James S. Prell

Bio: James S. Prell is an academic researcher from University of Oregon. The author has contributed to research in topics: Ion & Mass spectrometry. The author has an hindex of 28, co-authored 63 publications receiving 2627 citations. Previous affiliations of James S. Prell include University of California, Berkeley.

Attosecond band-gap dynamics in silicon

Abstract: Electron transfer from valence to conduction band states in semiconductors is the basis of modern electronics. Here, attosecond extreme ultraviolet (XUV) spectroscopy is used to resolve this process in silicon in real time. Electrons injected into the conduction band by few-cycle laser pulses alter the silicon XUV absorption spectrum in sharp steps synchronized with the laser electric field oscillations. The observed ~450-attosecond step rise time provides an upper limit for the carrier-induced band-gap reduction and the electron-electron scattering time in the conduction band. This electronic response is separated from the subsequent band-gap modifications due to lattice motion, which occurs on a time scale of 60 ± 10 femtoseconds, characteristic of the fastest optical phonon. Quantum dynamical simulations interpret the carrier injection step as light-field–induced electron tunneling.

Shapes and vorticities of superfluid helium nanodroplets

Abstract: Helium nanodroplets are considered ideal model systems to explore quantum hydrodynamics in self-contained, isolated superfluids. However, exploring the dynamic properties of individual droplets is experimentally challenging. In this work, we used single-shot femtosecond x-ray coherent diffractive imaging to investigate the rotation of single, isolated superfluid helium-4 droplets containing ~108 to 1011 atoms. The formation of quantum vortex lattices inside the droplets is confirmed by observing characteristic Bragg patterns from xenon clusters trapped in the vortex cores. The vortex densities are up to five orders of magnitude larger than those observed in bulk liquid helium. The droplets exhibit large centrifugal deformations but retain axially symmetric shapes at angular velocities well beyond the stability range of viscous classical droplets.

Infrared spectroscopy of cationized arginine in the gas phase: direct evidence for the transition from nonzwitterionic to zwitterionic structure.

Abstract: The gas-phase structures of protonated and alkali metal cationized arginine (Arg) and arginine methyl ester (ArgOMe) are investigated with infrared spectroscopy and ab initio calculations. Infrared spectra, measured in the hydrogen-stretch region, provide compelling evidence that arginine changes from its nonzwitterionic to zwitterionic form with increasing metal ion size, with the transition in structure occurring between lithium and sodium. For sodiated arginine, evidence for both forms is obtained from spectral deconvolution, although the zwitterionic form is predominant. Comparisons of the photodissociation spectra with spectra calculated for low-energy candidate structures provide additional insights into the detailed structures of these ions. Arg*Li+, ArgOMe*Li+, and ArgOMe*Na+ exist in nonzwitterionic forms in which the metal ion is tricoordinated with the amino acid, whereas Arg*Na+ and Arg*K+ predominately exist in a zwitterionic form where the protonated side chain donates one hydrogen bond to the N terminus of the amino acid and the metal ion is bicoordinated with the carboxylate group. Arg*H+ and ArgOMe*H+ have protonated side chains that form the same interaction with the N terminus as zwitterionic, alkali metal cationized arginine, yet both are unambiguously determined to be nonzwitterionic. Calculations indicate that for clusters with protonated side chains, structures with two strong hydrogen bonds are lowest in energy, in disagreement with these experimental results. This study provides new detailed structural assignments and interpretations of previously observed fragmentation patterns for these ions.

Sulfate ion patterns water at long distance.

Abstract: The chemical origins of the Hofmeister series are investigated using infrared photodissociation (IRPD) spectroscopy. IRPD spectra of SO(4)(2-)(H(2)O)(n) with up to 80 water molecules have a band at approximately 3710 cm(-1) for n > 43 but not for n < or = 43. This band corresponds to outer-shell water molecules with "free" OH groups similar to those at the surface of bulk water. These results indicate that the sulfate dianion has a long-range effect on water structure, and this effect is likely to be an important factor in its Hofmeister behavior.

Direct and simultaneous observation of ultrafast electron and hole dynamics in germanium.

Abstract: Understanding excited carrier dynamics in semiconductors is crucial for the development of photovoltaics and efficient photonic devices However, overlapping spectral features in optical pump-probe spectroscopy often render assignments of separate electron and hole carrier dynamics ambiguous Here, ultrafast electron and hole dynamics in germanium nanocrystalline thin films are directly and simultaneously observed by ultrafast transient absorption spectroscopy in the extreme ultraviolet at the germanium M4,5 edge We decompose the spectra into contributions of electronic state blocking and photo-induced band shifts at a carrier density of 8 × 1020 cm-3 Separate electron and hole relaxation times are observed as a function of hot carrier energies A first-order electron and hole decay of ∼1 ps suggests a Shockley-Read-Hall recombination mechanism The simultaneous observation of electrons and holes with extreme ultraviolet transient absorption spectroscopy paves the way for investigating few- to sub-femtosecond dynamics of both holes and electrons in complex semiconductor materials and across junctions

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Opportunities and challenges in long-read sequencing data analysis.

Abstract: Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long-read data are thus required, but the fast pace of development of such tools can be overwhelming. To assist in the design and analysis of long-read sequencing projects, we review the current landscape of available tools and present an online interactive database, long-read-tools.org, to facilitate their browsing. We further focus on the principles of error correction, base modification detection, and long-read transcriptomics analysis and highlight the challenges that remain.

X-Rays and Extreme Ultraviolet Radiation: Principles and Applications

Abstract: This self-contained, comprehensive book describes the fundamental properties of soft x-rays and extreme ultraviolet (EUV) radiation and discusses their applications in a wide variety of fields, including EUV lithography for semiconductor chip manufacture and soft x-ray biomicroscopy. The author begins by presenting the relevant basic principles such as radiation and scattering, wave propagation, diffraction, and coherence. He then goes on to examine a broad range of phenomena and applications. The topics covered include EUV lithography, biomicroscopy, spectromicroscopy, EUV astronomy, synchrotron radiation, and soft x-ray lasers. He also provides a great deal of useful reference material such as electron binding energies, characteristic emission lines and photo-absorption cross-sections. The book will be of great interest to graduate students and researchers in engineering, physics, chemistry, and the life sciences. It will also appeal to practicing engineers involved in semiconductor fabrication and materials science.

Global Λ hyperon polarization in nuclear collisions

Abstract: © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. The extreme energy densities generated by ultra-relativistic collisions between heavy atomic nuclei produce a state of matter that behaves surprisingly like a fluid, with exceptionally high temperature and low viscosity. Non-central collisions have angular momenta of the order of 1,000h, and the resulting fluid may have a strong vortical structure that must be understood to describe the fluid properly. The vortical structure is also of particular interest because the restoration of fundamental symmetries of quantum chromodynamics is expected to produce novel physical effects in the presence of strong vorticity. However, no experimental indications of fluid vorticity in heavy ion collisions have yet been found. Since vorticity represents a local rotational structure of the fluid, spin-orbit coupling can lead to preferential orientati on of particle spins along the direction of rotation. Here we present measurements of an alignment between the global angular momentum of a non-central collision and the spin of emitted particles (in this case the collision occurs between gold nuclei and produces Λ baryons), revealing that the fluid produced in heavy ion collisions is the most vortical system so far observed. (At high energies, this fluid is a quark-gluon plasma.) We find that Λ and hyperons show a positive polarization of the order of a few per cent, consistent with some hydrodynamic predictions. (A hyperon is a particle composed of three quarks, at least one of which is a strange quark; the remainder are up and down quarks, found in protons and neutrons.) A previous measurement that reported a null result, that is, zero polarization, at higher collision energies is seen to be consistent with the trend of our observations, though with larger statistical uncertainties. These data provide experimental access to the vortical structure of the nearly ideal liquid created in a heavy ion collision and should prove valuable in the development of hydrodynamic models that quantitatively connect observations to the theory of the strong force.