@article{1039,
abstract = {Molecular cooling techniques face the hurdle of dissipating translational as well as internal energy in the presence of a rich electronic, vibrational, and rotational energy spectrum. In our experiment, we create a translationally ultracold, dense quantum gas of molecules bound by more than 1000 wave numbers in the electronic ground state. Specifically, we stimulate with 80% efficiency, a two-photon transfer of molecules associated on a Feshbach resonance from a Bose-Einstein condensate of cesium atoms. In the process, the initial loose, long-range electrostatic bond of the Feshbach molecule is coherently transformed into a tight chemical bond. We demonstrate coherence of the transfer in a Ramsey-type experiment and show that the molecular sample is not heated during the transfer. Our results show that the preparation of a quantum gas of molecules in specific rovibrational states is possible and that the creation of a Bose-Einstein condensate of molecules in their rovibronic ground state is within reach.},
author = {Danzl, Johann G and Haller, Elmar and Gustavsson, Mattias and Mark, Manfred and Hart, Russell and Bouloufa, Nadia and Dulieu, Olivier and Ritsch, Helmut and Nägerl, Hanns},
journal = {Science},
number = {5892},
pages = {1062 -- 1066},
publisher = {American Association for the Advancement of Science},
title = {{Quantum gas of deeply bound ground state molecules}},
doi = {10.1126/science.1159909},
volume = {321},
year = {2008},
}
@article{965,
abstract = {We give many examples of applying Bogoliubov's forest formula to iterative solutions of various nonlinear equations. The same formula describes an extremely wide class of objects, from an ordinary quadratic equation to renormalization in quantum field theory.},
author = {Morozov, Alexei Y and Maksym Serbyn},
journal = {Theoretical and Mathematical Physics},
number = {2},
pages = {270 -- 293},
publisher = {Elsevier},
title = {{Nonlinear algebra and Bogoliubov's recursion}},
doi = {10.1007/s11232-008-0026-7},
volume = {154},
year = {2008},
}
@article{3734,
abstract = {Gene expression levels fluctuate even under constant external conditions. Much emphasis has usually been placed on the components of this noise that are due to randomness in transcription and translation. Here we focus on the role of noise associated with the inputs to transcriptional regulation; in particular, we analyze the effects of random arrival times and binding of transcription factors to their target sites along the genome. This contribution to the total noise sets a fundamental physical limit to the reliability of genetic control, and has clear signatures, but we show that these are easily obscured by experimental limitations and even by conventional methods for plotting the variance vs. mean expression level. We argue that simple, universal models of noise dominated by transcription and translation are inconsistent with the embedding of gene expression in a network of regulatory interactions. Analysis of recent experiments on transcriptional control in the early Drosophila embryo shows that these results are quantitatively consistent with the predicted signatures of input noise, and we discuss the experiments needed to test the importance of input noise more generally.},
author = {Gasper Tkacik and Gregor, Thomas and Bialek, William S},
journal = {PLoS One},
number = {7},
publisher = {Public Library of Science},
title = {{The role of input noise in transcriptional regulation}},
doi = {10.1371/journal.pone.0002774},
volume = {3},
year = {2008},
}
@article{3740,
abstract = {In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be possible to transmit much more than just one regulatory bit. Realizing this optimal information capacity would require that the dynamic range of TF concentrations used by the cell, the input/output relation of the regulatory module, and the noise in gene expression satisfy certain matching relations, which we derive. These results provide parameter-free, quantitative predictions connecting independently measurable quantities. Although we have considered only the simplified problem of a single gene responding to a single TF, we find that these predictions are in surprisingly good agreement with recent experiments on the Bicoid/Hunchback system in the early Drosophila embryo and that this system achieves approximately 90% of its theoretical maximum information transmission.},
author = {Gasper Tkacik and Callan,Curtis G and Bialek, William S},
journal = {PNAS},
number = {34},
pages = {12265 -- 12270},
publisher = {National Academy of Sciences},
title = {{Information flow and optimization in transcriptional regulation}},
doi = {10.1073/pnas.0806077105},
volume = {105},
year = {2008},
}
@article{3744,
abstract = {It is widely acknowledged that detailed timing of action potentials is used to encode information, for example, in auditory pathways; however, the computational tools required to analyze encoding through timing are still in their infancy. We present a simple example of encoding, based on a recent model of time-frequency analysis, in which units fire action potentials when a certain condition is met, but the timing of the action potential depends also on other features of the stimulus. We show that, as a result, spike-triggered averages are smoothed so much that they do not represent the true features of the encoding. Inspired by this example, we present a simple method, differential reverse correlations, that can separate an analysis of what causes a neuron to spike, and what controls its timing. We analyze with this method the leaky integrate-and-fire neuron and show the method accurately reconstructs the model's kernel.},
author = {Gasper Tkacik and Magnasco, Marcelo O},
journal = {Biosystems},
number = {1-2},
pages = {90 -- 100},
publisher = {Elsevier},
title = {{Decoding spike timing: The differential reverse-correlation method}},
doi = {10.1016/j.biosystems.2008.04.011},
volume = {93},
year = {2008},
}
@article{3751,
abstract = {Revealing the spectrum of combinatorial regulation of transcription at individual promoters is essential for understanding the complex structure of biological networks. However, the computations represented by the integration of various molecular signals at complex promoters are difficult to decipher in the absence of simple cis regulatory codes. Here we synthetically shuffle the regulatory architecture-operator sequences binding activators and repressors-of a canonical bacterial promoter. The resulting library of complex promoters allows for rapid exploration of promoter encoded logic regulation. Among all possible logic functions, NOR and ANDN promoter encoded logics predominate. A simple transcriptional cis regulatory code determines both logics, establishing a straightforward map between promoter structure and logic phenotype. The regulatory code is determined solely by the type of transcriptional regulation combinations: two repressors generate a NOR: NOT (a OR b) whereas a repressor and an activator generate an ANDN: a AND NOT b. Three-input versions of both logics, having an additional repressor as an input, are also present in the library. The resulting complex promoters cover a wide dynamic range of transcriptional strengths. Synthetic promoter shuffling represents a fast and efficient method for exploring the spectrum of complex regulatory functions that can be encoded by complex promoters. From an engineering point of view, synthetic promoter shuffling enables the experimental testing of the functional properties of complex promoters that cannot necessarily be inferred ab initio from the known properties of the individual genetic components. Synthetic promoter shuffling may provide a useful experimental tool for studying naturally occurring promoter shuffling.},
author = {Kinkhabwala, Ali and Guet, Calin C},
journal = {PLoS One},
number = {4},
publisher = {Public Library of Science},
title = {{Uncovering cis regulatory codes using synthetic promoter shuffling}},
doi = {10.1371/journal.pone.0002030},
volume = {3},
year = {2008},
}
@article{3822,
abstract = {Dentate gyrus granule cells transmit action potentials (APs) along their unmyelinated mossy fibre axons to the CA3 region. Although the initiation and propagation of APs are fundamental steps during neural computation, little is known about the site of AP initiation and the speed of propagation in mossy fibre axons. To address these questions, we performed simultaneous somatic and axonal whole-cell recordings from granule cells in acute hippocampal slices of adult mice at approximately 23 degrees C. Injection of short current pulses or synaptic stimulation evoked axonal and somatic APs with similar amplitudes. By contrast, the time course was significantly different, as axonal APs had a higher maximal rate of rise (464 +/- 30 V s(-1) in the axon versus 297 +/- 12 V s(-1) in the soma, mean +/- s.e.m.). Furthermore, analysis of latencies between the axonal and somatic signals showed that APs were initiated in the proximal axon at approximately 20-30 mum distance from the soma, and propagated orthodromically with a velocity of 0.24 m s(-1). Qualitatively similar results were obtained at a recording temperature of approximately 34 degrees C. Modelling of AP propagation in detailed cable models of granule cells suggested that a approximately 4 times higher Na(+) channel density ( approximately 1000 pS mum(-2)) in the axon might account for both the higher rate of rise of axonal APs and the robust AP initiation in the proximal mossy fibre axon. This may be of critical importance to separate dendritic integration of thousands of synaptic inputs from the generation and transmission of a common AP output.},
author = {Schmidt-Hieber, Christoph and Peter Jonas and Bischofberger, Josef},
journal = {Journal of Physiology},
number = {7},
pages = {1849 -- 57},
publisher = {Wiley-Blackwell},
title = {{Action potential initiation and propagation in hippocampal mossy fibre axons}},
doi = {10.1113/jphysiol.2007.150151 },
volume = {586},
year = {2008},
}
@article{3825,
abstract = {Fast-spiking parvalbumin-expressing basket cells (BCs) represent a major type of inhibitory interneuron in the hippocampus. These cells inhibit principal cells in a temporally precise manner and are involved in the generation of network oscillations. Although BCs show a unique expression profile of Ca(2+)-permeable receptors, Ca(2+)-binding proteins and Ca(2+)-dependent signalling molecules, physiological Ca(2+) signalling in these interneurons has not been investigated. To study action potential (AP)-induced dendritic Ca(2+) influx and buffering, we combined whole-cell patch-clamp recordings with ratiometric Ca(2+) imaging from the proximal apical dendrites of rigorously identified BCs in acute slices, using the high-affinity Ca(2+) indicator fura-2 or the low-affinity dye fura-FF. Single APs evoked dendritic Ca(2+) transients with small amplitude. Bursts of APs evoked Ca(2+) transients with amplitudes that increased linearly with AP number. Analysis of Ca(2+) transients under steady-state conditions with different fura-2 concentrations and during loading with 200 microm fura-2 indicated that the endogenous Ca(2+)-binding ratio was approximately 200 (kappa(S) = 202 +/- 26 for the loading experiments). The peak amplitude of the Ca(2+) transients measured directly with 100 microm fura-FF was 39 nm AP(-1). At approximately 23 degrees C, the decay time constant of the Ca(2+) transients was 390 ms, corresponding to an extrusion rate of approximately 600 s(-1). At 34 degrees C, the decay time constant was 203 ms and the corresponding extrusion rate was approximately 1100 s(-1). At both temperatures, continuous theta-burst activity with three to five APs per theta cycle, as occurs in vivo during exploration, led to a moderate increase in the global Ca(2+) concentration that was proportional to AP number, whereas more intense stimulation was required to reach micromolar Ca(2+) concentrations and to shift Ca(2+) signalling into a non-linear regime. In conclusion, dentate gyrus BCs show a high endogenous Ca(2+)-binding ratio, a small AP-induced dendritic Ca(2+) influx, and a relatively slow Ca(2+) extrusion. These specific buffering properties of BCs will sharpen the time course of local Ca(2+) signals, while prolonging the decay of global Ca(2+) signals.},
author = {Aponte, Yexica and Bischofberger, Josef and Peter Jonas},
journal = {Journal of Physiology},
number = {8},
pages = {2061 -- 75},
publisher = {Wiley-Blackwell},
title = {{Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus}},
doi = {10.1113/jphysiol.2007.147298},
volume = {586},
year = {2008},
}
@inproceedings{3878,
abstract = {We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing “reset” action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies.},
author = {Krishnendu Chatterjee and de Alfaro, Luca and Majumdar, Ritankar S},
pages = {91 -- 106},
publisher = {Springer},
title = {{The complexity of coverage}},
doi = {10.1007/978-3-540-89330-1_7},
volume = {5356},
year = {2008},
}
@inproceedings{4384,
abstract = {Model checking software transactional memories (STMs) is difficult because of the unbounded number, length, and delay of concurrent transactions and the unbounded size of the memory. We show that, under certain conditions, the verification problem can be reduced to a finite-state problem, and we illustrate the use of the method by proving the correctness of several STMs, including two-phase locking, DSTM, TL2, and optimistic concurrency control. The safety properties we consider include strict serializability and opacity; the liveness properties include obstruction freedom, livelock freedom, and wait freedom.
Our main contribution lies in the structure of the proofs, which are largely automated and not restricted to the STMs mentioned above. In a first step we show that every STM that enjoys certain structural properties either violates a safety or liveness requirement on some program with two threads and two shared variables, or satisfies the requirement on all programs. In the second step we use a model checker to prove the requirement for the STM applied to a most general program with two threads and two variables. In the safety case, the model checker constructs a simulation relation between two carefully constructed finite-state transition systems, one representing the given STM applied to a most general program, and the other representing a most liberal safe STM applied to the same program. In the liveness case, the model checker analyzes fairness conditions on the given STM transition system.},
author = {Guerraoui, Rachid and Thomas Henzinger and Jobstmann, Barbara and Vasu Singh},
pages = {372 -- 382},
publisher = {ACM},
title = {{Model checking transactional memories}},
doi = {10.1145/1375581.1375626},
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{3435,
abstract = {We develop a new method for estimating effective population sizes, Ne, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is ~0.43.},
author = {Jonathan Bollback and York, Thomas L and Nielsen, Rasmus},
journal = {Genetics},
number = {1},
pages = {497 -- 502},
publisher = {Genetics Society of America},
title = {{Estimation of 2Nes From Temporal Allele Frequency Data}},
doi = {10.1534/genetics.107.085019},
volume = {179},
year = {2008},
}
@inproceedings{3504,
abstract = {Simulation and bisimulation metrics for stochastic systems provide a quantitative gen- eralization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative μ-calculus and related probabilistic logics.
We present algorithms for computing the metrics on Markov decision processes (MDPs), turn- based stochastic games, and concurrent games. For turn-based games and MDPs, we provide a polynomial-time algorithm based on linear programming for the computation of the one-step metric distance between states. The algorithm improves on the previously known exponential-time algo- rithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known bound for Markov chains. For the bisimulation kernel of the metric, which corresponds to probabilistic bisimulation, our algorithm works in time O(n4) for both turn-based games and MDPs; improving the previously best known O(n9 · log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance between states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be accomplished via a reduction to the theory of real closed fields, involving a
formula with three quantifier alternations, yielding O(|G|O(|G|5)) time complexity, improving the previously known reduction with O(|G|O(|G|7)) time complexity. These algorithms can be iterated
to approximate the metrics using binary search.},
author = {Chatterjee, Krishnendu and De Alfaro, Luca and Majumdar, Ritankar and Raman, Vishwanath},
pages = {107 -- 118},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Algorithms for game metrics}},
doi = {10.4230/LIPIcs.FSTTCS.2008.1745},
volume = {2},
year = {2008},
}
@article{9457,
abstract = {Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation.},
author = {ZILBERMAN, Daniel and Coleman-Derr, Devin and Ballinger, Tracy and Henikoff, Steven},
issn = {1476-4687},
journal = {Nature},
keywords = {Multidisciplinary},
number = {7218},
pages = {125--129},
publisher = {Springer Nature},
title = {{Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks}},
doi = {10.1038/nature07324},
volume = {456},
year = {2008},
}
@article{2367,
abstract = {It was recently shown by Hansen that the Wigner-Yanase entropy is, for general states of quantum systems, not subadditive with respect to decomposition into two subsystems, although this property is known to hold for pure states. We investigate the question whether the weaker property of subadditivity for pure states with respect to decomposition into more than two subsystems holds. This property would have interesting applications in quantum chemistry. We show, however, that it does not hold in general, and provide a counterexample.},
author = {Robert Seiringer},
journal = {Letters in Mathematical Physics},
number = {3},
pages = {285 -- 288},
publisher = {Springer},
title = {{On the failure of subadditivity of the Wigner-Yanase entropy}},
doi = {10.1007/s11005-007-0159-x},
volume = {80},
year = {2007},
}
@article{2370,
abstract = {After recalling briefly the connection between spontaneous symmetry breaking and off-diagonal long-range order for models of magnets a general proof of spontaneous breaking of gauge symmetry as a consequence of Bose-Einstein condensation is presented. The proof is based on a rigorous validation of Bogoliubov's c-number substitution for the k = 0 mode operator α0.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Reports on Mathematical Physics},
number = {3},
pages = {389 -- 399},
publisher = {Elsevier},
title = {{Bose-Einstein condensation and spontaneous symmetry breaking}},
doi = {10.1016/S0034-4877(07)80074-7},
volume = {59},
year = {2007},
}
@article{2371,
abstract = {We give a proof of stability of relativistic matter with magnetic fields all the way up to the critical value of the nuclear charge Zα = 2/π.},
author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {479 -- 489},
publisher = {Springer},
title = {{Stability of relativistic matter with magnetic fields for nuclear charges up to the critical value}},
doi = {10.1007/s00220-007-0307-2},
volume = {275},
year = {2007},
}
@article{2372,
abstract = {The increasing interest in the Müller density-matrix-functional theory has led us to a systematic mathematical investigation of its properties. This functional is similar to the Hartree-Fock (HF) functional, but with a modified exchange term in which the square of the density matrix γ(x, x′) is replaced by the square of γ1 2 (x, x′). After an extensive introductory discussion of density-matrix-functional theory we show, among other things, that this functional is convex (unlike the HF functional) and that energy minimizing γ 's have unique densities ρ(r), which is a physically desirable property often absent in HF theory. We show that minimizers exist if N≤Z, and derive various properties of the minimal energy and the corresponding minimizers. We also give a precise statement about the equation for the orbitals of γ, which is more complex than for HF theory. We state some open mathematical questions about the theory together with conjectured solutions.},
author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer and Siedentop, Heinz K},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {5},
publisher = {American Physical Society},
title = {{Müller's exchange-correlation energy in density-matrix-functional theory}},
doi = {10.1103/PhysRevA.76.052517},
volume = {76},
year = {2007},
}
@article{2373,
abstract = {For the BCS equation with local two-body interaction λV(x), we give a rigorous analysis of the asymptotic behavior of the critical temperature as γ"0. We derive necessary and sufficient conditions onV(x) for the existence of a nontrivial solution for all values of γ>0.},
author = {Frank, Rupert L and Hainzl, Christian and Naboko, Serguei N and Robert Seiringer},
journal = {Journal of Geometric Analysis},
number = {4},
pages = {559 -- 567},
publisher = {Springer},
title = {{The critical temperature for the BCS equation at weak coupling}},
doi = {10.1007/BF02937429},
volume = {17},
year = {2007},
}
@article{2375,
abstract = {We give a Cwikel-Lieb-Rozenblum type bound on the number of bound states of Schrödinger operators with matrix-valued potentials using the functional integral method of Lieb. This significantly improves the constant in this inequality obtained earlier by Hundertmark.},
author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer},
journal = {Letters in Mathematical Physics},
number = {2-3},
pages = {107 -- 116},
publisher = {Springer},
title = {{Number of bound states of Schrödinger operators with matrix-valued potentials}},
doi = {10.1007/s11005-007-0211-x},
volume = {82},
year = {2007},
}
@inbook{2705,
author = {László Erdös},
booktitle = {Spectral Theory and Mathematical Physics: a Festschrift in Honor of Barry Simon's 60th Birthday },
editor = {Gesztesy, Fritz and Deift, Percy and Galvez, Percy and Perry, Peter and Schlag, Wilhelm},
pages = {401 -- 428},
publisher = {American Mathematical Society},
title = {{Recent developments in quantum mechanics with magnetic fields}},
volume = {76},
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},
}
@inproceedings{2091,
abstract = {We present a novel multi-scale representation and acquisition method for the animation of high-resolution facial geometry and wrinkles. We first acquire a static scan of the face including reflectance data at the highest possible quality. We then augment a traditional marker-based facial motion-capture system by two synchronized video cameras to track expression wrinkles. The resulting model consists of high-resolution geometry, motion-capture data, and expression wrinkles in 2D parametric form. This combination represents the facial shape and its salient features at multiple scales. During motion synthesis the motion-capture data deforms the high-resolution geometry using a linear shell-based mesh-deformation method. The wrinkle geometry is added to the facial base mesh using nonlinear energy optimization. We present the results of our approach for performance replay as well as for wrinkle editing. },
author = {Bernd Bickel and Botsch, Mario and Angst, Roland and Matusik, Wojciech and Otaduy, Miguel A and Pfister, Hanspeter and Groß, Markus S},
publisher = {ACM},
title = {{Multi scale capture of facial geometry and motion}},
doi = {doi:10.1145/1275808.1276419},
year = {2007},
}
@article{2093,
abstract = {We present a novel multi-scale representation and acquisition method for the animation of high-resolution facial geometry and wrinkles. We first acquire a static scan of the face including reflectance data at the highest possible quality. We then augment a traditional marker-based facial motion-capture system by two synchronized video cameras to track expression wrinkles. The resulting model consists of high-resolution geometry, motion-capture data, and expression wrinkles in 2D parametric form. This combination represents the facial shape and its salient features at multiple scales. During motion synthesis the motion-capture data deforms the high-resolution geometry using a linear shell-based mesh-deformation method. The wrinkle geometry is added to the facial base mesh using nonlinear energy optimization. We present the results of our approach for performance replay as well as for wrinkle editing. },
author = {Bernd Bickel and Botsch, Mario and Angst, Roland and Matusik, Wojciech and Otaduy, Miguel A and Pfister, Hanspeter and Groß, Markus S},
journal = {ACM Transactions on Graphics},
number = {3},
publisher = {ACM},
title = {{Multi scale capture of facial geometry and motion}},
doi = {10.1145/1276377.1276419},
volume = {26},
year = {2007},
}
@article{2118,
abstract = {We extend to infinite dimensions an explicit formula of Chill, Fašangová, Metafune, and Pallara for the optimal angle of analyticity of analytic Ornstein-Uhlenbeck semigroups. The main ingredient is an abstract representation of the Ornstein-Uhlenbeck operator in divergence form. },
author = {Jan Maas and van Neerven, Jan M},
journal = {Archiv der Mathematik},
number = {3},
pages = {226 -- 236},
publisher = {Birkhäuser},
title = {{On analytic Ornstein-Uhlenbeck semigroups in infinite dimensions}},
doi = {10.1007/s00013-007-2082-x},
volume = {89},
year = {2007},
}
@article{221,
author = {De La Bretèche, Régis and Browning, Timothy D},
journal = {Michigan Mathematical Journal},
number = {1},
pages = {51 -- 80},
publisher = {Project Euclid},
title = {{On Manin's conjecture for singular del Pezzo surfaces of degree four, I}},
doi = {10.1307/mmj/1177681985},
volume = {55},
year = {2007},
}
@article{222,
abstract = {Acknowledgements. The authors are grateful to Ulrich Derenthal and Brendan Hassett for several useful conversations relating to universal torsors for singular del Pezzo surfaces. Special thanks are due to Roger Heath–Brown whose ideas led us to the proof of Lemma 6. The paper was finalised while the first author was at the École Normale Supérieure, and the second author was at Oxford University supported by EPSRC grant number GR/R93155/01. The hospitality and financial support of these institutions is gratefully acknowledged. Finally, the authors would like to thank the anonymous referee for his careful reading of the manuscript and numerous useful suggestions.},
author = {de la Bretèche, Régis and Timothy Browning},
journal = {Mathematical Proceedings of the Cambridge Philosophical Society},
number = {3},
pages = {579 -- 605},
publisher = {Unknown},
title = {{On Manin's conjecture for singular del Pezzo surfaces of degree four, II}},
doi = {10.1017/S0305004107000205},
volume = {143},
year = {2007},
}
@article{223,
abstract = {Let Q be a non-singular diagonal quadratic form in at least four variables. We provide upper bounds for the number of integer solutions to the equation Q = 0, which lie in a box with sides of length 2B, as B → ∞. The estimates obtained are completely uniform in the coefficients of the form, and become sharper as they grow larger in modulus.},
author = {Timothy Browning},
journal = {Monatshefte fur Mathematik},
number = {1},
pages = {13 -- 38},
publisher = {Springer},
title = {{Density of integer solutions to diagonal quadratic forms}},
doi = {10.1007/s00605-007-0457-5},
volume = {152},
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},
}
@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{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},
}
@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{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{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},
}
@unpublished{3742,
abstract = {Recent work has shown that probabilistic models based on pairwise interactions-in the simplest case, the Ising model-provide surprisingly accurate descriptions of experiments on real biological networks ranging from neurons to genes. Finding these models requires us to solve an inverse problem: given experimentally measured expectation values, what are the parameters of the underlying Hamiltonian? This problem sits at the intersection of statistical physics and machine learning, and we suggest that more efficient solutions are possible by merging ideas from the two fields. We use a combination of recent coordinate descent algorithms with an adaptation of the histogram Monte Carlo method, and implement these techniques to take advantage of the sparseness found in data on real neurons. The resulting algorithm learns the parameters of an Ising model describing a network of forty neurons within a few minutes. This opens the possibility of analyzing much larger data sets now emerging, and thus testing hypotheses about the collective behaviors of these networks.},
author = {Broderick,Tamara and Dudik,Miroslav and Gasper Tkacik and Schapire,Robert E and Bialek, William S},
booktitle = {ArXiv},
publisher = {ArXiv},
title = {{Faster solutions of the inverse pairwise Ising problem}},
volume = {q-bio.QM},
year = {2007},
}
@article{4234,
abstract = {We study a generalised model of population growth in which the state variable is population growth rate instead of population size. Stochastic parametric perturbations, modelling phenotypic variability, lead to a Langevin system with two sources of multiplicative noise. The stationary probability distributions have two characteristic power-law scales. Numerical simulations show that noise suppresses the explosion of the growth rate which occurs in the deterministic counterpart. Instead, in different parameter regimes populations will grow with "anomalous" stochastic rates and (i) stabilise at "random carrying capacities", or (ii) go extinct in random times. Using logistic fits to reconstruct the simulated data, we find that even highly significant estimations do not recover or reflect information about the deterministic part of the process. Therefore, the logistic interpretation is not biologically meaningful. These results have implications for distinct model-aided calculations in biological situations because these kinds of estimations could lead to spurious conclusions. (c) 2006 Elsevier B.V. All rights reserved.},
author = {de Vladar, Harold and Pen, I.},
journal = {Physica A},
pages = {477 -- 485},
publisher = {Elsevier},
title = {{Determinism, noise, and spurious estimations in a generalised model of population growth}},
doi = {10.1016/j.physa.2006.06.025},
volume = {373},
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},
}
@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{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},
}
@inproceedings{2333,
author = {Lieb, Élliott H and Robert Seiringer and Solovej, Jan P},
pages = {239 -- 248},
publisher = {American Mathematical Society},
title = {{Ground-state energy of a dilute Fermi gas}},
doi = {10.1090/conm/412},
volume = {412},
year = {2006},
}
@inproceedings{2334,
author = {Robert Seiringer and Lieb, Élliott H and Yngvason, Jakob},
editor = {Zambrini, Jean-Claude},
publisher = {World Scientific Publishing},
title = {{One-dimensional behavior of dilute, trapped Bose gases in traps}},
doi = {10.1007/s00220-003-0993-3},
year = {2006},
}
@misc{2363,
abstract = { We prove that the Gross-Pitaevskii equation correctly describes the ground state energy and corresponding one-particle density matrix of rotating, dilute, trapped Bose gases with repulsive two-body interactions. We also show that there is 100% Bose-Einstein condensation. While a proof that the GP equation correctly describes non-rotating or slowly rotating gases was known for some time, the rapidly rotating case was unclear because the Bose (i.e., symmetric) ground state is not the lowest eigenstate of the Hamiltonian in this case. We have been able to overcome this difficulty with the aid of coherent states. Our proof also conceptually simplifies the previous proof for the slowly rotating case. In the case of axially symmetric traps, our results show that the appearance of quantized vortices causes spontaneous symmetry breaking in the ground state. },
author = {Lieb, Élliott H and Robert Seiringer},
booktitle = {Communications in Mathematical Physics},
number = {2},
pages = {505 -- 537},
publisher = {Springer},
title = {{Derivation of the Gross-Pitaevskii equation for rotating Bose gases}},
doi = {10.1007/s00220-006-1524-9},
volume = {264},
year = {2006},
}
@article{2364,
abstract = {We present an inequality that gives a lower bound on the expectation value of certain two-body interaction potentials in a general state on Fock space in terms of the corresponding expectation value for thermal equilibrium states of non-interacting systems and the difference in the free energy. This bound can be viewed as a rigorous version of first-order perturbation theory for many-body systems at positive temperature. As an application, we give a proof of the first two terms in a high density (and high temperature) expansion of the free energy of jellium with Coulomb interactions, both in the fermionic and bosonic case. For bosons, our method works above the transition temperature (for the non-interacting gas) for Bose-Einstein condensation.},
author = {Robert Seiringer},
journal = {Reviews in Mathematical Physics},
number = {3},
pages = {233 -- 253},
publisher = {World Scientific Publishing},
title = {{A correlation estimate for quantum many-body systems at positive temperature}},
doi = {10.1142/S0129055X06002632},
volume = {18},
year = {2006},
}
@article{2365,
abstract = {We consider a gas of fermions with non-zero spin at temperature T and chemical potential μ. We show that if the range of the interparticle interaction is small compared to the mean particle distance, the thermodynamic pressure differs to leading order from the corresponding expression for non-interacting particles by a term proportional to the scattering length of the interparticle interaction. This is true for any repulsive interaction, including hard cores. The result is uniform in the temperature as long as T is of the same order as the Fermi temperature, or smaller.},
author = {Robert Seiringer},
journal = {Communications in Mathematical Physics},
number = {3},
pages = {729 -- 757},
publisher = {Springer},
title = {{The thermodynamic pressure of a dilute fermi gas}},
doi = {10.1007/s00220-005-1433-3},
volume = {261},
year = {2006},
}
@article{2366,
abstract = {Inequalities are derived for power sums of the real part and the modulus of the eigenvalues of a Schrödinger operator with a complex-valued potential.},
author = {Frank, Rupert L and Laptev, Ari and Lieb, Élliott H and Robert Seiringer},
journal = {Letters in Mathematical Physics},
number = {3},
pages = {309 -- 316},
publisher = {Springer},
title = {{Lieb-Thirring inequalities for Schrödinger operators with complex-valued potentials}},
doi = {10.1007/s11005-006-0095-1},
volume = {77},
year = {2006},
}
@inbook{2369,
abstract = {One of the most remarkable recent developments in the study of ultracold Bose gases is the observation of a reversible transition from a Bose Einstein condensate to a state composed of localized atoms as the strength of a periodic, optical trapping potential is varied. In [1] a model of this phenomenon has been analyzed rigorously. The gas is a hard core lattice gas and the optical lattice is modeled by a periodic potential of strength λ. For small λ and temperature Bose- Einstein condensation (BEC) is proved to occur, while at large λ BEC disappears, even in the ground state, which is a Mott-insulator state with a characteristic gap. The inter-particle interaction is essential for this effect. This contribution gives a pedagogical survey of these results.},
author = {Aizenman, Michael and Lieb, Élliott H and Robert Seiringer and Solovej, Jan P and Yngvason, Jakob},
booktitle = {Mathematical Physics of Quantum Mechanics},
editor = {Asch, Joachim and Joye, Alain},
pages = {199 -- 215},
publisher = {Springer},
title = {{Bose-Einstein condensation as a quantum phase transition in an optical lattice}},
doi = {10.1007/b11573432},
volume = {690},
year = {2006},
}
@unpublished{573,
abstract = {Mitchison and Jozsa recently suggested that the "chained-Zeno" counterfactual computation protocol recently proposed by Hosten et al. is counterfactual for only one output of the computer. This claim was based on the existing abstract algebraic definition of counterfactual computation, and indeed according to this definition, their argument is correct. However, a more general definition (physically adequate) for counterfactual computation is implicitly assumed by Hosten et. al. Here we explain in detail why the protocol is counterfactual and how the "history tracking" method of the existing description inadequately represents the physics underlying the protocol. Consequently, we propose a modified definition of counterfactual computation. Finally, we comment on one of the most interesting aspects of the error-correcting protocol. },
author = {Hosten, Onur and Rakher, Matthew and Barreiro, Julio and Peters, Nicholas and Kwiat, Paul},
pages = {12},
publisher = {ArXiv},
title = {{Counterfactual computation revisited}},
year = {2006},
}
@unpublished{574,
abstract = {Vaidman, in a recent article adopts the method of 'quantum weak measurements in pre- and postselected ensembles' to ascertain whether or not the chained-Zeno counterfactual computation scheme proposed by Hosten et al. is counterfactual; which has been the topic of a debate on the definition of counterfactuality. We disagree with his conclusion, which brings up some interesting aspects of quantum weak measurements and some concerns about the way they are interpreted. },
author = {Hosten, Onur and Kwiat, Paul},
pages = {2},
publisher = {ArXiv},
title = {{Weak measurements and counterfactual computation}},
year = {2006},
}
@article{6151,
author = {Salecker, Iris and Häusser, Michael and de Bono, Mario},
issn = {1469-221X},
journal = {EMBO reports},
number = {6},
pages = {585--589},
publisher = {Wiley},
title = {{On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits}},
doi = {10.1038/sj.embor.7400713},
volume = {7},
year = {2006},
}
@article{1461,
abstract = {This note proves combinatorially that the intersection pairing on the middle-dimensional compactly supported cohomology of a toric hyperkähler variety is always definite, providing a large number of non-trivial L 2 harmonic forms for toric hyperkähler metrics on these varieties. This is motivated by a result of Hitchin about the definiteness of the pairing of L 2 harmonic forms on complete hyperkähler manifolds of linear growth.},
author = {Tamas Hausel and Swartz, Edward},
journal = {Proceedings of the American Mathematical Society},
number = {8},
pages = {2403 -- 2409},
publisher = {American Mathematical Society},
title = {{Intersection forms of toric hyperkähler varieties}},
doi = {10.1090/S0002-9939-06-08248-7},
volume = {134},
year = {2006},
}
@article{1462,
abstract = {A Fourier transform technique is introduced for counting the number of solutions of holomorphic moment map equations over a finite field. This technique in turn gives information on Betti numbers of holomorphic symplectic quotients. As a consequence, simple unified proofs are obtained for formulas of Poincaré polynomials of toric hyperkähler varieties (recovering results of Bielawski-Dancer and Hausel-Sturmfels), Poincaré polynomials of Hubert schemes of points and twisted Atiyah-Drinfeld-Hitchin-Manin (ADHM) spaces of instantons on ℂ2 (recovering results of Nakajima-Yoshioka), and Poincaré polynomials of all Nakajima quiver varieties. As an application, a proof of a conjecture of Kac on the number of absolutely indecomposable representations of a quiver is announced.},
author = {Tamas Hausel},
journal = {PNAS},
number = {16},
pages = {6120 -- 6124},
publisher = {National Academy of Sciences},
title = {{Betti numbers of holomorphic symplectic quotients via arithmetic Fourier transform}},
doi = {10.1073/pnas.0601337103},
volume = {103},
year = {2006},
}
@article{1033,
abstract = {Systems of three interacting particles are notorious for their complex physical behaviour. A landmark theoretical result in few-body quantum physics is Efimov\'s prediction1,2 of a universal set of bound trimer states appearing for three identical bosons with a resonant two-body interaction. Counterintuitively, these states even exist in the absence of a corresponding two-body bound state. Since the formulation of Efimov\'s problem in the context of nuclear physics 35 years ago, it has attracted great interest in many areas of physics3-8. However, the observation of Efimov quantum states has remained an elusive goal3,5. Here we report the observation of an Efimov resonance in an ultracold gas of caesium atoms. The resonance occurs in the range of large negative two-body scattering lengths, arising from the coupling of three free atoms to an Efimov trimer. Experimentally, we observe its signature as a giant three-body recombination loss9,10 when the strength of the two-body interaction is varied. We also detect a minimum 9,11,12 in the recombination loss for positive scattering lengths, indicating destructive interference of decay pathways. Our results confirm central theoretical predictions of Efimov physics and represent a starting point with which to explore the universal properties of resonantly interacting few-body systems7. While Feshbach resonances13,14 have provided the key to control quantum-mechanical interactions on the two-body level, Efimov resonances connect ultracold matter15 to the world of few-body quantum phenomena.},
author = {Kraemer, Tobias and Mark, Michael and Waldburger, Philipp and Danzl, Johann G and Chin, Cheng and Engeser, Bastian and Lange, Adam and Pilch, Karl and Jaakkola, Antti and Nägerl, Hanns and Grimm, Rudolf},
journal = {Nature},
number = {7082},
pages = {315 -- 318},
publisher = {Nature Publishing Group},
title = {{Evidence for Efimov quantum states in an ultracold gas of caesium atoms}},
doi = {10.1038/nature04626},
volume = {440},
year = {2006},
}
@inproceedings{1034,
abstract = {Three interacting particles form a system which is well known for its complex physical behavior. A landmark theoretical result in few-body quantum physics is Efimov\'s prediction of a universal set of weakly bound trimer states appearing for three identical bosons with a resonant two-body interaction [1, 2]. Surprisingly, these states even exist in the absence of a corresponding two-body bound state and their precise nature is largely independent of the particular type of the two-body interaction potential. Efimov\'s scenario has attracted great interest in many areas of physics; an experimental test however has not been achieved. We report the observation of an Efimov resonance in an ultracold thermal gas of cesium atoms [3]. The resonance occurs in the range of large negative two-body scattering lengths and arises from the coupling of three free atoms to an Efimov trimer. We observe its signature as a giant three-body recombination loss when the strength of the two-body interaction is varied near a Feshbach resonance. This resonance develops into a continuum resonance at non-zero collision energies, and we observe a shift of the resonance position as a function of temperature. We also report on a minimum in the recombination loss for positive scattering lengths, indicating destructive interference of decay pathways. Our results confirm central theoretical predictions of Efimov physics and represent a starting point from which to explore the universal properties of resonantly interacting few-body systems.},
author = {Nägerl, Hanns and Kraemer, Tobias and Mark, Michael and Waldburger, Philipp and Danzl, Johann G and Engeser, Bastian and Lange, Adam and Pilch, Karl and Jaakkola, Antti and Chin, Cheng and Grimm, Rudolf},
pages = {269 -- 277},
publisher = {AIP},
title = {{Experimental evidence for Efimov quantum states}},
doi = {10.1063/1.2400657},
volume = {869},
year = {2006},
}
@article{3755,
abstract = {A primitive example of adaptation in gene expression is the balance between the rate of synthesis and degradation of cellular RNA, which allows rapid responses to environmental signals. Here, we investigate how multidrug efflux pump systems mediate the dynamics of a simple drug-inducible system in response to a steady level of inducer. Using fluorescence correlation spectroscopy, we measured in real time within a single bacterium the transcription activity at the RNA level of the acrAB-TolC multidrug efflux pump system. When cells are exposed to constant level of anhydrotetracycline inducer and are adsorbed onto a poly-L-lysine-coated surface, we found that the acrAB-TolC promoter is steadily active. We also monitored the activity of the tet promoter to characterize the effect of this efflux system on the dynamics of drug-inducible transcription. We found that the transcriptional response of the tet promoter to a steady level of aTc rises and then falls back to its preinduction level. The rate of RNA degradation was constant throughout the transcriptional pulse, indicating that the modulation of intracellular inducer concentration alone can produce this pulsating response. Single-cell experiments together with numerical simulations suggest that such pulsating response in drug-inducible genetic systems is a property emerging from the dependence of drug-inducible transcription on multidrug efflux systems.},
author = {Le,Thuc T. and Emonet,Thierry and Harlepp, Sébastien and Calin Guet and Cluzel,Philippe},
journal = {Biophysical Journal},
number = {9},
pages = {3315 -- 3321},
publisher = {Biophysical Society},
title = {{Dynamical determinants of drug-inducible gene expression in a single bacterium}},
doi = {10.1529/biophysj.105.073353},
volume = {90},
year = {2006},
}
@article{3813,
abstract = {Hyperpolarization-activated channels (Ih or HCN channels) are widely expressed in principal neurons in the central nervous system. However, Ih in inhibitory GABAergic interneurons is less well characterized. We examined the functional properties of Ih in fast-spiking basket cells (BCs) of the dentate gyrus, using hippocampal slices from 17- to 21-day-old rats. Bath application of the Ih channel blocker ZD 7288 at a concentration of 30 microm induced a hyperpolarization of 5.7 +/- 1.5 mV, an increase in input resistance and a correlated increase in apparent membrane time constant. ZD 7288 blocked a hyperpolarization-activated current in a concentration-dependent manner (IC50, 1.4 microm). The effects of ZD 7288 were mimicked by external Cs+. The reversal potential of Ih was -27.4 mV, corresponding to a Na+ to K+ permeability ratio (PNa/PK) of 0.36. The midpoint potential of the activation curve of Ih was -83.9 mV, and the activation time constant at -120 mV was 190 ms. Single-cell expression analysis using reverse transcription followed by quantitative polymerase chain reaction revealed that BCs coexpress HCN1 and HCN2 subunit mRNA, suggesting the formation of heteromeric HCN1/2 channels. ZD 7288 increased the current threshold for evoking antidromic action potentials by extracellular stimulation, consistent with the expression of Ih in BC axons. Finally, ZD 7288 decreased the frequency of miniature inhibitory postsynaptic currents (mIPSCs) in hippocampal granule cells, the main target cells of BCs, to 70 +/- 4% of the control value. In contrast, the amplitude of mIPSCs was unchanged, consistent with the presence of Ih in inhibitory terminals. In conclusion, our results suggest that Ih channels are expressed in the somatodendritic region, axon and presynaptic elements of fast-spiking BCs in the hippocampus.},
author = {Aponte, Yexica and Lien, Cheng-Chang and Reisinger, Ellen and Peter Jonas},
journal = {Journal of Physiology},
number = {Pt 1},
pages = {229 -- 43},
publisher = {Wiley-Blackwell},
title = {{Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus}},
doi = {10.1113/jphysiol.2005.104042},
volume = {574},
year = {2006},
}
@article{4173,
abstract = {Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.},
author = {Link, Vinzenz and Shevchenko, Andrej and Heisenberg, Carl-Philipp J},
journal = {BMC Developmental Biology},
pages = {1 -- 9},
publisher = {BioMed Central},
title = {{Proteomics of early zebrafish embryos}},
doi = {10.1186/1471-213X-6-1},
volume = {6},
year = {2006},
}
@article{3009,
author = {Paciorek, Tomasz and Friml, Jirí},
journal = {Journal of Cell Science},
number = {7},
pages = {1199 -- 1202},
publisher = {Company of Biologists},
title = {{Auxin signaling}},
doi = {10.1242/jcs.02910},
volume = {119},
year = {2006},
}
@unpublished{3431,
abstract = {Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the retina, and show that pairwise interactions account for observed higher-order correlations. By first finding a representative ensemble for observed networks we can create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses.},
author = {Gasper Tkacik and Schneidman, E. and Berry, M. J. and Bialek, William S},
booktitle = {ArXiv},
pages = {1 -- 4},
publisher = {ArXiv},
title = {{Ising models for networks of real neurons}},
year = {2006},
}
@article{3695,
abstract = {We give an analytical and geometrical treatment of what it means to separate a Gaussian kernel along arbitrary axes in Ropfn, and we present a separation scheme that allows us to efficiently implement anisotropic Gaussian convolution filters for data of arbitrary dimensionality. Based on our previous analysis we show that this scheme is optimal with regard to the number of memory accesses and interpolation operations needed. The proposed method relies on nonorthogonal convolution axes and works completely in image space. Thus, it avoids the need for a fast Fourier transform (FFT)-subroutine. Depending on the accuracy and speed requirements, different interpolation schemes and methods to implement the one-dimensional Gaussian (finite impulse response and infinite impulse response) can be integrated. Special emphasis is put on analyzing the performance and accuracy of the new method. In particular, we show that without any special optimization of the source code, it can perform anisotropic Gaussian filtering faster than methods relying on the FFT.},
author = {Christoph Lampert and Wirjadi,Oliver},
journal = {IEEE Transactions on Image Processing (TIP)},
number = {11},
pages = {3501 -- 3513},
publisher = {IEEE},
title = {{An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter}},
doi = { 10.1109/TIP.2006.877501 },
volume = {15},
year = {2006},
}
@book{2335,
abstract = {This book contains a unique survey of the mathematically rigorous results about the quantum-mechanical many-body problem that have been obtained by the authors in the past seven years. It addresses a topic that is not only rich mathematically, using a large variety of techniques in mathematical analysis, but is also one with strong ties to current experiments on ultra-cold Bose gases and Bose-Einstein condensation. The book provides a pedagogical entry into an active area of ongoing research for both graduate students and researchers. It is an outgrowth of a course given by the authors for graduate students and post-doctoral researchers at the Oberwolfach Research Institute in 2004. The book also provides a coherent summary of the field and a reference for mathematicians and physicists active in research on quantum mechanics.},
author = {Lieb, Élliott H and Robert Seiringer and Solovej, Jan P and Yngvason, Jakob},
booktitle = {The mathematics of the Bose gas and its condensation},
publisher = {Birkhäuser},
title = {{The mathematics of the Bose gas and its condensation}},
volume = {34},
year = {2005},
}
@inbook{2336,
abstract = {
Now that the low temperature properties of quantum-mechanical many-body systems (bosons) at low density, ρ, can be examined experimentally it is appropriate to revisit some of the formulas deduced by many authors 4–5 decades ago, and to explore new regimes not treated before. For systems with repulsive (i.e. positive) interaction potentials the experimental low temperature state and the ground state are effectively synonymous — and this fact is used in all modeling. In such cases, the leading term in the energy/particle is 2πħ2 aρ/m where a is the scattering length of the two-body potential. Owing to the delicate and peculiar nature of bosonic correlations (such as the strange N 7/5 law for charged bosons), four decades of research failed to establish this plausible formula rigorously. The only previous lower bound for the energy was found by Dyson in 1957, but it was 14 times too small. The correct asymptotic formula has been obtained by us and this work will be presented. The reason behind the mathematical difficulties will be emphasized. A different formula, postulated as late as 1971 by Schick, holds in two dimensions and this, too, will be shown to be correct. With the aid of the methodology developed to prove the lower bound for the homogeneous gas, several other problems have been successfully addressed. One is the proof by us that the Gross-Pitaevskii equation correctly describes the ground state in the ‘traps’ actually used in the experiments. For this system it is also possible to prove complete Bose condensation and superfluidity as we have shown. On the frontier of experimental developments is the possibility that a dilute gas in an elongated trap will behave like a one-dimensional system; we have proved this mathematically. Another topic is a proof that Foldy’s 1961 theory of a high density Bose gas of charged particles correctly describes its ground state energy; using this we can also prove the N 7/5 formula for the ground state energy of the two-component charged Bose gas proposed by Dyson in 1967. All of this is quite recent work and it is hoped that the mathematical methodology might be useful, ultimately, to solve more complex problems connected with these interesting systems.},
author = {Lieb, Élliott H and Robert Seiringer and Solovej, Jan P and Yngvason, Jakob},
booktitle = {Perspectives in Analysis},
editor = {Benedicks, Michael and Jones, Peter W and Smirnov, Stanislav and Winckler, Björn},
pages = {97 -- 183},
publisher = {Springer},
title = {{The quantum-mechanical many-body problem: The Bose gas}},
doi = {10.1007/3-540-30434-7_9},
volume = {27},
year = {2005},
}
@article{2359,
abstract = {The validity of substituting a c-number z for the k = 0 mode operator a0 is established rigorously in full generality, thereby verifying one aspect of Bogoliubov's 1947 theory. This substitution not only yields the correct value of thermodynamic quantities such as the pressure or ground state energy, but also the value of |z|2 that maximizes the partition function equals the true amount of condensation in the presence of a gauge-symmetry-breaking term. This point had previously been elusive.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Physical Review Letters},
number = {8},
publisher = {American Physical Society},
title = {{Justification of c-number substitutions in bosonic hamiltonians}},
doi = {10.1103/PhysRevLett.94.080401},
volume = {94},
year = {2005},
}
@article{2361,
abstract = {The strong subadditivity of entropy plays a key role in several areas of physics and mathematics. It states that the entropy S[±]=- Tr(Ï±lnÏ±) of a density matrix Ï±123 on the product of three Hilbert spaces satisfies S[Ï±123]- S[Ï±12]≤S[Ï±23]-S[Ï±2]. We strengthen this to S[Ï±123]-S[Ï±12] ≤αnα(S[Ï±23α]-S[Ï±2α]), where the nα are weights and the Ï±23α are partitions of Ï±23. Correspondingly, there is a strengthening of the theorem that the map A|Trexp[L+lnA] is concave. As applications we prove some monotonicity and convexity properties of the Wehrl coherent state entropy and entropy inequalities for quantum gases.},
author = {Lieb, Élliott H and Robert Seiringer},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {6},
publisher = {American Physical Society},
title = {{Stronger subadditivity of entropy}},
doi = {10.1103/PhysRevA.71.062329},
volume = {71},
year = {2005},
}
@article{2362,
abstract = {Recent developments in the physics of low-density trapped gases make it worthwhile to verify old, well-known results that, while plausible, were based on perturbation theory and assumptions about pseudopotentials. We use and extend recently developed techniques to give a rigorous derivation of the asymptotic formula for the ground-state energy of a dilute gas of N fermions interacting with a short-range, positive potential of scattering length a. For spin-12 fermions, this is E∼E0+(22m)2πNa, where E0 is the energy of the noninteracting system and is the density. A similar formula holds in two dimensions (2D), with a replaced by ln(a2). Obviously this 2D energy is not the expectation value of a density-independent pseudopotential.},
author = {Lieb, Élliott H and Robert Seiringer and Solovej, Jan P},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {5},
publisher = {American Physical Society},
title = {{Ground state energy of the low density Fermi gas}},
doi = {10.1103/PhysRevA.71.053605},
volume = {71},
year = {2005},
}
@article{2867,
abstract = {The plant hormone auxin elicits many specific context-dependent developmental responses. Auxin promotes degradation of Aux/IAA proteins that prevent transcription factors of the auxin response factor (ARF) family from regulating auxin-responsive target genes. Aux/IAAs and ARFs are represented by large gene families in Arabidopsis. Here we show that stabilization of BDL/IAA12 or its sister protein IAA13 prevents MP/ARF5-dependent embryonic root formation whereas stabilized SHY2/IAA3 interferes with seedling growth. Although both bdl and shy2-2 proteins inhibited MP/ARF5-dependent reporter gene activation, shy2-2 was much less efficient than bdl to interfere with embryonic root initiation when expressed from the BDL promoter. Similarly, MP was much more efficient than ARF16 in this process. When expressed from the SHY2 promoter, both shy2-2 and bdl inhibited cell elongation and auxin-induced gene expression in the seedling hypocotyl. By contrast, gravitropism and auxin-induced gene expression in the root, which were promoted by functionally redundant NPH4/ARF7 and ARF19 proteins, were inhibited by shy2-2, but not by bdl protein. Our results suggest that auxin signals are converted into specific responses by matching pairs of coexpressed ARF and Aux/IAA proteins.},
author = {Weijers, Dolf and Eva Benková and Jäger, Katja E and Schlereth, Alexandra and Hamann, Thorsten and Kientz, Marika and Wilmoth, Jill C and Reed, Jason W and Jürgens, Gerd},
journal = {EMBO Journal},
number = {10},
pages = {1874 -- 1885},
publisher = {Wiley-Blackwell},
title = {{Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators}},
doi = {10.1038/sj.emboj.7600659},
volume = {24},
year = {2005},
}
@article{8028,
abstract = {Transmission of signals within the brain is essential for cognitive function, but it is not clear how neural circuits support reliable and accurate signal propagation over a sufficiently large dynamic range. Two modes of propagation have been studied: synfire chains, in which synchronous activity travels through feedforward layers of a neuronal network, and the propagation of fluctuations in firing rate across these layers. In both cases, a sufficient amount of noise, which was added to previous models from an external source, had to be included to support stable propagation. Sparse, randomly connected networks of spiking model neurons can generate chaotic patterns of activity. We investigate whether this activity, which is a more realistic noise source, is sufficient to allow for signal transmission. We find that, for rate-coded signals but not for synfire chains, such networks support robust and accurate signal reproduction through up to six layers if appropriate adjustments are made in synaptic strengths. We investigate the factors affecting transmission and show that multiple signals can propagate simultaneously along different pathways. Using this feature, we show how different types of logic gates can arise within the architecture of the random network through the strengthening of specific synapses.},
author = {Vogels, Tim P and Abbott, L. F.},
issn = {0270-6474},
journal = {Journal of Neuroscience},
number = {46},
pages = {10786--10795},
publisher = {Society for Neuroscience},
title = {{Signal propagation and logic gating in networks of integrate-and-fire neurons}},
doi = {10.1523/jneurosci.3508-05.2005},
volume = {25},
year = {2005},
}
@article{212,
abstract = {For any n ≧ 2, let F ∈ ℤ [ x 1, … , xn ] be a form of degree d≧ 2, which produces a geometrically irreducible hypersurface in ℙn–1. This paper is concerned with the number N(F;B) of rational points on F = 0 which have height at most B. For any ε > 0 we establish the estimate N(F; B) = O(B n− 2+ ε ), whenever either n ≦ 5 or the hypersurface is not a union of lines. Here the implied constant depends at most upon d, n and ε.},
author = {Timothy Browning and Heath-Brown, Roger},
journal = {Journal fur die Reine und Angewandte Mathematik},
number = {584},
pages = {83 -- 115},
publisher = {Walter de Gruyter and Co },
title = {{Counting rational points on hypersurfaces}},
doi = {https://doi.org/10.1515/crll.2005.2005.584.83},
year = {2005},
}
@article{214,
abstract = {Given an absolutely irreducible ternary form F, the purpose of this paper is to produce better upper bounds for the number of integer solutions to the equation F=0, that are restricted to lie in very lopsided boxes. As an application of the main result, a new paucity estimate is obtained for equal sums of two like powers.},
author = {Timothy Browning and Heath-Brown, Roger},
journal = {Mathematische Zeitschrift},
number = {2},
pages = {233 -- 247},
publisher = {Unknown},
title = {{Plane curves in boxes and equal sums of two powers}},
doi = {10.1007/s00209-004-0719-z},
volume = {251},
year = {2005},
}
@inbook{1444,
abstract = {The paper surveys the mirror symmetry conjectures of Hausel-Thaddeus and Hausel-Rodriguez-Villegas concerning the equality of certain Hodge numbers of SL(n, ℂ) vs. PGL(n, ℂ) flat connections and character varieties for curves, respectively. Several new results and conjectures and their relations to works of Hitchin, Gothen, Garsia-Haiman and Earl-Kirwan are explained. These use the representation theory of finite groups of Lie-type via the arithmetic of character varieties and lead to an unexpected conjecture for a Hard Lefschetz theorem for their cohomology.},
author = {Tamas Hausel},
booktitle = {Geometric Methods in Algebra and Number Theory},
pages = {193 -- 217},
publisher = {Springer},
title = {{Mirror symmetry and Langlands duality in the non-Abelian Hodge theory of a curve}},
doi = {10.1007/0-8176-4417-2_9},
volume = {235},
year = {2005},
}
@article{1447,
abstract = {Building on a recent paper [8], here we argue that the combinatorics of matroids are intimately related to the geometry and topology of toric hyperkähler varieties. We show that just like toric varieties occupy a central role in Stanley’s proof for the necessity of McMullen’s conjecture (or g-inequalities) about the classification of face vectors of simplicial polytopes, the topology of toric hyperkähler varieties leads to new restrictions on face vectors of matroid complexes. Namely in this paper we will give two proofs that the injectivity part of the Hard Lefschetz theorem survives for toric hyperkähler varieties. We explain how this implies the g-inequalities for rationally representable matroids. We show how the geometrical intuition in the first proof, coupled with results of Chari [3], leads to a proof of the g-inequalities for general matroid complexes, which is a recent result of Swartz [20]. The geometrical idea in the second proof will show that a pure O-sequence should satisfy the g-inequalities, thus showing that our result is in fact a consequence of a long-standing conjecture of Stanley.},
author = {Tamas Hausel},
journal = {Open Mathematics},
number = {1},
pages = {26 -- 38},
publisher = {Central European Science Journals},
title = {{Quaternionic geometry of matroids}},
doi = {10.2478/BF02475653},
volume = {3},
year = {2005},
}
@article{1463,
abstract = {We study an integration theory in circle equivariant cohomology in order to prove a theorem relating the cohomology ring of a hyperkähler quotient to the cohomology ring of the quotient by a maximal abelian subgroup, analogous to a theorem of Martin for symplectic quotients. We discuss applications of this theorem to quiver varieties, and compute as an example the ordinary and equivariant cohomology rings of a hyperpolygon space.},
author = {Tamas Hausel and Proudfoot, Nicholas J},
journal = {Topology},
number = {1},
pages = {231 -- 248},
publisher = {Elsevier},
title = {{Abelianization for hyperkähler quotients}},
doi = {10.1016/j.top.2004.04.002},
volume = {44},
year = {2005},
}
@article{3721,
abstract = {Recent advances in atomic force microscopy allowed globular and membrane proteins to be mechanically unfolded on a single-molecule level. Presented is an extension to the existing force spectroscopy experiments. While unfolding single bacteriorhodopsins from native purple membranes, small oscillation amplitudes (6–9nm) were supplied to the vertical displacement of the cantilever at a frequency of 3kHz. The phase and amplitude response of the cantilever-protein system was converted to reveal the elastic (conservative) and viscous (dissipative) contributions to the unfolding process. The elastic response (stiffness) of the extended parts of the protein were in the range of a few tens pN/nm and could be well described by the derivative of the wormlike chain model. Discrete events in the viscous response coincided with the unfolding of single secondary structure elements and were in the range of 1μNs/m. In addition, these force modulation spectroscopy experiments revealed novel mechanical unfolding intermediates of bacteriorhodopsin. We found that kinks result in a loss of unfolding cooperativity in transmembrane helices. Reconstructing force-distance spectra by the integration of amplitude-distance spectra verified their position, offering a novel approach to detect intermediates during the forced unfolding of single proteins.},
author = {Harald Janovjak and Mueller, Daniel J and Humphris, Andrew D},
journal = {Biophysical Journal},
number = {2},
pages = {1423 -- 1431},
publisher = {Biophysical Society},
title = {{Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins}},
doi = {10.1529/biophysj.104.052746},
volume = {88},
year = {2005},
}
@article{3741,
abstract = {In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here, we reformulate the clustering problem from an information theoretic perspective that avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster "prototype," does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures nonlinear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures.},
author = {Slonim,N. and Atwal,G. and Gasper Tkacik and Bialek, William S},
journal = {PNAS},
number = {51},
pages = {18297 -- 18302},
publisher = {National Academy of Sciences},
title = {{Information-based clustering}},
doi = {10.1073/pnas.0507432102},
volume = {102},
year = {2005},
}
@unpublished{3746,
abstract = {We address the practical problems of estimating the information relations that characterize large networks. Building on methods developed for analysis of the neural code, we show that reliable estimates of mutual information can be obtained with manageable computational effort. The same methods allow estimation of higher order, multi-information terms. These ideas are illustrated by analyses of gene expression, financial markets, and consumer preferences. In each case, information theoretic measures correlate with independent, intuitive measures of the underlying structures in the system.},
author = {Slonim,Noam and Atwal,Gurinder S and Gasper Tkacik and Bialek, William S},
booktitle = {ArXiv},
pages = {1 -- 11},
publisher = {ArXiv},
title = {{Estimating mutual information and multi-information in large networks}},
year = {2005},
}
@article{4252,
abstract = {Empirical studies of quantitative genetic variation have revealed robust patterns that are observed both across traits and across species. However, these patterns have no compelling explanation, and some of the observations even appear to be mutually incompatible. We review and extend a major class of theoretical models, ‘mutation–selection models’, that have been proposed to explain quantitative genetic variation. We also briefly review an alternative class of ‘balancing selection models’. We consider to what extent the models are compatible with the general observations, and argue that a key issue is understanding and modelling pleiotropy. We discuss some},
author = {Johnson, Toby and Nicholas Barton},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
number = {1459},
pages = {1411 -- 1425},
publisher = {Royal Society, The},
title = {{Theoretical models of selection and mutationon quantitative traits}},
doi = {10.1098/rstb.2005.1667},
volume = {360},
year = {2005},
}
@article{3416,
abstract = {In the last decade atomic force microscopy has been used to measure the mechanical stability of single proteins. These force spectroscopy experiments have shown that many water-soluble and membrane proteins unfold via one or more intermediates. Recently, Li and co-workers found a linear correlation between the unfolding force of the native state and the intermediate in fibronectin, which they suggested indicated the presence of a molecular memory or multiple unfolding pathways (1). Here, we apply two independent methods in combination with Monte Carlo simulations to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show that correlation analysis of unfolding forces is very sensitive to errors in force calibration of the instrument. In contrast, a comparison of relative forces provides a robust measure for the stability of unfolding intermediates. The proposed approach detects three energetically different states of α-helices E and D in trimeric BR. These states are not observed for monomeric BR and indicate that substantial information is hidden in forced unfolding experiments of single proteins.},
author = {Harald Janovjak and Sapra, Tanuj K and Mueller, Daniel J},
journal = {Biophysical Journal},
number = {5},
pages = {37 -- 39},
publisher = {Biophysical Society},
title = {{Complex stability of single proteins explored by forced unfolding experiments}},
doi = {10.1529/biophysj.105.059774},
volume = {88},
year = {2005},
}
@article{3426,
abstract = {We discuss the formation of graded morphogen profiles in a cell layer by nonlinear transport phenomena, important for patterning developing organisms. We focus on a process termed transcytosis, where morphogen transport results from the binding of ligands to receptors on the cell surface, incorporation into the cell, and subsequent externalization. Starting from a microscopic model, we derive effective transport equations. We show that, in contrast to morphogen transport by extracellular diffusion, transcytosis leads to robust ligand profiles which are insensitive to the rate of ligand production.},
author = {Bollenbach, Mark Tobias and Kruse, Karsten and Pantazis, Periklis and González Gaitán, Marcos and Jülicher, Frank},
journal = {Physical Review Letters},
number = {1},
publisher = {American Physical Society},
title = {{Robust formation of morphogen gradients}},
doi = {10.1103/PhysRevLett.94.018103},
volume = {94},
year = {2005},
}
@article{9514,
abstract = {Background:
DNA methylation occurs at preferred sites in eukaryotes. In Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. Targeting of cytosine methylation at selected loci has been found to sometimes involve histone H3 methylation and small interfering (si)RNAs. However, the relationship between different cytosine methylation pathways and their preferred targets is not known.
Results:
We used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. We found that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants.
Conclusion:
We conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. Thus, parallel pathways would be needed to maintain silencing of transposable elements.},
author = {Tran, Robert K. and ZILBERMAN, Daniel and de Bustos, Cecilia and Ditt, Renata F. and Henikoff, Jorja G. and Lindroth, Anders M. and Delrow, Jeffrey and Boyle, Tom and Kwong, Samson and Bryson, Terri D. and Jacobsen, Steven E. and Henikoff, Steven},
issn = {1465-6906},
journal = {Genome Biology},
number = {11},
publisher = {Springer Nature},
title = {{Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis}},
doi = {10.1186/gb-2005-6-11-r90},
volume = {6},
year = {2005},
}
@article{9491,
abstract = {Cytosine DNA methylation in vertebrates is widespread, but methylation in plants is found almost exclusively at transposable elements and repetitive DNA [1]. Within regions of methylation, methylcytosines are typically found in CG, CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and asymmetric sites appears to be maintained at each cell cycle by other mechanisms. We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters found at scattered sites throughout the genome. These clusters lack non-CG methylation and are preferentially found in genes, although they are relatively deficient toward the 5′ end. CG methylation clusters are present in lines derived from different accessions and in mutants that eliminate de novo methylation, indicating that CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine is mutagenic, the appearance of CG methylation clusters over evolutionary time predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G trinucleotides within transcribed regions. This is exactly what we find, implying that CG methylation clusters have contributed profoundly to plant gene evolution. We suggest that CG methylation clusters silence cryptic promoters that arise sporadically within transcription units.},
author = {Tran, Robert K. and Henikoff, Jorja G. and ZILBERMAN, Daniel and Ditt, Renata F. and Jacobsen, Steven E. and Henikoff, Steven},
issn = {1879-0445},
journal = {Current Biology},
number = {2},
pages = {154--159},
publisher = {Elsevier},
title = {{DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes}},
doi = {10.1016/j.cub.2005.01.008},
volume = {15},
year = {2005},
}
@article{2355,
abstract = {The BMV conjecture for traces, which states that Tr exp(A - λB) is the Laplace transform of a positive measure, is shown to be equivalent to two other statements: (i) The polynomial λ → Tr(A + λB) p has only non-negative coefficients for all A, B ≥ 0, p ∈ ℕ and (ii) λ → Tr(A + λB)-p is the Laplace transform of a positive measure for A, B ≥ 0, p > 0.},
author = {Lieb, Élliott H and Robert Seiringer},
journal = {Journal of Statistical Physics},
number = {1-2},
pages = {185 -- 190},
publisher = {Springer},
title = {{ Equivalent forms of the Bessis-Moussa-Villani conjecture}},
doi = {10.1023/B:JOSS.0000019811.15510.27},
volume = {115},
year = {2004},
}
@article{2356,
abstract = {Recent experimental and theoretical work has shown that there are conditions in which a trapped, low-density Bose gas behaves like the one-dimensional delta-function Bose gas solved years ago by Lieb and Liniger. This is an intrinsically quantum-mechanical phenomenon because it is not necessary to have a trap width that is the size of an atom - as might have been supposed - but it suffices merely to have a trap width such that the energy gap for motion in the transverse direction is large compared to the energy associated with the motion along the trap. Up to now the theoretical arguments have been based on variational - perturbative ideas or numerical investigations. In contrast, this paper gives a rigorous proof of the one-dimensional behavior as far as the ground state energy and particle density are concerned. There are four parameters involved: the particle number, N, transverse and longitudinal dimensions of the trap, r and L, and the scattering length a of the interaction potential. Our main result is that if r/L → 0 and N → ∞ the ground state energy and density can be obtained by minimizing a one-dimensional density functional involving the Lieb-Liniger energy density with coupling constant ∼ a/r 2. This density functional simplifies in various limiting cases and we identify five asymptotic parameter regions altogether. Three of these, corresponding to the weak coupling regime, can also be obtained as limits of a three-dimensional Gross-Pitaevskii theory. We also show that Bose-Einstein condensation in the ground state persists in a part of this regime. In the strong coupling regime the longitudinal motion of the particles is strongly correlated. The Gross-Pitaevskii description is not valid in this regime and new mathematical methods come into play.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {347 -- 393},
publisher = {Springer},
title = {{One-dimensional behavior of dilute, trapped Bose gases}},
doi = {10.1007/s00220-003-0993-3},
volume = {244},
year = {2004},
}
@article{2360,
abstract = {An optical lattice model developed that is similar to the Bose-Hubbard model to describe the transition between Bose-Einstein condensation (BEC) and a Mott insulator state was analyzed. It was found that the system was a hard core lattice gas at half of the maximum density and the optical lattice was modeled by a periodic potential of strength λ. It was also observed that the interparticle interaction was essential for this transition that occurred even in the ground state. The results show that all the essential features could be proved rigorously such as the existence of BEC for small λ and its suppression for a large λ.},
author = {Aizenman, Michael and Lieb, Élliott H and Robert Seiringer and Solovej, Jan P and Yngvason, Jakob},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {2},
pages = {023612 -- 1--0236121--2},
publisher = {American Physical Society},
title = {{Bose-Einstein quantum phase transition in an optical lattice model}},
doi = {10.1103/PhysRevA.70.023612},
volume = {70},
year = {2004},
}
@article{1456,
abstract = {We study the space of L2 harmonic forms on complete manifolds with metrics of fibred boundary or fibred cusp type. These metrics generalize the geometric structures at infinity of several different well-known classes of metrics, including asymptotically locally Euclidean manifolds, the (known types of) gravitational instantons, and also Poincaré metrics on ℚ-rank 1 ends of locally symmetric spaces and on the complements of smooth divisors in Kähler manifolds. The answer in all cases is given in terms of intersection cohomology of a stratified compactification of the manifold. The L2 signature formula implied by our result is closely related to the one proved by Dai and more generally by Vaillant and identifies Dai's τ-invariant directly in terms of intersection cohomology of differing perversities. This work is also closely related to a recent paper of Carron and the forthcoming paper of Cheeger and Dai. We apply our results to a number of examples, gravitational instantons among them, arising in predictions about L2 harmonic forms in duality theories in string theory.},
author = {Tamas Hausel and Hunsicker, Eugénie and Mazzeo, Rafe R},
journal = {Duke Mathematical Journal},
number = {3},
pages = {485 -- 548},
publisher = {Duke University Press},
title = {{Hodge cohomology of gravitational instantons}},
doi = {10.1215/S0012-7094-04-12233-X},
volume = {122},
year = {2004},
}
@article{1464,
abstract = {The moduli space of stable vector bundles on a Riemann surface is smooth when the rank and degree are coprime, and is diffeomorphic to the space of unitary connections of central constant curvature. A classic result of Newstead and Atiyah and Bott asserts that its rational cohomology ring is generated by the universal classes, that is, by the Kunneth components of the Chern classes of the universal bundle.
This paper studies the larger, non-compact moduli space of Higgs bundles, as introduced by Hitchin and Simpson, with values in the canonical bundle K. This is diffeomorphic to the space of all connections of central constant curvature, whether unitary or not. The main result of the paper is that, in the rank 2 case, the rational cohomology ring of this space is again generated by universal classes.
The spaces of Higgs bundles with values in K(n) for n > 0 turn out to be essential to the story. Indeed, we show that their direct limit has the homotopy type of the classifying space of the gauge group, and hence has cohomology generated by universal classes. 2000 Mathematics Subject Classification 14H60 (primary), 14D20, 14H81, 32Q55, 58D27 (secondary). },
author = {Tamas Hausel and Thaddeus, Michael},
journal = {Proceedings of the London Mathematical Society},
number = {3},
pages = {632 -- 658},
publisher = {Oxford University Press},
title = {{Generators for the cohomology ring of the moduli space of rank 2 higgs bundles}},
doi = {10.1112/S0024611503014618},
volume = {88},
year = {2004},
}
@article{3807,
abstract = {The time course of Mg(2+) block and unblock of NMDA receptors (NMDARs) determines the extent they are activated by depolarization. Here, we directly measure the rate of NMDAR channel opening in response to depolarizations at different times after brief (1 ms) and sustained (4.6 s) applications of glutamate to nucleated patches from neocortical pyramidal neurons. The kinetics of Mg(2+) unblock were found to be non-instantaneous and complex, consisting of a prominent fast component (time constant approximately 100 micros) and slower components (time constants 4 and approximately 300 ms), the relative amplitudes of which depended on the timing of the depolarizing pulse. Fitting a kinetic model to these data indicated that Mg(2+) not only blocks the NMDAR channel, but reduces both the open probability and affinity for glutamate, while enhancing desensitization. These effects slow the rate of NMDAR channel opening in response to depolarization in a time-dependent manner such that the slower components of Mg(2+) unblock are enhanced during depolarizations at later times after glutamate application. One physiological consequence of this is that brief depolarizations occurring earlier in time after glutamate application are better able to open NMDAR channels. This finding has important implications for spike-timing-dependent synaptic plasticity (STDP), where the precise (millisecond) timing of action potentials relative to synaptic inputs determines the magnitude and sign of changes in synaptic strength. Indeed, we find that STDP timing curves of NMDAR channel activation elicited by realistic dendritic action potential waveforms are narrower than expected assuming instantaneous Mg(2+) unblock, indicating that slow Mg(2+) unblock of NMDAR channels makes the STDP timing window more precise.},
author = {Kampa, Bjorn M and Clements, John and Peter Jonas and Stuart, Greg J},
journal = {Journal of Physiology},
number = {Pt 2},
pages = {337 -- 45},
publisher = {Wiley-Blackwell},
title = {{Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity}},
doi = {10.1113/jphysiol.2003.058842 },
volume = {556},
year = {2004},
}
@article{9517,
abstract = {Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense.},
author = {Xie, Zhixin and Johansen, Lisa K. and Gustafson, Adam M. and Kasschau, Kristin D. and Lellis, Andrew D. and ZILBERMAN, Daniel and Jacobsen, Steven E. and Carrington, James C.},
issn = {1545-7885},
journal = {PLoS Biology},
number = {5},
pages = {0642--0652},
publisher = {Public Library of Science},
title = {{Genetic and functional diversification of small RNA pathways in plants}},
doi = {10.1371/journal.pbio.0020104},
volume = {2},
year = {2004},
}
@article{9511,
abstract = {Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs. DNA and histone methylation are not always sufficient to maintain silencing, and RNA-based reinforcement can be needed to maintain as well as initiate it.},
author = {ZILBERMAN, Daniel and Henikoff, Steven},
issn = {1465-6906},
journal = {Genome Biology},
number = {12},
publisher = {Springer Nature},
title = {{Silencing of transposons in plant genomes: kick them when they're down}},
doi = {10.1186/gb-2004-5-12-249},
volume = {5},
year = {2004},
}
@article{9493,
abstract = {In a number of organisms, transgenes containing transcribed inverted repeats (IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA silencing also causes extensive cytosine methylation of homologous DNA in both the transgene "trigger" and any other homologous DNA sequences--"targets". Endogenous genomic sequences, including transposable elements and repeated elements, are also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4) is required for maintenance of DNA methylation at several endogenous loci and for the establishment of methylation at the FWA gene. Here, we show that mutation of AGO4 substantially reduces the maintenance of DNA methylation triggered by IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences, while the IR trigger sequences lose methylation in all sequence contexts. Finally, we find that AGO4 and the DRM methyltransferase genes are required for maintenance of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting that AGO4 may function downstream of siRNA production.},
author = {ZILBERMAN, Daniel and Cao, Xiaofeng and Johansen, Lisa K. and Xie, Zhixin and Carrington, James C. and Jacobsen, Steven E.},
issn = {1879-0445},
journal = {Current Biology},
number = {13},
pages = {1214--1220},
publisher = {Elsevier},
title = {{Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats}},
doi = {10.1016/j.cub.2004.06.055},
volume = {14},
year = {2004},
}
@inproceedings{2337,
author = {Lieb, Élliott H and Robert Seiringer},
editor = {Karpeshina, Yulia and Weikard, Rudi and Zeng, Yanni},
pages = {239 -- 250},
publisher = {American Mathematical Society},
title = {{Bose-Einstein condensation of dilute gases in traps }},
doi = {10.1090/conm/327/05818},
volume = {327},
year = {2003},
}
@article{2354,
abstract = {We investigate the ground state properties of a gas of interacting particles confined in an external potential in three dimensions and subject to rotation around an axis of symmetry. We consider the Gross-Pitaevskii (GP) limit of a dilute gas. Analysing both the absolute and the bosonic ground states of the system, we show, in particular, their different behaviour for a certain range of parameters. This parameter range is determined by the question whether the rotational symmetry in the minimizer of the GP functional is broken or not. For the absolute ground state, we prove that in the GP limit a modified GP functional depending on density matrices correctly describes the energy and reduced density matrices, independent of symmetry breaking. For the bosonic ground state this holds true if and only if the symmetry is unbroken.},
author = {Robert Seiringer},
journal = {Journal of Physics A: Mathematical and Theoretical},
number = {37},
pages = {9755 -- 9778},
publisher = {IOP Publishing Ltd.},
title = {{Ground state asymptotics of a dilute, rotating gas}},
doi = {10.1088/0305-4470/36/37/312},
volume = {36},
year = {2003},
}
@article{2357,
abstract = {The classic Poincaré inequality bounds the L q-norm of a function f in a bounded domain Ω ⊂ ℝ n in terms of some L p-norm of its gradient in Ω. We generalize this in two ways: In the first generalization we remove a set Τ from Ω and concentrate our attention on Λ = Ω \ Τ. This new domain might not even be connected and hence no Poincaré inequality can generally hold for it, or if it does hold it might have a very bad constant. This is so even if the volume of Τ is arbitrarily small. A Poincaré inequality does hold, however, if one makes the additional assumption that f has a finite L p gradient norm on the whole of Ω, not just on Λ. The important point is that the Poincaré inequality thus obtained bounds the L q-norm of f in terms of the L p gradient norm on Λ (not Ω) plus an additional term that goes to zero as the volume of Τ goes to zero. This error term depends on Τ only through its volume. Apart from this additive error term, the constant in the inequality remains that of the 'nice' domain Ω. In the second generalization we are given a vector field A and replace ∇ by ∇ + iA(x) (geometrically, a connection on a U(1) bundle). Unlike the A = 0 case, the infimum of ∥(∇ + iA)f∥ p over all f with a given ∥f∥ q is in general not zero. This permits an improvement of the inequality by the addition of a term whose sharp value we derive. We describe some open problems that arise from these generalizations.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Annals of Mathematics},
number = {3},
pages = {1067 -- 1080},
publisher = {Princeton University Press},
title = {{Poincaré inequalities in punctured domains}},
doi = {10.4007/annals.2003.158.1067 },
volume = {158},
year = {2003},
}
@article{2358,
abstract = {A study was conducted on the one-dimensional (1D) bosons in three-dimensional (3D) traps. A rigorous analysis was carried out on the parameter regions in which various types of 1D or 3D behavior occurred in the ground state. The four parameter regions include density, transverse, longitudinal dimensions and scattering length.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Physical Review Letters},
number = {15},
pages = {1504011 -- 1504014},
publisher = {American Physical Society},
title = {{One-dimensional Bosons in three-dimensional traps}},
doi = {10.1103/PhysRevLett.91.150401},
volume = {91},
year = {2003},
}
@article{1457,
abstract = {Among the major mathematical approaches to mirror symmetry are those of Batyrev-Borisov and Stromdnger-Yau-Zaslow (SYZ). The first is explicit and amenable to computation but is not clearly related to the physical motivation; the second is the opposite. Furthermore, it is far from obvious that mirror partners in one sense will also be mirror partners in the other. This paper concerns a class of examples that can be shown to satisfy the requirements of SYZ, but whose Hodge numbers are also equal. This provides significant evidence in support of SYZ. Moreover, the examples are of great interest in their own right: they are spaces of flat SLr-connections on a smooth curve. The mirror is the corresponding space for the Langlands dual group PGLr. These examples therefore throw a bridge from mirror symmetry to the duality theory of Lie groups and, more broadly, to the geometric Langlands program.},
author = {Tamas Hausel and Thaddeus, Michael},
journal = {Inventiones Mathematicae},
number = {1},
pages = {197 -- 229},
publisher = {Springer},
title = {{Mirror symmetry, langlands duality, and the Hitchin system}},
doi = {10.1007/s00222-003-0286-7},
volume = {153},
year = {2003},
}
@article{1458,
abstract = {The moduli space of stable bundles of rank $2$ and degree $1$ on a Riemann surface has rational cohomology generated by the so-called universal classes. The work of Baranovsky, King-Newstead, Siebert-Tian and Zagier provided a complete set of relations between these classes, expressed in terms of a recursion in the genus. This paper accomplishes the same thing for the noncompact moduli spaces of Higgs bundles, in the sense of Hitchin and Simpson. There are many more independent relations than for stable bundles, but in a sense the answer is simpler, since the formulas are completely explicit, not recursive. The results of Kirwan on equivariant cohomology for holomorphic circle actions are of key importance.},
author = {Tamas Hausel and Thaddeus, Michael},
journal = {Journal of the American Mathematical Society},
number = {2},
pages = {303 -- 329},
publisher = {American Mathematical Society},
title = {{Relations in the cohomology ring of the moduli space of rank 2 Higgs bundles}},
doi = {10.1090/S0894-0347-02-00417-4},
volume = {16},
year = {2003},
}
@article{1459,
abstract = {In this paper we explicitly calculate the analogue of the 't Hooft SU (2) Yang-Mills instantons on Gibbons-Hawking multi-centered gravitational instantons, which come in two parallel families: the multi-Eguchi-Hanson, or Ak ALE gravitational instantons and the multi-Taub-NUT spaces, or Ak ALF gravitational instantons. We calculate their energy and find the reducible ones. Following Kronheimer we also exploit the U(1) invariance of our solutions and study the corresponding explicit singular SU (2) magnetic monopole solutions of the Bogomolny equations on flat ℝ3.},
author = {Etesi, Gábor and Tamas Hausel},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {275 -- 288},
publisher = {Springer},
title = {{On Yang-Mills instantons over multi-centered gravitational instantons}},
doi = {10.1007/s00220-003-0806-8},
volume = {235},
year = {2003},
}
@article{166,
abstract = {For any number field k, upper bounds are established for the number of k-rational points of bounded height on non-singular del Pezzo surfaces defined over k, which are equipped with suitable conic bundle structures over k.},
author = {Browning, Timothy D and Swarbick Jones, M},
journal = {Proceedings of the Bonn session in analytic number theory and diophantine equations},
publisher = {Mathematisches Institut der Universität Bonn},
title = {{Counting rational points on del Pezzo surfaces of degree 5}},
volume = {360},
year = {2003},
}