Switched wave packets: A route to nonperturbative quantum control

The dynamic Stark effect due to a strong nonresonant but nonionizing laser field provides a route to quantum control via the creation of novel superposition states. We consider the creation of a field-free "switched" wave packet through adiabatic turn-on and sudden turn-off of a strong dynamic Stark interaction. There are two limiting cases for such wave packets. The first is a Raman-type coupling, illustrated by the creation of field-free molecular axis alignment. An experimental demonstration is given. The second case is that of dipole-type coupling, illustrated by the creation of charge localization in an array of quantum wells

Alignment enhancement of molecules embedded in helium nanodroplets by multiple laser pulses

We show experimentally that field-free one-dimensional (1D) alignment of 1,4-diiodobenzene molecules embedded in helium nanodroplets, induced by a single, linearly polarized 200-fs laser pulse, can be significantly enhanced by using two or four optimally synchronized laser pulses. The strongest degree of 1D alignment is obtained with four pulses and gives ⟨cos2θ⟩>0.60. Besides the immediate implications for molecular frame studies, our results pave the way for more general manipulation of rotational motion of molecules in He droplets

Stable kilohertz rate molecular beam laser ablation sources

A stable kilohertz (kHz) rate laser ablation/desorption supersonic molecular beam source for use in kHz rate laser experiments was discussed. The source was based based upon strong nonresonant interaction of a dithering laser focus with a rotating and translating solid rod. The kHz laser ablation of a high temperature refractory metal (niobium) for use in studied of metal clusters was also demonstrated. The kHz laser desorption and jet cooling of an involatile biomolecule (the DNA based guanine) for use in spectroscopic and dynamical studies was described.open151

Excited state wavepacket dynamics in NO 2 probed by strong-field ionization

We present an experimental femtosecond time-resolved study of the 399 nm excited state dynamics of nitrogen dioxide using channel-resolved above threshold ionization (CRATI) as the probe process. This method relies on photoelectron-photoion coincidence and covariance to correlate the strongfield photoelectron spectrum with ionic fragments, which label the channel. In all ionization channels observed, we report apparent oscillations in the ion and photoelectron yields as a function of pumpprobe delay. Further, we observe the presence of a persistent, time-invariant above threshold ionization comb in the photoelectron spectra associated with most ionization channels at long time delays. These observations are interpreted in terms of single-pump-photon excitation to the first excited electronic X˜ 2A1 state and multi-pump-photon excitations to higher-lying states. The short time delay (<100 fs) dynamics in the fragment channels show multi-photon pump signatures of higherlying neutral state dynamics, in data sets recorded with higher pump intensities. As expected for pumping NO2 at 399 nm, non-adiabatic coupling was seen to rapidly re-populate the ground state following excitation to the first excited electronic state, within 200 fs. Subsequent intramolecular vibrational energy redistribution results in the spreading of the ground state vibrational wavepacket into the asymmetric stretch coordinate, allowing the wavepacket to explore nuclear geometries in the asymptotic region of the ground state potential energy surface. Signatures of the vibrationally “hot” ground state wavepacket were observed in the CRATI spectra at longer time delays. This study highlights the complex and sometimes competing phenomena that can arise in strong-field ionization probing of excited state molecular dynamics

A mutate-and-map protocol for inferring base pairs in structured RNA

Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This experimental framework has been extensively revisited in the past decade with new strategies for high-throughput read-outs, chemical modification, and rapid data analysis. Recently, we have coupled the technique to high-throughput mutagenesis. Point mutations of a base-paired nucleotide can lead to exposure of not only that nucleotide but also its interaction partner. Carrying out the mutation and mapping for the entire system gives an experimental approximation of the molecules contact map. Here, we give our in-house protocol for this mutate-and-map strategy, based on 96-well capillary electrophoresis, and we provide practical tips on interpreting the data to infer nucleic acid structure.Comment: 22 pages, 5 figure

Genetic variation in the HLA region is associated with susceptibility to herpes zoster.

Herpes zoster, commonly referred to as shingles, is caused by the varicella zoster virus (VZV). VZV initially manifests as chicken pox, most commonly in childhood, can remain asymptomatically latent in nerve tissues for many years and often re-emerges as shingles. Although reactivation may be related to immune suppression, aging and female sex, most inter-individual variability in re-emergence risk has not been explained to date. We performed a genome-wide association analyses in 22,981 participants (2280 shingles cases) from the electronic Medical Records and Genomics Network. Using Cox survival and logistic regression, we identified a genomic region in the combined and European ancestry groups that has an age of onset effect reaching genome-wide significance (P&gt;1.0 × 10(-8)). This region tags the non-coding gene HCP5 (HLA Complex P5) in the major histocompatibility complex. This gene is an endogenous retrovirus and likely influences viral activity through regulatory functions. Variants in this genetic region are known to be associated with delay in development of AIDS in people infected by HIV. Our study provides further suggestion that this region may have a critical role in viral suppression and could potentially harbor a clinically actionable variant for the shingles vaccine

Lead Exposure: A Contributing Cause of the Current Breast Cancer Epidemic in Nigerian Women

Breast cancer incidence in Nigerian women has significantly increased during the past three decades in parallel with the rapid industrialization of that country. This suggested that the associated widespread contamination of the soil and of the water supplies by lead (Pb) and other industrial metals was a major contributing cause. Because of its many domestic, industrial, and automotive uses, Pb is of particular concern as it has been shown to promote the development of mammary tumors in murine mammary tumor virus-infected female C3H mice at levels as low of 0.5 ppm Pb in the drinking water. Lead belongs to the group of selenium-antagonistic elements that interact with selenium (Se), abolishing its anti-carcinogenic effect. Lead on chronic, low-level exposure in addition also accelerates tumor growth rates. Higher levels of Pb were found in blood and head hair samples of newly diagnosed patients with breast cancer, all with infiltrating ductal carcinoma, the most common form of breast cancer in Nigeria, seen at Obafemi Awolowo University, than in cancer-free controls from the same area. Evidence for interactions between Pb and Se was obtained from blood, hair, and tumor biopsy tissue analyses. Furthermore, the Pb levels in hair samples of the patients were directly correlated with the volumes of their tumors, in accord with the tumor growth-promoting effects of Pb. Conversely, Se levels in hair and blood were inversely correlated with the tumor volumes, consistent with the anti-proliferative effects of Se. Several other elements, e.g., Cd, Hg, Cr, Sn, and As, were detected in the scalp hair of the patients and the controls, although at significantly lower levels than those of Pb. However, correlation calculations revealed them also to interact with Se, suggesting that only a fraction of the Se in organs and tissues is actually present in bioactive forms. In metal-exposed subjects, a state of latent Se deficiency may exist, resulting in depressed immune functions and increased cancer susceptibility. Evidence is presented to show that Pb and other metals also interact with iodine, another vitally important essential trace element believed to protect against breast cancer development. Public health programs aiming at lowering the breast cancer risk of Nigerian women thus will have to include effective measures to protect the population from exposures to Pb and other industrial metals that are presently contaminating the environment and the water supplies

RNA secondary structure prediction from multi-aligned sequences

It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome. In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted. I systematically review and classify existing tools and algorithms for the problem, by utilizing the information employed in the tools and by adopting a unified viewpoint based on maximum expected gain (MEG) estimators. I believe that this classification will allow a deeper understanding of each tool and provide users with useful information for selecting tools for common secondary structure predictions.Comment: A preprint of an invited review manuscript that will be published in a chapter of the book `Methods in Molecular Biology'. Note that this version of the manuscript may differ from the published versio

Probing orbital structure of polyatomic molecules by high-order harmonic generation (vol 98, art no 203007, 2007)

Publisher’s Note: Probing Orbital Structure of Polyatomic Molecules by High-Order Harmonic Generation [Phys. Rev. Lett. 98, 203007 (2007)

Development and evolution of dentition pattern and tooth order in the Skates and Rays (Batoidea; Chondrichthyes)

Shark and ray (elasmobranch) dentitions are well known for their multiple generations of teeth, with isolated teeth being common in the fossil record. However, how the diverse dentitions characteristic of elasmobranchs form is still poorly understood. Data on the development and maintenance of the dental patterning in this major vertebrate group will allow comparisons to other morphologically diverse taxa, including the bony fishes, in order to identify shared pattern characters for the vertebrate dentition as a whole. Data is especially lacking from the Batoidea (skates and rays), hence our objective is to compile data on embryonic and adult batoid tooth development contributing to ordering of the dentition, from cleared and stained specimens and micro-CT scans, with 3D rendered models. We selected species (adult and embryonic) spanning phylogenetically significant batoid clades, such that our observations may raise questions about relationships within the batoids, particularly with respect to current molecular-based analyses. We include developmental data from embryos of recent model organisms Leucoraja erinacea and Raja clavata to evaluate the earliest establishment of the dentition. Characters of the batoid dentition investigated include alternate addition of teeth as offset successional tooth rows (versus single separate files), presence of a symphyseal initiator region (symphyseal tooth present, or absent, but with two parasymphyseal teeth) and a restriction to tooth addition along each jaw reducing the number of tooth families, relative to addition of successor teeth within each family. Our ultimate aim is to understand the shared characters of the batoids, and whether or not these dental characters are shared more broadly within elasmobranchs, by comparing these to dentitions in shark outgroups. These developmental morphological analyses will provide a solid basis to better understand dental evolution in these important vertebrate groups as well as the general plesiomorphic vertebrate dental condition