California Institute of Technology
Moore Laboratory, Mail Stop 136-93
1200 E. California Blvd
Pasadena, CA 91125
Phone: (626) 350-6973
I wrote my PhD thesis on "Control of RNA function by conformational design" under supervision of Ivo L. Hofacker at the Department of Theoretical Chemistry, University of Vienna. Feel free to download my CV for more details.
Here is a short list of keywords that illustrate my research interests.
- strand displacement system design
- bi-stable and multi-stable coformational design
- sequence design
- energy landscapes
- folding kinetics
- co-transcriptional folding
- conformational self-replication
Chemical reaction networks (CRNs)
- CRN equivalence
- formal language properties
- CRN condensation (coarse graining)
I use, contribute to, and develop various scientific open-source software projects, related to thermodynamic and kinetic modeling, energy landscapes, co-transcriptional folding, and nucleic acid strand displacement systems. The software can be found on GitHub, either in my personal repository, in the DNA Group repository or the ViennaRNA repository.
- Nuskell -- Nucleic acid strand displacement compiler [GitHub]
- Peppercorn -- Domain-level nucleic acid reaction enumeration [GitHub]
- CRNsimulator -- Simulate chemical reaction networks using ordinary differential equations [GitHub]
- dsdobjects -- Base classes for nucleic acid strand displacement programming [GitHub]
- Barriers -- Compute local minima and energy barriers of a landscape [GitHub]
- Treekin -- Compute folding dynamics on coarse grained version of an energy landscape [GitHub]
- ViennaRNA package -- The ViennaRNA Package [GitHub]
- RNAdesign.pl -- nucleic acid sequence design
- ribolands -- energy landscapes and folding kinetics of nucleic acids [GitHub]
- DrTransformer -- co-transcriptional folding
- BarMap -- co-transcriptional folding
Conferences, Talks & Posters
Have we met? An almost complete list of conferences I have visited in the past...
- 09/2017 - DNA23 - DNA Computing & Molecular Programming Conference, Austin: A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities [slides]
- 09/2016 - DNA22, Munich: Energy landscapes and folding kinetics of pairwise interacting RNAs [slides]
- 03/2016 - PhD Defense Talk, Vienna: Control of RNA function by conformational design [slides]
- 08/2015 - DNA21, Boston
- 02/2015 - TBI Winterseminar, Bled: BarMap & SundialsWrapper -- advanced RNA folding kinetics [slides]
- 02/2015 - GRC on RNA nanotechnolgy, Ventura: Design of XOR riboswitches [poster]
- 10/2014 - Herbstseminar Bioinformatik, Decin: Design of a circular RNA with prion-like behavior [slides]
- 08/2014 - ALIFE 14, New York: Design of a circular RNA with prion-like behavior [slides]
- 05/2014 - SSBSS 2014, Taormina: Sequence-controlled RNA self-processing: computational design, biochemical analysis and visualization by AFM [poster]
- 02/2014 - TBI Winterseminar, Bled: Folding kinetics of self-polymerizing RNA
- 10/2013 - Herbstseminar Bioinformatik, Decin: Circularization and multimerization of synthetic ribozymes [slides]
- 02/2013 - TBI Winterseminar, Bled: Design of self-processing RNA
- 10/2012 - Herbstseminar Bioinformatik, Decin: Design of self-processing ribozymes
- 02/2012 - TBI Winterseminar, Bled: Conformational design of self-organizing ribozymes
- 10/2011 - Herbstseminar Bioinformatik, Vysoka Lipa
- 02/2011 - TBI Winterseminar, Bled: Energy barriers in pseudoknot conformation space
- 10/2010 - Herbstseminar Bioinformatik, Vysoka Lipa: Design & future aspects of artificial RNA-switches in synthetic biology
- 02/2010 - TBI Winterseminar, Bled: Design of artificial RNA-switches
- Caltech Biology and Biological Engineering Division Fellowship
- NSF Grant CCF-1213127
- NSF Grant CCF-1317694 (“The Molecular Programming Project”)
- The Gordon and Betty Moore Foundation's Programmable Molecular Technology Initiative (PMTI)
- FWF SFB: F43 "RNA regulation of the transcriptome"
- FWF DK: W1207 "RNA Biologie"
- FWF International Programme: I670 "RNA-Funktionskontrolle durch strukturelles Design"
My most recent CV can be downloaded here