Chris Thachuk

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 14

Top Topics

Stochastic Simulation

Partition Function

Chemical Reaction

Top Venues

Theor. Comput. Sci.

J. Discrete Algorithms

Publications

Lancelot Wathieu, Gus Henry Smith, Luis Ceze, Chris Thachuk
Fridge Compiler: Optimal Circuits from Molecular Inventories. CMSB (2023)
Ahmed Shalaby, Chris Thachuk, Damien Woods
Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer. DNA (2023)
Tiernan Kennedy, Cadence Pearce, Chris Thachuk
Fast and Robust Strand Displacement Cascades via Systematic Design Strategies. DNA (2022)
Anne Condon, Monir Hajiaghayi, Chris Thachuk
Predicting Minimum Free Energy Structures of Multi-Stranded Nucleic Acid Complexes Is APX-Hard. DNA (2021)
Keenan Breik, Chris Thachuk, Marijn Heule, David Soloveichik
Computing properties of stable configurations of thermodynamic binding networks. Theor. Comput. Sci. 785 (2019)
Seung Woo Shin, Chris Thachuk, Erik Winfree
Verifying chemical reaction network implementations: A pathway decomposition approach. Theor. Comput. Sci. 765 (2019)
Stefan Badelt, Seung Woo Shin, Robert F. Johnson, Qing Dong, Chris Thachuk, Erik Winfree
A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities. DNA (2017)
Boya Wang, Chris Thachuk, Andrew D. Ellington, David Soloveichik
The Design Space of Strand Displacement Cascades with Toehold-Size Clamps. DNA (2017)
Keenan Breik, Lakshmi Prakash, Chris Thachuk, Marijn Heule, David Soloveichik
Computing properties of stable configurations of thermodynamic binding networks. CoRR (2017)
Sedigheh Zolaktaf, Frits Dannenberg, Xander Rudelis, Anne Condon, Joseph M. Schaeffer, Mark Schmidt, Chris Thachuk, Erik Winfree
Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates. DNA (2017)
David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods
Thermodynamic Binding Networks. CoRR (2017)
David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods
Thermodynamic Binding Networks. DNA (2017)
Ashwin Gopinath, David G. Kirkpatrick, Paul W. K. Rothemund, Chris Thachuk
Progressive Alignment of Shapes. CCCG (2016)
Marta Kwiatkowska, Andrew Phillips, Chris Thachuk
Preface. Theor. Comput. Sci. 632 (2016)
Frits Dannenberg, Marta Z. Kwiatkowska, Chris Thachuk, Andrew J. Turberfield
DNA walker circuits: computational potential, design, and verification. Nat. Comput. 14 (2) (2015)
Joseph Malcolm Schaeffer, Chris Thachuk, Erik Winfree
Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands. DNA (2015)
Chris Thachuk, Erik Winfree, David Soloveichik
Leakless DNA Strand Displacement Systems. DNA (2015)
Anne Condon, Ján Manuch, Chris Thachuk
The complexity of string partitioning. J. Discrete Algorithms 32 (2015)
Ho-Lin Chen, David Doty, Dhiraj Holden, Chris Thachuk, Damien Woods, Chun-Tao Yang
Fast Algorithmic Self-assembly of Simple Shapes Using Random Agitation. DNA (2014)
Ho-Lin Chen, David Doty, Dhiraj Holden, Chris Thachuk, Damien Woods, Chun-Tao Yang
Fast algorithmic self-assembly of simple shapes using random agitation. CoRR (2014)
Seung Woo Shin, Chris Thachuk, Erik Winfree
Verifying Chemical Reaction Network Implementations: A Pathway Decomposition Approach. CoRR (2014)
Chris Thachuk
Compressed indexes for text with wildcards. Theor. Comput. Sci. 483 (2013)
Chris Thachuk
Logically and Physically Reversible Natural Computing: A Tutorial. RC (2013)
Chris Thachuk
Indexing hypertext. J. Discrete Algorithms 18 (2013)
Frits Dannenberg, Marta Z. Kwiatkowska, Chris Thachuk, Andrew J. Turberfield
DNA Walker Circuits: Computational Potential, Design, and Verification. DNA (2013)
Chris Thachuk, Anne Condon
Space and Energy Efficient Computation with DNA Strand Displacement Systems. DNA (2012)
Anne Condon, Ján Manuch, Chris Thachuk
The complexity of string partitioning CoRR (2012)
Anne Condon, Chris Thachuk
Efficient codon optimization with motif engineering. J. Discrete Algorithms 16 (2012)
Anne Condon, Ján Manuch, Chris Thachuk
The Complexity of String Partitioning. CPM (2012)
Chris Thachuk
Succincter Text Indexing with Wildcards. CPM (2011)
Ján Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon
NP-completeness of the energy barrier problem without pseudoknots and temporary arcs. Nat. Comput. 10 (1) (2011)
Chris Thachuk
A Succinct Index for Hypertext. SPIRE (2011)
Anne Condon, Chris Thachuk
Efficient Codon Optimization with Motif Engineering. IWOCA (2011)
Chris Thachuk
Succincter Text Indexing with Wildcards CoRR (2011)
Anne Condon, Alan J. Hu, Ján Manuch, Chris Thachuk
Less Haste, Less Waste: On Recycling and Its Limits in Strand Displacement Systems. DNA (2011)
Chris Thachuk, Ján Manuch, Arash Rafiey, Leigh-Anne Mathieson, Ladislav Stacho, Anne Condon
An Algorithm for the Energy Barrier Problem Without Pseudoknots and Temporary Arcs. Pacific Symposium on Biocomputing (2010)
Ján Manuch, Murray Patterson, Sheung-Hung Poon, Chris Thachuk
Complexity of Finding Non-Planar Rectilinear Drawings of Graphs. Graph Drawing (2010)
Ján Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon
NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots. DNA (2009)
Chris Thachuk, Jose Crossa, Jorge Franco, Susanne Dreisigacker, Marilyn Warburton, Guy F. Davenport
Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures. BMC Bioinform. 10 (2009)
Anne Condon, Ján Manuch, Chris Thachuk
Complexity of a Collision-Aware String Partition Problem and Its Relation to Oligo Design for Gene Synthesis. COCOON (2008)
Chris Thachuk, Alena Shmygelska, Holger H. Hoos
A replica exchange Monte Carlo algorithm for protein folding in the HP model. BMC Bioinform. 8 (2007)
Chris Thachuk, Anne Condon
On the Design of Oligos for Gene Synthesis. BIBE (2007)