544–555.
Iglesias, J. Raymundo. (2001). Interoperability between bioinformatics tools: A logic programming approach. Lecture notes in computer science 1990 , pp. 153–168.
Ranjan, D. (2000). Data structures for order-sensitive predicates in parallel nondeterministic systems. Acta Informatica 37 (1) , pp. 21–43.
Ranjan, D. (2000). The temporal precedence problem. Algorithmica 28 (3) , pp. 288–306.
Ranjan, D. (1999). On the complexity of or-parallelism. New Generation Computing 17 (3) , pp. 285–307.
Alura, S. (1999). Session VA: Parallel Applications-Chair: CP Ravikumar, Indian Institute of Technology, Delhi A Parallel Monte Carlo Algorithm for Protein Accessible Surface Area Computation. Lecture Notes in Computer Science 1745 , pp. 339–348.
Harary, F. (1998). Breaking symmetry in complete graphs by orienting edges: asymptotic bounds. Information processing letters 67 (5) , pp. 227–230.
Ranjan, D. (1998). Efficient algorithms for the temporal precedence problem. Information processing letters 68 (2) , pp. 71–78.
Borchert, B. (1998). On the computational complexity of some classical equivalence relations on Boolean functions. Theory of Computing Systems 31 (6) , pp. 679–693.
Pontelli, E. (1998). The complexity of late-binding in dynamic object-oriented languages. Principles of Declarative Programming , pp. 213–229.
Asano, T. (1997). Space-filling curves and their use in the design of geometric data structures. Theoretical Computer Science 181 (1) , pp. 3–15.
Dubhashi, D. P. (1996). Balls and bins: A study in negative dependence. BRICS Report Series 3 (25).
Asano, T. (1996). Digital halftoning algorithms based on optimization criteria and their experimental evaluation. IEICE TRANSACTIONS on Fundamentals of Electronics, Communications and Computer Sciences 79 (4) , pp. 524–532.
Dubhashi, D. P. (1996). Negative dependence through the FKG inequality. BRICS Report Series 3 (27).
Leung, H. (1995). A simple proof on the decidability of equivalence between recursive and nonrecursive Datalog programs. Information processing letters 55 (5) , pp. 279–282.
Asano, T. (1995). Space filling curves and their use in the design of geometric data structures. LATIN’95: Theoretical Informatics , pp. 36–48.
Dubhashi, D. P. (1994). Some correlation inequalities for probabilistic analysis of algorithms. Max-Planck-Institut für Informatik.
Dubhashi, D. P. (1994). Stochastic majorisation: exploding some myths. Max-Planck-Institut für Informatik.
Chang, R. (1994). The random oracle hypothesis is false. Journal of Computer and System Sciences 49 (1) , pp. 24–39.
Ranjan, D. (1993). A tool for the analysis of manipulation. Information processing letters 45 (3) , pp. 117–121.
Dubhashi, D. P. (1993). Foundations of software technology and theoretical computer science (FSTTCS-93): 13th conference. Springer.
Ranjan, D. (1993). Improving known solutions is hard. computational complexity 3 (2) , pp. 168–185.
Borchert, B. (1993). The circuit subfunction relations are $ sum P_2 $-complete. Max-Planck-Institut für Informatik.
Chang, R. (1992). Relativization: a revisionistic retrospective. Bulletin of the EATCS 47 , pp. 144–153.
Ranjan, D. (1991). Improving known solutions is hard. Automata, Languages and Programming , pp. 381–392.
Ranjan, D. (1991). Space bounded computations: Review and new separation results. Theoretical Computer Science 80 (2) , pp. 289–302.
Hartmanis, J. (1990). Structural complexity theory: recent surprises. SWAT 90 , pp. 1–12.

Books

Hopkins, B. (2009). Resources for Teaching Discrete Mathematics: Classroom Projects, History Modules, and Articles. MAA.

Book Chapters

Ranjan, D. (2009). Counting Triangulations of a Convex Polygon Resources for Teaching Discrete Mathematics: Classroom Projects, History Modules, and Articles (pp. 209-215) Mathematical Association of America MAA Notes 74.
Barnett, J. (2009). Designing student projects for teaching and learning discrete mathematics and computer science via primary historical sources Recent Developments on Introducting a Historical Dimension in Mathematics Education Washington, D.C.: Mathematical Association of America.
Dal Palú, A. (2002). An Efficient Parallel Pointer Machine Algorithm for the NCA Problem Foundations of Information Technology in the Era of Network and Mobile Computing (pp. 157–168) Springer.

Conference Proceeding

Arumugam, K. (2017). A Machine Learning Approach for Efficient Parallel Simulation of Beam Dynamics on GPUs Parallel Processing (ICPP), 2017 46th International Conference on (pp. 462–471).
Arumugam, K. (2017). GPU-accelerated high-fidelity simulation of beam-beam effects in particle colliders Proceedings of the Summer Simulation Multi-Conference (pp. 5).
Terzic, B. (2017). Simulations of Coherent Synchrotron Radiation on Parallel Hybrid GPU/CPU Platform 8th Int. Particle Accelerator Conf.(IPAC’17), Copenhagen, Denmark, 14a 19 May, 2017 (pp. 3915–3917).
Haslam, D. (2016). Challenges in matching secondary structures in cryo-EM: An exploration Bioinformatics and Biomedicine (BIBM), 2016 IEEE International Conference on (pp. 1714–1719).
Terzic, B. (2016). High-Fidelity Simulations of Long-Term Beam-Beam Dynamics on GPUs 12th Int. Computational Accelerator Physics Conf.(ICAP’15), Shanghai, China, 12-16 October 2015 (pp. 40–43).
Arumugam, K. (2016). Memory-Efficient Parallel Simulation of Electron Beam Dynamics Using GPUs High Performance Computing (HiPC), 2016 IEEE 23rd International Conference on (pp. 212–221).
Walden, A. (2016). Optimizing a multiple right-hand side Dslash kernel for intel knights corner International Conference on High Performance Computing (pp. 390–401).
Biswas, A. (2015). A novel computational method for deriving protein secondary structure topologies using Cryo-EM density maps and multiple secondary structure predictions International Symposium on Bioinformatics Research and Applications (pp. 60–71).
Arumugam, K. (2015). High-fidelity simulation of collective effects in electron beams using an innovative parallel method Proceedings of the Conference on Summer Computer Simulation (pp. 1–10).
Biswas, A. (2014). Big data challenges for estimating genome assembler quality Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 653–660).
Dasari, N. Shailaja. (2014). Maximal clique enumeration for large graphs on hadoop framework Proceedings of the first workshop on Parallel programming for analytics applications (pp. 21–30).
Dasari, N. Shailaja. (2014). ParK: An efficient algorithm for k-core decomposition on multicore processors Big Data (Big Data), 2014 IEEE International Conference on (pp. 9–16).
Dasari, N. Shailaja. (2014). pbitMCE: A bit-based approach for maximal clique enumeration on multicore processors Parallel and Distributed Systems (ICPADS), 2014 20th IEEE International Conference on (pp. 478–485).
Nasr, K. Al. (2013). A constrained k-shortest path algorithm to rank the topologies of the protein secondary structure elements detected in cryoem volume maps Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics (pp. 749).
Arumugam, K. (2013). A memory efficient algorithm for adaptive multidimensional integration with multiple GPUs High Performance Computing (HiPC), 2013 20th International Conference on (pp. 169–175).
Arumugam, K. (2013). An efficient deterministic parallel algorithm for adaptive multidimensional numerical integration on GPUs Parallel Processing (ICPP), 2013 42nd International Conference on (pp. 486–491).
Biswas, A. (2013). Genome Assembly on a Multicore System Trust, Security and Privacy in Computing and Communications (TrustCom), 2013 12th IEEE International Conference on (pp. 1233–1240).
Dal Palü, A. (2013). MACHINE ALGORITHM FOR THE NCA PROBLEM Foundations of Information Technology in the Era of Network and Mobile Computing: IFIP 17th World Computer Congress—TC1 Stream/2nd IFIP International Conference on Theoretical Computer Science (TCS 2002) August 25–30, 2002, Montréal, Québec, Canada (pp. 157).
Al Nasr, K. (2012). Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (pp. 490–497).
Biswas, A. (2011). A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors Bioinformatics and Biomedicine (BIBM), 2011 IEEE International Conference on (pp. 160–163).
Dasari, N. Shailaja. (2011). High performance implementation of planted motif problem using suffix trees High Performance Computing and Simulation (HPCS), 2011 International Conference on (pp. 200–206).
Biswas, A. (2011). Parallelization of mira whole genome and est sequence assembler Workshop on Parallel Algorithms and Software for Analysis of Massive Graphs (ParGraph).
Dasari, N. S.. (2010). Solving Planted Motif Problem on GPU Vienna, Austria: The 19th International Conference on Parallel Architectures and Compilation Techniques (PACT).
Al Nasr, K. (2010). Enumeration of the Geometrically Constrained Alignments of the Secondary Structures Using Constraint Graph Chongqing: International Conference on Bioinformatics and Systems Biology (BSB 2010).
Ranjan, D. (2010). Upper and Lower I/O Bounds for Pebbling r-pyramids London: International Workshop on Combinatorial Algorithms (IWOCA2010).
Dasari, N. S.. (2010). An Efficient Multicore Implementation of Planted Motif Problem Caen: An Efficient Multicore Implementation.
Simon, B. (2010). Computational and Biological Approach to Understand the 3 UTR-mediated Posttranscriptional Regulation of Alfalfa Cytosolic Glutamine Synthetase Genes Hawaii: Proceedings of hte 2nd International Conference on Bioinformatics and Computational Biology (BICoB2010).
Vasudevan-Simon, B. (2009). Computational analysis using CisFind of the 3’UTR of cytosolic Glutamine synthetase genes involved in posttranscriptional regulation Bioinformatics and Biomedicine Workshop, 2009. BIBMW 2009. IEEE International Conference on (pp. 343–343).
Cloteaux, B. (2009). Lower Bounds for Accessing Information on Pure Pointer Machines (pp. 103-107) FCS '09: Proceedings of the International Conference on Foundations of Computer Science.
Pivkina, I. (2009). Historical Sources as a Teaching Tool Chattanooga, TN: Proceedings of the 40th ACM Technical Symposium on Computer Science Education 2009.
Beheshti, M. (2008). Work in Progress -CS0 Course Implementation in Computer Science IEEE Frontiers in Education 2008.
Barnett, J. (2008). Designing student projects for teaching and learning discrete mathematics and computer science via primary historical sources Mexico City: History and Pedagogy of Mathematics satellite meeting of the 11th International Congress on Mathematics Education.
Lodder, J. (2008). Historical Projects in Discrete Mathematics and Computer Science Monterrey: International Congress on Mathematics Education.
Ji, T. (2007). Computational Identification of Cis-regulatory Elements Associated with Pungency of Chili Peppers Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on (pp. 1188–1192).
Ji, T. (2007). Computational Indentification of Cis-regulatory Elements Associated with Pungency of Chili Peppers (pp. 1188-1192) IEEE Bioinformatics and Bio-Engineering 2007.
Ji, T. (2007). Tools for Cis-element Recognition and Phylogenetic Tree Construction Based on Conserved Patterns (pp. 1-6) Computers and their Applications 2007.
Alo, R. (2007). Work in Prgoress - Peer-Led Team Learning Implementation in Computer Science IEEE Frontiers in Education 2007.
Aló, R. A. (2007). Work in progress-peer-led team learning implementation in computer science Frontiers In Education Conference-Global Engineering: Knowledge Without Borders, Opportunities Without Passports, 2007. FIE’07. 37th Annual (pp. S4A–7).
Ji, T. (2007). Combination of Computational and Biological Appraoches for Cis-regulatory Element Recognition in Glutamine Synthetase Sequences Pattern Recognition in Bioinformatics 2007.
Pengelley, D. (2006). A Project in Algorithms based on a Primary Historical Source about Catalan Numbers ACM Technical symposium on Computer Science Education (SIGCSE 2006).
Cloteaux, B. (2006). Some separation results between classes of pointer algorithms Workshop on Description Complexity of Formal Systems.
Wu, Y. (2005). Computational Issues in Exploiting Dependent And-Parallelism in Logic Programming: Leftness Detection in Dynamic Search Trees (pp. 79-94) 12th International Conference on Logic Programming and Artificial Intelligence Reasoning (LPAR), Lecture Notes in Computer Science #3835.
Tang, D. (2004). Analysis of search based algorithms for satisfiability of propositional and quantified boolean formulas arising from circuit state space diameter problems International Conference on Theory and Applications of Satisfiability Testing (pp. 292–305).
He, J. (2004). Detecting local symmetry axis in 3-dimensional virus structures Proceedings of the second conference on Asia-Pacific bioinformatics-Volume 29 (pp. 265–270).
Son, T. Cao. (2003). An agent-based domain specific framework for rapid prototyping of applications in evolutionary biology International Workshop on Declarative Agent Languages and Technologies (pp. 76–96).
Wu, Y. (2003). On the complexity of dependent and-parallelism in logic programming ICLP (pp. 361–376).
Pontelli, E. (2002). /spl Phi/LOG: a domain specific language for solving phylogenetic inference problems Bioinformatics Conference, 2002. Proceedings. IEEE Computer Society (pp. 9–20).
Gupta, G. (2002). Semantics-based filtering 4th International Symposium on Practical Applications of Declarative Languages, PADL 2002.
Futamura, N. (2000). Efficient algorithms for protein solvent accessible surface area High Performance Computing in the Asia-Pacific Region, 2000. Proceedings. The Fourth International Conference/Exhibition on (pp. 586–592).
Aluru, S. (1999). A parallel Monte Carlo algorithm for protein accessible surface area computation HiPC (pp. 339–348).
Pontelli, E. (1997). On the complexity of parallel implementation of logic programs Foundations of Software Technology and Theoretical Computer Science (pp. 123–137).
Borchert, B. (1995). On the Computational Complexity of some Classical Equivalence Relations on... Forschungsberichte Mathematische Logik, Universitat Heidelberg, Bericht Nr. 18, Dezember.
Dubhashi, D. P. (1993). Searching, sorting and randomised algorithms for central elements and ideal counting in posets International Conference on Foundations of Software Technology and Theoretical Computer Science (pp. 436–443).
Ranjan, D. (1992). On randomized reductions to sparse sets Structure in Complexity Theory Conference, 1992., Proceedings of the Seventh Annual (pp. 239–242).
Chari, S. (1992). On the complexity of incremental computation International Symposium on Mathematical Foundations of Computer Science (pp. 172–180).
Panconesi, A. (1990). Quantifiers and approximation Proceedings of the twenty-second annual ACM symposium on Theory of computing (pp. 446–456).
Hartmanis, J. (1989). Space bounded computations: Review and new separation results Mathematical Foundations of Computer Science 1989 (pp. 49–66).

Presentations

Ranjan, D. ( 2006). Bioinformatics at NMSU .
Ranjan, D. ( 2005). NMSU Center for Research Excellence in Bioinformatics and Computational Biology .
  • Sage Graduate Fellowship, Cornell University
  • 2011: Outstanding Faculty Member, Iowa State University
  • 2009: NMSU Millionaire Researcher, New Mexico State University
  • 2008: NMSU Millionaire Researcher, New Mexico State University
  • 2007: University Research Council Distinguished Career Award for Exceptional Achievements in Creative Scholarly Activity, New Mexico State University
  • 2006: Outstanding Faculty Achievement Award, New Mexico State University
  • 1995: Morrison Award for the best Technical Presentation, Regional ACM Meeting at Ghost Ranch, New Mexico