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.     

The effect of solvent additives on morphology and excited-state dynamics in PCPDTBT:PCBM photovoltaic blends

The dependence of the thin film morphology and excited-state dynamics for the low-bandgap donor-acceptor copolymer poly[2,6-(4,4-bis-(2-ethylhexyl)-4H-cyclopenta[2,1-b;3,4-b']-dithiophene)-alt-4,7-(2,1,3-benzothiadiazole)] (PCPDTBT) in pristine films and in blends (1:2) with [6,6]-phenyl-C(61)-butyric acid methyl ester (PCBM) on the use of the solvent additive 1,8-octanedithiol (ODT) is studied by solid-state nuclear magnetic resonance (NMR) spectroscopy and broadband visible and near-infrared pump-probe transient absorption spectroscopy (TAS) covering a spectral range from 500-2000 nm. The latter allows monitoring of the dynamics of excitons, bound interfacial charge-transfer (CT) states, and free charge carriers over a time range from femto- to microseconds. The broadband pump-probe experiments reveal that excitons are not only generated in the polymer but also in PCBM-rich domains. Depending on the morphology controlled by the use of solvent additives, polymer excitons undergo mainly ultrafast dissociation (<100 fs) in blends prepared without ODT or diffusion-limited dissociation in samples prepared with ODT. Excitons generated in PCBM diffuse slowly to the interface in both samples and undergo dissociation on a time scale of several tens of picoseconds up to hundreds of picoseconds. In both samples a significant fraction of the excitons creates strongly bound interfacial CT states, which exhibit subnanosecond geminate recombination. The total internal quantum efficiency loss due to geminate recombination is estimated to be 50% in samples prepared without ODT and is found to be reduced to 30% with ODT, indicating that more free charges are generated in samples prepared with solvent additives. In samples prepared with ODT, the free charges exhibit clear intensity-dependent recombination dynamics, which can be modeled by Langevin-type recombination with a bimolecular recombination coefficient of 6.3 × 10(-11) cm(3) s(-1). In samples prepared without ODT, an additional nanosecond recombination of polaron pairs is observed in conjunction with an increased intensity-independent trap-assisted nongeminate recombination of charges. Furthermore, a comparison of the triplet-induced absorption spectra of PCPDTBT with the charge-induced absorption in PCPDTBT:PCBM blends reveals that triplets have a very similar excited-state absorption spectrum compared to the free charge carriers, however, in contrast have a distinct intensity-independent lifetime. Overall, our results suggest that whether free charges or strongly bound CT states are created upon dissociation of excitons at the PCPDTBT:PCBM interface is determined instantaneously upon exciton dissociation and that once formed strongly bound CT states rapidly recombine and thus are unlikely to dissociate into free charges. The observation of a significantly larger bimolecular recombination coefficient than previously determined for poly(3-hexylthiophen-2,5-diyl):PCBM (P3HT:PCBM) and PCDTBT:PCBM samples indicates that nongeminate recombination of free charges considerably competes with charge extraction in PCPDTBT:PCBM photovoltaic devices.     

Microstructural and domain effects in epitaxial CoFe2O4 films on MgO with perpendicular magnetic anisotropy

CoFe₂O₄ (CFO) epitaxial thin films of various thicknesses were grown on MgO substrates using the pulsed electron-beam deposition technique. The films have excellent in-plane coherence with the substrate, exhibit layer-by-layer growth and have well-defined thickness fringes in x-ray diffraction measurements. Atomic force microscopy (AFM) measurements indicate that misfit dislocations form in thicker films and the critical thickness for the dislocation formation is estimated. Perpendicular magnetic anisotropy in CFO due to epitaxial in-plane tensile strain from the substrate was found. A stripe-like domain structure in the demagnetized state is demonstrated using magnetic force microscopy (MFM), in agreement with previous predictions. Coercivity increased in thicker films, which is explained by domain wall pinning due to misfit dislocations at the CFO/MgO interface.     

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.     

Beyond benzyl grignards: facile generation of benzyl carbanions from styrenes

Benzylic functionalization is a convenient approach towards the conversion of readily available aromatic hydrocarbon feedstocks into more useful molecules. However, the formation of carbanionic benzyl species from benzyl halides or similar precursors is far from trivial. An alternative approach is the direct reaction of a styrene with a suitable coupling partner, but these reactions often involve the use of precious-metal transition-metal catalysts. Herein, we report the facile and convenient generation of reactive benzyl anionic species from styrenes. A Cu(I)-catalyzed Markovnikov hydroboration of the styrenic double bond by using a bulky pinacol borane source is followed by treatment with KOtBu to facilitate a sterically induced cleavage of the C-B bond to produce a benzylic carbanion. Quenching this intermediate with a variety of electrophiles, including CO(2), CS(2), isocyanates, and isothiocyanates, promotes C-C bond formation at the benzylic carbon atom. The utility of this methodology was demonstrated in a three-step, two-pot synthesis of the nonsteroidal anti-inflammatory drug (±)-flurbiprofen.     

Isothiourea-mediated asymmetric O- to C-carboxyl transfer of oxazolyl carbonates: structure-selectivity profiles and mechanistic studies

The structural motif within a series of tetrahydropyrimidine-based isothioureas necessary for generating high asymmetric induction in the asymmetric Steglich rearrangement of oxazolyl carbonates is fully explored, with crossover and dynamic (19)F?NMR experiments used to develop a mechanistic understanding of this transformation.