@article{1462,
  abstract     = {A Fourier transform technique is introduced for counting the number of solutions of holomorphic moment map equations over a finite field. This technique in turn gives information on Betti numbers of holomorphic symplectic quotients. As a consequence, simple unified proofs are obtained for formulas of Poincaré polynomials of toric hyperkähler varieties (recovering results of Bielawski-Dancer and Hausel-Sturmfels), Poincaré polynomials of Hubert schemes of points and twisted Atiyah-Drinfeld-Hitchin-Manin (ADHM) spaces of instantons on ℂ2 (recovering results of Nakajima-Yoshioka), and Poincaré polynomials of all Nakajima quiver varieties. As an application, a proof of a conjecture of Kac on the number of absolutely indecomposable representations of a quiver is announced.},
  author       = {Tamas Hausel},
  journal      = {PNAS},
  number       = {16},
  pages        = {6120 -- 6124},
  publisher    = {National Academy of Sciences},
  title        = {{Betti numbers of holomorphic symplectic quotients via arithmetic Fourier transform}},
  doi          = {10.1073/pnas.0601337103},
  volume       = {103},
  year         = {2006},
}

@article{13428,
  abstract     = {Mixtures of oppositely charged nanoparticles of various sizes and charge ratios precipitate only at the point of electroneutrality. This phenomenonspecific to the nanoscale and reminiscent of threshold precipitation of ionsis a consequence of the formation of core-and-shell nanoparticle aggregates, in which the shells are composed of like-charged particles and are stabilized by efficient electrostatic screening.},
  author       = {Kalsin, Alexander M. and Kowalczyk, Bartlomiej and Smoukov, Stoyan K. and Klajn, Rafal and Grzybowski, Bartosz A.},
  issn         = {1520-5126},
  journal      = {Journal of the American Chemical Society},
  keywords     = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis},
  number       = {47},
  pages        = {15046--15047},
  publisher    = {American Chemical Society},
  title        = {{Ionic-like behavior of oppositely charged nanoparticles}},
  doi          = {10.1021/ja0642966},
  volume       = {128},
  year         = {2006},
}

@article{13429,
  abstract     = {The fruitful core: Organic syntheses reported in the literature from 1850 to 2004 are analyzed with mathematical tools from network theory and statistical physics. There is a set of substances (the core) from which the majority of other organic compounds can be made (see picture; red: core, blue: periphery, green: islands). Search algorithms are used to identify small optimal sets of maximally useful chemicals.},
  author       = {Bishop, Kyle J. M. and Klajn, Rafal and Grzybowski, Bartosz A.},
  issn         = {1521-3773},
  journal      = {Angewandte Chemie International Edition},
  keywords     = {General Chemistry, Catalysis},
  number       = {32},
  pages        = {5348--5354},
  publisher    = {Wiley},
  title        = {{The core and most useful molecules in organic chemistry}},
  doi          = {10.1002/anie.200600881},
  volume       = {45},
  year         = {2006},
}

@article{13430,
  abstract     = {Dynamic self-assembly (DySA) processes occurring outside of thermodynamic equilibrium underlie many forms of adaptive and intellligent behaviors in natural systems. Relatively little, however, is known about the principles that govern DySA and the ways in which it can be extended to artificial ensembles. This article discusses recent advances in both the theory and the practice of nonequilibrium self-assembly. It is argued that a union of ideas from thermodynamics and dynamic systems' theory can provide a general description of DySA. In parallel, heuristic design rules can be used to construct DySA systems of increasing complexities based on a variety of suitable interactions/potentials on length scales from nanoscopic to macroscopic. Applications of these rules to magnetohydrodynamic DySA are also discussed.},
  author       = {Fialkowski, Marcin and Bishop, Kyle J. M. and Klajn, Rafal and Smoukov, Stoyan K. and Campbell, Christopher J. and Grzybowski, Bartosz A.},
  issn         = {1520-6106},
  journal      = {The Journal of Physical Chemistry B},
  keywords     = {Materials Chemistry, Surfaces, Coatings and Films, Physical and Theoretical Chemistry},
  number       = {6},
  pages        = {2482--2496},
  publisher    = {American Chemical Society},
  title        = {{Principles and implementations of dissipative (dynamic) self-assembly}},
  doi          = {10.1021/jp054153q},
  volume       = {110},
  year         = {2006},
}

@article{903,
  abstract     = {Background: Carcinogenesis typically involves multiple somatic mutations in caretaker (DNA repair) and gatekeeper (tumor suppressors and oncogenes) genes. Analysis of mutation spectra of the tumor suppressor that is most commonly mutated in human cancers, p53, unexpectedly suggested that somatic evolution of the p53 gene during tumorigenesis is dominated by positive selection for gain of function. This conclusion is supported by accumulating experimental evidence of evolution of new functions of p53 in tumors. These findings prompted a genome-wide analysis of possible positive selection during tumor evolution. Methods: A comprehensive analysis of probable somatic mutations in the sequences of Expressed Sequence Tags (ESTs) from malignant tumors and normal tissues was performed in order to access the prevalence of positive selection in cancer evolution. For each EST, the numbers of synonymous and non-synonymous substitutions were calculated. In order to identify genes with a signature of positive selection in cancers, these numbers were compared to: i) expected numbers and ii) the numbers for the respective genes in the ESTs from normal tissues. Results: We identified 112 genes with a signature of positive selection in cancers, i.e., a significantly elevated ratio of non-synonymous to synonymous substitutions, in tumors as compared to 37 such genes in an approximately equal-sized EST collection from normal tissues. A substantial fraction of the tumor-specific positive-selection candidates have experimentally demonstrated or strongly predicted links to cancer. Conclusion: The results of EST analysis should be interpreted with extreme caution given the noise introduced by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation of EST analysis is that multiple mutations amenable to statistical analysis can be detected only in relatively highly expressed genes. Nevertheless, the present results suggest that positive selection might affect a substantial number of genes during tumorigenic somatic evolution.},
  author       = {Babenko, Vladimir N and Basu, Malay K and Fyodor Kondrashov and Rogozin, Igor B and Koonin, Eugene V},
  journal      = {BMC Cancer},
  publisher    = {BioMed Central},
  title        = {{Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis}},
  doi          = {10.1186/1471-2407-6-36},
  volume       = {6},
  year         = {2006},
}

@article{9505,
  abstract     = {Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, whereas genes at either extreme are least likely. In turn, transcription is influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes.},
  author       = {Zilberman, Daniel and Gehring, Mary and Tran, Robert K. and Ballinger, Tracy and Henikoff, Steven},
  issn         = {1546-1718},
  journal      = {Nature Genetics},
  number       = {1},
  pages        = {61--69},
  publisher    = {Nature Publishing Group},
  title        = {{Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription}},
  doi          = {10.1038/ng1929},
  volume       = {39},
  year         = {2006},
}

@article{1033,
  abstract     = {Systems of three interacting particles are notorious for their complex physical behaviour. A landmark theoretical result in few-body quantum physics is Efimov\'s prediction1,2 of a universal set of bound trimer states appearing for three identical bosons with a resonant two-body interaction. Counterintuitively, these states even exist in the absence of a corresponding two-body bound state. Since the formulation of Efimov\'s problem in the context of nuclear physics 35 years ago, it has attracted great interest in many areas of physics3-8. However, the observation of Efimov quantum states has remained an elusive goal3,5. Here we report the observation of an Efimov resonance in an ultracold gas of caesium atoms. The resonance occurs in the range of large negative two-body scattering lengths, arising from the coupling of three free atoms to an Efimov trimer. Experimentally, we observe its signature as a giant three-body recombination loss9,10 when the strength of the two-body interaction is varied. We also detect a minimum 9,11,12 in the recombination loss for positive scattering lengths, indicating destructive interference of decay pathways. Our results confirm central theoretical predictions of Efimov physics and represent a starting point with which to explore the universal properties of resonantly interacting few-body systems7. While Feshbach resonances13,14 have provided the key to control quantum-mechanical interactions on the two-body level, Efimov resonances connect ultracold matter15 to the world of few-body quantum phenomena.},
  author       = {Kraemer, Tobias and Mark, Michael and Waldburger, Philipp and Danzl, Johann G and Chin, Cheng and Engeser, Bastian and Lange, Adam and Pilch, Karl and Jaakkola, Antti and Nägerl, Hanns and Grimm, Rudolf},
  journal      = {Nature},
  number       = {7082},
  pages        = {315 -- 318},
  publisher    = {Nature Publishing Group},
  title        = {{Evidence for Efimov quantum states in an ultracold gas of caesium atoms}},
  doi          = {10.1038/nature04626},
  volume       = {440},
  year         = {2006},
}

@inproceedings{1034,
  abstract     = {Three interacting particles form a system which is well known for its complex physical behavior. A landmark theoretical result in few-body quantum physics is Efimov\'s prediction of a universal set of weakly bound trimer states appearing for three identical bosons with a resonant two-body interaction [1, 2]. Surprisingly, these states even exist in the absence of a corresponding two-body bound state and their precise nature is largely independent of the particular type of the two-body interaction potential. Efimov\'s scenario has attracted great interest in many areas of physics; an experimental test however has not been achieved. We report the observation of an Efimov resonance in an ultracold thermal gas of cesium atoms [3]. The resonance occurs in the range of large negative two-body scattering lengths and arises from the coupling of three free atoms to an Efimov trimer. We observe its signature as a giant three-body recombination loss when the strength of the two-body interaction is varied near a Feshbach resonance. This resonance develops into a continuum resonance at non-zero collision energies, and we observe a shift of the resonance position as a function of temperature. We also report on a minimum in the recombination loss for positive scattering lengths, indicating destructive interference of decay pathways. Our results confirm central theoretical predictions of Efimov physics and represent a starting point from which to explore the universal properties of resonantly interacting few-body systems.},
  author       = {Nägerl, Hanns and Kraemer, Tobias and Mark, Michael and Waldburger, Philipp and Danzl, Johann G and Engeser, Bastian and Lange, Adam and Pilch, Karl and Jaakkola, Antti and Chin, Cheng and Grimm, Rudolf},
  pages        = {269 -- 277},
  publisher    = {AIP},
  title        = {{Experimental evidence for Efimov quantum states}},
  doi          = {10.1063/1.2400657},
  volume       = {869},
  year         = {2006},
}

@inproceedings{11929,
  abstract     = {Broder et al.'s [3] shingling algorithm and Charikar's [4] random projection based approach are considered "state-of-the-art" algorithms for finding near-duplicate web pages. Both algorithms were either developed at or used by popular web search engines. We compare the two algorithms on a very large scale, namely on a set of 1.6B distinct web pages. The results show that neither of the algorithms works well for finding near-duplicate pairs on the same site, while both achieve high precision for near-duplicate pairs on different sites. Since Charikar's algorithm finds more near-duplicate pairs on different sites, it achieves a better precision overall, namely 0.50 versus 0.38 for Broder et al.'s algorithm. We present a combined algorithm which achieves precision 0.79 with 79% of the recall of the other algorithms.},
  author       = {Henzinger, Monika H},
  booktitle    = {29th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval},
  location     = {Seattle, WA, United States},
  pages        = {284--291},
  publisher    = {Association for Computing Machinery},
  title        = {{Finding near-duplicate web pages: A large-scale evaluation of algorithms}},
  doi          = {10.1145/1148170.1148222},
  year         = {2006},
}

@inbook{3404,
  author       = {Harald Janovjak and Sawhney, Ravi K and Stark, Martin and Mueller, Daniel J},
  booktitle    = {Techniques in Microscopy for Biomedical Applications},
  pages        = {213 -- 284},
  publisher    = {World Scientific Publishing},
  title        = {{Atomic force microscopy}},
  volume       = {2},
  year         = {2006},
}

@article{3413,
  abstract     = {Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids.

Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded.

We discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state.},
  author       = {Kessler, Max and Gottschalk, Kay E and Harald Janovjak and Mueller, Daniel J and Gaub, Hermann},
  journal      = {Journal of Molecular Biology},
  number       = {2},
  pages        = {644 -- 654},
  publisher    = {Elsevier},
  title        = {{Bacteriorhodopsin folds into the membrane against an external force}},
  doi          = {10.1016/j.jmb.2005.12.065},
  volume       = {357},
  year         = {2006},
}

@article{3414,
  abstract     = {Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the folding intermediates of asingle NhaA polypeptide forming structural segments such as the Na+-binding site, transmembrane α-helices, and helical pairs. The folding rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed insight into a distinct folding hierarchy of an unfolded polypeptide into the native membrane protein structure. In some cases, however, the folding chain formed stable and kinetically trapped non-native structures, which could be assigned to misfolding events of the antiporter.},
  author       = {Kedrov, Alexej and Harald Janovjak and Ziegler,  Christine and Kühlbrandt, Werner and Mueller, Daniel J},
  journal      = {Journal of Molecular Biology},
  number       = {1},
  pages        = {2 -- 8},
  publisher    = {Elsevier},
  title        = {{Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli}},
  doi          = {10.1016/j.jmb.2005.10.028},
  volume       = {355},
  year         = {2006},
}

@misc{3415,
  author       = {Harald Janovjak and Kedrov, Alexej and Cisneros, David and Sapra, Tanuj K and Struckmeier, Jens and Mueller, Daniel J},
  booktitle    = {Neurobiology of Aging},
  pages        = {546 -- 561},
  publisher    = {Elsevier},
  title        = {{Imaging and detecting molecular interactions of single membrane proteins}},
  doi          = {10.1016/j.neurobiolaging.2005.03.031},
  volume       = {27},
  year         = {2006},
}

@unpublished{3431,
  abstract     = {Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the retina, and show that pairwise interactions account for observed higher-order correlations. By first finding a representative ensemble for observed networks we can create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses.},
  author       = {Gasper Tkacik and Schneidman, E. and Berry, M. J. and Bialek, William S},
  booktitle    = {ArXiv},
  pages        = {1 -- 4},
  publisher    = {ArXiv},
  title        = {{Ising models for networks of real neurons}},
  year         = {2006},
}

@article{3437,
  abstract     = {The mutational landscape model is a theoretical model describing sequence evolution in natural populations. However, recent experimental work has begun to test its predictions in laboratory populations of microbes. Several of these studies have focused on testing the prediction that the effects of beneficial mutations should be roughly exponentially distributed. The prediction appears to be borne out by most of these studies, at least qualitatively. Another study showed that a modified version of the model was able to predict, with reasonable accuracy, which of a ranked set of beneficial alleles will be fixed next. Although it remains to be seen whether the mutational landscape model adequately describes adaptation in organisms other than microbes, together these studies suggest that adaptive evolution has surprisingly general properties that can be successfully captured by theoretical models.},
  author       = {Betancourt, Andrea J and Jonathan Bollback},
  journal      = {Current Opinion in Genetics & Development},
  number       = {6},
  pages        = {618 -- 623},
  publisher    = {Elsevier},
  title        = {{Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution}},
  doi          = {10.1016/j.gde.2006.10.006},
  volume       = {16},
  year         = {2006},
}

@inproceedings{3449,
  abstract     = {We argue that games are expressive enough to encompass (history-based) access control, (resource) usage control (e.g., dynamic adaptive access control of reputation systems), accountability based controls (e.g., insurance), controls derived from rationality assumptions on participants (e.g., network mechanisms), and their composition. Building on the extensive research into games, we demonstrate that this expressive power coexists with a formal analysis framework comparable to that available for access control.},
  author       = {Krishnendu Chatterjee and Jagadeesan, Rhada and Pitcher, Corin},
  pages        = {70 -- 82},
  publisher    = {IEEE},
  title        = {{Games for controls}},
  doi          = {10.1109/CSFW.2006.14},
  year         = {2006},
}

@misc{3463,
  abstract     = {It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network.},
  author       = {Bischofberger, Joseph and Engel, Dominique and Frotscher, Michael and Peter Jonas},
  booktitle    = {Pflugers Archiv : European Journal of Physiology},
  number       = {3},
  pages        = {361 -- 372},
  publisher    = {Springer},
  title        = {{Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review)}},
  doi          = {10.1007/s00424-006-0093-2},
  volume       = {453},
  year         = {2006},
}

@inproceedings{3499,
  abstract     = {We study infinite stochastic games played by n-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players’ goals are not necessarily conflicting), and undiscounted. We show that if each player has an upward-closed objective, then there exists an ε-Nash equilibrium in memoryless strategies, for every ε>0; and exact Nash equilibria need not exist. Upward-closure of an objective means that if a set Z of infinitely repeating states is winning, then all supersets of Z of infinitely repeating states are also winning. Memoryless strategies are strategies that are independent of history of plays and depend only on the current state. We also study the complexity of finding values (payoff profile) of an ε-Nash equilibrium. We show that the values of an ε-Nash equilibrium in nonzero-sum concurrent games with upward-closed objectives for all players can be computed by computing ε-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives for all players and a polynomial procedure. As a consequence we establish that values of an ε-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME. },
  author       = {Krishnendu Chatterjee},
  pages        = {271 -- 286},
  publisher    = {Springer},
  title        = {{Nash equilibrium for upward-closed objectives}},
  doi          = {10.1007/11874683_18},
  volume       = {4207},
  year         = {2006},
}

@inproceedings{3500,
  abstract     = {The classical algorithm for solving Bu ̈chi games requires time O(n · m) for game graphs with n states and m edges. For game graphs with constant outdegree, the best known algorithm has running time O(n2/logn). We present two new algorithms for Bu ̈chi games. First, we give an algorithm that performs at most O(m) more work than the classical algorithm, but runs in time O(n) on infinitely many graphs of constant outdegree on which the classical algorithm requires time O(n2). Second, we give an algorithm with running time O(n · m · log δ(n)/ log n), where 1 ≤ δ(n) ≤ n is the outdegree of the game graph. Note that this algorithm performs asymptotically better than the classical algorithm if δ(n) = O(log n).},
  author       = {Krishnendu Chatterjee and Thomas Henzinger and Piterman, Nir},
  publisher    = {ACM},
  title        = {{Algorithms for Büchi Games}},
  year         = {2006},
}

@misc{3510,
  abstract     = {Embodiments automatically generate an accurate network of watertight NURBS patches from polygonal models of objects while automatically detecting and preserving character lines thereon. These embodiments generate from an initial triangulation of the surface, a hierarchy of progressively coarser triangulations of the surface by performing a sequence of edge contractions using a greedy algorithm that selects edge contractions by their numerical properties. Operations are also performed to connect the triangulations in the hierarchy using homeomorphisms that preserve the topology of the initial triangulation in the coarsest triangulation. A desired quadrangulation of the surface can then be generated by homeomorphically mapping edges of a coarsest triangulation in the hierarchy back to the initial triangulation. This quadrangulation is topologically consistent with the initial triangulation and is defined by a plurality of quadrangular patches. These quadrangular patches are linked together by a (U, V) mesh that is guaranteed to be continuous at patch boundaries. A grid is then preferably fit to each of the quadrangles in the resulting quadrangulation by decomposing each of the quadrangles into k.sup.2 smaller quadrangles. A watertight NURBS model may be generated from the resulting quadrangulation.},
  author       = {Edelsbrunner, Herbert and Fu, Ping and Nekhayev, Dmitry and Facello, Michael and Williams, Steven},
  title        = {{Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism}},
  year         = {2006},
}