@article{2383,
abstract = {We study the relativistic electron-positron field at positive temperature in the Hartree-Fock approximation. We consider both the case with and without exchange terms, and investigate the existence and properties of minimizers. Our approach is non-perturbative in the sense that the relevant electron subspace is determined in a self-consistent way. The present work is an extension of previous work by Hainzl, Lewin, Séré and Solovej where the case of zero temperature was considered.},
author = {Hainzl, Christian and Lewin, Mathieu and Robert Seiringer},
journal = {Reviews in Mathematical Physics},
number = {10},
pages = {1283 -- 1307},
publisher = {World Scientific Publishing},
title = {{A nonlinear model for relativistic electrons at positive temperature}},
doi = {10.1142/S0129055X08003547},
volume = {20},
year = {2008},
}
@inproceedings{2702,
abstract = {We review our proof that in a scaling limit, the time evolution of a quantum particle in a static random environment leads to a diffusion equation. In particular, we discuss the role of Feynman graph expansions and of renormalization.
},
author = {László Erdös and Salmhofer, Manfred and Yau, Horng-Tzer},
pages = {167 -- 182},
publisher = {World Scientific Publishing},
title = {{Feynman graphs and renormalization in quantum diffusion}},
doi = {10.1142/9789812833556_0011},
year = {2008},
}
@article{1763,
abstract = {The field of cavity quantum electrodynamics (QED), traditionally studied in atomic systems, has gained new momentum by recent reports of quantum optical experiments with solid-state semiconducting and superconducting systems. In cavity QED, the observation of the vacuum Rabi mode splitting is used to investigate the nature of matter-light interaction at a quantum-mechanical level. However, this effect can, at least in principle, be explained classically as the normal mode splitting of two coupled linear oscillators. It has been suggested that an observation of the scaling of the resonant atom-photon coupling strength in the Jaynes-Cummings energy ladder with the square root of photon number n is sufficient to prove that the system is quantum mechanical in nature. Here we report a direct spectroscopic observation of this characteristic quantum nonlinearity. Measuring the photonic degree of freedom of the coupled system, our measurements provide unambiguous spectroscopic evidence for the quantum nature of the resonant atom-field interaction in cavity QED. We explore atom-photon superposition states involving up to two photons, using a spectroscopic pump and probe technique. The experiments have been performed in a circuit QED set-up, in which very strong coupling is realized by the large dipole coupling strength and the long coherence time of a superconducting qubit embedded in a high-quality on-chip microwave cavity. Circuit QED systems also provide a natural quantum interface between flying qubits (photons) and stationary qubits for applications in quantum information processing and communication.},
author = {Johannes Fink and Göppl, M and Baur, Matthias P and Bianchetti, R and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas},
journal = {Nature},
number = {7202},
pages = {315 -- 318},
publisher = {Nature Publishing Group},
title = {{Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system}},
doi = {10.1038/nature07112},
volume = {454},
year = {2008},
}
@article{1765,
abstract = {High quality on-chip microwave resonators have recently found prominent new applications in quantum optics and quantum information processing experiments with superconducting electronic circuits, a field now known as circuit quantum electrodynamics (QED). They are also used as single photon detectors and parametric amplifiers. Here we analyze the physical properties of coplanar waveguide resonators and their relation to the materials properties for use in circuit QED. We have designed and fabricated resonators with fundamental frequencies from 2 to 9 GHz and quality factors ranging from a few hundreds to a several hundred thousands controlled by appropriately designed input and output coupling capacitors. The microwave transmission spectra measured at temperatures of 20 mK are shown to be in good agreement with theoretical lumped element and distributed element transmission matrix models. In particular, the experimentally determined resonance frequencies, quality factors, and insertion losses are fully and consistently explained by the two models for all measured devices. The high level of control and flexibility in design renders these resonators ideal for storing and manipulating quantum electromagnetic fields in integrated superconducting electronic circuits.},
author = {Göppl, M and Fragner, A and Baur, Matthias P and Bianchetti, R and Filipp, Stefan and Johannes Fink and Leek, Peter J and Puebla, G and Steffen, L. Kraig and Wallraff, Andreas},
journal = {Journal of Applied Physics},
number = {11},
publisher = {American Institute of Physics},
title = {{Coplanar waveguide resonators for circuit quantum electrodynamics}},
doi = {10.1063/1.3010859},
volume = {104},
year = {2008},
}
@article{2120,
abstract = {We consider the linear stochastic Cauchy problem dX (t) =AX (t) dt +B dWH (t), t≥ 0, where A generates a C0-semigroup on a Banach space E, WH is a cylindrical Brownian motion over a Hilbert space H, and B: H → E is a bounded operator. Assuming the existence of a unique minimal invariant measure μ∞, let Lp denote the realization of the Ornstein-Uhlenbeck operator associated with this problem in Lp (E, μ∞). Under suitable assumptions concerning the invariance of the range of B under the semigroup generated by A, we prove the following domain inclusions, valid for 1 < p ≤ 2: Image omitted. Here WHk, p (E, μinfin; denotes the kth order Sobolev space of functions with Fréchet derivatives up to order k in the direction of H. No symmetry assumptions are made on L p.},
author = {Jan Maas and van Neerven, Jan M},
journal = {Infinite Dimensional Analysis, Quantum Probability and Related Topics},
number = {4},
pages = {603 -- 626},
publisher = {World Scientific Publishing},
title = {{On the domain of non-symmetric Ornstein-Uhlenbeck operators in banach spaces}},
doi = {10.1142/S0219025708003245},
volume = {11},
year = {2008},
}
@article{2121,
abstract = {Let H be a separable real Hubert space and let double struck F sign = (ℱt)t∈[0,T] be the augmented filtration generated by an H-cylindrical Brownian motion (WH(t))t∈[0,T] on a probability space (Ω, ℱ ℙ). We prove that if E is a UMD Banach space, 1 ≤ p < ∞, and F ∈ double struck D sign1,p(Ω E) is ℱT-measurable, then F = double struck E sign(F) + ∫0T Pdouble struck F sign(DF) dW H, where D is the Malliavin derivative of F and P double struck F sign is the projection onto the F-adapted elements in a suitable Banach space of Lp-stochastically integrable ℒ(H, E)-valued processes.},
author = {van Neerven, Jan M and Jan Maas},
journal = {Electronic Communications in Probability},
pages = {151 -- 164},
publisher = {Institute of Mathematical Statistics},
title = {{A Clark-Ocone formula in UMD Banach spaces}},
volume = {13},
year = {2008},
}
@article{2146,
abstract = {We present an analytic model of thermal state-to-state rotationally inelastic collisions of polar molecules in electric fields. The model is based on the Fraunhofer scattering of matter waves and requires Legendre moments characterizing the “shape” of the target in the body-fixed frame as its input. The electric field orients the target in the space-fixed frame and thereby effects a striking alteration of the dynamical observables: both the phase and amplitude of the oscillations in the partial differential cross sections undergo characteristic field-dependent changes that transgress into the partial integral cross sections. As the cross sections can be evaluated for a field applied parallel or perpendicular to the relative velocity, the model also offers predictions about steric asymmetry. We exemplify the field-dependent quantum collision dynamics with the behavior of the Ne–OCS(Σ1) and Ar–NO(Π2) systems. A comparison with the close-coupling calculations available for the latter system [Chem. Phys. Lett.313, 491 (1999)] demonstrates the model’s ability to qualitatively explain the field dependence of all the scattering features observed.},
author = {Mikhail Lemeshko and Friedrich, Břetislav},
journal = {Journal of Chemical Physics},
number = {2},
publisher = {American Institute of Physics},
title = {{An analytic model of rotationally inelastic collisions of polar molecules in electric fields}},
doi = {10.1063/1.2948392},
volume = {129},
year = {2008},
}
@article{6146,
abstract = {Homeostasis of internal carbon dioxide (CO2) and oxygen (O2) levels is fundamental to all animals. Here we examine the CO2 response of the nematode Caenorhabditis elegans. This species inhabits rotting material, which typically has a broad CO2 concentration range. We show that well fed C. elegans avoid CO2 levels above 0.5%. Animals can respond to both absolute CO2 concentrations and changes in CO2 levels within seconds. Responses to CO2 do not reflect avoidance of acid pH but appear to define a new sensory response. Sensation of CO2 is promoted by the cGMP-gated ion channel subunits TAX-2 and TAX-4, but other pathways are also important. Robust CO2 avoidance in well fed animals requires inhibition of the DAF-16 forkhead transcription factor by the insulin-like receptor DAF-2. Starvation, which activates DAF-16, strongly suppresses CO2 avoidance. Exposure to hypoxia (<1% O2) also suppresses CO2 avoidance via activation of the hypoxia-inducible transcription factor HIF-1. The npr-1 215V allele of the naturally polymorphic neuropeptide receptor npr-1, besides inhibiting avoidance of high ambient O2 in feeding C. elegans, also promotes avoidance of high CO2. C. elegans integrates competing O2 and CO2 sensory inputs so that one response dominates. Food and allelic variation at NPR-1 regulate which response prevails. Our results suggest that multiple sensory inputs are coordinated by C. elegans to generate different coherent foraging strategies.},
author = {Bretscher, A. J. and Busch, K. E. and de Bono, Mario},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {23},
pages = {8044--8049},
publisher = {Proceedings of the National Academy of Sciences},
title = {{A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans}},
doi = {10.1073/pnas.0707607105},
volume = {105},
year = {2008},
}
@article{1460,
abstract = {We calculate the E-polynomials of certain twisted GL(n,ℂ)-character varieties Mn of Riemann surfaces by counting points over finite fields using the character table of the finite group of Lie-type GL(n, q) and a theorem proved in the appendix by N. Katz. We deduce from this calculation several geometric results, for example, the value of the topological Euler characteristic of the associated PGL(n,ℂ)-character variety. The calculation also leads to several conjectures about the cohomology of Mn: an explicit conjecture for its mixed Hodge polynomial; a conjectured curious hard Lefschetz theorem and a conjecture relating the pure part to absolutely indecomposable representations of a certain quiver. We prove these conjectures for n=2.},
author = {Tamas Hausel and Rodríguez Villegas, Fernando},
journal = {Inventiones Mathematicae},
number = {3},
pages = {555 -- 624},
publisher = {Springer},
title = {{Mixed Hodge polynomials of character varieties: With an appendix by Nicholas M. Katz}},
doi = {10.1007/s00222-008-0142-x},
volume = {174},
year = {2008},
}
@article{1036,
abstract = {We report on the control of interaction-induced dephasing of Bloch oscillations for an atomic Bose-Einstein condensate in an optical lattice. We quantify the dephasing in terms of the width of the quasimomentum distribution and measure its dependence on time for different interaction strengths which we control by means of a Feshbach resonance. For minimal interaction, the dephasing time is increased from a few to more than 20 thousand Bloch oscillation periods, allowing us to realize a BEC-based atom interferometer in the noninteracting limit.},
author = {Gustavsson, Mattias and Haller, Elmar and Mark, Manfred and Danzl, Johann G and Rojas Kopeinig, Gabriel and Nägerl, Hanns},
journal = {Physical Review Letters},
number = {8},
publisher = {American Physical Society},
title = {{Control of interaction-induced dephasing of bloch oscillations}},
doi = {10.1103/PhysRevLett.100.080404},
volume = {100},
year = {2008},
}
@article{1037,
abstract = {We experimentally demonstrate Cs2 Feshbach molecules well above the dissociation threshold, which are stable against spontaneous decay on the time scale of 1s. An optically trapped sample of ultracold dimers is prepared in a high rotational state and magnetically tuned into a region with a negative binding energy. The metastable character of these molecules arises from the large centrifugal barrier in combination with negligible coupling to states with low rotational angular momentum. A sharp onset of dissociation with increasing magnetic field is mediated by a crossing with a lower rotational dimer state and facilitates dissociation on demand with a well-defined energy.},
author = {Knoop, Steven and Mark, Michael and Ferlaino, Francesca and Danzl, Johann G and Kraemer, Tobias and Nägerl, Hanns and Grimm, Rudolf},
journal = {Physical Review Letters},
number = {8},
publisher = {American Physical Society},
title = {{Metastable feshbach molecules in high rotational states}},
doi = {10.1103/PhysRevLett.100.083002},
volume = {100},
year = {2008},
}
@article{1039,
abstract = {Molecular cooling techniques face the hurdle of dissipating translational as well as internal energy in the presence of a rich electronic, vibrational, and rotational energy spectrum. In our experiment, we create a translationally ultracold, dense quantum gas of molecules bound by more than 1000 wave numbers in the electronic ground state. Specifically, we stimulate with 80% efficiency, a two-photon transfer of molecules associated on a Feshbach resonance from a Bose-Einstein condensate of cesium atoms. In the process, the initial loose, long-range electrostatic bond of the Feshbach molecule is coherently transformed into a tight chemical bond. We demonstrate coherence of the transfer in a Ramsey-type experiment and show that the molecular sample is not heated during the transfer. Our results show that the preparation of a quantum gas of molecules in specific rovibrational states is possible and that the creation of a Bose-Einstein condensate of molecules in their rovibronic ground state is within reach.},
author = {Danzl, Johann G and Haller, Elmar and Gustavsson, Mattias and Mark, Manfred and Hart, Russell and Bouloufa, Nadia and Dulieu, Olivier and Ritsch, Helmut and Nägerl, Hanns},
journal = {Science},
number = {5892},
pages = {1062 -- 1066},
publisher = {American Association for the Advancement of Science},
title = {{Quantum gas of deeply bound ground state molecules}},
doi = {10.1126/science.1159909},
volume = {321},
year = {2008},
}
@article{965,
abstract = {We give many examples of applying Bogoliubov's forest formula to iterative solutions of various nonlinear equations. The same formula describes an extremely wide class of objects, from an ordinary quadratic equation to renormalization in quantum field theory.},
author = {Morozov, Alexei Y and Maksym Serbyn},
journal = {Theoretical and Mathematical Physics},
number = {2},
pages = {270 -- 293},
publisher = {Elsevier},
title = {{Nonlinear algebra and Bogoliubov's recursion}},
doi = {10.1007/s11232-008-0026-7},
volume = {154},
year = {2008},
}
@article{3734,
abstract = {Gene expression levels fluctuate even under constant external conditions. Much emphasis has usually been placed on the components of this noise that are due to randomness in transcription and translation. Here we focus on the role of noise associated with the inputs to transcriptional regulation; in particular, we analyze the effects of random arrival times and binding of transcription factors to their target sites along the genome. This contribution to the total noise sets a fundamental physical limit to the reliability of genetic control, and has clear signatures, but we show that these are easily obscured by experimental limitations and even by conventional methods for plotting the variance vs. mean expression level. We argue that simple, universal models of noise dominated by transcription and translation are inconsistent with the embedding of gene expression in a network of regulatory interactions. Analysis of recent experiments on transcriptional control in the early Drosophila embryo shows that these results are quantitatively consistent with the predicted signatures of input noise, and we discuss the experiments needed to test the importance of input noise more generally.},
author = {Gasper Tkacik and Gregor, Thomas and Bialek, William S},
journal = {PLoS One},
number = {7},
publisher = {Public Library of Science},
title = {{The role of input noise in transcriptional regulation}},
doi = {10.1371/journal.pone.0002774},
volume = {3},
year = {2008},
}
@article{3740,
abstract = {In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be possible to transmit much more than just one regulatory bit. Realizing this optimal information capacity would require that the dynamic range of TF concentrations used by the cell, the input/output relation of the regulatory module, and the noise in gene expression satisfy certain matching relations, which we derive. These results provide parameter-free, quantitative predictions connecting independently measurable quantities. Although we have considered only the simplified problem of a single gene responding to a single TF, we find that these predictions are in surprisingly good agreement with recent experiments on the Bicoid/Hunchback system in the early Drosophila embryo and that this system achieves approximately 90% of its theoretical maximum information transmission.},
author = {Gasper Tkacik and Callan,Curtis G and Bialek, William S},
journal = {PNAS},
number = {34},
pages = {12265 -- 12270},
publisher = {National Academy of Sciences},
title = {{Information flow and optimization in transcriptional regulation}},
doi = {10.1073/pnas.0806077105},
volume = {105},
year = {2008},
}
@article{3744,
abstract = {It is widely acknowledged that detailed timing of action potentials is used to encode information, for example, in auditory pathways; however, the computational tools required to analyze encoding through timing are still in their infancy. We present a simple example of encoding, based on a recent model of time-frequency analysis, in which units fire action potentials when a certain condition is met, but the timing of the action potential depends also on other features of the stimulus. We show that, as a result, spike-triggered averages are smoothed so much that they do not represent the true features of the encoding. Inspired by this example, we present a simple method, differential reverse correlations, that can separate an analysis of what causes a neuron to spike, and what controls its timing. We analyze with this method the leaky integrate-and-fire neuron and show the method accurately reconstructs the model's kernel.},
author = {Gasper Tkacik and Magnasco, Marcelo O},
journal = {Biosystems},
number = {1-2},
pages = {90 -- 100},
publisher = {Elsevier},
title = {{Decoding spike timing: The differential reverse-correlation method}},
doi = {10.1016/j.biosystems.2008.04.011},
volume = {93},
year = {2008},
}
@article{3751,
abstract = {Revealing the spectrum of combinatorial regulation of transcription at individual promoters is essential for understanding the complex structure of biological networks. However, the computations represented by the integration of various molecular signals at complex promoters are difficult to decipher in the absence of simple cis regulatory codes. Here we synthetically shuffle the regulatory architecture-operator sequences binding activators and repressors-of a canonical bacterial promoter. The resulting library of complex promoters allows for rapid exploration of promoter encoded logic regulation. Among all possible logic functions, NOR and ANDN promoter encoded logics predominate. A simple transcriptional cis regulatory code determines both logics, establishing a straightforward map between promoter structure and logic phenotype. The regulatory code is determined solely by the type of transcriptional regulation combinations: two repressors generate a NOR: NOT (a OR b) whereas a repressor and an activator generate an ANDN: a AND NOT b. Three-input versions of both logics, having an additional repressor as an input, are also present in the library. The resulting complex promoters cover a wide dynamic range of transcriptional strengths. Synthetic promoter shuffling represents a fast and efficient method for exploring the spectrum of complex regulatory functions that can be encoded by complex promoters. From an engineering point of view, synthetic promoter shuffling enables the experimental testing of the functional properties of complex promoters that cannot necessarily be inferred ab initio from the known properties of the individual genetic components. Synthetic promoter shuffling may provide a useful experimental tool for studying naturally occurring promoter shuffling.},
author = {Kinkhabwala, Ali and Guet, Calin C},
journal = {PLoS One},
number = {4},
publisher = {Public Library of Science},
title = {{Uncovering cis regulatory codes using synthetic promoter shuffling}},
doi = {10.1371/journal.pone.0002030},
volume = {3},
year = {2008},
}
@article{3822,
abstract = {Dentate gyrus granule cells transmit action potentials (APs) along their unmyelinated mossy fibre axons to the CA3 region. Although the initiation and propagation of APs are fundamental steps during neural computation, little is known about the site of AP initiation and the speed of propagation in mossy fibre axons. To address these questions, we performed simultaneous somatic and axonal whole-cell recordings from granule cells in acute hippocampal slices of adult mice at approximately 23 degrees C. Injection of short current pulses or synaptic stimulation evoked axonal and somatic APs with similar amplitudes. By contrast, the time course was significantly different, as axonal APs had a higher maximal rate of rise (464 +/- 30 V s(-1) in the axon versus 297 +/- 12 V s(-1) in the soma, mean +/- s.e.m.). Furthermore, analysis of latencies between the axonal and somatic signals showed that APs were initiated in the proximal axon at approximately 20-30 mum distance from the soma, and propagated orthodromically with a velocity of 0.24 m s(-1). Qualitatively similar results were obtained at a recording temperature of approximately 34 degrees C. Modelling of AP propagation in detailed cable models of granule cells suggested that a approximately 4 times higher Na(+) channel density ( approximately 1000 pS mum(-2)) in the axon might account for both the higher rate of rise of axonal APs and the robust AP initiation in the proximal mossy fibre axon. This may be of critical importance to separate dendritic integration of thousands of synaptic inputs from the generation and transmission of a common AP output.},
author = {Schmidt-Hieber, Christoph and Peter Jonas and Bischofberger, Josef},
journal = {Journal of Physiology},
number = {7},
pages = {1849 -- 57},
publisher = {Wiley-Blackwell},
title = {{Action potential initiation and propagation in hippocampal mossy fibre axons}},
doi = {10.1113/jphysiol.2007.150151 },
volume = {586},
year = {2008},
}
@article{3825,
abstract = {Fast-spiking parvalbumin-expressing basket cells (BCs) represent a major type of inhibitory interneuron in the hippocampus. These cells inhibit principal cells in a temporally precise manner and are involved in the generation of network oscillations. Although BCs show a unique expression profile of Ca(2+)-permeable receptors, Ca(2+)-binding proteins and Ca(2+)-dependent signalling molecules, physiological Ca(2+) signalling in these interneurons has not been investigated. To study action potential (AP)-induced dendritic Ca(2+) influx and buffering, we combined whole-cell patch-clamp recordings with ratiometric Ca(2+) imaging from the proximal apical dendrites of rigorously identified BCs in acute slices, using the high-affinity Ca(2+) indicator fura-2 or the low-affinity dye fura-FF. Single APs evoked dendritic Ca(2+) transients with small amplitude. Bursts of APs evoked Ca(2+) transients with amplitudes that increased linearly with AP number. Analysis of Ca(2+) transients under steady-state conditions with different fura-2 concentrations and during loading with 200 microm fura-2 indicated that the endogenous Ca(2+)-binding ratio was approximately 200 (kappa(S) = 202 +/- 26 for the loading experiments). The peak amplitude of the Ca(2+) transients measured directly with 100 microm fura-FF was 39 nm AP(-1). At approximately 23 degrees C, the decay time constant of the Ca(2+) transients was 390 ms, corresponding to an extrusion rate of approximately 600 s(-1). At 34 degrees C, the decay time constant was 203 ms and the corresponding extrusion rate was approximately 1100 s(-1). At both temperatures, continuous theta-burst activity with three to five APs per theta cycle, as occurs in vivo during exploration, led to a moderate increase in the global Ca(2+) concentration that was proportional to AP number, whereas more intense stimulation was required to reach micromolar Ca(2+) concentrations and to shift Ca(2+) signalling into a non-linear regime. In conclusion, dentate gyrus BCs show a high endogenous Ca(2+)-binding ratio, a small AP-induced dendritic Ca(2+) influx, and a relatively slow Ca(2+) extrusion. These specific buffering properties of BCs will sharpen the time course of local Ca(2+) signals, while prolonging the decay of global Ca(2+) signals.},
author = {Aponte, Yexica and Bischofberger, Josef and Peter Jonas},
journal = {Journal of Physiology},
number = {8},
pages = {2061 -- 75},
publisher = {Wiley-Blackwell},
title = {{Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus}},
doi = {10.1113/jphysiol.2007.147298},
volume = {586},
year = {2008},
}
@inproceedings{3878,
abstract = {We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing “reset” action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies.},
author = {Krishnendu Chatterjee and de Alfaro, Luca and Majumdar, Ritankar S},
pages = {91 -- 106},
publisher = {Springer},
title = {{The complexity of coverage}},
doi = {10.1007/978-3-540-89330-1_7},
volume = {5356},
year = {2008},
}
@inproceedings{4384,
abstract = {Model checking software transactional memories (STMs) is difficult because of the unbounded number, length, and delay of concurrent transactions and the unbounded size of the memory. We show that, under certain conditions, the verification problem can be reduced to a finite-state problem, and we illustrate the use of the method by proving the correctness of several STMs, including two-phase locking, DSTM, TL2, and optimistic concurrency control. The safety properties we consider include strict serializability and opacity; the liveness properties include obstruction freedom, livelock freedom, and wait freedom.
Our main contribution lies in the structure of the proofs, which are largely automated and not restricted to the STMs mentioned above. In a first step we show that every STM that enjoys certain structural properties either violates a safety or liveness requirement on some program with two threads and two shared variables, or satisfies the requirement on all programs. In the second step we use a model checker to prove the requirement for the STM applied to a most general program with two threads and two variables. In the safety case, the model checker constructs a simulation relation between two carefully constructed finite-state transition systems, one representing the given STM applied to a most general program, and the other representing a most liberal safe STM applied to the same program. In the liveness case, the model checker analyzes fairness conditions on the given STM transition system.},
author = {Guerraoui, Rachid and Thomas Henzinger and Jobstmann, Barbara and Vasu Singh},
pages = {372 -- 382},
publisher = {ACM},
title = {{Model checking transactional memories}},
doi = {10.1145/1375581.1375626},
year = {2008},
}
@article{3037,
author = {Feraru, Elena and Friml, Jirí},
journal = {Plant Physiology},
number = {4},
pages = {1553 -- 1559},
publisher = {American Society of Plant Biologists},
title = {{PIN polar targeting}},
doi = {10.1104/pp.108.121756},
volume = {147},
year = {2008},
}
@article{3307,
abstract = {A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.},
author = {Green, Richard E and Malaspinas, Anna-Sapfo and Krause, Johannes and Briggs, Adrian W and Johnson, Philip L and Caroline Uhler and Meyer, Matthias and Good, Jeffrey M and Maricic, Tomislav and Stenzel, Udo and Prüfer, Kay and Siebauer, Michael F and Burbano, Hernän A and Ronan, Michael T and Rothberg, Jonathan M and Egholm, Michael and Rudan, Pavao and Brajković, Dejana and Kućan, Željko and Gušić, Ivan and Wikström, Mårten K and Laakkonen, Liisa J and Kelso, Janet F and Slatkin, Montgomery and Pääbo, Svante H},
journal = {Cell},
pages = {416 -- 426},
publisher = {Cell Press},
title = {{A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing}},
doi = {10.1016/j.cell.2008.06.021},
volume = {134},
year = {2008},
}
@article{3435,
abstract = {We develop a new method for estimating effective population sizes, Ne, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is ~0.43.},
author = {Jonathan Bollback and York, Thomas L and Nielsen, Rasmus},
journal = {Genetics},
number = {1},
pages = {497 -- 502},
publisher = {Genetics Society of America},
title = {{Estimation of 2Nes From Temporal Allele Frequency Data}},
doi = {10.1534/genetics.107.085019},
volume = {179},
year = {2008},
}
@inproceedings{3504,
abstract = {Simulation and bisimulation metrics for stochastic systems provide a quantitative gen- eralization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative μ-calculus and related probabilistic logics.
We present algorithms for computing the metrics on Markov decision processes (MDPs), turn- based stochastic games, and concurrent games. For turn-based games and MDPs, we provide a polynomial-time algorithm based on linear programming for the computation of the one-step metric distance between states. The algorithm improves on the previously known exponential-time algo- rithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known bound for Markov chains. For the bisimulation kernel of the metric, which corresponds to probabilistic bisimulation, our algorithm works in time O(n4) for both turn-based games and MDPs; improving the previously best known O(n9 · log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance between states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be accomplished via a reduction to the theory of real closed fields, involving a
formula with three quantifier alternations, yielding O(|G|O(|G|5)) time complexity, improving the previously known reduction with O(|G|O(|G|7)) time complexity. These algorithms can be iterated
to approximate the metrics using binary search.},
author = {Chatterjee, Krishnendu and De Alfaro, Luca and Majumdar, Ritankar and Raman, Vishwanath},
pages = {107 -- 118},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Algorithms for game metrics}},
doi = {10.4230/LIPIcs.FSTTCS.2008.1745},
volume = {2},
year = {2008},
}
@article{2367,
abstract = {It was recently shown by Hansen that the Wigner-Yanase entropy is, for general states of quantum systems, not subadditive with respect to decomposition into two subsystems, although this property is known to hold for pure states. We investigate the question whether the weaker property of subadditivity for pure states with respect to decomposition into more than two subsystems holds. This property would have interesting applications in quantum chemistry. We show, however, that it does not hold in general, and provide a counterexample.},
author = {Robert Seiringer},
journal = {Letters in Mathematical Physics},
number = {3},
pages = {285 -- 288},
publisher = {Springer},
title = {{On the failure of subadditivity of the Wigner-Yanase entropy}},
doi = {10.1007/s11005-007-0159-x},
volume = {80},
year = {2007},
}
@article{2370,
abstract = {After recalling briefly the connection between spontaneous symmetry breaking and off-diagonal long-range order for models of magnets a general proof of spontaneous breaking of gauge symmetry as a consequence of Bose-Einstein condensation is presented. The proof is based on a rigorous validation of Bogoliubov's c-number substitution for the k = 0 mode operator α0.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Reports on Mathematical Physics},
number = {3},
pages = {389 -- 399},
publisher = {Elsevier},
title = {{Bose-Einstein condensation and spontaneous symmetry breaking}},
doi = {10.1016/S0034-4877(07)80074-7},
volume = {59},
year = {2007},
}
@article{2371,
abstract = {We give a proof of stability of relativistic matter with magnetic fields all the way up to the critical value of the nuclear charge Zα = 2/π.},
author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {479 -- 489},
publisher = {Springer},
title = {{Stability of relativistic matter with magnetic fields for nuclear charges up to the critical value}},
doi = {10.1007/s00220-007-0307-2},
volume = {275},
year = {2007},
}
@article{2372,
abstract = {The increasing interest in the Müller density-matrix-functional theory has led us to a systematic mathematical investigation of its properties. This functional is similar to the Hartree-Fock (HF) functional, but with a modified exchange term in which the square of the density matrix γ(x, x′) is replaced by the square of γ1 2 (x, x′). After an extensive introductory discussion of density-matrix-functional theory we show, among other things, that this functional is convex (unlike the HF functional) and that energy minimizing γ 's have unique densities ρ(r), which is a physically desirable property often absent in HF theory. We show that minimizers exist if N≤Z, and derive various properties of the minimal energy and the corresponding minimizers. We also give a precise statement about the equation for the orbitals of γ, which is more complex than for HF theory. We state some open mathematical questions about the theory together with conjectured solutions.},
author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer and Siedentop, Heinz K},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {5},
publisher = {American Physical Society},
title = {{Müller's exchange-correlation energy in density-matrix-functional theory}},
doi = {10.1103/PhysRevA.76.052517},
volume = {76},
year = {2007},
}
@article{2373,
abstract = {For the BCS equation with local two-body interaction λV(x), we give a rigorous analysis of the asymptotic behavior of the critical temperature as γ"0. We derive necessary and sufficient conditions onV(x) for the existence of a nontrivial solution for all values of γ>0.},
author = {Frank, Rupert L and Hainzl, Christian and Naboko, Serguei N and Robert Seiringer},
journal = {Journal of Geometric Analysis},
number = {4},
pages = {559 -- 567},
publisher = {Springer},
title = {{The critical temperature for the BCS equation at weak coupling}},
doi = {10.1007/BF02937429},
volume = {17},
year = {2007},
}
@article{2375,
abstract = {We give a Cwikel-Lieb-Rozenblum type bound on the number of bound states of Schrödinger operators with matrix-valued potentials using the functional integral method of Lieb. This significantly improves the constant in this inequality obtained earlier by Hundertmark.},
author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer},
journal = {Letters in Mathematical Physics},
number = {2-3},
pages = {107 -- 116},
publisher = {Springer},
title = {{Number of bound states of Schrödinger operators with matrix-valued potentials}},
doi = {10.1007/s11005-007-0211-x},
volume = {82},
year = {2007},
}
@inbook{2705,
author = {László Erdös},
booktitle = {Spectral Theory and Mathematical Physics: a Festschrift in Honor of Barry Simon's 60th Birthday },
editor = {Gesztesy, Fritz and Deift, Percy and Galvez, Percy and Perry, Peter and Schlag, Wilhelm},
pages = {401 -- 428},
publisher = {American Mathematical Society},
title = {{Recent developments in quantum mechanics with magnetic fields}},
volume = {76},
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},
}
@inproceedings{2091,
abstract = {We present a novel multi-scale representation and acquisition method for the animation of high-resolution facial geometry and wrinkles. We first acquire a static scan of the face including reflectance data at the highest possible quality. We then augment a traditional marker-based facial motion-capture system by two synchronized video cameras to track expression wrinkles. The resulting model consists of high-resolution geometry, motion-capture data, and expression wrinkles in 2D parametric form. This combination represents the facial shape and its salient features at multiple scales. During motion synthesis the motion-capture data deforms the high-resolution geometry using a linear shell-based mesh-deformation method. The wrinkle geometry is added to the facial base mesh using nonlinear energy optimization. We present the results of our approach for performance replay as well as for wrinkle editing. },
author = {Bernd Bickel and Botsch, Mario and Angst, Roland and Matusik, Wojciech and Otaduy, Miguel A and Pfister, Hanspeter and Groß, Markus S},
publisher = {ACM},
title = {{Multi scale capture of facial geometry and motion}},
doi = {doi:10.1145/1275808.1276419},
year = {2007},
}
@article{2093,
abstract = {We present a novel multi-scale representation and acquisition method for the animation of high-resolution facial geometry and wrinkles. We first acquire a static scan of the face including reflectance data at the highest possible quality. We then augment a traditional marker-based facial motion-capture system by two synchronized video cameras to track expression wrinkles. The resulting model consists of high-resolution geometry, motion-capture data, and expression wrinkles in 2D parametric form. This combination represents the facial shape and its salient features at multiple scales. During motion synthesis the motion-capture data deforms the high-resolution geometry using a linear shell-based mesh-deformation method. The wrinkle geometry is added to the facial base mesh using nonlinear energy optimization. We present the results of our approach for performance replay as well as for wrinkle editing. },
author = {Bernd Bickel and Botsch, Mario and Angst, Roland and Matusik, Wojciech and Otaduy, Miguel A and Pfister, Hanspeter and Groß, Markus S},
journal = {ACM Transactions on Graphics},
number = {3},
publisher = {ACM},
title = {{Multi scale capture of facial geometry and motion}},
doi = {10.1145/1276377.1276419},
volume = {26},
year = {2007},
}
@article{2118,
abstract = {We extend to infinite dimensions an explicit formula of Chill, Fašangová, Metafune, and Pallara for the optimal angle of analyticity of analytic Ornstein-Uhlenbeck semigroups. The main ingredient is an abstract representation of the Ornstein-Uhlenbeck operator in divergence form. },
author = {Jan Maas and van Neerven, Jan M},
journal = {Archiv der Mathematik},
number = {3},
pages = {226 -- 236},
publisher = {Birkhäuser},
title = {{On analytic Ornstein-Uhlenbeck semigroups in infinite dimensions}},
doi = {10.1007/s00013-007-2082-x},
volume = {89},
year = {2007},
}
@article{221,
author = {De La Bretèche, Régis and Browning, Timothy D},
journal = {Michigan Mathematical Journal},
number = {1},
pages = {51 -- 80},
publisher = {Project Euclid},
title = {{On Manin's conjecture for singular del Pezzo surfaces of degree four, I}},
doi = {10.1307/mmj/1177681985},
volume = {55},
year = {2007},
}
@article{222,
abstract = {Acknowledgements. The authors are grateful to Ulrich Derenthal and Brendan Hassett for several useful conversations relating to universal torsors for singular del Pezzo surfaces. Special thanks are due to Roger Heath–Brown whose ideas led us to the proof of Lemma 6. The paper was finalised while the first author was at the École Normale Supérieure, and the second author was at Oxford University supported by EPSRC grant number GR/R93155/01. The hospitality and financial support of these institutions is gratefully acknowledged. Finally, the authors would like to thank the anonymous referee for his careful reading of the manuscript and numerous useful suggestions.},
author = {de la Bretèche, Régis and Timothy Browning},
journal = {Mathematical Proceedings of the Cambridge Philosophical Society},
number = {3},
pages = {579 -- 605},
publisher = {Unknown},
title = {{On Manin's conjecture for singular del Pezzo surfaces of degree four, II}},
doi = {10.1017/S0305004107000205},
volume = {143},
year = {2007},
}
@article{223,
abstract = {Let Q be a non-singular diagonal quadratic form in at least four variables. We provide upper bounds for the number of integer solutions to the equation Q = 0, which lie in a box with sides of length 2B, as B → ∞. The estimates obtained are completely uniform in the coefficients of the form, and become sharper as they grow larger in modulus.},
author = {Timothy Browning},
journal = {Monatshefte fur Mathematik},
number = {1},
pages = {13 -- 38},
publisher = {Springer},
title = {{Density of integer solutions to diagonal quadratic forms}},
doi = {10.1007/s00605-007-0457-5},
volume = {152},
year = {2007},
}
@article{7753,
abstract = {In many species, females show reduced expression of a trait that is under sexual selection in males, and this expression is thought to be maintained through genetic associations with the male phenotype. However, there is also the potential for the female trait to convey an advantage in intrasexual conflicts over resources. We tested this hypothesis in a feral population of Soay sheep, in which males and females have a polymorphism for horn development, producing either full (normal horned), reduced (scurred) or no (polled, females only) horns. During the lambing period, females who possessed horns were more likely to initiate and win aggressive interactions, independent of age, weight and birthing status. The occurrence of aggression was also context dependent, decreasing over the lambing period and associated with local density. Our results demonstrate that a trait that confers benefits to males during intrasexual competition for mates may also be used by females in intrasexual competition over resources: males use weaponry to gain mates, whereas females use weaponry to gain food.},
author = {Robinson, Matthew Richard and Kruuk, Loeske E.B},
issn = {1744-9561},
journal = {Biology Letters},
number = {6},
pages = {651--654},
publisher = {The Royal Society},
title = {{Function of weaponry in females: The use of horns in intrasexual competition for resources in female Soay sheep}},
doi = {10.1098/rsbl.2007.0278},
volume = {3},
year = {2007},
}
@unpublished{6321,
abstract = {These lecture notes describe the current state of affairs for Manin's conjecture in the context of del Pezzo surfaces.},
author = {Browning, Timothy D},
booktitle = {arXiv},
title = {{The Manin conjecture in dimension 2}},
year = {2007},
}
@inbook{6323,
abstract = {This paper surveys recent progress towards the Manin conjecture for (singular and non-singular) del Pezzo surfaces. To illustrate some of the techniques available, an upper bound of the expected order of magnitude is established for a singular del Pezzo surface of degree four.},
author = {Browning, Timothy D},
booktitle = {A Tribute to Gauss and Dirichlet},
pages = {39--56},
publisher = {American Mathematical Society},
title = {{An overview of Manin's conjecture for del Pezzo surfaces}},
volume = {7},
year = {2007},
}
@article{128,
abstract = {A 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described. This long tuning range is achieved by simultaneously ramping the external cavity length with the laser injection current. The laser output pointing remains fixed, independent of its frequency because of the cover slip cavity design. This system is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate with lithium vapor and lithium atom beam experiments. },
author = {Carr, Adra and Serchest, Yancey and Waitukaitis, Scott R and Perreault, John and Lonij, Vincent and Cronin, Alexander},
journal = {Review of Scientific Instruments},
number = {10},
publisher = {American Institute of Physics},
title = {{Cover slip external cavity diode laser}},
doi = {10.1063/1.2801006},
volume = {78},
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{1035,
abstract = {We explore the rich internal structure of Cs2 Feshbach molecules. Pure ultracold molecular samples are prepared in a CO2 -laser trap, and a multitude of weakly bound states is populated by elaborate magnetic-field ramping techniques. Our methods use different Feshbach resonances as input ports and various internal level crossings for controlled state transfer. We populate higher partial-wave states of up to eight units of rotational angular momentum (l -wave states). We investigate the molecular structure by measurements of the magnetic moments for various states. Avoided level crossings between different molecular states are characterized through the changes in magnetic moment and by a Landau-Zener tunneling method. Based on microwave spectroscopy, we present a precise measurement of the magnetic-field-dependent binding energy of the weakly bound s -wave state that is responsible for the large background scattering length of Cs. This state is of particular interest because of its quantum-halo character.},
author = {Mark, Michael and Ferlaino, Francesca and Knoop, Steven and Danzl, Johann G and Kraemer, Tobias and Chin, Cheng and Nägerl, Hanns and Grimm, Rudolf},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {4},
publisher = {American Physical Society},
title = {{Spectroscopy of ultracold trapped cesium Feshbach molecules}},
doi = {10.1103/PhysRevA.76.042514},
volume = {76},
year = {2007},
}
@article{9149,
abstract = {The interaction of tidal currents with sea-floor topography results in the radiation of internal gravity waves into the ocean interior. These waves are called internal tides and their dissipation due to nonlinear wave breaking and concomitant three-dimensional turbulence could play an important role in the mixing of the abyssal ocean, and hence in controlling the large-scale ocean circulation.
As part of on-going work aimed at providing a theory for the vertical distribution of wave breaking over sea-floor topography, in this paper we investigate the instability of internal tides in a very simple linear model that helps us to relate the formation of unstable regions to simple features in the sea-floor topography. For two-dimensional tides over one-dimensional topography we find that the formation of overturning instabilities is closely linked to the singularities in the topography shape and that it is possible to have stable waves at the sea floor and unstable waves in the ocean interior above.
For three-dimensional tides over two-dimensional topography there is in addition an effect of geometric focusing of wave energy into localized regions of high wave amplitude, and we investigate this focusing effect in simple examples. Overall, we find that the distribution of unstable wave breaking regions can be highly non-uniform even for very simple idealized topography shapes.},
author = {BÜHLER, OLIVER and MULLER, Caroline J},
issn = {0022-1120},
journal = {Journal of Fluid Mechanics},
keywords = {Mechanical Engineering, Mechanics of Materials, Condensed Matter Physics},
pages = {1--28},
publisher = {Cambridge University Press},
title = {{Instability and focusing of internal tides in the deep ocean}},
doi = {10.1017/s0022112007007410},
volume = {588},
year = {2007},
}
@unpublished{3742,
abstract = {Recent work has shown that probabilistic models based on pairwise interactions-in the simplest case, the Ising model-provide surprisingly accurate descriptions of experiments on real biological networks ranging from neurons to genes. Finding these models requires us to solve an inverse problem: given experimentally measured expectation values, what are the parameters of the underlying Hamiltonian? This problem sits at the intersection of statistical physics and machine learning, and we suggest that more efficient solutions are possible by merging ideas from the two fields. We use a combination of recent coordinate descent algorithms with an adaptation of the histogram Monte Carlo method, and implement these techniques to take advantage of the sparseness found in data on real neurons. The resulting algorithm learns the parameters of an Ising model describing a network of forty neurons within a few minutes. This opens the possibility of analyzing much larger data sets now emerging, and thus testing hypotheses about the collective behaviors of these networks.},
author = {Broderick,Tamara and Dudik,Miroslav and Gasper Tkacik and Schapire,Robert E and Bialek, William S},
booktitle = {ArXiv},
publisher = {ArXiv},
title = {{Faster solutions of the inverse pairwise Ising problem}},
volume = {q-bio.QM},
year = {2007},
}
@article{4234,
abstract = {We study a generalised model of population growth in which the state variable is population growth rate instead of population size. Stochastic parametric perturbations, modelling phenotypic variability, lead to a Langevin system with two sources of multiplicative noise. The stationary probability distributions have two characteristic power-law scales. Numerical simulations show that noise suppresses the explosion of the growth rate which occurs in the deterministic counterpart. Instead, in different parameter regimes populations will grow with "anomalous" stochastic rates and (i) stabilise at "random carrying capacities", or (ii) go extinct in random times. Using logistic fits to reconstruct the simulated data, we find that even highly significant estimations do not recover or reflect information about the deterministic part of the process. Therefore, the logistic interpretation is not biologically meaningful. These results have implications for distinct model-aided calculations in biological situations because these kinds of estimations could lead to spurious conclusions. (c) 2006 Elsevier B.V. All rights reserved.},
author = {de Vladar, Harold and Pen, I.},
journal = {Physica A},
pages = {477 -- 485},
publisher = {Elsevier},
title = {{Determinism, noise, and spurious estimations in a generalised model of population growth}},
doi = {10.1016/j.physa.2006.06.025},
volume = {373},
year = {2007},
}
@article{3411,
abstract = {Mechanical single-molecule techniques offer exciting possibilities to investigate protein folding and stability in native environments at submolecular resolution. By applying a free-energy reconstruction procedure developed by Hummer and Szabo, which is based on a statistical theorem introduced by Jarzynski, we determined the unfolding free energy of the membrane proteins bacteriorhodopsin (BR), halorhodopsin, and the sodium-proton antiporter NhaA. The calculated energies ranged from 290.5kcal/mol for BR to 485.5kcal/mol for NhaA. For the remarkably stable BR, the equilibrium unfolding free energy was independent of pulling rate and temperature ranging between 18 and 42°C. Our experiments also revealed heterogeneous energetic properties in individual transmembrane helices. In halorhodopsin, the stabilization of a short helical segment yielded a characteristic signature in the energy profile. In NhaA, a pronounced peak was observed at a functionally important site in the protein. Since a large variety of single- and multispan membrane proteins can be tackled in mechanical unfolding experiments, our approach provides a basis for systematically elucidating energetic properties of membrane proteins with the resolution of individual secondary-structure elements.},
author = {Preiner, Johannes and Harald Janovjak and Rankl, Christian and Knaus, Helene and Cisneros, David A and Kedrov, Alexej and Kienberger, Ferry and Mueller, Daniel J and Hinterdorfer, Peter},
journal = {Biophysical Journal},
number = {3},
pages = {930 -- 937},
publisher = {Biophysical Society},
title = {{Free energy of membrane protein unfolding derived from single-molecule force measurements}},
doi = {10.1529/biophysj.106.096982},
volume = {93},
year = {2007},
}
@article{3427,
abstract = {We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case of transcytosis where morphogens undergo repeated rounds of internalization into cells and recycling. Based on a description on the cellular scale, we derive effective nonlinear transport equations in one and two dimensions which are valid on larger scales. We derive analytic expressions for the concentration dependence of the effective diffusion coefficient and the effective degradation rate. We discuss the effects of a directional bias on morphogen transport and those of the coupling of the morphogen and receptor kinetics. Furthermore, we discuss general properties of cellular transport processes such as the robustness of gradients and relate our results to recent experiments on the morphogen Decapentaplegic (Dpp) that acts in the wing disk of the fruit fly Drosophila.
© 2007 The American Physical Society},
author = {Bollenbach, Mark Tobias and Kruse, Karsten and Pantazis, Periklis and Gonzalez Gaitan, Marcos and Julicher, Frank},
journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics},
number = {1},
publisher = {American Institute of Physics},
title = {{Morphogen transport in epithelia}},
doi = {10.1103/PhysRevE.75.011901},
volume = {75},
year = {2007},
}