Publications

2025

• A roadmap towards the synthesis of Life

  Christine Kriebisch ... Karen Alim ... Erwin Frey Ulrich Gerland ... Job Boekhoven
  Chem 11, March 13, 2025.
  [ChemRxiv:10.26434/chemrxiv-2024-tnx83]

2014

• Single Cell Kinetics of Phenotypic Switching in the Arabinose Utilization System of E. coli

  J. Megerle G. Fritz S. A. Westermayer D. Brick R. Herrmann K. Jung J. O. Rädler U. Gerland
  PLoS ONE 9(2), e89532 (2014).

2013

• The paradox of dual roles in the RNA World: Resolving the conflict between stable folding and templating ability

  Nikola Ivica Benedikt Obermayer Gregory W. Campbell Sudha Rajamani Ulrich Gerland Irene A. Chen
  J. Mol. Evol. 77(3), 55-63 (2013).

• Optimization of collective enzyme activity via spatial localization

  Alexander Buchner Filipe Tostevin Florian Hinzpeter Ulrich Gerland
  J. Chem. Phys. 139, 135101 (2013).

• Biological Signal Processing with a Genetic Toggle Switch

  Patrick Hillenbrand Georg Fritz Ulrich Gerland
  PLoS ONE 8(7), e68345 (2013).

• Clustering and optimal arrangement of enzymes in reaction-diffusion systems

  Alexander Buchner Filipe Tostevin Ulrich Gerland
  Phys. Rev. Lett. 110, 208104 (2013).

• Escalation of Polymerization in a Thermal Gradient

  Christof B. Mast Severin Schink Ulrich Gerland Dieter Braun
  PNAS 2013 110 (20) 8030-8035.

• Towards a unified physical model of nucleosome patterns flanking transcription start sites

  Wolfram Möbius Brendan Osberg Alexander M. Tsankov Oliver J. Rando Ulrich Gerland
  PNAS 110, 5719-5724 (2013).

• Simulation of stochastic network dynamics via entropic matching

  Tiago Ramalho Marco Selig Ulrich Gerland Torsten A. Enßlin
  Phys. Rev. E 87, 022719 (2013).
  [arxiv:1209.3700]

• Cascade of Reduced Speed and Accuracy After Errors in Enzyme-Free Copying of Nucleic Acid Sequences

  Kevin Leu Eric Kervio Benedikt Obermayer Rebecca Turk-MacLeod Caterina Yuan Jesus-Mario Luevano Eric Chen Ulrich Gerland Clemens Richert Irene A. Chen
  J. Am. Chem. Soc., 135 (1), 354–366 (2013).

2012

• Deactivation of the E. coli pH stress sensor CadC by cadaverine

  Ina Haneburger Georg Fritz Nicole Jurkschat Larissa Tetsch Andreas Eichinger Arne Skerra Ulrich Gerland Kirsten Jung
  J. Mol. Biol 424 , 15-27 (2012).

• Quantitative analysis of the nanopore translocation dynamics of simple structured polynucleotides

  Severin Schink Sephan Renner Karen Alim Vera Arnaut Friedrich C. Simmel Ulrich Gerland
  Biophys. J. 102 (1), 85–95 (2012).

• Life: the physical underpinnings of replication

  R. Turk-MacLeod U. Gerland I. Chen
  published in "Astrochemistry and Astrobiology: Physical Chemistry in Action".
  [Springer Online]

2011

• Target search on a dynamic DNA molecule

  Thomas Schötz Richard A. Neher Ulrich Gerland
  Phys. Rev. E 84 (5), 051911 (2011).
  [arXiv:1109.3211]

• The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA

  Kevin Leu Benedikt Obermayer Sudha Rajamani Ulrich Gerland Irene A. Chen
  Nucl. Acids Res. 39, 8135-8147 (2011).

• Physical limits on cooperative protein-DNA binding and the kinetics of combinatorial transcription regulation

  Nico Geisel Ulrich Gerland
  Biophys. J. 101 (7), 1569-1579 (2011).
  [arXiv:1109.3351]

• Emergence of information transmission in a prebiotic RNA reactor

  Benedikt Obermayer Hubert Krammer Dieter Braun Ulrich Gerland
  Phys. Rev. Lett 107 (1), 018101 (2011).
  [arXiv:1105.3758]

2010

• Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy

  Stephan Renner Andrey Bessonov Ulrich Gerland Friedrich C. Simmel
  J. Phys. Condens. Matter 22 (45), 454119 (2010).

• Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites

  W. Möbius U. Gerland
  PLoS Comput. Biol. 6 (8), e1000891 (2010).
  [arXiv:1009.0169]

2009

• Induction kinetics of a conditional pH stress response system in Escherichia coli

  G. Fritz C. Koller K. Burdack I. Haneburger L. Tetsch K. Jung U. Gerland
  J. Mol. Biol. 393, 272–286 (2009).

• Triggering Enzymatic Activity with ForceTriggering Enzymatic Activity with Force

  H. Gumpp E. M. Puchner J. L. Zimmermann U. Gerland H. Gaub K. Blank
  Nano Lett. 9, 3290-3295 (2009).

• Evolutionary selection between alternative modes of gene regulation

  U. Gerland T. Hwa
  PNAS 106, 8841-8846 (2009).

• Anomalous scaling in nanopore translocation of structured heteropolymers

  M. McCauley R. Forties U. Gerland R. Bundschuh
  Phys. Biol. 6, 036006 (2009).
  [arXiv:0901.4850]

2008

• Spontaneous Unknotting of a Polymer Confined in a Nanochannel

  W. Möbius E. Frey U. Gerland
  Nano Lett. 8 (12), 4518–4522 (2008).
  [arXiv:0807.4091]

• Timing and Dynamics of Single Cell Gene Expression in the Arabinose Utilization System

  J. A. Megerle G. Fritz U. Gerland K. Jung J. O. Rädler
  Biophys. J. 95 (4), 2103-2115 (2008).

2007

• Designing sequential transcription logic: a simple genetic circuit for conditional memory

  G. Fritz N.E. Buchler T. Hwa U. Gerland
  Syst. Synth. Biol. 1 (2), 89-98 (2007).

• Optimal flexibility for conformational transitions in macromolecules

  R. Neher W. Möbius E. Frey U. Gerland
  Phys. Rev. Lett. 99, 178101 (2007).
  [arXiv:0704.1546]

2006

• Kinetic Accessibility of Buried DNA Sites in Nucleosomes

  W. Möbius R. A. Neher U. Gerland
  Phys. Rev. Lett. 97, 208102 (2006).
  [arXiv:q-bio/0605017]

• Intermediate phase in DNA melting

  R. Neher U. Gerland
  Phys. Rev. E 73 (3), 030902(R) (2006).
  [arXiv:q-bio/0509015]

• Dynamics of intramolecular recognition: Base-pairing in DNA/RNA near and far from equilibrium

  R. Bundschuh U. Gerland
  Eur. Phys. J. E 19, 319–329 (2006).

• A puzzle in DNA biophysics

  R. Bundschuh U. Gerland
  Eur. Phys. J. E 19, 347-349 (2006).

2005

• Coupled dynamics of RNA folding and nanopore translocation

  R. Bundschuh U. Gerland
  Phys. Rev. Lett. 95 (20), 208104 (2005).
  [arXiv:q-bio/0508004]

• Nonlinear protein degradation and the function of genetic circuits

  N.E. Buchler U. Gerland T. Hwa
  PNAS 102 (27), 9559-9564 (2005).

• DNA as a programmable viscoelastic nanoelement

  R.A. Neher U. Gerland
  Biophys. J. 89 (6), 3846-3855 (2005).
  [arXiv:q-bio/0506026]

• Transcriptional regulation by the numbers: models

  L. Bintu N.E. Buchler H.G. Garcia U. Gerland T. Hwa J. Kondev R. Phillips
  Current Opinion in Genetics & Development 15, 116 (2005).
  [PDF]

• Transcriptional regulation by the numbers: applications

  L. Bintu N.E. Buchler H.G. Garcia U. Gerland T. Hwa J. Kondev R. Phillips
  Current Opinion in Genetics & Development 15, 125 (2005).
  [PDF]

2004

• Dynamics of force-induced DNA slippage

  R. Neher U. Gerland
  Phys. Rev. Lett. 93, 198102 (2004).

• Translocation of structured polynucleotides through nanopores

  U. Gerland R. Bundschuh T. Hwa
  Phys. Biol. 1, 19 (2004).

2003

• Dynamics of Competitive Evolution on a Smooth Landscape

  W. Peng U. Gerland T. Hwa H. Levine
  Phys. Rev. Lett. 90, 088103 (2003).

• Mechanically probing the folding pathway of single RNA molecules

  U. Gerland R. Bundschuh T. Hwa
  Biophys. J. 84, 2831 (2003).

• On schemes of combinatorial transcription logic

  N. E. Buchler U. Gerland T. Hwa
  PNAS 100 (9), 5136-5141 (2003).

2002

• On the Selection and Evolution of Regulatory Binding Motifs

  U. Gerland T. Hwa
  J. Mol. Evol. 55, 386 (2002).

• Physical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction

  U. Gerland D. Moroz T. Hwa
  PNAS 99 (19), 12015-12020 (2002).

2001

• Force-induced denaturation of RNA

  U. Gerland R. Bundschuh T. Hwa
  Biophys. J. 81, 1324 (2001).