Publications
2012
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Severin Schink,
Sephan Renner,
Karen Alim,
Vera Arnaut,
Friedrich C. Simmel,
Ulrich Gerland,
Quantitative analysis of the nanopore translocation dynamics of simple structured polynucleotides,
Biophys. J. 102, 85–95 (2012).
2011
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Thomas Schötz,
Richard A. Neher,
Ulrich Gerland,
Target search on a dynamic DNA molecule,
Phys. Rev. E 84, 051911 (2011). [arXiv:1109.3211]
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Ina Haneburger,
Georg Fritz,
Nicole Jurkschat,
Larissa Tetsch,
Andreas Eichinger,
Arne Skerra,
Ulrich Gerland,
Kirsten Jung,
The feedback-inhibitor cadaverine suppresses pH response by binding to the pH susceptible site of CadC in Escherichia coli,
submitted for publication.
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Kevin Leu,
Benedikt Obermayer,
Sudha Rajamani,
Ulrich Gerland,
Irene A. Chen,
The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA,
Nucl. Acids Res. 39, 8135-8147 (2011).
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Nico Geisel,
Ulrich Gerland,
Physical limits on cooperative protein-DNA binding and the kinetics of combinatorial transcription regulation,
Biophys. J. 101, 1569-79 (2011). [arXiv:1109.3351]
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Benedikt Obermayer,
Hubert Krammer,
Dieter Braun,
Ulrich Gerland,
Emergence of information transmission in a prebiotic RNA reactor,
Phys. Rev. Lett 107, 018101 (2011). [arXiv:1105.3758]
2010
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Stephan Renner,
Andrey Bessonov,
Ulrich Gerland,
Friedrich C. Simmel,
Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy,
J. Phys.: Condens. Matter 22, 454119 (2010).
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W. Möbius,
U. Gerland,
Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites,
PLoS Comput Biol 6(8): e1000891 (2010). [arXiv:1009.0169]
2009
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G. Fritz,
C. Koller,
K. Burdack,
I. Haneburger,
L. Tetsch,
K. Jung,
U. Gerland,
Induction kinetics of a conditional pH stress response system in Escherichia coli,
J. Mol. Biol. 393, 272–286 (2009).
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H. Gumpp,
E. M. Puchner,
J. L. Zimmermann,
U. Gerland,
H. Gaub,
K. Blank,
Triggering Enzymatic Activity with ForceTriggering Enzymatic Activity with Force,
Nano Lett. 9, 3290-3295 (2009).
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U. Gerland,
T. Hwa,
Evolutionary selection between alternative modes of gene regulation,
PNAS 106, 8841-8846 (2009).
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M. McCauley,
R. Forties,
U. Gerland,
R. Bundschuh,
Anomalous scaling in nanopore translocation of structured heteropolymers,
Phys. Biol. 6, 036006 (2009). [arXiv:0901.4850]
2008
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W. Möbius,
E. Frey,
U. Gerland,
Spontaneous Unknotting of a Polymer Confined in a Nanochannel,
Nano Letters 8 (12), 4518–4522 (2008). [arXiv:0807.4091]
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J. A. Megerle,
G. Fritz,
U. Gerland,
K. Jung,
J. O. Rädler,
Timing and Dynamics of Single Cell Gene Expression in the Arabinose Utilization System,
Biophys. J. 95:2103-2115 (2008).
2007
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G. Fritz,
N.E. Buchler,
T. Hwa,
U. Gerland,
Designing sequential transcription logic: a simple genetic circuit for conditional memory,
Systems and Synthetic Biology 1, 89-98 (2007).
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R. Neher,
W. Möbius,
E. Frey,
U. Gerland,
Optimal flexibility for conformational transitions in macromolecules,
Phys. Rev. Lett. 99, 178101 (2007). [arXiv:0704.1546]
2006
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W. Möbius,
R. A. Neher,
U. Gerland,
Kinetic Accessibility of Buried DNA Sites in Nucleosomes,
Phys. Rev. Lett. 97, 208102 (2006). [arXiv:q-bio/0605017]
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R. Neher,
U. Gerland,
Intermediate phase in DNA melting,
Rev. E 73, 030902(R) (2006). [arXiv:q-bio/0509015]
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R. Bundschuh,
U. Gerland,
A puzzle in DNA biophysics,
Eur. Phys. J. E 19, 347-349 (2006).
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R. Bundschuh,
U. Gerland,
Dynamics of intramolecular recognition: Base-pairing in DNA/RNA near and far from equilibrium,
Eur. Phys. J. E 19, 319–329 (2006).
2005
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U. Gerland,
Programmierbare Gen-Logik,
BIOforum 1-2/2005, 44.
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R. Bundschuh,
U. Gerland,
Coupled dynamics of RNA folding and nanopore translocation.
[arXiv:q-bio/0508004]
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N.E. Buchler,
U. Gerland,
T. Hwa,
Nonlinear protein degradation and the function of genetic circuits,
PNAS 102, 9559 (2005).
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R.A. Neher,
U. Gerland,
DNA as a programmable viscoelastic nanoelement,
Biophysical Journal 89:3846-3855 (2005). [arXiv:q-bio/0506026]
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L. Bintu,
N.E. Buchler,
H.G. Garcia,
U. Gerland,
T. Hwa,
J. Kondev,
R. Phillips,
Transcriptional regulation by the numbers: models,
Current Opinion in Genetics & Development 15, 116 (2005). [PDF]
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L. Bintu,
N.E. Buchler,
H.G. Garcia,
U. Gerland,
T. Hwa,
J. Kondev,
R. Phillips,
Transcriptional regulation by the numbers: applications,
Current Opinion in Genetics & Development 15, 125 (2005). [PDF]
2004
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R. Neher,
U. Gerland,
Dynamics of force-induced DNA slippage,
Phys. Rev. Lett. 93, 198102 (2004).
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U. Gerland,
R. Bundschuh,
T. Hwa,
Translocation of structured polynucleotides through nanopores,
Phys. Biol. 1, 19 (2004).
2003
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W. Peng,
U. Gerland,
T. Hwa,
H. Levine,
Dynamics of Competitive Evolution on a Smooth Landscape,
Phys. Rev. Lett. 90, 088103 (2003).
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U. Gerland,
R. Bundschuh,
T. Hwa,
Mechanically probing the folding pathway of single RNA molecules,
Biophys. J. 84, 2831 (2003).
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N. E. Buchler,
U. Gerland,
T. Hwa,
On schemes of combinatorial transcription logic,
PNAS 100, 5136 (2003).
2002
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U. Gerland,
T. Hwa,
On the Selection and Evolution of Regulatory Binding Motifs,
J. Mol. Evol. 55, 386 (2002).
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U. Gerland,
D. Moroz,
T. Hwa,
Physical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction,
PNAS 99, 12015 (2002).
2001
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U. Gerland,
R. Bundschuh,
T. Hwa,
Force-induced denaturation of RNA,
Biophys. J. 81, 1324 (2001).