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PUBLICATIONS - Tobias Ambjörnsson


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Journal articles


55.
P.C. Torche, V Müller, F Westerlund, T Ambjörnsson,
Noise reduction in single time frame optical DNA maps,
PLOS One 12, e0179041 (2017).
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54.
L. Lizana, T. Ambjörnsson, M.A. Lomholt,
Tracer Particles in Two-Dimensional Elastic Networks Diffuse Logarithmically Slow,
J. Phys. A: Mathematical and Theoretical 50 034001 (2016).
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53.
V. Müller, F. Rajer, K. Frykholm, L.K. Nyberg, S. Quaderi, J. Fritzsche, E. Kristiansson, T. Ambjörnsson, L. Sandegren, F. Westerlund,
Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping.
Scientific Reports 6, 37938 (2016).
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52.
J.Jeffet, A. Kobo, T. Su, A. Grunwald, O. Green, A.N. Nilsson, E. Eisenberg, T. Ambjörnsson, F. Westerlund, E. Weinhold, D. Shabat, P.K. Purohit and Y. Ebenstein,
Super-Resolution Genome Mapping in Silicon Nanochannels,
ACS Nano 10, 9823 (2016).
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51.
Lena K. Nyberg, Saair Quaderi, Gustav Emilsson, Nahid Karami, Erik Lagerstedt, Vilhelm Müller, Charleston Noble, Susanna Hammarberg, Adam N. Nilsson, Fei Sjöberg, Joachim Fritzsche, Erik Kristiansson, Linus Sandegren, Tobias Ambjörnsson, and Fredrik Westerlund,
Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules,
Scientific Reports 6, 30410 (2016).
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50.
M. Nyberg, T. Ambjörnsson, L. Lizana,
A simple method to calculate first-passage time densities with arbitrary initial conditions,
New Journal of Physics 18, 063019 (2016).
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49.
V. Müller, N. Karami, L. K. Nyberg, C. Pichler, P. C. Torche Pedreschi, S. Quaderi, J. Fritzsche, T. Ambjörnsson, C. Åhrén, and F. Westerlund,
Rapid Tracing of Resistance Plasmids in a Nosocomial Outbreak Using Optical DNA Mapping,
ACS Infectious Diseases 2, 322 (2016)
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48.
V. Iarko, E. Werner, L. K. Nyberg, V. Müller, J. Fritzsche, T. Ambjörnsson, J. P. Beech, J. O. Tegenfeldt, K. Mehlig, F. Westerlund, B. Mehlig,
Extension of nano-confined DNA: quantitative comparison between experiment and theory,
Phys. Rev. E 92, 062701 (2015).
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47.
How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model,
M. Reiter-Schad, E. Werner, J. O. Tegenfeldt, B. Mehlig, and Tobias Ambjörnsson,
J. Chem. Phys. 143, 115101 (2015). E-print:arXiv:1505.01968
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46.
E. Werner, M. Reiter-Schad, T. Ambjörnsson, B. Mehlig,
Model for melting of confined DNA,
Phys. Rev. E 91, 060702(R) (2015). E-print: arXiv:1504.03082
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45.
C. Freitag, C. Noble, J. Fritzsche, F. Persson, A. N. Nilsson, M. Reiter-Schad, A.Graneli, T. Ambjörnsson, K. U. Mir and J. O. Tegenfeldt,
Visualizing the entire DNA from a chromosome in a single frame,
Biomicrofluidics 9, 044114 (2015).
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44.
A. Grunwald, M. Dahan, A. Giesbertz, A.N. Nilsson, L.K. Nyberg, E. Weinhold, T. Ambjörnsson, F. Westerlund, Y. Ebenstein,
Bacteriophage strain typing by rapid single molecule analysis,
Nucl. Ac. Res. 43, e117 (2015).
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43.
K. Frykholm, L. K Nyberg, E. Lagerstedt, C. Noble, J. Fritzsche, N. Karami, T. Ambjörnsson, L. Sandegren and F. Westerlund,
Fast size-determination of intact bacterial plasmids using nanofluidic channels,
Lab on a Chip 15, 2739 (2015).
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42.
S. Ahlberg T. Ambjörnsson and L. Lizana,
Many-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA,
New J. Phys. 17, 043036 (2015); E-print: arXiv:1502.02164.
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41.
C. Noble, A. N. Nilsson, C. Freitag, J. P. Beech, J. O. Tegenfeldt and T. Ambjörnsson,
A Fast and Scalable Algorithm for Alignment of Optical DNA Mappings,
Plos One, 10, e0121905 (2015)
E-print: arXiv:1311.6379
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40.
M. Alizadehheidari, E. Werner, C. Noble, M. Reiter-Schad, L. K. Nyberg, J. Fritzsche, B. Mehlig, J. O. Tegenfeldt, T. Ambjörnsson, F. Persson, and F. Westerlund,
Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics,
Macromolecules 48, 871 (2015).
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39.
R. Metzler, L. Sanders, M.A. Lomholt, L. Lizana, K. Fogelmark and Tobias Ambjörnsson,
Ageing single file motion,
Eur. Phys. J, Special Topics 223 3287 (2014). Special issue on "Brownian motion in confined geometries".
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38.
L.P. Sanders, M.A. Lomholt, L. Lizana, K. Fogelmark, M.A. Lomholt, R. Metzler and T. Ambjörnsson
Severe slowing-down of the dynamics in interacting many-body systems: aging, logarithmic subordination and ultraslow diffusion
New Journal of Physics 16, 113050 (2014). E-print: arXiv:1311.3790
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37.
R. Forslind, L.P. Sanders, T. Ambjörnsson and L. Lizana,
Non-Markovian effects in the first-passage dynamics of obstructed tracer particle diffusion in one-dimensional systems,
J. Chem. Phys. 141, 094902 (2014).
E-print: arXiv:1401.2933
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36.
A. N. Nilsson, G. Emilsson, L. Nyberg, C. Noble, L. Svensson Stadler, J. Fritzsche, E. R. B. Moore, J. O. Tegenfeldt, T. Ambjörnsson* and F. Westerlund*,
Competitive binding-based optical DNA mapping for fast identification of bacteria -- multi-ligand transfer matrix theory and experimental applications on E.coli, Nucl. Ac. Res. 42 e118 (2014)
* TA and FW contributed equally.
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35.
M.A. Lomholt and T. Ambjörnsson
Universality and non-universality for mobility in heterogeneous single-file systems and Rouse chains,
Phys. Rev. E 89, 032101 (2014).
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34.
L. Lizana, M.A. Lomholt and T. Ambjörnsson
Single-file diffusion with non-thermal initial conditions
Physica A 395, 148 (2014); E-print: arXiv:1304.1635
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33.
L.P. Sanders, B. Söderberg, D. Brockmann and T. Ambjörnsson
Perturbative solution to the SIS epidemic on networks
Phys. Rev. E 88, 032713 (2013)
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32.
M.A. Lomholt, L. Lizana, R. Metzler and T. Ambjörnsson
Microscopic Origin of the Logarithmic Time Evolution of Aging Processes in Complex Systems
Phys. Rev. Lett. 110, 208301 (2013); E-print: arXiv:1208.1383
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31.
Lloyd P. Sanders and T. Ambjörnsson,
First Passage Times for a Tracer Particle in Single File Diffusion and Fractional Brownian Motion,
J. Chem. Phys. 136 , 175103 ( (2012)
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30.
M.A. Lomholt, L. Lizana and T. Ambjörnsson,
Dissimilar bouncy walkers,
J. Chem. Phys. 134 , 045101 (2011).; E-print: arXiv:1011.5582
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29.
L. Lizana, T. Ambjörnsson, A. Taloni, E. Barkai and M.A. Lomholt,
Foundation of fractional Langevin equation: Harmonization of a many body problem,
Phys. Rev. E 81, 051118 (2010); E-print arXiv:0909.0881.
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28.
W. Ni, T. Ambjörnsson, S.P. Apell, H. Chen and J. Wang,
Observing Plasmonic-Molecular Resonance Coupling on Single Gold Nanorods,
Nano Lett. 10, 77 (2010);
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27.
L. Lizana and T. Ambjörnsson,
Diffusion of finite-sized hard-core interacting particles in a one-dimensional box: Tagged particle dynamics,
Phys. Rev. E. 80, 051103 (2009); E-print arXiv:0907.0567.
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26.
J.N. Pedersen, M.S. Hansen, T. Novotny, T. Ambjörnsson and R. Metzler,
Bubble merging in breathing DNA as a vicious walker problem in opposite potentials,
J. Chem. Phys. 130, 164117 (2009).
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25.
R. Metzler, T. Ambjörnsson, A. Hanke and H.C. Fogedby,
Single DNA denaturation and bubble dynamics,
Journal of Physics: Condensed Matter 21, 034111 (2009); special issue on DNA melting.
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24.
T. Ambjörnsson and R.J. Silbey,
Dynamics of two particles with a finite interaction potential in one dimension,
Journal of Chemical Physics 129, 165103 (2008); E-print arXiv:0803.2485.
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23.
T. Ambjörnsson, L. Lizana, M.A. Lomholt and R.J. Silbey,
Single-file diffusion with different diffusion constants,
Journal of Chemical Physics 129, 185106 (2008); E-print arXiv:0803.2485.
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22.
L. Lizana and T. Ambjörnsson,
Single-file diffusion in a box,
Phys. Rev. Lett. 100, 200601 (2008); E-print arXiv:0801.0563.
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21.
T. Novotny, J.N. Pedersen, T. Ambjörnsson, M.S. Hansen and R. Metzler,
Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials,
Europhys. Lett. 77, 48001 (2007); E-print cond-mat/0610752.
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20.
T. Ambjörnsson, M.A. Lomholt and P.L. Hansen,
Applying a potential across a biomembrane: electrostatic contribution to the bending rigidity and membrane instability,
Physical Review E 75, 051916 (2007); E-print cond-mat/0610355.
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19.
T. Ambjörnsson, S.K. Banik, O. Krichevsky and R. Metzler,
Breathing dynamics in heteropolymer DNA,
Biophys. J. 92, 2674 (2007); E-print q-bio/0611090.
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18.
R. Metzler, T. Ambjörnsson, A. Hanke, Y. Zhang and S. Levene,
Single DNA conformations and biological function,
J. Comput. Theoret. Nanoscience 4 1 (2007), E-print: Arxiv physics/0609139.
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17.
T. Ambjörnsson, S.K. Banik, M.A. Lomholt and R. Metzler,
Master equation approach to DNA-breathing in heteropolymer DNA,
Physical Review E 75, 021908 (2007); E-print cond-mat/0610547.
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16.
T. Ambjörnsson, S.K. Banik, O. Krichevsky and R. Metzler,
Sequence sensitivity of breathing dynamics in heteropolymer DNA,
Phys. Rev. Lett. 97, 128105 (2006); E-print q-bio.BM/0608036.
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15.
T. Ambjörnsson, G. Mukhopadhyay, S.P. Apell and M. Käll,
Resonant coupling between localized plasmons and anisotropic molecular coatings in ellipsoidal metal nanoparticles.
Phys. Rev. B 73, 085415 (2006); E-print physics/0601042.
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14.
R. Metzler and T. Ambjörnsson,
Dynamic approach to DNA breathing,
J. Biol. Phys. 31, 339 (2005).
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13.
M. Lomholt, T. Ambjörnsson and R. Metzler
Optimal target search on a fast folding polymer chain with volume exchange,
Phys. Rev. Lett. 95, 260603 (2005); E-print cond-mat/0510072.
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12.
T.Ambjörnsson and R. Metzler
Blinking statistics of a molecular beacon triggered by end-denaturation of DNA,
J. Phys: Cond. Matt. 17, S4305 (2005), special issue on diffusion in liquids, polymers, biophysics and chemical dynamics; E-print cond-mat/0508492.
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11.
T. Ambjörnsson, M. Lomholt and R. Metzler
Directed motion emerging from two coupled random process: Translocation of a chain through a membrane nanopore driven by binding proteins,
J. Phys: Cond. Matt. 17, S3945 (2005), special issue on molecular motors; E-print q-bio.BM/0508029.
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10.
S.K. Banik, T. Ambjörnsson and R. Metzler,
Stochastic approach to DNA breating dynamics,
Europhysics Letters 71, 852 (2005); E-print q-bio.BM/0506025.
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9.
R. Metzler and T. Ambjörnsson,
Sensing DNA - DNA as Nanosensor,
J. Comp. Theor. Nanosc. 2, 389 (2005); E-print cond-mat/0508490.
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8.
T. Ambjörnsson and R. Metzler,
Coupled dynamics of DNA-breathing and binding of proteins that selectively bind to single-stranded DNA,
Phys. Rev. E 72, 030901 (2005); E-print q-bio.BM/0411053.
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7.
T. Ambjörnsson and R. Metzler,
Binding dynamics of single-stranded DNA binding proteins to fluctuating bubbles in breathing DNA,
J. Phys: Cond. Matt. 17, S1841 (2005), special issue in honour of Lothar Schäfer.
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6.
T. Ambjörnsson and R. Metzler,
Chaperone assisted translocation,
Physical Biology 1, 77 (2004); E-print cond-mat/0405093.
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5.
T. Ambjörnsson, S.P.Apell and G.M.Mukhopadhyay,
Electromagnetic response of a dipole coupled ellipsoidal bilayer,
Phys. Rev. E 69, 031914 (2004).
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4.
T.Ambjörnsson and G.M.Mukhopadhyay,
Dipolar response of an ellipsoidal particle with an anisotropic coating,
J. Phys. A 36, 10651 (2003).
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3.
T. Ambjörnsson and S.P. Apell,
Ellipsoidal particles driven by intensity gradients through viscous fluids,
Phys. Rev. E. 67, 031917 (2003).
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2.
T. Ambjörnsson, S.P. Apell, Z. Konkoli, E.A. Di Marzio and J.J. Kasianowicz,
Charged polymer membrane translocation,
J. Chem. Phys. 117, 4063 (2002).
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1.
T. Ambjörnsson and S.P. Apell,
Nature of polarized excitons,
J. Chem. Phys 114, 3365 (2001).
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Conference proceedings


3.
R. Metzler, T. Ambjörnsson, M. A. Lomholt, and O. Krichevsky,
Dynamics of DNA conformations and DNA-protein interactions,
Invited contribution to J. T. Fourkas, P. Levitz, R. Overney, and M. Urbakh, Editors,
Dynamics in Small Confining Systems VI,
Materials Research Society Symposium Proceedings Vol. 899E, article 0899-N03-06.1 (2006).

2.
G. Mukhopadhyay, T. Ambjörnsson, S.P. Apell and M. Käll,
On the dipolar polarizability of ellipsoidal nano-particles with anisotropic coating,
Solid State Physics, Proceedings of the DAE Solid State Physics Symposium (2005),
Ed: V.K.Aswal, K.G.Bhushan and J.V.Yakhmi, vol. 50, page 265-266.

1.
R. Metzler and T. Ambjörnsson,
Dynamic approach to DNA breathing,
Proceedings of the 5th International Conference on Biological Physics
Gothenburgh (2004). (J. Biol. Phys. 31, 339 (2005).)

Theses


2.
T. Ambjörnsson,
Optical excitations in molecular aggregates,
Licentiate thesis, Chalmers University of Technology and Göteborg University (2000).

1.
T.Ambjörnsson,
Electromagnetic response of living matter,
Doctorate thesis, Chalmers University of Technology and Göteborg University (2003).
[ pdf-file ]

Lecture notes


2.
For the course Computational Physics (2009-2010) I rewrote previous lecture notes into six independent
lecture notes (see lecture notes 1-4 and 9-10).

1.
Lecture notes on biomembrane physics for the course Living State Physics, Chalmers University (1999-2001).

Miscellaneous


Nine of my publications (Publications 30, 26, 24, 22, 17, 16, 13, 8 and 5) were selected for the Virtual Journal of Biological Physics, which highlights topical research.

Publication 15 was selected for the Virtual journal of Nanoscale Science and Technology.

Publication 30 was selected for the January 2011 issue of JCP: BioChemical Physics, which features biophysical content from Journal of Chemical Physics.

Publication 38 was selected IOP Select.





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Last modified March 2015. e-mail:tobias.ambjornsson AT thep.lu.se