Inferring hidden Markov models from noisy time sequences: a method to alleviate degeneracy in molecular dynamics

We present a new method for inferring hidden Markov models from noisy time sequences without the necessity of assuming a model architecture, thus allowing for the detection of degenerate states. This is based on the statistical prediction techniques developed by Crutchfield et al., and generates so called causal state models, equivalent to hidden Markov models. This method is applicable to any continuous data which clusters around discrete values and exhibits multiple transitions between these values such as tethered particle motion data or Fluorescence Resonance Energy Transfer (FRET) spectra. The algorithms developed have been shown to perform well on simulated data, demonstrating the ability to recover the model used to generate the data under high noise, sparse data conditions and the ability to infer the existence of degenerate states. They have also been applied to new experimental FRET data of Holliday Junction dynamics, extracting the expected two state model and providing values for the transition rates in good agreement with previous results and with results obtained using existing maximum likelihood based methods.Comment: 19 pages, 9 figure

The order of the quantum chromodynamics transition predicted by the standard model of particle physics

We determine the nature of the QCD transition using lattice calculations for physical quark masses. Susceptibilities are extrapolated to vanishing lattice spacing for three physical volumes, the smallest and largest of which differ by a factor of five. This ensures that a true transition should result in a dramatic increase of the susceptibilities.No such behaviour is observed: our finite-size scaling analysis shows that the finite-temperature QCD transition in the hot early Universe was not a real phase transition, but an analytic crossover (involving a rapid change, as opposed to a jump, as the temperature varied). As such, it will be difficult to find experimental evidence of this transition from astronomical observations.Comment: 7 pages, 4 figure

Fermions and Type IIB Supergravity On Squashed Sasaki-Einstein Manifolds

We discuss the dimensional reduction of fermionic modes in a recently found class of consistent truncations of type IIB supergravity compactified on squashed five-dimensional Sasaki-Einstein manifolds. We derive the lower dimensional equations of motion and effective action, and comment on the supersymmetry of the resulting theory, which is consistent with N=4 gauged supergravity in $d=5$, coupled to two vector multiplets. We compute fermion masses by linearizing around two $AdS_{5}$ vacua of the theory: one that breaks N=4 down to N=2 spontaneously, and a second one which preserves no supersymmetries. The truncations under consideration are noteworthy in that they retain massive modes which are charged under a U(1) subgroup of the $R$-symmetry, a feature that makes them interesting for applications to condensed matter phenomena via gauge/gravity duality. In this light, as an application of our general results we exhibit the coupling of the fermions to the type IIB holographic superconductor, and find a consistent further truncation of the fermion sector that retains a single spin-1/2 mode.Comment: 43 pages, 2 figures, PDFLaTeX; v2: added references, typos corrected, minor change

Organic aerosol formation downwind from the Deepwater Horizon oil spill.

A large fraction of atmospheric aerosols are derived from organic compounds with various volatilities. A National Oceanic and Atmospheric Administration (NOAA) WP-3D research aircraft made airborne measurements of the gaseous and aerosol composition of air over the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico that occurred from April to August 2010. A narrow plume of hydrocarbons was observed downwind of DWH that is attributed to the evaporation of fresh oil on the sea surface. A much wider plume with high concentrations of organic aerosol (>25 micrograms per cubic meter) was attributed to the formation of secondary organic aerosol (SOA) from unmeasured, less volatile hydrocarbons that were emitted from a wider area around DWH. These observations provide direct and compelling evidence for the importance of formation of SOA from less volatile hydrocarbons

The interface between silicon and a high-k oxide

The ability to follow Moore's Law has been the basis of the tremendous success of the semiconductor industry in the past decades. To date, the greatest challenge for device scaling is the required replacement of silicon dioxide-based gate oxides by high-k oxides in transistors. Around 2010 high-k oxides are required to have an atomically defined interface with silicon without any interfacial SiO2 layer. The first clean interface between silicon and a high-K oxide has been demonstrated by McKee et al. Nevertheless, the interfacial structure is still under debate. Here we report on first-principles calculations of the formation of the interface between silicon and SrTiO3 and its atomic structure. Based on insights into how the chemical environment affects the interface, a way to engineer seemingly intangible electrical properties to meet technological requirements is outlined. The interface structure and its chemistry provide guidance for the selection process of other high-k gate oxides and for controlling their growth. Our study also shows that atomic control of the interfacial structure can dramatically improve the electronic properties of the interface. The interface presented here serves as a model for a variety of other interfaces between high-k oxides and silicon.Comment: 10 pages, 2 figures (one color

Negative emotions in informal feedback: The benefits of disappointment and drawbacks of anger

Using the emotions as social information (EASI) model, this study investigated the emotional, attitudinal and behavioral reactions to failure feedback by manipulating negative emotional displays (angry, disappointed or none) and the position level and relational distance of the feedback source. Undergraduate students (N = 260) responded to an organizational failure feedback vignette and completed a subsequent performance task. Results demonstrated that guilt was the complementary emotional experience following displays of disappointment, while reciprocal anger followed displays of anger. These emotional reactions served as important mediators between the emotional displays paired with the feedback message and participant responses of social behaviors, creative task performance and perceptions of the feedback source. In addition, our findings indicated that negative emotions can have positive organizational and interpersonal outcomes. Guilt in response to disappointed displays resulted in beneficial behaviors and attitudes, while anger in response to angry displays was socially detrimental. The emotion displayed during feedback provision also served as a consistent contextual factor that did not interact with the position level or relational distance of the feedback source to impact behavioral and attitudinal reactions. Overall, this study indicates that discrete negative emotions have unique social-functional properties that require further investigation.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

Schr\"odinger Deformations of AdS_3 x S^3

We study Schr\"odinger invariant deformations of the AdS_3 x S^3 x T^4 (or K3) solution of IIB supergravity and find a large class of solutions with integer and half-integer dynamical exponents. We analyze the supersymmetries preserved by our solutions and find an infinite number of solutions with four supersymmetries. We study the solutions holographically and find that the dual D1-D5 (or F1-NS5) CFT is deformed by irrelevant operators of spin one and two.Comment: 23 page

Impact of Scottish smoke-free legislation on smoking quit attempts and prevalence

<p><b>Objectives:</b> In Scotland, legislation was implemented in March 2006 prohibiting smoking in all wholly or partially enclosed public spaces. We investigated the impact on attempts to quit smoking and smoking prevalence.</p> <p><b>Methods:</b> We performed time series models using Box-Jenkins autoregressive integrated moving averages (ARIMA) on monthly data on the gross ingredient cost of all nicotine replacement therapy (NRT) prescribed in Scotland in 2003–2009, and quarterly data on self-reported smoking prevalence between January 1999 and September 2010 from the Scottish Household Survey.</p> <p><b>Results:</b> NRT prescription costs were significantly higher than expected over the three months prior to implementation of the legislation. Prescription costs peaked at £1.3 million in March 2006; £292,005.9 (95% CI £260,402.3, £323,609, p<0.001) higher than the monthly norm. Following implementation of the legislation, costs fell exponentially by around 26% per month (95% CI 17%, 35%, p<0.001). Twelve months following implementation, the costs were not significantly different to monthly norms. Smoking prevalence fell by 8.0% overall, from 31.3% in January 1999 to 23.7% in July–September 2010. In the quarter prior to implementation of the legislation, smoking prevalence fell by 1.7% (95% CI 2.4%, 1.0%, p<0.001) more than expected from the underlying trend.</p> <p><b>Conclusions:</b> Quit attempts increased in the three months leading up to Scotland's smoke-free legislation, resulting in a fall in smoking prevalence. However, neither has been sustained suggesting the need for additional tobacco control measures and ongoing support.</p&gt

Boundary Conditions and Unitarity: the Maxwell-Chern-Simons System in AdS_3/CFT_2

We consider the holography of the Abelian Maxwell-Chern-Simons (MCS) system in Lorentzian three-dimensional asymptotically-AdS spacetimes, and discuss a broad class of boundary conditions consistent with conservation of the symplectic structure. As is well-known, the MCS theory contains a massive sector dual to a vector operator in the boundary theory, and a topological sector consisting of flat connections dual to U(1) chiral currents; the boundary conditions we examine include double-trace deformations in these two sectors, as well as a class of boundary conditions that mix the vector operators with the chiral currents. We carefully study the symplectic product of bulk modes and show that almost all such boundary conditions induce instabilities and/or ghost excitations, consistent with violations of unitarity bounds in the dual theory.Comment: 50+1 pages, 6 figures, PDFLaTeX; v2: added references, corrected typo