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, where my group did modeling, image analysis, statistics and software development.
Brief CV
- 1993 - 1998. MSc, Theoretical Physics, Linköping University, Sweden
- 1998 - 2003, PhD, Gothenburg University, Sweden. 2003 - 2006. Postdoc, Nordic Institute for Theoretical Physics (NORDITA), Copenhagen, Denmark, group of Prof. Ralf Metzler.
- 2006 - 2008. Postdoc, Massachusetts Institute of Technology (MIT), Department of Chemistry, group of Prof. Robert Silbey.
- 2009 - 2015, Assistant Professor, Department of Astronomy and Theoretical Physics, Lund University
- 2016 - 2022. Senior University Lecturer, Department of Astronomy and Theoretical Physics, Lund University
- 2023-. Senior University Lecturer, Centre for Environmental and Climate Science, Lund University
Collaborators
I have a large network of collaborators from USA, India, China, Israel, Germany, Spain, Czech Republic, Denmark and Sweden.
Funding
Funding from several funding agencies such as The Swedish research council, Knut and Alice Wallenberg foundation, EU, The Erling-Persson Family Foundation, The Crafoord foundation, The Carl Tryggers foundation.
Software
My research group has made available several open source codes and software packages.
Please visit my profile in the Lund University Research portal for details.
Links
Publications
Displaying of publications. Sorted by year, then title.
Photophysical image analysis : Unsupervised probabilistic thresholding for images from electron-multiplying charge-coupled devices
Jens Krog, Albertas Dvirnas, Oskar E Ström, Jason P Beech, Jonas O Tegenfeldt, et al.
(2024) PLoS ONE, 19 p.0300122-0300122
Journal articleEquilibrium melting probabilities of a DNA molecule with a defect : An exact solution of the Poland-Scheraga model
Arthur Genthon, Albertas Dvirnas, Tobias Ambjörnsson
(2023) Journal of Chemical Physics, 159
Journal articleA simple cut and stretch assay to detect antimicrobial resistance genes on bacterial plasmids by single-molecule fluorescence microscopy
Gaurav Goyal, Elina Ekedahl, My Nyblom, Jens Krog, Erik Fröbrant, et al.
(2022) Scientific Reports, 12
Journal articleDetection of structural variations in densely-labelled optical DNA barcodes : A hidden Markov model approach
Albertas Dvirnas, Callum Stewart, Vilhelm Müller, Santosh Kumar Bikkarolla, Karolin Frykholm, et al.
(2021) PLoS ONE, 16
Journal articleCombining dense and sparse labeling in optical DNA mapping
Erik Torstensson, Gaurav Goyal, Anna Johnning, Fredrik Westerlund, Tobias Ambjörnsson
(2021) PLoS ONE, 16
Journal articleModeling protein target search in human chromosomes
Markus Nyberg, Tobias Ambjörnsson, Per Stenberg, Ludvig Lizana
(2021) Physical Review Research, 3
Journal articleA Predictive Model of Antibody Binding in the Presence of IgG-Interacting Bacterial Surface Proteins
Vibha Kumra Ahnlide, Therese de Neergaard, Martin Sundwall, Tobias Ambjörnsson, Pontus Nordenfelt
(2021) Frontiers in Immunology, 12
Journal articleCRISPR/CAS9 BASED DNA-COMBING ASSAY FOR DETECTING ANTIMICROBIAL RESISTANCE GENES ON PLASMIDS
Gaurav Goyal, Elina Ekedahl, My Nyblom, Jens Krog, Erik Torstensson, et al.
(2021) MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences , p.801-802
Conference paperCultivation-Free Typing of Bacteria Using Optical DNA Mapping
Vilhelm Müller, My Nyblom, Anna Johnning, Marie Wrande, Albertas Dvirnas, et al.
(2020) ACS Infectious Diseases, 6 p.1076-1084
Journal articleEnzyme-free optical DNA mapping of the human genome using competitive binding
Vilhelm Müller, Albertas Dvirnas, John Andersson, Vandana Singh, Sriram Kk, et al.
(2019) Nucleic Acids Research, 47
Journal articleOptical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak
Santosh K. Bikkarolla, Viveka Nordberg, Fredrika Rajer, Vilhelm Müller, Muhammad Humaun Kabir, et al.
(2019) mBio, 10
Journal articleBacterial identification by optical mapping of genomic DNA in nanofluidic channels
My Nyblom, Vilhelm Müller, Anna Johnning, Marie Wrande, Albertas Dvirnas, et al.
(2019) 23rd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2019 , p.821-822
Conference paperFitting a function to time-dependent ensemble averaged data
Karl Fogelmark, Michael A. Lomholt, Anders Irbäck, Tobias Ambjörnsson
(2018) Scientific Reports, 8
Journal articleThe resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis
Anna Johnning, Nahid Karami, Erika Tång Hallbäck, Vilhelm Müller, Lena Nyberg, et al.
(2018) Microbial Genomics, 4
Journal articleZero-crossing statistics for non-Markovian time series
Markus Nyberg, Ludvig Lizana, Tobias Ambjörnsson
(2018) Physical Review E, 97
Journal articleFacilitated sequence assembly using densely labeled optical DNA barcodes : A combinatorial auction approach
Albertas Dvirnas, Christoffer Pichler, Callum L. Stewart, Saair Quaderi, Lena K. Nyberg, et al.
(2018) PLoS ONE, 13
Journal articleStochastic unfolding of nanoconfined DNA : Experiments, model and Bayesian analysis
Jens Krog, Mohammadreza Alizadehheidari, Erik Werner, Santosh Kumar Bikkarolla, Jonas O. Tegenfeldt, et al.
(2018) Journal of Chemical Physics, 149
Journal articleTracer particle diffusion in a system with hardcore interacting particles
Simon Pigeon, Karl Fogelmark, Bo Söderberg, Gautam Mukhopadhyay, Tobias Ambjörnsson
(2017) Journal of Statistical Mechanics: Theory and Experiment, 2017
Journal articleNoise reduction in single time frame optical DNA maps
Paola C. Torche Pedreschi, Vilhelm Müller, Fredrik Westerlund, Tobias Ambjörnsson
(2017) PLoS ONE, 12
Journal articleTracer particles in two-dimensional elastic networks diffuse logarithmically slow
Ludvig Lizana, Tobias Ambjörnsson, Michael A. Lomholt
(2017) Journal of Physics A: Mathematical and Theoretical, 50
Journal articleDirect identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping
Vilhelm Müller, Fredrika Rajer, Karolin Frykholm, Lena K. Nyberg, Saair Quaderi, et al.
(2016) Scientific Reports, 6
Journal articleSuper-Resolution Genome Mapping in Silicon Nanochannels
Jonathan Jeffet, Asaf Kobo, Tianxiang Su, Assaf Grunwald, Ori Green, et al.
(2016) ACS Nano, 10 p.9823-9830
Journal articleRapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules
Lena K. Nyberg, Saair Quaderi, Gustav Emilsson, Nahid Karami, Erik Lagerstedt, et al.
(2016) Scientific Reports, 6
Journal articleA simple method to calculate first-passage time densities with arbitrary initial conditions
Markus Nyberg, Tobias Ambjörnsson, Ludvig Lizana
(2016) New Journal of Physics, 18
Journal articleRapid tracing of resistance plasmids in a nosocomial outbreak using optical DNA mapping
Vilhelm Müller, Nahid Karami, Lena K. Nyberg, Christoffer Pichler, Paola C. Torche Pedreschi, et al.
(2016) ACS Infectious Diseases, 2 p.322-328
Journal articleDetailed characterization of plasmids carrying resistance genes using optical DNA mapping
Vilhelm Müller, Lena K. Nyberg, Saair Quaderi, Erik Kristiansson, Tobias Ambjörnsson, et al.
(2016) 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016 , p.1561-1562
Conference paperVisualizing the entire DNA from a chromosome in a single frame
C. Freitag, Charleston Noble, J. Fritzsche, F. Persson, Michaela Reiter-Schad, et al.
(2015) Biomicrofluidics, 9
Journal articleA fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings.
Charleston Noble, Adam Nilsson, Camilla Freitag, Jason Beech, Jonas Tegenfeldt, et al.
(2015) PLoS ONE, 10
Journal articleMany-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA
Sebastian Ahlberg, Tobias Ambjörnsson, Ludvig Lizana
(2015) New Journal of Physics, 17
Journal articleNanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
Mohammadreza Alizadehheidari, Erik Werner, Charleston Noble, Michaela Reiter-Schad, Lena K. Nyberg, et al.
(2015) Macromolecules, 48 p.871-878
Journal articleModel for melting of confined DNA
E. Werner, Michaela Reiter-Schad, Tobias Ambjörnsson, B. Mehlig
(2015) Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), 91
Journal articleHow nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model.
Michaela Reiter-Schad, Erik Werner, Jonas Tegenfeldt, Bernhard Mehlig, Tobias Ambjörnsson
(2015) Journal of Chemical Physics, 143
Journal articleExtension of nanoconfined DNA: Quantitative comparison between experiment and theory
V. Iarko, E. Werner, L. K. Nyberg, V. Muller, J. Fritzsche, et al.
(2015) Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), 92
Journal articleFast size-determination of intact bacterial plasmids using nanofluidic channels
K. Frykholm, L. K. Nyberg, E. Lagerstedt, Charleston Noble, J. Fritzsche, et al.
(2015) Lab on a Chip, 15 p.2739-2743
Journal articleBacteriophage strain typing by rapid single molecule analysis.
Assaf Grunwald, Moran Dahan, Anna Giesbertz, Adam Nilsson, Lena K Nyberg, et al.
(2015) Nucleic Acids Research, 43 p.117-117
Journal articleSevere slowing-down and universality of the dynamics in disordered interacting many-body systems: ageing and ultraslow diffusion
Lloyd Sanders, Michael A. Lomholt, Ludvig Lizana, Karl Fogelmark, Ralf Metzler, et al.
(2014) New Journal of Physics, 16
Journal articleAgeing single file motion
R. Metzler, Lloyd Sanders, M. A. Lomholt, L. Lizana, Karl Fogelmark, et al.
(2014) The European Physical Journal. Special Topics, 223 p.3287-3293
Journal articleUniversality and nonuniversality of mobility in heterogeneous single-file systems and Rouse chains
Michael A. Lomholt, Tobias Ambjörnsson
(2014) Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), 89
Journal articleCompetitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli.
Adam Nilsson, Gustav Emilsson, Lena K Nyberg, Charleston Noble, Liselott Svensson Stadler, et al.
(2014) Nucleic Acids Research, 42 p.118-118
Journal articleNon-Markovian effects in the first-passage dynamics of obstructed tracer particle diffusion in one-dimensional systems.
Robin Forsling, Lloyd Sanders, Tobias Ambjörnsson, Ludvig Lizana
(2014) Journal of Chemical Physics, 141
Journal articleSingle-file diffusion with non-thermal initial conditions
Ludvig Lizana, Michael A. Lomholt, Tobias Ambjörnsson
(2014) Physica A: Statistical Mechanics and its Applications, 395 p.148-153
Journal articleNanoconfined circular DNA
M. Alizadehheidari, E. Werner, C. Noble, L. K. Nyberg, J. Fritzsche, et al.
(2014) 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014 , p.1353-1355
Conference paperIdentifying bacteria using DNA binding maps
Gustav Emilsson, Adam Nilsson, Lena K. Nyberg, Charleston Noble, Liselott Svensson Stadler, et al.
(2013) 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013, 1 p.473-475
Conference paperMicroscopic Origin of the Logarithmic Time Evolution of Aging Processes in Complex Systems
Michael A. Lomholt, Ludvig Lizana, Ralf Metzler, Tobias Ambjörnsson
(2013) Physical Review Letters, 110
Journal articlePerturbative solution to susceptible-infected-susceptible epidemics on networks.
Lloyd Sanders, Bo Söderberg, Dirk Brockmann, Tobias Ambjörnsson
(2013) Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), 88
Journal articleFirst passage times for a tracer particle in single file diffusion and fractional Brownian motion.
Lloyd Sanders, Tobias Ambjörnsson
(2012) Journal of Chemical Physics, 136
Journal articleDissimilar bouncy walkers
Michael A Lomholt, Ludvig Lizana, Tobias Ambjörnsson
(2011) Journal of Chemical Physics, 134
Journal articleObserving Plasmonic-Molecular Resonance Coupling on Single Gold Nanorods
Weihai Ni, Tobias Ambjörnsson, Sten Peter Apell, Huanjun Chen, Jianfang Wang
(2010) Nano Letters, 10 p.77-84
Journal articleFoundation of fractional Langevin equation: Harmonization of a many-body problem
Ludvig Lizana, Tobias Ambjörnsson, Alessandro Taloni, Eli Barkai, Michael A. Lomholt
(2010) Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), 81
Journal articleSingle DNA denaturation and bubble dynamics
Ralf Metzler, Tobias Ambjörnsson, Andreas Hanke, Hans C Fogedby
(2009) Journal of Physics: Condensed Matter, 21
Journal articleBubble merging in breathing DNA as a vicious walker problem in opposite potentials.
Jonas Pedersen, Mikael Sonne Hansen, Tomás Novotný, Tobias Ambjörnsson, Ralf Metzler
(2009) Journal of Chemical Physics, 130
Journal articleDiffusion of finite-sized hard-core interacting particles in a one-dimensional box: Tagged particle dynamics
L. Lizana, Tobias Ambjörnsson
(2009) Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), 80
Journal articleSingle-file dynamics with different diffusion constants
Tobias Ambjörnsson, Ludvig Lizana, Michael A. Lomholt, Robert J. Silbey
(2008) The Journal of chemical physics, 129
Journal articleDiffusion of two particles with a finite interaction potential in one dimension
Tobias Ambjörnsson, Robert J. Silbey
(2008) The Journal of chemical physics, 129 p.165103-165103
Journal articleSingle-File Diffusion in a Box
L. Lizana, T. Ambjörnsson
(2008) Physical Review Letters, 100
Journal articleBreathing Dynamics in Heteropolymer DNA
Tobias Ambjörnsson, Suman K. Banik, Oleg Krichevsky, Ralf Metzler
(2007) Biophysical Journal, 92 p.2674-2684
Journal articleSingle DNA conformations and biological function
Ralf Metzler, Tobias Ambjörnsson, Andreas Hanke, Yongli Zhang, Stephen Levene
(2007) Journal of Computational and Theoretical Nanoscience, 4 p.1-49
Journal article reviewBubble coalescence in breathing DNA: Two vicious walkers in opposite potentials
T. Novotny, Jonas Pedersen, T. Ambjörnsson, M. S. Hansen, R. Metzler
(2007) Europhysics Letters, 77
Journal articleApplying a potential across a biomembrane: Electrostatic contribution to the bending rigidity and membrane instability
Tobias Ambjörnsson, Michael A. Lomholt, Per Lyngs Hansen
(2007) Physical Review E, 75
Journal articleMaster equation approach to DNA breathing in heteropolymer DNA
Tobias Ambjörnsson, Suman K. Banik, Michael A. Lomholt, Ralf Metzler
(2007) Physical Review E, 75
Journal articleResonant coupling between localized plasmons and anisotropic molecular coatings in ellipsoidal metal nanoparticles
Tobias Ambjörnsson, Gautam Mukhopadhyay, S. Peter Apell, Mikael Käll
(2006) Physical Review B, 73
Journal articleSequence Sensitivity of Breathing Dynamics in Heteropolymer DNA
Tobias Ambjörnsson, Suman K. Banik, Oleg Krichevsky, Ralf Metzler
(2006) Physical Review Letters, 97
Journal articleBlinking statistics of a molecular beacon triggered by end-denaturation of DNA
Tobias Ambjörnsson, Ralf Metzler
(2005) Journal of Physics: Condensed Matter, 17 p.4305-4316
Journal articleDynamics of DNA conformations and DNA-protein interaction
Ralf Metzler, Tobias Ambjörnsson, Michael A. Lomholt, Oleg Krichevsky
(2005) Materials Research Society Symposium Proceedings, 899 p.7-18
Conference paperDynamic Approach to DNA Breathing
Ralf Metzler, Tobias Ambjörnsson
(2005) Journal of Biological Physics, 31 p.339-350
Journal articleDirected motion emerging from two coupled random processes: translocation of a chain through a membrane nanopore driven by binding proteins
Tobias Ambjörnsson, Michael A Lomholt, Ralf Metzler
(2005) Journal of Physics: Condensed Matter, 17 p.3945-3964
Journal articleStochastic approach to DNA breathing dynamics
S. K Banik, T Ambjörnsson, R Metzler
(2005) Europhysics Letters, 71 p.852-858
Journal articleSensing DNA–DNA as Nanosensor: A Perspective Towards Nanobiotechnology
Ralf Metzler, Tobias Ambjörnsson
(2005) Journal of Computational and Theoretical Nanoscience, 2 p.389-395
Journal articleBinding dynamics of single-stranded DNA binding proteins to fluctuating bubbles in breathing DNA
Tobias Ambjörnsson, Ralf Metzler
(2005) Journal of Physics: Condensed Matter, 17 p.1841-1869
Journal articleCoupled dynamics of DNA breathing and of proteins that selectively bind to single-stranded DNA
Tobias Ambjörnsson, Ralf Metzler
(2005) Physical Review E, 72
Journal articleOptimal Target Search on a Fast-Folding Polymer Chain with Volume Exchange
Michael A. Lomholt, Tobias Ambjörnsson, Ralf Metzler
(2005) Physical Review Letters, 95
Journal articleChaperone-assisted translocation
Tobias Ambjörnsson, Ralf Metzler
(2004) Physical Biology, 1 p.77-88
Journal articleOn the dipolar polarizability of ellipsoidal nano-particles with anisotropic coating
Tobias Ambjörnsson
(2004) Solid State Physics, Proceedings of the DAE Solid State Physics Symposium , p.265-265
Conference paperElectromagnetic response of a dipole-coupled ellipsoidal bilayer
T. Ambjörnsson, S. P. Apell, G. Mukhopadhyay
(2004) Physical Review E, 69
Journal articleDipolar response of an ellipsoidal particle with an anisotropic coating
T Ambjörnsson, G Mukhopadhyay
(2003) Journal of Physics A: Mathematical and General, 36 p.10651-10665
Journal articleEllipsoidal particles driven by intensity gradients through viscous fluids
T. Ambjörnsson, S. P. Apell
(2003) Physical Review E, 67
Journal articleCharged polymer membrane translocation
T. Ambjörnsson, S. P. Apell, Z. Konkoli, E. A. Di Marzio, J. J. Kasianowicz
(2002) The Journal of chemical physics, 117 p.4063-4073
Journal articleNature of polarized excitons
T. Ambjörnsson, S. P. Apell
(2001) The Journal of chemical physics, 114 p.3365-3372
Journal article
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