X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno-oncology.     

How useful are closed captions for learning mathematics via online video?

Closed captioning of instructional videos is a topic that has not seen much discussion despite its importance for hearing-impaired students and recent legal ramifications if videos are not appropriately captioned. In particular, it is unclear what best practice in captioning videos should be to benefit all learners in disciplines such as mathematics with a reliance on the development of visual explanation while providing audio narration. In this paper, we report on a study undertaken at an Australian university, to investigate the perceived level of usefulness of captions and their automatic translations in a mathematics course. We discovered that students broadly agreed that captions are a useful learning feature: to allow flexibility of where and when a video is watched, but also to help understand speaker accents, and clarify explanations that are difficult to hear in the recording. Due to the high levels of use and perceived educational benefits of closed captions in online video but limited literature, there is a significant need for new research in this area. An urgent discussion is needed to explore how students engage with closed captions, how they may support learning, and to investigate implications on instructional design of mathematical videos.     

Utilizing Lifetimes to Suppress Random Coil Features in 2D IR Spectra of Peptides

We report that the waiting time delay in 2D IR pulse sequences can be used to suppress signals from structurally disordered regions of amyloid fibrils. At a waiting time delay of 1.0 ps, the random coil vibrational modes of amylin fibrils are no longer detectable, leaving only the sharp excitonic vibrational features of the fibril β-sheets. Isotope labeling with (13)C(18)O reveals that structurally disordered residues decay faster than residues protected from solvent. Since structural disorder is usually accompanied by hydration, we conclude that the shorter lifetimes of random-coil residues is due to solvent exposure. These results indicate that 2D IR pulse sequences can utilize the waiting time to better resolve solvent-protected regions of peptides and that local mode lifetimes should be included in simulations of 2D IR spectra.     

On the formation mechanism for electrically generated exciplexes in a carbazole–pyridine copolymer

Although carbazole‐containing copolymers are frequently used as hole‐transporting host materials for polymer organic light‐emitting diodes (OLEDs), they often suffer from the formation of undesired exciplexes when the OLED is operated. The reason why exciplexes sometimes form for electrical excitation, yet not for optical excitation is not well understood. Here, we use luminescence measurements and quantum chemical calculations to investigate the mechanism of such exciplex formation for electrical excitation (electroplex formation) in a carbazole–pyridine copolymer. Our results suggest that the exciplex is formed via a positively charged interchain precursor complex. This complex is stabilized by interactions that involve the nitrogen lone pairs on both chain segments. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012     

A Relativistic Hidden-Variable Interpretation for the Massive Vector Field Based on Energy-Momentum Flows

This paper is motivated by the desire to formulate a relativistically covariant hidden-variable particle trajectory interpretation of the quantum theory of the vector field that is formulated in such a way as to allow the inclusion of gravity. We present a methodology for calculating the flows of rest energy and a conserved density for the massive vector field using the time-like eigenvectors and eigenvalues of the stress-energy-momentum tensor. Such flows may be used to define particle trajectories which follow the flow. This work extends our previous work which used a similar procedure for the scalar field. The massive, spin-one, complex vector field is discussed in detail and the flows of energy-momentum are illustrated in a simple example of standing waves in a plane.     

Quantifying induced electric field strengths during gene transfer to the intact rat vasculature

The application of appropriate electric fields to cells and tissues, termed electroporation, can result in efficient and safe gene transfer. We have shown previously that this approach results in high level gene transfer to and expression in the vasculature of living animals. This paper presents the results of an electric field distribution study of a rat mesenteric vasculature model using the Finite-Element Time-Domain (FETD) technique. A novelty of this work is the use of Debye dispersive dielectric parameters, as the electrical response of biological tissues is inherently frequency-dependent. The results compare fairly well with experimental findings.     

First measurements of the HCFC-142b trend from atmospheric chemistry experiment (ACE) solar occultation spectra

The first measurement of the HCFC-142b (CH₃CClF₂) trend near the tropopause has been derived from volume mixing ratio (VMR) measurements at northern and southern hemisphere mid-latitudes for the 2004–2008 time period from spaceborne solar occultation observations recorded at 0.02 cm⁻¹ resolution with the ACE (atmospheric chemistry experiment) Fourier transform spectrometer. The HCFC-142b molecule is currently the third most abundant HCFC (hydrochlorofluorocarbon) in the atmosphere and ACE measurements over this time span show a continuous rise in its volume mixing ratio. Monthly average measurements at northern and southern hemisphere mid-latitudes have similar increase rates that are consistent with surface trend measurements for a similar time span. A mean northern hemisphere profile for the time span shows a near constant VMR at 8–20 km altitude range, consistent on average for the same time span with in situ results. The nearly constant vertical VMR profile also agrees with model predictions of a long lifetime in the lower atmosphere.