Experimental free energy measurements of kinetic molecular states using fluctuation theorems

Recent advances in non-equilibrium statistical mechanics and single molecule technologies make it possible to extract free energy differences from irreversible work measurements in pulling experiments. To date, free energy recovery has been focused on native or equilibrium molecular states, whereas free energy measurements of kinetic states (i.e. finite lifetime states that are generated dynamically and are metastable) have remained unexplored. Kinetic states can play an important role in various domains of physics, such as nanotechnology or condensed matter physics. In biophysics, there are many examples where they determine the fate of molecular reactions: protein and peptide-nucleic acid binding, specific cation binding, antigen-antibody interactions, transient states in enzymatic reactions or the formation of transient intermediates and non-native structures in molecular folders. Here we demonstrate that it is possible to obtain free energies of kinetic states by applying extended fluctuation relations. This is shown by using optical tweezers to mechanically unfold and refold DNA structures exhibiting intermediate and misfolded kinetic states.Comment: main paper (16 pages, 5 figures) and supplementary information (22 pages, 14 figures

Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005

BACKGROUND The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.This work was partially supported by salaries from the NOAA Coral Reef Conservation Program to the NOAA Coral Reef Conservation Program authors. NOAA provided funding to Caribbean ReefCheck investigators to undertake surveys of bleaching and mortality. Otherwise, no funding from outside authors' institutions was necessary for the undertaking of this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

South East Pacific atmospheric composition and variability sampled along 20° S during VOCALS-REx

The VAMOS Ocean-Cloud-Atmosphere-Land Regional Experiment (VOCALS-REx) was conducted from 15 October to 15 November 2008 in the South East Pacific (SEP) region to investigate interactions between land, sea and atmosphere in this unique tropical eastern ocean environment and to improve the skill of global and regional models in representing the region. This study synthesises selected aircraft, ship and surface site observations from VOCALS-REx to statistically summarise and characterise the atmospheric composition and variability of the Marine Boundary Layer (MBL) and Free Troposphere (FT) along the 20° S parallel between 70° W and 85° W. Significant zonal gradients in mean MBL sub-micron aerosol particle size and composition, carbon monoxide, sulphur dioxide and ozone were seen over the campaign, with a generally more variable and polluted coastal environment and a less variable, more pristine remote maritime regime. Gradients in aerosol and trace gas concentrations were observed to be associated with strong gradients in cloud droplet number. The FT was often more polluted in terms of trace gases than the MBL in the mean; however increased variability in the FT composition suggests an episodic nature to elevated concentrations. This is consistent with a complex vertical interleaving of airmasses with diverse sources and hence pollutant concentrations as seen by generalised back trajectory analysis, which suggests contributions from both local and long-range sources. Furthermore, back trajectory analysis demonstrates that the observed zonal gradients both in the boundary layer and the free troposphere are characteristic of marked changes in airmass history with distance offshore – coastal boundary layer airmasses having been in recent contact with the local land surface and remote maritime airmasses having resided over ocean for in excess of ten days. Boundary layer composition to the east of 75° W was observed to be dominated by coastal emissions from sources to the west of the Andes, with evidence for diurnal pumping of the Andean boundary layer above the height of the marine capping inversion. Analysis of intra-campaign variability in atmospheric composition was not found to be significantly correlated with observed low-frequency variability in the large scale flow pattern; campaign-average interquartile ranges of CO, SO<sub>2</sub> and O<sub>3</sub> concentrations at all longitudes were observed to dominate over much smaller differences in median concentrations calculated between periods of different flow regimes. The campaign climatology presented here aims to provide a valuable dataset to inform model simulation and future process studies, particularly in the context of aerosol-cloud interaction and further evaluation of dynamical processes in the SEP region for conditions analogous to those during VOCALS-REx. To this end, our results are discussed in terms of coastal, transitional and remote spatial regimes in the MBL and FT and a gridded dataset are provided as a resource

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13

Expected Performance of the ATLAS Experiment - Detector, Trigger and Physics

A detailed study is presented of the expected performance of the ATLAS detector. The reconstruction of tracks, leptons, photons, missing energy and jets is investigated, together with the performance of b-tagging and the trigger. The physics potential for a variety of interesting physics processes, within the Standard Model and beyond, is examined. The study comprises a series of notes based on simulations of the detector and physics processes, with particular emphasis given to the data expected from the first years of operation of the LHC at CERN

Hunt for new phenomena using large jet multiplicities and missing transverse momentum with ATLAS in 4.7 fb−1 of s√=7TeV proton-proton collisions

Results are presented of a search for new particles decaying to large numbers of jets in association with missing transverse momentum, using 4.7 fb−1 of pp collision data at s√=7TeV collected by the ATLAS experiment at the Large Hadron Collider in 2011. The event selection requires missing transverse momentum, no isolated electrons or muons, and from ≥6 to ≥9 jets. No evidence is found for physics beyond the Standard Model. The results are interpreted in the context of a MSUGRA/CMSSM supersymmetric model, where, for large universal scalar mass m 0, gluino masses smaller than 840 GeV are excluded at the 95% confidence level, extending previously published limits. Within a simplified model containing only a gluino octet and a neutralino, gluino masses smaller than 870 GeV are similarly excluded for neutralino masses below 100 GeV

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured

A Search for Jet Handedness in Hadronic Z0Z^0 Decays

We have searched for signatures of polarization in hadronic jets from $Z^0 \to q \bar{q}$ decays using the ``jet handedness'' method. The polar angle asymmetry induced by the high SLC electron-beam polarization was used to separate quark jets from antiquark jets, expected to be left- and right-polarized, respectively. We find no evidence for jet handedness in our global sample or in a sample of light quark jets and we set upper limits at the 95% C.L. of 0.063 and 0.099 respectively on the magnitude of the analyzing power of the method proposed by Efremov {\it et al.}Comment: Revtex, 8 pages, 2 figure