@article{21154, abstract = {The crystal structure of the decamer sequence d(CCGGGACCGG)4 has previously been reported at 2.16 Å resolution as a four-way junction. Here, the structure of this sequence is reported at the significantly higher resolution of 1.6 Å, which is the highest resolution reported for a four-way junction. This allowed the unambiguous identification of an extensive hydration network with distinct patterns and solvent-mediated interactions that shed new light on the role of water in the formation and stabilization of junction structures.}, author = {Chakraborty, Arka and Mandal, Pradeep K and Gautham, Namasivayam}, issn = {1744-3091}, journal = {Acta Crystallographica Section F Structural Biology Communications}, number = {10}, pages = {1169--1174}, publisher = {International Union of Crystallography}, title = {{Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 Å resolution: New insights into solvent interactions}}, doi = {10.1107/s1744309112034926}, volume = {68}, year = {2012}, } @article{2125, abstract = {We consider a class of stochastic PDEs of Burgers type in spatial dimension 1, driven by space–time white noise. Even though it is well known that these equations are well posed, it turns out that if one performs a spatial discretization of the nonlinearity in the “wrong” way, then the sequence of approximate equations does converge to a limit, but this limit exhibits an additional correction term. This correction term is proportional to the local quadratic cross-variation (in space) of the gradient of the conserved quantity with the solution itself. This can be understood as a consequence of the fact that for any fixed time, the law of the solution is locally equivalent to Wiener measure, where space plays the role of time. In this sense, the correction term is similar to the usual Itô–Stratonovich correction term that arises when one considers different temporal discretizations of stochastic ODEs.}, author = {Hairer, Martin M and Jan Maas}, journal = {Annals of Probability}, number = {4}, pages = {1675 -- 1714}, publisher = {Institute of Mathematical Statistics}, title = {{A spatial version of the Itô-Stratonovich correction}}, doi = {10.1214/11-AOP662}, volume = {40}, year = {2012}, } @article{2127, abstract = {We study a new notion of Ricci curvature that applies to Markov chains on discrete spaces. This notion relies on geodesic convexity of the entropy and is analogous to the one introduced by Lott, Sturm, and Villani for geodesic measure spaces. In order to apply to the discrete setting, the role of the Wasserstein metric is taken over by a different metric, having the property that continuous time Markov chains are gradient flows of the entropy. Using this notion of Ricci curvature we prove discrete analogues of fundamental results by Bakry–Émery and Otto–Villani. Further, we show that Ricci curvature bounds are preserved under tensorisation. As a special case we obtain the sharp Ricci curvature lower bound for the discrete hypercube.}, author = {Erbar, Matthias and Jan Maas}, journal = {Archive for Rational Mechanics and Analysis}, number = {3}, pages = {997 -- 1038}, publisher = {Springer}, title = {{Ricci curvature of finite Markov chains via convexity of the entropy}}, doi = {10.1007/s00205-012-0554-z}, volume = {206}, year = {2012}, } @article{2128, abstract = {We introduce a technique for handling Whitney decompositions in Gaussian harmonic analysis and apply it to the study of Gaussian analogues of the classical tent spaces T 1,q of Coifman–Meyer–Stein.}, author = {Jan Maas and van Neerven, Jan M and Portal, Pierre}, journal = {Arkiv för Matematik}, number = {2}, pages = {379 -- 395}, publisher = {Springer}, title = {{Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure}}, doi = {10.1007/s11512-010-0143-z}, volume = {50}, year = {2012}, } @article{13407, abstract = {We show that diamagnetic particles can be remotely manipulated by a magnet by the reversible adsorption of dual-responsive, light-switchable/superparamagnetic nanoparticles down to their surface. Adsorption occurs upon exposure to UV light, and can be reversed thermally or by ambient light. The dynamic self-assembly of thin films of the dual-responsive nanoparticles induces attractive interactions between diamagnetic particles. We demonstrate that catalytic amounts of the dual-responsive nanoparticles are sufficient to magnetically guide and deliver the diamagnetic particles to desired locations, where they can then be released by disassembling the dynamic layers of superparamagnetic nanoparticles with visible light.}, author = {Chovnik, Olga and Balgley, Renata and Goldman, Joel R. and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {48}, pages = {19564--19567}, publisher = {American Chemical Society}, title = {{Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets}}, doi = {10.1021/ja309633v}, volume = {134}, year = {2012}, } @article{13408, abstract = {Well-defined metallic nanobowls can be prepared by extending the concept of a protecting group to colloidal synthesis. Magnetic nanoparticles are employed as “protecting groups” during the galvanic replacement of silver with gold. The replacement reaction is accompanied by spontantous dissociation of the protecting groups, leaving behind metallic nanobowls.}, author = {Ridelman, Yonatan and Singh, Gurvinder and Popovitz-Biro, Ronit and Wolf, Sharon G. and Das, Sanjib and Klajn, Rafal}, issn = {1613-6829}, journal = {Small}, keywords = {Biomaterials, Biotechnology, General Materials Science, General Chemistry}, number = {5}, pages = {654--660}, publisher = {Wiley}, title = {{Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles}}, doi = {10.1002/smll.201101882}, volume = {8}, year = {2012}, } @inproceedings{1384, abstract = {Software model checking, as an undecidable problem, has three possible outcomes: (1) the program satisfies the specification, (2) the program does not satisfy the specification, and (3) the model checker fails. The third outcome usually manifests itself in a space-out, time-out, or one component of the verification tool giving up; in all of these failing cases, significant computation is performed by the verification tool before the failure, but no result is reported. We propose to reformulate the model-checking problem as follows, in order to have the verification tool report a summary of the performed work even in case of failure: given a program and a specification, the model checker returns a condition Ψ - usually a state predicate - such that the program satisfies the specification under the condition Ψ - that is, as long as the program does not leave the states in which Ψ is satisfied. In our experiments, we investigated as one major application of conditional model checking the sequential combination of model checkers with information passing. We give the condition that one model checker produces, as input to a second conditional model checker, such that the verification problem for the second is restricted to the part of the state space that is not covered by the condition, i.e., the second model checker works on the problems that the first model checker could not solve. Our experiments demonstrate that repeated application of conditional model checkers, passing information from one model checker to the next, can significantly improve the verification results and performance, i.e., we can now verify programs that we could not verify before.}, author = {Beyer, Dirk and Henzinger, Thomas A and Keremoglu, Mehmet and Wendler, Philipp}, booktitle = {Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering}, location = {Cary, NC, USA}, publisher = {ACM}, title = {{Conditional model checking: A technique to pass information between verifiers}}, doi = {10.1145/2393596.2393664}, year = {2012}, } @article{1471, abstract = {Given a possibly reducible and non-reduced spectral cover π: X → C over a smooth projective complex curve C we determine the group of connected components of the Prym variety Prym(X/C). As an immediate application we show that the finite group of n-torsion points of the Jacobian of C acts trivially on the cohomology of the twisted SL n-Higgs moduli space up to the degree which is predicted by topological mirror symmetry. In particular this yields a new proof of a result of Harder-Narasimhan, showing that this finite group acts trivially on the cohomology of the twisted SL n stable bundle moduli space.}, author = {Tamas Hausel and Pauly, Christian}, journal = {Geometry and Topology}, number = {3}, pages = {1609 -- 1638}, publisher = {University of Warwick}, title = {{Prym varieties of spectral covers}}, doi = {10.2140/gt.2012.16.1609}, volume = {16}, year = {2012}, } @article{1472, abstract = {For G = GL 2, PGL 2, SL 2 we prove that the perverse filtration associated with the Hitchin map on the rational cohomology of the moduli space of twisted G-Higgs bundles on a compact Riemann surface C agrees with the weight filtration on the rational cohomology of the twisted G character variety of C when the cohomologies are identified via non-Abelian Hodge theory. The proof is accomplished by means of a study of the topology of the Hitchin map over the locus of integral spectral curves.}, author = {De Cataldo, Mark A and Tamas Hausel and Migliorini, Luca}, journal = {Annals of Mathematics}, number = {3}, pages = {1329 -- 1407}, publisher = {Princeton University Press}, title = {{Topology of hitchin systems and Hodge theory of character varieties: The case A 1}}, doi = {10.4007/annals.2012.175.3.7}, volume = {175}, year = {2012}, } @inbook{18737, abstract = {Supermassive black holes (SMBHs) are common in local galactic nuclei, and SMBHs as massive as several billion solar masses already exist at redshift z = 6. These earliest SMBHs may grow by the combination of radiation-pressure-limited accretion and mergers of stellar-mass seed BHs, left behind by the first generation of metal-free stars, or may be formed by more rapid direct collapse of gas in rare special environments where dense gas can accumulate without first fragmenting into stars. This chapter offers a review of these two competing scenarios, as well as some more exotic alternative ideas. It also briefly discusses how the different models may be distinguished in the future by observations with JWST, LISA and other instruments.}, author = {Haiman, Zoltán}, booktitle = {The First Galaxies}, editor = {Wiklind, Tommy and Mobasher, Bahram and Brumm, Volker}, isbn = {9783642323614}, issn = {2214-7985}, pages = {293--341}, publisher = {Springer Berlin Heidelberg}, title = {{The Formation of the First Massive Black Holes}}, doi = {10.1007/978-3-642-32362-1_6}, year = {2012}, } @article{1972, abstract = {Outer membrane protein F, a major component of the Escherichia coli outer membrane, was crystallized for the first time in lipidic mesophase of monoolein in novel space groups, P1 and H32. Due to ease of its purification and crystallization OmpF can be used as a benchmark protein for establishing membrane protein crystallization in meso, as a "membrane lyzozyme" The packing of porin trimers in the crystals of space group H32 is similar to natural outer membranes, providing the first high-resolution insight into the close to native packing of OmpF. Surprisingly, interaction between trimers is mediated exclusively by lipids, without direct protein-protein contacts. Multiple ordered lipids are observed and many of them occupy identical positions independently of the space group, identifying preferential interaction sites of lipid acyl chains. Presence of ordered aliphatic chains close to a positively charged area on the porin surface suggests a position for a lipopolysaccharide binding site on the surface of the major E. coli porins.}, author = {Efremov, Rouslan G and Leonid Sazanov}, journal = {Journal of Structural Biology}, number = {3}, pages = {311 -- 318}, publisher = {Academic Press}, title = {{Structure of Escherichia coli OmpF porin from lipidic mesophase}}, doi = {10.1016/j.jsb.2012.03.005}, volume = {178}, year = {2012}, } @misc{1976, abstract = {Complex I is a key enzyme of the respiratory chain in many organisms. This multi-protein complex with an intricate evolutionary history originated from the unification of prebuilt modules of hydrogenases and transporters. Using recently determined crystallographic structures of complex I we reanalyzed evolutionarily related complexes that couple oxidoreduction to trans-membrane ion translocation. Our analysis points to the previously unnoticed structural homology of the electron input module of formate dehydrogenlyases and subunit NuoG of complex I. We also show that all related to complex I hydrogenases likely operate via a conformation driven mechanism with structural changes generated in the conserved coupling site located at the interface of subunits NuoB/D/H. The coupling apparently originated once in evolutionary history, together with subunit NuoH joining hydrogenase and transport modules. Analysis of quinone oxidoreduction properties and the structure of complex I allows us to suggest a fully reversible coupling mechanism. Our model predicts that: 1) proton access to the ketone groups of the bound quinone is rigorously controlled by the protein, 2) the negative electric charge of the anionic ubiquinol head group is a major driving force for conformational changes.}, author = {Efremov, Rouslan G and Leonid Sazanov}, booktitle = {Biochimica et Biophysica Acta - Bioenergetics}, number = {10}, pages = {1785 -- 1795}, publisher = {Elsevier}, title = {{The coupling mechanism of respiratory complex i - A structural and evolutionary perspective}}, doi = {10.1016/j.bbabio.2012.02.015}, volume = {1817}, year = {2012}, } @article{492, abstract = {Background: Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.Results: We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.Conclusions: We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.}, author = {Galkovskyi, Taras and Mileyko, Yuriy and Bucksch, Alexander and Moore, Brad and Symonova, Olga and Price, Charles and Topp, Chrostopher and Iyer Pascuzzi, Anjali and Zurek, Paul and Fang, Suqin and Harer, John and Benfey, Philip and Weitz, Joshua}, journal = {BMC Plant Biology}, publisher = {BioMed Central}, title = {{GiA Roots: Software for the high throughput analysis of plant root system architecture}}, doi = {10.1186/1471-2229-12-116}, volume = {12}, year = {2012}, } @article{493, abstract = {The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students.The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs.}, author = {Tangermann, Michael and Müller, Klaus and Aertsen, Ad and Birbaumer, Niels and Braun, Christoph and Brunner, Clemens and Leeb, Robert and Mehring, Carsten and Miller, Kai and Müller Putz, Gernot and Nolte, Guido and Pfurtscheller, Gert and Preissl, Hubert and Schalk, Gerwin and Schlögl, Alois and Vidaurre, Carmen and Waldert, Stephan and Blankertz, Benjamin}, journal = {Frontiers in Neuroscience}, publisher = {Frontiers Research Foundation}, title = {{Review of the BCI competition IV}}, doi = {10.3389/fnins.2012.00055}, volume = {6}, year = {2012}, } @inproceedings{495, abstract = {An automaton with advice is a finite state automaton which has access to an additional fixed infinite string called an advice tape. We refine the Myhill-Nerode theorem to characterize the languages of finite strings that are accepted by automata with advice. We do the same for tree automata with advice.}, author = {Kruckman, Alex and Rubin, Sasha and Sheridan, John and Zax, Ben}, booktitle = {Proceedings GandALF 2012}, location = {Napoli, Italy}, pages = {238 -- 246}, publisher = {Open Publishing Association}, title = {{A Myhill Nerode theorem for automata with advice}}, doi = {10.4204/EPTCS.96.18}, volume = {96}, year = {2012}, } @inproceedings{496, abstract = {We study the expressive power of logical interpretations on the class of scattered trees, namely those with countably many infinite branches. Scattered trees can be thought of as the tree analogue of scattered linear orders. Every scattered tree has an ordinal rank that reflects the structure of its infinite branches. We prove, roughly, that trees and orders of large rank cannot be interpreted in scattered trees of small rank. We consider a quite general notion of interpretation: each element of the interpreted structure is represented by a set of tuples of subsets of the interpreting tree. Our trees are countable, not necessarily finitely branching, and may have finitely many unary predicates as labellings. We also show how to replace injective set-interpretations in (not necessarily scattered) trees by 'finitary' set-interpretations.}, author = {Rabinovich, Alexander and Rubin, Sasha}, location = {Dubrovnik, Croatia}, publisher = {IEEE}, title = {{Interpretations in trees with countably many branches}}, doi = {10.1109/LICS.2012.65}, year = {2012}, } @inproceedings{497, abstract = {One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm. © Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.}, author = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Kamath, Pritish}, location = {Fontainebleau, France}, pages = {167 -- 182}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Faster algorithms for alternating refinement relations}}, doi = {10.4230/LIPIcs.CSL.2012.167}, volume = {16}, year = {2012}, } @article{498, abstract = {Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration.}, author = {Pickup, Melinda and Field, David and Rowell, David and Young, Andrew}, journal = {Evolutionary Applications}, number = {8}, pages = {913 -- 924}, publisher = {Wiley-Blackwell}, title = {{Predicting local adaptation in fragmented plant populations: Implications for restoration genetics}}, doi = {10.1111/j.1752-4571.2012.00284.x}, volume = {5}, year = {2012}, } @misc{5377, abstract = {Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and ω-regular objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean-payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two- player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP- hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two- player pushdown games. Finally we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.}, author = {Chatterjee, Krishnendu and Velner, Yaron}, issn = {2664-1690}, pages = {33}, publisher = {IST Austria}, title = {{Mean-payoff pushdown games}}, doi = {10.15479/AT:IST-2012-0002}, year = {2012}, } @misc{5378, abstract = {One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm.}, author = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Kamath, Pritish}, issn = {2664-1690}, pages = {21}, publisher = {IST Austria}, title = {{Faster algorithms for alternating refinement relations}}, doi = {10.15479/AT:IST-2012-0001}, year = {2012}, }