Publications

M. Wolff, A. Schmid, P. Korber, U. Gerland (2021)
Effective Dynamics of Nucleosome Configurations at the Yeast PHO5 Promoter
https://elifesciences.org/articles/58394

L. Martini*, S. Brameyer*, E. Hoyer, K. Jung, U. Gerland (2021)
Dynamics of chromosomal target search by a membrane-integrated one-component receptor
PLoS Comput Biol 17(2): e1008680. https://doi.org/10.1371/journal.pcbi.1008680
* contributed equally

F. Tostevin*, M. Wigbers*, L. Søgaard-Andersen, U. Gerland (2021)
Four different mechanisms for switching cell polarity
PLoS Comput Biol 17(1): e1008587. https://doi.org/10.1371/journal.pcbi.1008587
*contributed equally

L. Carreira*, F. Tostevin*, U. Gerland, L. Søgaard-Andersen (2020)
Protein-protein interaction network controlling establishment and maintenance of switchable cell polarity in M. xanthus.
PLoS Genet 16: e1008877
*contributed equally

G. Giunta, H. Seyed-Allaei, U. Gerland (2020)
Cross-diffusion induced patterns for a single-step enzymatic reaction
Commun Phys 3, 167 (2020), arXiv:2006.02195

E. Biselli*, S. Schink*, U. Gerland (2020)
Slower growth of Escherichia coli leads to longer survival in carbon starvation due to a decrease in the maintenance rate
Mol Syst Biol (2020)16:e9478
*contributed equally

K. Ott, L. Martini, J. Lipfert, U. Gerland (2020)
Dynamics of the Buckling Transition in Double-Stranded DNA and RNA
Biophysical Journal

E. Oberbeckmann*, M. Wolff*, N. Krietenstein, M. Heron, J. L. Ellins, A. Schmid, S. Krebs, H. Blum, U. Gerland, Philipp Korber (2019)
Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
Genome Research
*contributed equally

F. Hinzpeter, F. Tostevin and U.Gerland (2019)
Regulation of reaction fluxes via enzyme sequestration and co-clustering
Journal of the Royal Society Interface

S. Schink*, E. Biselli*, C. Ammar, U. Gerland (2019) 
Death rate of E. coli during starvation is set by maintenance cost and biomass recycling. 
Cell Systems
*contributed equally

G.Fritz, N.Walker, U.Gerland (2019),
Heterogeneous Timing of Gene Induction as a Regulation Strategy
Journal of Molecular Biology

D. Szadkowski, A. Harms, L. A. Menezes Carreira, M. Wigbers, A. Potapova, K. Wuichet, D. Keilberg, U. Gerland, L. Søgaard-Andersen (2019)
Spatial control of the GTPase MglA by localized RomR–RomX GEF and MglB GAP activities enables Myxococcus xanthus motility
Nature Microbiology

M. Marczynski, B. Käsdorf, B. Altaner, A. Wenzler, U. Gerland, O. Lieleg (2018)
Transient binding promotes molecule penetration into mucin hydrogels by enhancing molecular partitioning
Biomaterials science

J. Nuebler, M. Wolff, B. Obermayer, W. Mobius, U. Gerland (2018)
Emergence of robust nucleosome patterns from an interplay of positioning mechanisms
bioRχiv, DOI: 10.1101/431445

C. Mast, F. Möller, M. Kreysing, S. Schink, B. Obermayer, U. Gerland, D. Braun (2018),
Toward living nanomachines,
Living machines: A handbook of research in biomimetics and biohybrid systems, 380-389, Oxford University Press, 978-0199674923

D. Erickson*, S. Schink*, V. Patsalo, J. Williamson, U. Gerland, T. Hwa (2017),
A global resource allocation strategy governs growth transition kinetics of Escherichia coli,
Nature, 551, 119–123 
*contributed equally

M. Mori*, S. Schink*, D. Erickson, U. Gerland, T. Hwa (2017),
Quantifying the benefit of a proteome reserve in fluctuating environments,
Nature Communications, 8, 1225
*contributed equally

F. Hinzpeter, U. Gerland, F. Tostevin (2017), 
Optimal Compartmentalization Strategies for Metabolic Microcompartments, 
Biophysical Journal, 112, 767-779

P. Hillenbrand, K. Maier, P. Cramer, U. Gerland (2016),
Inference of gene regulation functions from dynamic transcriptome data,
eLife 2016;10.7554/eLife.12188

H. Schramke, F. Tostevin, R. Heermann, U. Gerland, K. Jung (2016),
A Dual-Sensing Receptor Confers Robust Cellular Homeostasis,
Cell Reports (2016); DOI: 10.1016/j.celrep.2016.05.081

T. Göppel, V. Palyulin, U. Gerland (2016),
The efficiency of driving chemical reactions by a physical non-equilibrium is kinetically controlled,
Phys. Chem. Chem. Phys., 2016,18, 20135-20143

P. Hillenbrand, U. Gerland, G. Tkacik (2016),
Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information,
PLoS ONE 11(9): e0163628

S.A. Westermayer, G. Fritz, J. Gutierrez, J.A. Megerle, M.P.S. Weissl, K. Schnetz, U. Gerland, J. Rädler (2016),
Single-cell characterization of metabolic switching in the sugar phosphotransferase system of Escherichia coli,
Molecular Microbiology (2016) 100(3), 472–485

T. Ramalho, A. Meyer, A. Mückl, K. Kapsner, U. Gerland, F. C. Simmel (2016),
Single Cell Analysis of a Bacterial Sender-Receiver System,
PLoS ONE 11(1): e0145829.

B. Osberg, J. Nuebler, and U. Gerland (2015),
Adsorption-desorption kinetics of soft particles, 
Phys. Rev. Lett. 115, 088301.

Georg Fritz, Sebastian Dintner, Nicole Simone Treichel, Jara Radeck, Ulrich Gerland, Thorsten Mascher, and Susanne Gebhard (2015), 
A New Way of Sensing: Need-Based Activation of Antibiotic Resistance by a Flux-Sensing Mechanism,
mBio 6,  e00975-15.

Fabienna Arends, Sabine Sellner, Philipp Seifert, Ulrich Gerland, Markus Rehberg and Oliver Lieleg (2015), 
A microfluidics approach to study the accumulation of molecules at basal lamina interfaces, 
Lab Chip, 2015,15, 3326–3334

Laure Plener, Nicola Lorenz, Matthias Reiger, Tiago Ramalho, Ulrich Gerland, and Kirsten Jung (2015), 
The phosphorylation flow of the Vibrio harveyi quorum sensing cascade determines levels of phenotypic heterogeneity in the population, 
J. Bact., 197, 1747-1756.

C. Lieleg, P. Ketterer, J. Nuebler, J. Ludwigsen, U. Gerland, H. Dietz, F. Mueller-Planitz, and P. Korber (2015), 
Nucleosome spacing generated by ISWI and CHD1 remodelers is constant regardless of nucleosome density, 
Mol. Cell. Biol. 35, 1588-1605.

B. Osberg, J. Nuebler, P. Korber and U. Gerland (2014), 
Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays,
Nucleic Acids Research 42, 13633-13645.

G. Fritz, J. Megerle, S.A. Westermayer, D. Brick, R. Heermann, K. Jung, J.O. Rädler, and U. Gerland (2014),
Single Cell Kinetics of Phenotypic Switching in the Arabinose Utilization System of E. coli, 
PLoS One 9, e89532. 

N.A. Ivica, B. Obermayer, G.W. Campbell, S. Rajamani, U. Gerland, and I.A. Chen (2013),
The Paradox of Dual Roles in the RNA World: Resolving the Conflict Between Stable Folding and Templating Ability,
J. Mol. Evol. 77, 55–63.                   

A. Buchner, F. Tostevin, F. Hinzpeter and U. Gerland (2013), 
Optimization of collective enzyme activity via spatial localization, 
J. Chem. Phys. 139, 135101. 

A. Buchner, F. Tostevin, and U. Gerland (2013),
Clustering and optimal arrangement of enzymes in reaction-diffusion systems, 
Physical Review Letters 110, 208104.                   

P. Hillenbrand, G. Fritz, and U. Gerland (2013), 
Biological signal processing with a genetic toggle switch,
PLoS One 8, e68345   

C.B. Mast, S. Schink, U. Gerland, and D. Braun (2013), 
Escalation of Polymerization in a Thermal Gradient, 
Proc. Natl. Acad. Sci. USA 110, 8030–5.                   

W. Möbius, B. Osberg, A.M. Tsankov, O.J. Rando, and U. Gerland (2013), 
Toward a unified physical model of nucleosome patterns flanking transcription start sites, 
Proc. Natl. Acad. Sci. USA 110, 5719–5724. 

T. Ramalho, M. Selig, U. Gerland, and T.A. Enßlin (2013), 
Simulation of stochastic network dynamics via entropic matching, 
Physical Review E 87, 022719. 

K. Leu, E. Kervio, B. Obermayer, R. Turk-MacLeod, C. Yuan, J. Luevano, E. Chen, U. Gerland, C. Richert, and I.A. Chen (2013),  
Cascade of Reduced Speed and Accuracy After Errors in Enzyme-Free Copying of Nucleic Acid Sequences, 
J. Am. Chem. Soc. 135, 354–366. 

R. Turk-MacLeod, U. Gerland, and I. Chen (2013)
'Life: the physical underpinnings of replication' in 'Astrochemistry and Astrobiology: Physical Chemistry in Action'
Springer, New York; Eds. I.W.M. Smith, C.S. Cockell, S. Leach; ISBN 978-3-642-31729-3

I. Haneburger, G. Fritz, N. Jurkschat, L. Tetsch, A. Eichinger, A. Skerra, U. Gerland, K. Jung (2012), 
Deactivation of the E. coli pH Stress Sensor CadC by Cadaverine, 
Journal of Molecular Biology, 424, 15–27. 

S. Schink, S. Renner, K. Alim, V. Arnaut, F.C. Simmel, and U. Gerland (2012), 
Quantitative Analysis of the Nanopore Translocation Dynamics of Simple Structured Polynucleotides, 
Biophysical Journal 102, 85–95. 

T. Schötz, R.A. Neher, and U. Gerland (2011), 
Target search on a dynamic DNA molecule, 
Physical Review E 84, 051911.                   

N. Geisel and U. Gerland (2011),
Physical limits on cooperative protein-DNA binding and the kinetics of combinatorial transcription regulation, 
Biophysical Journal 101, 1569–79.                   

B. Obermayer, H. Krammer, D. Braun, and U. Gerland (2011), 
Emergence of information transmission in a prebiotic RNA reactor, 
Physical Review Letters 107, 018101.                   

K. Leu, B. Obermayer, S. Rajamani, U. Gerland, and I.A. Chen (2011), 
The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA, 
Nucleic Acids Research 39, 8135-47.                   

S. Renner, A. Bessonov, U. Gerland, and F.C. Simmel (2010), 
Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy,
J. Phys.: Condensed Matter 22, 454119.                   

W. Möbius and U. Gerland (2010), 
Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites, 
PLoS Comp. Biol. 6, e1000891.                   

H. Gumpp, E.M. Puchner, J.L. Zimmermann, U. Gerland, H.E. Gaub, and K. Blank (2009), 
Triggering enzymatic activity with force,
Nano Letters 9, 3290–3295.                   

G. Fritz, C. Koller, K. Burdack, L. Tetsch, I. Haneburger, K. Jung, and U. Gerland (2009), 
Induction kinetics of a conditional pH stress response system in Escherichia coli,
Journal of Molecular Biology 393, 272–286.                   

U. Gerland and T. Hwa (2009), 
Evolutionary selection between alternative modes of gene regulation,
Proc. Natl. Acad. Sci. USA 106, 8841–8846.                   

M. McCauley, R. Forties, U. Gerland, and R. Bundschuh (2009), 
Anomalous scaling in nanopore translocation of structured heteropolymers, 
Physical Biology 6, 036006.                   

W. Möbius, E. Frey, and U. Gerland (2008), 
Spontaneous Unknotting of a Polymer Confined in a Nanochannel, 
Nano Letters 8, 4518–4522.   

J. Megerle, G. Fritz, U. Gerland, K. Jung, J.O. Rädler (2008), 
Timing and dynamics of single cell gene expression in the arabinose utilization system, 
Biophysical Journal 95, 2103–2115. 

R. Neher, W. Möbius, E. Frey, U. Gerland (2007), 
Optimal Flexibility for Conformational Transitions in Macromolecules, 
Physical Review Letters 99, 178101.                   

G. Fritz, N. Buchler, T. Hwa and U. Gerland (2007), 
Designing sequential transcription logic: a simple genetic circuit for conditional memory, 
Systems and Synthetic Biology 1, 89–98.                   

W. Möbius, R. Neher, and U. Gerland (2006), 
Kinetic accessibility of buried DNA sites in nucleosomes, 
Physical Review Letters 97, 208102.                   

R. Bundschuh and U. Gerland (2006), 
A puzzle in DNA biophysics,
European Physical Journal E 19, 347–349.                   

R. Bundschuh and U. Gerland (2006), 
Dynamics of intramolecular recognition: Base-pairing in DNA/RNA near and far from equilibrium, 
European Physical Journal E 19, 319–329. 

R. Neher and U. Gerland (2006), 
Intermediate phase in DNA melting, 
Physical Review E 73, 030902 (rapid communication).   

R. Neher and U. Gerland (2005), 
DNA as a programmable viscoelastic nanoelement, 
Biophysical Journal 89, 3846–3855. 

R. Bundschuh and U. Gerland (2005), 
Coupled dynamics of RNA folding and nanopore translocation,
Physical Review Letters 95, 208104.                   

N.E. Buchler, U. Gerland, and T. Hwa (2005), 
Nonlinear protein degradation and the function of genetic circuits, 
Proc. Natl. Acad. Sci. USA 102, 9559–9564.                   

L. Bintu, N.E. Buchler, H. Garcia, U. Gerland, T. Hwa, J. Kondev, T. Kuhlman, and R. Phillips (2005), 
Transcriptional regulation by the numbers: applications, 
Curr. Opin. Genet. Dev. 15, 125-135.                   

L. Bintu, N.E. Buchler, H. Garcia, U. Gerland, T. Hwa, J. Kondev & R. Phillips (2005), 
Transcriptional regulation by the numbers: models, 
Curr. Opin. Genet. Dev. 15, 116-124.                   

U. Gerland (2005)
Programmierbare Gen-Logik
Bioforum 1-2, 44–45.

R. Neher and U. Gerland (2004), 
Dynamics of force-induced DNA slippage, 
Physical Review Letters 93, 198102.                   

U. Gerland, R. Bundschuh, and T. Hwa (2004), 
Translocation of structured polynucleotides through nanopores, 
Physical Biology 1, 19–26.                   

N.E. Buchler, U. Gerland, and T. Hwa (2003), 
On schemes of combinatorial transcription logic, 
Proc. Natl. Acad. Sci. USA 100, 5136–5141.                   

U. Gerland, R. Bundschuh, and T. Hwa (2003), 
Mechanically probing the folding pathway of single RNA molecules, 
Biophysical Journal 84, 2831–40.                   

W. Peng, U. Gerland, T. Hwa, and H. Levine (2003), 
Dynamics of competitive evolution on a smooth landscape, 
Physical Review Letters 90, 088103.                   

U. Gerland, J.D. Moroz, and T. Hwa (2002), 
Physical constraints and functional characteristics of Transcription Factor-DNA interaction, 
Proc. Natl. Acad. Sci. USA 99, 12105–10. 

U. Gerland and T. Hwa (2002), 
On the selection and evolution of regulatory binding motifs
Journal of Molecular Evolution 55, 386–400. 

U. Gerland, R. Bundschuh, and T. Hwa (2001), 
Force-induced denaturation of RNA, 
Biophysical Journal 81, 1324–32.                   

E.B. Bogomolny, U. Gerland, and C. Schmit (2001)
Singular statistics
Physical Review E 63, 036206

E.B. Bogomolny, U. Gerland, and C. Schmit (2001) 
Short-range plasma model for intermediate spectral statistics
Eur. Phys. J. B 19, 121–132.

U. Gerland, J. von Delft, T.A. Costi, and Y. Oreg (2000) 
Transmission phase shift of a quantum dot with Kondo correlations
Physical Review Letters 84, 3710–13

U. Gerland (1999)
Spectral statistics and dynamical localization: sharp transition in a generalized Sinai billiard
Physical Review Letters 83, 1139–42

E.B. Bogomolny, U. Gerland, and C. Schmit (1999) 
Models of intermediate spectral statistics
Physical Review E 59, R1315–19

U. Gerland and H.A. Weidenmüller (1996)
Weak localization in chaotic electron billiards: the effect of imperfect coupling to the leads
Europhysics Letters 35, 701–706