Exploring the conformational energy landscape of proteins

Proteins possess a complex energy landscape with a large number of local minima called conformational substates that are arranged in a hierarchical fashion. Here we discuss experiments aimed at the elucidation of the energy landscape in carbonmonoxy myoglobin (MbCO). In the highest tier of the hierarchy, a few taxonomic substates exist. Because of their small number, these substates are accessible to detailed structural investigations. Spectroscopic experiments are discussed that elucidate the role of protonations of amino acid side chains in creating the substates. The lower tiers of the hierarchy contain a large number of statistical substates. Substate interconversions are observed in the entire temperature range from below 1 K up to the denaturation temperature, indicating a wide spectrum of energy barriers that separate the substates

Strings in Homogeneous Background Spacetimes

The string equations of motion for some homogeneous (Kantowski-Sachs, Bianchi I and Bianchi IX) background spacetimes are given, and solved explicitly in some simple cases. This is motivated by the recent developments in string cosmology, where it has been shown that, under certain circumstances, such spacetimes appear as string-vacua. Both tensile and null strings are considered. Generally, it is much simpler to solve for the null strings since then we deal with the null geodesic equations of General Relativity plus some additional constraints. We consider in detail an ansatz corresponding to circular strings, and we discuss the possibility of using an elliptic-shape string ansatz in the case of homogeneous (but anisotropic) backgrounds.Comment: 25 pages, REVTE

A macroscopic multifractal analysis of parabolic stochastic PDEs

It is generally argued that the solution to a stochastic PDE with multiplicative noise---such as $\dot{u}=\frac12 u"+u\xi$, where $\xi$ denotes space-time white noise---routinely produces exceptionally-large peaks that are "macroscopically multifractal." See, for example, Gibbon and Doering (2005), Gibbon and Titi (2005), and Zimmermann et al (2000). A few years ago, we proved that the spatial peaks of the solution to the mentioned stochastic PDE indeed form a random multifractal in the macroscopic sense of Barlow and Taylor (1989; 1992). The main result of the present paper is a proof of a rigorous formulation of the assertion that the spatio-temporal peaks of the solution form infinitely-many different multifractals on infinitely-many different scales, which we sometimes refer to as "stretch factors." A simpler, though still complex, such structure is shown to also exist for the constant-coefficient version of the said stochastic PDE.Comment: 41 page

Resumming double logarithms in the QCD evolution of color dipoles

The higher-order perturbative corrections, beyond leading logarithmic accuracy, to the BFKL evolution in QCD at high energy are well known to suffer from a severe lack-of-convergence problem, due to radiative corrections enhanced by double collinear logarithms. Via an explicit calculation of Feynman graphs in light cone (time-ordered) perturbation theory, we show that the corrections enhanced by double logarithms (either energy-collinear, or double collinear) are associated with soft gluon emissions which are strictly ordered in lifetime. These corrections can be resummed to all orders by solving an evolution equation which is non-local in rapidity. This equation can be equivalently rewritten in local form, but with modified kernel and initial conditions, which resum double collinear logs to all orders. We extend this resummation to the next-to-leading order BFKL and BK equations. The first numerical studies of the collinearly-improved BK equation demonstrate the essential role of the resummation in both stabilizing and slowing down the evolution.Comment: 16 pages, 5 figure

Diffractive photon dissociation in the saturation regime from the Good and Walker picture

Combining the QCD dipole model with the Good and Walker picture, we formulate diffractive dissociation of a photon of virtuality Q^2 off a hadronic target, in the kinematical regime in which Q is close to the saturation scale and much smaller than the invariant mass of the diffracted system. We show how the obtained formula compares to the HERA data and discuss what can be learnt from such a phenomenology. In particular, we argue that diffractive observables in these kinematics provide useful pieces of information on the saturation regime of QCD.Comment: 17 pages, 7 figures, revte

solGS: a webbased tool for genomic selection

Background: Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide markers and statistical complexity, however, is a serious challenge in data management, analysis, and sharing. A bioinformatics infrastructure for data storage and access, and user-friendly web-based tool for analysis and sharing output is needed to make GS more practical for breeders. Results: We have developed a web-based tool, called solGS, for predicting genomic estimated breeding values (GEBVs) of individuals, using a Ridge-Regression Best Linear Unbiased Predictor (RR-BLUP) model. It has an intuitive web-interface for selecting a training population for modeling and estimating genomic estimated breeding values of selection candidates. It estimates phenotypic correlation and heritability of traits and selection indices of individuals. Raw data is stored in a generic database schema, Chado Natural Diversity, co-developed by multiple database groups. Analysis output is graphically visualized and can be interactively explored online or downloaded in text format. An instance of its implementation can be accessed at the NEXTGEN Cassava breeding database, http://cassavabase.org/solgs. Conclusions: solGS enables breeders to store raw data and estimate GEBVs of individuals online, in an intuitive and interactive workflow. It can be adapted to any breeding program.Background: Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide markers and statistical complexity, however, is a serious challenge in data management, analysis, and sharing. A bioinformatics infrastructure for data storage and access, and user-friendly web-based tool for analysis and sharing output is needed to make GS more practical for breeders. Results: We have developed a web-based tool, called solGS, for predicting genomic estimated breeding values (GEBVs) of individuals, using a Ridge-Regression Best Linear Unbiased Predictor (RR-BLUP) model. It has an intuitive web-interface for selecting a training population for modeling and estimating genomic estimated breeding values of selection candidates. It estimates phenotypic correlation and heritability of traits and selection indices of individuals. Raw data is stored in a generic database schema, Chado Natural Diversity, co-developed by multiple database groups. Analysis output is graphically visualized and can be interactively explored online or downloaded in text format. An instance of its implementation can be accessed at the NEXTGEN Cassava breeding database, http://cassavabase.org/solgs. Conclusions: solGS enables breeders to store raw data and estimate GEBVs of individuals online, in an intuitive and interactive workflow. It can be adapted to any breeding program.Background: Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide markers and statistical complexity, however, is a serious challenge in data management, analysis, and sharing. A bioinformatics infrastructure for data storage and access, and user-friendly web-based tool for analysis and sharing output is needed to make GS more practical for breeders. Results: We have developed a web-based tool, called solGS, for predicting genomic estimated breeding values (GEBVs) of individuals, using a Ridge-Regression Best Linear Unbiased Predictor (RR-BLUP) model. It has an intuitive web-interface for selecting a training population for modeling and estimating genomic estimated breeding values of selection candidates. It estimates phenotypic correlation and heritability of traits and selection indices of individuals. Raw data is stored in a generic database schema, Chado Natural Diversity, co-developed by multiple database groups. Analysis output is graphically visualized and can be interactively explored online or downloaded in text format. An instance of its implementation can be accessed at the NEXTGEN Cassava breeding database, http://cassavabase.org/solgs. Conclusions: solGS enables breeders to store raw data and estimate GEBVs of individuals online, in an intuitive and interactive workflow. It can be adapted to any breeding program.Background: Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide markers and statistical complexity, however, is a serious challenge in data management, analysis, and sharing. A bioinformatics infrastructure for data storage and access, and user-friendly web-based tool for analysis and sharing output is needed to make GS more practical for breeders. Results: We have developed a web-based tool, called solGS, for predicting genomic estimated breeding values (GEBVs) of individuals, using a Ridge-Regression Best Linear Unbiased Predictor (RR-BLUP) model. It has an intuitive web-interface for selecting a training population for modeling and estimating genomic estimated breeding values of selection candidates. It estimates phenotypic correlation and heritability of traits and selection indices of individuals. Raw data is stored in a generic database schema, Chado Natural Diversity, co-developed by multiple database groups. Analysis output is graphically visualized and can be interactively explored online or downloaded in text format. An instance of its implementation can be accessed at the NEXTGEN Cassava breeding database, http://cassavabase.org/solgs. Conclusions: solGS enables breeders to store raw data and estimate GEBVs of individuals online, in an intuitive and interactive workflow. It can be adapted to any breeding program

Enhanced Fusion-Evaporation Cross Sections in Neutron-Rich 132^{132}Sn on 64^{64}Ni

Evaporation residue cross sections have been measured with neutron-rich radioactive $^{132}$Sn beams on $^{64}$Ni in the vicinity of the Coulomb barrier. The average beam intensity was $2\times 10^{4}$ particles per second and the smallest cross section measured was less than 5 mb. Large subbarrier fusion enhancement was observed. Coupled-channels calculations taking into account inelastic excitation and neutron transfer underpredict the measured cross sections below the barrier.Comment: 4 pages including 1 table and 3 figure

SARS-CoV-2 / COVID-19 in patients on the Swiss national transplant waiting list.

The impact of coronavirus disease 2019 (COVID-19) on patients listed for solid organ transplantation has not been systematically investigated to date. Thus, we assessed occurrence and effects of infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on patients on the Swiss national waiting list for solid organ transplantation. Patient data were retrospectively extracted from the Swiss Organ Allocation System (SOAS). From 16 March to 31 May 2020, we included all patients listed for solid organ transplantation on the Swiss national waiting list who were tested positive for SARS-CoV-2. Severity of COVID-19 was categorised as follows: stage I, mild symptoms; stage II, moderate to severe symptoms; stage III, critical symptoms; stage IV, death. We compared the incidence rate (laboratory-confirmed cases of SARS-CoV-2), the hospital admission rate (number of admissions of SARS-CoV-2-positive individuals), and the case fatality rate (number of deaths of SARS-CoV-2-positive individuals) in our study population with the general Swiss population during the study period, calculating age-adjusted standardised incidence ratios and standardised mortality ratios, with 95% confidence intervals (CIs). A total of 1439 patients were registered on the Swiss national solid organ transplantation waiting list on 31 May 31 2020. Twenty-four (1.7%) waiting list patients were reported to test positive for SARS-CoV-2 in the study period. The median age was 56 years (interquartile range 45.3–65.8), and 14 (58%) were male. Of all patients tested positive for SARS-CoV-2, two patients were asymptomatic, 14 (58%) presented in COVID-19 stage I, 3 (13%) in stage II, and 5 (21%) in stage III. Eight patients (33%) were admitted to hospital, four (17%) required intensive care, and three (13%) mechanical ventilation. Twenty-two patients (92%) of all those infected recovered, but two male patients aged >65 years with multiple comorbidities died in hospital from respiratory failure. Comparing our study population with the general Swiss population, the age-adjusted standardised incidence ratio was 4.1 (95% CI 2.7–6.0). The overall rate of SARS-CoV-2 infections in candidates awaiting solid organ transplantation was four times higher than in the Swiss general population; however, the frequency of testing likely played a role. Given the small sample size of affected patients, conclusions have to be drawn cautiously and results need verification in larger cohorts

Non-equilibrium initial conditions from pQCD for RHIC and LHC

We calculate the initial non-equilibrium conditions from perturbative QCD (pQCD) within Glauber multiple scattering theory for $\sqrt s =200$ AGeV and $\sqrt s =5.5$ ATeV. At the soon available collider energies one will particularly test the small $x$ region of the parton distributions entering the cross sections. Therefore shadowing effects, previously more or less unimportant, will lead to new effects on variables such as particle multiplicities $dN/dy$, transverse energy production $d\bar{E}_T/dy$, and the initial temperature $T_i$. In this paper we will have a closer look on the effects of shadowing by employing different parametrizations for the shadowing effect for valence quarks, sea quarks and gluons. Since the cross sections at midrapidity are dominated by processes involving gluons the amount of their depletion is particularly important. We will therefore have a closer look on the results for $dN/dy$, $d\bar{E}_T/dy$, and $T_i$ by using two different gluon shadowing ratios, differing strongly in size. As a matter of fact, the calculated quantities differ significantly.Comment: typo in ref's removed, ack's added, no change in result

Q Qbar g contribution to diffractive J/psi electroproduction

We study the diffractive electroproduction of quarkonia from quark-antiquark-gluon states in the photon wave function. We show that these states contribute to the leading-power and leading-logarithm level. We suggest the measurement of J/psi production via inelastic diffraction to study color-transparency and color-opacity effects in the diffractive gluon distribution.Comment: Latex, 4 figures; v3: comments on color octet terms and on photoproduction expanded; results unchange