Non-Markovian polymer reaction kinetics

Describing the kinetics of polymer reactions, such as the formation of loops and hairpins in nucleic acids or polypeptides, is complicated by the structural dynamics of their chains. Although both intramolecular reactions, such as cyclization, and intermolecular reactions have been studied extensively, both experimentally and theoretically, there is to date no exact explicit analytical treatment of transport-limited polymer reaction kinetics, even in the case of the simplest (Rouse) model of monomers connected by linear springs. We introduce a new analytical approach to calculate the mean reaction time of polymer reactions that encompasses the non-Markovian dynamics of monomer motion. This requires that the conformational statistics of the polymer at the very instant of reaction be determined, which provides, as a by-product, new information on the reaction path. We show that the typical reactive conformation of the polymer is more extended than the equilibrium conformation, which leads to reaction times significantly shorter than predicted by the existing classical Markovian theory.Comment: Main text (7 pages, 5 figures) + Supplemantary Information (13 pages, 2 figures

GOPred: GO Molecular Function Prediction by Combined Classifiers

Functional protein annotation is an important matter for in vivo and in silico biology. Several computational methods have been proposed that make use of a wide range of features such as motifs, domains, homology, structure and physicochemical properties. There is no single method that performs best in all functional classification problems because information obtained using any of these features depends on the function to be assigned to the protein. In this study, we portray a novel approach that combines different methods to better represent protein function. First, we formulated the function annotation problem as a classification problem defined on 300 different Gene Ontology (GO) terms from molecular function aspect. We presented a method to form positive and negative training examples while taking into account the directed acyclic graph (DAG) structure and evidence codes of GO. We applied three different methods and their combinations. Results show that combining different methods improves prediction accuracy in most cases. The proposed method, GOPred, is available as an online computational annotation tool (http://kinaz.fen.bilkent.edu.tr/gopred)

Metallic, magnetic and molecular nanocontacts

Scanning tunnelling microscopy and break-junction experiments realize metallic and molecular nanocontacts that act as ideal one-dimensional channels between macroscopic electrodes. Emergent nanoscale phenomena typical of these systems encompass structural, mechanical, electronic, transport, and magnetic properties. This Review focuses on the theoretical explanation of some of these properties obtained with the help of first-principles methods. By tracing parallel theoretical and experimental developments from the discovery of nanowire formation and conductance quantization in gold nanowires to recent observations of emergent magnetism and Kondo correlations, we exemplify the main concepts and ingredients needed to bring together ab initio calculations and physical observations. It can be anticipated that diode, sensor, spin-valve and spin-filter functionalities relevant for spintronics and molecular electronics applications will benefit from the physical understanding thus obtained

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6  ×  6  ×  6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties

Convergent functional genomic studies of omega-3 fatty acids in stress reactivity, bipolar disorder and alcoholism

Omega-3 fatty acids have been proposed as an adjuvant treatment option in psychiatric disorders. Given their other health benefits and their relative lack of toxicity, teratogenicity and side effects, they may be particularly useful in children and in females of child-bearing age, especially during pregnancy and postpartum. A comprehensive mechanistic understanding of their effects is needed. Here we report translational studies demonstrating the phenotypic normalization and gene expression effects of dietary omega-3 fatty acids, specifically docosahexaenoic acid (DHA), in a stress-reactive knockout mouse model of bipolar disorder and co-morbid alcoholism, using a bioinformatic convergent functional genomics approach integrating animal model and human data to prioritize disease-relevant genes. Additionally, to validate at a behavioral level the novel observed effects on decreasing alcohol consumption, we also tested the effects of DHA in an independent animal model, alcohol-preferring (P) rats, a well-established animal model of alcoholism. Our studies uncover sex differences, brain region-specific effects and blood biomarkers that may underpin the effects of DHA. Of note, DHA modulates some of the same genes targeted by current psychotropic medications, as well as increases myelin-related gene expression. Myelin-related gene expression decrease is a common, if nonspecific, denominator of neuropsychiatric disorders. In conclusion, our work supports the potential utility of omega-3 fatty acids, specifically DHA, for a spectrum of psychiatric disorders such as stress disorders, bipolar disorder, alcoholism and beyond

Measurement of the tau lepton mass and an upper limit on the mass difference between tau(+) and tau(-)

The mass of the tau lepton has been measured in the decay mode tau -> 3 pi nu(tau) using a pseudomass technique. The result obtained from 414 fb(-1) of data collected with the Belle detector is M-tau=[1776.61 +/- 0.13(stat)+/- 0.35(sys)] MeV/c(2). The upper limit on the relative mass difference between positive and negative tau leptons is |M-tau(+)-M-tau(-)|/M-tau < 2.8x10(-4) at 90% confidence level

Measurement of inclusive D-s, D-0, and J/psi rates and determination of the B-s((*)) (B)over-bar(s)((*)) production fraction in b(b)over-bar events at the Upsilon(5S) resonance

The inclusive production of D-s, D-0, and J/psi mesons is studied using a 1.86 fb(-1) data sample collected on the Y(5S) resonance with the Belle detector at the KEKB asymmetric-energy e(+)e(-) collider. The number of bb events in this Y(5S) data sample is determined. We measure the branching fractions B(Y(5S) -> DsX)/2 = (23.6 +/- 1.2 +/- 3.6)%, B(Y(5S) -> (DX)-X-0)/2 = (53.8 +/- 2.0 +/- 3.4)%, and B(Y(5S) -> J/psi X)/2 = (1.030 +/- 0.080 +/- 0.067)%. From the D-s and D-0 inclusive branching fractions the ratio f(s) = (18.0 +/- 1.3 +/- 3.2)% of B-s((*)) B-s((*)) to the total bb quark pair production at the Y(5S) energy is obtained in a model-dependent way

Evidence for D-0-(D)over-bar(0) mixing

We observe evidence for D-0-(D) over bar (0) mixing by measuring the difference in the apparent lifetime when a D-0 meson decays to the CP eigenstates K+K- and pi(+)pi(-) and when it decays to the final state K-pi(+). We find the relative difference of the lifetimes y(CP) to be [1.31 +/- 0.32(stat)+/- 0.25(syst)]%, 3.2 standard deviations from zero. We also search for a CP asymmetry between D-0 and (D) over bar (0) decays; no evidence for CP violation is found. These results are based on 540 fb(-1) of data recorded by the Belle detector at the KEKB e(+)e(-) collider