Julius B. Kirkegaard

Theoretical Biophysics & Data Science

We do theoretical and data-centric research in a broad range of topics related to biology. We like to be jack-of-all-trades within our fields of study, fully aware that this means we remain masters of none. Some keywords of interests are:

— Stochastic Processes — Optimality — Computer Vision — Morphogenesis — Differentiable Programming — Fluid Mechanics — Ecology — Bayesian Analysis — Network optimization — Navigation — Protein Aggregation — Biofilms —

Publications

Google Scholar

Julius B Kirkegaard, Nikolay P Kutuzov, Rasmus Netterstrøm, Sune Darkner, Martin Lauritzen, François Lauze In Vivo Deep Learning Estimation of Diffusion Coefficients of Nanoparticles . Medical Image Computing and Computer Assisted Intervention 2024.
Albert Alonso, Julius B Kirkegaard Learning optimal integration of spatial and temporal information in noisy chemotaxis . PNAS Nexus 2024.
Yusuke Himeoka, Julius B Kirkegaard , Namiko Mitarai, Sandeep Krishna Roles of network topology in the relaxation dynamics of simple chemical reaction network models . Scientific Reports 2024.
Albert Alonso, Julius B Kirkegaard Fast detection of slender bodies in high density microscopy data . Communications Biology 2023.
Lars Erik J. Skjegstad, Jan F. Nickels, Kim Sneppen, Julius B Kirkegaard Epigenetic switching with asymmetric bridging interactions . Biophysical Journal 2023.
Julius B Kirkegaard, Kim Sneppen. Emerging diversity in a population of evolving intransitive dice. Phys. Rev. E 2022.
Interactive post
Julius B Kirkegaard Curvature Strains as a Global Orchestrator of Morphogensis. Phys. Rev. Research 2022.
Julius B Kirkegaard Simultaneous Curve Fitting of Functions and Differential Equations using Analytical Gradient Calculations. BMC Bioinformatics 2022.
Lichtenberg, Mads, Kragh, Kasper Nørskov, Fritz, Blaine, Julius B Kirkegaard, Tim Tolker-Nielsen, Thomas Bjarnsholt Cyclic-di-GMP signaling controls metabolic activity in Pseudomonas aeruginosa Cell reports 2022.
Fritz, Blaine, Kirkegaard, Julius B, Nielsen, Claus Henrik, Kirketerp-Møller, Klaus, Malone, Matthew, Bjarnsholt, Thomas Transcriptomic fingerprint of bacterial infection in lower extremity ulcers Apmis 2022.
Kirkegaard, Julius B, Sneppen, Kim Superspreading quantified from bursty epidemic trajectories Nature Scientific Reports 2021.
Kirkegaard, Julius B, Mathiesen, Joachim, Sneppen, Kim Airborne Pathogens in a Heterogeneous World: Superspreading & Mitigation. Nature Scientific Reports 2021.
Michele Perni, Annemieke van der Goot, Ryan Limbocker, Tjakko J van Ham, Francesco A Aprile, Catherine K Xu, Patrick Flagmeier, Karen Thijssen, Pietro Sormanni, Giuliana Fusco, Serene W Chen, Pavan K Challa, Julius B Kirkegaard, Romain F Laine, Kai Yu Ma, Martin BD Müller, Tessa Sinnige, Janet R Kumita, Samuel IA Cohen, Renée Seinstra, Gabriele S Kaminski Schierle, Clemens F Kaminski, Denise Barbut, Alfonso De Simone, Tuomas PJ Knowles, Michael Zasloff, Ellen AA Nollen, Michele Vendruscolo, Christopher M Dobson Comparative Studies in the A30P and A53T α-Synuclein C. elegans Strains to Investigate the Molecular Origins of Parkinson's Disease. Frontiers in Cell and Developmental Biology 2021.
Michele Perni, Quentin Peter, Pavan Challa, Tadas Kartanas, Pietro Sormanni, Julius Kirkegaard, Michele Vendruscolo, Chris Dobson, Tuomas Knowles Method of tracking a plurality of objects. U.S. Patent Application 2021.
Julius B Kirkegaard, Kim Sneppen Optimal transport flows for distributed production networks. Physical Review Letters 2020.
Julius B Kirkegaard, Bjarke F Nielsen, Ala Trusina, Kim Sneppen Self-assembly, buckling and density-invariant growth of three-dimensional vascular networks. Journal of the Royal Society Interface 2019.
Julius B Kirkegaard, Raymond E Goldstein The role of tumbling frequency and persistence in optimal run-and-tumble chemotaxis. IMA Journal of Applied Mathematics 2018.
Pierre A Haas, Stephanie SMH Höhn, Aurelia R Honerkamp-Smith, Julius B Kirkegaard, Raymond E Goldstein The noisy basis of morphogenesis: Mechanisms and mechanics of cell sheet folding inferred from developmental variability. PLoS biology 2018.
Julius B Kirkegaard Physical and Stochastic Aspects of Microorganism Behaviour. PhD Thesis 2018.
Michele Perni, Patrick Flagmeier, Ryan Limbocker, Roberta Cascella, Francesco A Aprile, Celine Galvagnion, Gabriella T Heller, Georg Meisl, Serene W Chen, Janet R Kumita, Pavan K Challa, Julius B Kirkegaard, Samuel IA Cohen, Benedetta Mannini, Denise Barbut, Ellen AA Nollen, Cristina Cecchi, Nunilo Cremades, Tuomas PJ Knowles, Fabrizio Chiti, Michael Zasloff, Michele Vendruscolo, Christopher M Dobson Multistep Inhibition of α-Synuclein Aggregation and Toxicity in Vitro and in Vivo by Trodusquemine. ACS chemical biology 2018.
Michele Perni, Pavan K Challa, Julius B Kirkegaard, Ryan Limbocker, Mandy Koopman, Maarten C Hardenberg, Pietro Sormanni, Thomas Müller, Kadi L Saar, Lianne WY Roode, Johnny Habchi, Giulia Vecchi, Nilumi Fernando, Samuel Casford, Ellen AA Nollen, Michele Vendruscolo, Christopher M Dobson, Tuomas PJ Knowles Massively parallel C. elegans tracking provides multi-dimensional fingerprints for phenotypic discovery. Journal of neuroscience methods 2018.
Michele Perni, Celine Galvagnion, Alexander Maltsev, Georg Meisl, Martin BD Mueller, Pavan K Challa, Julius B Kirkegaard, Patrick Flagmeier, Samuel IA Cohen, Roberta Cascella, Serene W Chen, Ryan Limboker, Pietro Sormanni, Gabriella T Heller, Francesco A Aprile, Nunilo Cremades, Cristina Cecchi, Fabrizio Chiti, Ellen AA Nollen, Tuomas PJ Knowles, Michele Vendruscolo, Adriaan Bax, Michael Zasloff, Christopher M Dobson A natural product inhibits the initiation of alpha-synuclein aggregation and suppresses its toxicity. Proceedings of the National Academy of Sciences of the United States of America 2017.
Patrick Varilly, Adam P Willard, Julius B Kirkegaard, Tuomas PJ Knowles, David Chandler Intra-chain organisation of hydrophobic residues controls inter-chain aggregation rates of amphiphilic polymers The Journal of chemical physics 2017.
Julius B Kirkegaard, Ambre Bouillant, Alan O Marron, Kyriacos C Leptos, Raymond E Goldstein Aerotaxis in the closest relatives of animals eLife 2016.
Julius B Kirkegaard, Raymond E Goldstein Filter-feeding, near-field flows, and the morphologies of colonial choanoflagellates. Physical Review E 2016.
Georg Meisl, Julius B Kirkegaard, Paolo Arosio, Thomas CT Michaels, Michele Vendruscolo, Christopher M Dobson, Sara Linse, Tuomas PJ Knowles Molecular mechanisms of protein aggregation from global fitting of kinetic models Nature protocols 2016.
Julius B Kirkegaard, Alan O Marron, Raymond E Goldstein Motility of colonial choanoflagellates and the statistics of aggregate random walkers Physical review letters 2016.
Thomas CT Michaels, Alexander J Dear, Julius B Kirkegaard, Kadi L Saar, David A Weitz, Tuomas PJ Knowles Fluctuations in the kinetics of linear protein self-assembly Physical review letters 2016.
Guillaume Lamour, Julius B Kirkegaard, Hongbin Li, Tuomas PJ Knowles, Jörg Gsponer Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains Source code for biology and medicine 2014.
Georg Meisl, Xiaoting Yang, Erik Hellstrand, Birgitta Frohm, Julius B Kirkegaard, Samuel IA Cohen, Christopher M Dobson, Sara Linse, Tuomas PJ Knowles Differences in nucleation behavior underlie the contrasting aggregation kinetics of the Aβ40 and Aβ42 peptides Proceedings of the National Academy of Sciences 2014.
Michael Caspersen, Julius Bier Kirkegaard Modelling electrolyte conductivity in a water electrolyzer cell International journal of hydrogen energy 2012.

Teaching

I teach Numerical Methods in Physics at the Niels Bohr Institute. This is an intense (7.5 ECTS) summer course that runs in August. It is meant for students who are already familiar with (preferably Python) programming, and who has made simple physical simulations before. We touch on the basis, theoretically and practially, of most simulation methods used in the physical sciences.

My lecture notes for the course can be downloaded here. If you are a teacher who wishes to use these, please reach out. A number of exercises are available for the notes.

People

Julius B. Kirkegaard
Principal Investigator
TT Assistant Professor
Department of Computer Science
Niels Bohr Institute
University of Copenhagen

2018 Ph.D. University of Cambridge
Supervisor: Raymond E. Goldstein
2014 M.Sc. University of Copenhagen
2012 B.Sc. University of Copenhagen

Current Grants

Previous Grants

Albert Alonso de la Fuente
PhD Student
Lars Erik Johnsen Skjegstad
PhD Student
Collaborators:
Kim Sneppen, Ala Trusina & Joachim Mathiesen
Niels Bohr Institute, University of Cambridge

Bjarke Frost Nielsen & Lone Simonsen
PandemiX Center, University of Roskilde

Mads Lichtenberg, Blaine Gabriel Fritz & Thomas Bjarnsholt
Costerton Biofilm Center, University of Copenhagen

Iris Anne Unterweger & Elke Ober
Center for Stem Cell Research and Developmental Biology (DanStem), University of Copenhagen

Michele Perni & Andrea Possenti
Wren Therapeutics & University of Cambridge

Georg Meisl
Department of Chemistry, University of Cambridge
Previous students:
Andreas Mosgaard
Bachelor Student

Contact

Julius B. Kirkegaard
University of Copenhagen
Department of Computer Science & Niels Bohr Institute
Universitetsparken 1
2100 Copenhagen Ø
Office 3-2-11
juki @ di.ku.dk