Observations of HONO by laser-induced fluorescence at the South Pole during ANTCI 2003

Observations of nitrous acid (HONO) by laser-induced fluorescence (LIF) at the South Pole taken during the Antarctic Troposphere Chemistry Investigation (ANTCI), which took place over the time period of Nov. 15, 2003 to Jan. 4, 2004, are presented here. The median observed mixing ratio of HONO 10 m above the snow was 5.8 pptv (mean value 6.3 pptv) with a maximum of 18.2 pptv on Nov 30th, Dec 1st, 3rd, 15th, 17th, 21st, 22nd, 25th, 27th and 28th. The measurement uncertainty is ±35%. The LIF HONO observations are compared to concurrent HONO observations performed by mist chamber/ion chromatography (MC/IC). The HONO levels reported by MC/IC are about 7.2 ± 2.3 times higher than those reported by LIF. Citation: Liao, W., A. T. Case, J. Mastromarino, D. Tan, and J. E. Dibb (2006), Observations of HONO by laser-induced fluorescence at the South Pole during ANTCI 2003, Geophys. Res. Lett., 33, L09810, doi:10.1029/2005GL025470

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing

Induction, Philosophical Conceptions of

How induction was understood took a substantial turn during the Renaissance. At the beginning, induction was understood as it had been throughout the medieval period, as a kind of propositional inference that is stronger the more it approximates deduction. During the Renaissance, an older understanding, one prevalent in antiquity, was rediscovered and adopted. By this understanding, induction identifies defining characteristics using a process of comparing and contrasting. Important participants in the change were Jean Buridan, humanists such as Lorenzo Valla and Rudolph Agricola, Paduan Aristotelians such as Agostino Nifo, Jacopo Zabarella, and members of the medical faculty, writers on philosophy of mind such as the Englishman John Case, writers of reasoning handbooks, and Francis Bacon

Comparative analysis of rigidity across protein families

We present a comparative study in which 'pebble game' rigidity analysis is applied to multiple protein crystal structures, for each of six different protein families. We find that the main-chain rigidity of a protein structure at a given hydrogen bond energy cutoff is quite sensitive to small structural variations, and conclude that the hydrogen bond constraints in rigidity analysis should be chosen so as to form and test specific hypotheses about the rigidity of a particular protein. Our comparative approach highlights two different characteristic patterns ('sudden' or 'gradual') for protein rigidity loss as constraints are removed, in line with recent results on the rigidity transitions of glassy networks

Picosecond electrical spectroscopy using monolithic GaAs circuits

This article describes an experimental apparatus for free-space mm-wave transmission measurements (spectroscopy). GaAs nonlinear transmission lines and sampling circuits are used as picosecond pulse generators and detectors, with planar monolithic bowtie antennas with associated substrate lenses used as the radiating and receiving elements. The received pulse is 270 mV amplitude and 2.4 ps rise time. Through Fourier transformation of the received pulse, 30–250 GHz measurements are demonstrated with <=0.3 dB (rms) accuracy

A Bi-Hamiltonian Formulation for Triangular Systems by Perturbations

A bi-Hamiltonian formulation is proposed for triangular systems resulted by perturbations around solutions, from which infinitely many symmetries and conserved functionals of triangular systems can be explicitly constructed, provided that one operator of the Hamiltonian pair is invertible. Through our formulation, four examples of triangular systems are exhibited, which also show that bi-Hamiltonian systems in both lower dimensions and higher dimensions are many and varied. Two of four examples give local 2+1 dimensional bi-Hamiltonian systems and illustrate that multi-scale perturbations can lead to higher-dimensional bi-Hamiltonian systems.Comment: 16 pages, to appear in J. Math. Phy

The radiation environment near the lunar surface: CRaTER observations and Geant4 simulations

[1] At the start of the Lunar Reconnaissance Orbiter mission in 2009, its Cosmic Ray Telescope for the Effects of Radiation instrument measured the radiation environment near the Moon during the recent deep solar minimum, when galactic cosmic rays (GCRs) were at the highest level observed during the space age. We present observations that show the combined effects of GCR primaries, secondary particles (“albedo”) created by the interaction of GCRs with the lunar surface, and the interactions of these particles in the shielding material overlying the silicon solid-state detectors of the Cosmic Ray Telescope for the Effects of Radiation. We use Geant4 to model the energy and angular distribution of the albedo particles, and to model the response of the sensor to the various particle species reaching the 50 kilometer altitude of the Lunar Reconnaissance Orbiter. Using simulations to gain insight into the observations, we are able to present preliminary energy-deposit spectra for evaluation of the radiation environment\u27s effects on other sensitive materials, whether biological or electronic, that would be exposed to a similar near-lunar environment

Monitoring the Low-Energy Gamma-Ray Sky Using Earth Occultation with GLAST GBM

Long term all-sky monitoring of the 20 keV – 2 MeV gamma-ray sky using the Earth occultation technique was demonstrated by the BATSE instrument on the Compton Gamma Ray Observatory. The principles and techniques used for the development of an end-to-end earth occultation data analysis system for BATSE can be extended to the GLAST Burst Monitor (GBM), resulting in multiband light curves and time-resolved spectra in the energy range 8 keV to above 1 MeV for known gamma-ray sources and transient outbursts, as well as the discovery of new sources of gamma-ray emission. In this paper we describe the application of the technique to the GBM. We also present the expected sensitivity for the GBM

GCR access to the Moon as measured by the CRaTER instrument on LRO

[1] Recent modeling efforts have yielded varying and conflicting results regarding the possibility that Earth\u27s magnetosphere is able to shield energetic particles of \u3e10 MeV at lunar distances. This population of particles consists of galactic cosmic rays as well as energetic particles that are accelerated by solar flares and coronal mass ejections. The Cosmic Ray Telescope for the Effects of Radiation (CRaTER) onboard the Lunar Reconnaissance Orbiter is in orbit about the Moon and is thus able to directly test these modeling results. Over the course of a month, CRaTER samples the upstream solar wind as well as various regions of Earth\u27s magnetotail. CRaTER data from multiple lunations demonstrate that Earth\u27s magnetosphere at lunar distances produces no measurable influence on energetic particle flux, even at the lowest energies (\u3e14 MeV protons) where any effect should be maximized. For particles with energies of 14–30 MeV, we calculate an upper limit (determined by counting statistics) on the amount of shielding caused by the magnetosphere of 1.7%. The high energy channel (\u3e500 MeV) provides an upper limit of 3.2%