Publications

Publications 2009

R. Pieruschka, A. Chavarría-Krauser, U. Schurr, S. Jahnke
Photosynthesis in lightfleck areas of homobaric and heterobaric leaves.
Journal of Experimental Botany, (electronic version Dec. 2009)

Chavarría-Krauser A., Jäger W.
Barodiffusion effects in bifurcating capillaries.
(2009), accepted by Computing and Visualization in Science

Di Ventura, B., Sourjik, V.
Self-arising equal partitioning of Min proteins during cytokinesis.
(2009), submitted to Genes and development, under review

Murray, C.M. Edwards, M.J. Tindall and P. K. Maini
From a discrete to a continuum model of cell dynamics in one dimension.
P.J.Phys Rev E 80 (3): 031912 (2009)

D. Hartmann
A multiscale model for red blood cell mechanics.
Modelling in Mechanobiology (electronic version) 17 pages, Springer 2009

T. Miura, D. Hartmann, M. Kiboshi, M. Komada, M. Ishibashi, K. Shiota
The cyst-branch difference in developing chick lung results from a different morphogen diffusion coefficient.
Mechanisms of Development. 126 (3-4), 160-172 (2009)

Mai Zahran, Isabella Daidone, Jeremy C. Smith, and Petra Imhof
Mechanism of DNA Recognition by the Restriction Enzyme EcoRV.
submitted to J. Mol. Biol.

Petra Imhof, Stefan Fischer, and Jeremy C. Smith
Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme.
EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis, Biochemistry 48 (2009) 9061-9075

L. Brun, B. Rupp, J. Ward, and F. Nédélec
A theory of microtubule catastrophes and their regulation.
PNAS vol 106 (50):21173-21178 (2009)

C. Fu, J. Ward, I. Loiodice, G. Velve-Casquillas, F. Nédélec and P. Tran
Phosophorylation-dependent anchoring of a kinesin-6 motor klp9p to the microtubule bundler ase1p is required for proper anaphase B.
Developmental Cell 17:257-67 (2009)

A. Dinarina, C. Pugieux, M. Mora Corral, M. Loose, J. Spatz, E. Karsenti and F. Nédélec
Chromatin shapes the mitotic spindle.
Cell 138:502-513 (2009)

M. Pinot, F. Chesnel, J.Z. Kubiak, I. Arnal, F. Nédélec and Z. Gueroui
Effects of confinement on the self-organization of microtubules and motors.
Current Biology 19 (11):954-60 (2009)

D. Foethke, T. Makushok, D. Brunner and F. Nédélec
Force and length-dependent catastrophe activities explain interphase microtubule organization in fission yeast.
Molecular Systems Biology 5:241-8 (2009)

Ptashnyk, M., Roose, T., Kirk, G.
Model of diffusion of strongly-sorbed solutes through soil allowing for slow access to and from sorption sites and time-dependent sorption reactions.
EJSS, accepted, 2009

Marcinak-Czochra, A., Ptashnyk, M.
Boundedness of solutions of a haptotaxis model.
M3AS: Mathematical Models and Methods in Applied Sciences, accepted, 2009

Ptashnyk, M., Roose, T.
Derivation of a macroscopic model for transport of strongly sorbed solutes in the soil using homogenization theory.
submitted to SIAM J Appl Math, 2000

Leitner, D., Klepsch,S., Ptashnyk, M., Marchant, A., Kirk, G., Schnepf, A.,Roose,T.
A dynamic model of nutrient uptake by root hairs based on homogenization.
New Phytologist, in press, 2009

Solon, J., Kaya-Copur, A., Colombelli, J., Brunner, D.
Pulsed forces timed by a ratchet-like mechanism drive directed tissue movement during dorsal closure.
Cell 137(7), 1331-1342. (2009)

Surovtsova I., Simus N., Lorenz Th., König A., Sahle S. and Kummer U.
Accessible methods for dynamical time-scale decomposition for biochemical systems.
Bioinformatics. 2009 25(21):2816-2823

Surovtsova I., Simus N., Sahle S. and Kummer U.
Time-dependent Approaches for Complexity Reduction for Biochemical Systems.
German Symposium on System Biology. May 12-15, 2009, Heidelberg. Publication in preparation

M.B. Ulmschneider, J.P. Ulmschneider
Implicit membrane models for peptide folding and insertion studies.
in Molecular Simulations and Biomembranes, Royal Society of Chemistry, 2009, in press

J. P. Ulmschneider, J. P. F. Doux, J. A. Killian, J. C. Smith, M. B. Ulmschneider
Peptide Partitioning and Folding into Lipid Bilayers.
JCTC 2009, 5, 2202-2205

J.P. Ulmschneider, M.B. Ulmschneider,
United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field.
JCTC 2009, 5 (7), 1803-1813

J.P. Ulmschneider, M.B. Ulmschneider
Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations.
Proteins 2009, 75, 586-597

A. Wedemeier, H. Merlitz, Chen-Xu Wu, J. Langowski
How proteins squeeze through polymer networks: a Cartesian lattice study?
J. Chem. Phys 131, 064905 (2009)

A. Wedemeier, H. Merlitz, Chen-Xu Wu, J. Langowski
Anomalous diffusion in the presence of mobile obstacles.
Europhys. Lett. 88, 38004 (2009)

M. Hellmann, Y. Deng, M. Weiss, D.W. Heermann
Phase transition of a two-dimensional, multiplicatively coupled XY-Potts model.
J. Phys. A 42, 225001 (2009)

J. Szymanski, C. Mayer, U. Hofmann-Rohrer, C. Kalla, I. Grummt, M. Weiss
Dynamic subcellular partitioning of the nucleolar transcription factor TIF-IA under ribotoxic stress.
Biochim. Biophys. Acta 1793, 1191 (2009)

J. Szymanski, M. Weiss
Elucidating the origin of anomalous diffusion in crowded fluids.
Phys. Rev. Lett. 103, 038102 (2009)

N. Malchus, M. Weiss
Elucidating anomalous protein diffusion in living cells with fluorescence correlation spectroscopy - facts and pitfalls.
J. Fluor., in press (2009)

D. Morozova, M. Weiss
On the role of acylation of transmembrane proteins.
Biophys. J., in press (2009)

J. Winkler, A. Seybert, L. Koenig, S. Pruggnaller, U. Haselmann, V. Sourjik, M. Weiss, A.S. Frangakis, A. Mogk & B. Bukau
Quantitative and spatio-temporal features of protein aggregation in E. coli and consequences on protein quality control and cellular aging.
EMBO J., in press (2009)