Tobias Ambjörnsson

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
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Equilibrium 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
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A 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
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Detection 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
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Combining dense and sparse labeling in optical DNA mapping

Erik Torstensson, Gaurav Goyal, Anna Johnning, Fredrik Westerlund, Tobias Ambjörnsson
(2021) PLoS ONE, 16
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Modeling protein target search in human chromosomes

Markus Nyberg, Tobias Ambjörnsson, Per Stenberg, Ludvig Lizana
(2021) Physical Review Research, 3
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A 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
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CRISPR/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
Konferensbidrag

Cultivation-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
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Enzyme-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
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Optical 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
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Bacterial 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
Konferensbidrag

Fitting a function to time-dependent ensemble averaged data

Karl Fogelmark, Michael A. Lomholt, Anders Irbäck, Tobias Ambjörnsson
(2018) Scientific Reports, 8
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The 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
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Zero-crossing statistics for non-Markovian time series

Markus Nyberg, Ludvig Lizana, Tobias Ambjörnsson
(2018) Physical Review E, 97
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Facilitated 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
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Stochastic 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
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Tracer 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
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Noise reduction in single time frame optical DNA maps

Paola C. Torche Pedreschi, Vilhelm Müller, Fredrik Westerlund, Tobias Ambjörnsson
(2017) PLoS ONE, 12
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Tracer 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
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Direct 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
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Super-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
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Rapid 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
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A simple method to calculate first-passage time densities with arbitrary initial conditions

Markus Nyberg, Tobias Ambjörnsson, Ludvig Lizana
(2016) New Journal of Physics, 18
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Rapid 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
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Detailed 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
Konferensbidrag

Visualizing 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
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A 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
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Many-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
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Nanoconfined 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
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Model 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
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How 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
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Extension 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
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Fast 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
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Bacteriophage 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
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Severe 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
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Ageing 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
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Universality 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
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Competitive 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
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Non-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
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Single-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
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Nanoconfined 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
Konferensbidrag

Identifying 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
Konferensbidrag

Microscopic 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
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Perturbative 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
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First passage times for a tracer particle in single file diffusion and fractional Brownian motion.

Lloyd Sanders, Tobias Ambjörnsson
(2012) Journal of Chemical Physics, 136
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Dissimilar bouncy walkers

Michael A Lomholt, Ludvig Lizana, Tobias Ambjörnsson
(2011) Journal of Chemical Physics, 134
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Observing 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
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Foundation 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
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Single DNA denaturation and bubble dynamics

Ralf Metzler, Tobias Ambjörnsson, Andreas Hanke, Hans C Fogedby
(2009) Journal of Physics: Condensed Matter, 21
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Bubble 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
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Diffusion 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
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Single-file dynamics with different diffusion constants

Tobias Ambjörnsson, Ludvig Lizana, Michael A. Lomholt, Robert J. Silbey
(2008) The Journal of chemical physics, 129
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Diffusion 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
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Single-File Diffusion in a Box

L. Lizana, T. Ambjörnsson
(2008) Physical Review Letters, 100
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Breathing Dynamics in Heteropolymer DNA

Tobias Ambjörnsson, Suman K. Banik, Oleg Krichevsky, Ralf Metzler
(2007) Biophysical Journal, 92 p.2674-2684
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Single 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
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Bubble 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
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Applying 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
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Master equation approach to DNA breathing in heteropolymer DNA

Tobias Ambjörnsson, Suman K. Banik, Michael A. Lomholt, Ralf Metzler
(2007) Physical Review E, 75
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Resonant 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
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Sequence Sensitivity of Breathing Dynamics in Heteropolymer DNA

Tobias Ambjörnsson, Suman K. Banik, Oleg Krichevsky, Ralf Metzler
(2006) Physical Review Letters, 97
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Blinking 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
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Dynamics 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
Konferensbidrag

Dynamic Approach to DNA Breathing

Ralf Metzler, Tobias Ambjörnsson
(2005) Journal of Biological Physics, 31 p.339-350
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Directed 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
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Tobias Ambjörnsson

Publikationer