@article{1044, abstract = {Control over all internal and external degrees of freedom of molecules at the level of single quantum states will enable a series of fundamental studies in physics and chemistry1,2. In particular, samples of ground-state molecules at ultralow temperatures and high number densities will facilitate new quantum-gas studies3 and future applications in quantum information science4. However, high phase-space densities for molecular samples are not readily attainable because efficient cooling techniques such as laser cooling are lacking. Here we produce an ultracold and dense sample of molecules in a single hyperfine level of the rovibronic ground state with each molecule individually trapped in the motional ground state of an optical lattice well. Starting from a zero-temperature atomic Mott-insulator state with optimized double-site occupancy6, weakly bound dimer molecules are efficiently associated on a Feshbach resonance7 and subsequently transferred to the rovibronic ground state by a stimulated four-photon process with >50% efficiency. The molecules are trapped in the lattice and have a lifetime of 8 s. Our results present a crucial step towards Bose-Einstein condensation of ground-state molecules and, when suitably generalized to polar heteronuclear molecules, the realization of dipolar quantum-gas phases in optical lattices8-10.}, author = {Danzl, Johann G and Mark, Manfred and Haller, Elmar and Gustavsson, Mattias and Hart, Russell and Aldegunde, Jesus and Hutson, Jeremy and Nägerl, Hanns}, journal = {Nature Physics}, number = {4}, pages = {265 -- 270}, publisher = {Nature Publishing Group}, title = {{An ultracold high-density sample of rovibronic ground-state molecules in an optical lattice}}, doi = {10.1038/nphys1533}, volume = {6}, year = {2010}, } @article{1045, abstract = {We report on the observation of confinement-induced resonances in strongly interacting quantum-gas systems with tunable interactions for one- and two-dimensional geometry. Atom-atom scattering is substantially modified when the s-wave scattering length approaches the length scale associated with the tight transversal confinement, leading to characteristic loss and heating signatures. Upon introducing an anisotropy for the transversal confinement we observe a splitting of the confinement-induced resonance. With increasing anisotropy additional resonances appear. In the limit of a two-dimensional system we find that one resonance persists.}, author = {Haller, Elmar and Mark, Manfred and Hart, Russell and Danzl, Johann G and Reichsöllner, Lukas and Melezhik, Vladimir and Schmelcher, Peter and Nägerl, Hanns}, journal = {Physical Review Letters}, number = {15}, publisher = {American Physical Society}, title = {{Confinement-induced resonances in low-dimensional quantum systems}}, doi = {10.1103/PhysRevLett.104.153203}, volume = {104}, year = {2010}, } @article{1046, abstract = {The phenomenon of matter-wave interference lies at the heart of quantum physics. It has been observed in various contexts in the limit of non-interacting particles as a single-particle effect. Here we observe and control matter-wave interference whose evolution is driven by interparticle interactions. In a multi-path matter-wave interferometer, the macroscopic manybody wave function of an interacting atomic Bose-Einstein condensate develops a regular interference pattern, allowing us to detect and directly visualize the effect of interaction-induced phase shifts. We demonstrate control over the phase evolution by inhibiting interaction-induced dephasing and by refocusing a dephased macroscopic matter wave in a spin-echo-type experiment. Our results show that interactions in a many-body system lead to a surprisingly coherent evolution, possibly enabling narrow-band and high-brightness matterwave interferometers based on atom lasers.}, author = {Gustavsson, Mattias and Haller, Elmar and Mark, Manfred and Danzl, Johann G and Hart, Russell and Daley, Andrew and Nägerl, Hanns}, journal = {New Journal of Physics}, publisher = {IOP Publishing Ltd.}, title = {{Interference of interacting matter waves}}, doi = {10.1088/1367-2630/12/6/065029}, volume = {12}, year = {2010}, } @article{1047, abstract = {Particles in a perfect lattice potential perform Bloch oscillations when subject to a constant force, leading to localization and preventing conductivity. For a weakly interacting Bose-Einstein condensate of Cs atoms, we observe giant center-of-mass oscillations in position space with a displacement across hundreds of lattice sites when we add a periodic modulation to the force near the Bloch frequency. We study the dependence of these "super" Bloch oscillations on lattice depth, modulation amplitude, and modulation frequency and show that they provide a means to induce linear transport in a dissipation-free lattice.}, author = {Haller, Elmar and Hart, Russell and Mark, Manfred and Danzl, Johann G and Reichsöllner, Lukas and Nägerl, Hanns}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{Inducing transport in a dissipation-free lattice with super bloch oscillations}}, doi = {10.1103/PhysRevLett.104.200403}, volume = {104}, year = {2010}, } @article{1049, abstract = {Quantum many-body systems can have phase transitions even at zero temperature; fluctuations arising from Heisenbergĝ€™s uncertainty principle, as opposed to thermal effects, drive the system from one phase to another. Typically, during the transition the relative strength of two competing terms in the systemĝ€™s Hamiltonian changes across a finite critical value. A well-known example is the Mottĝ€" Hubbard quantum phase transition from a superfluid to an insulating phase, which has been observed for weakly interacting bosonic atomic gases. However, for strongly interacting quantum systems confined to lower-dimensional geometry, a novel type of quantum phase transition may be induced and driven by an arbitrarily weak perturbation to the Hamiltonian. Here we observe such an effectĝ€"the sineĝ€"Gordon quantum phase transition from a superfluid Luttinger liquid to a Mott insulatorĝ€ "in a one-dimensional quantum gas of bosonic caesium atoms with tunable interactions. For sufficiently strong interactions, the transition is induced by adding an arbitrarily weak optical lattice commensurate with the atomic granularity, which leads to immediate pinning of the atoms. We map out the phase diagram and find that our measurements in the strongly interacting regime agree well with a quantum field description based on the exactly solvable sineĝ€"Gordon model. We trace the phase boundary all the way to the weakly interacting regime, where we find good agreement with the predictions of the one-dimensional Boseĝ€"Hubbard model. Our results open up the experimental study of quantum phase transitions, criticality and transport phenomena beyond Hubbard-type models in the context of ultracold gases.}, author = {Haller, Elmar and Hart, Russell and Mark, Manfred and Danzl, Johann G and Reichsöllner, Lukas and Gustavsson, Mattias and Dalmonte, Marcello and Pupillo, Guido and Nägerl, Hanns}, journal = {Nature}, number = {7306}, pages = {597 -- 600}, publisher = {Nature Publishing Group}, title = {{Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons}}, doi = {10.1038/nature09259}, volume = {466}, year = {2010}, } @inproceedings{758, abstract = {Set agreement [4] is a fundamental problem in distributed computing, in which processes collectively choose a small subset of values from a larger set of proposals. Set agreement has been extensively studied in both synchronous and asynchronous systems [10,11,3,5,8,9]. Real world distributed systems, however, are neither purely synchronous nor purely asynchronous. To describe such a system, Dwork et al. [6] introduced the idea of partial synchrony. They assume for every execution some (unknown) time GST (global stabilization time), after which the system is synchronous. In a recent paper [1,2], we study the complexity of set agreement in the context of partially synchronous systems, determining the minimum-sized window of synchrony in which set agreement can be solved. We show that at least ⌊t/k⌋ + 2 synchronous rounds are required for k-set agreement, where t < n is the number of crashes, and k is the agreement parameter of the set agreement task. We then introduce an algorithm that terminates in any window of synchrony of size at least ⌊t/k⌋ + 4 rounds. Together, these results tightly bound the inherent price of tolerating some asynchrony.}, author = {Alistarh, Dan-Adrian and Gilbert, Seth and Guerraoui, Rachid and Travers, Corentin}, pages = {404 -- 405}, publisher = {Springer}, title = {{Brief announcement: New bounds for partially synchronous set agreement}}, doi = {10.1007/978-3-642-15763-9_40}, volume = {6343 LNCS}, year = {2010}, } @article{7703, abstract = {By combining gene expression profiling with image registration, Tomer et al. (2010) find that the mushroom body of the segmented worm Platynereis dumerilii shares many features with the mammalian cerebral cortex. The authors propose that the mushroom body and cortex evolved from the same structure in the common ancestor of vertebrates and invertebrates.}, author = {Sweeney, Lora Beatrice Jaeger and Luo, Liqun}, issn = {0092-8674}, journal = {Cell}, number = {5}, pages = {679--681}, publisher = {Elsevier}, title = {{‘Fore brain: A hint of the ancestral cortex}}, doi = {10.1016/j.cell.2010.08.024}, volume = {142}, year = {2010}, } @article{8472, abstract = {Characterization of protein dynamics by solid-state NMR spectroscopy requires robust and accurate measurement protocols, which are not yet fully developed. In this study, we investigate the backbone dynamics of microcrystalline ubiquitin using different approaches. A rotational-echo double-resonance type (REDOR-type) methodology allows one to accurately measure 1H−15N order parameters in highly deuterated samples. We show that the systematic errors in the REDOR experiment are as low as 1% or even less, giving access to accurate data for the amplitudes of backbone mobility. Combining such dipolar-coupling-derived order parameters with autocorrelated and cross-correlated 15N relaxation rates, we are able to quantitate amplitudes and correlation times of backbone dynamics on picosecond and nanosecond time scales in a residue-resolved manner. While the mobility on picosecond time scales appears to have rather uniform amplitude throughout the protein, we unambiguously identify and quantitate nanosecond mobility with order parameters S2 as low as 0.8 in some regions of the protein, where nanosecond dynamics has also been revealed in solution state. The methodology used here, a combination of accurate dipolar-coupling measurements and different relaxation parameters, yields details about dynamics on different time scales and can be applied to solid protein samples such as amyloid fibrils or membrane proteins.}, author = {Schanda, Paul and Meier, Beat H. and Ernst, Matthias}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {45}, pages = {15957--15967}, publisher = {American Chemical Society}, title = {{Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy}}, doi = {10.1021/ja100726a}, volume = {132}, year = {2010}, } @article{8473, abstract = {β2-microglobulin (β2m), the light chain of class I major histocompatibility complex, is responsible for the dialysis-related amyloidosis and, in patients undergoing long term dialysis, the full-length and chemically unmodified β2m converts into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily, in common to other members of this family, experiences during its folding a long-lived intermediate associated to the trans-to-cis isomerization of Pro-32 that has been addressed as the precursor of the amyloid fibril formation. In this respect, previous studies on the W60G β2m mutant, showing that the lack of Trp-60 prevents fibril formation in mild aggregating condition, prompted us to reinvestigate the refolding kinetics of wild type and W60G β2m at atomic resolution by real-time NMR. The analysis, conducted at ambient temperature by the band selective flip angle short transient real-time two-dimensional NMR techniques and probing the β2m states every 15 s, revealed a more complex folding energy landscape than previously reported for wild type β2m, involving more than a single intermediate species, and shedding new light into the fibrillogenic pathway. Moreover, a significant difference in the kinetic scheme previously characterized by optical spectroscopic methods was discovered for the W60G β2m mutant.}, author = {Corazza, Alessandra and Rennella, Enrico and Schanda, Paul and Mimmi, Maria Chiara and Cutuil, Thomas and Raimondi, Sara and Giorgetti, Sofia and Fogolari, Federico and Viglino, Paolo and Frydman, Lucio and Gal, Maayan and Bellotti, Vittorio and Brutscher, Bernhard and Esposito, Gennaro}, issn = {0021-9258}, journal = {Journal of Biological Chemistry}, keywords = {Cell Biology, Biochemistry, Molecular Biology}, number = {8}, pages = {5827--5835}, publisher = {American Society for Biochemistry & Molecular Biology}, title = {{Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR}}, doi = {10.1074/jbc.m109.061168}, volume = {285}, year = {2010}, } @inbook{8506, author = {Hunt, Brian R. and Kaloshin, Vadim}, booktitle = {Handbook of Dynamical Systems}, isbn = {9780444531414}, issn = {1874-575X}, pages = {43--87}, publisher = {Elsevier}, title = {{Prevalence}}, doi = {10.1016/s1874-575x(10)00310-3}, volume = {3}, year = {2010}, } @inproceedings{8507, abstract = {We study a Cr nearly integrable Hamiltonian system defined on 𝕋3 × ℝ3. Let and µΣ1 be the restriction of Lebesgue measure on 𝕋3 × ℝ3 to ∑. We prove there is a perturbation , and an orbit (q(t), p(t)): ℝ → 𝕋3 × ℝ3 of the Hamiltonian equation such that .}, author = {Kaloshin, Vadim and ZHANG, KE and ZHENG, YONG}, booktitle = {XVIth International Congress on Mathematical Physics}, isbn = {9789814304627}, location = {Prague, Czech Republic}, pages = {314--322}, publisher = {World Scientific}, title = {{Almost dense orbit on energy surface}}, doi = {10.1142/9789814304634_0017}, year = {2010}, } @article{857, abstract = {The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, 3.5 × 10 9 yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.}, author = {Povolotskaya, Inna and Fyodor Kondrashov}, journal = {Nature}, number = {7300}, pages = {922 -- 926}, publisher = {Nature Publishing Group}, title = {{Sequence space and the ongoing expansion of the protein universe}}, doi = {10.1038/nature09105}, volume = {465}, year = {2010}, } @article{862, abstract = {A long-standing controversy in evolutionary biology is whether or not evolving lineages can cross valleys on the fitness landscape that correspond to low-fitness genotypes, which can eventually enable them to reach isolated fitness peaks1-9. Here we study the fitness landscapes traversed by switches between different AU and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles corresponding to GU and AC non-Watson-Crick intermediate states segregate within human populations at low frequencies, similar to those of non-synonymous alleles. Substitutions leading to a Watson-Crick switch are strongly correlated, especially in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial genome. Using these data we estimate that a typical Watson-Crick switch involves crossing a fitness valley of a depth of about 10-3 or even about 10-2, with AC intermediates being slightly more deleterious than GU intermediates. This compensatory evolution must proceed through rare intermediate variants that never reach fixation. The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs and other molecules implies that simultaneous fixation of two alleles that are individually deleterious may be a common phenomenon at the molecular level.}, author = {Meer, Margarita V and Kondrashov, Alexey S and Artzy-Randrup, Yael and Fyodor Kondrashov}, journal = {Nature}, number = {7286}, pages = {279 -- 282}, publisher = {Nature Publishing Group}, title = {{Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness}}, doi = {10.1038/nature08691}, volume = {464}, year = {2010}, } @article{872, abstract = {The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches. However, in the past few years genome-wide sequencing of closely related individuals has made it possible to estimate the rates of mutation directly at the level of the DNA, avoiding most of the problems associated with using indirect methods. Here, we review the methods used in the past with an emphasis on next generation sequencing, which may soon make the accurate measurement of spontaneous mutation rates a matter of routine.}, author = {Fyodor Kondrashov and Kondrashov, Alexey S}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, number = {1544}, pages = {1169 -- 1176}, publisher = {Royal Society, The}, title = {{Measurements of spontaneous rates of mutations in the recent past and the near future}}, doi = {10.1098/rstb.2009.0286}, volume = {365}, year = {2010}, } @article{884, abstract = {Background: Divergence of two independently evolving sequences that originated from a common ancestor can be described by two parameters, the asymptotic level of divergence E and the rate r at which this level of divergence is approached. Constant negative selection impedes allele replacements and, therefore, is routinely assumed to decelerate sequence divergence. However, its impact on E and on r has not been formally investigated.Results: Strong selection that favors only one allele can make E arbitrarily small and r arbitrarily large. In contrast, in the case of 4 possible alleles and equal mutation rates, the lowest value of r, attained when two alleles confer equal fitnesses and the other two are strongly deleterious, is only two times lower than its value under selective neutrality.Conclusions: Constant selection can strongly constrain the level of sequence divergence, but cannot reduce substantially the rate at which this level is approached. In particular, under any constant selection the divergence of sequences that accumulated one substitution per neutral site since their origin from the common ancestor must already constitute at least one half of the asymptotic divergence at sites under such selection.Reviewers: This article was reviewed by Drs. Nicolas Galtier, Sergei Maslov, and Nick Grishin.}, author = {Kondrashov, Alexey S and Povolotskaya, Inna and Ivankov, Dmitry N and Fyodor Kondrashov}, journal = {Biology Direct}, publisher = {BioMed Central}, title = {{Rate of sequence divergence under constant selection}}, doi = {10.1186/1745-6150-5-5}, volume = {5}, year = {2010}, } @article{89, abstract = {We demonstrate the operation of a device that can produce chitosan nanoparticles in a tunable size range from 50-300 nm with small size dispersion. A piezoelectric oscillator operated at megahertz frequencies is used to aerosolize a solution containing dissolved chitosan. The solvent is then evaporated from the aerosolized droplets in a heat pipe, leaving monodisperse nanoparticles to be collected. The nanoparticle size is controlled both by the concentration of the dissolved polymer and by the size of the aerosol droplets that are created. Our device can be used with any polymer or polymer/therapeutic combination that can be prepared in a homogeneous solution and vaporized.}, author = {Wright, Ian and Higginbotham, Andrew P and Baker, Shenda and Donnelly, Tom}, journal = {ACS Applied Materials and Interfaces}, number = {8}, pages = {2360 -- 2364}, publisher = {American Chemical Society}, title = {{Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution}}, doi = {10.1021/am100375w}, volume = {2}, year = {2010}, } @article{891, abstract = {Gene duplications and their subsequent divergence play an important part in the evolution of novel gene functions. Several models for the emergence, maintenance and evolution of gene copies have been proposed. However, a clear consensus on how gene duplications are fixed and maintained in genomes is lacking. Here, we present a comprehensive classification of the models that are relevant to all stages of the evolution of gene duplications. Each model predicts a unique combination of evolutionary dynamics and functional properties. Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications.}, author = {Innan, Hideki and Fyodor Kondrashov}, journal = {Nature Reviews Genetics}, number = {2}, pages = {97 -- 108}, publisher = {Nature Publishing Group}, title = {{The evolution of gene duplications: Classifying and distinguishing between models}}, doi = {10.1038/nrg2689}, volume = {11}, year = {2010}, } @article{901, abstract = {Background: Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome.Results: We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently.Reviewers: This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst).}, author = {Breen, Michael S and Fyodor Kondrashov}, journal = {Biology Direct}, publisher = {BioMed Central}, title = {{Mitochondrial pathogenic mutations are population-specific}}, doi = {10.1186/1745-6150-5-68}, volume = {5}, year = {2010}, } @article{9012, abstract = {In this Letter, we characterize experimentally the diffusiophoretic motion of colloids and λ-DNA toward higher concentration of solutes, using microfluidic technology to build spatially and temporally controlled concentration gradients. We then demonstrate that segregation and spatial patterning of the particles can be achieved from temporal variations of the solute concentration profile. This segregation takes the form of a strong trapping potential, stemming from an osmotically induced rectification mechanism of the solute time-dependent variations. Depending on the spatial and temporal symmetry of the solute signal, localization patterns with various shapes can be achieved. These results highlight the role of solute contrasts in out-of-equilibrium processes occurring in soft matter.}, author = {Palacci, Jérémie A and Abécassis, Benjamin and Cottin-Bizonne, Cécile and Ybert, Christophe and Bocquet, Lydéric}, issn = {10797114}, journal = {Physical Review Letters}, number = {13}, publisher = {American Physical Society}, title = {{Colloidal motility and pattern formation under rectified diffusiophoresis}}, doi = {10.1103/physrevlett.104.138302}, volume = {104}, year = {2010}, } @article{9013, abstract = {In this Letter, we investigate experimentally the nonequilibrium steady state of an active colloidal suspension under gravity field. The active particles are made of chemically powered colloids, showing self propulsion in the presence of an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated microfluidic device, made of permeable gel microstructures. Both the microdynamics of individual colloids and the global stationary state of the suspension under gravity are measured with optical microscopy. This yields a direct measurement of the effective temperature of the active system as a function of the particle activity, on the basis of the fluctuation-dissipation relationship. Our work is a first step in the experimental exploration of the out-of-equilibrium properties of active colloidal systems.}, author = {Palacci, Jérémie A and Cottin-Bizonne, Cécile and Ybert, Christophe and Bocquet, Lydéric}, issn = {10797114}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society }, title = {{Sedimentation and effective temperature of active colloidal suspensions}}, doi = {10.1103/physrevlett.105.088304}, volume = {105}, year = {2010}, }