New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...

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All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

This paper describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is composed of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additional absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 300 additional molecules important in different areas of atmospheric science have been added to the database. The compilation can be accessed through www.hitran.org. Most of the HITRAN data have now been cast into an underlying relational database structure that offers many advantages over the long-standing sequential text-based structure. The new structure empowers the user in many ways. It enables the incorporation of an extended set of fundamental parameters per transition, sophisticated line-shape formalisms, easy user-defined output formats, and very convenient searching, filtering, and plotting of data. A powerful application programming interface making use of structured query language (SQL) features for higher-level applications of HITRAN is also provided.

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The HITRAN 2008 molecular spectroscopic database

The role of extended and point defects, and key impurities such as C, O, and H, on the electrical and optical properties of GaN is reviewed. Recent progress in the development of high reliability contacts, thermal processing, dry and wet etching techniques, implantation doping and isolation, and gate insulator technology is detailed. Finally, the performance of GaN-based electronic and photonic devices such as field effect transistors, UV detectors, laser diodes, and light-emitting diodes is covered, along with the influence of process-induced or grown-in defects and impurities on the device physics.

Gan : processing, defects, and devices

Atomic and molecular data for the transitions of a number of astrophysically interesting species are summarized, in- cluding energy levels, statistical weights, Einstein A-coefficients and collisional rate coefficients. Available collisional data from quantum chemical calculations and experiments are extrapolated to higher energies (up to E/k ∼ 1000 K). These data, which are made publically available through the WWW at http://www.strw.leidenuniv.nl/∼moldata, are essential input for non-LTE line radiative transfer programs. An online version of a computer program for performing statistical equilibrium calcu- lations is also made available as part of the database. Comparisons of calculated emission lines using different sets of collisional rate coefficients are presented. This database should form an important tool in analyzing observations from current and future (sub)millimetre and infrared telescopes.

/pdf/an-atomic-and-molecular-database-for-analysis-of-4xud6qp5de.pdf

An atomic and molecular database for analysis of submillimetre line observations

Rotational spectrum of trans–trans diethyl ether in the ground and three excited vibrational states

A new analysis and additional measurements of the millimeter and submillimeter spectrum of methanol

Rotational transitions of a number of isotopic species of the hydrogen halides have been measured in the 1.0- to 0.38-mm wavelength region of the spectrum. These transitions have been measured with a submillimeter-wave spectrometer which employs a klystron-driven crystal harmonic generator and a 1.6\ifmmode^\circ\else\textdegree\fi{}K InSb photoconducting detector. The following results have been obtained: for H $^{35}\mathrm{Cl}$, ${B}_{0}=312 989.297\ifmmode\pm\else\textpm\fi{}0.020$ Mc/sec, ${D}_{0}=15.836$ Mc/sec, ${r}_{e}=1.274 5991$ \AA{}; for H $^{37}\mathrm{Cl}$, ${B}_{0}=312 519.121\ifmmode\pm\else\textpm\fi{}0.020$ Mc/sec, ${D}_{0}=15.788$ Mc/sec, ${r}_{e}=1.274 5990$ \AA{}; for D $^{35}\mathrm{Cl}$, ${B}_{0}=161 656.238\ifmmode\pm\else\textpm\fi{}0.014$ Mc/sec, ${D}_{0}=4.196\ifmmode\pm\else\textpm\fi{}0.003$ Mc/sec, ${r}_{e}=1.274 5990$ \AA{}; for D $^{37}\mathrm{Cl}$, ${B}_{0}=161 183.122\ifmmode\pm\else\textpm\fi{}0.016$ Mc/sec, ${D}_{0}=4.162\ifmmode\pm\else\textpm\fi{}0.003$ Mc/sec, ${r}_{e}=1.274 5988$ \AA{}; for H $^{127}\mathrm{I}$, ${B}_{0}=192 657.577\ifmmode\pm\else\textpm\fi{}0.019$ Mc/sec, ${D}_{0}=6.203\ifmmode\pm\else\textpm\fi{}0.003$ Mc/sec, ${r}_{e}=1.609 018$ \AA{}; for D $^{127}\mathrm{I}$, ${B}_{0}=97 537.092\ifmmode\pm\else\textpm\fi{}0.009$ Mc/sec, ${D}_{0}=1.578\ifmmode\pm\else\textpm\fi{}0.001$ Mc/sec, ${r}_{e}=1.609 018$ \AA{}; for D $^{79}\mathrm{Br}$, ${B}_{0}=127 357.639\ifmmode\pm\else\textpm\fi{}0.012$ Mc/sec, ${D}_{0}=2.6529\ifmmode\pm\else\textpm\fi{}0.0014$ Mc/sec, ${r}_{e}=1.414 4698$ \AA{}; for D $^{81}\mathrm{Br}$, ${B}_{0}=127 279.757\ifmmode\pm\else\textpm\fi{}0.017$ Mc/sec, ${D}_{0}=2.6479\ifmmode\pm\else\textpm\fi{}0.0020$ Mc/sec, ${r}_{e}=1.414 4698$ \AA{}; for D $^{19}\mathrm{F}$, ${B}_{0}=325 584.98\ifmmode\pm\else\textpm\fi{}0.300$ Mc/sec, ${D}_{0}=17.64$ Mc/sec, ${r}_{e}=0.916 914$ \AA{}.

Submillimeter-Wave Spectra and Equilibrium Structures of the Hydrogen Halides

Molecular force field and structure of water: Recent microwave results

A technique for enhancement of positive molecular ion concentrations in a glow discharge is presented. The technique consists of modifying an anomalous glow discharge by the addition of a longitudinal magnetic field of up to 300 G. Enhancements in the ion signal strength, as measured by millimeter and submillimeter wave spectroscopy, are approximately two orders of magnitude. Evidence is presented that the magnetic field increases the length of the ion rich negative glow by restricting inside a small diameter tube the ionizing electrons accelerated by the large cathode drop of an anomalous glow discharge.

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Frank C. De Lucia

Papers

Rotational spectrum of trans–trans diethyl ether in the ground and three excited vibrational states

A new analysis and additional measurements of the millimeter and submillimeter spectrum of methanol

Submillimeter-Wave Spectra and Equilibrium Structures of the Hydrogen Halides

Molecular force field and structure of water: Recent microwave results

The production of large concentrations of molecular ions in the lengthened negative glow region of a discharge