Radiative transfer in planetary atmospheres

Rheoretical techniques and observations at millimeter wavelengths are combined to study the atmosphere of planets and comets, planetary and satellite regoliths, and planetary rings. Analysis of the very high quality data on the 18 cm OH line observed in recent comets continued. The high spectral resolution and high signal-to-noise make these lines ideal for study of the kinematics in cometary comae. A model of the collisional quenching of the inversion of the lambda doublet responsible for the OH radio emission has been developed by P. Schloerb. For conditions appropriate to Halley's Comet, collisional quenching should lead radio observers to systematically underestimate the OH parent production rate by a factor of approximately 3 relative to its actual value, which is very consistent with differences observed between radio and ultraviolet-derived production rates. Modeling is likewise continuing for the profiles observed in the lowest rotational transition of HCN in Comet Halley in order to better estimate the excitation and hence the abundance of HCN, as well as the kinematics of parent molecules in the coma. A collaborative program to combine data from the 14 m antenna with interferometric data abtained at the Hat Creek Radio Observatory is allowing aperture synthesis mapping of Venus in the CO J=1-0 line

Orientation-dependent handedness and chiral design

Chirality occupies a central role in fields ranging from biological self-assembly to the design of optical metamaterials. The definition of chirality, as given by Lord Kelvin, associates chirality with the lack of mirror symmetry: the inability to superpose an object on its mirror image. While this definition has guided the classification of chiral objects for over a century, the quantification of handed phenomena based on this definition has proven elusive, if not impossible, as manifest in the paradox of chiral connectedness. In this work, we put forward a quantification scheme in which the handedness of an object depends on the direction in which it is viewed. While consistent with familiar chiral notions, such as the right-hand rule, this framework allows objects to be simultaneously right and left handed. We demonstrate this orientation dependence in three different systems - a biomimetic elastic bilayer, a chiral propeller, and optical metamaterial - and find quantitative agreement with chirality pseudotensors whose form we explicitly compute. The use of this approach resolves the existing paradoxes and naturally enables the design of handed metamaterials from symmetry principles

Boundary conditions for the paleoenvironment: Chemical and physical processes in the pre-solar nebula

Detailed study of the first interstellar hydrocarbon ring, cyclopropenylidene (C3H2), is continuing. The singly deuterated isotope of this molecule, C3HD, was observed in several cold interstellar clouds. The results of a large survey for C3H2 in galactic sources of various types will soon be completed. It appears that cyclopropenylidene is present in virtually all interstellar clouds of at least moderate density. In order to make the first determinations of the CO2/CO abundance ratio in interstellar sources, observations of protonated CO2 were pursued. The spectrum from 18.5 to 22 GHz for several interstellar clouds is being systematically measured. Particular attention is being given to the cold, dark clouds TMC-1 and L124N, which may be formation sites for solar mass stars. The phenomena of maser emission from molecules of methanol is being studied in certain interstellar clouds. A comparison of 1 millimeter continuum emission from dust with the column density of carbon monoxide as determined from the rare C(18)O isotope for 4 molecular clouds in the Galaxy is nearing completion. Papers published during the period of this report are listed

Rectification of energy and motion in non-equilibrium parity violating metamaterials

Uncovering new mechanisms for rectification of stochastic fluctuations has been a longstanding problem in non-equilibrium statistical mechanics. Here, using a model parity violating metamaterial that is allowed to interact with a bath of active energy consuming particles, we uncover new mechanisms for rectification of energy and motion. Our model active metamaterial can generate energy flows through an object in the absence of any temperature gradient. The nonreciprocal microscopic fluctuations responsible for generating the energy flows can further be used to power locomotion in, or exert forces on, a viscous fluid. Taken together, our analytical and numerical results elucidate how the geometry and inter-particle interactions of the parity violating material can couple with the non-equilibrium fluctuations of an active bath and enable rectification of energy and motion.Comment: 9 Pages + S

Molecular dynamics simulations of protein-membrane interactions focusing on PI3Kα and its oncogenic mutants : a thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in Computational Biochemistry at Massey University, Albany, New Zealand

The interactions between proteins and membranes are key to many aspects of biological function. Molecular dynamics simulations can provide insight into both atomic-level structural details and energetics of protein-membrane interactions. This thesis describes the development of a physiologically accurate brain lipid bilayer, and its use in molecular dynamics simulations to characterise how proteins that are important drug targets interact with the cell membrane. A method for rapidly identifying the orientation of a protein that interacts most favourably with a membrane was also developed and tested. The first chapter provides an introduction to molecular dynamics and its role in the context of this research. The second chapter details the development of a cellular membrane with a physiologically representative brain lipid composition. This was done through the testing of simple systems prior to the construction of two more complex lipid bilayers comprising phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylserine (PS), phosphatidylinositide 4,5 bisphosphate (PIP2), sphingomyelin, and cholesterol. The third chapter implements the brain lipid bilayer in the development of a rotational interaction energy screening method designed to predict the most favourable orientation of a protein with respect to the cellular membrane. The functionality of the method was validated through application to two membrane proteins commonly implicated in cancer: the phosphatase and tensin homolog (PTEN), and the p110α-p85α phosphatidyl-inositol kinase (PI3Kα) complex. The fourth chapter corresponds to the main focus of this research, the behaviour of wild type PI3Kα and two of its oncogenic mutants (E545K and H1047R) with regards to membrane and substrate interaction. It was primarily found that H1047R’s increased membrane affinity allowed it to sample a catalytically competent orientation independently of Ras, unlike the wild type. Furthermore, it was also found that the position of the C terminal tail with regards to the substrate binding pocket was crucial in the achievement of a catalytically competent position against the cellular membrane. The fifth and final chapter describes a cytochrome P450 system embedded in a cellular membrane. It was primarily found that the properties of its ingress and egress tunnels depended on the presence or absence of a substrate in the active site