Thomas Nowak

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Openings

I’m looking for excellent candidates for postdoc, PhD, and intern positions. If you’re interested in doing research with me, please write me an email.

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Research Interests

• distributed algorithms
• synthetic biology
• discrete-event systems
• wireless ad-hoc networks of mobile agents

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Projects

• DREAMY: Distributed Algorithms in Microbiological Systems (ANR)
• COSTXPRESS: Quantitative models of expression costs of synthetic genetic circuits (ANR)
• SAIF: Safe AI through Formal Methods
• MicroPILOTING: A microfluidic system for predictive interaction models of bacteria and microalgae cells (ANR)
• PROCEED/PREDICTABLE Predictive interaction models of bacteria and microalgae cells via a dedicated microfluidic device (Institut d’Alembert, Institut Farman, and OI BioProbe)

Past projects:

• DAB: Distributed Algorithms in Birth-Death Systems (DIM RFSI)
• HicDiesMeus: Highly Constrained Discrete Agents for Modeling Natural Systems (DigiCosme)
• ETSHI: Efficient Test Strategies for SARS-CoV-2 in Healthcare Institutions (Université Paris-Saclay/CARE)
• BACON: Bacterial Consensus (CNRS)
• COMBACT: Digital Communication Models for Bacteria (DIM RFSI)
• ABIDE: Algorithms in Birth-Death Systems (CNRS)
• DIGIT: Distributed Pulse Generation in Bacterial Colonies (DigiCosme)
• DEMO: Delay Models for Microbiological Circuits (CNRS)
• DICIMUS: Distributed Communication Models for Microbiological Circuits (Institut Farman)
• DEPEC MODE: Deriving Phage Communication Models (Université Paris-Saclay)

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Students and Post-Docs

• Gabriel Le Bouder, post-doc (co-supervised with Matthias Függer)
• Fabricio Cravo, PhD student, started in 2021 (co-supervised with Janna Burman and Matthias Függer)
• Mélanie Pietri, PhD student, started in 2023 (co-supervised with Sakina Bensalem, Matthias Függer, and Bruno Le Pioufle)
• Zhuofan Xu, PhD student, started in 2022 (co-supervised with Benedikt Bollig and Matthias Függer)
• Remi Baron, research intern (co-supervised with Fabricio Cravo and Matthias Függer)
• Azammat Charaf-Zadah, research intern (co-supervised with Benedikt Bollig and Matthias Függer)
• Luana Martins Ferraz, research intern (co-supervised with Matthias Függer)

Alumni:

• Elias Pinter, research intern (co-supervised with Matthias Függer)
• Berndt Uhlig, research intern (co-supervised with Benedikt Bollig and Matthias Függer)
• Antonia Baies, research intern (co-supervised with Benedikt Bollig and Matthias Függer)
• Thomas Sadigh Rezvani, research intern (co-supervised with Matthias Függer)
• Kevin Awoufack, research intern (co-supervised with Matthias Függer)
• Andrea Garcia, research intern (co-supervised with Matthias Függer)
• Josephine Ramirez, research intern (co-supervised with Matthias Függer)
• Shaunticlair Ruiz, research intern (co-supervised with Matthias Függer)
• Jessica Vipin, research intern (co-supervised with Matthias Függer)
• Margarita Shimanskaia, research intern (co-supervised with Matthias Függer)
• Thomas Chevet, post-doc (co-supervised with Matthias Függer)
• Gayathri Prakash, graduate research intern (co-supervised with Matthias Függer)
• Letícia Levin Diniz, graduate research intern (co-supervised with Matthias Függer)
• Artur Piana, graduate research intern (co-supervised with Matthias Függer)
• Anisse Belhadj, graduate research intern
• Sirajo Bakura, PhD student, started in 2018, defended in 2021 (co-supervised with Alain Lambert)
• Corbin Hopper, graduate research intern (co-supervised with Matthias Függer)
• Victoria Andaur, undergraduate research intern
• Bilal Manssouri, undergraduate research intern (co-supervised with Janna Burman)
• DaJung Cho, post-doc (co-supervised with Matthias Függer)
• Cheng-Yu Han, PhD student, started in 2015, defended in 2018 (co-supervised with Alain Lambert)
• Quentin Soubeyran, graduate research intern, École Polytechnique Research Internship Prize 2019

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Events

Workshops:

• CELLS 2022 (Computing among Cells) at DISC 2022, October 28, 2022, online
• CELLS 2021 (Computing among Cells) at DISC 2021, October 8, 2021, online
• CELLS 2020 (Computing among Cells) at DISC 2020, October 12, 2020, online
• CELLS 2019 (Computing among Cells) at DISC 2019 on October 14, 2019, in Budapest
• WENDY (Emergent Algorithms and Network Dynamics) on October 10-11, 2018, at Institut Henri Poincaré in Paris

Conferences:

• SSS 2018 (PC member), PODC 2019 (Publication Chair), PODC 2020 (PC member), DISC 2020 (PC member), SAND 2023 (PC member), SIROCCO 2023 (PC member), PODC 2024 (PC member)

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Teaching

• Fall 2023: Algorithmics and Bioinformatics (with S. Haar and M. Függer)
• Fall 2023: Initiation to Research: Synthetic Biology (with M. Függer)
• Fall 2023: Probabilistic Aspects of Computer Science (with S. Haddad)

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Publications

• An Allee-based Distributed Algorithm for Microbial Whole-Cell Sensors with F. Cravo and M. Függer, 2023.
  Accepted for publication in npj Systems Biology and Applications
  bioRxiv

• Topological Characterization of Task Solvability in General Models of Computation with H. Attiya and A. Castañeda, 2023.
  Extended abstract to be presented at DISC 2023
  arXiv

• Continuity of Thresholded Mode-Switched ODEs and Digital Circuit Delay Models with A. Ferdowsi, M. Függer, and U. Schmid, 2023.
  Extended abstract presented at HSCC 2023
  arXiv

• A synthetic communication system uncovers self-jamming of bacteriophage transmission with M. Függer, C. Hopper, M. Kushwaha, A. Pandi, and A. Pathania, 2022.
  bioRxiv

• MobsPy: A Meta-Species Language for Chemical Reaction Networks with F. Cravo, M. Függer, and G. Prakash, 2022.
  Extended abstract presented at CMSB 2022
  bioRxiv

• Stochastic Multi-Distribution Modeling of Inter-Contact Times with F. Cravo, 2022.
  Extended abstract presented at ICOIN 2022.

• Reaching Agreement in Competitive Microbial Systems with V. Andaur, J. Burman, M. Függer, M. Kushwaha, B. Manssouri, and J. Rybicki, 2022.
  arXiv

• Time-Optimal Self-Stabilizing Leader Election in Population Protocols with J. Burman, H. Chen, H. Chen, D. Doty, E. Severson, and C. Xu, 2021.
  Extended abstract presented at PODC 2021
  arXiv

• A Composable Glitch-Aware Delay Model with J. Maier, D. Öhlinger, U. Schmid, and M Függer, 2021.
  Extended abstract presented at GLSVLSI 2021
  arXiv

• New Bounds on the Periodicity Transient of the Powers of a Tropical Matrix: Using Cyclicity and Factor Rank with A. Kennedy-Cochran-Patrick, G. Merlet, and S. Sergeev, 2020.
  Linear Algebra and its Applications 611:279-309
  arXiv

• Digital Circuit Design for Biological and Silicon Computers with M. Függer and M. Kushwaha, 2020.
  Advances in Synthetic Biology
  HAL

• Distributed Computation with Continual Population Growth with D.-J. Cho, M. Függer, C. Hopper, M. Kushwaha, and Q. Soubeyran, 2020.
  Distributed Computing 35:547–569
  Extended abstract presented at DISC 2020 (video) (invited to special issue of Distributed Computing)
  arXiv

• Clock Synchronization with Exponential Smoothing for Dynamic Networks with S. Bakura and A. Lambert, 2020.
  Extended abstract presented at CISS 2020

• Byzantine Approximate Agreement on Graphs with J. Rybicki, 2019.
  Extended abstract presented at DISC 2019
  arXiv

• Topological Characterization of Consensus under General Message Adversaries with U. Schmid and K. Winkler, 2019.
  Extended abstract presented at PODC 2019
  arXiv
  

• Transistor-Level Analysis of Dynamic Delay Models with M. Függer, J. Maier, and U. Schmid, 2019.
  Extended abstract presented at ASYNC 2019

• On the Radius of Nonsplit Graphs and Information Dissemination in Dynamic Networks with M. Függer and K. Winkler, 2019.
  Discrete Applied Mathematics 282:257-264
  arXiv

• Fast Multidimensional Asymptotic and Approximate Consensus with M. Függer, 2018.
  Extended abstract presented at DISC 2018 (invited to special issue of Distributed Computing)
  arXiv

• Pulse Synchronization for Vehicular Networks with C.-Y. Han and A. Lambert, 2018.
  Extended abstract presented at IV 2018

• A Faithful Binary Circuit Models with Adversarial Noise with M. Függer, J. Maier, R. Najvirt, and U. Schmid, 2018.
  Extended abstract presented at DATE 2018 (best paper award finalist)
  arXiv

• Data Collection in Population Protocols with Non-uniformly Random Scheduler with J. Beauquier, J. Burman, S. Kutten, and C. Xu, 2017.
  Theoretical Computer Science 806:516-530
  Extended abstract presented at Algosensors 2017 (invited to special issue of Theoretical Computer Science)

• On the Tightness of Bounds for Transients and Weak CSR Expansions in Max-Plus Algebra with G. Merlet and S. Sergeev, 2017.
  Multilinear Algebra (2021)
  arXiv

• Tight Bounds for Asymptotic and Approximate Consensus with M. Függer and M. Schwarz, 2017.
  Journal of the ACM 68(6)
  Extended abstract presented at PODC 2018
  Brief announcement presented at DISC 2017
  arXiv

• Multidimensional Asymptotic Consensus in Dynamic Networks with B. Charron-Bost and M. Függer, 2016.
  arXiv

• Amortized Averaging Algorithms for Approximate Consensus with B. Charron-Bost and M. Függer, 2015.
  Extended abstract presented at ICALP 2016
  arXiv

• Fast Symbolic Computation of the Worst-Case Delay in Tandem Networks and Applications with A. Bouillard, 2015.
  Performance Evaluation 91:270-285

• Asymptotic Consensus Without Self-Confidence, 2015.
  Extended abstract presented at CDC 2015
  arXiv

• Experimental Validation of a Faithful Binary Circuit Model with M. Függer, R. Najvirt, U. Schmid, M. Hofbauer, and K. Schweiger, 2015.
  Extended abstract presented at GLSVLSI 2015

• Diffusive Clock Synchronization in Highly Dynamic Networks with B. Charron-Bost and M. Függer, 2015.
  Extended abstract presented at CISS 2015

• Approximate Consensus in Highly Dynamic Networks: The Role of Averaging Algorithms with B. Charron-Bost and M. Függer, 2014.
  Extended abstract presented at ICALP 2015
  arXiv

• Faithful Glitch Propagation in Binary Circuit Models with M. Függer, R. Najvirt, and U. Schmid, 2014.
  IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39(10):2784-2797
  Extended abstract presented at DATE 2015
  arXiv

• Weak CSR Expansions and Transience Bounds in Max-Plus Algebra with G. Merlet and S. Sergeev, 2013.
  Linear Algebra and its Applications 461:163-199
  arXiv

• Generalizations of Bounds on the Index of Convergence to Weighted Digraphs with G. Merlet, H. Schneider, and S. Sergeev, 2013.
  Discrete Applied Mathematics 178:121-134
  Extended abstract presented at CDC 2014
  arXiv

• Unfaithful Glitch Propagation in Existing Binary Circuit Models with M. Függer and U. Schmid, 2013.
  IEEE Transactions on Computers 65(3):964-978
  Extended abstract presented at ASYNC 2013
  arXiv

• Transience Bounds for Distributed Algorithms with B. Charron-Bost and M. Függer, 2013.
  Extended abstract presented at FORMATS 2013

• An Overview of Transience Bounds in Max-Plus Algebra with B. Charron-Bost, 2013.
  Contemporary Mathematics 616, pp. 277-289
  arXiv

• The Effect of Forgetting on the Performance of a Synchronizer with M. Függer, A. Kößler, U. Schmid, and M. Zeiner, 2013.
  Performance Evaluation 93:1-16
  Extended abstract presented at Algosensors 2013
  Brief announcement presented at SSS 2012

• General Transience Bounds in Tropical Linear Algebra via Nachtigall Decomposition with B. Charron-Bost, 2012.
  Extended abstract presented at TROPICAL-12

• New Transience Bounds for Max-Plus Linear Systems with B. Charron-Bost and M. Függer, 2012.
  Discrete Applied Mathematics 219:83-99
  Abstract and poster presented at Eurocomb 2013
  arXiv

• On the Performance of a Retransmission-Based Synchronizer with M. Függer and A. Kößler, 2011.
  Theoretical Computer Science 509:25-39
  Extended abstract presented at SIROCCO 2011 (invited to special issue of Theoretical Computer Science)

Theses

• Transient Behavior of Distributed Algorithms and Digital Circuit Models, PhD thesis, École polytechnique, 2014.
  PDF
• Topology in Distributed Computing, Master's thesis, Vienna University of Technology, 2010.
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• Implementation and Evaluation of a Support Vector Machine on an 8-bit Microcontroller, Bachelor's thesis, Vienna University of Technology, 2008.
  PDF

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Contact

Thomas Nowak
Laboratoire Méthodes Formelles
ENS Paris-Saclay
Room 2S57
4, avenue des Sciences
91190 Gif-sur-Yvette
France

Email: thomas@thomasnowak.net
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