A weakly nonlinear analysis of the magnetorotational instability in a model channel flow

We show by means of a perturbative weakly nonlinear analysis that the axisymmetric magnetorotational instability (MRI) of a viscous, resistive, incompressible rotating shear flow in a thin channel gives rise to a real Ginzburg-Landau equation for the disturbance amplitude. For small magnetic Prandtl number (${\cal P}_{\rm m}$), the saturation amplitude is $\propto \sqrt{{\cal P}_{\rm m}}$ and the resulting momentum transport scales as ${\cal R}^{-1}$, where $\cal R$ is the {\em hydrodynamic} Reynolds number. Simplifying assumptions, such as linear shear base flow, mathematically expedient boundary conditions and continuous spectrum of the vertical linear modes, are used to facilitate this analysis. The asymptotic results are shown to comply with numerical calculations using a spectral code. They suggest that the transport due to the nonlinearly developed MRI may be very small in experimental setups with ${\cal P}_{\rm m} \ll 1$.Comment: Accepted to Physical Review Letters - Nov. 30, 2006. In final for

Effects of dissipation in an adiabatic quantum search algorithm

We consider the effect of two different environments on the performance of the quantum adiabatic search algorithm, a thermal bath at finite temperature, and a structured environment similar to the one encountered in systems coupled to the electromagnetic field that exists within a photonic crystal. While for all the parameter regimes explored here, the algorithm performance is worsened by the contact with a thermal environment, the picture appears to be different when considering a structured environment. In this case we show that, by tuning the environment parameters to certain regimes, the algorithm performance can actually be improved with respect to the closed system case. Additionally, the relevance of considering the dissipation rates as complex quantities is discussed in both cases. More particularly, we find that the imaginary part of the rates can not be neglected with the usual argument that it simply amounts to an energy shift, and in fact influences crucially the system dynamics.Comment: 18 pages, 9 figure

Improved Error-Scaling for Adiabatic Quantum State Transfer

We present a technique that dramatically improves the accuracy of adiabatic state transfer for a broad class of realistic Hamiltonians. For some systems, the total error scaling can be quadratically reduced at a fixed maximum transfer rate. These improvements rely only on the judicious choice of the total evolution time. Our technique is error-robust, and hence applicable to existing experiments utilizing adiabatic passage. We give two examples as proofs-of-principle, showing quadratic error reductions for an adiabatic search algorithm and a tunable two-qubit quantum logic gate.Comment: 10 Pages, 4 figures. Comments are welcome. Version substantially revised to generalize results to cases where several derivatives of the Hamiltonian are zero on the boundar

Quantum algorithm for the Boolean hidden shift problem

The hidden shift problem is a natural place to look for new separations between classical and quantum models of computation. One advantage of this problem is its flexibility, since it can be defined for a whole range of functions and a whole range of underlying groups. In a way, this distinguishes it from the hidden subgroup problem where more stringent requirements about the existence of a periodic subgroup have to be made. And yet, the hidden shift problem proves to be rich enough to capture interesting features of problems of algebraic, geometric, and combinatorial flavor. We present a quantum algorithm to identify the hidden shift for any Boolean function. Using Fourier analysis for Boolean functions we relate the time and query complexity of the algorithm to an intrinsic property of the function, namely its minimum influence. We show that for randomly chosen functions the time complexity of the algorithm is polynomial. Based on this we show an average case exponential separation between classical and quantum time complexity. A perhaps interesting aspect of this work is that, while the extremal case of the Boolean hidden shift problem over so-called bent functions can be reduced to a hidden subgroup problem over an abelian group, the more general case studied here does not seem to allow such a reduction.Comment: 10 pages, 1 figur

High-resolution interrogation of functional elements in the noncoding genome

The noncoding genome affects gene regulation and disease, yet we lack tools for rapid identification and manipulation of noncoding elements. We developed a CRISPR screen using ∼18,000 single guide RNAs targeting > 700 kilobases surrounding the genes NF1, NF2, and CUL3, which are involved in BRAF inhibitor resistance in melanoma. We find that noncoding locations that modulate drug resistance also harbor predictive hallmarks of noncoding function. With a subset of regions at the CUL3 locus, we demonstrate that engineered mutations alter transcription factor occupancy and long-range and local epigenetic environments, implicating these sites in gene regulation and chemotherapeutic resistance. Through our expansion of the potential of pooled CRISPR screens, we provide tools for genomic discovery and for elucidating biologically relevant mechanisms of gene regulation.National Institutes of Health (U.S.) (Award F32-DK096822)National Institute of Mental Health (U.S.) (Grant 5DP1-MH100706)National Institute of Mental Health (U.S.) (Grant 1R01-MH110049

Regulatory control and the costs and benefits of biochemical noise

Experiments in recent years have vividly demonstrated that gene expression can be highly stochastic. How protein concentration fluctuations affect the growth rate of a population of cells, is, however, a wide open question. We present a mathematical model that makes it possible to quantify the effect of protein concentration fluctuations on the growth rate of a population of genetically identical cells. The model predicts that the population's growth rate depends on how the growth rate of a single cell varies with protein concentration, the variance of the protein concentration fluctuations, and the correlation time of these fluctuations. The model also predicts that when the average concentration of a protein is close to the value that maximizes the growth rate, fluctuations in its concentration always reduce the growth rate. However, when the average protein concentration deviates sufficiently from the optimal level, fluctuations can enhance the growth rate of the population, even when the growth rate of a cell depends linearly on the protein concentration. The model also shows that the ensemble or population average of a quantity, such as the average protein expression level or its variance, is in general not equal to its time average as obtained from tracing a single cell and its descendants. We apply our model to perform a cost-benefit analysis of gene regulatory control. Our analysis predicts that the optimal expression level of a gene regulatory protein is determined by the trade-off between the cost of synthesizing the regulatory protein and the benefit of minimizing the fluctuations in the expression of its target gene. We discuss possible experiments that could test our predictions.Comment: Revised manuscript;35 pages, 4 figures, REVTeX4; to appear in PLoS Computational Biolog

Chosen-ciphertext security from subset sum

We construct a public-key encryption (PKE) scheme whose security is polynomial-time equivalent to the hardness of the Subset Sum problem. Our scheme achieves the standard notion of indistinguishability against chosen-ciphertext attacks (IND-CCA) and can be used to encrypt messages of arbitrary polynomial length, improving upon a previous construction by Lyubashevsky, Palacio, and Segev (TCC 2010) which achieved only the weaker notion of semantic security (IND-CPA) and whose concrete security decreases with the length of the message being encrypted. At the core of our construction is a trapdoor technique which originates in the work of Micciancio and Peikert (Eurocrypt 2012

Magnetically Torqued Thin Accretion Disks

We compute the properties of a geometrically thin, steady accretion disk surrounding a central rotating, magnetized star. The magnetosphere is assumed to entrain the disk over a wide range of radii. The model is simplified in that we adopt two (alternate) ad hoc, but plausible, expressions for the azimuthal component of the magnetic field as a function of radial distance. We find a solution for the angular velocity profile tending to corotation close to the central star, and smoothly matching a Keplerian curve at a radius where the viscous stress vanishes. The value of this ''transition'' radius is nearly the same for both of our adopted B-field models. We then solve analytically for the torques on the central star and for the disk luminosity due to gravity and magnetic torques. When expressed in a dimensionless form, the resulting quantities depend on one parameter alone, the ratio of the transition radius to the corotation radius. For rapid rotators, the accretion disk may be powered mostly by spin-down of the central star. These results are independent of the viscosity prescription in the disk. We also solve for the disk structure for the special case of an optically thick alpha disk. Our results are applicable to a range of astrophysical systems including accreting neutron stars, intermediate polar cataclysmic variables, and T Tauri systems.Comment: 9 sharper figs, updated reference

The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells

The transcription factor BATF is required for interleukin 17 (IL-17)-producing helper T cell (TH17) and follicular helper T cell (TFH) differentiation. Here, we show that BATF also has a fundamental role in regulating effector CD8+ T cell differentiation. BATF-deficient CD8+ T cells show profound defects in effector expansion and undergo proliferative and metabolic catastrophe early after antigen encounter. BATF, together with IRF4 and Jun proteins, binds to and promotes early expression of genes encoding lineage-specific transcription-factors (T-bet and Blimp-1) and cytokine receptors, while paradoxically repressing genes encoding effector molecules (IFN-γ and granzyme B). Thus, BATF amplifies TCR-dependent transcription factor expression and augments inflammatory signal propagation but restrains effector gene expression. This checkpoint prevents irreversible commitment to an effector fate until a critical threshold of downstream transcriptional activity has been achieved

Quantum hypercomputation based on the dynamical algebra su(1,1)

An adaptation of Kieu's hypercomputational quantum algorithm (KHQA) is presented. The method that was used was to replace the Weyl-Heisenberg algebra by other dynamical algebra of low dimension that admits infinite-dimensional irreducible representations with naturally defined generalized coherent states. We have selected the Lie algebra $\mathfrak{su}(1,1)$, due to that this algebra posses the necessary characteristics for to realize the hypercomputation and also due to that such algebra has been identified as the dynamical algebra associated to many relatively simple quantum systems. In addition to an algebraic adaptation of KHQA over the algebra $\mathfrak{su}(1,1)$, we presented an adaptations of KHQA over some concrete physical referents: the infinite square well, the infinite cylindrical well, the perturbed infinite cylindrical well, the P{\"o}sch-Teller potentials, the Holstein-Primakoff system, and the Laguerre oscillator. We conclude that it is possible to have many physical systems within condensed matter and quantum optics on which it is possible to consider an implementation of KHQA.Comment: 25 pages, 1 figure, conclusions rewritten, typing and language errors corrected and latex format changed minor changes elsewhere and