Combinatorial–computational–chemoinformatics (C3) approach to finding and analyzing low-energy tautomers

Finding the most stable tautomer or a set of low-energy tautomers of molecules is critical in many aspects of molecular modelling or virtual screening experiments. Enumeration of low-energy tautomers of neutral molecules in the gas-phase or typical solvents can be performed by applying available organic chemistry knowledge. This kind of enumeration is implemented in a number of software packages and it is relatively reliable. However, in esoteric cases such as charged molecules in uncommon, non-aqueous solvents there is simply not enough available knowledge to make reliable predictions of low energy tautomers. Over the last few years we have been developing an approach to address the latter problem and we successfully applied it to discover the most stable anionic tautomers of nucleic acid bases that might be involved in the process of DNA damage by low-energy electrons and in charge transfer through DNA. The approach involves three steps: (1) combinatorial generation of a library of tautomers, (2) energy-based screening of the library using electronic structure methods, and (3) analysis of the information generated in step (2). In steps 1–3 we employ combinatorial, computational and chemoinformatics techniques, respectively. Therefore, this hybrid approach is named “Combinatorial*Computational*Chemoinformatics”, or just abbreviated as C3 (or C-cube) approach. This article summarizes our developments and most interesting methodological aspects of the C3 approach. It can serve as an example how to identify the most stable tautomers of molecular systems for which common chemical knowledge had not been sufficient to make definite predictions

Mild hydration of didecyldimethylammonium chloride modified DNA by 1H-nuclear magnetic resonance and by sorption isotherm

The gaseous phase hydration of deoxyribonucleic acid and didecyldimethylammonium chloride (C19H42ClN) complexes (DNA-DDCA) was observed using hydration kinetics, sorption isotherm, and high power nuclear magnetic resonance. Three bound water fractions were distinguished: (i) a very tightly bound water not removed by incubation over silica gel, (ii) a tightly bound water saturating with the hydration time t(1)(h) (0.596 +/- 0.04) h, and a loosely bound water fraction, (iii) with the hydration time t(2)(h) (20.9 +/- 1.3) h. Proton free induction decay was decomposed into the signal associated with the solid matrix of DNA-DDCA complex (T-2S approximate to 30 mu s) and two liquid signal components coming from tightly bound (T-2L1 approximate to 100 mu s) and from loosely bound water fraction (T-2L2 approximate to 1000 mu s)

Fluorescence Efficiency and Visible Re-emission Spectrum of Tetraphenyl Butadiene Films at Extreme Ultraviolet Wavelengths

A large number of current and future experiments in neutrino and dark matter detection use the scintillation light from noble elements as a mechanism for measuring energy deposition. The scintillation light from these elements is produced in the extreme ultraviolet (EUV) range, from 60 - 200 nm. Currently, the most practical technique for observing light at these wavelengths is to surround the scintillation volume with a thin film of Tetraphenyl Butadiene (TPB) to act as a fluor. The TPB film absorbs EUV photons and reemits visible photons, detectable with a variety of commercial photosensors. Here we present a measurement of the re-emission spectrum of TPB films when illuminated with 128, 160, 175, and 250 nm light. We also measure the fluorescence efficiency as a function of incident wavelength from 120 to 250 nm.Comment: 15 pages, 9 figures, Submitted to Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipmen

Precise 3D track reconstruction algorithm for the ICARUS T600 liquid argon time projection chamber detector

Liquid Argon Time Projection Chamber (LAr TPC) detectors offer charged particle imaging capability with remarkable spatial resolution. Precise event reconstruction procedures are critical in order to fully exploit the potential of this technology. In this paper we present a new, general approach of three-dimensional reconstruction for the LAr TPC with a practical application to track reconstruction. The efficiency of the method is evaluated on a sample of simulated tracks. We present also the application of the method to the analysis of real data tracks collected during the ICARUS T600 detector operation with the CNGS neutrino beam.Comment: Submitted to Advances in High Energy Physic

Search for anomalies in the {\nu}e appearance from a {\nu}{\mu} beam

We report an updated result from the ICARUS experiment on the search for {\nu}{\mu} ->{\nu}e anomalies with the CNGS beam, produced at CERN with an average energy of 20 GeV and travelling 730 km to the Gran Sasso Laboratory. The present analysis is based on a total sample of 1995 events of CNGS neutrino interactions, which corresponds to an almost doubled sample with respect to the previously published result. Four clear {\nu}e events have been visually identified over the full sample, compared with an expectation of 6.4 +- 0.9 events from conventional sources. The result is compatible with the absence of additional anomalous contributions. At 90% and 99% confidence levels the limits to possible oscillated events are 3.7 and 8.3 respectively. The corresponding limit to oscillation probability becomes consequently 3.4 x 10-3 and 7.6 x 10-3 respectively. The present result confirms, with an improved sensitivity, the early result already published by the ICARUS collaboration

A search for the analogue to Cherenkov radiation by high energy neutrinos at superluminal speeds in ICARUS

The OPERA collaboration has claimed evidence of superluminal {\nu}{_\mu} propagation between CERN and the LNGS. Cohen and Glashow argued that such neutrinos should lose energy by producing photons and e+e- pairs, through Z0 mediated processes analogous to Cherenkov radiation. In terms of the parameter delta=(v^2_nu-v^2_c)/v^2_c, the OPERA result implies delta = 5 x 10^-5. For this value of \delta a very significant deformation of the neutrino energy spectrum and an abundant production of photons and e+e- pairs should be observed at LNGS. We present an analysis based on the 2010 and part of the 2011 data sets from the ICARUS experiment, located at Gran Sasso National Laboratory and using the same neutrino beam from CERN. We find that the rates and deposited energy distributions of neutrino events in ICARUS agree with the expectations for an unperturbed spectrum of the CERN neutrino beam. Our results therefore refute a superluminal interpretation of the OPERA result according to the Cohen and Glashow prediction for a weak current analog to Cherenkov radiation. In particular no superluminal Cherenkov like e+e- pair or gamma emission event has been directly observed inside the fiducial volume of the "bubble chamber like" ICARUS TPC-LAr detector, setting the much stricter limit of delta < 2.5 10^-8 at the 90% confidence level, comparable with the one due to the observations from the SN1987A.Comment: 17 pages, 6 figure

Experimental search for the LSND anomaly with the ICARUS detector in the CNGS neutrino beam

We report an early result from the ICARUS experiment on the search for nu_mu to nu_e signal due to the LSND anomaly. The search was performed with the ICARUS T600 detector located at the Gran Sasso Laboratory, receiving CNGS neutrinos from CERN at an average energy of about 20 GeV, after a flight path of about 730 km. The LSND anomaly would manifest as an excess of nu_e events, characterized by a fast energy oscillation averaging approximately to sin^2(1.27 Dm^2_new L/ E_nu) = 1/2. The present analysis is based on 1091 neutrino events, which are about 50% of the ICARUS data collected in 2010-2011. Two clear nu_e events have been found, compared with the expectation of 3.7 +/- 0.6 events from conventional sources. Within the range of our observations, this result is compatible with the absence of a LSND anomaly. At 90% and 99% confidence levels the limits of 3.4 and 7.3 events corresponding to oscillation probabilities of 5.4 10^-3 and 1.1 10^-2 are set respectively. The result strongly limits the window of open options for the LSND anomaly to a narrow region around (Dm^2, sin^2(2 theta))_new = (0.5 eV^2, 0.005), where there is an overall agreement (90% CL) between the present ICARUS limit, the published limits of KARMEN and the published positive signals of LSND and MiniBooNE Collaborations.Comment: 10 pages, 7 figure

Search for anomalies in the neutrino sector with muon spectrometers and large LArTPC imaging detectors at CERN

A new experiment with an intense ~2 GeV neutrino beam at CERN SPS is proposed in order to definitely clarify the possible existence of additional neutrino states, as pointed out by neutrino calibration source experiments, reactor and accelerator experiments and measure the corresponding oscillation parameters. The experiment is based on two identical LAr-TPCs complemented by magnetized spectrometers detecting electron and muon neutrino events at Far and Near positions, 1600 m and 300 m from the proton target, respectively. The ICARUS T600 detector, the largest LAr-TPC ever built with a size of about 600 ton of imaging mass, now running in the LNGS underground laboratory, will be moved at the CERN Far position. An additional 1/4 of the T600 detector (T150) will be constructed and located in the Near position. Two large area spectrometers will be placed downstream of the two LAr-TPC detectors to perform charge identification and muon momentum measurements from sub-GeV to several GeV energy range, greatly complementing the physics capabilities. This experiment will offer remarkable discovery potentialities, collecting a very large number of unbiased events both in the neutrino and antineutrino channels, largely adequate to definitely settle the origin of the observed neutrino-related anomalies.Comment: Contribution to the European Strategy for Particle Physics - Open Symposium Preparatory Group, Kracow 10-12 September 201

Underground operation of the ICARUS T600 LAr-TPC: first results

Open questions are still present in fundamental Physics and Cosmology, like the nature of Dark Matter, the matter-antimatter asymmetry and the validity of the particle interaction Standard Model. Addressing these questions requires a new generation of massive particle detectors exploring the subatomic and astrophysical worlds. ICARUS T600 is the first large mass (760 ton) example of a novel detector generation able to combine the imaging capabilities of the old famous "bubble chamber" with an excellent energy measurement in huge electronic detectors. ICARUS T600 now operates at the Gran Sasso underground laboratory, studying cosmic rays, neutrino oscillation and proton decay. Physical potentialities of this novel telescope are presented through few examples of neutrino interactions reconstructed with unprecedented details. Detector design and early operation are also reported.Comment: 14 pages, 8 figures, 2 tables. Submitted to Jins