TY - GEN A1 - Ilgenfritz, Ernst-Michael A1 - Kerler, Werner A1 - Müller-Preussker, Michael A1 - Sternbeck, Andre A1 - Stüben, Hinnerk T1 - Probing the Aoki phase with N_f=2 Wilson fermions at finite temperature N2 - In this letter we report on a numerical investigation of the Aoki phase in the case of finite temperature which continues our former study at zero temperature. We have performed simulations with Wilson fermions at $\beta=4.6$ using lattices with temporal extension $N_{\tau}=4$. In contrast to the zero temperature case, the existence of an Aoki phase can be confirmed for a small range in $\kappa$ at $\beta=4.6$, however, shifted slightly to lower $\kappa$. Despite fine-tuning $\kappa$ we could not separate the thermal transition line from the Aoki phase. T3 - ZIB-Report - 05-48 KW - Wilson fermions KW - phase diagram KW - parity-flavor symmetry KW - Aoki phase KW - finite temperature Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8812 ER - TY - GEN A1 - Ilgenfritz, Ernst-Michael A1 - Kerler, Werner A1 - Müller-Preussker, Michael A1 - Sternbeck, André A1 - Stüben, Hinnerk T1 - A numerical reinvestigation of the Aoki phase with $N_f=2$ Wilson fermions at zero temperature N2 - We report on a numerical reinvestigation of the Aoki phase in lattice QCD with two flavors of Wilson fermions where the parity-flavor symmetry is spontaneously broken. For this purpose the Hybrid Monte Carlo algorithm was used and an explicit symmetry-breaking source term $h\bar{\psi} i \gamma_{5} \tau^{3}\psi$ was added to the Wilson fermion action. The order parameter $\langle\bar{\psi}i\gamma_{5}\tau^{3}\psi\rangle$ was studied at several values of $(\beta,\kappa,h)$ on lattices of sizes $4^4$ to $12^4$. Our largest lattices can be considered as infintely large allowing to extrapolate to $h=0$. The existence of a parity-flavor-breaking phase can be confirmed at $\beta=4.0$ and $\beta=4.3$ while we find no sign of parity-flavor-breaking at $\beta=4.6$ and $\beta=5.0$. T3 - ZIB-Report - 03-27 KW - Wilson fermions KW - phase diagram KW - parity-flavor symmetry KW - Aoki phase Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7492 ER - TY - GEN A1 - Ilgenfritz, Ernst-Michael A1 - Kerler, Werner A1 - Müller-Preussker, Michael A1 - Stüben, Hinnerk T1 - Parallel tempering and decorrelation of topological charge in full QCD N2 - The improvement of simulations of QCD with dynamical Wilson fermions by combining the Hybrid Monte Carlo algorithm with parallel tempering is studied on $10^4$ and $12^4$ lattices. As an indicator for decorrelation the topological charge is used. T3 - ZIB-Report - 00-25 KW - QCD KW - parallel tempering KW - topological charge Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5930 ER - TY - GEN A1 - Ilgenfritz, Ernst-Michael A1 - Kerler, Werner A1 - Müller-Preussker, Michael A1 - Stüben, Hinnerk T1 - Parallel tempering in full QCD with Wilson fermions N2 - We study the performance of QCD simulations with dynamical Wilson fermions by combining the Hybrid Monte Carlo algorithm with parallel tempering on $10^4$ and $12^4$ lattices. In order to compare tempered with standard simulations, covariance matrices between sub-ensembles have to be formulated and evaluated using the general properties of autocorrelations of the parallel tempering algorithm. We find that rendering the hopping parameter $\kappa$ dynamical does not lead to an essential improvement. We point out possible reasons for this observation and discuss more suitable ways of applying parallel tempering to QCD. T3 - ZIB-Report - 01-33 KW - QCD KW - parallel tempering KW - correlation analysis Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6593 ER - TY - JOUR A1 - Müller, A. A1 - Yan, D. A1 - Wulkow, Michael T1 - Molecular Parameters of Hyperbranched Polymers Made by Self-condensing Vinyl Polymerization, 1. Molecular weight distribution JF - Macromolecules Y1 - 1997 VL - 30 SP - 7015 ER - TY - CHAP A1 - Kornaropoulos, Evgenios I. A1 - Taylor, William R. A1 - Duda, Georg A1 - Ehrig, Rainald A1 - Matziolis, Georg A1 - Müller, Michael A1 - Wassilew, Georgi A1 - Asbach, Patrick A1 - Perka, Carsten A1 - Heller, Markus O. T1 - An imageless method to quantify the mechanical femoral-tibial angle based on the functional determination of joint centers and axes T2 - Annual meeting of the ESMAC 2009 Y1 - 2009 CY - London ER - TY - JOUR A1 - Kornaropoulos, Evgenios I. A1 - Taylor, William R. A1 - Duda, Georg A1 - Ehrig, Rainald A1 - Matziolis, Georg A1 - Müller, Michael A1 - Wassilew, Georgi A1 - Asbach, Patrick A1 - Perka, Carsten A1 - Heller, Markus O. T1 - Frontal plane alignment: An imageless method to predict the mechanical femoral–tibial angle (mFTA) based on functional determination of joint centres and axes JF - Gait & Posture Y1 - 2010 U6 - https://doi.org/10.1016/j.gaitpost.2009.10.006 VL - 31 IS - 2 SP - 204 EP - 208 ER - TY - JOUR A1 - Busch, Markus A1 - Müller, M. A1 - Wulkow, Michael T1 - The use of Simulation Techniques in Developing Kinetic Models for Polymerizations JF - Chem. Eng. Technol. Y1 - 2003 VL - 26 SP - 1031 ER - TY - JOUR A1 - Schrade, Katharina A1 - Tröger, Jessica A1 - Eldashan, Adeep A1 - Zühlke, Kerstin A1 - Abdul Azees, Kamal R. A1 - Elkins, Jonathan M. A1 - Neuenschwander, Martin A1 - Oder, Andreas A1 - Elkewedi, Mohamed A1 - Jaksch, Sarah A1 - Andrae, Karsten A1 - Li, Jinliang A1 - Fernandes, Jaoa A1 - Müller, Paul Markus A1 - Grunwald, Stephan A1 - Marino, Stephen F. A1 - Vukicevic, Tanja A1 - Eichhorst, Jenny A1 - Wiesner, Burkhard A1 - Weber, Marcus A1 - Kapiloff, Michael A1 - Rocks, Oliver A1 - Daumke, Oliver A1 - Wieland, Thomas A1 - Knapp, Stefan A1 - von Kries, Jens Peter A1 - Klussmann, Enno T1 - An AKAP-Lbc-RhoA interaction inhibitor promotes the translocation of aquaporin-2 to the plasma membrane of renal collecting duct principal cells JF - PLOS ONE N2 - Stimulation of renal collecting duct principal cells with antidiuretic hormone (arginine-vasopressin, AVP) results in inhibition of the small GTPase RhoA and the enrichment of the water channel aquaporin-2 (AQP2) in the plasma membrane. The membrane insertion facilitates water reabsorption from primary urine and fine-tuning of body water homeostasis. Rho guanine nucleotide exchange factors (GEFs) interact with RhoA, catalyze the exchange of GDP for GTP and thereby activate the GTPase. However, GEFs involved in the control of AQP2 in renal principal cells are unknown. The A-kinase anchoring protein, AKAP-Lbc, possesses GEF activity, specifically activates RhoA, and is expressed in primary renal inner medullary collecting duct principal (IMCD) cells. Through screening of 18,431 small molecules and synthesis of a focused library around one of the hits, we identified an inhibitor of the interaction of AKAP-Lbc and RhoA. This molecule, Scaff10-8, bound to RhoA, inhibited the AKAP-Lbc-mediated RhoA activation but did not interfere with RhoA activation through other GEFs or activities of other members of the Rho family of small GTPases, Rac1 and Cdc42. Scaff10-8 promoted the redistribution of AQP2 from intracellular vesicles to the periphery of IMCD cells. Thus, our data demonstrate an involvement of AKAP-Lbc-mediated RhoA activation in the control of AQP2 trafficking. Y1 - 2018 U6 - https://doi.org/10.1371/journal.pone.0191423 VL - 13 IS - 1 SP - e0191423 EP - e0191423 ER - TY - GEN A1 - Gleixner, Ambros A1 - Bastubbe, Michael A1 - Eifler, Leon A1 - Gally, Tristan A1 - Gamrath, Gerald A1 - Gottwald, Robert Lion A1 - Hendel, Gregor A1 - Hojny, Christopher A1 - Koch, Thorsten A1 - Lübbecke, Marco A1 - Maher, Stephen J. A1 - Miltenberger, Matthias A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Puchert, Christian A1 - Rehfeldt, Daniel A1 - Schlösser, Franziska A1 - Schubert, Christoph A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Viernickel, Jan Merlin A1 - Walter, Matthias A1 - Wegscheider, Fabian A1 - Witt, Jonas T. A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 6.0 N2 - The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version 6.0 of the SCIP Optimization Suite. Besides performance improvements of the MIP and MINLP core achieved by new primal heuristics and a new selection criterion for cutting planes, one focus of this release are decomposition algorithms. Both SCIP and the automatic decomposition solver GCG now include advanced functionality for performing Benders’ decomposition in a generic framework. GCG’s detection loop for structured matrices and the coordination of pricing routines for Dantzig-Wolfe decomposition has been significantly revised for greater flexibility. Two SCIP extensions have been added to solve the recursive circle packing problem by a problem-specific column generation scheme and to demonstrate the use of the new Benders’ framework for stochastic capacitated facility location. Last, not least, the report presents updates and additions to the other components and extensions of the SCIP Optimization Suite: the LP solver SoPlex, the modeling language Zimpl, the parallelization framework UG, the Steiner tree solver SCIP-Jack, and the mixed-integer semidefinite programming solver SCIP-SDP. T3 - ZIB-Report - 18-26 KW - constraint integer programming KW - linear programming KW - mixed-integer linear programming KW - mixed-integer nonlinear programming KW - optimization solver KW - branch-and-cut KW - branch-and-price KW - column generation framework KW - parallelization KW - mixed-integer semidefinite programming KW - Steiner tree optimization Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69361 SN - 1438-0064 ER - TY - JOUR A1 - Redemann, Stefanie A1 - Baumgart, Johannes A1 - Lindow, Norbert A1 - Shelley, Michael A1 - Nazockdast, Ehssan A1 - Kratz, Andrea A1 - Prohaska, Steffen A1 - Brugués, Jan A1 - Fürthauer, Sebastian A1 - Müller-Reichert, Thomas T1 - C. elegans chromosomes connect to centrosomes by anchoring into the spindle network JF - Nature Communications N2 - The mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient. Y1 - 2017 U6 - https://doi.org/10.1038/ncomms15288 VL - 8 IS - 15288 ER - TY - GEN A1 - Rusch, Beate A1 - Peters-Kottig, Wolfgang A1 - Ceynowa, Klaus A1 - Dinter, Joachim A1 - Dubberke, Ina A1 - Happel, Hans-Gerd A1 - Hilliger, Kirsten A1 - Kitaeva, Xenia A1 - Kleineberg, Michael A1 - Koch, Thorsten A1 - Mc Leod, Shirley A1 - Mutter, Moritz A1 - Müller, Anja A1 - Seeliger, Frank A1 - Segger, Elisabeth A1 - Stanek, Ursula A1 - Wiese, Robert A1 - Wrzesinski, Marcel T1 - KOBV Jahresbericht 2023-2024 T3 - KOBV-Jahresbericht - 2023-2024 Y1 - 2025 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-100440 SN - 0934-5892 VL - 2023-2024 CY - Berlin ER - TY - JOUR A1 - Okafornta, Chukwuebuka William A1 - Farhadifar, Reza A1 - Fabig, Gunar A1 - Wu, Hai-Yin A1 - Köckert, Maria A1 - Vogel, Martin A1 - Baum, Daniel A1 - Haase, Robert A1 - Shelley, Michael J. A1 - Needleman, Daniel J. A1 - Müller-Reichert, Thomas T1 - Cell size reduction scales spindle elongation but not chromosome segregation in C. elegans JF - bioRxiv N2 - How embryos adapt their internal cellular machinery to reductions in cell size during development remains a fundamental question in cell biology. Here, we use high-resolution lattice light-sheet fluorescence microscopy and automated image analysis to quantify lineage-resolved mitotic spindle and chromosome segregation dynamics from the 2– to 64–cell stages in Caenorhabditis elegans embryos. While spindle length scales with cell size across both wild-type and size-perturbed embryos, chromosome segregation dynamics remain largely invariant, suggesting that distinct mechanisms govern these mitotic processes. Combining femtosecond laser ablation with large-scale electron tomography, we find that central spindle microtubules mediate chromosome segregation dynamics and remain uncoupled from cell size across all stages of early development. In contrast, spindle elongation is driven by cortically anchored motor proteins and astral microtubules, rendering it sensitive to cell size. Incorporating these experimental results into an extended stoichiometric model for both the spindle and chromosomes, we find that allowing only cell size and microtubule catastrophe rates to vary reproduces elongation dynamics across development. The same model also accounts for centrosome separation and pronuclear positioning in the one-cell C. elegans embryo, spindle-length scaling across nematode species spanning ~100 million years of divergence, and spindle rotation in human cells. Thus, a unified stoichiometric framework provides a predictive, mechanistic account of spindle and nuclear dynamics across scales and species. Y1 - 2025 U6 - https://doi.org/10.1101/2025.10.13.681585 ER - TY - GEN A1 - Gamrath, Gerald A1 - Fischer, Tobias A1 - Gally, Tristan A1 - Gleixner, Ambros A1 - Hendel, Gregor A1 - Koch, Thorsten A1 - Maher, Stephen J. A1 - Miltenberger, Matthias A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Puchert, Christian A1 - Rehfeldt, Daniel A1 - Schenker, Sebastian A1 - Schwarz, Robert A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Vigerske, Stefan A1 - Weninger, Dieter A1 - Winkler, Michael A1 - Witt, Jonas T. A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 3.2 N2 - The SCIP Optimization Suite is a software toolbox for generating and solving various classes of mathematical optimization problems. Its major components are the modeling language ZIMPL, the linear programming solver SoPlex, the constraint integer programming framework and mixed-integer linear and nonlinear programming solver SCIP, the UG framework for parallelization of branch-and-bound-based solvers, and the generic branch-cut-and-price solver GCG. It has been used in many applications from both academia and industry and is one of the leading non-commercial solvers. This paper highlights the new features of version 3.2 of the SCIP Optimization Suite. Version 3.2 was released in July 2015. This release comes with new presolving steps, primal heuristics, and branching rules within SCIP. In addition, version 3.2 includes a reoptimization feature and improved handling of quadratic constraints and special ordered sets. SoPlex can now solve LPs exactly over the rational number and performance improvements have been achieved by exploiting sparsity in more situations. UG has been tested successfully on 80,000 cores. A major new feature of UG is the functionality to parallelize a customized SCIP solver. GCG has been enhanced with a new separator, new primal heuristics, and improved column management. Finally, new and improved extensions of SCIP are presented, namely solvers for multi-criteria optimization, Steiner tree problems, and mixed-integer semidefinite programs. T3 - ZIB-Report - 15-60 KW - mixed-integer linear and nonlinear programming KW - MIP solver KW - MINLP solver KW - linear programming KW - LP solver KW - simplex method KW - modeling KW - parallel branch-and-bound KW - branch-cut-and-price framework KW - generic column generation KW - Steiner tree solver KW - multi-criteria optimization KW - mixed-integer semidefinite programming Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57675 SN - 1438-0064 ER -