Articles In Academic Journals

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Year	Title
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. 578-586.
2017	GPU-accelerated high-fidelity simulation of beam-beam effects in particle colliders.  Simulation 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 GPUs.  23th 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 data.  Journal of Computational Biology. 837-843.
2015	ISQuest: Finding insertion sequences in prokaryotic sequence fragment data.  Bioinformatics. btv388.
2014	Simultaneous optimization of the cavity heat load and trip rates in linacs using a genetic algorithm.  Physical 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 Algorithm.  IEEE/ACM transactions on computational biology and bioinformatics. 1.
2013	High-performance implementation of planted motif problem on multicore and GPU.  Concurrency and Computation: Practice and Experience. 1340-1355.
2013	Primary historical sources in the classroom: Discrete mathematics and computer science.  AMC. 12.
2012	Improved efficiency in cryo-EM secondary structure topology determination from inaccurate data.  Journal of bioinformatics and computational biology. 1242006.
2012	Upper and lower I/O bounds for pebbling r-pyramids.  Journal of Discrete Algorithms. 2-12.
2012	Vertex isoperimetric parameter of a computation graph.  International Journal of Foundations of Computer Science. 941-964.
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. 189-201.
2011	Ranking valid topologies of the secondary structure elements using a constraint graph.  Journal of bioinformatics and computational biology. 415-430.
2009	Counting Triangulations of a Convex Polygon.  Resources 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. pdf.  Citeseer.
2007	Collaborative Research: Learning Discrete Mathematics and Computer Science via Primary Historical Sources
2007	Positive Influence and Negative Dependence.  Combinatorics, Probability, and Computing. 29-47.
2006	Sequential and Parallel Algorithms for the NCA Problem on Pure Pointer Machines.  Theoretical Computer Science. 108-135.
2005	A Simple Optimal Solution for the Temporal Precedence Problem on Pure Pointer Machines.  Theory of Computing Systems. 115-130.
2005	Identity Orientation of Complete Bipartite Graphs.  Discrete Mathematics. 173-182.
2004	A Comparative Study of 2QBF Algorithms..  SAT. 323-328.
2003	Design and implementation of a domain specific language for phylogenetic inference.  Journal of bioinformatics and computational biology. 201-230.
2003	The level-ancestor problem on pure pointer machines.  Information processing letters. 275-283.
2002	An optimal algorithm for finding NCA on pure pointer machines.  Algorithm Theory—SWAT 2002. 428-438.
2002	An optimal data structure to handle dynamic environments in non-deterministic computations.  Computer Languages, Systems & Structures. 181-201.
2002	Ancestor problems on pure pointer machines.  Lecture Notes in Computer Science. 263-277.
2002	Efficient parallel algorithms for solvent accessible surface area of proteins.  IEEE Transactions on Parallel and Distributed Systems. 544-555.
2001	Interoperability between bioinformatics tools: A logic programming approach.  Lecture Notes in Computer Science. 153-168.
2000	Data structures for order-sensitive predicates in parallel nondeterministic systems.  Acta Informatica. 21-43.
2000	The temporal precedence problem.  Algorithmica. 288-306.
1999	On the complexity of or-parallelism.  New 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 Computation.  Lecture Notes in Computer Science. 339-348.
1998	Breaking symmetry in complete graphs by orienting edges: asymptotic bounds.  Information processing letters. 227-230.
1998	Efficient algorithms for the temporal precedence problem.  Information processing letters. 71-78.
1998	On the computational complexity of some classical equivalence relations on Boolean functions.  Theory of Computing Systems. 679-693.
1998	The complexity of late-binding in dynamic object-oriented languages.  Principles of Declarative Programming. 213-229.
1997	Space-filling curves and their use in the design of geometric data structures.  Theoretical Computer Science. 3-15.
1996	Balls and bins: A study in negative dependence.  BRICS Report Series.
1996	Digital halftoning algorithms based on optimization criteria and their experimental evaluation.  IEICE TRANSACTIONS on Fundamentals of Electronics, Communications and Computer Sciences. 524-532.
1996	Negative dependence through the FKG inequality.  BRICS Report Series.
1995	A simple proof on the decidability of equivalence between recursive and nonrecursive Datalog programs.  Information processing letters. 279-282.
1995	Space filling curves and their use in the design of geometric data structures.  LATIN’95: Theoretical Informatics. 36-48.
1994	Some correlation inequalities for probabilistic analysis of algorithms.  Max-Planck-Institut für Informatik.
1994	Stochastic majorisation: exploding some myths.  Max-Planck-Institut für Informatik.
1994	The random oracle hypothesis is false.  Journal of Computer and System Sciences. 24-39.
1993	A tool for the analysis of manipulation.  Information processing letters. 117-121.
1993	Improving known solutions is hard.  computational complexity. 168-185.
1993	The circuit subfunction relations are $ sum P_2 $-complete.  Max-Planck-Institut für Informatik.
1993	of Proceedings: Foundations of software technology and theoretical computer science (FSTTCS-93): 13th conference.  Springer.
1992	Relativization: a revisionistic retrospective.  Bulletin of the EATCS. 144-153.
1991	Improving known solutions is hard.  Automata, Languages and Programming. 381-392.
1991	Space bounded computations: Review and new separation results.  Theoretical Computer Science. 289-302.
1990	Structural complexity theory: recent surprises.  SWAT 90. 1-12.

Books

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

Chapters

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Year	Title
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.
2002	An Efficient Parallel Pointer Machine Algorithm for the NCA Problem.  Foundations of Information Technology in the Era of Network and Mobile Computing. Springer.

Conference Papers

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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.