Meera Sitharam, Audrey St. John, Jessica Sidman, Handbook of Geometric Constraint Systems Principles 2018

Aysegul Ozkan, Meera Sitharam, Jose C. Flores-Canales, Rahul Prabhu, and Maria
Kurnikova, Baseline
Comparisons of Complementary Sampling Methods for Assembly Driven by
Short-Ranged Pair Potentials toward Fast and Flexible HybridizationJournal
of Chemical Theory and Computation 2021, 17, 3.

PDF

Ruijin Wu, Rahul Prabhu, Aysegul Ozkan, and Meera Sitharam,
Rapid prediction of crucial hotspot interactions for icosahedral viral
capsid self-assembly by energy landscape atlasing validated by mutagenesis,
PLoS computational biology 16.10 (2020): e1008357.

PDF

Rahul Prabhu, Meera Sitharam, Aysegul Ozkan, and Ruijin Wu. Atlasing
of assembly landscapes using distance geometry and graph rigidity,
2020. Journal of Chemical Information and Modeling. 2020, 60, 10, 4924–4957.

PDF

Meera Sitharam, Andrew Vince, Menghan Wang, Miklós Bóna Symmetry in Sphere-based Assembly Configuration Spaces Symmetry Journal 2016

Aysegul Ozkan, Meera Sitharam, Best of Both Worlds: Uniform sampling in Cartesian and Cayley Molecular Assembly Configuration Space 2014

Aysegul Ozkan, Jose C. Flores-Canales, Meera Sitharam, Maria Kurnikova Fast and Flexible Geometric Method For Enhancing MC Sampling of Compact Configurations For Protein Docking Problem 2014

M. Sitharam, Modeling Supramolecular Assembly Discrete and Topological Methods in biology, Springer volume, Ed N. Jonoschka and M. Saito, 2013

R. Wu, A. Ozkan, A. Bennett, M. Agbandje-Mckenna, M. Sitharam, Robustness of icosahedral viral shell assembly predicted by configuration space atlasing using EASAL Proceedings of ACM-Bioinformatics and Computational biology 2012

Aysegul Ozkan, James Pence, J. Peters, M. Sitharam EASAL- Efficient Atlasing of Assembly Landscapes: theory, algorithms, applications and software architecture Journal version on ArXiv 2012

Aysegul Ozkan, Meera Sitharam, “EASAL: efficient atlasing, search and analysis of assembly landscapes,” Proceedings of IEEE BiCoB, New Orleans, March, 2011. Journal version in preparation.

M. B'ona, M. Sitharam, A. Vince, Tree orbits under permutation group action: algorithms, enumeration and application to virus assembly (arxiv). , Bulletin of Mathematical Biology, 2011 DOI: 10.1007/s11538-010-9606-4

M. B'ona, M. Sitharam ``Icosahedral group action and virus assembly pathway probability," Accepted to Computational and Mathematical methods in medicine special issue on Mathematical Virology (Stockley and Twarock ed.s), 2008

M. Sitharam, M. Agbandje-McKenna, ``Sampling Virus assembly pathways: avoiding dynamics using geometric constraint decomposition," Accepted to Journal of Computational Biology, 2006

M. Sitharam, M. B'ona Combinatorial enumeration of symmetric macromolecular assembly pathways Accepted to the international conference on bioinformatics and applications, ICBA 2004.

M. Sitharam, M. Agbandje-Mckenna ``Modeling Virus self-assembly pathways using computational algebra and geometry,'' Proceedings of the Applications of Computer Algebra Symposium, ACA 2004.

** Geometric Constraints, Rigidity, Configuration Spaces **

Daniel Irving Bernstein, Sean Dewar, Steven J. Gortler, Anthony Nixon, Meera Sitharam, Louis Theran Maximum likelihood thresholds via graph rigidity 2021. Preprint available on arXiv:1910.05390.

William Sims and Meera Sitharam Flip Paths Between Lattice Triangulations 2021. Prepint available on arXiv:2008.11292.

Youngquist, Jeremy, Meera Sitharam, and Jörg Peters.
A slice-traversal algorithm for very large mapped volumetric models. Computer-Aided Design, volume 141, pages 103102, 2021.

PDF

Meera Sitharam, Andrew Vince The Maximum Matroid of a Graph Preprint available on arXiv:1910.05390.

Sadjadi, Mahdi, Varda F. Hagh, Mingyu Kang, Meera Sitharam, Robert Connelly, Steven J. Gortler, Louis Theran, Miranda Holmes-Cerfon, and Michael F. Thorpe.
Realizations of Isostatic Material Frameworks. physica status solidi (b), pages 2000555, 2021.

PDF

Aysegul Ozkan, Rahul Prabhu, Troy Baker, James Pence, Jorg Peters, and Meera
Sitharam. Algorithm 990:
Efficient Atlasing and Search of Configuration Spaces of Point-Sets Constrained
by Distance Intervals. ACM Trans. Math. Softw., 44(4):48:1–48:30, July
2018.

VIDEO available,
PDF

Meera Sitharam, Jeremy Youngquist, Maxwell Nolan, Jörg Peters
Corner-Sharing Tetrahedra for Modeling Micro-Structure,
Computer-Aided Design, 14 (2019): 164-178.

PDF

Meera Sitharam, Troy Baker Overview and Preliminaries In Meera Sitharam, Audrey St John, Jessica Sidman, editors, Handbook of Geometric Constraint Systems Principles, chapter 1, pages 1–18. CRC Press, 2018

Troy Baker, Meera Sitharam, Rahul Prabhu Geometric Constraint Decomposition: The General Case In Meera Sitharam, Audrey St John, Jessica Sidman, editors, Handbook of Geometric Constraint Systems Principles, chapter 7, pages 285–310. CRC Press, 2018

Meera Sitharam, Menghan Wang, Joel Willoughby, Rahul Prabhu Cayley Configuration Spaces In Meera Sitharam, Audrey St John, Jessica Sidman, editors, Handbook of Geometric Constraint Systems Principles, chapter 10, pages 181–198. CRC Press, 2018

Menghan Wang, Meera Sitharam Combinatorial Rigidity and Independence of Generalized Pinned Subspace-Incidence Constraint Systems Proceedings of the ADG 2015

Meera Sitharam, Joel Willoughby On Flattenability of Graphs Proceedings of the ADG 2015.

Troy Baker, Meera Sitharam, Menghan Wang, Joel Willoughby Optimal Decomposition and Recombination of Isostatic Geometric Constraint Systems for Designing Layered Materials Computer Aided Geometric Design 2015

Menghan Wang, Meera Sitharam Cayley Analysis of Mechanism Configuration Spaces using CayMos: Software Functionalities and Architecture> ACM TOMS 2015

M. Sitharam, M. Wang
How the Beast really moves: Cayley
analysis of mechanism realization spaces using CayMos,
Proceedings of
SIAM Solid and Physical Modeling, 2013, and also in

Computer-Aided
Design, Volume 46, January 2014, Pages 205-210, ISSN 0010-4485,
CayMos web-accessible software and videos

Meera Sitharam, Menghan Wang, Heping Gao, Cayley analysis of 1-dof tree-decomposable linkages Part I: algebraic complexity> 2013

Meera Sitharam, Menghan Wang, Heping Gao,
,
Cayley analysis of 1-dof tree-decomposable linkages Part II:
combinatorial characterization
2013

CayMos sourcecode is deposited on Google code

J. Cheng, M. Sitharam, I. Streinu, Nucleation-free 3D rigidity short preliminary version appeared in: Proceedings of Canadian Conf on Comput. Geom. 2009 (full journal version 2013),

J. Cheng, M. Sitharam ``Better bounds for rank of 3D rigidity matroid of general graphs,'' Preliminary short version appeared in proceedings of FWCG 2010. Accepted to J. Combinatorial Theory, B, 2013

M. Sitharam, Y. Zhou, J. Peters Reconciling Combinatorial Preprocessors for Geometric constraint systems International Journal of Computational Geometry and Applications, 20(6):631–651, 2010.

K. Haller, A. Lee, M. Sitharam, I. Streinu, N. White `` Body-and-Cad constraint systems'' ACM-SAC Geometric constraints and Reasoning, 2009 and FwCG 2008. Computational Geometry Theory and Applications. CoRR abs/1006.1126: (2010) To appear

M. Sitharam, J. Peters, Y. Zhou, ``Combinatorial optimization of algebraic complexity of minimal geometric constraint sytems'' Journal of Symbolic Computation, 2010

M. Sitharam, H. Gao Characterizing graphs with convex configuration spaces (arXiv) Discrete and Computational Geometry 2009.

H. Gao, M. Sitharam `` Henneberg graphs with efficient configuration spaces'' ACM-SAC Geometric constraints and Reasoning, 2009.

H. Gao, M. Sitharam Characterizing 1-dof Henneberg graphs with efficient configuration spaces (arXiv) 2008.

M. Sitharam "Characterizing Well-formed systems of incidences for resolving collections of rigid bodies" IJCGA, Vol. 16, 5-6, 2006

M. Sitharam, J. Oung, A. Arbree and Y. Zhou, "Mixing features and variational constraints in 3D" CAD 2006

M. Sitharam, A. Arbree, Y. Zhou, N. Kohareswaran "Solution management and navigation for 3D geometric constraint systems" ACM TOG 2006

H. Gao, M. Sitharam "Combinatorial Characterization of underconstrained sytems,'' Proc. ASCM 2005.

X-S. Gao, M. Sitharam "Geometric constraint solving: underconstrained systems,'' Proc. ASCM 2005.

Jorg Peters and JianHua Fan and Meera Sitharam and Yong Zhou, Elimination in generically rigid 3{\sf D} geometric constraint systems, Proceedings of Algebraic Geometry and Geometric Modeling,Nice, 27-29 September 2004, Springer Verlag, 1-16, 2005.

M. Sitharam ``Combinatorial approaches to geometric constraint solving: problems, progress, directions,'' AMS-DIMACS book on computer aided design and manufacturing. Edited by Dutta, Janardhan, Smid. 2005.

M. Sitharam, Y.Zhou "A tractable, approximate characterization of combinatorial rigidity in 3D" 5th Automated Deduction in Geometry, ADG 2004.

M. Sitharam, Y.Zhou, J. Peters "Solving minimally decomposed 3D geometric constraint systems: optimizing algebraic complexity" 5th to Automated Deduction in Geometry, ADG 2004. Talk given at ACA 2004.

C. Hoffman, M. Sitharam, B. Yuan, ``Making constraint solvers useable: overconstraints,'' (pdf file) CAD, 2004.

J-J. Oung, M. Sitharam, B. Moro, A. Arbree,
FRONTIER: fully enabling geometric constraints for
feature based modeling and assembly (pdf file)

gzipped ps file
Proceedings of ACM Solid Modeling symposium, 2001.

C. Hoffman, A. Lomonosov, M. Sitharam,
Decomposition of Geometric Constraints Part I: performance
measures,
(pdf file)

gzipped ps file
Journal of Symbolic Computation Vol. 31, No. 4, April 2001

C. Hoffman, A. Lomonosov, M. Sitharam,
Decomposition of Geometric Constraints Part II: new algorithms,
(pdf file)

C. Hoffman, A. Lomonosov, M. Sitharam,
Planning Geometric constraint decompositions via
graph transformations
(pdf file)

gzipped ps file
Proceedings of AGTIVE '99 (Graph Transformations with
Industrial Relevance), Springer lecture notes,
LNCS 1779, eds Nagl, Schurr, Munch,
pp. 309-324, 1999.

C. Hoffman,
M. Sitharam,
A. Lomonosov,
``Geometric constraint decomposition,''
(pdf file)

gzipped ps file
in
"Geometric Constraint Solving
and Applications", Springer Verlag, Edited
by Beat Br\" uderlin and Dieter Roller, 1998.

M. Sitharam,
C. Hoffman,
A. Lomonosov,
Finding dense subgraphs of constraint graphs,
(pdf file)

gzipped ps file
Constraint Programming '97,
Lecture Notes in Computer Science 1330,
G. Smolka Ed.,
Springer Verlag, pp. 463-478, 1997.

A. Lomonosov, M. Sitharam ``Stability, Optimality and Complexity in Network games with pricing and player dropouts,'' SCPE (Scalable computing) journal, 2007

A. Lomonosov, M. Sitharam, K. Park ``Stability in network games'' JCSS, 2004.

A. Lomonosov, M. Sitharam, K. Park ``Stability vs. Optimality tradeoffs in network games'' AIMS track of the 18th SAC (symposium on applied computing) 2003.

Kihong Park, Meera Sitharam, Shaogang Chen,
Quality of service provision in noncooperative networks
with diverse user requirements,
(pdf file)

gzipped ps file
Decision Support Systems,
Special Issue on Information and Computation Economies,
vol. 28,
pp 101--122,
2000.

Shaogang Chen, Kihong Park, Meera Sitharam,
On the Ordering Properties of GPS Routers for Multi-Class QoS
Provision,
(pdf file)

gzipped ps file
Proceedings of the
SPIE Conference on
Performance and Control of Network Systems, Nov. 1998.

Kihong Park, Meera Sitharam, Shaogang Chen,
Quality of Service Provision in Noncooperative Networks: Heterogenous Pref
erences, Multi-Dimensional QoS Vectors, and Burstiness,
(pdf file)

gzipped ps file
Proceedings of the
International Conference on Information and Computation Economies, ICE
Oct. 1998.

Xiang Gao, Meera Sitharam, and Adrian E. Roitberg.
Bounds on the Jensen gap, and implications for mean-concentrated distributions.
The Australian Journal of Mathematical
Analysis and Applications (AJMAA)
Volume 16, Issue 2, Article 14, pp. 1-18, 2019.

PDF

Sitharam, Meera, Mohamad Tarifi, and Menghan Wang.
Combinatorial rigidity of incidence systems and application to
dictionary learning. Journal of Symbolic Computation 88 (2018): 21-46.

PDF

Meera Sitharam, Mohamad Tarifi, Menghan Wang ''An Incidence Geometry approach to Dictionary Learning" Proceedings of CCCG 2014

Mohamad Tarifi, Meera Sitharam, Jeff Ho "Learning Hierarchical Sparse Representations using Iterative Dictionary Learning and Dimension Reduction" Proceedings of BICA, 2011

O. Boykin, M. Sitharam, P. Tiep, P. Wocjan ``Orthogonal decomposition of lie algebras and Mutually Unbiased Bases'' Quantum Information and Computation, 2007

O. Boykin, M. Sitharam, M. Tarifi, P. Wocjan
``Nonextendibility of Mutually Unbiased Bases''

ArXiv subsuming version
Quantum Information Processing 2007

S. Riis, M. Sitharam,
Uniformly generated submodules of permutation modules,
(pdf file)

gzipped ps file
Journal of Pure and Applied Algebra
Vol 160, No 3, 285-318, 2001.

M. Belcher, S.Hicks, M. Sitharam
Equiseparations,
(pdf file)

gzipped ps file
Proceedings of ACM-SE conference, Mar. 2001.

M. Sitharam, T. Straney,
``Sampling Boolean functions over finite abelian groups and applications''
(pdf file)

gzipped ps file
Springer Journal of Applied Algebra (AAECC), Vol 11, No. 2,
pp 89-110, 2000.

S. Riis, M. Sitharam,
``Hard propositional tautologies and the symmetric group,''
(pdf file)

gzipped ps file
Oxford University Press: Logic journal of the IGPL,
Vol. 8, No. 6, 2000.

M. Sitharam, T. Straney,
``Derandomized learning, testing and fooling of Boolean functions over
finite abelian groups''
(pdf file)

gzipped ps file
International Journal of Foundations of CS.
Vol 12, No. 4 , 491-516, 2001

M. Sitharam, T. Straney,
``Derandomized learning of Boolean functions,''
(pdf file)

gzipped ps file
Proceedings of Algorithmic Learning Theory 1997, Lecture notes in Artificial Intelligence,
subseries of Lecture Notes in Computer Science, 1316,
Ming Li and Akira Maruoka Ed.s,
Springer-Verlag, 1997,
pp. 100-115.

S. Riis, M. Sitharam ``Generating hard tautologies using predicate logic and the symmetric group,'' Proceedings of the Workshop on Logic, Language, Information and Computation, Wollic, 1998.

B. Anderson, M. Sitharam, J. Jackson,
``How to obtain a polynomial that satisfies Descartes' law
of signs for a given sign sequence?''
(pdf file)

American Mathematical Monthly, May 1998.

S. Riis, M. Sitharam, ``Nonconstant degree lower bounds imply linear degree lower bounds,'' Appears in the Electronic Colloquium on Computational Complexity, Oct 97, Kent State TR Aug 97, Talks given at DIMACS Algebraic complexity workshop, Summer 1999; talks given at the Complexity lower bounds workshop at the Fields institute, Feb. 98, Midwest Theory Seminar, Dec. 97.

M. Sitharam,
``Pseudorandom generators and learning algorithms
for AC^0,''
(pdf file)

gzipped ps file
Computational Complexity (5), 1995, 248-266.
Appeared in proceedings of ACM Symposium on the Theory of Computing, 1994.

M.Sitharam,
``Evaluating spectral norms for functions
computed by constant depth circuit with symmetric gates,''
(pdf file)

gzipped ps file
Computational Complexity (5),
1995, 167-189.

M. Sitharam,
``Approximation from spaces of functions over the cube,
complexity lower bounds, derandomization, and learning algorithms,''
(pdf file)

gzipped ps file
Kent State TR May 96.
Appears in Electronic Colloquium on Computational Complexity, 96.

M.Sitharam, P. Enflo,
``Stable bases and complexity lower bounds,''
(pdf file)

gzipped ps file
Kent State TR May 96.
Appears in Electronic Colloquium on Computational Complexity, 96.

M. Sitharam, D.Joseph
``Kolmogorov complexity,
restricted nondeterminism and generalized spectra,''
(pdf file)

Symposium on the Theoretical Aspects of CS,
Lecture Notes in CS 415,
Rouen, France,
C. Choffrut and T. Lengauer, eds.,
Feb. 1990,
pp. 152-164.

M. Sitharam, D. Bruschi, A. Bertoni, D. Joseph,
P.Young,
``Generalized Boolean hierarchies and the Boolean
hierarchy over RP,''
(pdf file)

gzipped ps file
Foundations of Computation Theory, Lecture Notes in
CS 380,
Szeged, Hungary,
J. Csirik, J. Demetrovics, and F. Gecseg eds.
Aug. 1989,
pp. 35-46.

M. Sitharam,
``Generalized Boolean hierarchies,''
(pdf file)

gzipped ps file
University of Wisconsin Ph.D thesis and TR

A. Cavaretta, M. Sitharam, ``Variational properties of tensor product Bernstein Bezi\' er operators,'' Journal of Approximation theory, Vol. 72, No. 1, 1993, pp. 34-39.

J. Peters, M. Sitharam, ``Stability of $C^1$ cubics at the vertices of an underlying triangulation,'' SIAM J. Numerical analysis, Vol. 29, No. 2, 1992, pp. 528-533.

J. Peters, M. Sitharam
``Stability of $m$-variate $C^1$ interpolation,''
(pdf file)

Journal of Approximation Theory and its Applications,
Vol. 9, No. 1,
1993, pp. 18-32.

M. Sitharam, J. Peters ``Questions in general multivariate $C^1$ interpolation'' Proceedings of the NATO-ASI conference on Approximation Theory, Maratea, Italy, May 1991

M. Sitharam, J. Peters`` Graph-theoretic methods for bivariate $C^1$ cubic interpolation,'' Proceedings of the SIAM conference on Discrete Mathematics, Atlanta, June 1990

M. Sitharam, M. Tarifi, M. Wang "Rigidity of pinned line incidences to give provable bounds for Dictionary learning"

R. Wu, A. Ozkan, A. Bennett, M. Agbandje-Mckenna, M. Sitharam "Conclusive validation of EASAL's predictions of crucial interface interactions viral shell assembly"

J. Cheng, M. Sitharam "An algorithmic characterization of a family of abstract rigidity matroids over general graphs"

M. Sitharam, R. Wu, A. Ozkan "Configurational Entropy computation for small flexible molecular conformation and assembly systems" "

U. Chittamuru, M. Sitharam

``
Efficient parametrization and sampling of configuration space for 2-trees in
3D''

In preparation

O. Boykin, M. Sitharam, M. Tarifi, P. Wocjan ``Real Mutually Unbiased Bases'' '' In preparation

C. Borcea, M. Sitharam, I. Streinu `` The admissible polytope of edge distances for 2D realizations of partial 2-trees '' In preparation

A. Lomonosov, M. Sitharam ``Graph density based decomposition in geometric constraint solving'' 3 papers, based on Andrew's PhD thesis

M. Sitharam, Y. Zhou " Characterizing Rigidity of Angle constraint systems in 2D. " based on Yong's PhD thesis, 2006

O. Boykin, M. Sitharam, P. Wocjan `` On Monomiality of Mutually Unbiased Bases " In preparation.

M. Sitharam,
``FRONTIER, an opensource 3D geometric constraint solver: architecture
(Part I)

``FRONTIER, an opensource 3D geometric constraint solver: new algorithms
(Part II)
Research Monograph, in preparation.

P. Dandekar, M. Sitharam, A. Vince `` Constructions and bounds related to Dvoretzky's theorem and applications in threshold circuit size and communication complexity'' Pranav's thesis

M. Sitharam " Non-naturalizing proofs and algebraic complexity lower bounds: the role of symm etry and stability. "

M. Sitharam
``Datamining to capture geometric design intent,''
(pdf file)

gzipped ps file

K. Park, M. Sitharam, S. Chen, ``Quality of service provision in noncooperative network environments,'' Purdue University TR, Aug 97.

L. Robitaille, M. Sitharam , ``Asymptotic lengths of curve families and their fractal dimension,'' (ps file) Kent State TR, Aug 1996.

M. Sitharam, A. Lomonosov, ``Dense subgraph detection,'' Kent State University Tech. Report, January 1997.

V. Dimitrijevic, M. Sitharam, ``Lower bounds in algebraic models'' Kent State University Tech. Report, 1995, master's project

M. Sitharam, D. Hines ``Short discrete proofs of real zero existence for special cases of polynomial inequalities, and applications to geometric constraint problems,'' Kent State TR, Summer 1996.

M. Sitharam, B. Anderson ``Solving systems of polynomial inequalities arising from generalizations of the Budan-Fourier theorem,'' talk given at the Kent AMS conference in Nov. 95. Kent State TR, Spring 1996.

L. Hannah, M. Sitharam, ``Non-linear weight distributions of codes and circuit complexity lower bounds,'' Kent State TR, Summer 1996.

M. Sitharam, K. Mcevoy ``An HP-starbase toolkit for visualizing 2-D algebraic varieties,'' Kent State TR, Summer 1996.

M. Sitharam, M. Dowd ``Shannon bounds for functions over $Z_2^n$,'' Kent State University Tech. Report, 1992