The Crystalline Structure of Copper Phthalocyanine Films on ZnO(11̅00)

The structure of copper phthalocyanine (CuPc) thin films (5-100 nm) deposited on single-crystal ZnO(11?00) substrates by organic molecular beam deposition was determined from grazing-incidence X-ray diffraction reciprocal space maps. The crystal structure was identified as the metastable polymorph α-CuPc, but the molecular stacking was found to vary depending on the film thickness: for thin films, a herringbone arrangement was observed, whereas for films thicker than 10 nm, coexistence of both the herringbone and brickstone arrangements was found. We propose a modified structure for the herringbone phase with a larger monoclinic β angle, which leads to intrastack Cu-Cu distances closer to those in the brickstone phase. This structural basis enables an understanding of the functional properties (e.g., light absorption and charge transport) of (opto)electronic devices fabricated from CuPc/ZnO hybrid systems.     

Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch

Experiments demonstrate that Mg(2+) is crucial for structure and function of RNA systems, yet the detailed molecular mechanism of Mg(2+) action on RNA is not well understood. We investigate the interplay between RNA and Mg(2+) at atomic resolution through ten 2-μs explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations. The structure, including three stemloops, is very stable on this time scale. Simulations reveal that outer-sphere coordinated Mg(2+) ions fluctuate on the same time scale as the RNA, and that their dynamics couple. Locally, Mg(2+) association affects RNA conformation through tertiary bridging interactions; globally, increasing Mg(2+) concentration slows RNA fluctuations. Outer-sphere Mg(2+) ions responsible for these effects account for 80% of Mg(2+) in our simulations. These ions are transiently bound to the RNA, maintaining interactions, but shuttled from site to site. Outer-sphere Mg(2+) are separated from the RNA by a single hydration shell, occupying a thin layer 3-5 ? from the RNA. Distribution functions reveal that outer-sphere Mg(2+) are positioned by electronegative atoms, hydration layers, and a preference for the major groove. Diffusion analysis suggests transient outer-sphere Mg(2+) dynamics are glassy. Since outer-sphere Mg(2+) ions account for most of the Mg(2+) in our simulations, these ions may change the paradigm of Mg(2+)-RNA interactions. Rather than a few inner-sphere ions anchoring the RNA structure surrounded by a continuum of diffuse ions, we observe a layer of outer-sphere coordinated Mg(2+) that is transiently bound but strongly coupled to the RNA.     

Diagnosis and prediction of rebounds in financial markets

We introduce the concept of “negative bubbles” as the mirror (but not necessarily exactly symmetric) image of standard financial bubbles, in which positive feedback mechanisms may lead to transient accelerating price falls. To model these negative bubbles, we adapt the Johansen-Ledoit-Sornette (JLS) model of rational expectation bubbles with a hazard rate describing the collective buying pressure of noise traders. The price fall occurring during a transient negative bubble can be interpreted as an effective random down payment that rational agents accept to pay in the hope of profiting from the expected occurrence of a possible rally. We validate the model by showing that it has significant predictive power in identifying the times of major market rebounds. This result is obtained by using a general pattern recognition method that combines the information obtained at multiple times from a dynamical calibration of the JLS model. Error diagrams, Bayesian inference and trading strategies suggest that one can extract genuine information and obtain real skill from the calibration of negative bubbles with the JLS model. We conclude that negative bubbles are in general predictably associated with large rebounds or rallies, which are the mirror images of the crashes terminating standard bubbles.     

A theoretical study of the structure and stability of borohydride on 3d transition metals

The adsorption of borohydride on 3d transition metals (Cr, Mn, Fe, Co, Ni and Cu) was studied using first principles calculations within spin-polarized density functional theory. Magnetic effect on the stability of borohydride is noted. Molecular adsorption is favorable on Co, Ni and Cu, which is characterized by the strong s–d_zz hybridization of the adsorbate-substrate states. Dissociated adsorption structure yielding one or two H adatom fragments on the surface is observed for Cr, Mn and Fe.     

Observation of transverse Anderson localization in an optical fiber

We utilize transverse Anderson localization as the waveguiding mechanism in optical fibers with random transverse refractive index profiles. Using experiments and numerical simulations, we show that the transverse localization results in an effective propagating beam diameter that is comparable to that of a typical index-guiding optical fiber.     

A Hybrid Differential Dynamic Programming Algorithm for Constrained Optimal Control Problems. Part 2: Application

In the first part of this paper series, a new solver, called HDDP, was presented for solving constrained, nonlinear optimal control problems. In the present paper, the algorithm is extended to include practical safeguards to enhance robustness, and four illustrative examples are used to evaluate the main algorithm and some variants. The experiments involve both academic and applied problems to show that HDDP is capable of solving a wide class of constrained, nonlinear optimization problems. First, the algorithm is verified to converge in a single iteration on a simple multi-phase quadratic problem with trivial dynamics. Successively, more complicated constrained optimal control problems are then solved demonstrating robust solutions to problems with as many as 7 states, 25 phases, 258 stages, 458 constraints, and 924 total control variables. The competitiveness of HDDP, with respect to general-purpose, state-of-the-art NLP solvers, is also demonstrated.     

Facile identification of photocleavable reactive metabolites and oxidative stress biomarkers in proteins via mass spectrometry

Described herein is a method which combines bond selective fragmentation by photodissociation with online liquid chromatographic separation and mass spectrometric analysis. Photoexcitation of proteins or peptides with 266-nm light does not normally yield abundant fragmentation; however, incorporation of a suitable carbon-sulfur or carbon-halogen bond that is proximal to a chromophore allows access to direct dissociation pathways, resulting in homolytic cleavage of these bonds. Radicals generated through this process can cause further dissociation of the peptide backbone, which is useful for site specifically identifying the point of modification. Two specific applications of this technique for peptide analysis in model systems are presented: (1) identification of reactive metabolites which covalently modify cysteine residues, and (2) characterization of halogenated tyrosine residues which are biomarkers related to oxidative stress. In both cases, these naturally occurring post translational modifications create photocleavable bonds which can be fragmented by 266-nm light. The selectivity offered by photodissociation allows facile identification of the peptides of interest even in complex mixtures, and subsequent selective radical directed backbone fragmentation pinpoints the site of modification. This combination greatly simplifies data analysis and provides more confident assignments.     

Imaging longitudinal changes in articular cartilage and bone following doxycycline treatment in a rabbit anterior cruciate ligament transection model of osteoarthritis

Objective

The development of osteoarthritis following traumatic anterior cruciate ligament (ACL) injury is well established. However, few reliable indicators of early osteoarthritic changes have been established, which has limited the development of effective therapies. T_1ρ and T₂ mapping techniques have the ability to provide highly accurate and quantitative measurements of articular cartilage degeneration in vivo. Relating these cartilaginous changes to high-resolution bone-densitometric evaluations of the late-stage osteoarthritic bone is crucial in elucidating the mechanisms of development of traumatic osteoarthritis (OA) and potential therapies for early- or late-stage intervention.

Methods

Twelve rabbits were monitored with in vivo magnetic resonance imaging (MRI) scans following ACL transection surgery with a contralateral leg sham operation. Six of the rabbits were treated with oral doxycycline for the duration of the experiment. At 12 weeks, the excised knees from three animals from each group (n=6 overall) were subjected to micro-computed tomography (CT) analysis.

Results

Consistent with previous studies, initial elevations in T_1ρ and T₂ values in ACL-transected animals were observed with relative normalization towards values see in sham-operated legs over the 12-week study. This biphasic pattern could hold diagnostic potential to differentiate osteoarthritic cartilage by tracking the relative proportions of T_1ρ and T₂ values as they rise with inflammation then fall as collagen and proteoglycan loss leads to further dehydration. The addition of doxycycline resulted in inconclusive, yet potentially interesting, cartilaginous changes in several compartments of the rabbit legs. Micro-CT studies demonstrated decreased bone densitometrics in ACL-transected knees. Correlation studies suggest that the cartilaginous changes may be associated with some aspects of bony change and the development of OA.

Conclusion

We conclude that there are definite relationships between cartilaginous changes as seen on MRI and late-stage microstructural bony changes after traumatic ACL injury in rabbits. In addition, doxycycline may show promise in mitigating early-stage cartilage damage that may serve to lessen late-stage osteoarthritic changes. This study demonstrates the ability to track OA progression and therapeutic efficacy with imaging modalities in vivo.     

Nuclear data for space radiation

Human space flight requires protecting astronauts from the harmful effects of space radiation. The availability of measured nuclear cross-section data needed for these studies is reviewed in the present paper. The energy range of interest for radiation protection is approximately 100 MeV/n–10 GeV/n. The majority of data are for projectile fragmentation partial and total cross-sections, including both charge changing and isotopic cross-sections. The cross-section data are organized into categories which include charge changing, elemental, isotopic for total, single and double differential with respect to momentum, energy and angle. Gaps in the data relevant to space radiation protection are discussed and recommendations for future experiments are made.