@article{2383, abstract = {We study the relativistic electron-positron field at positive temperature in the Hartree-Fock approximation. We consider both the case with and without exchange terms, and investigate the existence and properties of minimizers. Our approach is non-perturbative in the sense that the relevant electron subspace is determined in a self-consistent way. The present work is an extension of previous work by Hainzl, Lewin, Séré and Solovej where the case of zero temperature was considered.}, author = {Hainzl, Christian and Lewin, Mathieu and Robert Seiringer}, journal = {Reviews in Mathematical Physics}, number = {10}, pages = {1283 -- 1307}, publisher = {World Scientific Publishing}, title = {{A nonlinear model for relativistic electrons at positive temperature}}, doi = {10.1142/S0129055X08003547}, volume = {20}, year = {2008}, } @inproceedings{2702, abstract = {We review our proof that in a scaling limit, the time evolution of a quantum particle in a static random environment leads to a diffusion equation. In particular, we discuss the role of Feynman graph expansions and of renormalization. }, author = {László Erdös and Salmhofer, Manfred and Yau, Horng-Tzer}, pages = {167 -- 182}, publisher = {World Scientific Publishing}, title = {{Feynman graphs and renormalization in quantum diffusion}}, doi = {10.1142/9789812833556_0011}, year = {2008}, } @article{3037, author = {Feraru, Elena and Friml, Jirí}, journal = {Plant Physiology}, number = {4}, pages = {1553 -- 1559}, publisher = {American Society of Plant Biologists}, title = {{PIN polar targeting}}, doi = {10.1104/pp.108.121756}, volume = {147}, year = {2008}, } @article{3307, abstract = {A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.}, author = {Green, Richard E and Malaspinas, Anna-Sapfo and Krause, Johannes and Briggs, Adrian W and Johnson, Philip L and Caroline Uhler and Meyer, Matthias and Good, Jeffrey M and Maricic, Tomislav and Stenzel, Udo and Prüfer, Kay and Siebauer, Michael F and Burbano, Hernän A and Ronan, Michael T and Rothberg, Jonathan M and Egholm, Michael and Rudan, Pavao and Brajković, Dejana and Kućan, Željko and Gušić, Ivan and Wikström, Mårten K and Laakkonen, Liisa J and Kelso, Janet F and Slatkin, Montgomery and Pääbo, Svante H}, journal = {Cell}, pages = {416 -- 426}, publisher = {Cell Press}, title = {{A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing}}, doi = {10.1016/j.cell.2008.06.021}, volume = {134}, year = {2008}, } @article{11113, abstract = {The nuclear envelope (NE), a double membrane enclosing the nucleus of eukaryotic cells, controls the flow of information between the nucleoplasm and the cytoplasm and provides a scaffold for the organization of chromatin and the cytoskeleton. In dividing metazoan cells, the NE breaks down at the onset of mitosis and then reforms around segregated chromosomes to generate the daughter nuclei. Recent data from intact cells and cell-free nuclear assembly systems suggest that the endoplasmic reticulum (ER) is the source of membrane for NE assembly. At the end of mitosis, ER membrane tubules are targeted to chromatin via tubule ends and reorganized into flat nuclear membrane sheets by specific DNA-binding membrane proteins. In contrast to previous models, which proposed vesicle fusion to be the principal mechanism of NE formation, these new studies suggest that the nuclear membrane forms by the chromatin-mediated reshaping of the ER.}, author = {Anderson, Daniel J. and HETZER, Martin W}, issn = {1477-9137}, journal = {Journal of Cell Science}, keywords = {Cell Biology}, number = {2}, pages = {137--142}, publisher = {The Company of Biologists}, title = {{Shaping the endoplasmic reticulum into the nuclear envelope}}, doi = {10.1242/jcs.005777}, volume = {121}, year = {2008}, } @article{11114, abstract = {We present a miniaturized pull-down method for the detection of protein-protein interactions using standard affinity chromatography reagents. Binding events between different proteins, which are color-coded with quantum dots (QDs), are visualized on single affinity chromatography beads by fluorescence microscopy. The use of QDs for single molecule detection allows the simultaneous analysis of multiple protein-protein binding events and reduces the amount of time and material needed to perform a pull-down experiment.}, author = {Schulte, Roberta and Talamas, Jessica and Doucet, Christine and HETZER, Martin W}, issn = {1932-6203}, journal = {PLoS ONE}, keywords = {Multidisciplinary}, number = {4}, publisher = {Public Library of Science}, title = {{Single bead affinity detection (SINBAD) for the analysis of protein-protein interactions}}, doi = {10.1371/journal.pone.0002061}, volume = {3}, year = {2008}, } @article{128, abstract = {A 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described. This long tuning range is achieved by simultaneously ramping the external cavity length with the laser injection current. The laser output pointing remains fixed, independent of its frequency because of the cover slip cavity design. This system is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate with lithium vapor and lithium atom beam experiments. }, author = {Carr, Adra and Serchest, Yancey and Waitukaitis, Scott R and Perreault, John and Lonij, Vincent and Cronin, Alexander}, journal = {Review of Scientific Instruments}, number = {10}, publisher = {American Institute of Physics}, title = {{Cover slip external cavity diode laser}}, doi = {10.1063/1.2801006}, volume = {78}, year = {2007}, } @article{9149, abstract = {The interaction of tidal currents with sea-floor topography results in the radiation of internal gravity waves into the ocean interior. These waves are called internal tides and their dissipation due to nonlinear wave breaking and concomitant three-dimensional turbulence could play an important role in the mixing of the abyssal ocean, and hence in controlling the large-scale ocean circulation. As part of on-going work aimed at providing a theory for the vertical distribution of wave breaking over sea-floor topography, in this paper we investigate the instability of internal tides in a very simple linear model that helps us to relate the formation of unstable regions to simple features in the sea-floor topography. For two-dimensional tides over one-dimensional topography we find that the formation of overturning instabilities is closely linked to the singularities in the topography shape and that it is possible to have stable waves at the sea floor and unstable waves in the ocean interior above. For three-dimensional tides over two-dimensional topography there is in addition an effect of geometric focusing of wave energy into localized regions of high wave amplitude, and we investigate this focusing effect in simple examples. Overall, we find that the distribution of unstable wave breaking regions can be highly non-uniform even for very simple idealized topography shapes.}, author = {Bühler, Oliver and Muller, Caroline J}, issn = {0022-1120}, journal = {Journal of Fluid Mechanics}, keywords = {mechanical engineering, mechanics of materials, condensed matter physics}, pages = {1--28}, publisher = {Cambridge University Press}, title = {{Instability and focusing of internal tides in the deep ocean}}, doi = {10.1017/s0022112007007410}, volume = {588}, year = {2007}, } @article{7753, abstract = {In many species, females show reduced expression of a trait that is under sexual selection in males, and this expression is thought to be maintained through genetic associations with the male phenotype. However, there is also the potential for the female trait to convey an advantage in intrasexual conflicts over resources. We tested this hypothesis in a feral population of Soay sheep, in which males and females have a polymorphism for horn development, producing either full (normal horned), reduced (scurred) or no (polled, females only) horns. During the lambing period, females who possessed horns were more likely to initiate and win aggressive interactions, independent of age, weight and birthing status. The occurrence of aggression was also context dependent, decreasing over the lambing period and associated with local density. Our results demonstrate that a trait that confers benefits to males during intrasexual competition for mates may also be used by females in intrasexual competition over resources: males use weaponry to gain mates, whereas females use weaponry to gain food.}, author = {Robinson, Matthew Richard and Kruuk, Loeske E.B}, issn = {1744-9561}, journal = {Biology Letters}, number = {6}, pages = {651--654}, publisher = {The Royal Society}, title = {{Function of weaponry in females: The use of horns in intrasexual competition for resources in female Soay sheep}}, doi = {10.1098/rsbl.2007.0278}, volume = {3}, year = {2007}, } @inbook{167, abstract = {This book contains research articles on Diophantine Geometry, written by participants of a research program held at the Ennio De Giorgi Mathematical Research Center in Pisa, Italy, during the period April – July 2005. The authors are eminent experts in the field. Several subfields of the main topic are presented; the volume thus is particularly useful to get a broad overview of recent research developments.}, author = {Browning, Timothy D and Heath Brown, Roger}, booktitle = {Diophantine Geometry}, editor = {Zannier, Umberto}, pages = {93 -- 100}, publisher = {Edizioni della Normale}, title = {{Simultaneous equal sums of three powers}}, volume = {4}, year = {2007}, } @article{1762, abstract = {In quantum information science, the phase of a wave function plays an important role in encoding information. Although most experiments in this field rely on dynamic effects to manipulate this information, an alternative approach is to use geometric phase, which has been argued to have potential fault tolerance. We demonstrated the controlled accumulation of a geometric phase, Berry's phase, in a superconducting qubit; we manipulated the qubit geometrically by means of microwave radiation and observed the accumulated phase in an interference experiment. We found excellent agreement with Berry's predictions and also observed a geometry-dependent contribution to dephasing.}, author = {Leek, Peter J and Johannes Fink and Blais, Alexandre and Bianchetti, R and Göppl, M and Gambetta, Jay M and Schuster, David I and Frunzio, Luigi and Schoelkopf, Robert J and Wallraff, Andreas}, journal = {Science}, number = {5858}, pages = {1889 -- 1892}, publisher = {American Association for the Advancement of Science}, title = {{Observation of Berry's phase in a solid-state qubit}}, doi = {10.1126/science.1149858}, volume = {318}, year = {2007}, } @article{13425, abstract = {Nanoparticles (NPs) decorated with ligands combining photoswitchable dipoles and covalent cross-linkers can be assembled by light into organized, three-dimensional suprastructures of various types and sizes. NPs covered with only few photoactive ligands form metastable crystals that can be assembled and disassembled “on demand” by using light of different wavelengths. For higher surface concentrations, self-assembly is irreversible, and the NPs organize into permanently cross-linked structures including robust supracrystals and plastic spherical aggregates.}, author = {Klajn, Rafal and Bishop, Kyle J. M. and Grzybowski, Bartosz A.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {25}, pages = {10305--10309}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Light-controlled self-assembly of reversible and irreversible nanoparticle suprastructures}}, doi = {10.1073/pnas.0611371104}, volume = {104}, year = {2007}, } @unpublished{6321, abstract = {These lecture notes describe the current state of affairs for Manin's conjecture in the context of del Pezzo surfaces.}, author = {Browning, Timothy D}, booktitle = {arXiv}, title = {{The Manin conjecture in dimension 2}}, year = {2007}, } @inbook{6323, abstract = {This paper surveys recent progress towards the Manin conjecture for (singular and non-singular) del Pezzo surfaces. To illustrate some of the techniques available, an upper bound of the expected order of magnitude is established for a singular del Pezzo surface of degree four.}, author = {Browning, Timothy D}, booktitle = {A Tribute to Gauss and Dirichlet}, pages = {39--56}, publisher = {American Mathematical Society}, title = {{An overview of Manin's conjecture for del Pezzo surfaces}}, volume = {7}, year = {2007}, } @article{1035, abstract = {We explore the rich internal structure of Cs2 Feshbach molecules. Pure ultracold molecular samples are prepared in a CO2 -laser trap, and a multitude of weakly bound states is populated by elaborate magnetic-field ramping techniques. Our methods use different Feshbach resonances as input ports and various internal level crossings for controlled state transfer. We populate higher partial-wave states of up to eight units of rotational angular momentum (l -wave states). We investigate the molecular structure by measurements of the magnetic moments for various states. Avoided level crossings between different molecular states are characterized through the changes in magnetic moment and by a Landau-Zener tunneling method. Based on microwave spectroscopy, we present a precise measurement of the magnetic-field-dependent binding energy of the weakly bound s -wave state that is responsible for the large background scattering length of Cs. This state is of particular interest because of its quantum-halo character.}, author = {Mark, Michael and Ferlaino, Francesca and Knoop, Steven and Danzl, Johann G and Kraemer, Tobias and Chin, Cheng and Nägerl, Hanns and Grimm, Rudolf}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {4}, publisher = {American Physical Society}, title = {{Spectroscopy of ultracold trapped cesium Feshbach molecules}}, doi = {10.1103/PhysRevA.76.042514}, volume = {76}, year = {2007}, } @article{9487, abstract = {Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals. In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic background. However, the extent and function of demethylation by DEMETER-LIKE (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA hypermethylation. Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist. Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the overall distribution of WT DNA methylation. Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation.}, author = {Penterman, Jon and Zilberman, Daniel and Huh, Jin Hoe and Ballinger, Tracy and Henikoff, Steven and Fischer, Robert L.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {16}, pages = {6752--6757}, publisher = {National Academy of Sciences}, title = {{DNA demethylation in the Arabidopsis genome}}, doi = {10.1073/pnas.0701861104}, volume = {104}, year = {2007}, } @article{9524, abstract = {Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA methylation has an important role in many aspects of biology, including development and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies. Combining these techniques with DNA microarrays and high-throughput sequencing has made the mapping of DNA methylation feasible on a genome-wide scale. Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests.}, author = {Zilberman, Daniel and Henikoff, Steven}, issn = {1477-9129}, journal = {Development}, number = {22}, pages = {3959--3965}, publisher = {The Company of Biologists}, title = {{Genome-wide analysis of DNA methylation patterns}}, doi = {10.1242/dev.001131}, volume = {134}, year = {2007}, } @article{3411, abstract = {Mechanical single-molecule techniques offer exciting possibilities to investigate protein folding and stability in native environments at submolecular resolution. By applying a free-energy reconstruction procedure developed by Hummer and Szabo, which is based on a statistical theorem introduced by Jarzynski, we determined the unfolding free energy of the membrane proteins bacteriorhodopsin (BR), halorhodopsin, and the sodium-proton antiporter NhaA. The calculated energies ranged from 290.5kcal/mol for BR to 485.5kcal/mol for NhaA. For the remarkably stable BR, the equilibrium unfolding free energy was independent of pulling rate and temperature ranging between 18 and 42°C. Our experiments also revealed heterogeneous energetic properties in individual transmembrane helices. In halorhodopsin, the stabilization of a short helical segment yielded a characteristic signature in the energy profile. In NhaA, a pronounced peak was observed at a functionally important site in the protein. Since a large variety of single- and multispan membrane proteins can be tackled in mechanical unfolding experiments, our approach provides a basis for systematically elucidating energetic properties of membrane proteins with the resolution of individual secondary-structure elements.}, author = {Preiner, Johannes and Harald Janovjak and Rankl, Christian and Knaus, Helene and Cisneros, David A and Kedrov, Alexej and Kienberger, Ferry and Mueller, Daniel J and Hinterdorfer, Peter}, journal = {Biophysical Journal}, number = {3}, pages = {930 -- 937}, publisher = {Biophysical Society}, title = {{Free energy of membrane protein unfolding derived from single-molecule force measurements}}, doi = {10.1529/biophysj.106.096982}, volume = {93}, year = {2007}, } @article{3427, abstract = {We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case of transcytosis where morphogens undergo repeated rounds of internalization into cells and recycling. Based on a description on the cellular scale, we derive effective nonlinear transport equations in one and two dimensions which are valid on larger scales. We derive analytic expressions for the concentration dependence of the effective diffusion coefficient and the effective degradation rate. We discuss the effects of a directional bias on morphogen transport and those of the coupling of the morphogen and receptor kinetics. Furthermore, we discuss general properties of cellular transport processes such as the robustness of gradients and relate our results to recent experiments on the morphogen Decapentaplegic (Dpp) that acts in the wing disk of the fruit fly Drosophila. © 2007 The American Physical Society}, author = {Bollenbach, Mark Tobias and Kruse, Karsten and Pantazis, Periklis and Gonzalez Gaitan, Marcos and Julicher, Frank}, journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics}, number = {1}, publisher = {American Institute of Physics}, title = {{Morphogen transport in epithelia}}, doi = {10.1103/PhysRevE.75.011901}, volume = {75}, year = {2007}, } @inproceedings{3561, abstract = {The main result of this paper is an extension of de Silva's Weak Delaunay Theorem to smoothly embedded curves and surfaces in Euclidean space. Assuming a sufficiently fine sampling, we prove that i + 1 points in the sample span an i-simplex in the restricted Delaunay triangulation iff every subset of the i + 1 points has a weak witness.}, author = {Attali, Dominique and Herbert Edelsbrunner and Mileyko, Yuriy}, pages = {143 -- 150}, publisher = {ACM}, title = {{Weak witnesses for Delaunay triangulations of submanifolds}}, doi = {10.1145/1236246.1236267}, year = {2007}, }