Abstract:
The key to understanding the fundamental processes of catalysis is the transition state (TS): indeed, catalysis is a transition-state molecular recognition event. Practical objectives, such as the design of TS analogues as potential drugs, or the design of synthetic catalysts (including catalytic antibodies), require prior knowledge of the TS structure to be mimicked. Examples, both old and new, of computational modelling studies are discussed, which illustrate this fundamental concept. It is shown that reactant binding is intrinsically inhibitory, and that attempts to design catalysts that focus simply upon attractive interactions in a binding site may fail. Free-energy changes along the reaction coordinate for SN2 methyl transfer catalysed by the enzyme catechol-O-methyl transferase are described and compared with those for a model reaction in water, as computed by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulations. The case is discussed of molecular recognition in a xylanase enzyme that stabilises its sugar substrate in a (normally unfavourable) boat conformation and in which a single-atom mutation affects the free-energy of activation dramatically.

Abstract:
Recent evidence indicates that the Universe is open, i.e., spatially hyperbolic, longstanding theoretical preferences to the contrary notwithstanding. This makes it possible to select a vacuum state, Fock space, and particle definition for a quantized field, by requiring concordance with ordinary flat-spacetime theory at late times. The particle-number basis states thus identified span the physical state space of the field at all times. This construction is demonstrated here explicitly for a massive, minimally coupled, linear scalar field in an open, radiation-dominated Friedmann-Robertson-Walker spacetime.

Abstract:
A numerical scheme is described for accurately accommodating oblique, non-aligned, boundaries, on a three-dimensional cartesian grid. The scheme gives second-order accuracy in the solution for potential of Poisson's equation using compact difference stencils involving only nearest neighbors. Implementation for general "Robin" boundary conditions and for boundaries between media of different dielectric constant for arbitrary-shaped regions is described in detail. The scheme also provides for the interpolation of field (potential gradient) which, despite first-order peak errors immediately adjacent to the boundaries, has overall second order accuracy, and thus provides with good accuracy what is required in particle-in-cell codes: the force. Numerical tests on the implementation confirm the scalings and the accuracy.

Abstract:
Scalar particles--i.e., scalar-field excitations--in de Sitter space exhibit behavior unlike either classical particles in expanding space or quantum particles in flat spacetime. Their energies oscillate forever, and their interactions are spread out in energy. Here it is shown that these features characterize not only normal-mode excitations spread out over all space, but localized particles or wave packets as well. Both one-particle and coherent states of a massive, minimally coupled scalar field in de Sitter space, associated with classical wave packets, are constructed explicitly. Their energy expectation values and corresponding Unruh-DeWitt detector response functions are calculated. Numerical evaluation of these quantities for a simple set of classical wave packets clearly displays these novel features. Hence, given the observed accelerating expansion of the Universe, it is possible that observation of an ultralow-mass scalar particle could yield direct confirmation of distinct predictions of quantum field theory in curved spacetime.

Abstract:
A frequent and well-founded criticism of the maximum a posteriori (MAP) and minimum mean squared error (MMSE) estimates of a continuous parameter \gamma taking values in a differentiable manifold \Gamma is that they are not invariant to arbitrary ``reparameterizations'' of \Gamma. This paper clarifies the issues surrounding this problem, by pointing out the difference between coordinate invariance, which is a sine qua non for a mathematically well-defined problem, and diffeomorphism invariance, which is a substantial issue, and then provides a solution. We first show that the presence of a metric structure on \Gamma can be used to define coordinate-invariant MAP and MMSE estimates, and we argue that this is the natural way to proceed. We then discuss the choice of a metric structure on \Gamma. By imposing an invariance criterion natural within a Bayesian framework, we show that this choice is essentially unique. It does not necessarily correspond to a choice of coordinates. In cases of complete prior ignorance, when Jeffreys' prior is used, the invariant MAP estimate reduces to the maximum likelihood estimate. The invariant MAP estimate coincides with the minimum message length (MML) estimate, but no discretization or approximation is used in its derivation.

Abstract:
Traditionally, high initial capital costs and lengthy payback periods have been identified as the most significant barriers that limit the diffusion of solar photovoltaic (PV) systems. In November, 2006, the Ontario Power Authority (OPA) introduced the Renewable Energy Standard Offer Program (RESOP), offering owners of solar PV systems with a generation capacity under 10 MW a 20 year contract to sell electricity back to the grid at a guaranteed rate of CAD $0.42/kWh. While it is the intent of incentive programs such as the RESOP to begin to lower financial barriers in order to increase the uptake of solar PV systems, there is no guarantee that the level of participation will in fact rise. The "on-the-ground" manner in which consumers interact with such an incentive program ultimately determines its effectiveness. This paper analyzes the relationship between the RESOP and solar PV system consumers. Experiences of current RESOP participants are presented, wherein the factors that are either hindering or promoting utilization of the RESOP and the adoption of solar PV systems are identified.

Abstract:
The ion-drag force on a spherical dust particle immersed in a flowing plasma with external electric field is self-consistently calculated using the Particle In Cell code SCEPTIC in the entire range of charge-exchange collisionality. Our results, not based on questionable approximations, extend prior analytic calculations valid only in a few limiting regimes. Particular attention is given to the force direction, shown never to be directed opposite to the flow except in the continuum limit, where other forces are of much stronger magnitude.

Abstract:
We show that a smooth embedding of a closed 3-manifold in S^3 x R can be isotoped so that every generic level divides S^3 x t into two handlebodies (i.e., is Heegaard) provided the original embedding has a unique local maximum with respect to the R coordinate. This allows uniqueness of embeddings to be studied via the mapping class group of surfaces and the Schoenflies conjecture is considered in this light. We also give a necessary and sufficient condition that a 3-manifold connected summed with arbitrarily many copies of S^1 x S^2 embeds in R^4.

Abstract:
This paper considers filtered polynomial approximations on the unit sphere $\mathbb{S}^d\subset \mathbb{R}^{d+1}$, obtained by truncating smoothly the Fourier series of an integrable function $f$ with the help of a "filter" $h$, which is a real-valued continuous function on $[0,\infty)$ such that $h(t)=1$ for $t\in[0,1]$ and $h(t)=0$ for $t\ge2$. The resulting "filtered polynomial approximation" (a spherical polynomial of degree $2L-1$) is then made fully discrete by approximating the inner product integrals by an $N$-point cubature rule of suitably high polynomial degree of precision, giving an approximation called "filtered hyperinterpolation". In this paper we require that the filter $h$ and all its derivatives up to $\lfloor\tfrac{d-1}{2}\rfloor$ are absolutely continuous, while its right and left derivatives of order $\lfloor \tfrac{d+1}{2}\rfloor$ exist everywhere and are of bounded variation. Under this assumption we show that for a function $f$ in the Sobolev space $W^s_p(\mathbb{S}^d),\ 1\le p\le \infty$, both approximations are of the optimal order $ L^{-s}$, in the first case for $s>0$ and in the second fully discrete case for $s>d/p$.

Abstract:
A central objective in neuroscience is to understand how neurons interact. Such functional interactions have been estimated using signals recorded with different techniques and, consequently, different temporal resolutions. For example, spike data often have sub-millisecond resolution while some imaging techniques may have a resolution of many seconds. Here we use multi-electrode spike recordings to ask how similar functional connectivity inferred from slower timescale signals is to the one inferred from fast timescale signals. We find that functional connectivity is relatively robust to low-pass filtering—dropping by about 10% when low pass filtering at 10 hz and about 50% when low pass filtering down to about 1 Hz—and that estimates are robust to high levels of additive noise. Moreover, there is a weak correlation for physiological filters such as hemodynamic or Ca2+ impulse responses and filters based on local field potentials. We address the origin of these correlations using simulation techniques and find evidence that the similarity between functional connectivity estimated across timescales is due to processes that do not depend on fast pair-wise interactions alone. Rather, it appears that connectivity on multiple timescales or common-input related to stimuli or movement drives the observed correlations. Despite this qualification, our results suggest that techniques with intermediate temporal resolution may yield good estimates of the functional connections between individual neurons.