A Smooth Transition from Powerlessness to Absolute Power

We study the phase transition of the coalitional manipulation problem for generalized scoring rules. Previously it has been shown that, under some conditions on the distribution of votes, if the number of manipulators is $o(\sqrt{n})$, where $n$ is the number of voters, then the probability that a random profile is manipulable by the coalition goes to zero as the number of voters goes to infinity, whereas if the number of manipulators is $\omega(\sqrt{n})$, then the probability that a random profile is manipulable goes to one. Here we consider the critical window, where a coalition has size $c\sqrt{n}$, and we show that as $c$ goes from zero to infinity, the limiting probability that a random profile is manipulable goes from zero to one in a smooth fashion, i.e., there is a smooth phase transition between the two regimes. This result analytically validates recent empirical results, and suggests that deciding the coalitional manipulation problem may be of limited computational hardness in practice.Comment: 22 pages; v2 contains minor changes and corrections; v3 contains minor changes after comments of reviewer

Magnetic Monopole in Noncommutative Space-Time and Wu-Yang Singularity-Free Gauge Transformations

We investigate the validity of the Dirac Quantization Condition (DQC) for magnetic monopoles in noncommutative space-time. We use an approach which is based on an extension of the method introduced by Wu and Yang. To study the effects of noncommutativity of space-time, we consider the gauge transformations of $U_\star(1)$ gauge fields and use the corresponding deformed Maxwell's equations. Using a perturbation expansion in the noncommutativity parameter $\theta$, we show that the DQC remains unmodified up to the first order in the expansion parameter. The result is obtained for a class of noncommutative source terms, which reduce to the Dirac delta function in the commutative limit.Comment: 18 pages. Relation to relevant literature clarified in the conclusions, 6 references adde

Differential freezeout and pion interferometry at RHIC from covariant transport theory

Puzzling discrepancies between recent pion interferometry data on Au+Au reactions at s^1/2 = 130 and 200 AGeV from RHIC and predictions based on ideal hydrodynamics are analyzed in terms of covariant parton transport theory. The discrepancies of out and longitudinal radii are significantly reduced when the finite opacity of the gluon plasma is taken into account.Comment: 4 pages, 3 EPS figures. Submitted to PR

Universal Flow-Driven Conical Emission in Ultrarelativistic Heavy-Ion Collisions

The double-peak structure observed in soft-hard hadron correlations is commonly interpreted as a signature for a Mach cone generated by a supersonic jet interacting with the hot and dense medium created in ultrarelativistic heavy-ion collisions. We show that it can also arise due to averaging over many jet events in a transversally expanding background. We find that the jet-induced away-side yield does not depend on the details of the energy-momentum deposition in the plasma, the jet velocity, or the system size. Our claim can be experimentally tested by comparing soft-hard correlations induced by heavy-flavor jets with those generated by light-flavor jets.Comment: 4 pages, 3 figure

Near Zone Navier-Stokes Analysis of Heavy Quark Jet Quenching in an N\mathcal{N} =4 SYM Plasma

The near zone energy-momentum tensor of a supersonic heavy quark jet moving through a strongly-coupled $\mathcal{N}=4$ SYM plasma is analyzed in terms of first-order Navier-Stokes hydrodynamics. It is shown that the hydrodynamical description of the near quark region worsens with increasing quark velocities. For realistic quark velocities, $v=0.99$, the non-hydrodynamical region is located at a narrow band surrounding the quark with a width of approximately $3/\pi T$ in the direction parallel to the quark's motion and with a length of roughly $10/\pi T$ in the perpendicular direction. Our results can be interpreted as an indication of the presence of coherent Yang-Mills fields where deviation from hydrodynamics is at its maximum. In the region where hydrodynamics does provide a good description of the system's dynamics, the flow velocity is so small that all the nonlinear terms can be dropped. Our results, which are compatible with the thermalization timescales extracted from elliptic flow measurements, suggest that if AdS/CFT provides a good description of the RHIC system, the bulk of the quenched jet energy has more than enough time to locally thermalize and become encoded in the collective flow. The resulting flow pattern close to the quark, however, is shown to be considerably different than the superposition of Mach cones and diffusion wakes observed at large distances.Comment: new revised version, 11 figures, as published in PR

Ellipsoid Localisation Microscopy

Multilayered protein coats are crucial to the dormancy, robustness, and germination of bacterial spores. In Bacillus subtilis spores, the coat contains over 70 distinct proteins. Identifying which proteins reside in each layer may provide insight into their distinct functions. We present image analysis methods that determine the order and geometry of concentric protein layers by fitting a model description for a spheroidal fluorescent shell image to optical micrographs of spores incorporating fluorescent fusion proteins. The radius of a spherical protein shell can be determined with <10 nm error by fitting an equation to widefield fluorescence micrographs. Ellipsoidal shell axes can be fitted with comparable precision. The layer orders inferred for B. subtilis and B. megaterium are consistent with measurements in the literature. The aspect ratio of elongated spores and the tendency of some proteins to localize near their poles can be quantified, enabling measurement of structural anisotropy.We gratefully acknowledge support from MedImmune through the Beacon collaboration, the EPSRC Centre for Doctoral Training in Sensor Technologies and Applications (EP/L015889/1), and thank Clemens Kaminski, Romain Laine and Jose Casas-Finet for inspiring discussions.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.bpj.2015.09.02

High pTp_T Azimuthal Asymmetry in Non-central A+A at RHIC

The high $p_{\rm T}>3$ GeV azimuthal asymmetry, $v_2(p_{\rm T})$, in non-central nuclear collisions at RHIC is shown to be a sensitive measure of the initial parton density distribution of the produced quark-gluon plasma. A generalization of the Gyulassy-Levai-Vitev (GLV) non-abelian energy loss formalism including Bjorken 1+1D expansion as well as important kinematic constraints is used.Comment: 4 pages, Revtex, bbox.sty, 4 eps figures, references added, minor corrections, Phys.Rev.Lett versio

Dirac Quantization Condition for Monopole in Noncommutative Space-Time

Since the structure of space-time at very short distances is believed to get modified possibly due to noncommutativity effects and as the Dirac Quantization Condition (DQC), $\mu e = \frac{N}{2}\hbar c$, probes the magnetic field point singularity, a natural question arises whether the same condition will still survive. We show that the DQC on a noncommutative space in a model of dynamical noncommutative quantum mechanics remains the same as in the commutative case to first order in the noncommutativity parameter $\theta$, leading to the conjecture that the condition will not alter in higher orders.Comment: 11 page

Testing the Resolving Power of 2-D K^+ K^+ Interferometry

Adopting a procedure previously proposed to quantitatively study two-dimensional pion interferometry, an equivalent 2-D chi^2 analysis was performed to test the resolving power of that method when applied to less favorable conditions, i.e., if no significant contribution from long lived resonances is expected, as in kaon interferometry. For that purpose, use is made of the preliminary E859 K^+ K^+ interferometry data from Si+Au collisions at 14.6 AGeV/c. As expected, less sensitivity is achieved in the present case, although it still is possible to distinguish two distinct decoupling geometries. The present analysis seems to favor scenarios with no resonance formation at the AGS energy range, if the preliminary K^+ K^+ data are confirmed. The possible compatibility of data with zero decoupling proper time interval, conjectured by the 3-D experimental analysis, is also investigated and is ruled out when considering more realistic dynamical models with expanding sources. These results, however, clearly evidence the important influence of the time emission interval on the source effective transverse dimensions. Furthermore, they strongly emphasize that the static Gaussian parameterization, commonly used to fit data, cannot be trusted under more realistic conditions, leading to distorted or even wrong interpretation of the source parameters!Comment: 11 pages, RevTeX, 4 Postscript figures include

Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability

Bryan S. Der, Ron Jacak, Brian Kuhlman, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of AmericaChristien Kluwe, Aleksandr E. Miklos, Andrew D. Ellington , Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of AmericaChristien Kluwe, Aleksandr E. Miklos, George Georgiou, Andrew D. Ellington, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of AmericaAleksandr E. Miklos, Andrew D. Ellington , Applied Research Laboratories, University of Texas at Austin, Austin, Texas, United States of AmericaSergey Lyskov, Jeffrey J. Gray, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of AmericaBrian Kuhlman, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of AmericaReengineering protein surfaces to exhibit high net charge, referred to as “supercharging”, can improve reversibility of unfolding by preventing aggregation of partially unfolded states. Incorporation of charged side chains should be optimized while considering structural and energetic consequences, as numerous mutations and accumulation of like-charges can also destabilize the native state. A previously demonstrated approach deterministically mutates flexible polar residues (amino acids DERKNQ) with the fewest average neighboring atoms per side chain atom (AvNAPSA). Our approach uses Rosetta-based energy calculations to choose the surface mutations. Both protocols are available for use through the ROSIE web server. The automated Rosetta and AvNAPSA approaches for supercharging choose dissimilar mutations, raising an interesting division in surface charging strategy. Rosetta-supercharged variants of GFP (RscG) ranging from −11 to −61 and +7 to +58 were experimentally tested, and for comparison, we re-tested the previously developed AvNAPSA-supercharged variants of GFP (AscG) with +36 and −30 net charge. Mid-charge variants demonstrated ~3-fold improvement in refolding with retention of stability. However, as we pushed to higher net charges, expression and soluble yield decreased, indicating that net charge or mutational load may be limiting factors. Interestingly, the two different approaches resulted in GFP variants with similar refolding properties. Our results show that there are multiple sets of residues that can be mutated to successfully supercharge a protein, and combining alternative supercharge protocols with experimental testing can be an effective approach for charge-based improvement to refolding.This work was supported by the Defense Advanced Research Projects Agency (HR-0011-10-1-0052 to A.E.) and the Welch Foundation (F-1654 to A.E.), the National Institutes of Health grants GM073960 (B.K.) and R01-GM073151 (J.G. and S.L.), the Rosetta Commons (S.L.), the National Science Foundation graduate research fellowship (2009070950 to B.D.), the UNC Royster Society Pogue fellowship (B.D.), and National Institutes of Health grant T32GM008570 for the UNC Program in Molecular and Cellular Biophysics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Center for Systems and Synthetic BiologyCellular and Molecular BiologyApplied Research LaboratoriesEmail: [email protected]