@inproceedings{3223, abstract = {“Hash then encrypt” is an approach to message authentication, where first the message is hashed down using an ε-universal hash function, and then the resulting k-bit value is encrypted, say with a block-cipher. The security of this scheme is proportional to εq2, where q is the number of MACs the adversary can request. As ε is at least 2−k, the best one can hope for is O(q2/2k) security. Unfortunately, such small ε is not achieved by simple hash functions used in practice, such as the polynomial evaluation or the Merkle-Damg ̊ard construction, where ε grows with the message length L. The main insight of this work comes from the fact that, by using ran- domized message preprocessing via a short random salt p (which must then be sent as part of the authentication tag), we can use the “hash then encrypt” paradigm with suboptimal “practical” ε-universal hash func- tions, and still improve its exact security to optimal O(q2/2k). Specif- ically, by using at most an O(logL)-bit salt p, one can always regain the optimal exact security O(q2/2k), even in situations where ε grows polynomially with L. We also give very simple preprocessing maps for popular “suboptimal” hash functions, namely polynomial evaluation and the Merkle-Damg ̊ard construction. Our results come from a general extension of the classical Carter- Wegman paradigm, which we believe is of independent interest. On a high level, it shows that public randomization allows one to use the potentially much smaller “average-case” collision probability in place of the “worst-case” collision probability ε.}, author = {Dodis, Yevgeniy and Krzysztof Pietrzak}, pages = {414 -- 433}, publisher = {Springer}, title = {{Improving the security of MACs via randomized message preprocessing}}, doi = {10.1007/978-3-540-74619-5_26}, volume = {4593}, year = {2007}, } @article{3305, abstract = {The accumulation of deleterious mutations plays a major role in evolution, and key to this are the interactions between their fitness effects, known as epistasis. Whether mutations tend to interact synergistically (with multiple mutations being more deleterious than would be expected from their individual fitness effects) or antagonistically is important for a variety of evolutionary questions, particularly the evolution of sex. Unfortunately, the experimental evidence on the prevalence and strength of epistasis is mixed and inconclusive. Here we study theoretically whether synergistic or antagonistic epistasis is likely to be favored by evolution and by how much. We find that in the presence of recombination, evolution favors less synergistic or more antagonistic epistasis whenever mutations that change the epistasis in this direction are possible. This is because evolution favors increased buffering against the effects of deleterious mutations. This suggests that we should not expect synergistic epistasis to be widespread in nature and hence that the mutational deterministic hypothesis for the advantage of sex may not apply widely.}, author = {Desai, Michael M and Daniel Weissman and Feldman, Marcus W}, journal = {Genetics}, number = {2}, pages = {1001 -- 10}, publisher = {Genetics Society of America}, title = {{Evolution can favor antagonistic epistasis}}, doi = {10.1534/genetics.107.075812}, volume = {177}, year = {2007}, } @article{11115, abstract = {The formation of the nuclear envelope (NE) around chromatin is a major membrane-remodelling event that occurs during cell division of metazoa. It is unclear whether the nuclear membrane reforms by the fusion of NE fragments or if it re-emerges from an intact tubular network of the endoplasmic reticulum (ER). Here, we show that NE formation and expansion requires a tubular ER network and occurs efficiently in the presence of the membrane fusion inhibitor GTPγS. Chromatin recruitment of membranes, which is initiated by tubule-end binding, followed by the formation, expansion and sealing of flat membrane sheets, is mediated by DNA-binding proteins residing in the ER. Thus, chromatin plays an active role in reshaping of the ER during NE formation.}, author = {Anderson, Daniel J. and HETZER, Martin W}, issn = {1476-4679}, journal = {Nature Cell Biology}, keywords = {Cell Biology}, number = {10}, pages = {1160--1166}, publisher = {Springer Nature}, title = {{Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum}}, doi = {10.1038/ncb1636}, volume = {9}, year = {2007}, } @article{11116, abstract = {The metazoan nuclear envelope (NE) breaks down and re-forms during each cell cycle. Nuclear pore complexes (NPCs), which allow nucleocytoplasmic transport during interphase, assemble into the re-forming NE at the end of mitosis. Using in vitro NE assembly, we show that the vertebrate homologue of MEL-28 (maternal effect lethal), a recently discovered NE component in Caenorhabditis elegans, functions in postmitotic NPC assembly. MEL-28 interacts with the Nup107–160 complex (Nup for nucleoporin), an important building block of the NPC, and is essential for the recruitment of the Nup107–160 complex to chromatin. We suggest that MEL-28 acts as a seeding point for NPC assembly.}, author = {Franz, Cerstin and Walczak, Rudolf and Yavuz, Sevil and Santarella, Rachel and Gentzel, Marc and Askjaer, Peter and Galy, Vincent and HETZER, Martin W and Mattaj, Iain W and Antonin, Wolfram}, issn = {1469-3178}, journal = {EMBO reports}, keywords = {Genetics, Molecular Biology, Biochemistry}, number = {2}, pages = {165--172}, publisher = {EMBO}, title = {{MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly}}, doi = {10.1038/sj.embor.7400889}, volume = {8}, year = {2007}, } @article{7780, abstract = {We used single-channel electrical recordings and Langevin molecular dynamics simulations to explore the electrophoretic translocation of various β-hairpin peptides across the staphylococcal α-hemolysin (αHL) protein pore at single-molecule resolution. The β-hairpin peptides, which varied in their folding properties, corresponded to the C terminal residues of the B1 domain of protein G. The translocation time was strongly dependent on the electric force and was correlated with the folding features of the β-hairpin peptides. Highly unfolded peptides entered the pore in an extended conformation, resulting in fast single-file translocation events. In contrast, the translocation of the folded β-hairpin peptides occurred more slowly. In this case, the β-hairpin peptides traversed the αHL pore in a misfolded or fully folded conformation. This study demonstrates that the interaction between a polypeptide and a β-barrel protein pore is dependent on the folding features of the polypeptide. }, author = {Goodrich, Carl Peter and Kirmizialtin, Serdal and Huyghues-Despointes, Beatrice M. and Zhu, Aiping and Scholtz, J. Martin and Makarov, Dmitrii E. and Movileanu, Liviu}, issn = {1520-6106}, journal = {The Journal of Physical Chemistry B}, number = {13}, pages = {3332--3335}, publisher = {American Chemical Society}, title = {{Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations}}, doi = {10.1021/jp071364h}, volume = {111}, year = {2007}, } @article{7781, abstract = {Males are predicted to compete for reproductive opportunities, with sexual selection driving the evolution of large body size and weaponry through the advantage they confer for access to females. Few studies have explored potential trade‐offs of investment in secondary sexual traits between different components of fitness or tested for sexually antagonistic selection pressures. These factors may provide explanations for observed polymorphisms in both form and quality of secondary sexual traits. We report here an analysis of selection on horn phenotype in a feral population of Soay sheep (Ovis aries) on the island of Hirta, St. Kilda, Scotland. Soay sheep display a phenotypic polymorphism for horn type with males growing either normal or reduced (scurred) horns, and females growing either normal, scurred, or no (polled) horns; further variation in size exists within horn morphs. We show that horn phenotype and the size of the trait displayed is subject to different selection pressures in males and females, generating sexually antagonistic selection. Furthermore, there was evidence of a trade‐off between breeding success and longevity in normal‐horned males, with both the normal horn type and larger horn size being associated with greater annual breeding success but reduced longevity. Therefore, selection through lifetime breeding success was not found to act upon horn phenotype in males. In females, a negative association of annual breeding success within the normal‐horned phenotype did not result in a significant difference in lifetime fitness when compared to scurred individuals, as no significant difference in longevity was found. However, increased horn size within this group was negatively associated with breeding success and longevity. Females without horns (polled) suffered reduced longevity and thus reduced lifetime breeding success relative the other horn morphs. Our results therefore suggest that trade‐offs between different components of fitness and antagonistic selection between the sexes may maintain genetic variation for secondary sexual traits within a population.}, author = {Robinson, Matthew Richard and Pilkington, Jill G. and Clutton-Brock, Tim H. and Pemberton, Josephine M. and Kruuk, Loeske E.B.}, issn = {0014-3820}, journal = {Evolution}, number = {10}, pages = {2168--2181}, publisher = {Wiley}, title = {{Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep}}, doi = {10.1111/j.0014-3820.2006.tb01854.x}, volume = {60}, year = {2007}, } @article{8027, abstract = {Gating deficits and hallucinatory sensations are prominent symptoms of schizophrenia. Comparing these abnormalities with the failure modes of network models is an interesting way to explore how they arise. We present a network model that can both propagate and gate signals. The model exhibits effects reminiscent of clinically observed pathologies when the balance between excitation and inhibition that it requires is not properly maintained.}, author = {Vogels, Tim P and Abbott, L.}, issn = {0176-3679}, journal = {Pharmacopsychiatry}, number = {S 1}, pages = {S73--S77}, publisher = {Thieme}, title = {{Gating deficits in model networks: A path to schizophrenia?}}, doi = {10.1055/s-2007-992130}, volume = {40}, year = {2007}, } @article{8483, abstract = {Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of α-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of α-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes.}, author = {Schanda, Paul and Forge, V. and Brutscher, B.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {27}, pages = {11257--11262}, publisher = {National Academy of Sciences}, title = {{Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy}}, doi = {10.1073/pnas.0702069104}, volume = {104}, year = {2007}, } @article{8484, abstract = {A series of sequential, intra-residue, and bi-directional BEST H–N–CA, H–N–CO, and H–N–CB pulse sequences is presented that extends the BEST concept introduced recently for fast multidimensional protein NMR [Schanda et al., J. Am. Chem. Soc. 128 (2006) 9042] to the complete set of experiments required for sequential resonance assignment. We demonstrate for the protein ubiquitin that 3D BEST H–N–C correlation spectra can be recorded on a 600 MHz NMR spectrometer equipped with a cryogenic probe in only a few minutes of acquisition time with sufficient sensitivity to detect all expected cross peaks.}, author = {Lescop, Ewen and Schanda, Paul and Brutscher, Bernhard}, issn = {1090-7807}, journal = {Journal of Magnetic Resonance}, number = {1}, pages = {163--169}, publisher = {Elsevier}, title = {{A set of BEST triple-resonance experiments for time-optimized protein resonance assignment}}, doi = {10.1016/j.jmr.2007.04.002}, volume = {187}, year = {2007}, } @article{8485, abstract = {High signal to noise is a necessity for the quantification of NMR spectral parameters to be translated into accurate and precise restraints on protein structure and dynamics. An important source of long-range structural information is obtained from 1H–1H residual dipolar couplings (RDCs) measured for weakly aligned molecules. For sensitivity reasons, such measurements are generally performed on highly deuterated protein samples. Here we show that high sensitivity is also obtained for protonated protein samples if the pulse schemes are optimized in terms of longitudinal relaxation efficiency and J-mismatch compensated coherence transfer. The new sensitivity-optimized quantitative J-correlation experiment yields important signal gains reaching factors of 1.5 to 8 for individual correlation peaks when compared to previously proposed pulse schemes.}, author = {Schanda, Paul and Lescop, Ewen and Falge, Mirjam and Sounier, Rémy and Boisbouvier, Jérôme and Brutscher, Bernhard}, issn = {0925-2738}, journal = {Journal of Biomolecular NMR}, keywords = {Spectroscopy, Biochemistry}, pages = {47--55}, publisher = {Springer Nature}, title = {{Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons}}, doi = {10.1007/s10858-006-9138-2}, volume = {38}, year = {2007}, } @article{8486, abstract = {A technique is described that allows reducing acquisition times of multidimensional NMR experiments by extensive spectral folding. The method is simple and has many interesting applications for NMR studies of molecular structure, dynamics, and kinetics.}, author = {Lescop, Ewen and Schanda, Paul and Rasia, Rodolfo and Brutscher, Bernhard}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {10}, pages = {2756--2757}, publisher = {American Chemical Society}, title = {{Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy}}, doi = {10.1021/ja068949u}, volume = {129}, year = {2007}, } @article{8487, abstract = {Following unidirectional biophysical events such as the folding of proteins or the equilibration of binding interactions, requires experimental methods that yield information at both atomic-level resolution and at high repetition rates. Toward this end a number of different approaches enabling the rapid acquisition of 2D NMR spectra have been recently introduced, including spatially encoded “ultrafast” 2D NMR spectroscopy and SOFAST HMQC NMR. Whereas the former accelerates acquisitions by reducing the number of scans that are necessary for completing arbitrary 2D NMR experiments, the latter operates by reducing the delay between consecutive scans while preserving sensitivity. Given the complementarities between these two approaches it seems natural to combine them into a single tool, enabling the acquisition of full 2D protein NMR spectra at high repetition rates. We demonstrate here this capability with the introduction of “ultraSOFAST” HMQC NMR, a spatially encoded and relaxation-optimized approach that can provide 2D protein correlation spectra at ∼1 s repetition rates for samples in the ∼2 mM concentration range. The principles, relative advantages, and current limitations of this new approach are discussed, and its application is exemplified with a study of the fast hydrogen−deuterium exchange characterizing amide sites in Ubiquitin.}, author = {Gal, Maayan and Schanda, Paul and Brutscher, Bernhard and Frydman, Lucio}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {5}, pages = {1372--1377}, publisher = {American Chemical Society}, title = {{UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates}}, doi = {10.1021/ja066915g}, volume = {129}, year = {2007}, } @article{8511, abstract = {Here we study an amazing phenomenon discovered by Newhouse [S. Newhouse, Non-density of Axiom A(a) on S2, in: Proc. Sympos. Pure Math., vol. 14, Amer. Math. Soc., 1970, pp. 191–202; S. Newhouse, Diffeomorphisms with infinitely many sinks, Topology 13 (1974) 9–18; S. Newhouse, The abundance of wild hyperbolic sets and nonsmooth stable sets of diffeomorphisms, Publ. Math. Inst. Hautes Études Sci. 50 (1979) 101–151]. It turns out that in the space of Cr smooth diffeomorphisms Diffr(M) of a compact surface M there is an open set U such that a Baire generic diffeomorphism f ∈ U has infinitely many coexisting sinks. In this paper we make a step towards understanding “how often does a surface diffeomorphism have infinitely many sinks.” Our main result roughly says that with probability one for any positive D a surface diffeomorphism has only finitely many localized sinks either of cyclicity bounded by D or those whose period is relatively large compared to its cyclicity. It verifies a particular case of Palis’ Conjecture saying that even though diffeomorphisms with infinitely many coexisting sinks are Baire generic, they have probability zero. One of the key points of the proof is an application of Newton Interpolation Polynomials to study the dynamics initiated in [V. Kaloshin, B. Hunt, A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I, Ann. of Math., in press, 92 pp.; V. Kaloshin, A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II, preprint, 85 pp.].}, author = {Gorodetski, A. and Kaloshin, Vadim}, issn = {0001-8708}, journal = {Advances in Mathematics}, keywords = {General Mathematics}, number = {2}, pages = {710--797}, publisher = {Elsevier}, title = {{How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency}}, doi = {10.1016/j.aim.2006.03.012}, volume = {208}, year = {2007}, } @article{8512, abstract = {For diffeomorphisms of smooth compact finite-dimensional manifolds, we consider the problem of how fast the number of periodic points with period n grows as a function of n. In many familiar cases (e.g., Anosov systems) the growth is exponential, but arbitrarily fast growth is possible; in fact, the first author has shown that arbitrarily fast growth is topologically (Baire) generic for C2 or smoother diffeomorphisms. In the present work we show that, by contrast, for a measure-theoretic notion of genericity we call “prevalence”, the growth is not much faster than exponential. Specifically, we show that for each ρ,δ>0, there is a prevalent set of C1+ρ (or smoother) diffeomorphisms for which the number of periodic n points is bounded above by exp(Cn1+δ) for some C independent of n. We also obtain a related bound on the decay of hyperbolicity of the periodic points as a function of n, and obtain the same results for 1-dimensional endomorphisms. The contrast between topologically generic and measure-theoretically generic behavior for the growth of the number of periodic points and the decay of their hyperbolicity show this to be a subtle and complex phenomenon, reminiscent of KAM theory. Here in Part I we state our results and describe the methods we use. We complete most of the proof in the 1-dimensional C2-smooth case and outline the remaining steps, deferred to Part II, that are needed to establish the general case. The novel feature of the approach we develop in this paper is the introduction of Newton Interpolation Polynomials as a tool for perturbing trajectories of iterated maps.}, author = {Kaloshin, Vadim and Hunt, Brian}, issn = {0003-486X}, journal = {Annals of Mathematics}, number = {1}, pages = {89--170}, publisher = {Princeton University Press}, title = {{Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I}}, doi = {10.4007/annals.2007.165.89}, volume = {165}, year = {2007}, } @article{860, abstract = {We identified a mutation in the CRYGD gene (P23S) of the γ-crystallin gene cluster that is associated with a polymorphic congenital cataract that occurs with frequency of ∼0.3% in a human population. To gain insight into the molecular mechanism of the pathogenesis of γ-crystallin isoforms, we undertook an evolutionary analysis of the available mammalian and newly obtained primate sequences of the γ-crystallin genes. The cataract-associated serine at site 23 corresponds to the ancestral state, since it was found in CRYGD of a lower primate and all the surveyed nonprimate mammals. Crystallin proteins include two structurally similar domains, and substitutions in mammalian CRYGD protein at site 23 of the first domain were always associated with substitutions in the structurally reciprocal sites 109 and 136 of the second domain. These data suggest that the cataractogenic effect of serine at site 23 in the N-terminal domain of CRYGD may be compensated indirectly by amino acid changes in a distal domain. We also found that gene conversion was a factor in the evolution of the γ-crystallin gene cluster throughout different mammalian clades. The high rate of gene conversion observed between the functional CRYGD gene and two primate γ-crystallin pseudogenes (CRYGEP1 and CRYGFP1) coupled with a surprising finding of apparent negative selection in primate pseudogenes suggest a deleterious impact of recently derived pseudogenes involved in gene conversion in the γ-crystallin gene cluster.}, author = {Plotnikova, Olga V and Fyodor Kondrashov and Vlasov, Peter K and Grigorenko, Anastasia P and Ginter, Evgeny K and Rogaev, Evgeny I}, journal = {American Journal of Human Genetics}, number = {1}, pages = {32 -- 43}, publisher = {Cell Press}, title = {{Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state}}, doi = {10.1086/518616}, volume = {81}, year = {2007}, } @article{861, abstract = {Background: Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. Description: We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. Conclusion: We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.}, author = {Popadin, Konstantin Yu and Mamirova, Leila A and Fyodor Kondrashov}, journal = {BMC Bioinformatics}, publisher = {BioMed Central}, title = {{A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures}}, doi = {10.1186/1471-2105-8-441}, volume = {8}, year = {2007}, } @article{879, abstract = {Having an extra copy of a gene is thought to provide some functional redundancy, which results in a higher rate of evolution in duplicated genes. In this article, we estimate the impact of gene duplication on the selection of tuf paralogs, and we find that in the absence of gene conversion, tuf paralogs have evolved significantly slower than when gene conversion has been a factor in their evolution. Thus, tuf gene copies evolve under a selective pressure that ensures their functional uniformity, and gene conversion reduces selection against amino acid substitutions that affect the function of the encoded protein, EF-Tu.}, author = {Fyodor Kondrashov and Gurbich, Tatiana A and Vlasov, Peter K}, journal = {Trends in Genetics}, number = {5}, pages = {215 -- 218}, publisher = {Elsevier}, title = {{Selection for functional uniformity of tuf duplicates in γ-proteobacteria}}, doi = {10.1016/j.tig.2007.03.002}, volume = {23}, year = {2007}, } @inbook{167, abstract = {This book contains research articles on Diophantine Geometry, written by participants of a research program held at the Ennio De Giorgi Mathematical Research Center in Pisa, Italy, during the period April – July 2005. The authors are eminent experts in the field. Several subfields of the main topic are presented; the volume thus is particularly useful to get a broad overview of recent research developments.}, author = {Browning, Timothy D and Heath Brown, Roger}, booktitle = {Diophantine Geometry}, editor = {Zannier, Umberto}, pages = {93 -- 100}, publisher = {Edizioni della Normale}, title = {{Simultaneous equal sums of three powers}}, volume = {4}, year = {2007}, } @article{1750, abstract = {The authors investigate the composition profile of SiGe islands after capping with Si to form quantum dots, using a two step etching procedure and atomic force microscopy. Initially, the Si capping layers are removed by etching selectively Si over Ge and then the composition of the disclosed islands is addressed by selectively etching Ge over Si. For samples grown at 580 °C the authors show that even when overgrowth leads to a flat Si surface and the islands undergo strong morphological changes, a Ge-rich core region is still preserved in the dot. At high growth and overgrowth temperatures (740 °C), the experiments show that the newly formed base of the buried islands is more Si rich than their top. Furthermore, the authors find that for the growth conditions used, no lateral motion takes place during capping.}, author = {Georgios Katsaros and Stoffel, Mathieu and Rastelli, Armando and Schmidt, Oliver G and Kern, Klaus and Tersoff, Jerry}, journal = {Applied Physics Letters}, number = {1}, publisher = {American Institute of Physics}, title = {{Three-dimensional isocompositional profiles of buried SiGeSi (001) islands}}, doi = {10.1063/1.2752730}, volume = {91}, year = {2007}, } @article{1762, abstract = {In quantum information science, the phase of a wave function plays an important role in encoding information. Although most experiments in this field rely on dynamic effects to manipulate this information, an alternative approach is to use geometric phase, which has been argued to have potential fault tolerance. We demonstrated the controlled accumulation of a geometric phase, Berry's phase, in a superconducting qubit; we manipulated the qubit geometrically by means of microwave radiation and observed the accumulated phase in an interference experiment. We found excellent agreement with Berry's predictions and also observed a geometry-dependent contribution to dephasing.}, author = {Leek, Peter J and Johannes Fink and Blais, Alexandre and Bianchetti, R and Göppl, M and Gambetta, Jay M and Schuster, David I and Frunzio, Luigi and Schoelkopf, Robert J and Wallraff, Andreas}, journal = {Science}, number = {5858}, pages = {1889 -- 1892}, publisher = {American Association for the Advancement of Science}, title = {{Observation of Berry's phase in a solid-state qubit}}, doi = {10.1126/science.1149858}, volume = {318}, year = {2007}, }