@unpublished{574, abstract = {Vaidman, in a recent article adopts the method of 'quantum weak measurements in pre- and postselected ensembles' to ascertain whether or not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}}, doi = {10.48550/arXiv.quant-ph/0612159}, year = {2006}, } @inproceedings{577, abstract = {Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) are high-efficiency single-photon detectors which have multi-photon counting capability. While both the VLPCs and the SSPMs have inferred internal quantum efficiencies above 93%, the actual measured values for both the detectors were in fact limited to less than 88%, attributed to in-coupling losses. We are currently improving this overall detection efficiency via a) custom anti-reflection coating the detectors and the in-coupling fibers, b) implementing a novel cryogenic design to reduce transmission losses and, c) using low-noise electronics to obtain a better signal-to-noise ratio.}, author = {Rangarajan, Radhika and Altepeter, Joseph and Jeffrey, Evan and Stoutimore, Micah and Peters, Nicholas and Hosten, Onur and Kwiat, Paul}, booktitle = {Optics East}, issn = {0277-786X}, location = {Boston, Massachusetts, United States}, publisher = {SPIE}, title = {{High-efficiency single-photon detectors}}, doi = {10.1117/12.686117}, year = {2006}, } @inproceedings{578, abstract = {A source of single photons allows secure quantum key distribution, in addition, to being a critical resource for linear optics quantum computing. We describe our progress on deterministically creating single photons from spontaneous parametric downconversion, an extension of the Pittman, Jacobs and Franson scheme [Phys. Rev A, v66, 042303 (2002)]. Their idea was to conditionally prepare single photons by measuring one member of a spontaneously emitted photon pair and storing the remaining conditionally prepared photon until a predetermined time, when it would be "deterministically" released from storage. Our approach attempts to improve upon this by recycling the pump pulse in order to decrease the possibility of multiple-pair generation, while maintaining a high probability of producing a single pair. Many of the challenges we discuss are central to other quantum information technologies, including the need for low-loss optical storage, switching and detection, and fast feed-forward control.}, author = {Peters, Nicholas and Arnold, Keith and Vandevender, Aaron and Jeffrey, Evan and Rangarajan, Radhika and Hosten, Onur and Barreiro, Julio and Altepeter, Joseph and Kwiat, Paul}, booktitle = {Quantum Communications and Quantum Imaging IV}, location = {San DIego, CA, United States}, publisher = {SPIE}, title = {{Towards a quasi-deterministic single-photon source}}, doi = {10.1117/12.684702}, volume = {6305}, year = {2006}, } @article{579, abstract = {The logic underlying the coherent nature of quantum information processing often deviates from intuitive reasoning, leading to surprising effects. Counterfactual computation constitutes a striking example: the potential outcome of a quantum computation can be inferred, even if the computer is not run 1. Relying on similar arguments to interaction-free measurements 2 (or quantum interrogation3), counterfactual computation is accomplished by putting the computer in a superposition of 'running' and 'not running' states, and then interfering the two histories. Conditional on the as-yet-unknown outcome of the computation, it is sometimes possible to counterfactually infer information about the solution. Here we demonstrate counterfactual computation, implementing Grover's search algorithm with an all-optical approach4. It was believed that the overall probability of such counterfactual inference is intrinsically limited1,5, so that it could not perform better on average than random guesses. However, using a novel 'chained' version of the quantum Zeno effect6, we show how to boost the counterfactual inference probability to unity, thereby beating the random guessing limit. Our methods are general and apply to any physical system, as illustrated by a discussion of trapped-ion systems. Finally, we briefly show that, in certain circumstances, counterfactual computation can eliminate errors induced by decoherence. }, author = {Hosten, Onur and Rakher, Matthew and Barreiro, Julio and Peters, Nicholas and Kwiat, Paul}, issn = {1476-4687}, journal = {Nature}, number = {7079}, pages = {949 -- 952}, publisher = {Nature Publishing Group}, title = {{Counterfactual quantum computation through quantum interrogation}}, doi = {10.1038/nature04523}, volume = {439}, year = {2006}, } @inproceedings{583, abstract = {Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) facilitate efficient single-photon detection. We are attempting to improve their efficiency, previously limited to < 88% by coupling losses, via anti-reflection coatings, better electronics and cryogenics.}, author = {Rangarajan, Radhika and Peters, Nicholas and Hosten, Onur and Altepeter, Joseph and Jeffrey, Evan and Kwiat, Paul}, booktitle = {Conference on Lasers and Electro-Optics}, issn = {2160-9004}, location = {Long Beach, CA, United States}, publisher = {IEEE}, title = {{Improved single-photon detection}}, doi = {10.1109/CLEO.2006.4628641}, 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{6152, author = {Rogers, Candida and Persson, Annelie and Cheung, Benny and de Bono, Mario}, issn = {0960-9822}, journal = {Current Biology}, number = {7}, pages = {649--659}, publisher = {Elsevier}, title = {{Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans}}, doi = {10.1016/j.cub.2006.03.023}, volume = {16}, year = {2006}, } @article{2066, abstract = {Although the X chromosome is usually similar to the autosomes in size and cytogenetic appearance, theoretical models predict that its hemizygosity in males may cause unusual patterns of evolution. The sequencing of several genomes has indeed revealed differences between the X chromosome and the autosomes in the rates of gene divergence, patterns of gene expression and rates of gene movement between chromosomes. A better understanding of these patterns should provide valuable information on the evolution of genes located on the X chromosome. It could also suggest solutions to more general problems in molecular evolution, such as detecting selection and estimating mutational effects on fitness}, author = {Beatriz Vicoso and Charlesworth, Brian}, journal = {Nature Reviews Genetics}, number = {8}, pages = {645 -- 653}, publisher = {Nature Publishing Group}, title = {{Evolution on the X chromosome: Unusual patterns and processes}}, doi = {10.1038/nrg1914}, volume = {7}, year = {2006}, } @inproceedings{2077, abstract = {We present an adaptive animation method for electrical discharges. Electrical discharges can be simulated using the dielectric breakdown model. Regular discretization of the governing Laplace equation leads to huge equation systems, and the computational cost of solving the equations quickly becomes prohibitive at high resolutions, especially for simulations in 3D. In contrast, our method discretizes the Laplace equation on an adaptive octree, reducing the size of the problem significantly, and making simulations of high resolution 3D datasets and even 3D animations feasible. In order to enhance realism for lightning animations, we propose a particle simulation that animates the residual positive charge. Thus, interaction of electrical discharges with their surroundings can be simulated.}, author = {Bernd Bickel and Wicke, Martin and Gross, Markus}, publisher = {IOS Press}, title = {{Adaptive simulation of electrical discharges}}, 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{8488, abstract = {We demonstrate for different protein samples that three-dimensional HNCO and HNCA correlation spectra may be recorded in a few minutes acquisition time using the band-selective excitation short-transient sequences presented here. This opens new perspectives for the NMR structural investigation of unstable protein samples and real-time site-resolved studies of protein kinetics.}, author = {Schanda, Paul and Van Melckebeke, Hélène and Brutscher, Bernhard}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {28}, pages = {9042--9043}, publisher = {American Chemical Society}, title = {{Speeding up three-dimensional protein NMR experiments to a few minutes}}, doi = {10.1021/ja062025p}, volume = {128}, year = {2006}, } @article{8489, abstract = {Structure elucidation of proteins by either NMR or X‐ray crystallography often requires the screening of a large number of samples for promising protein constructs and optimum solution conditions. For large‐scale screening of protein samples in solution, robust methods are needed that allow a rapid assessment of the folding of a polypeptide under diverse sample conditions. Here we present HET‐SOFAST NMR, a highly sensitive new method for semi‐quantitative characterization of the structural compactness and heterogeneity of polypeptide chains in solution. On the basis of one‐dimensional 1H HET‐SOFAST NMR data, obtained on well‐folded, molten globular, partially‐ and completely unfolded proteins, we define empirical thresholds that can be used as quantitative benchmarks for protein compactness. For 15N‐enriched protein samples, two‐dimensional 1H‐15N HET‐SOFAST correlation spectra provide site‐specific information about the structural heterogeneity along the polypeptide chain.}, author = {Schanda, Paul and Forge, Vincent and Brutscher, Bernhard}, issn = {0749-1581}, journal = {Magnetic Resonance in Chemistry}, number = {S1}, pages = {S177--S184}, publisher = {Wiley}, title = {{HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains}}, doi = {10.1002/mrc.1825}, volume = {44}, year = {2006}, } @article{8490, abstract = {We demonstrate the feasibility of recording 1H–15N correlation spectra of proteins in only one second of acquisition time. The experiment combines recently proposed SOFAST-HMQC with Hadamard-type 15N frequency encoding. This allows site-resolved real-time NMR studies of kinetic processes in proteins with an increased time resolution. The sensitivity of the experiment is sufficient to be applicable to a wide range of molecular systems available at millimolar concentration on a high magnetic field spectrometer.}, author = {Schanda, Paul and Brutscher, Bernhard}, issn = {1090-7807}, journal = {Journal of Magnetic Resonance}, keywords = {Nuclear and High Energy Physics, Biophysics, Biochemistry, Condensed Matter Physics}, number = {2}, pages = {334--339}, publisher = {Elsevier}, title = {{Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR}}, doi = {10.1016/j.jmr.2005.10.007}, volume = {178}, year = {2006}, } @article{8513, author = {Kaloshin, Vadim and Saprykina, Maria}, issn = {1553-5231}, journal = {Discrete & Continuous Dynamical Systems - A}, number = {2}, pages = {611--640}, publisher = {American Institute of Mathematical Sciences (AIMS)}, title = {{Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits}}, doi = {10.3934/dcds.2006.15.611}, volume = {15}, year = {2006}, } @article{8514, abstract = {We study the extent to which the Hausdorff dimension of a compact subset of an infinite-dimensional Banach space is affected by a typical mapping into a finite-dimensional space. It is possible that the dimension drops under all such mappings, but the amount by which it typically drops is controlled by the ‘thickness exponent’ of the set, which was defined by Hunt and Kaloshin (Nonlinearity12 (1999), 1263–1275). More precisely, let $X$ be a compact subset of a Banach space $B$ with thickness exponent $\tau$ and Hausdorff dimension $d$. Let $M$ be any subspace of the (locally) Lipschitz functions from $B$ to $\mathbb{R}^{m}$ that contains the space of bounded linear functions. We prove that for almost every (in the sense of prevalence) function $f \in M$, the Hausdorff dimension of $f(X)$ is at least $\min\{ m, d / (1 + \tau) \}$. We also prove an analogous result for a certain part of the dimension spectra of Borel probability measures supported on $X$. The factor $1 / (1 + \tau)$ can be improved to $1 / (1 + \tau / 2)$ if $B$ is a Hilbert space. Since dimension cannot increase under a (locally) Lipschitz function, these theorems become dimension preservation results when $\tau = 0$. We conjecture that many of the attractors associated with the evolution equations of mathematical physics have thickness exponent zero. We also discuss the sharpness of our results in the case $\tau > 0$.}, author = {OTT, WILLIAM and HUNT, BRIAN and Kaloshin, Vadim}, issn = {0143-3857}, journal = {Ergodic Theory and Dynamical Systems}, number = {3}, pages = {869--891}, publisher = {Cambridge University Press}, title = {{The effect of projections on fractal sets and measures in Banach spaces}}, doi = {10.1017/s0143385705000714}, volume = {26}, year = {2006}, } @inproceedings{8515, abstract = {We consider the evolution of a set carried by a space periodic incompressible stochastic flow in a Euclidean space. We report on three main results obtained in [8, 9, 10] concerning long time behaviour for a typical realization of the stochastic flow. First, at time t most of the particles are at a distance of order √t away from the origin. Moreover, we prove a Central Limit Theorem for the evolution of a measure carried by the flow, which holds for almost every realization of the flow. Second, we show the existence of a zero measure full Hausdorff dimension set of points, which escape to infinity at a linear rate. Third, in the 2-dimensional case, we study the set of points visited by the original set by time t. Such a set, when scaled down by the factor of t, has a limiting non random shape.}, author = {Kaloshin, Vadim and DOLGOPYAT, D. and KORALOV, L.}, booktitle = {XIVth International Congress on Mathematical Physics}, isbn = {9789812562012}, location = {Lisbon, Portugal}, pages = {290--295}, publisher = {World Scientific}, title = {{Long time behaviour of periodic stochastic flows}}, doi = {10.1142/9789812704016_0026}, year = {2006}, } @article{854, abstract = {Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch - the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ∼1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene.}, author = {Rogaev, Evgeny and Moliaka, Yuri and Malyarchuk, Boris and Kondrashov, Fyodor and Derenko, Miroslava and Chumakov, Ilya and Grigorenko, Anastasia}, issn = {1545-7885}, journal = {PLoS Biology}, number = {3}, pages = {0403 -- 0410}, publisher = {Public Library of Science}, title = {{Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius}}, doi = {10.1371/journal.pbio.0040073}, volume = {4}, year = {2006}, } @article{868, abstract = {Background: The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in animal tissues has been reported. In order to clarify the status of the MS and ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic study. Results: Using sequence similarity searches, we identified MS genes in arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in the numerous sequenced genomes of placental mammals. The regions of the placental mammals' genomes expected to code for malate synthase, as determined by comparison of the gene orders in vertebrate genomes, show clear similarity to the opossum MS sequence but contain stop codons, indicating that the MS gene became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable in animals other than the nematodes that possess a bifunctional, fused ICL-MS gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal gene transfer events that probably went in both directions between several bacterial and eukaryotic lineages. The strongest evidence was obtained for the acquisition of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the corresponding operonic organization by the common ancestor of the nematodes. Conclusion: The distribution of the MS and ICL genes in animals suggests that either they encode alternative enzymes of the glyoxylate cycle that are not orthologous to the known MS and ICL or the animal MS acquired a new function that remains to be characterized. Regardless of the ultimate solution to this conundrum, the genes for the glyoxylate cycle enzymes present a remarkable variety of evolutionary events including unusual horizontal gene transfer from bacteria to animals.}, author = {Fyodor Kondrashov and Koonin, Eugene V and Morgunov, Igor G and Finogenova, Tatiana V and Kondrashova, Marie N}, journal = {Biology Direct}, publisher = {BioMed Central}, title = {{Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation}}, doi = {10.1186/1745-6150-1-31}, volume = {1}, year = {2006}, } @article{869, abstract = {The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, and the rate of their evolution is used as a proxy for mutation rate. We subdivide all sites into four classes in terms of the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold synonymous sites and intron sites residing outside transposable elements. The distribution of the rate of evolution across all synonymous sites is trimodal. Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed by G, is ∼10% below that at such intron sites. In contrast, rate of evolution at postCpreG synonymous sites is ∼30% above that at such intron sites. Finally, synonymous and intron postC and preG sites evolve at similar rates. The relationship between the levels of polymorphism at the corresponding synonymous and intron sites is very similar to that between their rates of evolution. Within every class, synonymous sites are occupied by G or C much more often than intron sites, whose nucleotide composition is consistent with neutral mutation-drift equilibrium. These patterns suggest that synonymous sites are under weak selection in favor of G and C, with the average coefficient s∼0.25/Ne∼10-5, where Ne is the effective population size. Such selection decelerates evolution and reduces variability at sites with symmetric mutation, but has the opposite effects at sites where the favored nucleotides are more mutable. The amino-acid composition of proteins dictates that many synonymous sites are CpGprone, which causes them, on average, to evolve faster and to be more polymorphic than intron sites. An average genotype carries ∼107 suboptimal nucleotides at synonymous sites, implying synergistic epistasis in selection against them.}, author = {Kondrashov, Fyodor and Ogurtsov, Aleksey and Kondrashov, Alexey}, issn = {1095-8541}, journal = {Journal of Theoretical Biology}, keywords = {Mutation, Selection, Synonymous site, Evolution, Genetic drift}, number = {4}, pages = {616 -- 626}, publisher = {Elsevier}, title = {{Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites}}, doi = {10.1016/j.jtbi.2005.10.020}, volume = {240}, year = {2006}, }