Time-resolved RNA SHAPE chemistry

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry yields quantitative RNA secondary and tertiary structure information at single nucleotide resolution. SHAPE takes advantage of the discovery that the nucleophilic reactivity of the ribose 2'-hydroxyl group is modulated by local nucleotide flexibility in the RNA backbone. Flexible nucleotides are reactive toward hydroxyl-selective electrophiles, whereas constrained nucleotides are unreactive. Initial versions of SHAPE chemistry, which employ isatoic anhydride derivatives that react on the minute time scale, are emerging as the ideal technology for monitoring equilibrium structures of RNA in a wide variety of biological environments. Here, we extend SHAPE chemistry to a benzoyl cyanide scaffold to make possible facile time-resolved kinetic studies of RNA in approximately 1 s snapshots. We then use SHAPE chemistry to follow the time-dependent folding of an RNase P specificity domain RNA. Tertiary interactions form in two distinct steps with local tertiary contacts forming an order of magnitude faster than long-range interactions. Rate-determining tertiary folding requires minutes despite that no non-native interactions must be disrupted to form the native structure. Instead, overall folding is limited by simultaneous formation of interactions approximately 55 A distant in the RNA. Time-resolved SHAPE holds broad potential for understanding structural biogenesis and the conformational interconversions essential to the functions of complex RNA molecules at single nucleotide resolution.     

Designing functionalized porphyrins capable of pseudo-2D self-assembly on surfaces

A crystallography-instructed strategy to highly ordered layering of porphyrins with different topologies on HOPG is developed based on meso-tetraarylporphyrins bearing 2-ethoxyethanol side chains as "sticky ends". These sticky ends are capable of displaying directive hydrogen bonding motifs with the inherent D4h symmetry of the porphyrins. Solvent effects are shown to have an important role in fabricating the adsorption. Metalation and subsequent axial ligation was a key controlling factor in the topology of the layer, leading to pseudo-2D structures on HOPG.     

M + Ng potential energy curves including spin-orbit coupling for M = K, Rb, Cs and Ng = He, Ne, Ar

The X(2)Σ(1/2)(+), A(2)Π(1∕2), A(2)Π(3∕2), and B(2)Σ(1/2)(+) potential energy curves and associated dipole matrix elements are computed for M + Ng at the spin-orbit multi-reference configuration interaction level, where M = K, Rb, Cs and Ng = He, Ne, Ar. Dissociation energies and equilibrium positions for all minima are identified and corresponding vibrational energy levels are computed. Difference potentials are used together with the quasistatic approximation to estimate the position of satellite peaks of collisionally broadened D2 lines. The comparison of potential energy curves for different alkali atom and noble gas atom combinations is facilitated by using the same level of theory for all nine M + Ng pairs.     

Determination of sublimation rate of 2,4,6-trinitrotoluene (TNT) nano thin films using UV-absorbance spectroscopy

We report the in situ measurements of the sublimation rate and activation energy of continuous nanofilms of 2,4,6-trinitrotoluene (TNT) in air using UV absorbance spectroscopy. The films were prepared using acetone-dissolved TNT by simple spin coating deposition technique. Unlike traditional mass loss techniques, this new method is independent of the surface area of the sample which contributes to errors in determining physical parameters accurately in both bulk and thin films of materials. The calculated activation energy and temperature-dependent sublimation rates agree well with the reported values for TNT thin films. The results suggest that UV absorbance spectroscopy is an efficient tool in measuring thermodynamic properties in the nanometer scale for materials with absorbance in the UV region of the electromagnetic spectrum.     

Guidance Trajectories for Spacecraft Rendezvous

In a previous paper of Miele et al. (J. Optim. Theory Appl. 132(1), 2007), we employed the single-subarc sequential gradient-restoration algorithm to optimize the three-dimensional rendezvous between a target spacecraft in a planar circular orbit and a chaser spacecraft with an initial separation distance and separation velocity. The achieved continuous solutions are characterized by two, three, or four subarcs depending on the performance index (time, fuel) and the constraints. In this paper, based on the solutions in Miele et al. (J. Optim. Theory Appl. 132(1), 2007), we employ the multiple-subarc sequential gradient-restoration algorithm to produce pieced guidance trajectories implementable in real time via constant control components. In other words, in this investigation, we force the controls to behave as parameters in each subarc. With the above understanding, we investigate four problems: (P1) minimum time, fuel free; (P2) minimum fuel, time free; (P3) minimum time, fuel given; (P4) minimum fuel, time given. Problem P1 results in a two-subarc solution, each subarc with constant controls: a max-thrust accelerating subarc followed by a max-thrust braking subarc. Problem P2 results in a four-subarc solution, each subarc with constant controls: an initial coasting subarc, followed by a max-thrust braking subarc, followed by another coasting subarc, followed by another max-thrust braking subarc. Problems P3 and P4 result in two, three, or four-subarc solutions depending on the performance index and the constraints, albeit with constant controls in each subarc. For each of the problems studied, the performance index of the multiple-subarc pieced guidance trajectory approximates well the performance index of the single-subarc continuous optimal trajectory of Miele et al. (J. Optim. Theory Appl. 132(1), 2007) as well as the performance index of the multiple-subarc pieced optimal trajectory: the pairwise relative differences in performance index are less than 1/100. This research was supported by NSF under Grant CMS-0218878.     

Laser-excited molecular fluorescence of CaOH in an air-acetylene flame

Pulsed laser-excited molecular fluorescence of CaOH and SrOH in an air-acetylene flame have been investigated. The spectra were examined in the wavelength region from ca. 500 to 700 nm. A preliminary energy level diagram is proposed for CaOH. Results are also given for SrOH.     

Similarity solutions of radially symmetric two-phase flow

When both the diffusivityD and fractional flow functionf have a power law dependence on the water content , i.e.D=D _o andf=⁺¹, the nonlinear transport equation for radially symmetric two phase flow can, in certain circumstances, be reduced to a weakly coupled system of two first order nonlinear ordinary differential equations. Numerical solutions of these equations for a constant flux boundary conditionV _wo and comparison with experimental data are given. In particular, when the fluxV _wo and a are related byV _wo( + 1)/D _o=2, a new fully explicit analytical solution is found as (r, t)=(1 – r ²/4D _ot)^1/ forr ² < 4D _ot/ and (r, t)=0 forr ² 4D _ot/ We show that the existence of this exact soution is due to the presence of a Lagrangian symmetry.