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At least 451 records · Page 25

Time-resolved inner-shell photoelectron spectroscopy: From a bound molecule to an isolated atom

Due to its element and site specificity, inner-shell photoelectron spectroscopy is a widely used technique to probe the chemical structure of matter. Here, we show that time-resolved inner-shell photoelectron spectroscopy can be employed to observe ultrafast chemical reactions and the electronic response to the nuclear motion with high sensitivity. The ultraviolet dissociation of iodomethane (CH 3 I) is investigated by ionization above the iodine 4d edge, using time-resolved inner-shell photoelectron and photoion spectroscopy. The dynamics observed in the photoelectron spectra appear earlier and are faster than those seen in the iodine fragments. Finally, the experimental results are interpreted using crystal-field and spin-orbit configuration interaction calculations, and demonstrate that time-resolved inner-shell photoelectron spectroscopy is a powerful tool to directly track ultrafast structural and electronic transformations in gas-phase molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗

Mapping sea ice leads with a coupled numeric/symbolic system

A method is presented which facilitates the detection and delineation of leads with single-channel Landsat data by coupling numeric and symbolic procedures. The procedure consists of three steps: (1) using the dynamic threshold method, an image is mapped to a lead/no lead binary image; (2) the likelihood of fragments to be real leads is examined with a set of numeric rules; and (3) pairs of objects are examined geometrically and merged where possible. The processing ends when all fragments are merged and statistical characteristics are determined, and a map of valid lead objects are left which summarizes useful physical in the lead complexes. Direct implementation of domain knowledge and rapid prototyping are two benefits of the rule-based system. The approach is found to be more successfully applied to mid- and high-level processing, and the system can retrieve statistics about sea-ice leads as well as detect the leads.

Key, J.↗

Time-Resolved Probing of the Iodobenzene C-Band Using XUV-Induced Electron Transfer Dynamics

Time-resolved extreme ultraviolet spectroscopy was used to investigate photodissociation within the iodobenzene C-band. The carbon–iodine bond of iodobenzene was photolyzed at 200 nm, and the ensuing dynamics were probed at 10.3 nm (120 eV) over a 4 ps range. Two product channels were observed and subsequently isolated by using a global fitting method. Their onset times and energetics were assigned to distinct electron transfer dynamics initiated following site-selective ionization of the iodine photoproducts, enabling the electronic states of the phenyl fragments to be identified using a classical over-the-barrier model for electron transfer. In combination with previous theoretical work, this allowed the corresponding neutral photochemistry to be assigned to (1) dissociation via the 7B2, 8A2, and 8B1 states to give ground-state phenyl, Ph(X), and spin–orbit excited iodine and (2) dissociation through the 7A1 and 8B2 states to give excited-state phenyl, Ph(A), and ground-state iodine. The branching ratio was determined to be 87 ± 4% Ph(X) and 13 ± 4% Ph(A). Similarly, the corresponding amount of energy deposited into the internal phenyl modes in these channels was determined to be 44 ± 10 and 65 ± 21%, respectively, and upper bounds to the channel rise times were found to be 114 ± 6 and 310 ± 60 fs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Communication: XFAIMS—eXternal Field Ab Initio Multiple Spawning for electron-nuclear dynamics triggered by short laser pulses

Attoscience is an emerging field where attosecond pulses or few cycle IR pulses are used to pump and probe the correlated electron-nuclear motion of molecules. We present the trajectory-guided eXternal Field Ab Initio Multiple Spawning (XFAIMS) method that models such experiments “on-the-fly,” from laser pulse excitation to fragmentation or nonadiabatic relaxation to the ground electronic state. For the photoexcitation of the LiH molecule, we show that XFAIMS gives results in close agreement with numerically exact quantum dynamics simulations, both for atto- and femtosecond laser pulses. As a result, we then show the ability of XFAIMS to model the dynamics in polyatomic molecules by studying the effect of nuclear motion on the photoexcitation of a sulfine (H 2 CSO).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural and dynamical characteristics of tropomyosin epitopes as the major allergens in shrimp

Highlights: • The epitope region in tropomyosin was more stable than the non-epitope region. • The difference between epitope and non-epitope regions was largest at low pHs. • Lower content of Ala cluster is involved in higher stability of the epitope region. Ingestion of marine invertebrates often causes food allergy, where the major allergens have been reported to be derived from tropomyosin (TM). Intact or the digestive fragments of food allergens generally show resistance to digestion, which is usually attributable to the structural stability (or rigidity). The difference in the structural and dynamical characteristics between the epitope and the non-epitope regions in TM has not yet been well understood. In the present study, molecular dynamics simulation was performed at constant pHs for shrimp TM. By analyzing the main-chain dihedral angle fluctuations and local α-helix contents, we found that the epitope regions are more stable than the non-epitope counterparts, providing a possible physical reason for the resistance to digestion in the epitopes regions. The difference of the structural stability between the epitope and the non-epitope regions was largest at low pHs, even though pH dependence of the structural stability in itself was not significant in both regions. The lower content of the Ala cluster in the epitope region is considered to cause the higher stability of the epitope region.

60 APPLIED LIFE SCIENCES↗

Site-specific interrogation of an ionic chiral fragment during photolysis using an X-ray free-electron laser

Abstract Short-wavelength free-electron lasers with their ultrashort pulses at high intensities have originated new approaches for tracking molecular dynamics from the vista of specific sites. X-ray pump X-ray probe schemes even allow to address individual atomic constituents with a ‘trigger’-event that preludes the subsequent molecular dynamics while being able to selectively probe the evolving structure with a time-delayed second X-ray pulse. Here, we use a linearly polarized X-ray photon to trigger the photolysis of a prototypical chiral molecule, namely trifluoromethyloxirane (C 3 H 3 F 3 O), at the fluorine K-edge at around 700 eV. The created fluorine-containing fragments are then probed by a second, circularly polarized X-ray pulse of higher photon energy in order to investigate the chemically shifted inner-shell electrons of the ionic mother-fragment for their stereochemical sensitivity. We experimentally demonstrate and theoretically support how two-color X-ray pump X-ray probe experiments with polarization control enable XFELs as tools for chiral recognition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The dynamical origins of the dark comets and a proposed evolutionary track

So-called ‘dark comets’ are small, morphologically inactive near-Earth objects (NEOs) that exhibit nongravitational accelerations inconsistent with radiative effects. These objects exhibit short rotational periods (minutes to hours), where measured. We find that the strengths required to prevent catastrophic disintegration are consistent with those measured in cometary nuclei and expected in rubble pile objects. We hypothesize that these dark comets are the end result of a rotational fragmentation cascade, which is consistent with their measured physical properties. We calculate the predicted size-frequency distribution for objects evolving under this model. Using dynamical simulations, we further demonstrate that the majority of these bodies originated from the 𝜈6 resonance, implying the existence of volatiles in the current inner main belt. Moreover, one of the dark comets, (523599) 2003 RM, likely originated from the outer main belt, although a JFC origin is also plausible. These results provide strong evidence that volatiles from a reservoir in the inner main belt are present in the near-Earth environment.

Aster G Taylor↗

First-principles study of crystalline and amorphous AlMgB{sub 14}-based materials

We report first-principles investigations of crystalline and amorphous boron and M1{sub x}M2{sub y}X{sub z}B{sub 14−z} (M1, M2 = Al, Mg, Li, Na, Y; X = Ti, C, Si) phases (so-called “BAM” materials). Phase stability is analyzed in terms of formation energy and dynamical stability. The atomic configurations as well as the electronic and phonon density states of these phases are compared. Amorphous boron consists of distorted icosahedra, icosahedron fragments, and dioctahedra, connected by an amorphous network. The presence of metal atoms in amorphous BAM materials precludes the formation of icosahedra. For all the amorphous structures considered here, the Fermi level is located in the mobility gap independent of the number of valence electrons. The intra-icosahedral vibrations are localized in the range of 800 cm{sup −1}, whereas the inter-icosahedral vibrations appear at higher wavenumbers. The amorphization leads to an enhancement of the vibrations in the range of 1100–1250 cm{sup −1}. The mechanical properties of BAM materials are investigated at equilibrium and under shear and tensile strain. The anisotropy of the ideal shear and tensile strengths is explained in terms of a layered structure of the B{sub 12} units. The strength of amorphous BAM materials is lower than that of the crystalline counterparts because of the partial fragmentation of the boron icosahedra in amorphous structures. The strength enhancement found experimentally for amorphous boron-based films is very likely related to an increase in film density, and the presence of oxygen impurities. For crystalline BAM materials, the icosahedra are preserved during elongation upon tension as well as upon shear in the (010)[100] slip system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Intricate Crystal Structure of Dihydrolipoamide Dehydrogenase (E3) with its Binding Protein: Multiple Copies, Dynamic and Static Disorders

Human E3 and binding protein E3BP are two components of the pyruvate dehydrogenase complex. Crystallization of E3 with 221-amino acid fragment of E3BP (E3BPdd) led to crystals that diffracted to a resolution of 2.6 Angstroms. Structure determination involved molecular replacement using a dimer of E3 homolog as a search model and de novo building of the E3BPdd peptide. Solution was achieved by inclusion of one E3 dimer at a time, followed by refinement until five E3 dimers were located. This complete content of E3 provided electron density maps suitable for tracing nine peptide chains of E3BPdd, eight of them being identified with partial occupancies. Final content of the asymmetric unit consists of five E3 dimers, each binding one E3BPdd molecule. In four of these molecular complexes, E3BPdd is in static disorder resulting in E3BPdd binding to either one or the other monomer of the E3 dimer. However, E3BPdd of the fifth E3 dimer forms specific contacts that lock it at one monomer. In addition to this static disorder, E3BPdd reveals high mobility in the limited space of the crystal lattice. Support from NIH and NASA.

Makal, A.↗

Conformer-Specific Dissociation Dynamics in Dimethyl Methylphosphonate Radical Cation

The dynamics of the dimethyl methylphosphonate (DMMP) radical cation after production by strong field adiabatic ionization have been investigated. Pump-probe experiments using strong field 1300 nm pulses to adiabatically ionize DMMP and a 800 nm non-ionizing probe induce coherent oscillations of the parent ion yield with a period of about 45 fs. The yields of two fragments, PO 2 C 2 H 7 + and PO 2 CH 4 + , oscillate approximately out of phase with the parent ion, but with a slight phase shift relative to each other. We use electronic structure theory and nonadiabatic surface hopping dynamics to understand the underlying dynamics. The results show that while the cation oscillates on the ground state along the P=O bond stretch coordinate, the probe excites population to higher electronic states that can lead to fragments PO 2 C 2 H 7 + and PO 2 CH 4 + . The computational results combined with the experimental observations indicate that the two conformers of DMMP that are populated under experimental conditions exhibit different dynamics after being excited to the higher electronic states of the cation leading to different dissociation products. These results highlight the potential usefulness of these pump-probe measurements as a tool to study conformer-specific dynamics in molecules of biological interest.

59 BASIC BIOLOGICAL SCIENCES↗

Sunspots and the physics of magnetic flux tubes. X - On the hydrodynamic instability of buoyant fields

The hydrodynamics of cylindrical buoyant bubbles (magnetic flux tubes) in an atmosphere is examined. Their dynamical stability is considered, with particular attention to the Rayleigh-Taylor and Kelvin-Helmholtz instabilities. The instabilities are sufficient to cause fragmentation in the absence of some strong stabilizing effect such as surface tension or an internal azimuthal magnetic field. The results of the stability analysis are first applied to rising gas bubbles in liquids. Then, since agreement with the experimental data is found, the results are applied to the similar problem of the rising magnetic flux in the sun. Magnetic flux tubes in a fluid velocity field are intrinsically unstable, unless twisted. With the known dynamical limits on the degree of twisting, an upper limit on the diameter of the order of a few hundred kilometers is found for the stability of individual flux tubes in the photosphere. Observations show that tubes, except when clustered to form sunspots, are generally not larger than this amount. Therefore, it is suggested that the hydrodynamic instability of larger tubes is a prime cause of their absence from the solar photosphere.

Tsinganos, K. C.↗

Heavy ion beam physics at Facility for Rare Isotope Beams

The Facility for Rare Isotope Beams (FRIB) will be the world's premier rare-isotope beam facility. Experiments with the majority (~80%) of the isotope predicted to exist will become available. The FRIB facility is based on a superconducting (SC) heavy ion linac with output energy above 200 MeV/u for any ions at beam power of 400 kW. FRIB includes a target facility for in-flight production of rare isotopes. A three-stage fragment separator will be used to prepare fast rare isotope beams with high-purity for nuclear physics experiments. The installation work of the accelerator and experimental systems is approaching completion and multi-stage beam commissioning activities started in summer 2017 with expected project completion in early 2022. In conclusion, the commencement of operation for users' experiments is planned immediately following the project completion.

43 PARTICLE ACCELERATORS↗

Microscopic calculation of fission product yields with particle-number projection

Fission fragments' charge and mass distribution is an important input to applications ranging from basic science to energy production or nuclear nonproliferation. In simulations of nucleosynthesis or calculations of superheavy elements, these quantities must be computed from models, as they are needed in nuclei where no experimental information is available. Until now, standard techniques to estimate these distributions were not capable of accounting for fine-structure effects, such as the odd-even staggering of the charge distributions. In this work, we combine a fully microscopic collective model of fission dynamics with a recent extension of the particle number projection formalism to provide the highest-fidelity prediction of the primary fission fragment distributions for the neutron-induced fission of 235 U and 239 Pu. Here, we show that particle-number projection is an essential ingredient to reproduce odd-even staggering in the charge yields and benchmark the performance of various empirical probability laws that could simulate its effect. This new approach also enables for the first time the realistic determination of two-dimensional isotopic yields within nuclear density functional theory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Isotope effects in dynamics of water isotopologues induced by core ionization at an x-ray free-electron laser

Dynamical response of water exposed to x-rays is of utmost importance in a wealth of science areas. We exposed isolated water isotopologues to short x-ray pulses from a free-electron laser and detected momenta of all produced ions in coincidence. By combining experimental results and theoretical modeling, we identify significant structural dynamics with characteristic isotope effects in H 2 O 2+ , D 2 O 2+ , and HDO 2+ , such as asymmetric bond elongation and bond-angle opening, leading to two-body or three-body fragmentation on a timescale of a few femtoseconds. A method to disentangle the sequences of events taking place upon the consecutive absorption of two x-ray photons is described. The obtained deep look into structural properties and dynamics of dissociating water isotopologues provides essential insights into the underlying mechanisms.

47 OTHER INSTRUMENTATION↗

Explicit 3D continuum fracture modeling with smooth particle hydrodynamics

Impact phenomena shaped our solar system. As usual for most solar system processes, the scales are far different than we can address directly in the laboratory. Impact velocities are often much higher than we can achieve, sizes are often vastly larger, and most impacts take place in an environment where the only gravitational force is the mutual pull of the impactors. The Smooth Particle Hydrodynamics (SPH) technique has been applied in the past to the simulations of giant impacts. In these simulations, the colliding objects were so massive (at least a sizeable fraction of the Earth's mass) that material strength was negligible compared to gravity. This assumption can no longer be made when the bodies are much smaller. To this end, we have developed a 3D SPH code that includes a strength model to which we have added a von Mises yielding relation for stresses beyond the Hugoniot Elastic Limit. At the lower stresses associated with brittle failure, we use a rate-dependent strength based on the nucleation of incipient flaws whose number density is given by a Weibull distribution. Following Grady and Kipp and Melosh et al., we introduce a state variable D ('damage'), 0 less than D less than 1, which expresses the local reduction in strength due to crack growth under tensile loading. Unfortunately for the hydrodynamics, Grady and Kipp's model predicts which fragments are the most probable ones and not the ones that are really formed. This means, for example, that if a given laboratory experiment is modeled, the fragment distribution obtained from the Grady-Kipp theory would be equivalent to a ensemble average over many realizations of the experiment. On the other hand, the hydrodynamics itself is explicit and evolves not an ensemble average but very specific fragments. Hence, there is a clear incompatibility with the deterministic nature of the hydrodynamics equations and the statistical approach of the Grady-Kipp dynamical fracture model. We remedy these shortcomings by making the incipient flaw distribution explicit, i.e., particles carry activation strains which are distributed at random with a probability of occurrence given by the Weibull distribution. If the local principal axis strain exceeds this limit, damage starts to grow. By growing explicit cracks together with statistical cracks (damage) at the sub-particle scale, we ensure that material strength and fragmentation is independent of model resolution. We tested our scheme by simulating laboratory impact experiments on basalt spheres.

Benz, W.↗

Effect of glycosylation on an immunodominant region in the V1V2 variable domain of the HIV-1 envelope gp120 protein

Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal to the disulfide linkages at the base of the surface-exposed variable domains. To dissect the influence of glycans on the conformation these regions, we focused on an antigenic peptide fragment from a disulfide bridge-bounded region spanning the V1 and V2 hyper-variable domains of HIV-1 gp120. We used replica exchange molecular dynamics (MD) simulations to investigate how glycosylation influences its conformation and stability. Simulations were performed with and without N-linked glycosylation at two sites that are highly conserved across HIV-1 isolates (N156 and N160); both are contacts for recognition by V1V2-targeted broadly neutralizing antibodies against HIV-1. Glycosylation stabilized the pre-existing conformations of this peptide construct, reduced its propensity to adopt other secondary structures, and provided resistance against thermal unfolding. Simulations performed in the context of the Env trimer also indicated that glycosylation reduces flexibility of the V1V2 region, and provided insight into glycan-glycan interactions in this region. These stabilizing effects were influenced by a combination of factors, including the presence of a disulfide bond between the Cysteines at 131 and 157, which increased the formation of beta-strands. Together, these results provide a mechanism for conservation of disulfide linkage proximal glycosylation adjacent to the variable domains of gp120 and begin to explain how this could be exploited to enhance the immunogenicity of those regions. Furthermore, these studies suggest that glycopeptide immunogens can be designed to stabilize the most relevant Env conformations to focus the immune response on key neutralizing epitopes.

59 BASIC BIOLOGICAL SCIENCES↗

Multiple time step integrators in ab initio molecular dynamics

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗