Beräkningsvetenskap med fokus på bionanofysik

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Research overview

I have a broad expertise within the fields of theoretical biological physics, equilibrium and non-equilibrium statistical physics, mathematical physics and nanophysics. I worked with several experimental partners from the fields of physics, chemistry and nanoscience.

Examples of research topics

• Data analysis and modeling for particle tracking 
• Optical DNA mapping (DNA barcoding)
• Modeling of biophysical processes at the nanoscale
• Crowding effects on tracer particle dynamics in many-body systems
• Single-file diffusion
• Epidemiology on networks
• Localized surface plasmons in metallic nanoparticles
• Electric and electromagnetic response of biomembranes
• DNA breathing dynamics and protein binding dynamics
• Translocation of biopolymers through nanopores
• Fluroscence of molecules near metallic surfaces
• Interaction between optical electromagnetic fields and molecular aggregates

Group members 

• Erik Clarkson, PhD student 2024 - present
• Mikkel Peter Andersen,  PhD student, 2024 - present
• Jakob Gunnarsson, BSc student, 2025
• Christoffer Karlsson, BSC student, 2025

Previous members

• Lauri Eckle, BSc student, 2025
• Albertas Dvirnas, post-doc 2022- 
• Dibyayjoti Mohanta, post-doc 2022- 
• Steffi Schijf, BSc student 2022-2023.
• Erik Clarkson, MSc student, 2022.
• Simon Tropp, MSc student, 2022.
• Jake Lumsden, MSc student, 2022.
• Albertas Dvirnas, PhD student, 2017-2022.
• Lennart Golks, Master student, 2020-2021.
• Nirvika Chouhan, Research intern (through Jobbsprånget) 2020-2021.
• Dolev Illouz, Master student 2020.
• Magnus Brander, Master student 2019-2020.
• Jens Krog, Post-doc 2018-2020.
• Wensi Zhu, Master student 2017-2018.
• Magnus Brander, Bachelor student 2018.
• Terje Stenström, Bachelor student 2017.
• Henrik Nordanger, Master student 2016, project worker 2017.
• Callum Stewart, Master student 2016-2017,
• Lisa Rämisch, Summer research intern 2017. 
• Arthur Genthon, Exchange master student (Ecole Normale Superieure Paris-Saclay) 2019
• Saair Quaderi, Visting researcher 2015-2017.
• Vibha Kumra, Bachelor student 2016.
• Hemant Kumar, Visting researcher (Indian Institute of Technology, Delhi) 2016.
• Johannes Isaksson, Bachelor student 2016.
• Christoffer Pichler, Masters student 2015.
• Paola Torche, Bachelor student 2015.
• Erik Lagerstedt, Masters student 2014.
• Michaela Schad, PhD student 2010-2015.
• Erik Lagerstedt, Bachelor student 2011.
• Susanna Hammarberg, Summer research intern 2014.
• Charleston Noble, Researcher 2013-2014.
• Lloyd Sanders, PhD student 2010-2014.
• Adam Nilsson, Masters student 2013.
• Simon Pigeon, Post-doc 2012-2013.
• Karl Fogelmark, Master student and research intern 2010-2011.

List of past and present collaborators (alphabetical order)

• Peter Apell, Chalmers University, Sweden.
• Suman Banik, Bose Institute, India.
• Eli Barkai, Bar Ilan University, Israel.
• Dirk Brockmann, Northwestern University, USA.
• Yuval Ebenstein, Tel Aviv University, Israel.
• Per Lyngs Hansen, University of Southern Denmark, Denmark.
• John Kasianowicz, National Institute of Standards and Technology, USA.
• Peter Jönsson, Physical chemistry, Lund University
• Oleg Krichevsky, Ben-Gurion University, Israel.
• Zoran Konkoli, Chalmers University, Sweden.
• Mikael Käll, Chalmers University, Sweden.
• Ludvig Lizana, Umeå University, Denmark.
• Michael Lomholt, University of Southern Denmark, Denmark.
• Ed Di Marzio, National Institute of Standards and Technology, USA.
• Ralf Metzler, Technical University Munich, Germany.
• Gautam Mukhopadhyay, Indian Institute of Technology Bombay, India.
• Weihai Ni, Universidade de Vigo, Spain.
• Pontus Nordenfelt, Division of Infection Medicine, Lund University.
• Tomas Novotny, Charles University, Czech Republic.
• Jonas Pedersen, Technical University of Denmark, Denmark.
• Robert Silbey, Massachusetts Institute of Technology, USA.
• Alessandro Taloni, Tel Aviv University, Israel.
• Jonas Tegenfeldt, Lund University and Göteborg University, Sweden.
• Jianfang Wang, Chinese University of Hong Kong.
• Fredrik Westerlund, Chalmers University, Sweden.

Grants

• 2023-2027: VR, project grant: Connecting the dots: probabilistic mapping of biomolecular paths in fluorescence microscopy, PI.
• 2022-2024: Barncancerfonden, Optical DNA mapping for improved diagnostics for children with leukemia, co-PI. PI: Fredrik Westerlund.
• 2022-2024:The Erling-Persson Family Foundation, Next generation diagnostic of bacterial infections, co-PI. PI: Fredrik Westerlund.
• 2018-2019: Crafoord Foundation, Detecting antibiotic resistance genes on plasmids using high-throughput and cell-phone microscopy based optical DNA mappings, PI.
• 2017-2020: The Erling-Persson Family Foundation, A novel ultrafast method for detecting multiresistant bacteria in intensive care units, co-PI. PI: Fredrik Westerlund. 
• 2015-2019: VR, project grant,  Non-equilibrium biophysics in nano-confined systems, Grant ID: 2014-4305, PI. 
• 2015-2019: EU, BeyondSeq -- Genomic diagnostics beyond the sequence, PI: Yuval Ebenstein.
• 2012-2013, Carl Tryggers Stiftelse. Classifying DNA Melting Maps for Ultra-fast Identification of Species, PI. 
• 2011-2012, The Crafoord Foundation. Nanoscale tracer dynamics in many-body heterogenous soft matter systems, PI.
• 2010-2014: VR, project grant, Modeling of nanoscale biophysical  processes and label-free detection using metallic nanoparticles, PI.
• 2006-2011: The Knut and Alice Wallenberg Foundation. Bio-nano-sensor physics. Post-doc grant + repatriation, PI.

Software 

• WLS-ICE - Weighted Least Squares Including Correlation in Error. 
  The latest release of the software is available at: https://github.com/impaktor/wlsice/
  The associated methods are described in this publication: https://doi.org/10.1038/s41598-018-24983-y
• Filter-function for reducing noise in DNA barcodes. Code: https://figshare.com/s/a63df3aac07777ed878d Methods described in: https://doi.org/10.1371/journal.pone.0179041
• Simulation package for interacting particles jumping on a lattice. Code: https://github.com/impaktor/diffusion  Methods described in: https://doi.org/10.1088/1742-5468/aa9db3
• Bayesian data analysis package for unfolding DNA molecules in nano-channels. Code: https://github.com/krogjens/dna_unfolding Methods described in: https://doi.org/10.1063/1.5051319
• Hidden Markov Model for detecting structural variations in DNA barcodes. Code: https://gitlab.com/dnadevcode/hmmsv Methods described in: https://doi.org/10.1371/journal.pone.0259670
• Data analysis of dually labeled DNA barcodes. Code: https://gitlab.com/dnadevcode/cdsodm ; Methods described in: https://doi.org/10.1371/journal.pone.0260489
• Software for DNA melting predictions, https://github.com/Arthur-Genthon/dna-melting-defect Methods are described in: https://doi.org/10.1063/5.0168915 
• Photophysical image analysis for EMCCD camera imaging, https://zenodo.org/records/10531777 Methods are described in: https://doi.org/10.1371/journal.pone.0300122 
•  Random sampling of ligand arrangements, https://github.com/dibyajyoti41/ligandbinding Methods are described in: https://doi.org/10.1103/PhysRevE.111.014412 
• Bayesian and frequentist analyses of two-state single-molecule diffusion trajectories, https://github.com/ewclarkson/BayFreq-2state Methods described in: https://doi.org/10.1088/1751-8121/add064 

   

   

   

Current 

• FYTN15/FMFN25 Statistical Mechanics (course coordinator/lecturer) 
• FYTN05 Theoretical Biophysics (lecturer) 
• Stochastic Thermodynamics, PhD level, 2025

Previous 

• FYTN03 Computational Physics (course coordinator/lecturer), 2009-2019
• FYTK02/FYTM03/FYTM04, degree project in theoretical physics (course coordinator), 2015-2018, 2020-2022.
• Morphomatics, Chalmers University (lecturer), 2001-2002  
• Living State Physics, Chalmers University (lecturer), 1999-2001
• Teaching Assistant for several courses at Chalmers University of Technology and Göteborg University, 1998-2003