Path-integral and Coarse-graining Strategies for Complex Molecular Phenomena

Molecular simulation provides a powerful tool for connecting molecular-level processes to physical observables. However, the facility to make those connections relies upon the application and development of theoretical methods that permit appropriate descriptions of the systems or processes to be studied. In this thesis, we utilize molecular simulation to study and predict two phenomena with very different theoretical challenges, beginning with (1) lithium-ion transport behavior in polymers and following with (2) equilibrium isotope effects with relevance to position-specific and clumped isotope studies. In the case of ion transport in polymers, there is motivation to use molecular simulation to provide guidance in polymer electrolyte design, but the length and timescales relevant for ion diffusion in polymers preclude the use of direct molecular dynamics simulation to compute ion diffusivities in more than a handful of candidate systems. In the case of equilibrium isotope effects, the thermodynamic driving forces for isotopic fractionation are often fundamentally quantum mechanical in nature, and the high precision of experimental instruments demands correspondingly accurate theoretical approaches. Herein, we describe respectively coarse-graining and path-integral strategies to address outstanding questions in these two subject areas.

Direct simulation of quantum dynamics in complex systems

Accurate simulation of quantum dynamics in complex systems poses a fundamental theoretical challenge with immediate application to problems in biological catalysis, charge transfer, and solar energy conversion. The varied length- and timescales that characterize these kinds of processes necessitate development of novel simulation methodology that can both accurately evolve the coupled quantum and classical degrees of freedom and also be easily applicable to large, complex systems. In the following dissertation, the problems of quantum dynamics in complex systems are explored through direct simulation using path-integral methods as well as application of state-of-the-art analytical rate theories.

Direct simulation of proton-coupled electron transfer reaction dynamics and mechanisms

Proton-coupled electron transfer (PCET) reactions are ubiquitous throughout chemistry and biology. However, challenges arise in both the the experimental and theoretical investigation of PCET reactions; the rare-event nature of the reactions and the coupling between quantum mechanical electron- and proton-transfer with the slower classical dynamics of the surrounding environment necessitates the development of robust simulation methodology. In the following dissertation, novel path-integral based methods are developed and employed for the direct simulation of the reaction dynamics and mechanisms of condensed-phase PCET.

Two new integral transforms and their applications

This thesis is in two parts. In Part I the independent variable θ in the trigonometric form of Legendre's equation is extended to the range ( -∞, ∞). The associated spectral representation is an infinite integral transform whose kernel is the analytic continuation of the associated Legendre function of the second kind into the complex θ-plane. This new transform is applied to the problems of waves on a spherical shell, heat flow on a spherical shell, and the gravitational potential of a sphere. In each case the resulting alternative representation of the solution is more suited to direct physical interpretation than the standard forms.

In Part II separation of variables is applied to the initial-value problem of the propagation of acoustic waves in an underwater sound channel. The Epstein symmetric profile is taken to describe the variation of sound with depth. The spectral representation associated with the separated depth equation is found to contain an integral and a series. A point source is assumed to be located in the channel. The nature of the disturbance at a point in the vicinity of the channel far removed from the source is investigated.

Nearly free molecular heat transfer from a sphere

Consider a sphere immersed in a rarefied monatomic gas with zero mean flow. The distribution function of the molecules at infinity is chosen to be a Maxwellian. The boundary condition at the body is diffuse reflection with perfect accommodation to the surface temperature. The microscopic flow of particles about the sphere is modeled kinetically by the Boltzmann equation with the Krook collision term. Appropriate normalizations in the near and far fields lead to a perturbation solution of the problem, expanded in terms of the ratio of body diameter to mean free path (inverse Knudsen number). The distribution function is found directly in each region, and intermediate matching is demonstrated. The heat transfer from the sphere is then calculated as an integral over this distribution function in the inner region. Final results indicate that the heat transfer may at first increase over its free flow value before falling to the continuum level.

Oscillatory integral operators related to pointwise convergence of Schrödinger operators

In this thesis we consider smooth analogues of operators studied in connection with the pointwise convergence of the solution, u(x,t), (x,t) ∈ ℝ^n x ℝ, of the free Schrodinger equation to the given initial data. Such operators are interesting examples of oscillatory integral operators with degenerate phase functions, and we develop strategies to capture the oscillations and obtain sharp L^2 → L^2 bounds. We then consider, for fixed smooth t(x), the restriction of u to the surface (x,t(x)). We find that u(x,t(x)) ∈ L^2(D^n) when the initial data is in a suitable L^2-Sobolev space H^8 (ℝ^n), where s depends on conditions on t.

Integral finite surgeries on knots in S^3

Using the correction terms in Heegaard Floer homology, we prove that if a knot in S³ admits a positive integral T-, O-, or I-type surgery, it must have the same knot Floer homology as one of the knots given in our complete list, and the resulting manifold is orientation-preservingly homeomorphic to the p-surgery on the corresponding knot.

Investigations of noise and of quantum interference in proximity effect bridges

This work reports investigations upon weakly superconducting proximity effect bridges. These bridges, which exhibit the Josephson effects, are produced by bisecting a superconductor with a short (<1µ) region of material whose superconducting transition temperature is below that of the adjacent superconductors. These bridges are fabricated from layered refractory metal thin films whose transition temperature will depend upon the thickness ratio of the materials involved. The thickness ratio is changed in the area of the bridge to lower its transition temperature. This is done through novel photolithographic techniques described in the text, Chapter 2.

If two such proximity effect bridges are connected in parallel, they form a quantum interferometer. The maximum zero voltage current through this circuit is periodically modulated by the magnetic flux through the circuit. At a constant bias current, the modulation of the critical current produces a modulation in the dc voltage across the bridge. This change in dc voltage has been found to be the result of a change in the internal dissipation in the device. A simple model using lumped circuit theory and treating the bridges as quantum oscillators of frequency ω = 2eV/h, where V is the time average voltage across the device, has been found to adequately describe the observed voltage modulation.

The quantum interferometers have been converted to a galvanometer through the inclusion of an integral thin film current path which couples magnetic flux through the interferometer. Thus a change in signal current produces a change in the voltage across the interferometer at a constant bias current. This work is described in Chapter 3 of the text.

The sensitivity of any device incorporating proximity effect bridges will ultimately be determined by the fluctuations in their electrical parameters. He have measured the spectral power density of the voltage fluctuations in proximity effect bridges using a room temperature electronics and a liquid helium temperature transformer to match the very low (~ 0.1 Ω) impedances characteristic of these devices.

We find the voltage noise to agree quite well with that predicted by phonon noise in the normal conduction through the bridge plus a contribution from the superconducting pair current through the bridge which is proportional to the ratios of this current to the time average voltage across the bridge. The total voltage fluctuations are given by <V^2(f ) > = 4kTR^2_d I/V where R_d is the dynamic resistance, I the total current, and V the voltage across the bridge . An additional noise source appears with a strong 1/f^(n) dependence , 1.5 < n < 2, if the bridges are fabricated upon a glass substrate. This excess noise, attributed to thermodynamic temperature fluctuations in the volume of the bridge, increases dramatically on a glass substrate due to the greatly diminished thermal diffusivity of the glass as compared to sapphire.

Symmetric representation of an integral domain over a subdomain

Let F(θ) be a separable extension of degree n of a field F. Let Δ and D be integral domains with quotient fields F(θ) and F respectively. Assume that Δ ᴝ D. A mapping φ of Δ into the n x n D matrices is called a Δ/D rep if (i) it is a ring isomorphism and (ii) it maps d onto dI_n whenever d ϵ D. If the matrices are also symmetric, φ is a Δ/D symrep.

Every Δ/D rep can be extended uniquely to an F(θ)/F rep. This extension is completely determined by the image of θ. Two Δ/D reps are called equivalent if the images of θ differ by a D unimodular similarity. There is a one-to-one correspondence between classes of Δ/D reps and classes of Δ ideals having an n element basis over D.

The condition that a given Δ/D rep class contain a Δ/D symrep can be phrased in various ways. Using these formulations it is possible to (i) bound the number of symreps in a given class, (ii) count the number of symreps if F is finite, (iii) establish the existence of an F(θ)/F symrep when n is odd, F is an algebraic number field, and F(θ) is totally real if F is formally real (for n = 3 see Sapiro, “Characteristic polynomials of symmetric matrices” Sibirsk. Mat. Ž. 3 (1962) pp. 280-291), and (iv) study the case D = Z, the integers (see Taussky, “On matrix classes corresponding to an ideal and its inverse” Illinois J. Math. 1 (1957) pp. 108-113 and Faddeev, “On the characteristic equations of rational symmetric matrices” Dokl. Akad. Nauk SSSR 58 (1947) pp. 753-754).

The case D = Z and n = 2 is studied in detail. Let Δ’ be an integral domain also having quotient field F(θ) and such that Δ’ ᴝ Δ. Let φ be a Δ/Z symrep. A method is given for finding a Δ’/Z symrep ʘ such that the Δ’ ideal class corresponding to the class of ʘ is an extension to Δ’ of the Δ ideal class corresponding to the class of φ. The problem of finding all Δ/Z symreps equivalent to a given one is studied.