Ulrich Gerland

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Physical constraints and functional characteristics of transcription factor-DNA interaction
    Ulrich Gerland
    Department of Physics, University of California at San Diego, La Jolla, CA 92093 0319, USA
    Proc Natl Acad Sci U S A 99:12015-20. 2002
  2. ncbi request reprint On the selection and evolution of regulatory DNA motifs
    Ulrich Gerland
    Department of Physics, University of California, San Diego, La Jolla, CA 92093 0319, USA
    J Mol Evol 55:386-400. 2002
  3. pmc Mechanically probing the folding pathway of single RNA molecules
    Ulrich Gerland
    Department of Physics, University of California at San Diego, La Jolla 92093 0319, USA
    Biophys J 84:2831-40. 2003
  4. ncbi request reprint Translocation of structured polynucleotides through nanopores
    Ulrich Gerland
    Department of Physics and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093 0319, USA
    Phys Biol 1:19-26. 2004
  5. ncbi request reprint Dynamics of competitive evolution on a smooth landscape
    Weiqun Peng
    Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, California 92093 0319, USA
    Phys Rev Lett 90:088103. 2003
  6. ncbi request reprint Coupled dynamics of RNA folding and nanopore translocation
    Ralf Bundschuh
    Department of Physics, The Ohio State University, Columbus, Ohio 43210 1117, USA
    Phys Rev Lett 95:208104. 2005
  7. doi request reprint Anomalous scaling in nanopore translocation of structured heteropolymers
    Malcolm McCauley
    Department of Physics, The Ohio State University, Columbus, OH 43210 1117, USA
    Phys Biol 6:036006. 2009
  8. pmc On schemes of combinatorial transcription logic
    Nicolas E Buchler
    Department of Physics and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093 0319, USA
    Proc Natl Acad Sci U S A 100:5136-41. 2003
  9. pmc Toward a unified physical model of nucleosome patterns flanking transcription start sites
    Wolfram Möbius
    Department of Physics, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 110:5719-24. 2013
  10. pmc DNA as a programmable viscoelastic nanoelement
    Richard A Neher
    Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig Maximilians Universitat Munchen, Munich, Germany
    Biophys J 89:3846-55. 2005

Collaborators

Detail Information

Publications17

  1. pmc Physical constraints and functional characteristics of transcription factor-DNA interaction
    Ulrich Gerland
    Department of Physics, University of California at San Diego, La Jolla, CA 92093 0319, USA
    Proc Natl Acad Sci U S A 99:12015-20. 2002
    ..We suggest further experiments to test whether this is a general feature for a large class of TFs...
  2. ncbi request reprint On the selection and evolution of regulatory DNA motifs
    Ulrich Gerland
    Department of Physics, University of California, San Diego, La Jolla, CA 92093 0319, USA
    J Mol Evol 55:386-400. 2002
    ..We discuss possible experimental approaches to resolve open questions raised by our study...
  3. pmc Mechanically probing the folding pathway of single RNA molecules
    Ulrich Gerland
    Department of Physics, University of California at San Diego, La Jolla 92093 0319, USA
    Biophys J 84:2831-40. 2003
    ..We compare and relate our results to recent experiments by Liphardt et al. (2001)...
  4. ncbi request reprint Translocation of structured polynucleotides through nanopores
    Ulrich Gerland
    Department of Physics and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093 0319, USA
    Phys Biol 1:19-26. 2004
    ..Our analysis suggests that, with this added spatial resolution, nanopores could be transformed into a powerful experimental tool to study the folding of nucleic acids...
  5. ncbi request reprint Dynamics of competitive evolution on a smooth landscape
    Weiqun Peng
    Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, California 92093 0319, USA
    Phys Rev Lett 90:088103. 2003
    ..Analytical results obtained on the motion of the pulse agree with simulations. Furthermore, finite population correction to the mean-field results are found to be insignificant...
  6. ncbi request reprint Coupled dynamics of RNA folding and nanopore translocation
    Ralf Bundschuh
    Department of Physics, The Ohio State University, Columbus, Ohio 43210 1117, USA
    Phys Rev Lett 95:208104. 2005
    ..We find that the transient formation of base pairs that do not occur in the ground state can significantly speed up translocation...
  7. doi request reprint Anomalous scaling in nanopore translocation of structured heteropolymers
    Malcolm McCauley
    Department of Physics, The Ohio State University, Columbus, OH 43210 1117, USA
    Phys Biol 6:036006. 2009
    ..We explain the behavior in the molten phase and the qualitative trend in the glassy phase theoretically...
  8. pmc On schemes of combinatorial transcription logic
    Nicolas E Buchler
    Department of Physics and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093 0319, USA
    Proc Natl Acad Sci U S A 100:5136-41. 2003
    ..This may be a key factor limiting the genome-wide adoption of complex transcription control in bacteria. Implications of our findings for combinatorial transcription control in eukaryotes are discussed...
  9. pmc Toward a unified physical model of nucleosome patterns flanking transcription start sites
    Wolfram Möbius
    Department of Physics, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 110:5719-24. 2013
    ..We therefore establish a basis for a physical description of nucleosome patterns that can serve as a null model for sequence-specific effects at individual genes and in models of transcription regulation...
  10. pmc DNA as a programmable viscoelastic nanoelement
    Richard A Neher
    Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig Maximilians Universitat Munchen, Munich, Germany
    Biophys J 89:3846-55. 2005
    ..Based on our findings, we suggest new dynamical roles for DNA in artificial nanoscale devices. The basepairing dynamics described here is also relevant for the extension of repetitive sequences inside genomic DNA...
  11. ncbi request reprint Intermediate phase in DNA melting
    Richard A Neher
    Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, LMU Munchen, Theresienstrasse 37, 80333 München, Germany
    Phys Rev E Stat Nonlin Soft Matter Phys 73:030902. 2006
    ..This continuous transition is in many aspects analogous to Bose-Einstein condensation. When the sequence is weakly disordered, the contour length changes discontinuously with temperature...
  12. ncbi request reprint Kinetic accessibility of buried DNA sites in nucleosomes
    Wolfram Möbius
    Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, LMU Munchen, Theresienstrasse 37, 80333 München, Germany
    Phys Rev Lett 97:208102. 2006
    ..Close inspection reveals a surprising physical effect of flexibility-assisted barrier crossing, which we characterize within a toy model, the "semiflexible Brownian rotor."..
  13. ncbi request reprint Dynamics of force-induced DNA slippage
    Richard A Neher
    Department of Physics and CeNS, LMU Munchen, Theresienstrasse 37, 80333 München, Germany
    Phys Rev Lett 93:198102. 2004
    ..We predict a viscoelastic behavior for periodic DNA with time and force scales that can be programmed into its sequence...
  14. pmc Transcriptional regulation by the numbers: applications
    Lacramioara Bintu
    Physics Department, Brandeis University, Waltham, MA 02454, USA
    Curr Opin Genet Dev 15:125-35. 2005
    ..g. of genetic networks) without the need to invoke the biochemical details of every component. Moreover, it can be used to generate hypotheses on the likely mechanisms of transcriptional control...
  15. pmc Transcriptional regulation by the numbers: models
    Lacramioara Bintu
    Physics Department, Brandeis University, Waltham, MA 02454, USA
    Curr Opin Genet Dev 15:116-24. 2005
    ..This analysis culminates in an expression for the probability of RNA polymerase binding at the promoter of interest as a function of the number of regulatory proteins in the cell...
  16. pmc Timing and dynamics of single cell gene expression in the arabinose utilization system
    Judith A Megerle
    Department für Physik und CeNS, Ludwig Maximilians Universitat, Munich, Germany
    Biophys J 95:2103-15. 2008
    ..Our findings support the idea that the heterogeneous timing of gene induction is causally related to a broad distribution of uptake proteins at the time of sugar addition...
  17. pmc Nonlinear protein degradation and the function of genetic circuits
    Nicolas E Buchler
    Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 102:9559-64. 2005
    ..Our results suggest that cooperative stability needs to be considered explicitly and characterized quantitatively in any systematic experimental or theoretical study of gene circuits...