Tracing transient charges in expanding clusters

We study transient charges formed in methane clusters following ionization by intense near-infrared laser pulses. Cluster ionization by 400-fs (I=1×1014 W/cm2) pulses is highly efficient, resulting in the observation of a dominant C3+ ion contribution. The C4+ ion yield is very small but is strongly enhanced by applying a time-delayed weak near-infrared pulse. We conclude that most of the valence electrons are removed from their atoms during the laser-cluster interaction and that electrons from the nanoplasma recombine with ions and populate Rydberg states when the cluster expands, leading to a decrease of the average charge state of individual ions. Furthermore, we find clear bound-state signatures in the electron kinetic energy spectrum, which we attribute to Auger decay taking place in expanding clusters. Such nonradiative processes lead to an increase of the final average ion charge state that is measured in experiments. Our results suggest that it is crucial to include both recombination and nonradiative decay processes for the understanding of recorded ion charge spectra

MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long-timescale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large lengthscales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time- and lengthscales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step towards MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported

Ionization avalanching in clusters ignited by extreme-ultraviolet driven seed electrons

We study the ionization dynamics of Ar clusters exposed to ultrashort near-infrared (NIR) laser pulses for intensities well below the threshold at which tunnel ionization ignites nanoplasma formation. We find that the emission of highly charged ions up to Ar$^{8+}$ can be switched on with unit contrast by generating only a few seed electrons with an ultrashort extreme ultraviolet (XUV) pulse prior to the NIR field. Molecular dynamics simulations can explain the experimental observations and predict a generic scenario where efficient heating via inverse bremsstrahlung and NIR avalanching are followed by resonant collective nanoplasma heating. The temporally and spatially well-controlled injection of the XUV seed electrons opens new routes for controlling avalanching and heating phenomena in nanostructures and solids, with implications for both fundamental and applied laser-matter science.Comment: 5 pages, 4 figure

Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes

Quantum dynamical simulations of vibrational spectroscopy have been carried out for glycine dipeptide (CH3-CO-NH-CH2-CO-NH-CH3). Conformational structure and dynamics are modeled in terms of the two Ramachandran dihedral angles of the molecular backbone. Potential energy surfaces and harmonic frequencies are obtained from electronic structure calculations at the density functional theory (B3LYP/6-31+G(d)) level. The ordering of the energetically most stable isomers (C7 and C5) is reversed upon inclusion of the quantum mechanical zero point vibrational energy. Vibrational spectra of various isomers show distinct differences, mainly in the region of the amide modes, thereby relating conformational structures and vibrational spectra. Conformational dynamics is modeled by propagation of quantum mechanical wave packets. Assuming a directed energy transfer to the torsional degrees of freedom, transitions between the C7 and C5 minimum energy structures occur on a sub-picosecond timescale (700 ... 800 fs). Vibrationally non-adiabatic effects are investigated for the case of the coupled, fundamentally excited amide I states. Using a two state-two mode model, the resulting wave packet dynamics is found to be strongly non-adiabatic due to the presence of a seam of the two potential energy surfaces. Initially prepared adiabatic vibrational states decay upon conformational change on a timescale of 200 ... 500 fs with population transfer of more than 50 % between the coupled amide I states. Also the vibrational energy transport between localized (excitonic) amide I vibrational states is strongly influenced by torsional dynamics of the molecular backbone where both enhanced and reduced decay rates are found. All these observations should allow the detection of conformational changes by means of time-dependent vibrational spectroscopy

Intense XUV pulses from a compact HHG setup using a single harmonic

We report on a compact and spectrally intense extreme-ultraviolet (XUV) source, which is based on high-harmonic generation (HHG) driven by 395 nm pulses. In order to minimize the XUV virtual source size and to maximize the XUV flux, HHG is performed several Rayleigh lengths away from the driving laser focal plane in a high-density gas jet. As a result, a high focused XUV intensity of 5 × 1013 W cm−2 is achieved, using a beamline with a length of only two meters and a modest driving laser pulse energy of 3 mJ. The high XUV intensity is demonstrated by performing a nonlinear ionization experiment in argon, using an XUV spectrum that is dominated by a single harmonic at 22 eV. Ion charge states up to Ar3+ are observed, which requires the absorption of at least four XUV photons. The high XUV intensity and the narrow bandwidth are ideally suited for a variety of applications including photoelectron spectroscopy, the coherent control of resonant transitions and the imaging of nanoscale structures

Barcoding and interspecific relationships of Macaronesian Weevils (Coleoptera: Curculionoidea)

In dieser integrativ-taxonomischen Studie werden für 468 der 735 bisher beschriebenen lauri-makaronesischen Arten und Unterarten der Rüsselkäfer (Curculionoidea) mitochondriale CO1-Barcodes in 1388 Proben vorgelegt. Ein Bayes‘scher Baum (elektronisches Supplement) gibt Einblicke in die Beziehungen innerhalb der Arten und Unterarten, ohne ein phylogenetisches Gesamtbild oberhalb der Gattungsebene anzustreben. Mit Ausnahme einiger weniger diskutierter Fälle erlaubt der vorliegende Datensatz von DNA-Barcodes eine zuverlässige Re-Identifizierung und bemerkenswerte Differenzierung von Arten und wird die Entdeckung und Beschreibung neuer Rüsselkäfer-Arten - sowie deren (Re-) Synonymisierung - von den Kanaren, Madeira, und den Azoren beschleunigen. Nur in einem einzigen Fall, bei den eingewanderten, verwandten Arten Rhinoncus castor und R. bruchoides (Ceutorhynchinae) aus Madeira, ergab die molekulare (Re-)Identifizierung einen unauflösbaren Widerspruch zu unserer morphologischen Artbestimmung. In den meisten Fällen wurden die morphologischen Bestimmungen zuvor durch Vergleiche mit dem Typenmaterial untermauert und sequenzierte Exemplare wurden in einer Referenzsammlung für spätere Nachbestimmungen hinterlegt.In an integrative taxonomic approach, this study presents mitochondrial CO1 barcodes for 468 of the 735 so far described Lauri-Macaronesian weevil (Curculionoidea) species and subspecies in 1388 samples. A Bayesian tree (electronic supplement) provides insights into within-species relationships, without aiming at phylogenetic accuracy above genus level. With the exception of a few discussed cases, the present dataset of DNA barcodes allows a reliable re-identification and remarkable differentiation of species and will accelerate the discovery of new weevil species from the Canary, Madeira and Azores archipelagos. Only in a single case, the similar species Rhinoncus castor and R. bruchoides (Ceutorhynchinae) from Madeira, did the molecular (re)identification reveal an unresolvable contradiction with our morphological species identification. In many cases, morphological determinations were bolstered by comparisons with the type material. Sequenced specimens were mounted and deposited in a reference collection for later re-determinations

Rare-Gas Clusters in Intense Extreme-Ultraviolet Pulses from a High-Order Harmonic Source

We report evidence for two previously unidentified effects in the ionization of rare-gas clusters by intense extreme-ultraviolet pulses. First, electron spectra indicate multistep photoemission with increasing isotropy for larger clusters due to electron-atom collisions. Second, very slow (meV) electrons are interpreted as the first experimental evidence for Rydberg-like atomic state formation in the nanoplasma expansion. Only small fractions of Xe2+ ions were found, in sharp contrast to previous results recorded under comparable conditions [Murphy et al., Phys. Rev. Lett. 101, 203401 (2008)]