Stefan Badelt
Institute for Theoretical Chemistry
University of Vienna
Währingerstrasse 17/3/307
1090 Vienna, Austria
stef@tbi.univie.ac.at <gpg-key.asc>
http://www.tbi.univie.ac.at/~stef

I am a postdoc in Ivo L. Hofacker's Theoretical Biochemistry Group (tbi) at the University of Vienna. My research activities include a software project to simulate cotranscriptional folding of large RNA molecules, the development of a foundational, coarse-grained, biophysical model for kinetic folding of multistranded nucleic acid systems, and a sequence design software for multistranded nucleic acid systems that integrates thermodynamic optimization with optimization of selected kinetic parameters. Before my present appointment, I studied Molecular Biology at the University of Vienna with focus on computational RNA design (using both thermodynamic and kinetic models of RNA folding), and I worked as a postdoc in Erik Winfree's DNA and Natural Algorithms Group, Caltech to develop a compiler framework that unifies the design of complex nucleic acid "strand displacement" systems and formal verification. Feel free to download my CV for more details.

June, 2020

Nucleic acids

• strand displacement system design
• bi-stable and multi-stable conformational design
• sequence design
• energy landscapes
• folding kinetics
• co-transcriptional folding
• conformational self-replication
• ribozymes
• riboswitches

Chemical reaction networks (CRNs)

• CRN equivalence
• formal language properties
• CRN condensation (coarse graining)

• 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

• 06/2019 - MPP2 Finale Workshop, Caltech: A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities [slides]
• 04/2019 - FNANO19, Snowbird: Enumeration, condensation and simulation of pseudoknot-free domain-level DNA strand displacement systems [slides]
• 01/2019 - GRC on RNA nanotechnolgy, Ventura: Compilation and verification of nucleic acid reaction networks [poster]
• 07/2018 - VEMDP, Oxford: Equivalence of chemical reaction networks in a CRN-to-DNA compiler framework [slides]
• 02/2018 - 33rd TBI Winterseminar, Bled: Reaction enumeration and condensation of domain-level strand displacement systems [slides]
• 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 - 30th 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]
• 10/2013 - DK RNA Biology Retreat, Krumbach: Design and Analysis of self-polymerizing RNA
• 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

previous projects:

• Caltech Biology and Biological Engineering Division Fellowship
• NSF Grant 1643606 INSPIRE: Computational Parameterization of Nucleic Acid Secondary Structure Models
• NSF Grant 1213127
• NSF Grant 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