TY - CONF AB - We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi, and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs for probabilistic finite automata and present an almost complete characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems for probabilistic automata on infinite words. AU - Chatterjee, Krishnendu AU - Henzinger, Thomas A ID - 3857 TI - Probabilistic Automata on infinite words: decidability and undecidability results VL - 6252 ER - TY - CONF AB - We study observation-based strategies for partially-observable Markov decision processes (POMDPs) with parity objectives. An observation-based strategy relies on partial information about the history of a play, namely, on the past sequence of observations. We consider qualitative analysis problems: given a POMDP with a parity objective, decide whether there exists an observation-based strategy to achieve the objective with probability 1 (almost-sure winning), or with positive probability (positive winning). Our main results are twofold. First, we present a complete picture of the computational complexity of the qualitative analysis problem for POMDPs with parity objectives and its subclasses: safety, reachability, Büchi, and coBüchi objectives. We establish several upper and lower bounds that were not known in the literature. Second, we give optimal bounds (matching upper and lower bounds) for the memory required by pure and randomized observation-based strategies for each class of objectives. AU - Chatterjee, Krishnendu AU - Doyen, Laurent AU - Henzinger, Thomas A ID - 3855 TI - Qualitative analysis of partially-observable Markov Decision Processes VL - 6281 ER - TY - CHAP AU - Juhás, Gabriel AU - Kazlov, Igor AU - Juhásová, Ana ID - 5940 SN - 0302-9743 T2 - Applications and Theory of Petri Nets TI - Instance Deadlock: A Mystery behind Frozen Programs ER - TY - JOUR AB - It is not well understood how the human Mediator complex, transcription factor IIH and RNA polymerase II (Pol II) work together with activators to initiate transcription. Activator binding alters Mediator structure, yet the functional consequences of such structural shifts remain unknown. The p53 C terminus and its activation domain interact with different Mediator subunits, and we find that each interaction differentially affects Mediator structure; strikingly, distinct p53-Mediator structures differentially affect Pol II activity. Only the p53 activation domain induces the formation of a large pocket domain at the Mediator-Pol II interaction site, and this correlates with activation of stalled Pol II to a productively elongating state. Moreover, we define a Mediator requirement for TFIIH-dependent Pol II C-terminal domain phosphorylation and identify substantial differences in Pol II C-terminal domain processing that correspond to distinct p53-Mediator structural states. Our results define a fundamental mechanism by which p53 activates transcription and suggest that Mediator structural shifts trigger activation of stalled Pol II complexes. AU - Meyer, Krista AU - Lin, Shih AU - Bernecky, Carrie A AU - Gao, Yuefeng AU - Taatjes, Dylan ID - 598 IS - 6 JF - Nature Structural and Molecular Biology TI - P53 activates transcription by directing structural shifts in Mediator VL - 17 ER - TY - JOUR AB - Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes' ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from shortly after the Bristol strain was isolated until methods to freeze C. elegans were developed. We find that during this time the two strains have accumulated 1208 genetic differences. We describe phenotypic variation between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and highlight 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication. AU - Weber, Katherine P. AU - De, Subhajyoti AU - Kozarewa, Iwanka AU - Turner, Daniel J. AU - Babu, M. Madan AU - de Bono, Mario ID - 6142 IS - 11 JF - PLoS ONE SN - 1932-6203 TI - Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans VL - 5 ER - TY - CHAP AB - Sinclair Ross’s novel As for Me and My House has long since been canonized as Canadian prairie fiction. Accordingly, it has been the subject of many critical studies and academic papers. Most commentators have concentrated on such literary issues as the representation of the western landscape or the reliability of the female narrator. But so far little consideration has been given to the social and cultural implications of the novel. Few attempts have been made to analyze the text from a cultural perspective including such social markers as class, gender and ethnicity. That is all the more surprising because Sinclair Ross has often been credited for being a realistic author and As for Me and My House has often been interpreted as a regional novel characteristic of a particular time and place. AU - Zacharasiewicz, Waldemar AU - Kirsch, Fritz Peter ID - 619 T2 - Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l'Ouest canadien TI - “This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House ER - TY - JOUR AB - Stroke is a major public health problem leading to high rates of death and disability in adults. Excessive stimulation of N-methyl-D-aspartate receptors (NMDARs) and the resulting neuronal nitric oxide synthase (nNOS) activation are crucial for neuronal injury after stroke insult. However, directly inhibiting NMDARs or nNOS can cause severe side effects because they have key physiological functions in the CNS. Here we show that cerebral ischemia induces the interaction of nNOS with postsynaptic density protein-95 (PSD-95). Disrupting nNOS-PSD-95 interaction via overexpressing the N-terminal amino acid residues 1-133 of nNOS (nNOS-N(1-133)) prevented glutamate-induced excitotoxicity and cerebral ischemic damage. Given the mechanism of nNOS-PSD-95 interaction, we developed a series of compounds and discovered a small-molecular inhibitor of the nNOS-PSD-95 interaction, ZL006. This drug blocked the ischemia-induced nNOS-PSD-95 association selectively, had potent neuroprotective activity in vitro and ameliorated focal cerebral ischemic damage in mice and rats subjected to middle cerebral artery occlusion (MCAO) and reperfusion. Moreover, it readily crossed the blood-brain barrier, did not inhibit NMDAR function, catalytic activity of nNOS or spatial memory, and had no effect on aggressive behaviors. Thus, this new drug may serve as a treatment for stroke, perhaps without major side effects. AU - Zhou, L AU - Li, F AU - Xu, Haibing AU - Luo, CX AU - Wu, HY AU - Zhu, MM AU - Lu, W AU - Ji, X AU - Zhou, QG AU - Zhu, DY ID - 6198 IS - 12 JF - Nature Medicine SN - 1078-8956 TI - Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95 VL - 16 ER - TY - JOUR AB - We study the average order of the divisor function, as it ranges over the values of binary quartic forms that are reducible over ℚ. AU - Bretèche, Régis de la AU - Browning, Timothy D ID - 6320 IS - 646 JF - Crelles Journal TI - Le problème des diviseurs pour des formes binaires de degré 4 VL - 2010 ER - TY - JOUR AB - We report resonant ultrasound spectroscopy (RUS), dilatometry/magnetostriction, magnetotransport, magnetization, specific-heat, and 119Sn Mössbauer spectroscopy measurements on SnTe and Sn0.995Cr0.005Te. Hall measurements at T=77 K indicate that our Bridgman-grown single crystals have a p-type carrier concentration of 3.4×1019 cm−3 and that our Cr-doped crystals have an n-type concentration of 5.8×1022 cm−3. Although our SnTe crystals are diamagnetic over the temperature range 2≤T≤1100 K, the Cr-doped crystals are room-temperature ferromagnets with a Curie temperature of 294 K. For each sample type, three-terminal capacitive dilatometry measurements detect a subtle 0.5 μm distortion at Tc≈85 K. Whereas our RUS measurements on SnTe show elastic hardening near the structural transition, pointing to co-elastic behavior, similar measurements on Sn0.995Cr0.005Te show a pronounced softening, pointing to ferroelastic behavior. Effective Debye temperature, θD, values of SnTe obtained from 119Sn Mössbauer studies show a hardening of phonons in the range 60–115 K (θD=162 K) as compared with the 100–300 K range (θD=150 K). In addition, a precursor softening extending over approximately 100 K anticipates this collapse at the critical temperature and quantitative analysis over three decades of its reduced modulus finds ΔC44/C44=A|(T−T0)/T0|−κ with κ=0.50±0.02, a value indicating a three-dimensional softening of phonon branches at a temperature T0∼75 K, considerably below Tc. We suggest that the differences in these two types of elastic behaviors lie in the absence of elastic domain-wall motion in the one case and their nucleation in the other. AU - Salje, E. K. H. AU - Safarik, D. J. AU - Modic, Kimberly A AU - Gubernatis, J. E. AU - Cooley, J. C. AU - Taylor, R. D. AU - Mihaila, B. AU - Saxena, A. AU - Lookman, T. AU - Smith, J. L. AU - Fisher, R. A. AU - Pasternak, M. AU - Opeil, C. P. AU - Siegrist, T. AU - Littlewood, P. B. AU - Lashley, J. C. ID - 7078 IS - 18 JF - Physical Review B SN - 1098-0121 TI - Tin telluride: A weakly co-elastic metal VL - 82 ER - TY - JOUR AB - We have observed that reacting Pb:Te:Ag:Se in a 1:1:1.9:1 molar ratio gives rise to what appears to be a predominantly single-phase alloy, which crystallizes in the PbSe cF8 fcc structure. However, further investigation of the structure using energy dispersive x-ray analysis reveals the presence of two phases, PbSe and β-Ag2Te, with identical lattice parameters. The total thermal conductivity of the formed alloy is remarkably low for a crystalline material, κT<0.6W∕mK at 675K, it is reproducible, and in addition, the compound has good mechanical properties. AU - Drymiotis, Fivos R. AU - Drye, Tyler B. AU - Wang, Yisha AU - He, Jian AU - Rhodes, Daniel AU - Modic, Kimberly A AU - Cawthorne, Samantha AU - Zhang, Qiu Run ID - 7079 IS - 3 JF - Journal of Applied Physics SN - 0021-8979 TI - Structure formation and very low thermal conductivity in Pb:Te:Ag:Se mixtures VL - 107 ER - TY - JOUR AB - The decomposition reaction of H2O2 aqueous solutions (H2O2 - H2O + 1/2O2) catalyzed by transition metal oxide powders has been compared with the charging voltage of nonaqueous Li-O2 cells containing the same catalyst. An inverse linear relationship between Ln k (rate constant for the H2O2 decomposition) and the charging voltage has been found, despite differences in media and possible mechanistic differences. The results suggest that the decomposition may be a reliable, useful, and fast screening tool for materials that promote the charging process of the Li-O2 battery and may ultimately give insight into the charging mechanism. AU - Giordani, V. AU - Freunberger, Stefan Alexander AU - Bruce, P. G. AU - Tarascon, J.-M. AU - Larcher, D. ID - 7318 IS - 12 JF - Electrochemical and Solid-State Letters SN - 1099-0062 TI - H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells VL - 13 ER - TY - CONF AB - Most people believe that renaming is easy: simply choose a name at random; if more than one process selects the same name, then try again. We highlight the issues that occur when trying to implement such a scheme and shed new light on the read-write complexity of randomized renaming in an asynchronous environment. At the heart of our new perspective stands an adaptive implementation of a randomized test-and-set object, that has poly-logarithmic step complexity per operation, with high probability. Interestingly, our implementation is anonymous, as it does not require process identifiers. Based on this implementation, we present two new randomized renaming algorithms. The first ensures a tight namespace of n names using O( n log4 n) total steps, with high probability. This significantly improves on the complexity of the best previously known namespace-optimal algorithms. The second algorithm achieves a namespace of size k (1 + ε) using O( k log4 k / log2 (1 + ε) ) total steps, both with high probability, where k is the total contention in the execution. It is the first adaptive randomized renaming algorithm, and it improves on existing deterministic solutions by providing a smaller namespace, and by lowering step complexity. AU - Alistarh, Dan-Adrian AU - Attiya, Hagit AU - Gilbert, Seth AU - Giurgiu, Andrei AU - Guerraoui, Rachid ID - 754 TI - Fast randomized test-and-set and renaming VL - 6343 LNCS ER - TY - CONF AB - Gossip, also known as epidemic dissemination, is becoming an increasingly popular technique in distributed systems. Yet, it has remained a partially open question: how robust are such protocols? We consider a natural extension of the random phone-call model (introduced by Karp et al. [1]), and we analyze two different notions of robustness: the ability to tolerate adaptive failures, and the ability to tolerate oblivious failures. For adaptive failures, we present a new gossip protocol, TrickleGossip, which achieves near-optimal O(n log 3 n) message complexity. To the best of our knowledge, this is the first epidemic-style protocol that can tolerate adaptive failures. We also show a direct relation between resilience and message complexity, demonstrating that gossip protocols which tolerate a large number of adaptive failures need to use a super-linear number of messages with high probability. For oblivious failures, we present a new gossip protocol, CoordinatedGossip, that achieves optimal O(n) message complexity. This protocol makes novel use of the universe reduction technique to limit the message complexity. AU - Alistarh, Dan-Adrian AU - Gilbert, Seth AU - Guerraoui, Rachid AU - Zadimoghaddam, Morteza ID - 755 IS - PART 2 TI - How efficient can gossip be? (On the cost of resilient information exchange) VL - 6199 LNCS ER - TY - CONF AB - This paper studies non-cryptographic authenticated broadcast in radio networks subject to malicious failures. We introduce two protocols that address this problem. The first, NeighborWatchRB, makes use of a novel strategy in which honest devices monitor their neighbors for malicious behavior. Second, we present a more robust variant, MultiPathRB, that tolerates the maximum possible density of malicious devices per region, using an elaborate voting strategy. We also introduce a new proof technique to show that both protocols ensure asymptotically optimal running time. We demonstrate the fault tolerance of our protocols through extensive simulation. Simulations show the practical superiority of the NeighborWatchRB protocol (an advantage hidden in the constants of the asymptotic complexity). The NeighborWatchRB protocol even performs relatively well when compared to the simple, fast epidemic protocols commonly used in the radio setting, protocols that tolerate no malicious faults. We therefore believe that the overhead for ensuring authenticated broadcast is reasonable, especially in applications that use authenticated broadcast only when necessary, such as distributing an authenticated digest. AU - Alistarh, Dan-Adrian AU - Gilbert, Seth AU - Guerraoui, Rachid AU - Milošević, Žarko AU - Newport, Calvin ID - 756 TI - Securing every bit: Authenticated broadcast in radio networks ER - TY - CONF AB - 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. AU - Alistarh, Dan-Adrian AU - Gilbert, Seth AU - Guerraoui, Rachid AU - Travers, Corentin ID - 758 TI - Brief announcement: New bounds for partially synchronous set agreement VL - 6343 LNCS ER - TY - JOUR AB - 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. AU - Wright, Ian AU - Higginbotham, Andrew P AU - Baker, Shenda AU - Donnelly, Tom ID - 89 IS - 8 JF - ACS Applied Materials and Interfaces TI - Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution VL - 2 ER - TY - JOUR AB - 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. AU - Innan, Hideki AU - Fyodor Kondrashov ID - 891 IS - 2 JF - Nature Reviews Genetics TI - The evolution of gene duplications: Classifying and distinguishing between models VL - 11 ER - TY - JOUR AB - 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. AU - Palacci, Jérémie A AU - Abécassis, Benjamin AU - Cottin-Bizonne, Cécile AU - Ybert, Christophe AU - Bocquet, Lydéric ID - 9012 IS - 13 JF - Physical Review Letters SN - 00319007 TI - Colloidal motility and pattern formation under rectified diffusiophoresis VL - 104 ER - TY - JOUR AB - 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. AU - Palacci, Jérémie A AU - Cottin-Bizonne, Cécile AU - Ybert, Christophe AU - Bocquet, Lydéric ID - 9013 IS - 8 JF - Physical Review Letters SN - 00319007 TI - Sedimentation and effective temperature of active colloidal suspensions VL - 105 ER - TY - JOUR AB - 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). AU - Breen, Michael S AU - Fyodor Kondrashov ID - 901 JF - Biology Direct TI - Mitochondrial pathogenic mutations are population-specific VL - 5 ER - TY - JOUR AB - We have found a new way to express the solutions of the RSM (Reynolds Stress Model) equations that allows us to present the turbulent diffusivities for heat, salt and momentum in a way that is considerably simpler and thus easier to implement than in previous work. The RSM provides the dimensionless mixing efficiencies Γα (α stands for heat, salt and momentum). However, to compute the diffusivities, one needs additional information, specifically, the dissipation ε. Since a dynamic equation for the latter that includes the physical processes relevant to the ocean is still not available, one must resort to different sources of information outside the RSM to obtain a complete Mixing Scheme usable in OGCMs. As for the RSM results, we show that the Γα’s are functions of both Ri and Rρ (Richardson number and density ratio representing double diffusion, DD); the Γα are different for heat, salt and momentum; in the case of heat, the traditional value Γh = 0.2 is valid only in the presence of strong shear (when DD is inoperative) while when shear subsides, NATRE data show that Γh can be three times as large, a result that we reproduce. The salt Γs is given in terms of Γh. The momentum Γm has thus far been guessed with different prescriptions while the RSM provides a well defined expression for Γm(Ri, Rρ). Having tested Γh, we then test the momentum Γm by showing that the turbulent Prandtl number Γm/Γh vs. Ri reproduces the available data quite well. As for the dissipation ε, we use different representations, one for the mixed layer (ML), one for the thermocline and one for the ocean’s bottom. For the ML, we adopt a procedure analogous to the one successfully used in PB (planetary boundary layer) studies; for the thermocline, we employ an expression for the variable εN−2 from studies of the internal gravity waves spectra which includes a latitude dependence; for the ocean bottom, we adopt the enhanced bottom diffusivity expression used by previous authors but with a state of the art internal tidal energy formulation and replace the fixed Γα = 0.2 with the RSM result that brings into the problem the Ri, Rρ dependence of the Γα; the unresolved bottom drag, which has thus far been either ignored or modeled with heuristic relations, is modeled using a formalism we previously developed and tested in PBL studies. We carried out several tests without an OGCM. Prandtl and flux Richardson numbers vs. Ri. The RSM model reproduces both types of data satisfactorily. DD and Mixing efficiency Γh(Ri, Rρ). The RSM model reproduces well the NATRE data. Bimodal ε-distribution. NATRE data show that ε(Ri < 1) ≈ 10ε(Ri > 1), which our model reproduces. Heat to salt flux ratio. In the Ri ≫ 1 regime, the RSM predictions reproduce the data satisfactorily. NATRE mass diffusivity. The z-profile of the mass diffusivity reproduces well the measurements at NATRE. The local form of the mixing scheme is algebraic with one cubic equation to solve. AU - Canuto, V.M. AU - Howard, A.M. AU - Cheng, Y. AU - Muller, Caroline J AU - Leboissetier, A. AU - Jayne, S.R. ID - 9145 IS - 3-4 JF - Ocean Modelling KW - Computer Science (miscellaneous) KW - Geotechnical Engineering and Engineering Geology KW - Atmospheric Science KW - Oceanography SN - 1463-5003 TI - Ocean turbulence, III: New GISS vertical mixing scheme VL - 34 ER - TY - JOUR AB - The factors governing the rate of change in the amount of atmospheric water vapor are analyzed in simulations of climate change. The global-mean amount of water vapor is estimated to increase at a differential rate of 7.3% K − 1 with respect to global-mean surface air temperature in the multi-model mean. Larger rates of change result if the fractional change is evaluated over a finite change in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean column water vapor range from 6 to 12% K − 1 depending on latitude. Clausius–Clapeyron scaling is directly evaluated using an invariant distribution of monthly-mean relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor in the tropics and mid-latitudes, but they largely cancel in the global mean. A purely thermodynamic scaling based on a saturated troposphere gives a higher global rate of 7.9% K − 1. Surface specific humidity increases at a rate of 5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there are widespread decreases in surface relative humidity over land (by more than 1% K − 1 in many regions), and it is argued that decreases of this magnitude could result from the land/ocean contrast in surface warming. AU - O’Gorman, P A AU - Muller, Caroline J ID - 9146 IS - 2 JF - Environmental Research Letters KW - Renewable Energy KW - Sustainability and the Environment KW - Public Health KW - Environmental and Occupational Health KW - General Environmental Science SN - 1748-9326 TI - How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? VL - 5 ER - TY - JOUR AB - Most eukaryotic cells sense and respond to the mechanical properties of their surroundings. This can strongly influence their collective behavior in embryonic development, tissue function, and wound healing. We use a deformable substrate to measure collective behavior in cell motion due to substrate mediated cell-cell interactions. We quantify spatial and temporal correlations in migration velocity and substrate deformation, and show that cooperative cell-driven patterns of substrate deformation mediate long-distance mechanical coupling between cells and control collective cell migration. AU - Angelini, Thomas AU - Hannezo, Edouard B AU - Trepat, Xavier AU - Fredberg, Jeffrey AU - Weitz, David ID - 920 IS - 16 JF - Physical Review Letters TI - Cell migration driven by cooperative substrate deformation patterns VL - 104 ER - TY - JOUR AB - Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops. AU - Zemach, Assaf AU - Kim, M. Yvonne AU - Silva, Pedro AU - Rodrigues, Jessica A. AU - Dotson, Bradley AU - Brooks, Matthew D. AU - Zilberman, Daniel ID - 9485 IS - 43 JF - Proceedings of the National Academy of Sciences SN - 0027-8424 TI - Local DNA hypomethylation activates genes in rice endosperm VL - 107 ER - TY - JOUR AB - Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries. AU - Zemach, Assaf AU - Zilberman, Daniel ID - 9489 IS - 17 JF - Current Biology SN - 0960-9822 TI - Evolution of eukaryotic DNA methylation and the pursuit of safer sex VL - 20 ER - TY - JOUR AB - 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. AU - Corazza, Alessandra AU - Rennella, Enrico AU - Schanda, Paul AU - Mimmi, Maria Chiara AU - Cutuil, Thomas AU - Raimondi, Sara AU - Giorgetti, Sofia AU - Fogolari, Federico AU - Viglino, Paolo AU - Frydman, Lucio AU - Gal, Maayan AU - Bellotti, Vittorio AU - Brutscher, Bernhard AU - Esposito, Gennaro ID - 8473 IS - 8 JF - Journal of Biological Chemistry KW - Cell Biology KW - Biochemistry KW - Molecular Biology SN - 0021-9258 TI - Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR VL - 285 ER - TY - JOUR AB - 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. AU - Schanda, Paul AU - Meier, Beat H. AU - Ernst, Matthias ID - 8472 IS - 45 JF - Journal of the American Chemical Society SN - 0002-7863 TI - Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy VL - 132 ER - TY - CONF AB - 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 . AU - Kaloshin, Vadim AU - ZHANG, KE AU - ZHENG, YONG ID - 8507 SN - 9789814304627 T2 - XVIth International Congress on Mathematical Physics TI - Almost dense orbit on energy surface ER - TY - CHAP AU - Hunt, Brian R. AU - Kaloshin, Vadim ID - 8506 SN - 1874-575X T2 - Handbook of Dynamical Systems TI - Prevalence VL - 3 ER - TY - JOUR AB - 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. AU - Povolotskaya, Inna AU - Fyodor Kondrashov ID - 857 IS - 7300 JF - Nature TI - Sequence space and the ongoing expansion of the protein universe VL - 465 ER - TY - JOUR AB - 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. AU - Meer, Margarita V AU - Kondrashov, Alexey S AU - Artzy-Randrup, Yael AU - Fyodor Kondrashov ID - 862 IS - 7286 JF - Nature TI - Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness VL - 464 ER - TY - JOUR AB - 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. AU - Fyodor Kondrashov AU - Kondrashov, Alexey S ID - 872 IS - 1544 JF - Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences TI - Measurements of spontaneous rates of mutations in the recent past and the near future VL - 365 ER - TY - JOUR AB - 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. AU - Kondrashov, Alexey S AU - Povolotskaya, Inna AU - Ivankov, Dmitry N AU - Fyodor Kondrashov ID - 884 JF - Biology Direct TI - Rate of sequence divergence under constant selection VL - 5 ER - TY - JOUR AB - Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes. AU - Zemach, Assaf AU - McDaniel, Ivy E. AU - Silva, Pedro AU - Zilberman, Daniel ID - 9452 IS - 5980 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Genome-wide evolutionary analysis of eukaryotic DNA methylation VL - 328 ER - TY - JOUR AB - Crosses between closely related species give two contrasting results. One result is that species hybrids may be inferior to their parents, for example, being less fertile [1]. The other is that F1 hybrids may display superior performance (heterosis), for example with increased vigour [2]. Although various hypotheses have been proposed to account for these two aspects of hybridisation, their biological basis is still poorly understood [3]. To gain further insights into this issue, we analysed the role that variation in gene expression may play. We took a conserved trait, flower asymmetry in Antirrhinum, and determined the extent to which the underlying regulatory genes varied in expression among closely related species. We show that expression of both genes analysed, CYC and RAD, varies significantly between species because of cis-acting differences. By making a quantitative genotype-phenotype map, using a range of mutant alleles, we demonstrate that the species lie on a plateau in gene expression-morphology space, so that the variation has no detectable phenotypic effect. However, phenotypic differences can be revealed by shifting genotypes off the plateau through genetic crosses. Our results can be readily explained if genomes are free to evolve within an effectively neutral zone in gene expression space. The consequences of this drift will be negligible for individual loci, but when multiple loci across the genome are considered, we show that the variation may have significant effects on phenotype and fitness, causing a significant drift load. By considering these consequences for various gene-expression-fitness landscapes, we conclude that F1 hybrids might be expected to show increased performance with regard to conserved traits, such as basic physiology, but reduced performance with regard to others. Thus, our study provides a new way of explaining how various aspects of hybrid performance may arise through natural variation in gene activity. AU - Rosas, Ulises AU - Barton, Nicholas H AU - Copsey, Lucy AU - Barbier De Reuille, Pierre AU - Coen, Enrico ID - 3779 IS - 7 JF - PLoS Biology TI - Cryptic variation between species and the basis of hybrid performance VL - 8 ER - TY - GEN AU - Rosas, Ulises AU - Barton, Nicholas H AU - Copsey, Lucy AU - Barbier De Reuille, Pierre AU - Coen, Enrico ID - 9764 TI - Heterosis and the drift load ER - TY - JOUR AB - The four microsporangia of the flowering plant anther develop from archesporial cells in the L2 of the primordium. Within each microsporangium, developing microsporocytes are surrounded by concentric monolayers of tapetal, middle layer and endothecial cells. How this intricate array of tissues, each containing relatively few cells, is established in an organ possessing no formal meristems is poorly understood. We describe here the pivotal role of the LRR receptor kinase EXCESS MICROSPOROCYTES 1 (EMS1) in forming the monolayer of tapetal nurse cells in Arabidopsis. Unusually for plants, tapetal cells are specified very early in development, and are subsequently stimulated to proliferate by a receptor-like kinase (RLK) complex that includes EMS1. Mutations in members of this EMS1 signalling complex and its putative ligand result in male-sterile plants in which tapetal initials fail to proliferate. Surprisingly, these cells continue to develop, isolated at the locular periphery. Mutant and wild-type microsporangia expand at similar rates and the ‘tapetal’ space at the periphery of mutant locules becomes occupied by microsporocytes. However, induction of late expression of EMS1 in the few tapetal initials in ems1 plants results in their proliferation to generate a functional tapetum, and this proliferation suppresses microsporocyte number. Our experiments also show that integrity of the tapetal monolayer is crucial for the maintenance of the polarity of divisions within it. This unexpected autonomy of the tapetal ‘lineage’ is discussed in the context of tissue development in complex plant organs, where constancy in size, shape and cell number is crucial. AU - Feng, Xiaoqi AU - Dickinson, Hugh G. ID - 12199 IS - 14 JF - Development KW - Developmental Biology KW - Molecular Biology KW - Anther Tapetum KW - Arabidopsis KW - Cell Fate Establishment KW - EMS1 KW - Reproductive Cell Lineage SN - 1477-9129 TI - Tapetal cell fate, lineage and proliferation in the Arabidopsis anther VL - 137 ER - TY - JOUR AB - Key steps in the evolution of the angiosperm anther include the patterning of the concentrically organized microsporangium and the incorporation of four such microsporangia into a leaf-like structure. Mutant studies in the model plant Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the cell lineages culminating in the different cell types present in the microsporangium (the microsporocytes, the tapetum, and the middle and endothecial layers), and (ii) some of the genes responsible for specifying their fates. However, the processes that confer polarity on the developing anther and position the microsporangia within it remain unclear. Certainly, data from a range of experimental strategies suggest that hormones play a central role in establishing polarity and the patterning of the anther initial, and may be responsible for locating the microsporangia. But the fact that microsporangia were originally positioned externally suggests that their development is likely to be autonomous, perhaps with the reproductive cells generating signals controlling the growth and division of the investing anther epidermis. These possibilities are discussed in the context of the expression of genes which initiate and maintain male and female reproductive development, and in the perspective of our current views of anther evolution. AU - Feng, Xiaoqi AU - Dickinson, Hugh G. ID - 12200 IS - 2 JF - Biochemical Society Transactions KW - Biochemistry KW - Anther Development KW - Arabidopsis KW - Cell Fate KW - Microsporangium KW - Polarity KW - Receptor Kinase SN - 0300-5127 TI - Cell–cell interactions during patterning of the Arabidopsis anther VL - 38 ER - TY - JOUR AB - A range (Au, Pt, Pd) of metal nanoparticles (MNPs) has been prepared and functionalized with (a) redox-active stalks containing tetrathiafulvalene (TTF) units, (b) [2]pseudorotaxanes formed between these stalks and cyclobis(paraquat-p-phenylene) (CBPQT4+) rings, and (c) bistable [2]rotaxane molecules where the dumbbell component contains a 1,5-dioxynaphthalene (DNP) unit, as well as a TTF unit, encircled by a CBPQT4+ ring. It transpires that the molecules present in (a) and (c) and the supermolecules described in (b) retain their switching characteristics, previously observed in solution, when they are immobilized onto MNPs. Moreover, their oxidation potentials depend on the fraction, χ, of the molecules or supermolecules on the surface of the nanoparticles. A variation in χ affects the oxidation potentials of the TTF units to the extent that switching can be subjected to fine tuning as a result. Specifically, increasing χ results in positive shifts (i) in the oxidation potentials of the TTF unit in (a)−(c) and (ii) the reduction potentials of the CBPQT4+ rings in (c). These shifts can be attributed to an increase in the electrostatic potential surrounding the MNPs. Both the magnitude and the direction of these shifts are reproduced by a model, based on the Poisson−Boltzmann equation coupled with charge-regulating boundary conditions. Furthermore, the kinetics of relaxation from the metastable state coconformation (MSCC) to the ground-state coconformation (GSCC) of the bistable [2]rotaxane molecules also depends on χ, as well as on the nanoparticle diameter. Increasing either of these parameters accelerates the rate of relaxation from the MSCC to the GSCC. This rate is a function of (i) the activation energy for the relaxation process associated with the bistable [2]rotaxane molecules in solution and (ii) the electrostatic potential surrounding the MNPs. The electrostatic potential depends on (i) the diameter of the MNPs, (ii) the amount of the bistable [2]rotaxane molecules on the surface of the MNPs, and (iii) the equilibrium distribution of the CBPQT4+ rings between the DNP and TTF recognition sites in the GSCC. This electrostatic potential has also been quantified using the Poisson−Boltzmann equation, leading to faithful estimates of the rate constants. AU - Coskun, Ali AU - Wesson, Paul J. AU - Klajn, Rafal AU - Trabolsi, Ali AU - Fang, Lei AU - Olson, Mark A. AU - Dey, Sanjeev K. AU - Grzybowski, Bartosz A. AU - Stoddart, J. Fraser ID - 13410 IS - 12 JF - Journal of the American Chemical Society KW - Colloid and Surface Chemistry KW - Biochemistry KW - General Chemistry KW - Catalysis SN - 0002-7863 TI - Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory VL - 132 ER - TY - JOUR AB - The immobilization of molecular switches onto inorganic supports has recently become a hot topic as it can give rise to novel hybrid materials in which the properties of the two components are mutually enhanced. Even more attractive is the concept of “transferring” the switchable characteristics of single layers of organic molecules onto the underlying inorganic components, rendering them responsive to external stimuli as well. Of the various molecular switches studied, azobenzene (AB) has arguably attracted most attention due to its simple molecular structure, and because its “trigger” (light) is a noninvasive one, it can be delivered instantaneously, and into a precise location. In order to fully realize its potential, however, it is necessary to immobilize AB onto solid supports. It is the goal of this manuscript to comprehensively yet concisely review such hybrid systems which comprise AB forming well-defined self-assembled monolayers (SAMs) on planar and curved (colloidal and nanoporous) inorganic surfaces. I discuss methods to immobilize AB derivatives onto surfaces, strategies to ensure efficient AB isomerization, ways to monitor the switching process, properties of these switchable hybrid materials, and, last but not least, their emerging applications. AU - Klajn, Rafal ID - 13409 IS - 12 JF - Pure and Applied Chemistry KW - General Chemical Engineering KW - General Chemistry SN - 0033-4545 TI - Immobilized azobenzenes for the construction of photoresponsive materials VL - 82 ER - TY - JOUR AB - Nanoparticles (NPs) and molecular/supramolecular switches have attracted considerable interest during the past decade on account of their unique properties and prominent roles in the fields of organic chemistry and materials science. Materials derived from the combination of these two components are now emerging in the literature. This critical review evaluates materials which comprise NPs functionalised with well-defined self-assembled monolayers of molecular and supramolecular switches. We draw attention to the fact that immobilisation of switches on NPs does not, in general, hamper their switching ability, although it can impart new properties on the supporting particles. This premise leads us to the discussion of systems in which switching on the surfaces of NPs can be used to modulate reversibly a range of NP properties—optical, fluorescent, electrical, magnetic—as well as the controlled release of small molecules. Finally, we discuss examples in which molecular switches direct reversible self-assembly of NPs (308 references). AU - Klajn, Rafal AU - Stoddart, J. Fraser AU - Grzybowski, Bartosz A. ID - 13412 IS - 6 JF - Chemical Society Reviews KW - General Chemistry SN - 0306-0012 TI - Nanoparticles functionalised with reversible molecular and supramolecular switches VL - 39 ER - TY - JOUR AB - Photoresponsive gold nanoparticles dispersed in a solid/frozen matrix provide a basis for sensors that “remember” whether the sample has ever exceeded the melting temperature of the matrix. The operation of these sensors rests on the ability to photoinduce metastable electric dipoles on NP surfaces – upon melting, these dipoles drive NP aggregation, precipitation, and crosslinking. These events are manifested by a pronounced color change. AU - Klajn, Rafal AU - Browne, Kevin P. AU - Soh, Siowling AU - Grzybowski, Bartosz A. ID - 13411 IS - 13 JF - Small KW - Biomaterials KW - Biotechnology KW - General Materials Science KW - General Chemistry SN - 1613-6810 TI - Nanoparticles that “remember” temperature VL - 6 ER - TY - CONF AB - We introduce two-level discounted games played by two players on a perfect-information stochastic game graph. The upper level game is a discounted game and the lower level game is an undiscounted reachability game. Two-level games model hierarchical and sequential decision making under uncertainty across different time scales. We show the existence of pure memoryless optimal strategies for both players and an ordered field property for such games. We show that if there is only one player (Markov decision processes), then the values can be computed in polynomial time. It follows that whether the value of a player is equal to a given rational constant in two-level discounted games can be decided in NP intersected coNP. We also give an alternate strategy improvement algorithm to compute the value. AU - Chatterjee, Krishnendu AU - Majumdar, Ritankar ID - 3852 TI - Discounting in games across time scales VL - 25 ER - TY - THES AU - Pflicke, Holger ID - 3962 SN - 2663-337X TI - Dendritic cell migration across basement membranes in the skin ER - TY - CONF AB - Depth-bounded processes form the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. In this paper we develop an adequate domain of limits for the well-structured transition systems that are induced by depth-bounded processes. An immediate consequence of our result is that there exists a forward algorithm that decides the covering problem for this class. Unlike backward algorithms, the forward algorithm terminates even if the depth of the process is not known a priori. More importantly, our result suggests a whole spectrum of forward algorithms that enable the effective verification of a large class of mobile systems. AU - Wies, Thomas AU - Zufferey, Damien AU - Henzinger, Thomas A ED - Ong, Luke ID - 4361 TI - Forward analysis of depth-bounded processes VL - 6014 ER - TY - JOUR AB - Most fisheries involving spiny lobsters of the genus Palinurus have been over exploited during the last decades, so there is a raising concern about management decisions for these valuable resources. A total of 13 microsatellite DNA loci recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave amplifications and showed polymorphism in all species, with gene diversity values varying from 0.65060.077 SD (Palinurus barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth distribution was taken into account, shallower waters pecies consistently showed larger historical effective population sizes than their deeper-water counterparts. This could explain why deeper-water species are more sensitive to overfishing, and would indicate that overexploitation may have a larger impact on their long-term genetic diversity. AU - Palero, Ferran AU - Abello, Pere AU - Macpherson, E. AU - Matthee, C. AU - Pascual, Marta ID - 3785 IS - 4 JF - Journal of Crustacean Biology SN - 0278-0372 TI - Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata) VL - 30 ER - TY - JOUR AB - 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. AU - Sweeney, Lora Beatrice Jaeger AU - Luo, Liqun ID - 7703 IS - 5 JF - Cell SN - 0092-8674 TI - ‘Fore brain: A hint of the ancestral cortex VL - 142 ER - TY - CHAP AB - This chapter tackles a difficult challenge: presenting signal processing material to non-experts. This chapter is meant to be comprehensible to people who have some math background, including a course in linear algebra and basic statistics, but do not specialize in mathematics, engineering, or related fields. Some formulas assume the reader is familiar with matrices and basic matrix operations, but not more advanced material. Furthermore, we tried to make the chapter readable even if you skip the formulas. Nevertheless, we include some simple methods to demonstrate the basics of adaptive data processing, then we proceed with some advanced methods that are fundamental in adaptive signal processing, and are likely to be useful in a variety of applications. The advanced algorithms are also online available [30]. In the second part, these techniques are applied to some real-world BCI data. AU - Schlögl, Alois AU - Vidaurre, Carmen AU - Müller, Klaus-Robert ED - Graimann, Bernhard ED - Pfurtscheller, Gert ED - Allison, Brendan ID - 14983 SN - 1612-3018 T2 - Brain-Computer Interfaces TI - Adaptive Methods in BCI Research - An Introductory Tutorial ER - TY - JOUR AB - One possible way to produce ultra-cold, high-phase-space-density quantum gases of molecules in the rovibronic ground state is given by molecule association from quantum-degenerate atomic gases on a Feshbach resonance and subsequent coherent optical multi-photon transfer into the rovibronic ground state. In ultra-cold samples of Cs2 molecules, we observe two-photon dark resonances that connect the intermediate rovibrational level |v=73,J=2 with the rovibrational ground state |v=0,J=0 of the singlet X 1 ∑ g + ground-state potential. For precise dark resonance spectroscopy we exploit the fact that it is possible to efficiently populate the level |v=73,J=2 by two-photon transfer from the dissociation threshold with the stimulated Raman adiabatic passage (STIRAP) technique. We find that at least one of the two-photon resonances is sufficiently strong to allow future implementation of coherent STIRAP transfer of a molecular quantum gas to the rovibrational ground state |v=0,J=0. AU - Mark, Manfred AU - Danzl, Johann G AU - Haller, Elmar AU - Gustavsson, Mattias AU - Bouloufa, Nadia AU - Dulieu, Olivier AU - Salami, Houssam AU - Bergeman, Thomas AU - Ritsch, Helmut AU - Hart, Russell AU - Nägerl, Hanns ID - 1038 IS - 2 JF - Applied Physics B: Lasers and Optics TI - Dark resonances for ground-state transfer of molecular quantum gases VL - 95 ER - TY - JOUR AB - Ultracold atomic physics offers myriad possibilities to study strongly correlated many-body systems in lower dimensions. Typically, only ground-state phases are accessible. Using a tunable quantum gas of bosonic cesium atoms, we realized and controlled in one-dimensional geometry a highly excited quantum phase that is stabilized in the presence of attractive interactions by maintaining and strengthening quantum correlations across a confinement-induced resonance. We diagnosed the crossover from repulsive to attractive interactions in terms of the stiffness and energy of the system. Our results open up the experimental study of metastable, excited, many-body phases with strong correlations and their dynamical properties. AU - Haller, Elmar AU - Gustavsson, Mattias AU - Mark, Manfred AU - Danzl, Johann G AU - Hart, Russell AU - Pupillo, Guido AU - Nägerl, Hanns ID - 1040 IS - 5945 JF - Science TI - Realization of an excited, strongly correlated quantum gas Phase VL - 325 ER - TY - JOUR AB - We demonstrate efficient transfer of ultracold molecules into a deeply bound rovibrational level of the singlet ground state potential in the presence of an optical lattice. The overall molecule creation efficiency is 25%, and the transfer efficiency to the rovibrational level |v = 73, J = 2) is above 80%. We find that the molecules in |v = 73, J = 2) are trapped in the optical lattice, and that the lifetime in the lattice is limited by optical excitation by the lattice light. The molecule trapping time for a lattice depth of 15 atomic recoil energies is about 20 ms. We determine the trapping frequency by the lattice phase and amplitude modulation technique. It will now be possible to transfer the molecules to the rovibrational ground state |v = 0, J = 0) in the presence of the optical lattice. AU - Danzl, Johann G AU - Mark, Manfred AU - Haller, Elmar AU - Gustavsson, Mattias AU - Hart, Russell AU - Liem, Andreas AU - Zellmer, Holger AU - Nägerl, Hanns ID - 1041 JF - New Journal of Physics TI - Deeply bound ultracold molecules in an optical lattice VL - 11 ER - TY - JOUR AB - One possibility for the creation of ultracold, high phase space density quantum gases of molecules in the rovibronic ground state relies on first associating weakly-bound molecules from quantum-degenerate atomic gases on a Feshbach resonance and then transferring the molecules via several steps of coherent two-photon stimulated Raman adiabatic passage (STIRAP) into the rovibronic ground state. Here, in ultracold samples of Cs2 Feshbach molecules produced out of ultracold samples of Cs atoms, we observe several optical transitions to deeply-bound rovibrational levels of the excited 0 u+ molecular potentials with high resolution. At least one of these transitions, although rather weak, allows efficient STIRAP transfer into the deeply-bound vibrational level v = 73> of the singlet X 1Σg+ ground state potential, as recently demonstrated (J. G. Danzl, E. Haller, M. Gustavsson, M. J. Mark, R. Hart, N. Bouloufa, O. Dulieu, H. Ritsch, and H.-C. Nägerl, Science, 2008, 321, 1062). From this level, the rovibrational ground state v = 0, J = 0> can be reached with one more transfer step. In total, our results show that coherent ground state transfer for Cs2 is possible using a maximum of two successive two-photon STIRAP processes or one single four-photon STIRAP process. AU - Danzl, Johann G AU - Mark, Manfred AU - Haller, Elmar AU - Gustavsson, Mattias AU - Bouloufa, Nadia AU - Dulieu, Olivier AU - Ritsch, Helmut AU - Hart, Russell AU - Nägerl, Hanns ID - 1043 JF - Faraday Discussions TI - Precision molecular spectroscopy for ground state transfer of molecular quantum gases VL - 142 ER - TY - JOUR AB - In order to better understand magnetic reconnection and particle acceleration in solar flares, we compare the RHESSI hard X-ray (HXR) footpoint motions of three flares with a detailed study of the corresponding topology given by a Magnetic Charge Topology model. We analyze the relationship between the footpoint motions and topological spine lines and find that the examined footpoint sources move along spine lines. We present a three-dimensional topological model in which this movement can be understood. As reconnection proceeds, flux is transferred between the reconnecting domains, causing the separator to move. The movement of the separator\'s chromospheric ends, identified with the HXR footpoints, is along those spine lines on which the separator ends. AU - Des Jardins, Angela AU - Canfield, Richard AU - Longcope, Dana AU - Fordyce, Crystal AU - Waitukaitis, Scott R ID - 110 IS - 2 JF - The Astrophysical Journal TI - Reconnection in three dimensions: The role of spines in three eruptive flares VL - 693 ER - TY - JOUR AB - Thin streams of liquid commonly break up into characteristic droplet patterns owing to the surface-tension-driven PlateauRayleigh instability 1-3. Very similar patterns are observed when initially uniform streams of dry granular material break up into clusters of grains4-6, even though flows of macroscopic particles are considered to lack surface tension7,8. Recent studies on freely falling granular streams tracked fluctuations in the stream profile9, but the clustering mechanism remained unresolved because the full evolution of the instability could not be observed. Here we demonstrate that the cluster formation is driven by minute, nanoNewton cohesive forces that arise from a combination of van der Waals interactions and capillary bridges between nanometre-scale surface asperities. Our experiments involve high-speed video imaging of the granular stream in the co-moving frame, control over the properties of the grain surfaces and the use of atomic force microscopy to measure grain-grain interactions. The cohesive forces that we measure correspond to an equivalent surface tension five orders of magnitude below that, of ordinary liquids. We find that, the shapes of these weakly cohesive, non-thermal clusters of macroscopic particles closely resemble droplets resulting from thermally induced rupture of liquid nanojets 10-12. AU - Royer, John AU - Evans, Daniel AU - Oyarte, Loreto AU - Guo, Qiti AU - Kapit, Eliot AU - Möbius, Matthias AU - Waitukaitis, Scott R AU - Jaeger, Heinrich ID - 111 IS - 7250 JF - Nature TI - High-speed tracking of rupture and clustering in freely falling granular streams VL - 459 ER - TY - JOUR AB - Over the last decade, the nuclear envelope (NE) has emerged as a key component in the organization and function of the nuclear genome. As many as 100 different proteins are thought to specifically localize to this double membrane that separates the cytoplasm and the nucleoplasm of eukaryotic cells. Selective portals through the NE are formed at sites where the inner and outer nuclear membranes are fused, and the coincident assembly of ∼30 proteins into nuclear pore complexes occurs. These nuclear pore complexes are essential for the control of nucleocytoplasmic exchange. Many of the NE and nuclear pore proteins are thought to play crucial roles in gene regulation and thus are increasingly linked to human diseases. AU - HETZER, Martin W AU - Wente, Susan R. ID - 11103 IS - 5 JF - Developmental Cell KW - Developmental Biology KW - Cell Biology KW - General Biochemistry KW - Genetics and Molecular Biology KW - Molecular Biology SN - 1534-5807 TI - Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes VL - 17 ER - TY - JOUR AB - Formation of the nuclear envelope (NE) around segregated chromosomes occurs by the reshaping of the endoplasmic reticulum (ER), a reservoir for disassembled nuclear membrane components during mitosis. In this study, we show that inner nuclear membrane proteins such as lamin B receptor (LBR), MAN1, Lap2β, and the trans-membrane nucleoporins Ndc1 and POM121 drive the spreading of ER membranes into the emerging NE via their capacity to bind chromatin in a collaborative manner. Despite their redundant functions, decreasing the levels of any of these trans-membrane proteins by RNAi-mediated knockdown delayed NE formation, whereas increasing the levels of any of them had the opposite effect. Furthermore, acceleration of NE formation interferes with chromosome separation during mitosis, indicating that the time frame over which chromatin becomes membrane enclosed is physiologically relevant and regulated. These data suggest that functionally distinct classes of chromatin-interacting membrane proteins, which are present at nonsaturating levels, collaborate to rapidly reestablish the nuclear compartment at the end of mitosis. AU - Anderson, Daniel J. AU - Vargas, Jesse D. AU - Hsiao, Joshua P. AU - HETZER, Martin W ID - 11106 IS - 2 JF - Journal of Cell Biology KW - Cell Biology SN - 0021-9525 TI - Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo VL - 186 ER - TY - JOUR AB - Nucleocytoplasmic transport occurs exclusively through nuclear pore complexes (NPCs) embedded in pores formed by inner and outer nuclear membrane fusion. The mechanism for de novo pore and NPC biogenesis remains unclear. Reticulons (RTNs) and Yop1/DP1 are conserved membrane protein families required to form and maintain the tubular endoplasmic reticulum (ER) and the postmitotic nuclear envelope. In this study, we report that members of the RTN and Yop1/DP1 families are required for nuclear pore formation. Analysis of Saccharomyces cerevisiae prp20-G282S and nup133Δ NPC assembly mutants revealed perturbations in Rtn1–green fluorescent protein (GFP) and Yop1-GFP ER distribution and colocalization to NPC clusters. Combined deletion of RTN1 and YOP1 resulted in NPC clustering, nuclear import defects, and synthetic lethality with the additional absence of Pom34, Pom152, and Nup84 subcomplex members. We tested for a direct role in NPC biogenesis using Xenopus laevis in vitro assays and found that anti-Rtn4a antibodies specifically inhibited de novo nuclear pore formation. We hypothesize that these ER membrane–bending proteins mediate early NPC assembly steps. AU - Dawson, T. Renee AU - Lazarus, Michelle D. AU - HETZER, Martin W AU - Wente, Susan R. ID - 11107 IS - 5 JF - Journal of Cell Biology KW - Cell Biology SN - 0021-9525 TI - ER membrane–bending proteins are necessary for de novo nuclear pore formation VL - 184 ER - TY - JOUR AB - In dividing cells, nuclear pore complexes (NPCs) disassemble during mitosis and reassemble into the newly forming nuclei. However, the fate of nuclear pores in postmitotic cells is unknown. Here, we show that NPCs, unlike other nuclear structures, do not turn over in differentiated cells. While a subset of NPC components, like Nup153 and Nup50, are continuously exchanged, scaffold nucleoporins, like the Nup107/160 complex, are extremely long-lived and remain incorporated in the nuclear membrane during the entire cellular life span. Besides the lack of nucleoporin expression and NPC turnover, we discovered an age-related deterioration of NPCs, leading to an increase in nuclear permeability and the leaking of cytoplasmic proteins into the nucleus. Our finding that nuclear “leakiness” is dramatically accelerated during aging and that a subset of nucleoporins is oxidatively damaged in old cells suggests that the accumulation of damage at the NPC might be a crucial aging event. AU - D'Angelo, Maximiliano A. AU - Raices, Marcela AU - Panowski, Siler H. AU - HETZER, Martin W ID - 11108 IS - 2 JF - Cell KW - General Biochemistry KW - Genetics and Molecular Biology SN - 0092-8674 TI - Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells VL - 136 ER - TY - JOUR AB - Nuclear-pore complexes (NPCs) are large protein channels that span the nuclear envelope (NE), which is a double membrane that encloses the nuclear genome of eukaryotes. Each of the typically 2,000–4,000 pores in the NE of vertebrate cells is composed of multiple copies of 30 different proteins known as nucleoporins. The evolutionarily conserved NPC proteins have the well-characterized function of mediating the transport of molecules between the nucleoplasm and the cytoplasm. Mutations in nucleoporins are often linked to specific developmental defects and disease, and the resulting phenotypes are usually interpreted as the consequences of perturbed nuclear transport activity. However, recent evidence suggests that NPCs have additional functions in chromatin organization and gene regulation, some of which might be independent of nuclear transport. Here, we review the transport-dependent and transport-independent roles of NPCs in the regulation of nuclear function and gene expression. AU - Capelson, Maya AU - HETZER, Martin W ID - 11105 IS - 7 JF - EMBO reports KW - Genetics KW - Molecular Biology KW - Biochemistry SN - 1469-221X TI - The role of nuclear pores in gene regulation, development and disease VL - 10 ER - TY - CONF AB - We study the problem of matching bidders to items where each bidder i has general, strictly monotonic utility functions u i,j (p j ) expressing her utility of being matched to item j at price p j . For this setting we prove that a bidder optimal outcome always exists, even when the utility functions are non-linear and non-continuous. Furthermore, we give an algorithm to find such a solution. Although the running time of this algorithm is exponential in the number of items, it is polynomial in the number of bidders. AU - Dütting, Paul AU - Henzinger, Monika H AU - Weber, Ingmar ID - 11799 SN - 1611-3349 T2 - 5th International Workshop on Internet and Network Economics TI - Bidder optimal assignments for general utilities VL - 5929 ER - TY - CONF AB - As the World Wide Web is growing rapidly, it is getting increasingly challenging to gather representative information about it. Instead of crawling the web exhaustively one has to resort to other techniques like sampling to determine the properties of the web. A uniform random sample of the web would be useful to determine the percentage of web pages in a specific language, on a topic or in a top level domain. Unfortunately, no approach has been shown to sample the web pages in an unbiased way. Three promising web sampling algorithms are based on random walks. They each have been evaluated individually, but making a comparison on different data sets is not possible. We directly compare these algorithms in this paper. We performed three random walks on the web under the same conditions and analyzed their outcomes in detail. We discuss the strengths and the weaknesses of each algorithm and propose improvements based on experimental results. AU - Baykan, Eda AU - Henzinger, Monika H AU - Keller, Stefan F. AU - de Castelberg, Sebastian AU - Kinzler, Markus ID - 11912 SN - 1868-8969 T2 - 26th International Symposium on Theoretical Aspects of Computer Science TI - A comparison of techniques for sampling web pages VL - 3 ER - TY - CONF AB - Given only the URL of a web page, can we identify its topic? This is the question that we examine in this paper. Usually, web pages are classified using their content, but a URL-only classifier is preferable, (i) when speed is crucial, (ii) to enable content filtering before an (objection-able) web page is downloaded, (iii) when a page's content is hidden in images, (iv) to annotate hyperlinks in a personalized web browser, without fetching the target page, and (v) when a focused crawler wants to infer the topic of a target page before devoting bandwidth to download it. We apply a machine learning approach to the topic identification task and evaluate its performance in extensive experiments on categorized web pages from the Open Directory Project (ODP). When training separate binary classifiers for each topic, we achieve typical F-measure values between 80 and 85, and a typical precision of around 85. We also ran experiments on a small data set of university web pages. For the task of classifying these pages into faculty, student, course and project pages, our methods improve over previous approaches by 13.8 points of F-measure. AU - Baykan, Eda AU - Henzinger, Monika H AU - Marian, Ludmila AU - Weber, Ingmar ID - 11905 SN - 978-1-60558-487-4 T2 - 18th International World Wide Web Conference TI - Purely URL-based topic classification ER - TY - CONF AB - In the origin detection problem an algorithm is given a set S of documents, ordered by creation time, and a query document D. It needs to output for every consecutive sequence of k alphanumeric terms in D the earliest document in $S$ in which the sequence appeared (if such a document exists). Algorithms for the origin detection problem can, for example, be used to detect the "origin" of text segments in D and thus to detect novel content in D. They can also find the document from which the author of D has copied the most (or show that D is mostly original.) We concentrate on solutions that use only a fixed amount of memory. We propose novel algorithms for this problem and evaluate them together with a large number of previously published algorithms. Our results show that (1) detecting the origin of text segments efficiently can be done with very high accuracy even when the space used is less than 1% of the size of the documents in $S$, (2) the precision degrades smoothly with the amount of available space, (3) various estimation techniques can be used to increase the performance of the algorithms. AU - Abdel Hamid, Ossama AU - Behzadi, Behshad AU - Christoph, Stefan AU - Henzinger, Monika H ID - 11906 SN - 978-160558487-4 T2 - 18th International World Wide Web Conference TI - Detecting the origin of text segments efficiently ER - TY - JOUR AB - We investigate the transferability of an enhanced temperature-index melt model that was developed and tested on Haut Glacier d’Arolla, Switzerland, in the 2001 season. The model’s empirical parameters (temperature factor, TF, and shortwave radiation factor, SRF) are recalibrated for: (1) other locations on Haut Glacier d’Arolla; (2) subperiods of distinct meteorological conditions; (3) different years on Haut Glacier d’Arolla; and (4) other glaciers in different years. The model parameters are optimized against simulations of an energy-balance model validated against ablation observations. Results are compared with those obtained with the original parameters. The model works very well when applied to other sites, seasons and glaciers, with the exception of overcast conditions. Differences are due to underestimation of high melt rates. The parameter values are associated with the prevailing energy-balance conditions, showing that high SRF are obtained on clear-sky days, whereas higher TF are typical of locations where glacier winds prevail and turbulent fluxes are high. We also provide a range of parameters clearly associated with the site’s location and its meteorological characteristics that could help to assign parameter values to sites where few data are available. AU - Carenzo, Marco AU - Pellicciotti, Francesca AU - Rimkus, Stefan AU - Burlando, Paolo ID - 12654 IS - 190 JF - Journal of Glaciology SN - 0022-1430 TI - Assessing the transferability and robustness of an enhanced temperature-index glacier-melt model VL - 55 ER - TY - JOUR AB - We discuss the inclusion of the subsurface heat-conduction flux into the calculation of the energy balance and ablation at the glacier–atmosphere interface. Data from automatic weather stations are used to force an energy-balance model at several locations on alpine glaciers and at one site in the dry Andes of central Chile. The heat-conduction flux is computed using a two-layer scheme, assuming that 36% of the net shortwave radiation is absorbed by the surface layer and that the rest penetrates into the snowpack. We compare simulations conducted with and without subsurface heat flux. Results show that assuming a surface temperature of zero degrees leads to a larger overestimation of melt at the sites in the accumulation area (10.4–13.3%) than in the ablation area (0.5–2.8%), due to lower air temperatures and the presence of snow. The difference between simulations with and without heat conduction is also high at the beginning and end of the ablation season (up to 29% for the first 15 days of the season), when air temperatures are lower and snow covers the glacier surface, while they are of little importance during periods of sustained melt at all the locations investigated. AU - Pellicciotti, Francesca AU - Carenzo, Marco AU - Helbing, Jakob AU - Rimkus, Stefan AU - Burlando, Paolo ID - 12655 IS - 50 JF - Annals of Glaciology SN - 0260-3055 TI - On the role of subsurface heat conduction in glacier energy-balance modelling VL - 50 ER - TY - JOUR AB - The nervous system of seeing animals derives information about optic flow in two subsequent steps. First, local motion vectors are calculated from moving retinal images, and second, the spatial distribution of these vectors is analyzed on the dendrites of large downstream neurons. In dipteran flies, this second step relies on a set of motion-sensitive lobula plate tangential cells (LPTCs), which have been studied in great detail in large fly species. Yet, studies on neurons that convey information to LPTCs and neuroanatomical investigations that enable a mechanistic understanding of the underlying dendritic computations in LPTCs are rare. We investigated the subcellular distribution of nicotinic acetylcholine receptors (nAChRs) on two sets of LPTCs: vertical system (VS) and horizontal system (HS) cells in Drosophila melanogaster. In this paper, we describe that both cell types express Dα7-type nAChR subunits specifically on higher order dendritic branches, similar to the expression of gamma aminobutyric acid (GABA) receptors. These findings support a model in which directional selectivity of LPTCs is achieved by the dendritic integration of excitatory, cholinergic, and inhibitory GABA-ergic input from local motion detectors with opposite preferred direction. Nonetheless, whole-cell recordings in mutant flies without Dα7 nAChRs revealed that direction selectivity of VS and HS cells is largely retained. In addition, mutant LPTCs were responsive to acetylcholine and remaining nAChR receptors were labeled by α-bungarotoxin. These results in LPTCs with genetically manipulated excitatory input synapses suggest a robust cellular implementation of dendritic processing that warrants direction selectivity. The underlying mechanism that ensures appropriate nAChR-mediated synaptic currents and the functional implications of separate sets or heteromultimeric nAChRs can now be addressed in this system. AU - Raghu, Shamprasad V AU - Maximilian Jösch AU - Sigrist, Stephan J AU - Borst, Alexander AU - Reiff, Dierk F ID - 1302 IS - 1-2 JF - Journal of Neurogenetics TI - Synaptic organization of lobula plate tangential cells in Drosophila: Dα7 cholinergic receptors VL - 23 ER - TY - CHAP AB - Let g be a cubic polynomial with integer coefficients and n>9 variables, and assume that the congruence g=0 modulo p^k is soluble for all prime powers p^k. We show that the equation g=0 has infinitely many integer solutions when the cubic part of g defines a projective hypersurface with singular locus of dimension <n-10. The proof is based on the Hardy-Littlewood circle method. AU - Browning, Timothy D AU - Heath Brown, Roger ID - 164 T2 - Analytic Number Theory: Essays in honour of Klaus Roth TI - Integral points on cubic hypersurfaces ER - TY - CONF AB - We survey the state of affairs for the distribution of ℚ-rational points on non-singular del Pezzo surfaces of low degree, highlighting the recent resolution of Manin's conjecture for a non-singular del Pezzo surface of degree 4 by la Bretèche and Browning. AU - Timothy Browning ED - Aoki, Takashi ED - Kanemitsu, Shigeru ED - Liu, Jianya ID - 165 TI - Resent progress on the quantitative arithmetic of del Pezzo surfaces VL - 6 ER - TY - CHAP AB - The arithmetic of ternary diagonal equation is considered for degree d >1, with the outcome that the set of coefficients for which the equation admits a non-zero integer solution is shown to have density zero. AU - Timothy Browning AU - Dietmann, Rainer ID - 168 T2 - Quadratic Forms - algebra, arithmetic and geometry TI - Solubility of Fermat equations VL - 493 ER - TY - JOUR AB - Morphogens act as graded positional cues to control cell fate specification in many developing tissues. This concept, in which a signaling gradient regulates differential gene expression in a concentration-dependent manner, has received considerable experimental support. Nevertheless, several recent studies have challenged the straightforward model of morphogen activity. In particular, the observation that pattern formation is a dynamic process has raised questions about the influence of time on morphogen activity. Here we propose that the spatiotemporal dynamics of the cellular response to a morphogen gradient depend on a combination of temporal alterations to the morphogen gradient itself, the dynamics of its signal transduction and downstream interactions between target genes. AU - Kutějová, Eva AU - Briscoe, James AU - Anna Kicheva ID - 1718 IS - 4 JF - Current Opinion in Genetics & Development TI - Temporal dynamics of patterning by morphogen gradients VL - 19 ER - TY - JOUR AB - How morphogen gradients are formed in target tissues is a key question for understanding the mechanisms of morphological patterning. Here, we review different mechanisms of morphogen gradient formation from theoretical and experimental points of view. First, a simple, comprehensive overview of the underlying biophysical principles of several mechanisms of gradient formation is provided. We then discuss the advantages and limitations of different experimental approaches to gradient formation analysis. AU - Wartlick, Ortrud AU - Anna Kicheva AU - González-Gaitán, Marcos A ID - 1720 IS - 3 JF - Cold Spring Harbor perspectives in biology TI - Morphogen gradient formation VL - 1 ER - TY - JOUR AB - We present an ideal realization of the Tavis-Cummings model in the absence of atom number and coupling fluctuations by embedding a discrete number of fully controllable superconducting qubits at fixed positions into a transmission line resonator. Measuring the vacuum Rabi mode splitting with one, two, and three qubits strongly coupled to the cavity field, we explore both bright and dark dressed collective multiqubit states and observe the discrete N scaling of the collective dipole coupling strength. Our experiments demonstrate a novel approach to explore collective states, such as the W state, in a fully globally and locally controllable quantum system. Our scalable approach is interesting for solid-state quantum information processing and for fundamental multiatom quantum optics experiments with fixed atom numbers. AU - Johannes Fink AU - Bianchetti, R AU - Baur, Matthias P AU - Göppl, M AU - Steffen, L. Kraig AU - Filipp, Stefan AU - Leek, Peter J AU - Blais, Alexandre AU - Wallraff, Andreas ID - 1769 IS - 8 JF - Physical Review Letters TI - Dressed collective qubit states and the Tavis-Cummings model in circuit QED VL - 103 ER - TY - JOUR AB - We present spectroscopic measurements of the Autler-Townes doublet and the sidebands of the Mollow triplet in a driven superconducting qubit. The ground to first excited state transition of the qubit is strongly pumped while the resulting dressed qubit spectrum is probed with a weak tone. The corresponding transitions are detected using dispersive readout of the qubit coupled off resonantly to a microwave transmission line resonator. The observed frequencies of the Autler-Townes and Mollow spectral lines are in good agreement with a dispersive Jaynes-Cummings model taking into account higher excited qubit states and dispersive level shifts due to off-resonant drives. AU - Baur, Matthias P AU - Filipp, Stefan AU - Bianchetti, R AU - Johannes Fink AU - Göppl, M AU - Steffen, L. Kraig AU - Leek, Peter J AU - Blais, Alexandre AU - Wallraff, Andreas ID - 1767 IS - 24 JF - Physical Review Letters TI - Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit VL - 102 ER - TY - JOUR AB - We demonstrate the time-resolved driving of two-photon blue sideband transitions between superconducting qubits and a transmission line resonator. As an example of using these sideband transitions for a two-qubit operation, we implement a pulse sequence that first entangles one qubit with the resonator and subsequently distributes the entanglement between two qubits. We show the generation of 75% fidelity Bell states by this method. The full density matrix of the two-qubit system is extracted using joint measurement and quantum state tomography and shows close agreement with numerical simulation. AU - Leek, Peter J AU - Filipp, Stefan AU - Maurer, Patrick AU - Baur, Matthias P AU - Bianchetti, R AU - Johannes Fink AU - Göppl, M AU - Steffen, L. Kraig AU - Wallraff, Andreas ID - 1766 IS - 18 JF - Physical Review B - Condensed Matter and Materials Physics TI - Using sideband transitions for two-qubit operations in superconducting circuits VL - 79 ER - TY - JOUR AB - Quantum state tomography is an important tool in quantum information science for complete characterization of multiqubit states and their correlations. Here we report a method to perform a joint simultaneous readout of two superconducting qubits dispersively coupled to the same mode of a microwave transmission line resonator. The nonlinear dependence of the resonator transmission on the qubit state dependent cavity frequency allows us to extract the full two-qubit correlations without the need for single-shot readout of individual qubits. We employ standard tomographic techniques to reconstruct the density matrix of two-qubit quantum states. AU - Filipp, Stefan AU - Maurer, Patrick AU - Leek, Peter J AU - Baur, Matthias P AU - Bianchetti, R AU - Johannes Fink AU - Göppl, M AU - Steffen, L. Kraig AU - Gambetta, Jay M AU - Blais, Alexandre AU - Wallraff, Andreas ID - 1768 IS - 20 JF - Physical Review Letters TI - Two-qubit state tomography using a joint dispersive readout VL - 102 ER - TY - JOUR AB - The quantum state of a superconducting qubit nonresonantly coupled to a transmission line resonator can be determined by measuring the quadrature amplitudes of an electromagnetic field transmitted through the resonator. We present experiments in which we analyze in detail the dynamics of the transmitted field as a function of the measurement frequency for both weak continuous and pulsed measurements. We find excellent agreement between our data and calculations based on a set of Bloch-type differential equations for the cavity field derived from the dispersive Jaynes-Cummings Hamiltonian including dissipation. We show that the measured system response can be used to construct a measurement operator from which the qubit population can be inferred accurately. Such a measurement operator can be used in tomographic methods to reconstruct single and multiqubit states in ensemble-averaged measurements. AU - Bianchetti, R AU - Filipp, Stefan AU - Baur, Matthias P AU - Johannes Fink AU - Göppl, M AU - Leek, Peter J AU - Steffen, L. Kraig AU - Blais, Alexandre AU - Wallraff, Andreas ID - 1770 IS - 4 JF - Physical Review A - Atomic, Molecular, and Optical Physics TI - Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics VL - 80 ER - TY - JOUR AB - The exceptionally strong coupling realizable between superconducting qubits and photons stored in an on-chip microwave resonator allows for the detailed study of matter-light interactions in the realm of circuit quantum electrodynamics (QED). Here we investigate the resonant interaction between a single transmon-type multilevel artificial atom and weak thermal and coherent fields. We explore up to three photon dressed states of the coupled system in a linear response heterodyne transmission measurement. The results are in good quantitative agreement with a generalized Jaynes-Cummings model. Our data indicate that the role of thermal fields in resonant cavity QED can be studied in detail using superconducting circuits. AU - Johannes Fink AU - Baur, Matthias P AU - Bianchetti, R AU - Filipp, Stefan AU - Göppl, M AU - Leek, Peter J AU - Steffen, L. Kraig AU - Blais, Alexandre AU - Wallraff, Andreas ID - 1771 JF - Physica Scripta T TI - Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics VL - T137 ER - TY - JOUR AB - The detection of approaching objects, such as looming predators, is necessary for survival. Which neurons and circuits mediate this function? We combined genetic labeling of cell types, two-photon microscopy, electrophysiology and theoretical modeling to address this question. We identify an approach-sensitive ganglion cell type in the mouse retina, resolve elements of its afferent neural circuit, and describe how these confer approach sensitivity on the ganglion cell. The circuit's essential building block is a rapid inhibitory pathway: it selectively suppresses responses to non-approaching objects. This rapid inhibitory pathway, which includes AII amacrine cells connected to bipolar cells through electrical synapses, was previously described in the context of night-time vision. In the daytime conditions of our experiments, the same pathway conveys signals in the reverse direction. The dual use of a neural pathway in different physiological conditions illustrates the efficiency with which several functions can be accommodated in a single circuit. AU - Münch, Thomas A AU - Da Silveira, Ravá A AU - Sandra Siegert AU - Viney, Tim J AU - Awatramani, Gautam B AU - Roska, Botond M ID - 1799 IS - 10 JF - Nature Neuroscience TI - Approach sensitivity in the retina processed by a multifunctional neural circuit VL - 12 ER - TY - JOUR AB - The mammalian brain is assembled from thousands of neuronal cell types that are organized in distinct circuits to perform behaviorally relevant computations. Transgenic mouse lines with selectively marked cell types would facilitate our ability to dissect functional components of complex circuits. We carried out a screen for cell type-specific green fluorescent protein expression in the retina using BAC transgenic mice from the GENSAT project. Among others, we identified mouse lines in which the inhibitory cell types of the night vision and directional selective circuit were selectively labeled. We quantified the stratification patterns to predict potential synaptic connectivity between marked cells of different lines and found that some of the lines enabled targeted recordings and imaging of cell types from developing or mature retinal circuits. Our results suggest the potential use of a stratification-based screening approach for characterizing neuronal circuitry in other layered brain structures, such as the neocortex. AU - Sandra Siegert AU - Scherf, Brigitte G AU - Del Punta, Karina AU - Didkovsky, Nick AU - Heintz, Nathaniel M AU - Roska, Botond M ID - 1798 IS - 9 JF - Nature Neuroscience TI - Genetic address book for retinal cell types VL - 12 ER - TY - JOUR AB - Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus. A key mechanism that underlies this response is the slow, activity-dependent removal of responding molecules to a pool which is unavailable to respond immediately to the input. This mechanism is implemented in different ways in various biological systems and has traditionally been studied separately for each. Here we highlight the common aspects of this principle, shared by many biological systems, and suggest a unifying theoretical framework. We study theoretically a class of models which describes the general mechanism and allows us to distinguish its universal from system-specific features. We show that under general conditions, regardless of the details of kinetics, molecule availability encodes an averaging over past activity and feeds back multiplicatively on the system output. The kinetics of recovery from unavailability determines the effective memory kernel inside the feedback branch, giving rise to a variety of system-specific forms of adaptive response—precise or input-dependent, exponential or power-law—as special cases of the same model. AU - Tamar Friedlander AU - Brenner, Naama ID - 1825 IS - 52 JF - PNAS TI - Adaptive response by state-dependent inactivation VL - 106 ER - TY - JOUR AB - Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source of reactive oxygen species, which may be one of the causes of aging. Dysfunction of complex I is implicated in many human neurodegenerative diseases. We have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 Å resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of reactive oxygen species production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide-binding pocket, as well as small but significant shifts of several α-helices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby iron-sulfur clusters N2 and N6a/b. Cluster N2 is the electron donor to quinone and is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines. AU - Berrisford, John M AU - Leonid Sazanov ID - 1971 IS - 43 JF - Journal of Biological Chemistry TI - Structural basis for the mechanism of respiratory complex I VL - 284 ER - TY - JOUR AB - In animal and plant cells, mitotic chromatin locally generates microtubules that self-organize into a mitotic spindle, and its dimensions and bipolar symmetry are essential for accurate chromosome segregation. By immobilizing microscopic chromatin-coated beads on slide surfaces using a microprinting technique, we have examined the effect of chromatin on the dimensions and symmetry of spindles in Xenopus laevis cytoplasmic extracts. While circular spots with diameters around 14-18 μm trigger bipolar spindle formation, larger spots generate an incorrect number of poles. We also examined lines of chromatin with various dimensions. Their length determined the number of poles that formed, with a 6 × 18 μm rectangular patch generating normal spindle morphology. Around longer lines, multiple poles formed and the structures were disorganized. While lines thinner than 10 μm generated symmetric structures, thicker lines induced the formation of asymmetric structures where all microtubules are on the same side of the line. Our results show that chromatin defines spindle shape and orientation. For a video summary of this article, see the PaperFlick file available with the online Supplemental Data. AU - Dinarina, Ana AU - Pugieux, Céline AU - Corral, Maria M AU - Martin Loose AU - Spatz, Joachim P AU - Karsenti, Éric AU - Nédélec, François J ID - 1984 IS - 3 JF - Cell TI - Chromatin shapes the mitotic spindle VL - 138 ER - TY - JOUR AB - During many cellular processes such as cell division, polarization and motility, the plasma membrane does not only represent a passive physical barrier, but also provides a highly dynamic platform for the interplay between lipids, membrane binding proteins and cytoskeletal elements. Even though many regulators of these interactions are known, their mutual interdependence appears to be highly complex and difficult to study in a living cell. Over the past few years, in vitro studies on membrane-cytoskeleton interactions using biomimetic membranes turned out to be extremely helpful to get better mechanistic insight into the dynamics of these processes. In this review, we discuss some of the recent developments using in vitro assays to dissect the role of the players involved: lipids in the membrane, proteins binding to membranes and proteins binding to membrane proteins. We also summarize advantages and disadvantages of supported lipid bilayers as model membrane. AU - Martin Loose AU - Schwille, Petra ID - 1983 IS - 1 JF - Journal of Structural Biology TI - Biomimetic membrane systems to study cellular organization VL - 168 ER - TY - JOUR AU - Beatriz Vicoso AU - Charlesworth, Brian ID - 2067 IS - 4 JF - Genetics TI - Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster VL - 181 ER - TY - JOUR AB - In Drosophila, there is a consistent deficit of male-biased genes on the X chromosome. It has been suggested that male-biased genes may evolve from initially unbiased genes as a result of increased expression levels in males. If transcription rates are limited, a large increase in expression in the testis may be harder to achieve for single-copy X-linked genes than for autosomal genes, because they are already hypertranscribed due to dosage compensation. This hypothesis predicts that the larger the increase in expression required to make a male-biased gene, the lower the chance of this being achievable if it is located on the X chromosome. Consequently, highly expressed male-biased genes should be located on the X chromosome less often than lowly expressed male-biased genes. This pattern is observed in our analysis of publicly available data, where microarray data or EST data are used to detect male-biased genes in D. melanogaster and to measure their expression levels. This is consistent with the idea that limitations in transcription rates may prevent male-biased genes from accumulating on the X chromosome. AU - Beatriz Vicoso AU - Charlesworth, Brian ID - 2068 IS - 5 JF - Journal of Molecular Evolution TI - The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation? VL - 68 ER - TY - JOUR AB - Current models of X-linked and autosomal evolutionary rates often assume that the effective population size of the X chromosome (NeX) is equal to three-quarters of the autosomal population size (NeA). However, polymorphism studies of Drosophila melanogaster and D. simulans suggest that there are often significant deviations from this value. We have computed fixation rates of beneficial and deleterious mutations at X-linked and autosomal sites when this occurs. We find that NeX/NeA is a crucial parameter for the rates of evolution of X-linked sites compared to autosomal sites. Faster-X evolution due to the fixation of beneficial mutations can occur under a much wider range of levels of dominance when NeX/N eA > 3/4. We also examined various parameters that are known to influence the rates of evolution at X-linked and autosomal sites, such as different mutation rates in males and females and mutations that are sexually antagonistic, to determine which cases can lead to faster-X evolution. We show that, when the rate of nonsynonymous evolution is normalized by the rate of neutral evolution, a sex difference in mutation rate has no influence on the conditions for faster-X evolution. AU - Beatriz Vicoso AU - Charlesworth, Brian ID - 2069 IS - 9 JF - Evolution TI - Effective population size and the faster-X effect: An extended model VL - 63 ER - TY - JOUR AB - In many eukaryotic organisms, gender is determined by a pair of heteromorphic sex chromosomes. Degeneration of the non-recombining Y chromosome is a general facet of sex chromosome evolution. Selective pressure to restore expression levels of X-linked genes relative to autosomes accompanies Y-chromosome degeneration, thus driving the evolution of dosage compensation mechanisms. This review focuses on evolutionary aspects of dosage compensation, in light of recent advances in comparative and functional genomics that have substantially increased our understanding of the molecular mechanisms of dosage compensation and how it evolved. We review processes involved in sex chromosome evolution, and discuss the dynamic interaction between Y degeneration and the acquisition of dosage compensation. We compare mechanisms of dosage compensation and the origin of dosage compensation genes between different taxa and comment on sex chromosomes that apparently lack compensation mechanisms. Finally, we discuss how dosage compensation systems can also influence the evolution of well-established sex chromosomes. AU - Beatriz Vicoso AU - Bachtrog, Doris ID - 2070 IS - 5 JF - Chromosome Research TI - Progress and prospects toward our understanding of the evolution of dosage compensation VL - 17 ER - TY - CONF AB - This paper introduces a data-driven representation and modeling technique for simulating non-linear heterogeneous soft tissue. It simplifies the construction of convincing deformable models by avoiding complex selection and tuning of physical material parameters, yet retaining the richness of non-linear heterogeneous behavior. We acquire a set of example deformations of a real object, and represent each of them as a spatially varying stress-strain relationship in a finite-element model. We then model the material by non-linear interpolation of these stress-strain relationships in strain-space. Our method relies on a simple-to-build capture system and an efficient run-time simulation algorithm based on incremental loading, making it suitable for interactive computer graphics applications. We present the results of our approach for several non-linear materials and biological soft tissue, with accurate agreement of our model to the measured data. AU - Bernd Bickel AU - Bac̈her, Moritz AU - Otaduy, Miguel A AU - Matusik, Wojciech AU - Pfister, Hanspeter AU - Groß, Markus S ID - 2094 IS - 3 TI - Capture and modeling of non-linear heterogeneous soft tissue VL - 28 ER - TY - JOUR AB - Let (E, H, μ) be an abstract Wiener space and let DV : = V D, where D denotes the Malliavin derivative and V is a closed and densely defined operator from H into another Hilbert space under(H, {combining low line}). Given a bounded operator B on under(H, {combining low line}), coercive on the range over(R (V), -), we consider the operators A : = V* B V in H and under(A, {combining low line}) : = V V* B in under(H, {combining low line}), as well as the realisations of the operators L : = DV* B DV and under(L, {combining low line}) : = DV DV* B in Lp (E, μ) and Lp (E, μ ; under(H, {combining low line})) respectively, where 1 < p < ∞. Our main result asserts that the following four assertions are equivalent: (1)D (sqrt(L)) = D (DV) with {norm of matrix} sqrt(L) f {norm of matrix}p {minus tilde} {norm of matrix} DV f {norm of matrix}p for f ∈ D (sqrt(L));(2)under(L, {combining low line}) admits a bounded H∞-functional calculus on over(R (DV), -);(3)D (sqrt(A)) = D (V) with {norm of matrix} sqrt(A) h {norm of matrix} {minus tilde} {norm of matrix} V h {norm of matrix} for h ∈ D (sqrt(A));(4)under(A, {combining low line}) admits a bounded H∞-functional calculus on over(R (V), -). Moreover, if these conditions are satisfied, then D (L) = D (DV2) ∩ D (DA). The equivalence (1)-(4) is a non-symmetric generalisation of the classical Meyer inequalities of Malliavin calculus (where under(H, {combining low line}) = H, V = I, B = frac(1, 2) I). A one-sided version of (1)-(4), giving Lp-boundedness of the Riesz transform DV / sqrt(L) in terms of a square function estimate, is also obtained. As an application let -A generate an analytic C0-contraction semigroup on a Hilbert space H and let -L be the Lp-realisation of the generator of its second quantisation. Our results imply that two-sided bounds for the Riesz transform of L are equivalent with the Kato square root property for A. The boundedness of the Riesz transform is used to obtain an Lp-domain characterisation for the operator L. AU - Jan Maas AU - van Neerven, Jan M ID - 2119 IS - 8 JF - Journal of Functional Analysis TI - Boundedness of Riesz transforms for elliptic operators on abstract Wiener spaces VL - 257 ER - TY - CONF AB - The local atomic structure of PbTiO3, BaTiO3, and KNbO3 perovskite-type crystals and K x Na1 − x NbO3 solid solutions in different phases is investigated using the angular dependence of the pre-edge structure of the Ti and Nb K X-ray absorption spectra and the EXAFS data. In noncubic phases, a considerable deviation of the local structure from the structure determined from diffraction data is observed only for the tetragonal phase of the BaTiO3 crystal. It is revealed that, in the cubic phase of niobates, the niobium atoms are characterized by significant displacements from the centrosymmetric positions along the threefold axes, so that they are close in the magnitude and the direction to the displacements in the low-temperatures rhombohedral phases. AU - Vedrinskiǐ, Rostislav V AU - Kraǐzman, V. L AU - Mikhail Lemeshko AU - Nazarenko, Elena S AU - Novakovich, Alexander A AU - Reznichenko, Larisa A AU - Fokin, Vladimir N AU - Shuvaeva, Victoria A ID - 2136 IS - 7 TI - Local atomic structure of niobates and titanates from X-ray absorption spectroscopic data VL - 51 ER - TY - JOUR AB - Relying on the quantization rule of Raab and Friedrich [Phys. Rev. A (2009) in press], we derive simple and accurate formulae for the number of rotational states supported by a weakly bound vibrational level of a diatomic molecular ion. We also provide analytic estimates of the rotational constants of any such levels up to threshold for dissociation and obtain a criterion for determining whether a given weakly bound vibrational level is rotationless. The results depend solely on the long-range part of the molecular potential. AU - Mikhail Lemeshko AU - Frierich, Bretislav ID - 2137 IS - 1 JF - Journal of Atomic and Molecular Sciences TI - Rotational structure of weakly bound molecular ions VL - 1 ER - TY - JOUR AB - We investigate the effects of a magnetic field on the dynamics of rotationally inelastic collisions of open-shell molecules (Σ2, Σ3, and Π2) with closed-shell atoms. Our treatment makes use of the Fraunhofer model of matter wave scattering and its recent extension to collisions in electric [M. Lemeshko and B. Friedrich, J. Chem. Phys. 129, 024301 (2008)] and radiative fields [M. Lemeshko and B. Friedrich, Int. J. Mass. Spec. 280, 19 (2009)]. A magnetic field aligns the molecule in the space-fixed frame and thereby alters the effective shape of the diffraction target. This significantly affects the differential and integral scattering cross sections. We exemplify our treatment by evaluating the magnetic-field-dependent scattering characteristics of the He-CaH (XΣ+2), He-O2 (XΣ–3), and He-OH (XΠΩ2) systems at thermal collision energies. Since the cross sections can be obtained for different orientations of the magnetic field with respect to the relative velocity vector, the model also offers predictions about the frontal-versus-lateral steric asymmetry of the collisions. The steric asymmetry is found to be almost negligible for the He-OH system, weak for the He-CaH collisions, and strong for the He-O2. While odd ΔM transitions dominate the He-OH [J=3/2,f→J′,e/f] integral cross sections in a magnetic field parallel to the relative velocity vector, even ΔM transitions prevail in the case of the He-CaH (X2Σ+) and He-O2 (XΣ−3) collision systems. For the latter system, the magnetic field opens inelastic channels that are closed in the absence of the field. These involve the transitions N=1,J=0→N′, J′ with J′=N′. AU - Mikhail Lemeshko AU - Friedrich, Břetislav ID - 2149 IS - 1 JF - Physical Review A - Atomic, Molecular, and Optical Physics TI - Collisions of paramagnetic molecules in magnetic fields: An analytic model based on Fraunhofer diffraction of matter waves VL - 79 ER - TY - JOUR AB - We examine the effects of a linearly polarized nonresonant radiative field on the dynamics of rotationally inelastic Na+ + N2 collisions at eV collision energies. Our treatment is based on the Fraunhofer model of matter wave scattering and its recent extension to collisions in electric fields [M. Lemeshko, B. Friedrich, J. Chem. Phys. 129 (2008) 024301]. The nonresonant radiative field changes the effective shape of the target molecule by aligning it in the space-fixed frame. This markedly alters the differential and integral scattering cross-sections. As the cross-sections can be evaluated for a polarization of the radiative field collinear or perpendicular to the relative velocity vector, the model also offers predictions about steric asymmetry of the collisions. AU - Mikhail Lemeshko AU - Friedrich, Břetislav ID - 2150 IS - 1-3 JF - International Journal of Mass Spectrometry TI - The effect of a nonresonant radiative field on low-energy rotationally inelastic Na+ + N2 collisions VL - 280 ER - TY - JOUR AB - We develop an analytic model of thermal state-to-state rotationally inelastic collisions of asymmetric-top molecules with closed-shell atoms in electric fields and apply it to the Ar-H2O collision system. The predicted cross sections as well as the steric asymmetry of the collisions show at fields up to 150 kV/cm characteristic field-dependent features which can be experimentally tested. Particularly suitable candidates for such tests are the 000 → 220 and 101→ 221 channels, arising from the relaxation of the field-free selection rules due to the hybridization of J states by the field. Averaging over the M' product channels is found to largely obliterate the orientation effects brought about by the field. AU - Mikhail Lemeshko AU - Friedrich, Břetislav ID - 2192 IS - 52 JF - Journal of Physical Chemistry A TI - Model analysis of rotationally inelastic Ar + H2O scattering in an electric field VL - 113 ER - TY - JOUR AB - By making use of the quantization rule of Raab and Friedrich [Phys. Rev. A 78, 022707 (2008)], we derive simple and accurate formulae for the number of rotational states supported by a weakly bound vibrational level of a diatomic molecule and the rotational constants of any such levels up to the threshold, and provide a criterion for determining whether a given weakly bound vibrational level is rotationless. The results depend solely on the long-range part of the molecular potential and are applicable to halo molecules. AU - Mikhail Lemeshko AU - Friedrich, Břetislav ID - 2191 IS - 5 JF - Physical Review A - Atomic, Molecular, and Optical Physics TI - Rotational and rotationless states of weakly bound molecules VL - 79 ER - TY - JOUR AB - We show that weakly bound molecules can be probed by "shaking" in a pulsed nonresonant laser field. The field introduces a centrifugal term which expels the highest vibrational level from the potential that binds it. Our numerical simulations applied to the Rb2 and KRb Feshbach molecules indicate that shaking by feasible laser pulses can be used to accurately recover the square of the vibrational wave function and, by inversion, also the long-range part of the molecular potential. AU - Mikhail Lemeshko AU - Friedrich, Břetislav ID - 2193 IS - 5 JF - Physical Review Letters TI - Probing weakly bound molecules with nonresonant light VL - 103 ER - TY - JOUR AB - The Manin conjecture is established for a split singular del Pezzo surface of degree four, with singularity type A4. AU - Timothy Browning AU - Derenthal, Ulrich ID - 226 IS - 3 JF - Annales de l'Institut Fourier TI - Manin's conjecture for a quartic del Pezzo surface with A4 singularity VL - 59 ER - TY - BOOK AB - Winner of the Ferran Sunyer i Balaguer Prize 2009. First attempt to systematically survey the range of available tools from analytic number theory that can be applied to study the density of rational points on projective varieties. Designed to rapidly guide the reader to the many areas of ongoing research in the domain. Provides an extensive bibliography. AU - Browning, Timothy D ID - 227 SN - 0743-1643 TI - Quantitative Arithmetic of Projective Varieties VL - 277 ER - TY - JOUR AB - Let X be a projective non-singular quartic hypersurface of dimension 39 or more, which is defined over . We show that X() is non-empty provided that X() is non-empty and X has p-adic points for every prime p. AU - Timothy Browning AU - Heath-Brown, Roger ID - 228 IS - 629 JF - Journal fur die Reine und Angewandte Mathematik TI - Rational points on quartic hypersurfaces ER - TY - JOUR AB - An upper bound of the expected order of magnitude is established for the number of ℚ-rational points of bounded height on Châtelet surfaces defined over ℚ. AU - Timothy Browning ID - 229 IS - 1 JF - Mathematische Annalen TI - Linear growth for Châtelet surfaces VL - 346 ER -