@article{3009,
author = {Paciorek, Tomasz and Friml, Jirí},
journal = {Journal of Cell Science},
number = {7},
pages = {1199 -- 1202},
publisher = {Company of Biologists},
title = {{Auxin signaling}},
doi = {10.1242/jcs.02910},
volume = {119},
year = {2006},
}
@article{3010,
abstract = {The formation of the leaf vascular pattern has fascinated biologists for centuries. In the early leaf primordium, complex networks of procambial cells emerge from homogeneous subepidermal tissue. The molecular nature of the underlying positional information is unknown, but various lines of evidence implicate gradually restricted transport routes of the plant hormone auxin in defining sites of procambium formation. Here we show that a crucial member of the AtPIN family of auxin-efflux-associated proteins, AtPIN1, is expressed prior to pre-procambial and procambial cell fate markers in domains that become restricted toward sites of procambium formation. Subcellular AtPIN1 polarity indicates that auxin is directed to distinct "convergence points" in the epidermis, from where it defines the positions of major veins. Integrated polarities in all emerging veins indicate auxin drainage toward pre-existing veins, but veins display divergent polarities as they become connected at both ends. Auxin application and transport inhibition reveal that convergence point positioning and AtPIN1 expression domain dynamics are self-organizing, auxin-transport-dependent processes. We derive a model for self-regulated, reiterative patterning of all vein orders and postulate at its onset a common epidermal auxin-focusing mechanism for major-vein positioning and phyllotactic patterning.},
author = {Scarpella, Enrico and Marcos, Danielle and Jirí Friml and Berleth, Thomas},
journal = {Genes and Development},
number = {8},
pages = {1015 -- 1027},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{Control of leaf vascular patterning by polar auxin transport}},
doi = {10.1101/gad.1402406},
volume = {20},
year = {2006},
}
@article{3011,
abstract = {Polar flow of the phytohormone auxin requires plasma membrane‐associated PIN proteins and underlies multiple developmental processes in plants. Here we address the importance of the polarity of subcellular PIN localization for the directionality of auxin transport in Arabidopsis thaliana. Expression of different PINs in the root epidermis revealed the importance of PIN polar positions for directional auxin flow and root gravitropic growth. Interfering with sequence-embedded polarity signals directly demonstrates that PIN polarity is a primary factor in determining the direction of auxin flow in meristematic tissues. This finding provides a crucial piece in the puzzle of how auxin flow can be redirected via rapid changes in PIN polarity.},
author = {Wiśniewska, Justyna and Xu, Jian and Seifertová, Daniela and Brewer, Philip B and Růžička, Kamil and Blilou, Ikram and Rouquié, David and Eva Benková and Scheres, Ben and Jirí Friml},
journal = {Science},
number = {5775},
publisher = {American Association for the Advancement of Science},
title = {{Polar PIN localization directs auxin flow in plants}},
doi = {10.1126/science.1121356},
volume = {312},
year = {2006},
}
@article{3012,
abstract = {Intercellular flow of the phytohormone auxin underpins multiple developmental processes in plants. Plant-specific pin-formed (PIN) proteins and several phosphoglycoprotein (PGP) transporters are crucial factors in auxin transport-related development, yet the molecular function of PINs remains unknown. Here, we show that PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. Conditional gain-of-function alleles and quantitative measurements of auxin accumulation in Arabidopsis and tobacco cultured cells revealed that the action of PINs in auxin efflux is distinct from PGP, rate-limiting, specific to auxins, and sensitive to auxin transport inhibitors. This suggests a direct involvement of PINs in catalyzing cellular auxin efflux.},
author = {Petrášek, Jan and Mravec, Jozef and Bouchard, Rodolphe and Blakeslee, Joshua and Melinda Abas and Seifertová, Daniela and Wiśniewska, Justyna and Tadele, Zerihun and Kubeš, Martin and Čovanová, Milada and Dhonukshe, Pankaj and Skůpa, Petr and Eva Benková and Perry, Lucie and Křeček, Pavel and Lee, Ok Ran and Fink, Gerald R and Geisler, Markus and Murphy, Angus S and Luschnig, Christian and Zažímalová, Eva and Jirí Friml},
journal = {Science},
number = {5775},
pages = {914 -- 918},
publisher = {American Association for the Advancement of Science},
title = {{PIN proteins perform a rate-limiting function in cellular auxin efflux}},
doi = {10.1126/science.1123542},
volume = {312},
year = {2006},
}
@article{3013,
abstract = {There is a growing demand for methods that allow rapid and reliable in situ localization of proteins in plant cells. The immunocytochemistry protocol presented here can be used routinely to observe protein localization patterns in tissue sections of various plant species. This protocol is especially suitable for plant species with more-complex tissue architecture (such as maize, Zea mays), which makes it difficult to use an easier whole-mount procedure for protein localization. To facilitate the antibody-antigen reaction, it is necessary to include a wax-embedding and tissue-sectioning step. The protocol consists of the following procedures: chemical fixation of tissue, dehydration, wax embedding, sectioning, dewaxing, rehydration, blocking and antibody incubation. The detailed protocol, recommended controls and troubleshooting are presented here, along with examples of applications.},
author = {Paciorek, Tomasz and Sauer, Michael and Balla, Jozef and Wiśniewska, Justyna and Jirí Friml},
journal = {Nature Protocols},
number = {1},
pages = {104 -- 107},
publisher = {Nature Publishing Group},
title = {{Immunocytochemical technique for protein localization in sections of plant tissues}},
doi = {10.1038/nprot.2006.16},
volume = {1},
year = {2006},
}
@article{3014,
abstract = {Plant biology is currently confronted with an overflow of expression profile data provided by high-throughput microarray transcription analyses. However, the tissue and cellular resolution of these techniques is limited. Thus, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here we present an in situ mRNA hybridization method that is routinely used in the analysis of gene expression patterns. The protocol is optimized for mRNA localizations in sectioned tissue of Arabidopsis seedlings including embryos, roots, hypocotyls, young primary leaves and flowers. The detailed protocol, recommended controls and troubleshooting are presented along with examples of application. The total time for the process is 10 days.},
author = {Brewer, Philip B and Heisler, Marcus G and Hejátko, Jan and Jirí Friml and Eva Benková},
journal = {Nature Protocols},
number = {3},
pages = {1462 -- 1467},
publisher = {Nature Publishing Group},
title = {{In situ hybridization for mRNA detection in Arabidopsis tissue sections}},
doi = {10.1038/nprot.2006.226},
volume = {1},
year = {2006},
}
@article{3015,
abstract = {As the field of plant molecular biology is swiftly advancing, a need has been created for methods that allow rapid and reliable in situ localization of proteins in plant cells. Here we describe a whole-mount 'immunolocalization' technique for various plant tissues, including roots, hypocotyls, cotyledons, young primary leaves and embryos of Arabidopsis thaliana and other species. The detailed protocol, recommended controls and troubleshooting are presented, along with examples of applications. The protocol consists of five main procedures: tissue fixation, tissue permeation, blocking, primary and secondary antibody incubation. Notably, the first procedure (tissue fixation) includes several steps (4-12) that are absolutely necessary for protein localization in hypocotyls, cotyledons and young primary leaves but should be omitted for other tissues. The protocol is usually done in 3 days, but could also be completed in 2 days.},
author = {Sauer, Michael and Paciorek, Tomasz and Eva Benková and Jirí Friml},
journal = {Nature Protocols},
number = {1},
pages = {98 -- 103},
publisher = {Nature Publishing Group},
title = {{Immunocytochemical techniques for whole mount in situ protein localization in plants}},
doi = {10.1038/nprot.2006.15},
volume = {1},
year = {2006},
}
@article{3016,
abstract = {Plant development is characterized by a profound ability to regenerate and form tissues with new axes of polarity. An unsolved question concerns how the position within a tissue and cues from neighboring cells are integrated to specify the polarity of individual cells. The canalization hypothesis proposes a feedback effect of the phytohormone auxin on the directionality of intercellular auxin flow as a means to polarize tissues. Here we identify a cellular and molecular mechanism for canalization. Local auxin application, wounding, or auxin accumulation during de novo organ formation lead to rearrangements in the subcellular polar localization of PIN auxin transport components. This auxin effect on PIN polarity is cell-specific, does not depend on PIN transcription, and involves the Aux/IAA-ARF (indole-3-acetic acid-auxin response factor) signaling pathway. Our data suggest that auxin acts as polarizing cue, which links individual cell polarity with tissue and organ polarity through control of PIN polar targeting. This feedback regulation provides a conceptual framework for polarization during multiple regenerative and patterning processes in plants.},
author = {Sauer, Michael and Balla, Jozef and Luschnig, Christian and Wiśniewska, Justyna and Reinöhl, Vilém and Friml, Jirí and Benková, Eva},
journal = {Genes and Development},
number = {20},
pages = {2902 -- 2911},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity}},
doi = {10.1101/gad.390806},
volume = {20},
year = {2006},
}
@article{3017,
abstract = {The plant hormone auxin plays crucial roles in regulating plant growth development, including embryo and root patterning, organ formation, vascular tissue differentiation and growth responses to environmental stimuli. Asymmetric auxin distribution patterns have been observed within tissues, and these so-called auxin gradients change dynamically during different developmental processes. Most auxin is synthesized in the shoot and distributed directionally throughout the plant. This polar auxin transport is mediated by auxin influx and efflux facilitators, whose subcellular polar localizations guide the direction of auxin flow. The polar localization of PIN auxin efflux carriers changes in response to developmental and external cues in order to channel auxin flow in a regulated manner for organized growth. Auxin itself modulates the expression and subcellular localization of PIN proteins, contributing to a complex pattern of feedback regulation. Here we review the available information mainly from studies of a model plant, Arabidopsis thaliana, on the generation of auxin gradients, the regulation of polar auxin transport and further downstream cellular events.},
author = {Tanaka, Hirokazu and Dhonukshe, Pankaj and Brewer, Philip and Friml, Jirí},
journal = {Cellular and Molecular Life Sciences},
number = {23},
pages = {2738 -- 2754},
publisher = {Birkhäuser},
title = {{Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development}},
doi = {10.1007/s00018-006-6116-5},
volume = {63},
year = {2006},
}
@article{3018,
abstract = {The directional flow of the plant hormone auxin mediates multiple developmental processes, including patterning and tropisms. Apical and basal plasma membrane localization of AUXIN-RESISTANT1 (AUX1) and PIN-FORMED1 (PIN1) auxin transport components underpins the directionality of intercellular auxin flow in Arabidopsis thaliana roots. Here, we examined the mechanism of polar trafficking of AUX1. Real-time live cell analysis along with subcellular markers revealed that AUX1 resides at the apical plasma membrane of protophloem cells and at highly dynamic subpopulations of Golgi apparatus and endosomes in all cell types. Plasma membrane and intracellular pools of AUX1 are interconnected by actin-dependent constitutive trafficking, which is not sensitive to the vesicle trafficking inhibitor brefeldin A. AUX1 subcellular dynamics are not influenced by the auxin influx inhibitor NOA but are blocked by the auxin efflux inhibitors TIBA and PBA. Furthermore, auxin transport inhibitors and interference with the sterol composition of membranes disrupt polar AUX1 distribution at the plasma membrane. Compared with PIN1 trafficking, AUX1 dynamics display different sensitivities to trafficking inhibitors and are independent of the endosomal trafficking regulator ARF GEF GNOM. Hence, AUX1 uses a novel trafficking pathway in plants that is distinct from PIN trafficking, providing an additional mechanism for the fine regulation of auxin transport.},
author = {Kleine-Vehn, Jürgen and Dhonukshe, Pankaj and Swarup, Ranjan and Bennett, Malcolm and Jirí Friml},
journal = {Plant Cell},
number = {11},
pages = {3171 -- 3181},
publisher = {American Society of Plant Biologists},
title = {{Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1}},
doi = {10.1105/tpc.106.042770},
volume = {18},
year = {2006},
}
@article{3020,
abstract = {High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here, we present an in situ mRNA hybridization method that is routinely used for the analysis of plant gene expression patterns. The protocol is optimized for whole mount mRNA localizations in Arabidopsis seedling tissues including embryos, roots, hypocotyls and young primary leaves. It can also be used for comparable tissues in other species. Part of the protocol can also be automated and performed by a liquid handling robot. Here we present a detailed protocol, recommended controls and troubleshooting, along with examples of several applications. The total time to carry out the entire procedure is ∼7 d, depending on the tissue used.},
author = {Hejátko, Jan and Blilou, Ikram and Brewer, Philip B and Jirí Friml and Scheres, Ben and Eva Benková},
journal = {Nature Protocols},
number = {4},
pages = {1939 -- 1946},
publisher = {Nature Publishing Group},
title = {{In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples}},
doi = {10.1038/nprot.2006.333},
volume = {1},
year = {2006},
}
@article{3152,
abstract = {The basic concepts of the molecular machinery that mediates cell migration have been gleaned from cell culture systems. However, the three-dimensional environment within an organism presents migrating cells with a much greater challenge. They must move between and among other cells while interpreting multiple attractive and repulsive cues to choose their proper path. They must coordinate their cell adhesion with their surroundings and know when to start and stop moving. New insights into the control of these remaining mysteries have emerged from genetic dissection and live imaging of germ cell migration in Drosophila, zebrafish, and mouse embryos. In this review, we first describe germ cell migration in cellular and mechanistic detail in these different model systems. We then compare these systems to highlight the emerging principles. Finally, we contrast the migration of germ cells with that of immune and cancer cells to outline the conserved and different mechanisms.},
author = {Kunwar, Prabhat S and Daria Siekhaus and Lehmann, Ruth},
journal = {Annual Review of Cell and Developmental Biology},
pages = {237 -- 265},
publisher = {Annual Reviews},
title = {{In vivo migration A germ cell perspective}},
doi = {10.1146/annurev.cellbio.22.010305.103337},
volume = {22},
year = {2006},
}
@inproceedings{3180,
abstract = {One of the most exciting advances in early vision has been the development of efficient energy minimization algorithms. Many early vision tasks require labeling each pixel with some quantity such as depth or texture. While many such problems can be elegantly expressed in the language of Markov Random Fields (MRF's), the resulting energy minimization problems were widely viewed as intractable. Recently, algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: for example, such methods form the basis for almost all the top-performing stereo methods. Unfortunately, most papers define their own energy function, which is minimized with a specific algorithm of their choice. As a result, the tradeoffs among different energy minimization algorithms are not well understood. In this paper we describe a set of energy minimization benchmarks, which we use to compare the solution quality and running time of several common energy minimization algorithms. We investigate three promising recent methods - graph cuts, LBP, and tree-reweighted message passing - as well as the well-known older iterated conditional modes (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching and interactive segmentation. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods with minimal overhead. We expect that the availability of our benchmarks and interface will make it significantly easier for vision researchers to adopt the best method for their specific problems. Benchmarks, code, results and images are available at http://vision.middlebury.edu/MRF.},
author = {Szeliski, Richard S and Zabih, Ramin and Scharstein, Daniel and Veksler, Olga and Vladimir Kolmogorov and Agarwala, Aseem and Tappen, Marshall F and Rother, Carsten},
pages = {16 -- 29},
publisher = {Springer},
title = {{A comparative study of energy minimization methods for Markov random fields}},
doi = {10.1007/11744047_2},
volume = {3952},
year = {2006},
}
@inproceedings{3184,
abstract = {Algorithms for discrete energy minimization play a fundamental role for low-level vision. Known techniques include graph cuts, belief propagation (BP) and recently introduced tree-reweighted message passing (TRW). So far, the standard benchmark for their comparison has been a 4-connected grid-graph arising in pixel-labelling stereo. This minimization problem, however, has been largely solved: recent work shows that for many scenes TRW finds the global optimum. Furthermore, it is known that a 4-connecled grid-graph is a poor stereo model since it does not take occlusions into account. We propose the problem of stereo with occlusions as a new test bed for minimization algorithms. This is a more challenging graph since it has much larger connectivity, and it also serves as a better stereo model. An attractive feature of this problem is that increased connectivity does not result in increased complexity of message passing algorithms. Indeed, one contribution of this paper is to show that sophisticated implementations of BP and TRW have the same time and memory complexity as that of 4-connecled grid-graph stereo. The main conclusion of our experimental study is that for our problem graph cut outperforms both TRW and BP considerably. TRW achieves consistently a lower energy than BP. However, as connectivity increases the speed of convergence of TRW becomes slower. Unlike 4-connected grids, the difference between the energy of the best optimization method and the lower bound of TRW appears significant. This shows the hardness of the problem and motivates future research.},
author = {Vladimir Kolmogorov and Rother, Carsten},
pages = {1 -- 15},
publisher = {Springer},
title = {{Comparison of energy minimization algorithms for highly connected graphs}},
doi = {10.1007/11744047_1},
volume = {3952 LNCS},
year = {2006},
}
@article{3185,
abstract = {This paper describes models and algorithms for the real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from color/contrast or from stereo alone is known to be error-prone. Here, color, contrast, and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended six-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive color model that is learned on-the-fly and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead, the stereo match likelihood is marginalized over disparities to evaluate foreground and background hypotheses and then fused with a contrast-sensitive color model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than either stereo or color/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.},
author = {Vladimir Kolmogorov and Criminisi, Antonio and Blake, Andrew and Cross, Geoffrey and Rother, Carsten},
journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
number = {9},
pages = {1480 -- 1492},
publisher = {IEEE},
title = {{Probabilistic fusion of stereo with color and contrast for bilayer segmentation}},
doi = {10.1109/TPAMI.2006.193},
volume = {28},
year = {2006},
}
@inproceedings{3186,
abstract = {We introduce a new approach to modelling gradient flows of contours and surfaces. While standard variational methods (e.g. level sets) compute local interface motion in a differential fashion by estimating local contour velocity via energy derivatives, we propose to solve surface evolution PDEs by explicitly estimating integral motion of the whole surface. We formulate an optimization problem directly based on an integral characterization of gradient flow as an infinitesimal move of the (whole) surface giving the largest energy decrease among all moves of equal size. We show that this problem can be efficiently solved using recent advances in algorithms for global hypersurface optimization [4, 2, 11]. In particular, we employ the geo-cuts method [4] that uses ideas from integral geometry to represent continuous surfaces as cuts on discrete graphs. The resulting interface evolution algorithm is validated on some 2D and 3D examples similar to typical demonstrations of level-set methods. Our method can compute gradient flows of hypersurfaces with respect to a fairly general class of continuous functional and it is flexible with respect to distance metrics on the space of contours/surfaces. Preliminary tests for standard L2 distance metric demonstrate numerical stability, topological changes and an absence of any oscillatory motion.},
author = {Boykov, Yuri and Vladimir Kolmogorov and Cremers, Daniel and Delong, Andrew},
pages = {409 -- 422},
publisher = {Springer},
title = {{An integral solution to surface evolution PDEs via geo cuts}},
doi = {10.1007/11744078_32},
volume = {3953},
year = {2006},
}
@inproceedings{3188,
abstract = {We introduce the term cosegmentation which denotes the task of segmenting simultaneously the common parts of an image pair. A generative model for cosegmentation is presented. Inference in the model leads to minimizing an energy with an MRF term encoding spatial coherency and a global constraint which attempts to match the appearance histograms of the common parts. This energy has not been proposed previously and its optimization is challenging and NP-hard. For this problem a novel optimization scheme which we call trust region graph cuts is presented. We demonstrate that this framework has the potential to improve a wide range of research: Object driven image retrieval, video tracking and segmentation, and interactive image editing. The power of the framework lies in its generality, the common part can be a rigid/non-rigid object (or scene), observed from different viewpoints or even similar objects of the same class.},
author = {Rother, Carsten and Vladimir Kolmogorov and Minka, Thomas P and Blake, Andrew},
pages = {993 -- 1000},
publisher = {IEEE},
title = {{Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs}},
doi = {10.1109/CVPR.2006.91},
year = {2006},
}
@inproceedings{3189,
abstract = {This paper presents an algorithm capable of real-time separation of foreground from background in monocular video sequences. Automatic segmentation of layers from colour/contrast or from motion alone is known to be error-prone. Here motion, colour and contrast cues are probabilistically fused together with spatial and temporal priors to infer layers accurately and efficiently. Central to our algorithm is the fact that pixel velocities are not needed, thus removing the need for optical flow estimation, with its tendency to error and computational expense. Instead, an efficient motion vs non-motion classifier is trained to operate directly and jointly on intensity-change and contrast. Its output is then fused with colour information. The prior on segmentation is represented by a second order, temporal, Hidden Markov Model, together with a spatial MRF favouring coherence except where contrast is high. Finally, accurate layer segmentation and explicit occlusion detection are efficiently achieved by binary graph cut. The segmentation accuracy of the proposed algorithm is quantitatively evaluated with respect to existing ground-truth data and found to be comparable to the accuracy of a state of the art stereo segmentation algorithm. Fore-ground/background segmentation is demonstrated in the application of live background substitution and shown to generate convincingly good quality composite video.},
author = {Criminisi, Antonio and Cross, Geoffrey and Blake, Andrew and Vladimir Kolmogorov},
pages = {53 -- 60},
publisher = {IEEE},
title = {{Bilayer segmentation of live video}},
doi = {10.1109/CVPR.2006.69},
volume = {1},
year = {2006},
}
@article{3190,
abstract = {Algorithms for discrete energy minimization are of fundamental importance in computer vision. In this paper, we focus on the recent technique proposed by Wainwright et al. (Nov. 2005)- tree-reweighted max-product message passing (TRW). It was inspired by the problem of maximizing a lower bound on the energy. However, the algorithm is not guaranteed to increase this bound - it may actually go down. In addition, TRW does not always converge. We develop a modification of this algorithm which we call sequential tree-reweighted message passing. Its main property is that the bound is guaranteed not to decrease. We also give a weak tree agreement condition which characterizes local maxima of the bound with respect to TRW algorithms. We prove that our algorithm has a limit point that achieves weak tree agreement. Finally, we show that, our algorithm requires half as much memory as traditional message passing approaches. Experimental results demonstrate that on certain synthetic and real problems, our algorithm outperforms both the ordinary belief propagation and tree-reweighted algorithm in (M. J. Wainwright, et al., Nov. 2005). In addition, on stereo problems with Potts interactions, we obtain a lower energy than graph cuts.},
author = {Vladimir Kolmogorov},
journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
number = {10},
pages = {1568 -- 1583},
publisher = {IEEE},
title = {{Convergent tree reweighted message passing for energy minimization}},
doi = {10.1109/TPAMI.2006.200},
volume = {28},
year = {2006},
}
@inproceedings{3214,
abstract = {The Feistel-network is a popular structure underlying many block-ciphers where the cipher is constructed from many simpler rounds, each defined by some function which is derived from the secret key.
Luby and Rackoff showed that the three-round Feistel-network – each round instantiated with a pseudorandom function secure against adaptive chosen plaintext attacks (CPA) – is a CPA secure pseudorandom permutation, thus giving some confidence in the soundness of using a Feistel-network to design block-ciphers.
But the round functions used in actual block-ciphers are – for efficiency reasons – far from being pseudorandom. We investigate the security of the Feistel-network against CPA distinguishers when the only security guarantee we have for the round functions is that they are secure against non-adaptive chosen plaintext attacks (nCPA). We show that in the information-theoretic setting, four rounds with nCPA secure round functions are sufficient (and necessary) to get a CPA secure permutation. Unfortunately, this result does not translate into the more interesting pseudorandom setting. In fact, under the so-called Inverse Decisional Diffie-Hellman assumption the Feistel-network with four rounds, each instantiated with a nCPA secure pseudorandom function, is in general not a CPA secure pseudorandom permutation.},
author = {Maurer, Ueli M and Oswald, Yvonne A and Krzysztof Pietrzak and Sjödin, Johan},
pages = {391 -- 408},
publisher = {Springer},
title = {{Luby Rackoff ciphers from weak round functions }},
doi = {10.1007/11761679_24},
volume = {4004},
year = {2006},
}
@inproceedings{3215,
abstract = {Most cryptographic primitives such as encryption, authentication or secret sharing require randomness. Usually one assumes that perfect randomness is available, but those primitives might also be realized under weaker assumptions. In this work we continue the study of building secure cryptographic primitives from imperfect random sources initiated by Dodis and Spencer (FOCS’02). Their main result shows that there exists a (high-entropy) source of randomness allowing for perfect encryption of a bit, and yet from which one cannot extract even a single weakly random bit, separating encryption from extraction. Our main result separates encryption from 2-out-2 secret sharing (both in the information-theoretic and in the computational settings): any source which can be used to achieve one-bit encryption also can be used for 2-out-2 secret sharing of one bit, but the converse is false, even for high-entropy sources. Therefore, possibility of extraction strictly implies encryption, which in turn strictly implies 2-out-2 secret sharing.},
author = {Dodis, Yevgeniy and Krzysztof Pietrzak and Przydatek, Bartosz},
pages = {601 -- 616},
publisher = {Springer},
title = {{Separating sources for encryption and secret sharing}},
doi = {10.1007/11681878_31},
volume = {3876},
year = {2006},
}
@inproceedings{3216,
abstract = {We prove a new upper bound on the advantage of any adversary for distinguishing the encrypted CBC-MAC (EMAC) based on random permutations from a random function. Our proof uses techniques recently introduced in [BPR05], which again were inspired by [DGH + 04].
The bound we prove is tight — in the sense that it matches the advantage of known attacks up to a constant factor — for a wide range of the parameters: let n denote the block-size, q the number of queries the adversary is allowed to make and ℓ an upper bound on the length (i.e. number of blocks) of the messages, then for ℓ ≤ 2 n/8 and q≥ł2 the advantage is in the order of q 2/2 n (and in particular independent of ℓ). This improves on the previous bound of q 2ℓΘ(1/ln ln ℓ)/2 n from [BPR05] and matches the trivial attack (which thus is basically optimal) where one simply asks random queries until a collision is found.},
author = {Krzysztof Pietrzak},
pages = {168 -- 179},
publisher = {Springer},
title = {{A tight bound for EMAC}},
doi = {10.1007/11787006_15},
volume = {4052},
year = {2006},
}
@inproceedings{3217,
abstract = {To prove that a secure key-agreement protocol exists one must at least show P ≠NP. Moreover any proof that the sequential composition of two non-adaptively secure pseudorandom functions is secure against at least two adaptive queries must falsify the decisional Diffie-Hellman assumption, a standard assumption from public-key cryptography. Hence proving any of this two seemingly unrelated statements would require a significant breakthrough. We show that at least one of the two statements is true.
To our knowledge this gives the first positive cryptographic result (namely that composition implies some weak adaptive security) which holds in Minicrypt, but not in Cryptomania, i.e. under the assumption that one-way functions exist, but public-key cryptography does not.},
author = {Krzysztof Pietrzak},
pages = {328 -- 338},
publisher = {Springer},
title = {{Composition implies adaptive security in minicrypt}},
doi = {10.1007/11761679_20},
volume = {4004},
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},
}
@article{8488,
abstract = {We demonstrate for different protein samples that three-dimensional HNCO and HNCA correlation spectra may be recorded in a few minutes acquisition time using the band-selective excitation short-transient sequences presented here. This opens new perspectives for the NMR structural investigation of unstable protein samples and real-time site-resolved studies of protein kinetics.},
author = {Schanda, Paul and Van Melckebeke, Hélène and Brutscher, Bernhard},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis},
number = {28},
pages = {9042--9043},
publisher = {American Chemical Society},
title = {{Speeding up three-dimensional protein NMR experiments to a few minutes}},
doi = {10.1021/ja062025p},
volume = {128},
year = {2006},
}
@article{8489,
abstract = {Structure elucidation of proteins by either NMR or X‐ray crystallography often requires the screening of a large number of samples for promising protein constructs and optimum solution conditions. For large‐scale screening of protein samples in solution, robust methods are needed that allow a rapid assessment of the folding of a polypeptide under diverse sample conditions. Here we present HET‐SOFAST NMR, a highly sensitive new method for semi‐quantitative characterization of the structural compactness and heterogeneity of polypeptide chains in solution. On the basis of one‐dimensional 1H HET‐SOFAST NMR data, obtained on well‐folded, molten globular, partially‐ and completely unfolded proteins, we define empirical thresholds that can be used as quantitative benchmarks for protein compactness. For 15N‐enriched protein samples, two‐dimensional 1H‐15N HET‐SOFAST correlation spectra provide site‐specific information about the structural heterogeneity along the polypeptide chain.},
author = {Schanda, Paul and Forge, Vincent and Brutscher, Bernhard},
issn = {0749-1581},
journal = {Magnetic Resonance in Chemistry},
number = {S1},
pages = {S177--S184},
publisher = {Wiley},
title = {{HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains}},
doi = {10.1002/mrc.1825},
volume = {44},
year = {2006},
}
@article{8490,
abstract = {We demonstrate the feasibility of recording 1H–15N correlation spectra of proteins in only one second of acquisition time. The experiment combines recently proposed SOFAST-HMQC with Hadamard-type 15N frequency encoding. This allows site-resolved real-time NMR studies of kinetic processes in proteins with an increased time resolution. The sensitivity of the experiment is sufficient to be applicable to a wide range of molecular systems available at millimolar concentration on a high magnetic field spectrometer.},
author = {Schanda, Paul and Brutscher, Bernhard},
issn = {1090-7807},
journal = {Journal of Magnetic Resonance},
keywords = {Nuclear and High Energy Physics, Biophysics, Biochemistry, Condensed Matter Physics},
number = {2},
pages = {334--339},
publisher = {Elsevier},
title = {{Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR}},
doi = {10.1016/j.jmr.2005.10.007},
volume = {178},
year = {2006},
}
@article{8513,
author = {Kaloshin, Vadim and Saprykina, Maria},
issn = {1553-5231},
journal = {Discrete & Continuous Dynamical Systems - A},
number = {2},
pages = {611--640},
publisher = {American Institute of Mathematical Sciences (AIMS)},
title = {{Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits}},
doi = {10.3934/dcds.2006.15.611},
volume = {15},
year = {2006},
}
@article{8514,
abstract = {We study the extent to which the Hausdorff dimension of a compact subset of an infinite-dimensional Banach space is affected by a typical mapping into a finite-dimensional space. It is possible that the dimension drops under all such mappings, but the amount by which it typically drops is controlled by the ‘thickness exponent’ of the set, which was defined by Hunt and Kaloshin (Nonlinearity12 (1999), 1263–1275). More precisely, let $X$ be a compact subset of a Banach space $B$ with thickness exponent $\tau$ and Hausdorff dimension $d$. Let $M$ be any subspace of the (locally) Lipschitz functions from $B$ to $\mathbb{R}^{m}$ that contains the space of bounded linear functions. We prove that for almost every (in the sense of prevalence) function $f \in M$, the Hausdorff dimension of $f(X)$ is at least $\min\{ m, d / (1 + \tau) \}$. We also prove an analogous result for a certain part of the dimension spectra of Borel probability measures supported on $X$. The factor $1 / (1 + \tau)$ can be improved to $1 / (1 + \tau / 2)$ if $B$ is a Hilbert space. Since dimension cannot increase under a (locally) Lipschitz function, these theorems become dimension preservation results when $\tau = 0$. We conjecture that many of the attractors associated with the evolution equations of mathematical physics have thickness exponent zero. We also discuss the sharpness of our results in the case $\tau > 0$.},
author = {OTT, WILLIAM and HUNT, BRIAN and Kaloshin, Vadim},
issn = {0143-3857},
journal = {Ergodic Theory and Dynamical Systems},
number = {3},
pages = {869--891},
publisher = {Cambridge University Press},
title = {{The effect of projections on fractal sets and measures in Banach spaces}},
doi = {10.1017/s0143385705000714},
volume = {26},
year = {2006},
}
@inproceedings{8515,
abstract = {We consider the evolution of a set carried by a space periodic incompressible stochastic flow in a Euclidean space. We
report on three main results obtained in [8, 9, 10] concerning long time behaviour for a typical realization of the stochastic flow. First, at time t most of the particles are at a distance of order √t away from the origin. Moreover, we prove a Central Limit Theorem for the evolution of a measure carried by the flow, which holds for almost every realization of the flow. Second, we show the existence of a zero measure full Hausdorff dimension set of points, which
escape to infinity at a linear rate. Third, in the 2-dimensional case, we study the set of points visited by the original set by time t. Such a set, when scaled down by the factor of t, has a limiting non random shape.},
author = {Kaloshin, Vadim and DOLGOPYAT, D. and KORALOV, L.},
booktitle = {XIVth International Congress on Mathematical Physics},
isbn = {9789812562012},
location = {Lisbon, Portugal},
pages = {290--295},
publisher = {World Scientific},
title = {{Long time behaviour of periodic stochastic flows}},
doi = {10.1142/9789812704016_0026},
year = {2006},
}
@article{854,
abstract = {Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch - the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ∼1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene.},
author = {Rogaev, Evgeny I and Moliaka, Yuri K and Malyarchuk, Boris A and Fyodor Kondrashov and Derenko, Miroslava V and Chumakov, Ilya M and Grigorenko, Anastasia P},
journal = {PLoS Biology},
number = {3},
pages = {0403 -- 0410},
publisher = {Public Library of Science},
title = {{Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius}},
doi = {10.1371/journal.pbio.0040073},
volume = {4},
year = {2006},
}
@inproceedings{4431,
abstract = {We summarize some current trends in embedded systems design and point out some of their characteristics, such as the chasm between analytical and computational models, and the gap between safety-critical and best-effort engineering practices. We call for a coherent scientific foundation for embedded systems design, and we discuss a few key demands on such a foundation: the need for encompassing several manifestations of heterogeneity, and the need for constructivity in design. We believe that the development of a satisfactory Embedded Systems Design Science provides a timely challenge and opportunity for reinvigorating computer science.},
author = {Thomas Henzinger and Sifakis, Joseph},
pages = {1 -- 15},
publisher = {Springer},
title = {{The embedded systems design challenge}},
doi = {10.1007/11813040_1},
volume = {4085},
year = {2006},
}
@inproceedings{4432,
abstract = {We add freeze quantifiers to the game logic ATL in order to specify real-time objectives for games played on timed structures. We define the semantics of the resulting logic TATL by restricting the players to physically meaningful strategies, which do not prevent time from diverging. We show that TATL can be model checked over timed automaton games. We also specify timed optimization problems for physically meaningful strategies, and we show that for timed automaton games, the optimal answers can be approximated to within any degree of precision.},
author = {Thomas Henzinger and Prabhu, Vinayak S},
pages = {1 -- 17},
publisher = {Springer},
title = {{Timed alternating-time temporal logic}},
doi = {10.1007/11867340_1},
volume = {4202},
year = {2006},
}
@inproceedings{4436,
abstract = {We present an assume-guarantee interface algebra for real-time components. In our formalism a component implements a set of task sequences that share a resource. A component interface consists of an arrival rate function and a latency for each task sequence, and a capacity function for the shared resource. The interface specifies that the component guarantees certain task latencies depending on assumptions about task arrival rates and allocated resource capacities. Our algebra defines compatibility and refinement relations on interfaces. Interface compatibility can be checked on partial designs, even when some component interfaces are yet unknown. In this case interface composition computes as new assumptions the weakest constraints on the unknown components that are necessary to satisfy the specified guarantees. Interface refinement is defined in a way that ensures that compatible interfaces can be refined and implemented independently. Our algebra thus formalizes an interface-based design methodology that supports both the incremental addition of new components and the independent stepwise refinement of existing components. We demonstrate the flexibility and efficiency of the framework through simulation experiments.},
author = {Thomas Henzinger and Matic, Slobodan},
pages = {253 -- 266},
publisher = {IEEE},
title = {{An interface algebra for real-time components}},
doi = {10.1109/RTAS.2006.11},
year = {2006},
}
@inproceedings{4437,
abstract = {The synthesis of reactive systems requires the solution of two-player games on graphs with ω-regular objectives. When the objective is specified by a linear temporal logic formula or nondeterministic Büchi automaton, then previous algorithms for solving the game require the construction of an equivalent deterministic automaton. However, determinization for automata on infinite words is extremely complicated, and current implementations fail to produce deterministic automata even for relatively small inputs. We show how to construct, from a given nondeterministic Büchi automaton, an equivalent nondeterministic parity automaton that is good for solving games with objective . The main insight is that a nondeterministic automaton is good for solving games if it fairly simulates the equivalent deterministic automaton. In this way, we omit the determinization step in game solving and reactive synthesis. The fact that our automata are nondeterministic makes them surprisingly simple, amenable to symbolic implementation, and allows an incremental search for winning strategies.},
author = {Thomas Henzinger and Piterman, Nir},
pages = {395 -- 410},
publisher = {Springer},
title = {{Solving games without determinization}},
doi = {10.1007/11874683_26},
volume = {4207},
year = {2006},
}
@article{4451,
abstract = {One source of complexity in the μ-calculus is its ability to specify an unbounded number of switches between universal (AX) and existential (EX) branching modes. We therefore study the problems of satisfiability, validity, model checking, and implication for the universal and existential fragments of the μ-calculus, in which only one branching mode is allowed. The universal fragment is rich enough to express most specifications of interest, and therefore improved algorithms are of practical importance. We show that while the satisfiability and validity problems become indeed simpler for the existential and universal fragments, this is, unfortunately, not the case for model checking and implication. We also show the corresponding results for the alternation-free fragment of the μ-calculus, where no alternations between least and greatest fixed points are allowed. Our results imply that efforts to find a polynomial-time model-checking algorithm for the μ-calculus can be replaced by efforts to find such an algorithm for the universal or existential fragment.},
author = {Thomas Henzinger and Kupferman, Orna and Majumdar, Ritankar S},
journal = {Theoretical Computer Science},
number = {2},
pages = {173 -- 186},
publisher = {Elsevier},
title = {{On the universal and existential fragments of the mu-calculus}},
doi = {10.1016/j.tcs.2005.11.015},
volume = {354},
year = {2006},
}
@inproceedings{4523,
abstract = {We consider the problem if a given program satisfies a specified safety property. Interesting programs have infinite state spaces, with inputs ranging over infinite domains, and for these programs the property checking problem is undecidable. Two broad approaches to property checking are testing and verification. Testing tries to find inputs and executions which demonstrate violations of the property. Verification tries to construct a formal proof which shows that all executions of the program satisfy the property. Testing works best when errors are easy to find, but it is often difficult to achieve sufficient coverage for correct programs. On the other hand, verification methods are most successful when proofs are easy to find, but they are often inefficient at discovering errors. We propose a new algorithm, Synergy, which combines testing and verification. Synergy unifies several ideas from the literature, including counterexample-guided model checking, directed testing, and partition refinement.This paper presents a description of the Synergy algorithm, its theoretical properties, a comparison with related algorithms, and a prototype implementation called Yogi.},
author = {Gulavani, Bhargav S and Thomas Henzinger and Kannan, Yamini and Nori, Aditya V and Rajamani, Sriram K},
pages = {117 -- 127},
publisher = {ACM},
title = {{Synergy: A new algorithm for property checking}},
doi = {10.1145/1181775.1181790},
year = {2006},
}
@inproceedings{4526,
abstract = {We designed and implemented a new programming language called Hierarchical Timing Language (HTL) for hard realtime systems. Critical timing constraints are specified within the language,and ensured by the compiler. Programs in HTL are extensible in two dimensions without changing their timing behavior: new program modules can be added, and individual program tasks can be refined. The mechanism supporting time invariance under parallel composition is that different program modules communicate at specified instances of time. Time invariance under refinement is achieved by conservative scheduling of the top level. HTL is a coordination language, in that individual tasks can be implemented in "foreign" languages. As a case study, we present a distributed HTL implementation of an automotive steer-by-wire controller.},
author = {Ghosal, Arkadeb and Thomas Henzinger and Iercan, Daniel and Kirsch, Christoph M and Sangiovanni-Vincentelli, Alberto},
pages = {132 -- 141},
publisher = {ACM},
title = {{A hierarchical coordination language for interacting real-time tasks}},
doi = {10.1145/1176887.1176907},
year = {2006},
}
@inproceedings{4528,
abstract = {Computational modeling of biological systems is becoming increasingly common as scientists attempt to understand biological phenomena in their full complexity. Here we distinguish between two types of biological models mathematical and computational - according to their different representations of biological phenomena and their diverse potential. We call the approach of constructing computational models of biological systems executable biology, as it focuses on the design of executable computer algorithms that mimic biological phenomena. We give an overview of the main modeling efforts in this direction, and discuss some of the new challenges that executable biology poses for computer science and biology. We argue that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research, driving biology towards a more precise engineering discipline.},
author = {Fisher, Jasmin and Thomas Henzinger},
pages = {1675 -- 1682},
publisher = {IEEE},
title = {{Executable biology}},
doi = {10.1109/WSC.2006.322942},
year = {2006},
}
@inproceedings{4538,
abstract = {A stochastic graph game is played by two players on a game graph with probabilistic transitions. We consider stochastic graph games with ω-regular winning conditions specified as parity objectives. These games lie in NP ∩ coNP. We present a strategy improvement algorithm for stochastic parity games; this is the first non-brute-force algorithm for solving these games. From the strategy improvement algorithm we obtain a randomized subexponential-time algorithm to solve such games.},
author = {Krishnendu Chatterjee and Thomas Henzinger},
pages = {512 -- 523},
publisher = {Springer},
title = {{Strategy improvement and randomized subexponential algorithms for stochastic parity games}},
doi = {10.1007/11672142_42},
volume = {3884},
year = {2006},
}
@inproceedings{4539,
abstract = {Games on graphs with ω-regular objectives provide a model for the control and synthesis of reactive systems. Every ω-regular objective can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. While for one-shot liveness (reachability) objectives, classical and finitary liveness coincide, for repeated liveness (Büchi) objectives, the finitary formulation is strictly stronger. In this work we study games with finitary parity and Streett (fairness) objectives. We prove the determinacy of these games, present algorithms for solving these games, and characterize the memory requirements of winning strategies. Our algorithms can be used, for example, for synthesizing controllers that do not let the response time of a system increase without bound.},
author = {Krishnendu Chatterjee and Thomas Henzinger},
pages = {257 -- 271},
publisher = {Springer},
title = {{Finitary winning in omega-regular games}},
doi = {10.1007/11691372_17},
volume = {3920},
year = {2006},
}
@inproceedings{4549,
abstract = {We present a compositional theory of system verification, where specifications assign real-numbered costs to systems. These costs can express a wide variety of quantitative system properties, such as resource consumption, price, or a measure of how well a system satisfies its specification. The theory supports the composition of systems and specifications, and the hiding of variables. Boolean refinement relations are replaced by real-numbered distances between descriptions of a system at different levels of detail. We show that the classical Boolean rules for compositional reasoning have quantitative counterparts in our setting. While our general theory allows costs to be specified by arbitrary cost functions, we also consider a class of linear cost functions, which give rise to an instance of our framework where all operations are computable in polynomial time.},
author = {Krishnendu Chatterjee and de Alfaro, Luca and Faella, Marco and Thomas Henzinger and Majumdar, Ritankar S and Stoelinga, Mariëlle},
pages = {179 -- 188},
publisher = {IEEE},
title = {{Compositional quantitative reasoning}},
doi = {10.1109/QEST.2006.11},
year = {2006},
}
@article{4550,
abstract = {In 2-player non-zero-sum games, Nash equilibria capture the options for rational behavior if each player attempts to maximize her payoff. In contrast to classical game theory, we consider lexicographic objectives: first, each player tries to maximize her own payoff, and then, the player tries to minimize the opponent's payoff. Such objectives arise naturally in the verification of systems with multiple components. There, instead of proving that each component satisfies its specification no matter how the other components behave, it sometimes suffices to prove that each component satisfies its specification provided that the other components satisfy their specifications. We say that a Nash equilibrium is secure if it is an equilibrium with respect to the lexicographic objectives of both players. We prove that in graph games with Borel winning conditions, which include the games that arise in verification, there may be several Nash equilibria, but there is always a unique maximal payoff profile of a secure equilibrium. We show how this equilibrium can be computed in the case of ω-regular winning conditions, and we characterize the memory requirements of strategies that achieve the equilibrium.},
author = {Krishnendu Chatterjee and Thomas Henzinger and Jurdziński, Marcin},
journal = {Theoretical Computer Science},
number = {1-2},
pages = {67 -- 82},
publisher = {Elsevier},
title = {{Games with secure equilibria}},
doi = {10.1016/j.tcs.2006.07.032},
volume = {365},
year = {2006},
}
@inproceedings{4551,
abstract = {We consider Markov decision processes (MDPs) with multiple discounted reward objectives. Such MDPs occur in design problems where one wishes to simultaneously optimize several criteria, for example, latency and power. The possible trade-offs between the different objectives are characterized by the Pareto curve. We show that every Pareto-optimal point can be achieved by a memoryless strategy; however, unlike in the single-objective case, the memoryless strategy may require randomization. Moreover, we show that the Pareto curve can be approximated in polynomial time in the size of the MDP. Additionally, we study the problem if a given value vector is realizable by any strategy, and show that it can be decided in polynomial time; but the question whether it is realizable by a deterministic memoryless strategy is NP-complete. These results provide efficient algorithms for design exploration in MDP models with multiple objectives.
This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, and the NSF grants CCR-0225610, CCR-0234690, and CCR-0427202. },
author = {Krishnendu Chatterjee and Majumdar, Ritankar S and Thomas Henzinger},
pages = {325 -- 336},
publisher = {Springer},
title = {{Markov decision processes with multiple objectives}},
doi = {10.1007/11672142_26},
volume = {3884},
year = {2006},
}
@inproceedings{4552,
abstract = {A concurrent reachability game is a two-player game played on a graph: at each state, the players simultaneously and independently select moves; the two moves determine jointly a probability distribution over the successor states. The objective for player 1 consists in reaching a set of target states; the objective for player 2 is to prevent this, so that the game is zero-sum. Our contributions are two-fold. First, we present a simple proof of the fact that in concurrent reachability games, for all epsilon > 0, memoryless epsilon-optimal strategies exist. A memoryless strategy is independent of the history of plays, and an epsilon-optimal strategy achieves the objective with probability within epsilon of the value of the game. In contrast to previous proofs of this fact, which rely on the limit behavior of discounted games using advanced Puisieux series analysis, our proof is elementary and combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration) algorithm for concurrent games with reachability objectives.},
author = {Krishnendu Chatterjee and de Alfaro, Luca and Thomas Henzinger},
pages = {291 -- 300},
publisher = {IEEE},
title = {{Strategy improvement for concurrent reachability games}},
doi = {10.1109/QEST.2006.48},
year = {2006},
}
@inproceedings{4574,
abstract = {Many software model checkers are based on predicate abstraction. If the verification goal depends on pointer structures, the approach does not work well, because it is difficult to find adequate predicate abstractions for the heap. In contrast, shape analysis, which uses graph-based heap abstractions, can provide a compact representation of recursive data structures. We integrate shape analysis into the software model checker Blast. Because shape analysis is expensive, we do not apply it globally. Instead, we ensure that, like predicates, shape graphs are computed and stored locally, only where necessary for proving the verification goal. To achieve this, we extend lazy abstraction refinement, which so far has been used only for predicate abstractions, to three-valued logical structures. This approach does not only increase the precision of model checking, but it also increases the efficiency of shape analysis. We implemented the technique by extending Blast with calls to Tvla.},
author = {Beyer, Dirk and Thomas Henzinger and Théoduloz, Grégory},
pages = {532 -- 546},
publisher = {Springer},
title = {{Lazy shape analysis}},
doi = {10.1007/11817963_48},
volume = {4144},
year = {2006},
}
@unpublished{573,
abstract = {Mitchison and Jozsa recently suggested that the "chained-Zeno" counterfactual computation protocol recently proposed by Hosten et al. is counterfactual for only one output of the computer. This claim was based on the existing abstract algebraic definition of counterfactual computation, and indeed according to this definition, their argument is correct. However, a more general definition (physically adequate) for counterfactual computation is implicitly assumed by Hosten et. al. Here we explain in detail why the protocol is counterfactual and how the "history tracking" method of the existing description inadequately represents the physics underlying the protocol. Consequently, we propose a modified definition of counterfactual computation. Finally, we comment on one of the most interesting aspects of the error-correcting protocol. },
author = {Hosten, Onur and Rakher, Matthew and Barreiro, Julio and Peters, Nicholas and Kwiat, Paul},
pages = {12},
publisher = {ArXiv},
title = {{Counterfactual computation revisited}},
year = {2006},
}
@unpublished{574,
abstract = {Vaidman, in a recent article adopts the method of 'quantum weak measurements in pre- and postselected ensembles' to ascertain whether or not the chained-Zeno counterfactual computation scheme proposed by Hosten et al. is counterfactual; which has been the topic of a debate on the definition of counterfactuality. We disagree with his conclusion, which brings up some interesting aspects of quantum weak measurements and some concerns about the way they are interpreted. },
author = {Hosten, Onur and Kwiat, Paul},
pages = {2},
publisher = {ArXiv},
title = {{Weak measurements and counterfactual computation}},
year = {2006},
}
@inproceedings{577,
abstract = {Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) are high-efficiency single-photon detectors which have multi-photon counting capability. While both the VLPCs and the SSPMs have inferred internal quantum efficiencies above 93%, the actual measured values for both the detectors were in fact limited to less than 88%, attributed to in-coupling losses. We are currently improving this overall detection efficiency via a) custom anti-reflection coating the detectors and the in-coupling fibers, b) implementing a novel cryogenic design to reduce transmission losses and, c) using low-noise electronics to obtain a better signal-to-noise ratio.},
author = {Rangarajan, Radhika and Altepeter, Joseph B and Jeffrey, Evan R and Stoutimore, Micah J and Peters, Nicholas A and Onur Hosten and Kwiat, Paul G},
publisher = {SPIE},
title = {{High-efficiency single-photon detectors}},
doi = {10.1117/12.686117},
volume = {6372},
year = {2006},
}
@inproceedings{578,
abstract = {A source of single photons allows secure quantum key distribution, in addition, to being a critical resource for linear optics quantum computing. We describe our progress on deterministically creating single photons from spontaneous parametric downconversion, an extension of the Pittman, Jacobs and Franson scheme [Phys. Rev A, v66, 042303 (2002)]. Their idea was to conditionally prepare single photons by measuring one member of a spontaneously emitted photon pair and storing the remaining conditionally prepared photon until a predetermined time, when it would be "deterministically" released from storage. Our approach attempts to improve upon this by recycling the pump pulse in order to decrease the possibility of multiple-pair generation, while maintaining a high probability of producing a single pair. Many of the challenges we discuss are central to other quantum information technologies, including the need for low-loss optical storage, switching and detection, and fast feed-forward control.},
author = {Peters, Nicholas A and Arnold, Keith J and VanDevender, Aaron P and Jeffrey, Evan R and Rangarajan, Radhika and Onur Hosten and Barreiro, Julio T and Altepeter, Joseph B and Kwiat, Paul G},
publisher = {SPIE},
title = {{Towards a quasi-deterministic single-photon source}},
doi = {10.1117/12.684702},
volume = {6305},
year = {2006},
}
@article{579,
abstract = {The logic underlying the coherent nature of quantum information processing often deviates from intuitive reasoning, leading to surprising effects. Counterfactual computation constitutes a striking example: the potential outcome of a quantum computation can be inferred, even if the computer is not run 1. Relying on similar arguments to interaction-free measurements 2 (or quantum interrogation3), counterfactual computation is accomplished by putting the computer in a superposition of 'running' and 'not running' states, and then interfering the two histories. Conditional on the as-yet-unknown outcome of the computation, it is sometimes possible to counterfactually infer information about the solution. Here we demonstrate counterfactual computation, implementing Grover's search algorithm with an all-optical approach4. It was believed that the overall probability of such counterfactual inference is intrinsically limited1,5, so that it could not perform better on average than random guesses. However, using a novel 'chained' version of the quantum Zeno effect6, we show how to boost the counterfactual inference probability to unity, thereby beating the random guessing limit. Our methods are general and apply to any physical system, as illustrated by a discussion of trapped-ion systems. Finally, we briefly show that, in certain circumstances, counterfactual computation can eliminate errors induced by decoherence. },
author = {Onur Hosten and Rakher, Matthew T and Barreiro, Julio T and Peters, Nicholas A and Kwiat, Paul G},
journal = {Nature},
number = {7079},
pages = {949 -- 952},
publisher = {Nature Publishing Group},
title = {{Counterfactual quantum computation through quantum interrogation}},
doi = {10.1038/nature04523},
volume = {439},
year = {2006},
}
@inproceedings{583,
abstract = {Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) facilitate efficient single-photon detection. We are attempting to improve their efficiency, previously limited to < 88% by coupling losses, via anti-reflection coatings, better electronics and cryogenics.},
author = {Rangarajan, Radhika and Peters, Nicholas A and Onur Hosten and Altepeter, Joseph B and Jeffrey, Evan R and Kwiat, Paul G},
publisher = {IEEE},
title = {{Improved single-photon detection}},
doi = {10.1109/CLEO.2006.4628641},
year = {2006},
}
@inproceedings{7326,
abstract = {Often the properties of a single cell are considered as representative for a complete polymer electrolyte fuel cell stack or even a fuel cell system. In some cases this comes close, however, in many real cases differences on several scales become important. Cell interaction phenomena in fuel cell stacks that arise from inequalities between adjacent cells are investigated in detail experimentally. For that, a specialized 2-cell stack with advanced localized diagnostics was developed. The results show that inequalities propagate by electrical coupling, inhomogeneous cell polarization and inducing in-plane current in the common bipolar plate. The effects of the different loss-mechanisms are analyzed and quantified. },
author = {Büchi, Felix N. and Freunberger, Stefan Alexander and Santis, Marco},
booktitle = {ECS Transactions},
location = {Cancun, Mexico},
number = {1},
pages = {963--968},
publisher = {ECS},
title = {{What is learned beyond the scale of single cells?}},
doi = {10.1149/1.2356215},
volume = {3},
year = {2006},
}
@article{7327,
abstract = {Propagation of performance changes to adjacent cells in polymer electrolyte fuel cell stacks is studied by means of voltage monitoring and local current density measurements in peripheral cells of the stack. A technical fuel cell stack has been modified by implementing two independent reactant and coolant supplies in order to deliberately change the performance of one cell (anomalous cell) and study the coupling phenomena to adjacent cells (coupling cells), while keeping the working conditions of the later cell-group unaltered.
Two anomalies are studied: (i) air starvation and (ii) thermal anomaly, in a single anomalous cell in the stack and their coupling to adjacent cells. The results have shown that anomalies inducing considerable changes in the local current density of the anomalous cell (such as air starvation) propagate to adjacent cells affecting their performance. The propagation of local current density changes takes place via the common bipolar plate due to its finite thickness and in-plane conductivity. Consequently, anomalies which do not strongly influence the local current density distribution (such as a thermal anomaly under the studied working conditions) do not propagate to adjacent cells.},
author = {Santis, Marco and Freunberger, Stefan Alexander and Papra, Matthias and Wokaun, Alexander and Büchi, Felix N.},
issn = {0378-7753},
journal = {Journal of Power Sources},
number = {2},
pages = {1076--1083},
publisher = {Elsevier},
title = {{Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks}},
doi = {10.1016/j.jpowsour.2006.06.007},
volume = {161},
year = {2006},
}
@article{7328,
abstract = {An experimental technique for measuring the current density distribution with a resolution smaller than the channel/rib scale of the flow field in polymer electrolyte fuel cells (PEFCs) is presented. The electron conductors in a plane perpendicular to the channel direction are considered as two-dimensional resistors. Hence, the current density is obtained from the solution of Laplace's equation with the potentials at current collector and reaction layer as boundary conditions. Using ohmic drop for calculating the local current, detailed knowledge of all resistances involved is of prime importance. In particular, the contact resistance between the gas diffusion layer (GDL) and flow field rib, as well as GDL bulk conductivity, are strongly dependent on clamping pressure. They represent a substantial amount of the total ohmic drop and therefore require careful consideration. The detailed experimental setup as well as the concise procedure for quantitative data evaluation is described. Finally, the method is applied successfully to a cell operated on pure oxygen and air up to high current densities. The results show that electrical and ionic resistances seem to govern the current distribution at low current regimes, whereas mass transport limitations locally hamper the current production at high loads.},
author = {Freunberger, Stefan Alexander and Reum, Mathias and Evertz, Jörg and Wokaun, Alexander and Büchi, Felix N.},
issn = {0013-4651},
journal = {Journal of The Electrochemical Society},
number = {11},
publisher = {The Electrochemical Society},
title = {{Measuring the current distribution in PEFCs with sub-millimeter resolution}},
doi = {10.1149/1.2345591},
volume = {153},
year = {2006},
}
@article{7329,
abstract = {A novel measurement principle for measuring the current distribution in polymer electrolyte fuel cells (PEFCs) is introduced. It allows, in contrast to all other known techniques, for the first time for a resolution smaller than the channel/rib scale of the flow field in PEFCs. The current density is obtained by considering the electron conductors in the cell as a two-dimensional resistor with the voltage drop caused by the current. The method was applied to a cell operated on oxygen up to high current densities. The results show that the ohmic resistances govern the current distribution in the low current regime, whereas mass transport limitations hamper the current production under the land at high loads.},
author = {Freunberger, Stefan Alexander and Reum, Mathias and Wokaun, Alexander and Büchi, Felix N.},
issn = {1388-2481},
journal = {Electrochemistry Communications},
number = {9},
pages = {1435--1438},
publisher = {Elsevier},
title = {{Expanding current distribution measurement in PEFCs to sub-millimeter resolution}},
doi = {10.1016/j.elecom.2006.05.032},
volume = {8},
year = {2006},
}
@article{7330,
abstract = {Polymer electrolyte fuel cells (PE fuel cells) working with air at low stoichiometries (<2.0) and standard electrochemical components show a high degree of inhomogeneity in the current density distribution over the active area. An inhomogeneous current density distribution leads to a non-uniform utilization of the active area, which could negatively affect the time of life of the cells. Furthermore, it is also believed to lower cell performance. In this work, the homogenization of the current density, realized by means of tailored cathodes with along-the-air-channel redistributed catalyst loadings, is investigated. The air stoichiometry range for which a homogenization of the current density is achieved depends upon the gradient with which the catalyst is redistributed along the air channel. A gentle increasing catalyst loading profile homogenizes the current density at relatively higher air stoichiometries, while a steeper profile is suited better for lower air stoichiometries. The results show that a homogenization of the current density by means of redistributed catalyst loading has negative effects on cell performance. Model calculations corroborate the experimental findings on homogenization of the current density and deliver an explanation for the decrease in cell performance.},
author = {Santis, M. and Freunberger, Stefan Alexander and Reiner, A. and Büchi, F.N.},
issn = {0013-4686},
journal = {Electrochimica Acta},
number = {25},
pages = {5383--5393},
publisher = {Elsevier},
title = {{Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients}},
doi = {10.1016/j.electacta.2006.02.008},
volume = {51},
year = {2006},
}
@article{7331,
abstract = {A previously developed mathematical model for water management and current density distribution in a polymer electrolyte fuel cell (PEFCs) is employed to investigate the effects of cooling strategies on cell performance. The model describes a two-dimensional slice through the cell along the channels and through the entire cell sandwich including the coolant channels and the bipolar plate. Arbitrary flow arrangements of fuel, oxidant, and coolant stream directions can be described. Due to the serious impact of temperature on all processes in the PEFC, both the relative direction of the coolant stream to the gas streams and its mass flow turns out to significantly affect the cell performance. Besides influencing the electrochemical reaction and all kinds of mass transfer temperature, variations predominantly alter the local membrane hydration distribution and subseqently its conductivity.},
author = {Freunberger, Stefan Alexander and Wokaun, Alexander and Büchi, Felix N.},
issn = {0013-4651},
journal = {Journal of The Electrochemical Society},
number = {5},
publisher = {The Electrochemical Society},
title = {{In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance}},
doi = {10.1149/1.2185282},
volume = {153},
year = {2006},
}
@article{7332,
abstract = {A quasi-two-dimensional, along-the-channel mass and heat-transfer model for a proton exchange membrane fuel cell (PEFC) is described and validated against experimental current distribution data. The model is formulated in a dimensional manner, i.e., local transport phenomena are treated one-dimensional in through-plane direction and coupled in-plane by convective transport in the gas and coolant channels. Thus, a two-dimensional slice running through the repetitive unit of a cell from the anode channel via membrane-electrode assembly (MEA) and cathode channel to the coolant channel and from inlet to outlet is modeled. The aim of the work is to elucidate the influence of operating conditions such as feed gas humidities and stoichiometric ratios on the along-the-channel current density distribution and to identify the distinct underlying voltage loss mechanisms. Furthermore, a complicated technical flow field is modeled by a combination of co- and counterflow subdomains and compared with experimental current densities.},
author = {Freunberger, Stefan Alexander and Santis, Marco and Schneider, Ingo A. and Wokaun, Alexander and Büchi, Felix N.},
issn = {0013-4651},
journal = {Journal of The Electrochemical Society},
number = {2},
publisher = {The Electrochemical Society},
title = {{In-plane effects in large-scale PEMFCs}},
doi = {10.1149/1.2150150},
volume = {153},
year = {2006},
}
@article{1715,
abstract = {Background: Cell-to-cell communication at the synapse involves synaptic transmission as well as signaling mediated by growth factors, which provide developmental and plasticity cues. There is evidence that a retrograde, presynaptic transforming growth factor-β (TGF-β) signaling event regulates synapse development and function in Drosophila. Results: Here we show that a postsynaptic TGF-β signaling event occurs during larval development. The type I receptor Thick veins (Tkv) and the R-Smad transcription factor Mothers-against-dpp (Mad) are localized postsynaptically in the muscle. Furthermore, Mad phosphorylation occurs in regions facing the presynaptic active zones of neurotransmitter release within the postsynaptic subsynaptic reticulum (SSR). In order to monitor in real time the levels of TGF-β signaling in the synapse during synaptic transmission, we have established a FRAP assay to measure Mad nuclear import/export in the muscle. We show that Mad nuclear trafficking depends on stimulation of the muscle. Conclusions: Our data suggest a mechanism linking synaptic transmission and postsynaptic TGF-β signaling that may coordinate nerve-muscle development and function.},
author = {Dudu, Veronika and Bittig, Thomas and Entchev, Eugeni and Kicheva, Anna and Julicher, Frank and González Gaitán, Marcos},
journal = {Current Biology},
number = {7},
pages = {625 -- 635},
publisher = {Cell Press},
title = {{Postsynaptic mad signaling at the Drosophila neuromuscular junction}},
doi = {10.1016/j.cub.2006.02.061},
volume = {16},
year = {2006},
}
@article{1745,
abstract = {SiGe islands grown by deposition of 10 monolayers of Ge on Si(0 0 1) at 740 °C were investigated by using a combination of selective wet chemical etching and atomic force microscopy. The used etchant, a solution consisting of ammonium hydroxide and hydrogen peroxide, shows a high selectivity of Ge over SixGe1-x and is characterized by relatively slow etching rates for Si-rich alloys. By performing successive etching experiments on the same sample area, we are able to gain a deeper insight into the lateral displacement the islands undergo during post growth annealing.},
author = {Georgios Katsaros and Rastelli, Armando and Stoffel, Mathieu and Isella, Giovanni and Von Känel, Hans and Bittner, Alexander M and Tersoff, Jerry and Denker, Ulrich and Schmidt, Oliver G and Costantini, Giovanni and Kern, Klaus},
journal = {Surface Science},
number = {12},
pages = {2608 -- 2613},
publisher = {Elsevier},
title = {{Investigating the lateral motion of SiGe islands by selective chemical etching}},
doi = {10.1016/j.susc.2006.04.027},
volume = {600},
year = {2006},
}
@article{1746,
abstract = {A microscopic picture for the GaAs overgrowth of self-organized InAs/GaAs(001) quantum dots is developed. Scanning tunneling microscopy measurements reveal two capping regimes: the first being characterized by a dot shrinking and a backward pyramid-to-dome shape transition. This regime is governed by fast dynamics resulting in island morphologies close to thermodynamic equilibrium. The second regime is marked by a true overgrowth and is controlled by kinetically limited surface diffusion processes. A simple model is developed to describe the observed structural changes which are rationalized in terms of energetic minimization driven by lattice mismatch and alloying.},
author = {Costantini, Giovanni and Rastelli, Armando and Manzano, Carlos and Acosta-Diaz, P and Songmuang, Rudeeson and Georgios Katsaros and Schmidt, Oliver G and Kern, Klaus},
journal = {Physical Review Letters},
number = {22},
publisher = {American Physical Society},
title = {{Interplay between thermodynamics and kinetics in the capping of InAs/GaAs (001) quantum dots}},
doi = {10.1103/PhysRevLett.96.226106},
volume = {96},
year = {2006},
}
@article{1747,
abstract = {We report on recent advances in the understanding of surface processes occurring during growth and post-growth annealing of strained islands which may find application as self-assembled quantum dots. We investigate the model system SiGe/Si(0 0 1) by a new approach based on "reading the footprints" which islands leave on the substrate during their growth and evolution. Such footprints consist of trenches carved in the Si substrate. We distinguish between surface footprints and footprints buried below the islands. The former allow us to discriminate islands which are in the process of growing from those which are shrinking. Islands with steep morphologies grow at the expense of smaller and shallower islands, consistent with the kinetics of anomalous coarsening. While shrinking, islands change their shape according to thermodynamic predictions. Buried footprints are investigated by removing the SiGe epilayer by means of selective wet chemical etching. Their reading shows that: (i) during post-growth annealing islands move laterally because of surface-mediated Si-Ge intermixing; (ii) a tree-ring structure of trenches is created by dislocated islands during their "cyclic" growth. This allows us to distinguish coherent from dislocated islands and to establish whether the latter are the result of island coalescence.},
author = {Rastelli, Armando and Stoffel, Mathieu and Georgios Katsaros and Tersoff, Jerry and Denker, Ulrich and Merdzhanova, Tsvetelina and Kar, Gouranga S and Costantini, Giovanni and Kern, Klaus and Von Känel, Hans and Schmidt, Oliver G},
journal = {Microelectronics Journal},
number = {12},
pages = {1471 -- 1476},
publisher = {Elsevier},
title = {{Reading the footprints of strained islands}},
doi = {10.1016/j.mejo.2006.05.029},
volume = {37},
year = {2006},
}
@article{1748,
abstract = {The authors apply selective wet chemical etching and atomic force microscopy to reveal the three-dimensional shape of SiGeSi (001) islands after capping with Si. Although the "self-assembled quantum dots" remain practically unaffected by capping in the temperature range of 300-450 °C, significant morphological changes take place on the Si surface. At 450 °C, the morphology of the capping layer (Si matrix) evolves toward an intriguing semifacetted structure, which we call a "ziggurat," giving the misleading impression of a stepped SiGe island shape.},
author = {Georgios Katsaros and Rastelli, Armando and Stoffel, Mathieu and Costantini, Giovanni and Schmidt, Oliver G and Kern, Klaus and Tersoff, Jerry and Müller, Elisabeth and Von Känel, Hans},
journal = {Applied Physics Letters},
number = {25},
publisher = {American Institute of Physics},
title = {{Evolution of buried semiconductor nanostructures and origin of stepped surface mounds during capping}},
doi = {10.1063/1.2405876},
volume = {89},
year = {2006},
}
@article{1796,
abstract = {Drugs that block the entry of human immunodeficiency virus type 1 (HIV-1) into host cells abrogate the establishment of a productive infection and should ideally diminish the chances of HIV-1 developing resistance. This review will give an overview of the mechanism by which the envelope glycoprotein mediates HIV-1 entry and will summarize current drug developments.},
author = {Sandra Siegert and Schnierle, Peter and Schnierle, Barbara S},
journal = {Mini-Reviews in Medicinal Chemistry},
number = {5},
pages = {557 -- 562},
publisher = {Bentham Science Publishers},
title = {{Novel anti-viral therapy: Drugs that block HIV entry at different target sites}},
doi = {10.2174/138955706776876267},
volume = {6},
year = {2006},
}
@article{1961,
abstract = {Respiratory complex I plays a central role in cellular energy production in bacteria and mitochondria. Its dysfunction is implicated in many human neurodegenerative diseases, as well as in aging. The crystal structure of the hydrophilic domain (peripheral arm) of complex I from Thermus thermophilus has been solved at 3.3 angstrom resolution. This subcomplex consists of eight subunits and contains all the redox centers of the enzyme, including nine iron-sulfur clusters. The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway, and of the distal cluster Nia, a possible antioxidant. The structure reveals new aspects of the mechanism and evolution of the enzyme. The terminal cluster N2 is coordinated, uniquely, by two consecutive cysteines. The novel subunit Nqo15 has a similar fold to the mitochondrial iron chaperone frataxin, and it may be involved in iron-sulfur cluster regeneration in the complex.
},
author = {Leonid Sazanov and Hinchliffe, Philip },
journal = {Science},
number = {5766},
pages = {1430 -- 1436},
publisher = {American Association for the Advancement of Science},
title = {{Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus}},
doi = {10.1126/science.1123809},
volume = {311},
year = {2006},
}
@article{1966,
abstract = {The hydrophilic domain (peripheral arm) of the proton-translocating NADH:quinone oxidoreductase (complex I) from the thermophilic organism Thermus thermophilus HB8 has been purified and characterized. The subcomplex is stable in sodium dodecyl sulfate up to 80 °C. Of nine iron-sulfur clusters, four to five (one or two binuclear and three tetranuclear) could be detected by EPR in the NADH-reduced enzyme. The preparation consists of eight different polypeptides. Seven of them have been positively identified by peptide mass mapping and N-terminal sequencing as known hydrophilic subunits of T. thermophilus complex I. The eighth polypeptide copurified with the subcomplex at all stages, is strongly associated with the other subunits, and is present in crystals of the subcomplex, used for X-ray data collection. Therefore, it has been identified as a novel complex I subunit and named Nqo15. It is encoded in a locus separate from the nqo operon, containing the 14 other known complex I genes. ORFs encoding Nqo15 homologues are present in the genomes of the closest relatives of T. thermophilus. Our data show that, contrary to previous assumptions, bacterial complex I can contain proteins in addition to a "core" complement of 14 subunits.},
author = {Hinchliffe, Philip and Carroll, Joe D and Leonid Sazanov},
journal = {Biochemistry},
number = {14},
pages = {4413 -- 4420},
publisher = {ACS},
title = {{Identification of a novel subunit of respiratory complex I from Thermus thermophilus}},
doi = {10.1021/bi0600998},
volume = {45},
year = {2006},
}
@article{6151,
author = {Salecker, Iris and Häusser, Michael and de Bono, Mario},
issn = {1469-221X},
journal = {EMBO reports},
number = {6},
pages = {585--589},
publisher = {Wiley},
title = {{On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits}},
doi = {10.1038/sj.embor.7400713},
volume = {7},
year = {2006},
}
@article{6152,
author = {Rogers, Candida and Persson, Annelie and Cheung, Benny and de Bono, Mario},
issn = {0960-9822},
journal = {Current Biology},
number = {7},
pages = {649--659},
publisher = {Elsevier},
title = {{Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans}},
doi = {10.1016/j.cub.2006.03.023},
volume = {16},
year = {2006},
}
@article{868,
abstract = {Background: The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in animal tissues has been reported. In order to clarify the status of the MS and ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic study. Results: Using sequence similarity searches, we identified MS genes in arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in the numerous sequenced genomes of placental mammals. The regions of the placental mammals' genomes expected to code for malate synthase, as determined by comparison of the gene orders in vertebrate genomes, show clear similarity to the opossum MS sequence but contain stop codons, indicating that the MS gene became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable in animals other than the nematodes that possess a bifunctional, fused ICL-MS gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal gene transfer events that probably went in both directions between several bacterial and eukaryotic lineages. The strongest evidence was obtained for the acquisition of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the corresponding operonic organization by the common ancestor of the nematodes. Conclusion: The distribution of the MS and ICL genes in animals suggests that either they encode alternative enzymes of the glyoxylate cycle that are not orthologous to the known MS and ICL or the animal MS acquired a new function that remains to be characterized. Regardless of the ultimate solution to this conundrum, the genes for the glyoxylate cycle enzymes present a remarkable variety of evolutionary events including unusual horizontal gene transfer from bacteria to animals.},
author = {Fyodor Kondrashov and Koonin, Eugene V and Morgunov, Igor G and Finogenova, Tatiana V and Kondrashova, Marie N},
journal = {Biology Direct},
publisher = {BioMed Central},
title = {{Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation}},
doi = {10.1186/1745-6150-1-31},
volume = {1},
year = {2006},
}
@article{869,
abstract = {The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, and the rate of their evolution is used as a proxy for mutation rate. We subdivide all sites into four classes in terms of the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold synonymous sites and intron sites residing outside transposable elements. The distribution of the rate of evolution across all synonymous sites is trimodal. Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed by G, is ∼10% below that at such intron sites. In contrast, rate of evolution at postCpreG synonymous sites is ∼30% above that at such intron sites. Finally, synonymous and intron postC and preG sites evolve at similar rates. The relationship between the levels of polymorphism at the corresponding synonymous and intron sites is very similar to that between their rates of evolution. Within every class, synonymous sites are occupied by G or C much more often than intron sites, whose nucleotide composition is consistent with neutral mutation-drift equilibrium. These patterns suggest that synonymous sites are under weak selection in favor of G and C, with the average coefficient s∼0.25/Ne∼10-5, where Ne is the effective population size. Such selection decelerates evolution and reduces variability at sites with symmetric mutation, but has the opposite effects at sites where the favored nucleotides are more mutable. The amino-acid composition of proteins dictates that many synonymous sites are CpGprone, which causes them, on average, to evolve faster and to be more polymorphic than intron sites. An average genotype carries ∼107 suboptimal nucleotides at synonymous sites, implying synergistic epistasis in selection against them.},
author = {Fyodor Kondrashov and Ogurtsov, Aleksey Yu and Kondrashov, Alexey S},
journal = {Journal of Theoretical Biology},
number = {4},
pages = {616 -- 626},
publisher = {Elsevier},
title = {{Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites}},
doi = {10.1016/j.jtbi.2005.10.020},
volume = {240},
year = {2006},
}
@article{873,
abstract = {New genes commonly appear through complete or partial duplications of pre-existing genes. Duplications of long DNA segments are constantly produced by rare mutations, may become fixed in a population by selection or random drift, and are subject to divergent evolution of the paralogous sequences after fixation, although gene conversion can impede this process. New data shed some light on each of these processes. Mutations which involve duplications can occur through at least two different mechanisms, backward strand slippage during DNA replication and unequal crossing-over. The background rate of duplication of a complete gene in humans is 10-9-10-10 per generation, although many genes located within hot-spots of large-scale mutation are duplicated much more often. Many gene duplications affect fitness strongly, and are responsible, through gene dosage effects, for a number of genetic diseases. However, high levels of intrapopulation polymorphism caused by presence or absence of long, gene-containing DNA segments imply that some duplications are not under strong selection. The polymorphism to fixation ratios appear to be approximately the same for gene duplications and for presumably selectively neutral nucleotide substitutions, which, according to the McDonald-Kreitman test, is consistent with selective neutrality of duplications. However, this pattern can also be due to negative selection against most of segregating duplications and positive selection for at least some duplications which become fixed. Patterns in post-fixation evolution of duplicated genes do not easily reveal the causes of fixations. Many gene duplications which became fixed recently in a variety of organisms were positively selected because the increased expression of the corresponding genes was beneficial. The effects of gene dosage provide a unified framework for studying all phases of the life history of a gene duplication. Application of well-known methods of evolutionary genetics to accumulating data on new, polymorphic, and fixed duplication will enhance our understanding of the role of natural selection in the evolution by gene duplication.},
author = {Fyodor Kondrashov and Kondrashov, Alexey S},
journal = {Journal of Theoretical Biology},
number = {2},
pages = {141 -- 151},
publisher = {Elsevier},
title = {{Role of selection in fixation of gene duplications}},
doi = {10.1016/j.jtbi.2005.08.033},
volume = {239},
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{1461,
abstract = {This note proves combinatorially that the intersection pairing on the middle-dimensional compactly supported cohomology of a toric hyperkähler variety is always definite, providing a large number of non-trivial L 2 harmonic forms for toric hyperkähler metrics on these varieties. This is motivated by a result of Hitchin about the definiteness of the pairing of L 2 harmonic forms on complete hyperkähler manifolds of linear growth.},
author = {Tamas Hausel and Swartz, Edward},
journal = {Proceedings of the American Mathematical Society},
number = {8},
pages = {2403 -- 2409},
publisher = {American Mathematical Society},
title = {{Intersection forms of toric hyperkähler varieties}},
doi = {10.1090/S0002-9939-06-08248-7},
volume = {134},
year = {2006},
}
@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{1033,
abstract = {Systems of three interacting particles are notorious for their complex physical behaviour. A landmark theoretical result in few-body quantum physics is Efimov\'s prediction1,2 of a universal set of bound trimer states appearing for three identical bosons with a resonant two-body interaction. Counterintuitively, these states even exist in the absence of a corresponding two-body bound state. Since the formulation of Efimov\'s problem in the context of nuclear physics 35 years ago, it has attracted great interest in many areas of physics3-8. However, the observation of Efimov quantum states has remained an elusive goal3,5. Here we report the observation of an Efimov resonance in an ultracold gas of caesium atoms. The resonance occurs in the range of large negative two-body scattering lengths, arising from the coupling of three free atoms to an Efimov trimer. Experimentally, we observe its signature as a giant three-body recombination loss9,10 when the strength of the two-body interaction is varied. We also detect a minimum 9,11,12 in the recombination loss for positive scattering lengths, indicating destructive interference of decay pathways. Our results confirm central theoretical predictions of Efimov physics and represent a starting point with which to explore the universal properties of resonantly interacting few-body systems7. While Feshbach resonances13,14 have provided the key to control quantum-mechanical interactions on the two-body level, Efimov resonances connect ultracold matter15 to the world of few-body quantum phenomena.},
author = {Kraemer, Tobias and Mark, Michael and Waldburger, Philipp and Danzl, Johann G and Chin, Cheng and Engeser, Bastian and Lange, Adam and Pilch, Karl and Jaakkola, Antti and Nägerl, Hanns and Grimm, Rudolf},
journal = {Nature},
number = {7082},
pages = {315 -- 318},
publisher = {Nature Publishing Group},
title = {{Evidence for Efimov quantum states in an ultracold gas of caesium atoms}},
doi = {10.1038/nature04626},
volume = {440},
year = {2006},
}
@inproceedings{1034,
abstract = {Three interacting particles form a system which is well known for its complex physical behavior. A landmark theoretical result in few-body quantum physics is Efimov\'s prediction of a universal set of weakly bound trimer states appearing for three identical bosons with a resonant two-body interaction [1, 2]. Surprisingly, these states even exist in the absence of a corresponding two-body bound state and their precise nature is largely independent of the particular type of the two-body interaction potential. Efimov\'s scenario has attracted great interest in many areas of physics; an experimental test however has not been achieved. We report the observation of an Efimov resonance in an ultracold thermal gas of cesium atoms [3]. The resonance occurs in the range of large negative two-body scattering lengths and arises from the coupling of three free atoms to an Efimov trimer. We observe its signature as a giant three-body recombination loss when the strength of the two-body interaction is varied near a Feshbach resonance. This resonance develops into a continuum resonance at non-zero collision energies, and we observe a shift of the resonance position as a function of temperature. We also report on a minimum in the recombination loss for positive scattering lengths, indicating destructive interference of decay pathways. Our results confirm central theoretical predictions of Efimov physics and represent a starting point from which to explore the universal properties of resonantly interacting few-body systems.},
author = {Nägerl, Hanns and Kraemer, Tobias and Mark, Michael and Waldburger, Philipp and Danzl, Johann G and Engeser, Bastian and Lange, Adam and Pilch, Karl and Jaakkola, Antti and Chin, Cheng and Grimm, Rudolf},
pages = {269 -- 277},
publisher = {AIP},
title = {{Experimental evidence for Efimov quantum states}},
doi = {10.1063/1.2400657},
volume = {869},
year = {2006},
}
@article{2066,
abstract = {Although the X chromosome is usually similar to the autosomes in size and cytogenetic appearance, theoretical models predict that its hemizygosity in males may cause unusual patterns of evolution. The sequencing of several genomes has indeed revealed differences between the X chromosome and the autosomes in the rates of gene divergence, patterns of gene expression and rates of gene movement between chromosomes. A better understanding of these patterns should provide valuable information on the evolution of genes located on the X chromosome. It could also suggest solutions to more general problems in molecular evolution, such as detecting selection and estimating mutational effects on fitness},
author = {Beatriz Vicoso and Charlesworth, Brian},
journal = {Nature Reviews Genetics},
number = {8},
pages = {645 -- 653},
publisher = {Nature Publishing Group},
title = {{Evolution on the X chromosome: Unusual patterns and processes}},
doi = {10.1038/nrg1914},
volume = {7},
year = {2006},
}
@inproceedings{2077,
abstract = {We present an adaptive animation method for electrical discharges. Electrical discharges can be simulated using the dielectric breakdown model. Regular discretization of the governing Laplace equation leads to huge equation systems, and the computational cost of solving the equations quickly becomes prohibitive at high resolutions, especially for simulations in 3D. In contrast, our method discretizes the Laplace equation on an adaptive octree, reducing the size of the problem significantly, and making simulations of high resolution 3D datasets and even 3D animations feasible. In order to enhance realism for lightning animations, we propose a particle simulation that animates the residual positive charge. Thus, interaction of electrical discharges with their surroundings
can be simulated.},
author = {Bernd Bickel and Wicke, Martin and Gross, Markus},
publisher = {IOS Press},
title = {{Adaptive simulation of electrical discharges}},
year = {2006},
}
@inproceedings{2088,
abstract = {We have measured 3D face geometry, skin reflectance, and subsurface scattering using custom-built devices for 149 subjects of varying age, gender, and race. We developed a novel skin reflectance model whose parameters can be estimated from measurements. The model decomposes the large amount of measured skin data into a spatially-varying analytic BRDF, a diffuse albedo map, and diffuse subsurface scattering. Our model is intuitive, physically plausible, and - since we do not use the original measured data - easy to edit as well. High-quality renderings come close to reproducing real photographs. The analysis of the model parameters for our sample population reveals variations according to subject age, gender, skin type, and external factors (e.g., sweat, cold, or makeup). Using our statistics, a user can edit the overall appearance of a face (e.g., changing skin type and age) or change small-scale features using texture synthesis (e.g., adding moles and freckles). We are making the collected statistics publicly available to the research community for applications in face synthesis and analysis. },
author = {Weyrich, Tim and Matusik, Wojciech and Pfister, Hanspeter and Bernd Bickel and Donner, Craig and Tu, Chien and McAndless, Janet M and Lee, Jinho and Ngan, Addy and Jensen, Henrik W and Groß, Markus S},
pages = {1013 -- 1024},
publisher = {ACM},
title = {{Analysis of human faces using a measurement-based skin reflectance model}},
doi = {10.1145/1179352.1141987},
year = {2006},
}
@article{2089,
abstract = {We have measured 3D face geometry, skin reflectance, and subsurface scattering using custom-built devices for 149 subjects of varying age, gender, and race. We developed a novel skin reflectance model whose parameters can be estimated from measurements. The model decomposes the large amount of measured skin data into a spatially-varying analytic BRDF, a diffuse albedo map, and diffuse subsurface scattering. Our model is intuitive, physically plausible, and - since we do not use the original measured data - easy to edit as well. High-quality renderings come close to reproducing real photographs. The analysis of the model parameters for our sample population reveals variations according to subject age, gender, skin type, and external factors (e.g., sweat, cold, or makeup). Using our statistics, a user can edit the overall appearance of a face (e.g., changing skin type and age) or change small-scale features using texture synthesis (e.g., adding moles and freckles). We are making the collected statistics publicly available to the research community for applications in face synthesis and analysis.},
author = {Weyrich, Tim and Matusik, Wojciech and Pfister, Hanspeter and Bernd Bickel and Donner, Craig and Tu, Chien and McAndless, Janet M and Lee, Jinho and Ngan, Addy and Jensen, Henrik W and Groß, Markus S},
journal = {ACM Transactions on Graphics},
number = {3},
pages = {1013 -- 1024},
publisher = {ACM},
title = {{Analysis of human faces using a measurement-based skin reflectance model}},
doi = {10.1145/1141911.1141987},
volume = {25},
year = {2006},
}
@inproceedings{2090,
author = {Bernd Bickel and Weyrich, Tim and Matusik, Wojciech and Pfister, Hanspeter and Donner, Craig and Tu, Chien and McAndless, Janet M and Lee, Jinho and Ngan, Addy and Jensen, Henrik W and Groß, Markus S},
publisher = {ACM},
title = {{Processing and editing of faces using a measurement-based skin reflectance model}},
doi = {10.1145/1179849.1180059},
year = {2006},
}
@article{213,
abstract = {For any integers d,n ≥2, let X ⊂ Pn be a non‐singular hypersurface of degree d that is defined over the rational numbers. The main result in this paper is a proof that the number of rational points on X which have height at most B is O(Bn − 1 + ɛ), for any ɛ > 0. The implied constant in this estimate depends at most upon d, ɛ and n. 2000 Mathematics Subject Classification 11D45 (primary), 11G35, 14G05 (secondary).},
author = {Timothy Browning and Heath-Brown, Roger and Starr, Jason M},
journal = {Proceedings of the London Mathematical Society},
number = {2},
pages = {273 -- 303},
publisher = {John Wiley and Sons Ltd},
title = {{The density of rational points on non-singular hypersurfaces, II}},
doi = {https://doi.org/10.1112/S0024611506015784},
volume = {93},
year = {2006},
}
@article{2134,
abstract = {Predissociation of the N+2 C 2Σ+u(v') vibrational levels with v' ≥ 3 was observed via dispersed C 2Σ+u → X 2Σ+g fluorescence in the spectral range of 165–208 nm after resonant 1s−1π*(vr) excitation of N2 and its subsequent autoionization into the N+2 C state. This range is dominated by lines in atomic nitrogen, by overlapped C 2Σ+u(v') → X 2Σ+g(v'') vibrational band sequences with Δv = const and broad unresolved band systems (D, (2))2Πg(v') → A2Πu(v'') in the N+2 molecular ion. With very high fluorescence resolution of about 0.1 nm FWHM individual C 2Σ+u(v') → X 2Σ+g(v'') vibrational bands have been resolved. Calculation of the observed fluorescence spectra by taking into account predissociation and molecular rotation describes well the shape of both individual vibrational bands C 2Σ+u(v') → X 2Σ+g(v'') and the whole band system.},
author = {Ehresmann, Arno and Werner, Lutz and Klumpp, Stefan and Demekhin, Ph V and Mikhail Lemeshko and Sukhorukov, V. L and Schartner, Karl H and Schmoranzer, Hans P},
journal = {Journal of Physics B: Atomic, Molecular and Optical Physics},
number = {6},
pages = {L119 -- L126},
publisher = {IOP Publishing Ltd.},
title = {{Predissociation of the N+2(C 2Σ+u) state observed via C 2Σ+u → X 2Σ+g fluorescence after resonant 1s−1π* excitation of N2 molecule}},
doi = {10.1088/0953-4075/39/6/L03},
volume = {39},
year = {2006},
}
@article{2142,
abstract = {Fluorescence from fragments formed after the de-excitation of the N*2(1s−1π*) resonance has been measured in the spectral range of 135–190 nm. This range is dominated by lines in atomic nitrogen and lines formed by overlapping C2Σ+u(v') → X2Σ+g(v'') bands with Δv = const in the N+2 molecular ion which result from the spectator Auger decays of the N*2(1s−1π*(vr)) resonances. Ab initio calculations of the corresponding potential curves and transition probabilities showed that the observed irregular intensity dependence of the C2Σ+u(v') → X2Σ+g(v'')(Δv = const) fluorescence lines on the vibrational quantum number vr is due to transitions between vibrational levels during the reaction N2(v0 = 0)→ N*2(1s−1π*(vr)) Longrightarrow C2Σ+u(v') → X2Σ+g(v'').},
author = {Ehresmann, Arno and Werner, Lutz and Klumpp, Stefan and Lucht, S and Schmoranzer, Hans P and Mickat, Sascha and Schill, Rüdiger H and Schartner, Karl H and Demekhin, Philipp and Mikhail Lemeshko and Sukhorukov, Victor L},
journal = {Journal of Physics B: Atomic, Molecular and Optical Physics},
number = {2},
pages = {283 -- 304},
publisher = {IOP Publishing Ltd.},
title = {{Studying the N+2(C2Σ+u → X2Σ+g) fluorescence excited via the 1s−1π* resonance}},
doi = {10.1088/0953-4075/39/2/006},
volume = {39},
year = {2006},
}
@article{2144,
abstract = {Temperature dependent preedge and extended x-ray absorption fine structure measurements at the Zr K edge for the perovskite-type zirconates Pb Zr0.515 Ti0.485 O3 (PZT), PbZr O3 (PZ), and BaZr O3 are performed. To carry out a more accurate study of the weak reconstruction of the local atomic structure we employed a combination of two techniques: (i) analysis of the preedge fine structure, and (ii) analysis of the Fourier transform of the difference between χ (k) functions obtained at different temperatures. A detailed investigation of local atomic structure in the cubic phase for all the crystals is also performed. It is shown that neither the displacive nor the order-disorder model can describe correctly the changes of local atomic structure during phase transitions in PZ and PZT. A spherical model describing the local atomic structure of perovskite-type crystals suffering structural phase transitions is proposed.},
author = {Vedrinskiǐ, Rostislav V and Nazarenko, Elena S and Mikhail Lemeshko and Nassif, Vivian M and Proux, Olivier and Novakovich, Alexander A and Joly, Yves},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {13},
publisher = {American Physical Society},
title = {{Temperature dependent XAFS studies of local atomic structure of the perovskite-type zirconates}},
doi = {10.1103/PhysRevB.73.134109},
volume = {73},
year = {2006},
}
@article{215,
abstract = {For any n≥3, let F ∈ Z[X0,...,Xn ] be a form of degree d *≥5 that defines a non-singular hypersurface X ⊂ Pn . The main result in this paper is a proof of the fact that the number N (F ; B) of Q-rational points on X which have height at most B satisfiesN (F ; B) = Od,ε,n (Bn −1+ε ), for any ε > 0. The implied constant in this estimate depends at most upon d, ε and n. New estimates are also obtained for the number of representations of a positive integer as the sum of three dth powers, and for the paucity of integer solutions to equal sums of like polynomials.*},
author = {Timothy Browning and Heath-Brown, Roger},
journal = {Bulletin of the London Mathematical Society},
number = {3},
pages = {401 -- 410},
publisher = {Wiley-Blackwell},
title = {{The density of rational points on non-singular hypersurfaces, I}},
doi = {10.1112/S0024609305018412},
volume = {38},
year = {2006},
}
@article{216,
abstract = {For any N ≥ 2, let Z ⊂ ℙN be a geometrically integral algebraic variety of degree d. This article is concerned with the number Nz(B) of ℚ-rational points on Z which have height at most B. For any ε > 0, we establish the estimate NZ(B) = O d,ε,N(Bdim Z+ε), provided that d ≥ 6. As indicated, the implied constant depends at most on d, ε, and N.},
author = {Timothy Browning and Heath-Brown, Roger and Salberger, Per},
journal = {Duke Mathematical Journal},
number = {3},
pages = {545 -- 578},
publisher = {Unknown},
title = {{Counting rational points on algebraic varieties}},
doi = {10.1215/S0012-7094-06-13236-2},
volume = {132},
year = {2006},
}
@article{218,
abstract = {This paper is concerned with the average order of certain arithmetic functions, as they range over the values taken by binary forms.},
author = {de la Bretèche, Régis and Timothy Browning},
journal = {Acta Arithmetica},
number = {3},
pages = {291 -- 304},
publisher = {Instytut Matematyczny},
title = {{Sums of arithmetic functions over values of binary forms}},
doi = {10.4064/aa125-3-6},
volume = {125},
year = {2006},
}
@inproceedings{2333,
author = {Lieb, Élliott H and Robert Seiringer and Solovej, Jan P},
pages = {239 -- 248},
publisher = {American Mathematical Society},
title = {{Ground-state energy of a dilute Fermi gas}},
doi = {10.1090/conm/412},
volume = {412},
year = {2006},
}
@inproceedings{2334,
author = {Robert Seiringer and Lieb, Élliott H and Yngvason, Jakob},
editor = {Zambrini, Jean-Claude},
publisher = {World Scientific Publishing},
title = {{One-dimensional behavior of dilute, trapped Bose gases in traps}},
doi = {10.1007/s00220-003-0993-3},
year = {2006},
}
@misc{2363,
abstract = { We prove that the Gross-Pitaevskii equation correctly describes the ground state energy and corresponding one-particle density matrix of rotating, dilute, trapped Bose gases with repulsive two-body interactions. We also show that there is 100% Bose-Einstein condensation. While a proof that the GP equation correctly describes non-rotating or slowly rotating gases was known for some time, the rapidly rotating case was unclear because the Bose (i.e., symmetric) ground state is not the lowest eigenstate of the Hamiltonian in this case. We have been able to overcome this difficulty with the aid of coherent states. Our proof also conceptually simplifies the previous proof for the slowly rotating case. In the case of axially symmetric traps, our results show that the appearance of quantized vortices causes spontaneous symmetry breaking in the ground state. },
author = {Lieb, Élliott H and Robert Seiringer},
booktitle = {Communications in Mathematical Physics},
number = {2},
pages = {505 -- 537},
publisher = {Springer},
title = {{Derivation of the Gross-Pitaevskii equation for rotating Bose gases}},
doi = {10.1007/s00220-006-1524-9},
volume = {264},
year = {2006},
}
@article{2364,
abstract = {We present an inequality that gives a lower bound on the expectation value of certain two-body interaction potentials in a general state on Fock space in terms of the corresponding expectation value for thermal equilibrium states of non-interacting systems and the difference in the free energy. This bound can be viewed as a rigorous version of first-order perturbation theory for many-body systems at positive temperature. As an application, we give a proof of the first two terms in a high density (and high temperature) expansion of the free energy of jellium with Coulomb interactions, both in the fermionic and bosonic case. For bosons, our method works above the transition temperature (for the non-interacting gas) for Bose-Einstein condensation.},
author = {Robert Seiringer},
journal = {Reviews in Mathematical Physics},
number = {3},
pages = {233 -- 253},
publisher = {World Scientific Publishing},
title = {{A correlation estimate for quantum many-body systems at positive temperature}},
doi = {10.1142/S0129055X06002632},
volume = {18},
year = {2006},
}
@article{2365,
abstract = {We consider a gas of fermions with non-zero spin at temperature T and chemical potential μ. We show that if the range of the interparticle interaction is small compared to the mean particle distance, the thermodynamic pressure differs to leading order from the corresponding expression for non-interacting particles by a term proportional to the scattering length of the interparticle interaction. This is true for any repulsive interaction, including hard cores. The result is uniform in the temperature as long as T is of the same order as the Fermi temperature, or smaller.},
author = {Robert Seiringer},
journal = {Communications in Mathematical Physics},
number = {3},
pages = {729 -- 757},
publisher = {Springer},
title = {{The thermodynamic pressure of a dilute fermi gas}},
doi = {10.1007/s00220-005-1433-3},
volume = {261},
year = {2006},
}
@article{2366,
abstract = {Inequalities are derived for power sums of the real part and the modulus of the eigenvalues of a Schrödinger operator with a complex-valued potential.},
author = {Frank, Rupert L and Laptev, Ari and Lieb, Élliott H and Robert Seiringer},
journal = {Letters in Mathematical Physics},
number = {3},
pages = {309 -- 316},
publisher = {Springer},
title = {{Lieb-Thirring inequalities for Schrödinger operators with complex-valued potentials}},
doi = {10.1007/s11005-006-0095-1},
volume = {77},
year = {2006},
}
@inbook{2368,
abstract = {The recent experimental success in creating Bose-Einstein condensates of alkali atoms, honored by the Nobel prize awards in 2001 [1,5], led to renewed interest in the mathematical description of interacting Bose gases.},
author = {Robert Seiringer},
booktitle = {Large Coulomb Systems},
editor = {Dereziński, Jan and Siedentop, Heinz},
pages = {249 -- 274},
publisher = {Springer},
title = {{Dilute, trapped Bose gases and Bose-Einstein condensation}},
doi = {10.1007/3-540-32579-4_6},
volume = {695},
year = {2006},
}
@inbook{2369,
abstract = {One of the most remarkable recent developments in the study of ultracold Bose gases is the observation of a reversible transition from a Bose Einstein condensate to a state composed of localized atoms as the strength of a periodic, optical trapping potential is varied. In [1] a model of this phenomenon has been analyzed rigorously. The gas is a hard core lattice gas and the optical lattice is modeled by a periodic potential of strength λ. For small λ and temperature Bose- Einstein condensation (BEC) is proved to occur, while at large λ BEC disappears, even in the ground state, which is a Mott-insulator state with a characteristic gap. The inter-particle interaction is essential for this effect. This contribution gives a pedagogical survey of these results.},
author = {Aizenman, Michael and Lieb, Élliott H and Robert Seiringer and Solovej, Jan P and Yngvason, Jakob},
booktitle = {Mathematical Physics of Quantum Mechanics},
editor = {Asch, Joachim and Joye, Alain},
pages = {199 -- 215},
publisher = {Springer},
title = {{Bose-Einstein condensation as a quantum phase transition in an optical lattice}},
doi = {10.1007/b11573432},
volume = {690},
year = {2006},
}