TY - JOUR
AB - Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population.
AU - Weissman, Daniel
AU - Feldman, Marcus
AU - Fisher, Daniel
ID - 3303
IS - 4
JF - Genetics
TI - The rate of fitness-valley crossing in sexual populations
VL - 186
ER -
TY - JOUR
AB - We use methods from combinatorics and algebraic statistics to study analogues of birth-and-death processes that have as their state space a finite subset of the m-dimensional lattice and for which the m matrices that record the transition probabilities in each of the lattice directions commute pairwise. One reason such processes are of interest is that the transition matrix is straightforward to diagonalize, and hence it is easy to compute n step transition probabilities. The set of commuting birth-and-death processes decomposes as a union of toric varieties, with the main component being the closure of all processes whose nearest neighbor transition probabilities are positive. We exhibit an explicit monomial parametrization for this main component, and we explore the boundary components using primary decomposition.
AU - Evans, Steven N
AU - Sturmfels, Bernd
AU - Caroline Uhler
ID - 3306
JF - The Annals of Applied Probability
TI - Commuting birth and death processes
VL - 20
ER -
TY - JOUR
AB - We study multivariate normal models that are described by linear constraints on the inverse of the covariance matrix. Maximum likelihood estimation for such models leads to the problem of maximizing the determinant function over a spectrahedron, and to the problem of characterizing the image of the positive definite cone under an arbitrary linear projection. These problems at the interface of statistics and optimization are here examined from the perspective of convex algebraic geometry.
AU - Sturmfels, Bernd
AU - Caroline Uhler
ID - 3308
IS - 4
JF - Annals of the Institute of Statistical Mathematics
TI - Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry
VL - 62
ER -
TY - CONF
AB - These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throughout the notes is transcriptional regulation in genetic regulatory networks. We present tools from information theory and statistical physics that can be used to analyze noisy nonlinear biological networks, and build generative and predictive models of regulatory processes.
AU - Gasper Tkacik
ID - 3430
TI - Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics
ER -
TY - JOUR
AB - How seizures start is a major question in epilepsy research. Preictal EEG changes occur in both human patients and animal models, but their underlying mechanisms and relationship with seizure initiation remain unknown. Here we demonstrate the existence, in the hippocampal CA1 region, of a preictal state characterized by the progressive and global increase in neuronal activity associated with a widespread buildup of low-amplitude high-frequency activity (HFA) (> 100 Hz) and reduction in system complexity. HFA is generated by the firing of neurons, mainly pyramidal cells, at much lower frequencies. Individual cycles of HFA are generated by the near-synchronous (within similar to 5 ms) firing of small numbers of pyramidal cells. The presence of HFA in the low-calcium model implicates nonsynaptic synchronization; the presence of very similar HFA in the high-potassium model shows that it does not depend on an absence of synaptic transmission. Immediately before seizure onset, CA1 is in a state of high sensitivity in which weak depolarizing or synchronizing perturbations can trigger seizures. Transition to seizure is characterized by a rapid expansion and fusion of the neuronal populations responsible for HFA, associated with a progressive slowing of HFA, leading to a single, massive, hypersynchronous cluster generating the high-amplitude low-frequency activity of the seizure.
AU - Jiruska, Premysl
AU - Csicsvari, Jozsef L
AU - Powell, Andrew
AU - Fox, John
AU - Chang, Wei
AU - Vreugdenhil, Martin
AU - Li, Xiaoli
AU - Palus, Milan
AU - Bujan, Alejandro
AU - Dearden, Richard
AU - Jefferys, John
ID - 3538
IS - 16
JF - Journal of Neuroscience
TI - High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro
VL - 30
ER -
TY - CONF
AB - Depth-bounded processes form the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. In this paper we develop an adequate domain of limits for the well-structured transition systems that are induced by depth-bounded processes. An immediate consequence of our result is that there exists a forward algorithm that decides the covering problem for this class. Unlike backward algorithms, the forward algorithm terminates even if the depth of the process is not known a priori. More importantly, our result suggests a whole spectrum of forward algorithms that enable the effective verification of a large class of mobile systems.
AU - Wies, Thomas
AU - Zufferey, Damien
AU - Henzinger, Thomas A
ED - Ong, Luke
ID - 4361
TI - Forward analysis of depth-bounded processes
VL - 6014
ER -
TY - JOUR
AB - Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops.
AU - Zemach, Assaf
AU - Kim, M. Yvonne
AU - Silva, Pedro
AU - Rodrigues, Jessica A.
AU - Dotson, Bradley
AU - Brooks, Matthew D.
AU - ZILBERMAN, Daniel
ID - 9485
IS - 43
JF - Proceedings of the National Academy of Sciences
SN - 0027-8424
TI - Local DNA hypomethylation activates genes in rice endosperm
VL - 107
ER -
TY - JOUR
AB - Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries.
AU - Zemach, Assaf
AU - ZILBERMAN, Daniel
ID - 9489
IS - 17
JF - Current Biology
SN - 0960-9822
TI - Evolution of eukaryotic DNA methylation and the pursuit of safer sex
VL - 20
ER -
TY - JOUR
AB - Let X be a projective non-singular quartic hypersurface of dimension 39 or more, which is defined over . We show that X() is non-empty provided that X() is non-empty and X has p-adic points for every prime p.
AU - Timothy Browning
AU - Heath-Brown, Roger
ID - 228
IS - 629
JF - Journal fur die Reine und Angewandte Mathematik
TI - Rational points on quartic hypersurfaces
ER -
TY - JOUR
AB - An upper bound of the expected order of magnitude is established for the number of ℚ-rational points of bounded height on Châtelet surfaces defined over ℚ.
AU - Timothy Browning
ID - 229
IS - 1
JF - Mathematische Annalen
TI - Linear growth for Châtelet surfaces
VL - 346
ER -
TY - JOUR
AB - We prove the Lee-Huang-Yang formula for the ground state energy of the 3D Bose gas with repulsive interactions described by the exponential function, in a simultaneous limit of weak coupling and high density. In particular, we show that the Bogoliubov approximation is exact in an appropriate parameter regime, as far as the ground state energy is concerned.
AU - Giuliani, Alessandro
AU - Robert Seiringer
ID - 2384
IS - 5-6
JF - Journal of Statistical Physics
TI - The ground state energy of the weakly interacting Bose gas at high density
VL - 135
ER -
TY - JOUR
AB - We consider an ultracold rotating Bose gas in a harmonic trap close to the critical angular velocity, so that the system can be considered to be confined to the lowest Landau level. With this assumption we prove that the Gross-Pitaevskii energy functional accurately describes the ground-state energy of the corresponding N -body Hamiltonian with contact interaction provided the total angular momentum L is much less than N2. While the Gross-Pitaevskii energy is always an obvious variational upper bound to the ground-state energy, a more refined analysis is needed to establish it as an exact lower bound. We also discuss the question of Bose-Einstein condensation in the parameter range considered. Coherent states together with inequalities in spaces of analytic functions are the main technical tools.
AU - Lieb, Élliott H
AU - Robert Seiringer
AU - Yngvason, Jakob
ID - 2385
IS - 6
JF - Physical Review A - Atomic, Molecular, and Optical Physics
TI - Yrast line of a rapidly rotating Bose gas: Gross-Pitaevskii regime
VL - 79
ER -
TY - JOUR
AB - We prove exponential decay of the off-diagonal correlation function in the two-dimensional homogeneous Bose gas when a2 ρ is small and the temperature T satisfies T> 4πρ ln | ln (a2 ρ) |. Here, a is the scattering length of the repulsive interaction potential and ρ is the density. To the leading order in a2 ρ, this bound agrees with the expected critical temperature for superfluidity. In the three-dimensional Bose gas, exponential decay is proved when T- Tc (0) Tc (0) >5 a ρ1/3, where Tc (0) is the critical temperature of the ideal gas. While this condition is not expected to be sharp, it gives a rigorous upper bound on the critical temperature for Bose-Einstein condensation.
AU - Robert Seiringer
AU - Ueltschi, Daniel
ID - 2386
IS - 1
JF - Physical Review B - Condensed Matter and Materials Physics
TI - Rigorous upper bound on the critical temperature of dilute Bose gases
VL - 80
ER -
TY - JOUR
AB - We consider a system of trapped spinless bosons interacting with a repulsive potential and subject to rotation. In the limit of rapid rotation and small scattering length, we rigorously show that the ground state energy converges to that of a simplified model Hamiltonian with contact interaction projected onto the Lowest Landau Level. This effective Hamiltonian models the bosonic analogue of the Fractional Quantum Hall Effect (FQHE). For a fixed number of particles, we also prove convergence of states; in particular, in a certain regime we show convergence towards the bosonic Laughlin wavefunction. This is the first rigorous justification of the effective FQHE Hamiltonian for rapidly rotating Bose gases. We review previous results on this effective Hamiltonian and outline open problems.
AU - Lewin, Mathieu
AU - Robert Seiringer
ID - 2387
IS - 5
JF - Journal of Statistical Physics
TI - Strongly correlated phases in rapidly rotating Bose gases
VL - 137
ER -
TY - JOUR
AB - This paper provides self-contained proof of a theorem relating probabilistic coherence of forecasts to their non-domination by rival forecasts with respect to any proper scoring rule. The theorem recapitulates insights achieved by other investigators, and clarifies the connection of coherence and proper scoring rules to Bregman divergence.
AU - Predd, Joel B
AU - Robert Seiringer
AU - Lieb, Élliott H
AU - Osherson, Daniel N
AU - Poor, Harold V
AU - Kulkarni, Sanjeev R
ID - 2388
IS - 10
JF - IEEE Transactions on Information Theory
TI - Probabilistic coherence and proper scoring rules
VL - 55
ER -
TY - CONF
AB - Let EMBEDk→d be the following algorithmic problem: Given a finite simplicial complex K of dimension at most k, does there exist a (piecewise linear) embedding of K into ℝd? Known results easily imply polynomiality of EMBEDk→2 (k = 1, 2; the case k = 1, d = 2 is graph planarity) and of EMBEDk→2k for all k ≥ 3 (even if k is not considered fixed). We show that the celebrated result of Novikov on the algorithmic unsolvability of recognizing the 5-sphere implies that EMBED d→d and EMBED(d-1)→d are undecidable for each d ≥ 5. Our main result is NP-hardness of EMBED2→4 and, more generally, of EMBEDk→d for all k, d with d ≥ 4 and d ≥ k ≥ (2d - 2)/3.
AU - Matoušek, Jiří
AU - Martin Tancer
AU - Uli Wagner
ID - 2433
TI - Hardness of embedding simplicial complexes in ℝd
ER -
TY - JOUR
AB - G protein-coupled receptors (GPCRs) have critical functions in intercellular communication. Although a wide range of different receptors have been identified in the same cells, the mechanism by which signals are integrated remains elusive. The ability of GPCRs to form dimers or larger hetero-oligomers is thought to generate such signal integration. We examined the molecular mechanisms responsible for the GABAB receptor-mediated potentiation of the mGlu receptor signalling reported in Purkinje neurons. We showed that this effect does not require a physical interaction between both receptors. Instead, it is the result of a more general mechanism in which the βγ subunits produced by the Gi-coupled GABAB receptor enhance the mGlu-mediated Gq response. Most importantly, this mechanism could be generally applied to other pairs of Gi- and Gq-coupled receptors and the signal integration varied depending on the time delay between activation of each receptor. Such a mechanism helps explain specific properties of cells expressing two different Gi- and Gq-coupled receptors activated by a single transmitter, or properties of GPCRs naturally coupled to both types of the G protein.
AU - Rives, Marie L
AU - Vol, Claire
AU - Fukazawa, Yugo
AU - Tinel, Norbert
AU - Trinquet, Eric
AU - Ayoub, Mohammed A
AU - Ryuichi Shigemoto
AU - Pin, Jean-Philippe
AU - Prezèau, Laurent
ID - 2499
IS - 15
JF - EMBO Journal
TI - Crosstalk between GABAB and mGlu1a receptors reveals new insight into GPCR signal integration
VL - 28
ER -
TY - JOUR
AB - Recent theoretical work has provided a basic understanding of signal propagation in networks of spiking neurons, but mechanisms for gating and controlling these signals have not been investigated previously. Here we introduce an idea for the gating of multiple signals in cortical networks that combines principles of signal propagation with aspects of balanced networks. Specifically, we studied networks in which incoming excitatory signals are normally cancelled by locally evoked inhibition, leaving the targeted layer unresponsive. Transmission can be gated 'on' by modulating excitatory and inhibitory gains to upset this detailed balance. We illustrate gating through detailed balance in large networks of integrate-and-fire neurons. We show successful gating of multiple signals and study failure modes that produce effects reminiscent of clinically observed pathologies. Provided that the individual signals are detectable, detailed balance has a large capacity for gating multiple signals.
AU - Vogels, Tim P
AU - Abbott, L F
ID - 8026
IS - 4
JF - Nature Neuroscience
SN - 1097-6256
TI - Gating multiple signals through detailed balance of excitation and inhibition in spiking networks
VL - 12
ER -
TY - JOUR
AB - We have developed a tunable source of Mie scale microdroplet aerosols that can be used for the generation of energetic ions. To demonstrate this potential, a terawatt Ti: Al2 O3 laser focused to 2×10 19 W/cm2 was used to irradiate heavy water (D2 O) aerosols composed of micron-scale droplets. Energetic deuterium ions, which were generated in the laser-droplet interaction, produced deuterium-deuterium fusion with approximately 2×10^3 fusion neutrons measured per joule of incident laser energy.
AU - Higginbotham, Andrew P
AU - Semonin, Octavi
AU - Bruce, S
AU - Chan, C
AU - Maindi, M
AU - Donnelly, Tom
AU - Maurer, M
AU - Bang, Woosuk
AU - Churina, I.V
AU - Osterholz, Jens
AU - Kim, I
AU - Bernstein, Aaron
AU - Ditmire, Todd
ID - 88
IS - 6
JF - Review of Scientific Instruments
TI - Generation of Mie size microdroplet aerosols with applications in laser-driven fusion experiments
VL - 80
ER -
TY - JOUR
AB - We demonstrate the time-resolved driving of two-photon blue sideband transitions between superconducting qubits and a transmission line resonator. As an example of using these sideband transitions for a two-qubit operation, we implement a pulse sequence that first entangles one qubit with the resonator and subsequently distributes the entanglement between two qubits. We show the generation of 75% fidelity Bell states by this method. The full density matrix of the two-qubit system is extracted using joint measurement and quantum state tomography and shows close agreement with numerical simulation.
AU - Leek, Peter J
AU - Filipp, Stefan
AU - Maurer, Patrick
AU - Baur, Matthias P
AU - Bianchetti, R
AU - Johannes Fink
AU - Göppl, M
AU - Steffen, L. Kraig
AU - Wallraff, Andreas
ID - 1766
IS - 18
JF - Physical Review B - Condensed Matter and Materials Physics
TI - Using sideband transitions for two-qubit operations in superconducting circuits
VL - 79
ER -
TY - JOUR
AB - We present spectroscopic measurements of the Autler-Townes doublet and the sidebands of the Mollow triplet in a driven superconducting qubit. The ground to first excited state transition of the qubit is strongly pumped while the resulting dressed qubit spectrum is probed with a weak tone. The corresponding transitions are detected using dispersive readout of the qubit coupled off resonantly to a microwave transmission line resonator. The observed frequencies of the Autler-Townes and Mollow spectral lines are in good agreement with a dispersive Jaynes-Cummings model taking into account higher excited qubit states and dispersive level shifts due to off-resonant drives.
AU - Baur, Matthias P
AU - Filipp, Stefan
AU - Bianchetti, R
AU - Johannes Fink
AU - Göppl, M
AU - Steffen, L. Kraig
AU - Leek, Peter J
AU - Blais, Alexandre
AU - Wallraff, Andreas
ID - 1767
IS - 24
JF - Physical Review Letters
TI - Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit
VL - 102
ER -
TY - JOUR
AB - Quantum state tomography is an important tool in quantum information science for complete characterization of multiqubit states and their correlations. Here we report a method to perform a joint simultaneous readout of two superconducting qubits dispersively coupled to the same mode of a microwave transmission line resonator. The nonlinear dependence of the resonator transmission on the qubit state dependent cavity frequency allows us to extract the full two-qubit correlations without the need for single-shot readout of individual qubits. We employ standard tomographic techniques to reconstruct the density matrix of two-qubit quantum states.
AU - Filipp, Stefan
AU - Maurer, Patrick
AU - Leek, Peter J
AU - Baur, Matthias P
AU - Bianchetti, R
AU - Johannes Fink
AU - Göppl, M
AU - Steffen, L. Kraig
AU - Gambetta, Jay M
AU - Blais, Alexandre
AU - Wallraff, Andreas
ID - 1768
IS - 20
JF - Physical Review Letters
TI - Two-qubit state tomography using a joint dispersive readout
VL - 102
ER -
TY - JOUR
AB - We present an ideal realization of the Tavis-Cummings model in the absence of atom number and coupling fluctuations by embedding a discrete number of fully controllable superconducting qubits at fixed positions into a transmission line resonator. Measuring the vacuum Rabi mode splitting with one, two, and three qubits strongly coupled to the cavity field, we explore both bright and dark dressed collective multiqubit states and observe the discrete N scaling of the collective dipole coupling strength. Our experiments demonstrate a novel approach to explore collective states, such as the W state, in a fully globally and locally controllable quantum system. Our scalable approach is interesting for solid-state quantum information processing and for fundamental multiatom quantum optics experiments with fixed atom numbers.
AU - Johannes Fink
AU - Bianchetti, R
AU - Baur, Matthias P
AU - Göppl, M
AU - Steffen, L. Kraig
AU - Filipp, Stefan
AU - Leek, Peter J
AU - Blais, Alexandre
AU - Wallraff, Andreas
ID - 1769
IS - 8
JF - Physical Review Letters
TI - Dressed collective qubit states and the Tavis-Cummings model in circuit QED
VL - 103
ER -
TY - JOUR
AB - The quantum state of a superconducting qubit nonresonantly coupled to a transmission line resonator can be determined by measuring the quadrature amplitudes of an electromagnetic field transmitted through the resonator. We present experiments in which we analyze in detail the dynamics of the transmitted field as a function of the measurement frequency for both weak continuous and pulsed measurements. We find excellent agreement between our data and calculations based on a set of Bloch-type differential equations for the cavity field derived from the dispersive Jaynes-Cummings Hamiltonian including dissipation. We show that the measured system response can be used to construct a measurement operator from which the qubit population can be inferred accurately. Such a measurement operator can be used in tomographic methods to reconstruct single and multiqubit states in ensemble-averaged measurements.
AU - Bianchetti, R
AU - Filipp, Stefan
AU - Baur, Matthias P
AU - Johannes Fink
AU - Göppl, M
AU - Leek, Peter J
AU - Steffen, L. Kraig
AU - Blais, Alexandre
AU - Wallraff, Andreas
ID - 1770
IS - 4
JF - Physical Review A - Atomic, Molecular, and Optical Physics
TI - Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics
VL - 80
ER -
TY - JOUR
AB - The exceptionally strong coupling realizable between superconducting qubits and photons stored in an on-chip microwave resonator allows for the detailed study of matter-light interactions in the realm of circuit quantum electrodynamics (QED). Here we investigate the resonant interaction between a single transmon-type multilevel artificial atom and weak thermal and coherent fields. We explore up to three photon dressed states of the coupled system in a linear response heterodyne transmission measurement. The results are in good quantitative agreement with a generalized Jaynes-Cummings model. Our data indicate that the role of thermal fields in resonant cavity QED can be studied in detail using superconducting circuits.
AU - Johannes Fink
AU - Baur, Matthias P
AU - Bianchetti, R
AU - Filipp, Stefan
AU - Göppl, M
AU - Leek, Peter J
AU - Steffen, L. Kraig
AU - Blais, Alexandre
AU - Wallraff, Andreas
ID - 1771
JF - Physica Scripta T
TI - Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics
VL - T137
ER -
TY - JOUR
AB - Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus. A key mechanism that underlies this response is the slow, activity-dependent removal of responding molecules to a pool which is unavailable to respond immediately to the input. This mechanism is implemented in different ways in various biological systems and has traditionally been studied separately for each. Here we highlight the common aspects of this principle, shared by many biological systems, and suggest a unifying theoretical framework. We study theoretically a class of models which describes the general mechanism and allows us to distinguish its universal from system-specific features. We show that under general conditions, regardless of the details of kinetics, molecule availability encodes an averaging over past activity and feeds back multiplicatively on the system output. The kinetics of recovery from unavailability determines the effective memory kernel inside the feedback branch, giving rise to a variety of system-specific forms of adaptive response—precise or input-dependent, exponential or power-law—as special cases of the same model.
AU - Tamar Friedlander
AU - Brenner, Naama
ID - 1825
IS - 52
JF - PNAS
TI - Adaptive response by state-dependent inactivation
VL - 106
ER -
TY - JOUR
AB - Let (E, H, μ) be an abstract Wiener space and let DV : = V D, where D denotes the Malliavin derivative and V is a closed and densely defined operator from H into another Hilbert space under(H, {combining low line}). Given a bounded operator B on under(H, {combining low line}), coercive on the range over(R (V), -), we consider the operators A : = V* B V in H and under(A, {combining low line}) : = V V* B in under(H, {combining low line}), as well as the realisations of the operators L : = DV* B DV and under(L, {combining low line}) : = DV DV* B in Lp (E, μ) and Lp (E, μ ; under(H, {combining low line})) respectively, where 1 < p < ∞. Our main result asserts that the following four assertions are equivalent: (1)D (sqrt(L)) = D (DV) with {norm of matrix} sqrt(L) f {norm of matrix}p {minus tilde} {norm of matrix} DV f {norm of matrix}p for f ∈ D (sqrt(L));(2)under(L, {combining low line}) admits a bounded H∞-functional calculus on over(R (DV), -);(3)D (sqrt(A)) = D (V) with {norm of matrix} sqrt(A) h {norm of matrix} {minus tilde} {norm of matrix} V h {norm of matrix} for h ∈ D (sqrt(A));(4)under(A, {combining low line}) admits a bounded H∞-functional calculus on over(R (V), -). Moreover, if these conditions are satisfied, then D (L) = D (DV2) ∩ D (DA). The equivalence (1)-(4) is a non-symmetric generalisation of the classical Meyer inequalities of Malliavin calculus (where under(H, {combining low line}) = H, V = I, B = frac(1, 2) I). A one-sided version of (1)-(4), giving Lp-boundedness of the Riesz transform DV / sqrt(L) in terms of a square function estimate, is also obtained. As an application let -A generate an analytic C0-contraction semigroup on a Hilbert space H and let -L be the Lp-realisation of the generator of its second quantisation. Our results imply that two-sided bounds for the Riesz transform of L are equivalent with the Kato square root property for A. The boundedness of the Riesz transform is used to obtain an Lp-domain characterisation for the operator L.
AU - Jan Maas
AU - van Neerven, Jan M
ID - 2119
IS - 8
JF - Journal of Functional Analysis
TI - Boundedness of Riesz transforms for elliptic operators on abstract Wiener spaces
VL - 257
ER -
TY - JOUR
AB - Relying on the quantization rule of Raab and Friedrich [Phys. Rev. A (2009) in press], we derive simple and accurate formulae for the number of rotational states supported by a weakly bound vibrational level of a diatomic molecular ion. We also provide analytic estimates of the rotational constants of any such levels up to threshold for dissociation and obtain a criterion for determining whether a given weakly bound vibrational level is rotationless. The results depend solely on the long-range part of the molecular potential.
AU - Mikhail Lemeshko
AU - Frierich, Bretislav
ID - 2137
IS - 1
JF - Journal of Atomic and Molecular Sciences
TI - Rotational structure of weakly bound molecular ions
VL - 1
ER -
TY - JOUR
AB - We investigate the effects of a magnetic field on the dynamics of rotationally inelastic collisions of open-shell molecules (Σ2, Σ3, and Π2) with closed-shell atoms. Our treatment makes use of the Fraunhofer model of matter wave scattering and its recent extension to collisions in electric [M. Lemeshko and B. Friedrich, J. Chem. Phys. 129, 024301 (2008)] and radiative fields [M. Lemeshko and B. Friedrich, Int. J. Mass. Spec. 280, 19 (2009)]. A magnetic field aligns the molecule in the space-fixed frame and thereby alters the effective shape of the diffraction target. This significantly affects the differential and integral scattering cross sections. We exemplify our treatment by evaluating the magnetic-field-dependent scattering characteristics of the He-CaH (XΣ+2), He-O2 (XΣ–3), and He-OH (XΠΩ2) systems at thermal collision energies. Since the cross sections can be obtained for different orientations of the magnetic field with respect to the relative velocity vector, the model also offers predictions about the frontal-versus-lateral steric asymmetry of the collisions. The steric asymmetry is found to be almost negligible for the He-OH system, weak for the He-CaH collisions, and strong for the He-O2. While odd ΔM transitions dominate the He-OH [J=3/2,f→J′,e/f] integral cross sections in a magnetic field parallel to the relative velocity vector, even ΔM transitions prevail in the case of the He-CaH (X2Σ+) and He-O2 (XΣ−3) collision systems. For the latter system, the magnetic field opens inelastic channels that are closed in the absence of the field. These involve the transitions N=1,J=0→N′, J′ with J′=N′.
AU - Mikhail Lemeshko
AU - Friedrich, Břetislav
ID - 2149
IS - 1
JF - Physical Review A - Atomic, Molecular, and Optical Physics
TI - Collisions of paramagnetic molecules in magnetic fields: An analytic model based on Fraunhofer diffraction of matter waves
VL - 79
ER -
TY - JOUR
AB - We examine the effects of a linearly polarized nonresonant radiative field on the dynamics of rotationally inelastic Na+ + N2 collisions at eV collision energies. Our treatment is based on the Fraunhofer model of matter wave scattering and its recent extension to collisions in electric fields [M. Lemeshko, B. Friedrich, J. Chem. Phys. 129 (2008) 024301]. The nonresonant radiative field changes the effective shape of the target molecule by aligning it in the space-fixed frame. This markedly alters the differential and integral scattering cross-sections. As the cross-sections can be evaluated for a polarization of the radiative field collinear or perpendicular to the relative velocity vector, the model also offers predictions about steric asymmetry of the collisions.
AU - Mikhail Lemeshko
AU - Friedrich, Břetislav
ID - 2150
IS - 1-3
JF - International Journal of Mass Spectrometry
TI - The effect of a nonresonant radiative field on low-energy rotationally inelastic Na+ + N2 collisions
VL - 280
ER -
TY - JOUR
AB - By making use of the quantization rule of Raab and Friedrich [Phys. Rev. A 78, 022707 (2008)], we derive simple and accurate formulae for the number of rotational states supported by a weakly bound vibrational level of a diatomic molecule and the rotational constants of any such levels up to the threshold, and provide a criterion for determining whether a given weakly bound vibrational level is rotationless. The results depend solely on the long-range part of the molecular potential and are applicable to halo molecules.
AU - Mikhail Lemeshko
AU - Friedrich, Břetislav
ID - 2191
IS - 5
JF - Physical Review A - Atomic, Molecular, and Optical Physics
TI - Rotational and rotationless states of weakly bound molecules
VL - 79
ER -
TY - JOUR
AB - We develop an analytic model of thermal state-to-state rotationally inelastic collisions of asymmetric-top molecules with closed-shell atoms in electric fields and apply it to the Ar-H2O collision system. The predicted cross sections as well as the steric asymmetry of the collisions show at fields up to 150 kV/cm characteristic field-dependent features which can be experimentally tested. Particularly suitable candidates for such tests are the 000 → 220 and 101→ 221 channels, arising from the relaxation of the field-free selection rules due to the hybridization of J states by the field. Averaging over the M' product channels is found to largely obliterate the orientation effects brought about by the field.
AU - Mikhail Lemeshko
AU - Friedrich, Břetislav
ID - 2192
IS - 52
JF - Journal of Physical Chemistry A
TI - Model analysis of rotationally inelastic Ar + H2O scattering in an electric field
VL - 113
ER -
TY - JOUR
AB - We show that weakly bound molecules can be probed by "shaking" in a pulsed nonresonant laser field. The field introduces a centrifugal term which expels the highest vibrational level from the potential that binds it. Our numerical simulations applied to the Rb2 and KRb Feshbach molecules indicate that shaking by feasible laser pulses can be used to accurately recover the square of the vibrational wave function and, by inversion, also the long-range part of the molecular potential.
AU - Mikhail Lemeshko
AU - Friedrich, Břetislav
ID - 2193
IS - 5
JF - Physical Review Letters
TI - Probing weakly bound molecules with nonresonant light
VL - 103
ER -
TY - GEN
AB - We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs of [GO09] and present a precise characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems.
AU - Chatterjee, Krishnendu
ID - 5392
SN - 2664-1690
TI - Probabilistic automata on infinite words: Decidability and undecidability results
ER -
TY - GEN
AB - Gist is a tool that (a) solves the qualitative analysis problem of turn-based probabilistic games with ω-regular objectives; and (b) synthesizes reasonable environment assumptions for synthesis of unrealizable specifications. Our tool provides efficient implementations of several reduction based techniques to solve turn-based probabilistic games, and uses the analysis of turn-based probabilistic games for synthesizing environment assumptions for unrealizable specifications.
AU - Chatterjee, Krishnendu
AU - Henzinger, Thomas A
AU - Jobstmann, Barbara
AU - Radhakrishna, Arjun
ID - 5393
SN - 2664-1690
TI - Gist: A solver for probabilistic games
ER -
TY - GEN
AB - We consider two-player games played on graphs with request-response and finitary Streett objectives. We show these games are PSPACE-hard, improving the previous known NP-hardness. We also improve the lower bounds on memory required by the winning strategies for the players.
AU - Chatterjee, Krishnendu
AU - Henzinger, Thomas A
AU - Horn, Florian
ID - 5394
SN - 2664-1690
TI - Improved lower bounds for request-response and finitary Streett games
ER -
TY - GEN
AB - We study observation-based strategies for partially-observable Markov decision processes (POMDPs) with omega-regular objectives. An observation-based strategy relies on partial information about the history of a play, namely, on the past sequence of observa- tions. We consider the qualitative analysis problem: given a POMDP with an omega-regular objective, whether there is an observation-based strategy to achieve the objective with probability 1 (almost-sure winning), or with positive probability (positive winning). Our main results are twofold. First, we present a complete picture of the computational complexity of the qualitative analysis of POMDPs with parity objectives (a canonical form to express omega-regular objectives) and its subclasses. Our contribution consists in establishing several upper and lower bounds that were not known in literature. Second, we present optimal bounds (matching upper and lower bounds) on the memory required by pure and randomized observation-based strategies for the qualitative analysis of POMDPs with parity objectives and its subclasses.
AU - Chatterjee, Krishnendu
AU - Doyen, Laurent
AU - Henzinger, Thomas A
ID - 5395
SN - 2664-1690
TI - Qualitative analysis of partially-observable Markov decision processes
ER -
TY - JOUR
AB - The human CDK8 subcomplex (CDK8, cyclin C, Med12, and Med13) negatively regulates transcription in ways not completely defined; past studies suggested CDK8 kinase activity was required for its repressive function. Using a reconstituted transcription system together with recombinant or endogenous CDK8 subcomplexes, we demonstrate that, in fact, Med12 and Med13 are critical for subcomplex-dependent repression, whereas CDK8 kinase activity is not. A hallmark of activated transcription is efficient reinitiation from promoter-bound scaffold complexes that recruit a series of pol II enzymes to the gene. Notably, the CDK8 submodule strongly represses even reinitiation events, suggesting a means to fine tune transcript levels. Structural and biochemical studies confirm the CDK8 submodule binds the Mediator leg/tail domain via the Med13 subunit, and this submodule-Mediator association precludes pol II recruitment. Collectively, these results reveal the CDK8 subcomplex functions as a simple switch that controls the Mediator-pol II interaction to help regulate transcription initiation and reinitiation events. As Mediator is generally required for expression of protein-coding genes, this may reflect a common mechanism by which activated transcription is shut down in human cells.
AU - Knuesel, Matthew
AU - Meyer, Krista
AU - Bernecky, Carrie A
AU - Taatjes, Dylan
ID - 599
IS - 4
JF - Genes and Development
TI - The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function
VL - 23
ER -
TY - CHAP
AB - Let g be a cubic polynomial with integer coefficients and n>9 variables, and assume that the congruence g=0 modulo p^k is soluble for all prime powers p^k. We show that the equation g=0 has infinitely many integer solutions when the cubic part of g defines a projective hypersurface with singular locus of dimension <n-10. The proof is based on the Hardy-Littlewood circle method.
AU - Browning, Timothy D
AU - Heath Brown, Roger
ID - 164
T2 - Analytic Number Theory: Essays in honour of Klaus Roth
TI - Integral points on cubic hypersurfaces
ER -
TY - JOUR
AB - One possible way to produce ultra-cold, high-phase-space-density quantum gases of molecules in the rovibronic ground state is given by molecule association from quantum-degenerate atomic gases on a Feshbach resonance and subsequent coherent optical multi-photon transfer into the rovibronic ground state. In ultra-cold samples of Cs2 molecules, we observe two-photon dark resonances that connect the intermediate rovibrational level |v=73,J=2 with the rovibrational ground state |v=0,J=0 of the singlet X 1 ∑ g + ground-state potential. For precise dark resonance spectroscopy we exploit the fact that it is possible to efficiently populate the level |v=73,J=2 by two-photon transfer from the dissociation threshold with the stimulated Raman adiabatic passage (STIRAP) technique. We find that at least one of the two-photon resonances is sufficiently strong to allow future implementation of coherent STIRAP transfer of a molecular quantum gas to the rovibrational ground state |v=0,J=0.
AU - Mark, Manfred
AU - Danzl, Johann G
AU - Haller, Elmar
AU - Gustavsson, Mattias
AU - Bouloufa, Nadia
AU - Dulieu, Olivier
AU - Salami, Houssam
AU - Bergeman, Thomas
AU - Ritsch, Helmut
AU - Hart, Russell
AU - Nägerl, Hanns
ID - 1038
IS - 2
JF - Applied Physics B: Lasers and Optics
TI - Dark resonances for ground-state transfer of molecular quantum gases
VL - 95
ER -
TY - JOUR
AB - Ultracold atomic physics offers myriad possibilities to study strongly correlated many-body systems in lower dimensions. Typically, only ground-state phases are accessible. Using a tunable quantum gas of bosonic cesium atoms, we realized and controlled in one-dimensional geometry a highly excited quantum phase that is stabilized in the presence of attractive interactions by maintaining and strengthening quantum correlations across a confinement-induced resonance. We diagnosed the crossover from repulsive to attractive interactions in terms of the stiffness and energy of the system. Our results open up the experimental study of metastable, excited, many-body phases with strong correlations and their dynamical properties.
AU - Haller, Elmar
AU - Gustavsson, Mattias
AU - Mark, Manfred
AU - Danzl, Johann G
AU - Hart, Russell
AU - Pupillo, Guido
AU - Nägerl, Hanns
ID - 1040
IS - 5945
JF - Science
TI - Realization of an excited, strongly correlated quantum gas Phase
VL - 325
ER -
TY - JOUR
AB - We demonstrate efficient transfer of ultracold molecules into a deeply bound rovibrational level of the singlet ground state potential in the presence of an optical lattice. The overall molecule creation efficiency is 25%, and the transfer efficiency to the rovibrational level |v = 73, J = 2) is above 80%. We find that the molecules in |v = 73, J = 2) are trapped in the optical lattice, and that the lifetime in the lattice is limited by optical excitation by the lattice light. The molecule trapping time for a lattice depth of 15 atomic recoil energies is about 20 ms. We determine the trapping frequency by the lattice phase and amplitude modulation technique. It will now be possible to transfer the molecules to the rovibrational ground state |v = 0, J = 0) in the presence of the optical lattice.
AU - Danzl, Johann G
AU - Mark, Manfred
AU - Haller, Elmar
AU - Gustavsson, Mattias
AU - Hart, Russell
AU - Liem, Andreas
AU - Zellmer, Holger
AU - Nägerl, Hanns
ID - 1041
JF - New Journal of Physics
TI - Deeply bound ultracold molecules in an optical lattice
VL - 11
ER -
TY - JOUR
AB - One possibility for the creation of ultracold, high phase space density quantum gases of molecules in the rovibronic ground state relies on first associating weakly-bound molecules from quantum-degenerate atomic gases on a Feshbach resonance and then transferring the molecules via several steps of coherent two-photon stimulated Raman adiabatic passage (STIRAP) into the rovibronic ground state. Here, in ultracold samples of Cs2 Feshbach molecules produced out of ultracold samples of Cs atoms, we observe several optical transitions to deeply-bound rovibrational levels of the excited 0 u+ molecular potentials with high resolution. At least one of these transitions, although rather weak, allows efficient STIRAP transfer into the deeply-bound vibrational level v = 73> of the singlet X 1Σg+ ground state potential, as recently demonstrated (J. G. Danzl, E. Haller, M. Gustavsson, M. J. Mark, R. Hart, N. Bouloufa, O. Dulieu, H. Ritsch, and H.-C. Nägerl, Science, 2008, 321, 1062). From this level, the rovibrational ground state v = 0, J = 0> can be reached with one more transfer step. In total, our results show that coherent ground state transfer for Cs2 is possible using a maximum of two successive two-photon STIRAP processes or one single four-photon STIRAP process.
AU - Danzl, Johann G
AU - Mark, Manfred
AU - Haller, Elmar
AU - Gustavsson, Mattias
AU - Bouloufa, Nadia
AU - Dulieu, Olivier
AU - Ritsch, Helmut
AU - Hart, Russell
AU - Nägerl, Hanns
ID - 1043
JF - Faraday Discussions
TI - Precision molecular spectroscopy for ground state transfer of molecular quantum gases
VL - 142
ER -
TY - JOUR
AB - As part of an ongoing effort to develop a parameterization of wave-induced abyssal mixing, the authors derive an heuristic model for nonlinear wave breaking and energy dissipation associated with internal tides. Then the saturation and dissipation of internal tides for idealized and observed topography samples are investigated. One of the main results is that the wave-induced mixing could be more intense and more confined to the bottom than previously assumed in numerical models. Furthermore, in this model wave breaking and mixing clearly depend on the small scales of the topography below 10 km or so, which is below the current resolution of global bathymetry. This motivates the use of a statistical approach to represent the unresolved topography when addressing the role of internal tides in mixing the deep ocean.
AU - MULLER, Caroline J
AU - Bühler, Oliver
ID - 9147
IS - 9
JF - Journal of Physical Oceanography
KW - Oceanography
SN - 1520-0485
TI - Saturation of the internal tides and induced mixing in the abyssal ocean
VL - 39
ER -
TY - JOUR
AB - Several observational studies have shown a tight relationship between tropical precipitation and column‐integrated water vapor. We show that the observed relationship in the tropics between column‐integrated water vapor, precipitation, and its variance can be qualitatively reproduced by a simple and physically motivated two‐layer model. It has previously been argued that features of this relationship could be explained by analogy with the theory of continuous phase transitions. Instead, our model explicitly assumes that the onset of precipitation is governed by a stability threshold involving boundary‐layer water vapor. This allows us to explain the precipitation‐humidity relationship over a broader range of water vapor values, and may explain the observed temperature dependence of the relationship.
AU - MULLER, Caroline J
AU - Back, Larissa E.
AU - O'Gorman, Paul A.
AU - Emanuel, Kerry A.
ID - 9148
IS - 16
JF - Geophysical Research Letters
KW - General Earth and Planetary Sciences
KW - Geophysics
SN - 0094-8276
TI - A model for the relationship between tropical precipitation and column water vapor
VL - 36
ER -
TY - GEN
AB - Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the salamander retina responding to natural movies. We show that pairwise interactions between neurons account for observed higher-order correlations, and that for groups of 10 or more neurons pairwise interactions can no longer be regarded as small perturbations in an independent system. We then construct network ensembles that generalize the network instances observed in the experiment, and study their thermodynamic behavior and coding capacity. Based on this construction, we can also create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses. We examine closely two such behaviors that could be relevant for neural code: tuning of the network to the critical point to maximize the ability to encode diverse stimuli, and using the metastable states of the Ising Hamiltonian as neural code words.
AU - Gasper Tkacik
AU - Schneidman, Elad
AU - Berry, Michael J
AU - Bialek, William S
ID - 3732
T2 - ArXiv
TI - Spin glass models for a network of real neurons
VL - q-bio.NC
ER -
TY - JOUR
AB - There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, View the MathML source, tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, SH, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum View the MathML source gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is View the MathML source; this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large SΩ), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits.
AU - Barton, Nicholas H
AU - Coe, Jason
ID - 3775
IS - 2
JF - Journal of Theoretical Biology
TI - On the application of statistical physics to evolutionary biology
VL - 259
ER -
TY - JOUR
AB - Why are sinistral snails so rare? Two main hypotheses are that selection acts against the establishment of new coiling morphs, because dextral and sinistral snails have trouble mating, or else a developmental constraint prevents the establishment of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in which sinistrals are rare, and populations of Partula suturalis, in which sinistrals are common, as well as a mathematical model, to understand the circumstances by which new morphs evolve. The main finding is that the sinistral genotype is associated with reduced egg viability in L. stagnalis, but in P. suturalis individuals of sinistral and dextral genotype appear equally fecund, implying a lack of a constraint. As positive frequency-dependent selection against the rare chiral morph in P. suturalis also operates over a narrow range (< 3%), the results suggest a model for chiral evolution in snails in which weak positive frequency-dependent selection may be overcome by a negative frequency-dependent selection, such as reproductive character displacement. In snails, there is not always a developmental constraint. As the direction of cleavage, and thus the directional asymmetry of the entire body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans, sipunculids and nemerteans), it remains an open question as to whether this is because of a constraint and/or because most taxa do not have a conspicuous external asymmetry (like a shell) upon which selection can act.
AU - Davison, Angus
AU - Barton, Nicholas H
AU - Clarke, Bryan
ID - 3780
IS - 8
JF - Journal of Evolutionary Biology
TI - The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails
VL - 22
ER -
TY - CONF
AB - In this paper we extend the work of Alfaro, Henzinger et al. on interface theories for component-based design. Existing interface theories often fail to capture functional relations between the inputs and outputs of an interface. For example, a simple synchronous interface that takes as input a number n ≥ 0 and returns, at the same time, as output n + 1, cannot be expressed in existing theories. In this paper we provide a theory of relational interfaces, where such input-output relations can be captured. Our theory supports synchronous interfaces, both stateless and stateful. It includes explicit notions of environments and pluggability, and satisfies fundamental properties such as preservation of refinement by composition, and characterization of pluggability by refinement. We achieve these properties by making reasonable restrictions on feedback loops in interface compositions.
AU - Tripakis, Stavros
AU - Lickly, Ben
AU - Henzinger, Thomas A
AU - Lee, Edward
ID - 3837
T2 - EMSOFT '09 Proceedings of the seventh ACM international conference on Embedded software
TI - On relational interfaces
ER -
TY - CONF
AB - We compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. These languages —matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models— all describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, ease of use, and the support they provide for checking the well-formedness of a model and for analyzing a model.
AU - Henzinger, Thomas A
AU - Jobstmann, Barbara
AU - Wolf, Verena
ID - 3841
TI - Formalisms for specifying Markovian population models
VL - 5797
ER -