Publications

2022

Samuel W. Schaffter, Kuan-Lin Chen, Jackson O’Brien, Madeline Noble, Arvind Murugan & Rebecca Schulman. Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks. Nature Chemistry. 10.7281/T1/UBSZF1 2022 Link to Original

Yi Li, Christopher Maffeo, Himanshu Joshi, Aleksei Aksimentiev, Brice Ménard, Rebecca Schulman, Lossless end-to-end transport of small molecules through micron-length DNA nanochannels. bioRXiv. 10.1101/2022.04.13.488239 2022 Download

Misha Rubanov, Phillip Dorsey, Dominic Scalise,  & Rebecca Schulman,  Sequential Activation of Spatially Localized Oligonucleotides. ChemRxiv. 10.26434/chemrxiv-2022-4jcv6 2022 Download

Pepijn G. Moerman, Huang Fang, Thomas E. Videbæk, W. Benjamin Rogers, Rebecca Schulman. A simple method to reprogram the binding specificity of DNA-coated colloids that crystallize. arXiv 10.48550/arXiv.2206.00952 2022 Download 

Pepijn Moerman, Momcilo Gavrilov, Taekjip Ha., Rebecca Schulman*. Catalytic DNA Polymerization Can Be Expedited by Active Product Release. Angewandte Chemie, 10.26434/chemrxiv-2022-3k98v, 2022  Download  Supplemental Materials Link to Original

Phillip J. Dorsey, Dominic Scalise, and Rebecca Schulman*.Enabling Spatiotemporal Regulation within Biomaterials using DNA reaction-diffusion waveguides. bioRxiv, 10.1101/2022.02.26.482105, 2022 Download Supplemental Materials

Naresh Niranjan Dhanasekar, Yi Li and Rebecca Schulman*. The ion permeability of DNA nanotube channels. bioRxiv, 10.1101/2022.03.04.482952, 2022 Download Supplemental Materials

2021

Samuel Schaffter, Kuan-Lin Chen, Jackson O’Brien, Madeline Noble, Arvind Murugan and Rebecca Schulman
Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks
Nature Portfolio, 10.21203/rs.3.rs-247740/v1, 2021 Download  Supplemental Material Link to Original

Sisi Jia, Siew Cheng Phua, Yuta Nihongaki, Yizeng Li, Michael Pacella, Yi Li, Abdul Mohammed, Sean Sun, Takanari Inoue and Rebecca Schulman
Growth and site-specific organization of micron-scale biomolecular devices on living mammalian cells
Nature Communications, 12, pp 5729, 10.1038/s41467-021-25890, 2021  Download  Link to Original  Supplemental Materials

2020

Samuel Schaffter, Dominic Scalise, Terence Murphy, Anusha Patel and Rebecca Schulman
Feedback regulation of crystal growth by buffering monomer concentration
Nature Communications, 11(1) pp 6057,10.1038/241467-020-19882-8, 2020 Download  Supplemental Material  Link to Original  Associated Data and Code

Samuel Schaffter, Joanna Schneider, Deepak Agrawal, Michael Pacella, Eric Rothchild, Terence Murphy and Rebecca Schulman
Reconfiguring DNA Nanotube Architectures via Selective Regulation of Terminating Structures
ACS Nano, 14, 10, pp 13451–13462, 10.1021/acsnano.0c05340, 2020. Download Supplemental Material  Link to Original

Ruohong Shi, Joshua Fern, Weinan Xu, Sisi Jia, Qi Huang, Gayatri Pahapale, Rebecca Schulman and David H. Gracias
Multicomponent DNA Polymerization Motor Gels
Small, 16, 2002946, 10.1002/smll.202002946, 2020. Download  Supplemental Material  Link to Original

Philip Dorsey, Dominic Scalise and Rebecca Schulman
DNA Reaction-Diffusion Attractor Patterns
Angewandte Chemie, 60, pp 338,10.1002/anie.202009756, 2020. Download  Supplemental Material  Link to Original  German Edition

Pepijn Moerman and Rebecca Schulman
DNA Computation Improves Diagnostic Workflows
Nature Nanotechnology, 15, pp 626–627,10.1038/241565-020-0710-9, 2020. Download  Link to Original

Xinyu Cui, Dominic Scalise and Rebecca Schulman
Powering DNA Strand-displacement Reactions with a Continuous Flow Reactor
Natural Computing, 20, 4,  pp 821–827, 10.1007/s11047-020-09795-2, 2020. Download  Supplemental Material  Link to Original

Deepak Agrawal and Rebecca Schulman
Modular protein-oligonucleotide signal exchange
Nucleic Acids Research, 48, 12, pp 6431-6444, 2020. Download  Supplemental Material  Link to Original

Dominic Scalise, Moshe Rubanov, Katherine Miller, Leo Potters, Madeline Noble and Rebecca Schulman
Programming the Sequential Release of DNA
ACS Synthetic Biology, 9(4), pp 749-755, 2020. Download  Supplemental Materials  Link to Original

Michael Pacella, Vahid Mardanlou, Siddhart Agarwal, Anusha Patel, Elizabeth Jelezniakov, Abdul Mohammed, Elisa Franco and Rebecca Schulman
Characterizing the Length-Dependence of DNA Nanotube End-to-End Joining Rates
Molecular Systems Design & Engineering, 5, pp 544-558, 2020. Download  Link to Original

2019

Phillip Dorsey, Misha Rubanov, Wenlu Wang and Rebecca Schulman
Digital maskless photolithographic patterning of DNA-functionalized poly(ethylene glycol) diacrylate hydrogels with visible light enabling photo-directed release of oligonucleotides
ACS Macro Letters, 8, pp 1133-1140, 2019. Download  Supplemental Materials  Link to Original

Samuel Schaffter and Rebecca Schulman
Building in vitro transcriptional regulatory networks that integrate multiple functional circuit motifs
Nature Chemistry,11, pp 829-838, 2019. Download   Link to Original  Supplementary Materials

Yi Li and Rebecca Schulman
DNA Nanotubes that Self-Heal in Serum
Nano Letters, 19 (6), pp 3751-3760, 2019. Download  Supplementary Material  Link to Original  Supplementary movies

Yi Li and Rebecca Schulman
Talking across the Membrane
Nature Chemistry, 11, pp 18-20, 2019. Download Link to Original

Dominic Scalise and Rebecca Schulman
Control of Matter at the Molecular Scale with DNA Circuits
Annual Review of Biomedical Engineering, 21, pp 469-493, 2019. Download  Link to Original

2018

John Zenk, Matthew Billups and Rebecca Schulman
Optimizing Component-Component Interaction Energies in the Self-Assembly of Finite, Multicomponent Structures
ACS Omega, 3 (12), pp 18753 – 18761, 2018. Download  Supplementary Material  Link to Original

Dominic Scalise, Nisita Dutta and Rebecca Schulman
DNA Strand Buffers
Journal of the American Chemical Society, 140 (38), pp 12068-12076,  2018. Download  Supplementary material  Link to Original

Joshua Fern and Rebecca Schulman
Modular DNA strand-displacement controllers for directing material expansion
Nature Communications 9, Article 3766, 2018. Download Supplementary material Link to original

Samuel W. Schaffter, Leopold N. Green, Joanna Schneider, Hari KK Subramanian, Rebecca Schulman and Elisa Franco
T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures
Nucleic Acids Research, 46 (10), pp 5332-5343, 2018. Download Supplementary material Link to original

2017

Friedrich C. Simmel and Rebecca Schulman.
Self-organizing materials built with DNA
Materials Research Society (MRS) Bulletin, 42 (12), pp 913-919, 2017. Download Link to original

Angelo Cangialosi, ChangKyu Yoon, Jiayu Liu, Qi Huang, Jingkai Guo, Thao D. Nguyen, David H. Gracias and Rebecca Schulman.
DNA Sequence-Directed Shape Change of Photopatterned Hydrogels via High-Degree Swelling
Science 357, pp 1126-1130, 2017. Download Supplementary material Supplementary movies Link to original

Deepak K. Agrawal, Ruoyu Jiang, Seth Reinhart, Abdul M. Mohammed, Tyler D. Jorgenson and Rebecca Schulman.
Terminating DNA Tile Assembly with Nanostructured Caps
ACS Nano, 11 (10), pp 9770-9779, 2017. Download Supplementary material Supplementary movies Link to original  Erratum

Joshua Fern and Rebecca Schulman.
Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium
ACS Synthetic Biology, 6 (9), pp 1774-1783, 2017. Download Supplementary material Link to original

Abdul M Mohammed, Petr Sulc, John Zenk and Rebecca Schulman.
Self-Assembling DNA Nanotubes to Connect Molecular Landmarks.
Nature Nanotechnology 12, pp 312-316, 2017. Download Supplementary material Supplementary movies Link to original

John Zenk, Dominic Scalise, Kai-Yuan Wang, Philip Dorsey, Joshua Fern, Ariana Cruz and Rebecca Schulman.
Stable DNA-Based Reaction-Diffusion Patterns 
RSC Advances, 7, pp 18032-18040, 2017. Download Supplementary material Link to original

Tyler D. Jorgenson, Abdul M Mohammed, Deepak K. Agrawal and Rebecca Schulman.
Self-Assembly of Hierarchical DNA Nanotube Architectures with Well-Defined Geometries.
ACS Nano, 17, pp 1927-1936, 2017. Download Supplementary material Link to original

Abdul M Mohammed, Lourdes Velazquez, Allison Chisenhall, Daniel Schiffels, Deborah K Fygenson and Rebecca Schulman.
Self-Assembly of Precisely Defined DNA Nanotube Superstructures Using DNA Origami Seeds.
Nanoscale, 9, pp 522-526, 2017. Download Supplementary material Link to original

2016

Joshua Fern, Dominic Scalise, Angelo Cangialosi, Dylan Howie, Leo Potters and Rebecca Schulman.
DNA Strand-Displacement Timer Circuits.
ACS Synthetic Biology, 6, 190-193, 2016. Download Supplementary material Link to original

John Zenk, Chanon Tuntivate and Rebecca Schulman.
Kinetics and Thermodynamics of Watson-Crick Base Pairing Driven DNA Origami Dimerization.
Journal of the American Chemical Society, 138, 3346-3354, 2016. Download Supplementary materialLink to original

Joshua Fern, Jennifer Lu and Rebecca Schulman.
The Energy Landscape for the Self-Assembly of a Two-Dimensional DNA Origami Complex.
ACS Nano, 10, 1836-1844, 2016. Download Supplementary material Link to original

2015

Deepak K. Agrawal, Elisa Franco and Rebecca Schulman.
A self-regulating biomolecular comparator for processing oscillatory signals
Journal of The Royal Society Interface 12.111, 20150586, 2015. Download Supplementary material Link to original

Rebecca Schulman, Christina Wright and Erik Winfree.
Increasing Redundancy Exponentially Reduces Error Rates during Algorithmic Self-Assembly
ACS Nano 9, 5760-5771, 2015. Download Supplementary material Link to original.

Rebecca Schulman and David Doty.
Designing Ordered Nucleic Acid Self-Assembly Processes.
Current Opinion in Structural Biology 31, 57-63, 2015. Download Link to original

2014

Dominic Scalise and Rebecca Schulman.
Emulating Cellular Automata in Chemical Reaction-Diffusion Networks.
In Proceedings of the 20th Annual Conference on DNA Computing and Molecular Programming, 2014. Download Link to original.
Natural Computing, online first Download Link to original.

John Zenk and Rebecca Schulman.
An Assembly Funnel Makes Biomolecular Complex Assembly Efficient.
PLoS One 9 (10): e11123, 2014. Download Link to original.

Dominic Scalise and Rebecca Schulman.
Designing modular reaction-diffusion programs for complex pattern formation.
Technology 02 55-66, 2014. Download Link to original.

2013

Abdul M. Mohammed and Rebecca Schulman.
Directing Self-Assembly of DNA Nanotubes Using Programmable Seeds.
Nano Letters 13 (9) 4006-4013, 2013. Download Supplementary Material Link to original
Simulation code (matlab scripts) (All files are collected into a single zip archive.)

2012

Stephen Whitelam, Rebecca Schulman and Lester O. Hedges.
Self-assembly of multicomponent structures in and out of equilibrium.
Physical Review Letters 109 (26) 265506, 2012. Download Supplementary Material Link to original

Rebecca Schulman, Bernard Yurke and Erik Winfree.
Robust Self-Replication of Combinatorial Information via Crystal Growth and Scission.
Proceedings of the National Academy of Science, 109 (17) 6405-6410, 2012.
Download Supplementary Material Link to original

Rebecca Schulman and Erik Winfree.
Simple Evolution of Complex Crystal Species.
Natural Computing, 11, 187-197, 2012. Link

2011 and Before

Rebecca Schulman.
Beyond Biology: Designing a New Mechanism for Self-Replication and Evolution at the Nanoscale.
In Proceedings of the Conference on Genetics and Evolutionary Computation (GECCO), 2011. Link

Rebecca Schulman and Bernard Yurke.
A Molecular Algorithm for Path Self-Assembly in 3 Dimensions.
In Proceedings of Robotics: Science and Systems, 2010. Link

Rebecca Schulman and Erik Winfree.
Simple Evolution of Complex Crystal Species.
In Proceedings of the 16th Annual Conference on DNA Computing and Molecular Programming, 2010. Link

Rebecca Schulman and Erik Winfree.
Programmable control of nucleation for algorithmic self-assembly.
SIAM Journal of Scientific Computing , 39 (4) 1581-1616, 2009. Link or ArXiv version

Robert Barish1, Rebecca Schulman1, Paul Rothemund and Erik Winfree.
An Information-Bearing Seed for Algorithmic Self-Assembly.
Proceedings of the National Academy of Sciences USA, 106 (15), 6054-–6059, 2009. Link

Rebecca Schulman and Erik Winfree.
How Crystals that Sense and Respond to Their Environments Could Evolve.
Natural Computing, 7 (2) 219-237, 2008. Link

Rebecca Schulman and Erik Winfree.
Synthesis of Crystals with a Programmable Barrier to Nucleation.
Proceedings of the National Academy of Sciences USA, 104 (39), 15236-15241, 2007. Link

Ho-Lin Chen1,Rebecca Schulman1, Ashish Goel and Erik Winfree.
Reducing Facet Nucleation During Algorithmic Self-Assembly.
Nano Letters, 7 (9), 2913-2919, 2007. Link

Rebecca Schulman and Erik Winfree.
Self-Replication and Evolution of DNA Crystals.
In Proceedings of the VIIIth European Conference on Artificial Life, 2005. Link

Rebecca Schulman and Erik Winfree.
Programmable Control of Nucleation for Algorithmic Self-Assembly (Extended Abstract).
In Proceedings of the 10th Annual Conference on DNA-Based Computation, 2004. Link

Rebecca Schulman, Shaun Lee, Nick Papadakis and Erik Winfree.
One-dimensional boundaries for DNA tile self-assembly.
In Proceedings of the 9th Annual Conference on DNA-Based Computation, 2003. Link

1These authors contributed equally to this work