Quantitative microarray profiling of DNA-binding molecules

A high-throughput Cognate Site Identity (CSI) microarray platform interrogating all 524 800 10-base pair variable sites is correlated to quantitative DNase I footprinting data of DNA binding pyrrole-imidazole polyamides. An eight-ring hairpin polyamide programmed to target the 5 bp sequence 5'-TACGT-3' within the hypoxia response element (HRE) yielded a CSI microarray-derived sequence motif of 5'-WWACGT-3' (W = A,T). A linear beta-linked polyamide programmed to target a (GAA)3 repeat yielded a CSI microarray-derived sequence motif of 5'-AARAARWWG-3' (R = G,A). Quantitative DNase I footprinting of selected sequences from each microarray experiment enabled quantitative prediction of Ka values across the microarray intensity spectrum.     

Evaluating uranium radiochronometry by single-collector mass spectrometry for nuclear forensics: a multi-instrument investigation

Radiochronometric data, a key signature in evaluating the provenance and process history of nuclear material out of regulatory control, are conventionally acquired via multi-collector mass spectrometry. Here we explore the potential of age-dating by single-collector mass spectrometry. To evaluate model age accuracy/precision across different instrument designs, we performed ²³⁰Th–²³⁴U and ²³¹Pa–²³⁵U radiochronometry of CRM 125-A using two single-collector and one multi-collector plasma source mass spectrometers. Single-collector instruments produce accurate model ages for this uranium standard and thus hold promise for nuclear forensics radiochronometry. Increased acquisition of age information via multiple instrument designs will bolster the global response to nuclear interdictions.

     

A Terminal Chlorophosphinidene Complex

Terminal, electrophilic phosphinidene complexes (M=PR) are attractive platforms for PR-transfer to organic substrates. In contrast to aryl- or alkylphosphinidene complexes terminal chlorophosphinidenes (M=PCl) have only been proposed as transient intermediates but isolable example remain elusive. Here we present the transfer of PCl from chloro-substituted dibenzo-7λ³-phosphanorbornadiene to a square-planar osmium(II) PNP pincer complex to give the first isolable, terminal chlorophosphinidene complex with remarkable thermal stability. Os=P bonding was examined computationally giving rise to highly covalent {Os^II=P^ICl} double bonding.     

Intra-dot relaxation and dephasing rates from time-resolved photoluminescence from InAs quantum dot ensembles

An ensemble of InAs quantum dots with ground state transition energies centered at 1.216 eV and density 10¹¹dots/cm² has been studied by time-resolved photoluminescence (PL). The wavelength of the 100-fs excitation pulse was tuned through the ground (excited) state transitions, resulting in resonant (optical phonon sideband) PL. The decay of the PL was time resolved with a streak camera in the interval 1.5–3 ns to avoid scattered laser light. The intensity of the PL was recorded with its polarization both parallel with and perpendicular to the excitation polarization (along one of the crystal’s cleave axes); the ratio is 2.22 at low temperatures and low excitation. A phenomenological rate equation analysis is made, separating the excitations into two classes, one polarized along the excitation polarization and the other unpolarized (either that way immediately after the excitation pulse or scattered from the first class). Excellent fits to the data lead to the conclusion that both classes decay radiatively with a lifetime of 1 ns, and a transfer from the polarized to the unpolarized species takes place with a distribution time of 12 ns at low temperatures and low excitation, dropping rapidly toward zero for temperatures above 30 K and for intense excitation levels. The polarization of a coherently excited ground state exciton should dephase with a rate equal to the sum of the radiative rate plus the inverse of this distribution time.     

In situ and tomographic analysis of dislocation/grain boundary interactions in α-titanium

In situ straining in the transmission electron microscope and diffraction-contrast electron tomography have been applied to the investigation of dislocation/grain boundary and dislocation/twin boundary interactions in α-Ti. It was found that, similar to FCC materials, the transfer of dislocations across grain boundaries is governed primarily by the minimization of the magnitude of the Burgers vector of the residual grain boundary dislocation. That is, grain boundary strain energy density minimization determines the selection of the emitted slip system.     

A radioactive tracer dilution method to determine the mass of molten salt

A new technique for molten salt mass determination, termed radioactive tracer dilution, that uses ²²Na as a tracer was validated at bench scale. It has been a challenging problem to determine the mass of molten salt in irregularly shaped containers, where a highly radioactive, high-temperature molten salt was used to process nuclear spent/used fuel during electrochemical recycling (pyro-processing) or for coolant/fuel salt from molten salt reactors. A radioactive source with known activity is dissolved into the salt. After a complete mixture, a small amount of the salt is sampled and measured in terms of its mass and radioactivity. By finding the ratio of the mass to radioactivity, the unknown salt mass in the original container can be precisely determined.

     

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

The main protease (M^pro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of M^pro, a cysteine protease, have been determined, facilitating structure-based drug design. M^pro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41–Cys145, M^pro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nucleophile Cys145 have been debated in previous studies of SARS-CoV M^pro, but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 M^pro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of M^pro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an α-ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored N_δ (HD) and N_ϵ (HE) protonation of His41 and His164, respectively, the α-ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 M^pro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.

The main protease (M^pro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics.     

ZnO nanowire transistors

ZnO nanowire field-effect transistors (FETs) were fabricated and studied in vacuum and a variety of ambient gases from 5 to 300 K. In air, these n-type nanowire transistors have among the highest mobilities yet reported for ZnO FETs (mu(e) = 13 +/- 5 cm(2) V(-1) s(-1)), with carrier concentrations averaging 5.2 +/- 2.5 x 10(17) cm(-3) and on-off current ratios ranging from 10(5) to 10(7). Four probe measurements show that the resistivity of the Ti/Au-ZnO contacts is 0.002-0.02 Omega.cm. The performance characteristics of the nanowire transistors are intimately tied to the presence and nature of adsorbed surface species. In addition, we describe a dynamic gate effect that seems to involve mobile surface charges and causes hysteresis in the transconductance, among other effects.     

Bounding surface actions on hyperbolic spaces

Given an isometric action of the fundamental group of a closed orientable surface on a δ-hyperbolic space, we find a standard generating set whose translation distances are bounded above in terms of the hyperbolicity constant δ, the genus of the surface, and the injectivity radius of the action, which we assume to be strictly positive.