Density functional theory embedding for correlated wavefunctions

Methods that exploit the intrinsic locality of molecular interactions show significant promise in making tractable the electronic structure calculation of large-scale systems. In particular, embedded density functional theory (e-DFT) offers a formally exact approach to electronic structure calculations in which the interactions between subsystems are evaluated in terms of their electronic density. In the following dissertation, methodological advances of embedded density functional theory are described, numerically tested, and applied to real chemical systems.

First, we describe an e-DFT protocol in which the non-additive kinetic energy component of the embedding potential is treated exactly. Then, we present a general implementation of the exact calculation of the non-additive kinetic potential (NAKP) and apply it to molecular systems. We demonstrate that the implementation using the exact NAKP is in excellent agreement with reference Kohn-Sham calculations, whereas the approximate functionals lead to qualitative failures in the calculated energies and equilibrium structures.

Next, we introduce density-embedding techniques to enable the accurate and stable calculation of correlated wavefunction (CW) in complex environments. Embedding potentials calculated using e-DFT introduce the effect of the environment on a subsystem for CW calculations (WFT-in-DFT). We demonstrate that WFT-in-DFT calculations are in good agreement with CW calculations performed on the full complex.

We significantly improve the numerics of the algorithm by enforcing orthogonality between subsystems by introduction of a projection operator. Utilizing the projection-based embedding scheme, we rigorously analyze the sources of error in quantum embedding calculations in which an active subsystem is treated using CWs, and the remainder using density functional theory. We show that the embedding potential felt by the electrons in the active subsystem makes only a small contribution to the error of the method, whereas the error in the nonadditive exchange-correlation energy dominates. We develop an algorithm which corrects this term and demonstrate the accuracy of this corrected embedding scheme.

The search for gravitational waves from the coalescence of black hole binary systems in data from the LIGO and Virgo detectors. Or: A dark walk through a random forest

The LIGO and Virgo gravitational-wave observatories are complex and extremely sensitive strain detectors that can be used to search for a wide variety of gravitational waves from astrophysical and cosmological sources. In this thesis, I motivate the search for the gravitational wave signals from coalescing black hole binary systems with total mass between 25 and 100 solar masses. The mechanisms for formation of such systems are not well-understood, and we do not have many observational constraints on the parameters that guide the formation scenarios. Detection of gravitational waves from such systems — or, in the absence of detection, the tightening of upper limits on the rate of such coalescences — will provide valuable information that can inform the astrophysics of the formation of these systems. I review the search for these systems and place upper limits on the rate of black hole binary coalescences with total mass between 25 and 100 solar masses. I then show how the sensitivity of this search can be improved by up to 40% by the the application of the multivariate statistical classifier known as a random forest of bagged decision trees to more effectively discriminate between signal and non-Gaussian instrumental noise. I also discuss the use of this classifier in the search for the ringdown signal from the merger of two black holes with total mass between 50 and 450 solar masses and present upper limits. I also apply multivariate statistical classifiers to the problem of quantifying the non-Gaussianity of LIGO data. Despite these improvements, no gravitational-wave signals have been detected in LIGO data so far. However, the use of multivariate statistical classification can significantly improve the sensitivity of the Advanced LIGO detectors to such signals.

Band structure and transport properties of simple cubic tellurium-base alloys

The electrical transport properties and lattice spacings of simple cubic Te-Au, Te-Au-Fe, and Te-Au-Mn alloys, prepared by rapid quenching from the liquid state, hove been measured and correlated with a proposed bond structure. The variations of superconducting transition temperature, absolute thermoelectric power, and lattice spacing with Te concentration all showed related anomalies in the binary Te-Au alloys. The unusual behavior of these properties has been interpreted by using nearly free electron theory to predict the effect of the second Brillouin zone boundary on the area of the Fermi surface, and the electronic density of states. The behavior of the superconducting transition temperature and the lattice parameter as Fe and Mn ore added further supports the proposed interpretation as well as providing information on the existence of localized magnetic states in the ternary alloys. In addition, it was found that a very distinct bond structure effect on the transition temperatures of the Te-Au-Fe alloys could be identified.

The needle in the hundred square degree haystack: The hunt for binary neutron star mergers with LIGO and Palomar Transient Factory

The Advanced LIGO and Virgo experiments are poised to detect gravitational waves (GWs) directly for the first time this decade. The ultimate prize will be joint observation of a compact binary merger in both gravitational and electromagnetic channels. However, GW sky locations that are uncertain by hundreds of square degrees will pose a challenge. I describe a real-time detection pipeline and a rapid Bayesian parameter estimation code that will make it possible to search promptly for optical counterparts in Advanced LIGO. Having analyzed a comprehensive population of simulated GW sources, we describe the sky localization accuracy that the GW detector network will achieve as each detector comes online and progresses toward design sensitivity. Next, in preparation for the optical search with the intermediate Palomar Transient Factory (iPTF), we have developed a unique capability to detect optical afterglows of gamma-ray bursts (GRBs) detected by the Fermi Gamma-ray Burst Monitor (GBM). Its comparable error regions offer a close parallel to the Advanced LIGO problem, but Fermi's unique access to MeV-GeV photons and its near all-sky coverage may allow us to look at optical afterglows in a relatively unexplored part of the GRB parameter space. We present the discovery and broadband follow-up observations (X-ray, UV, optical, millimeter, and radio) of eight GBM-IPTF afterglows. Two of the bursts (GRB 130702A / iPTF13bxl and GRB 140606B / iPTF14bfu) are at low redshift (z=0.145 and z = 0.384, respectively), are sub-luminous with respect to "standard" cosmological bursts, and have spectroscopically confirmed broad-line type Ic supernovae. These two bursts are possibly consistent with mildly relativistic shocks breaking out from the progenitor envelopes rather than the standard mechanism of internal shocks within an ultra-relativistic jet. On a technical level, the GBM--IPTF effort is a prototype for locating and observing optical counterparts of GW events in Advanced LIGO with the Zwicky Transient Facility.

Essays on Correlated Equilibrium and Voter Turnout

This thesis consists of three essays in the areas of political economy and game theory, unified by their focus on the effects of pre-play communication on equilibrium outcomes.

Communication is fundamental to elections. Chapter 2 extends canonical voter turnout models, where citizens, divided into two competing parties, choose between costly voting and abstaining, to include any form of communication, and characterizes the resulting set of Aumann's correlated equilibria. In contrast to previous research, high-turnout equilibria exist in large electorates and uncertain environments. This difference arises because communication can coordinate behavior in such a way that citizens find it incentive compatible to follow their correlated signals to vote more. The equilibria have expected turnout of at least twice the size of the minority for a wide range of positive voting costs.

In Chapter 3 I introduce a new equilibrium concept, called subcorrelated equilibrium, which fills the gap between Nash and correlated equilibrium, extending the latter to multiple mediators. Subcommunication equilibrium similarly extends communication equilibrium for incomplete information games. I explore the properties of these solutions and establish an equivalence between a subset of subcommunication equilibria and Myerson's quasi-principals' equilibria. I characterize an upper bound on expected turnout supported by subcorrelated equilibrium in the turnout game.

Chapter 4, co-authored with Thomas Palfrey, reports a new study of the effect of communication on voter turnout using a laboratory experiment. Before voting occurs, subjects may engage in various kinds of pre-play communication through computers. We study three communication treatments: No Communication, a control; Public Communication, where voters exchange public messages with all other voters, and Party Communication, where messages are exchanged only within one's own party. Our results point to a strong interaction effect between the form of communication and the voting cost. With a low voting cost, party communication increases turnout, while public communication decreases turnout. The data are consistent with correlated equilibrium play. With a high voting cost, public communication increases turnout. With communication, we find essentially no support for the standard Nash equilibrium turnout predictions.

Technology for Single Cell Protein Analysis in Immunology and Cancer Prognostics

The first chapter of this thesis deals with automating data gathering for single cell microfluidic tests. The programs developed saved significant amounts of time with no loss in accuracy. The technology from this chapter was applied to experiments in both Chapters 4 and 5.

The second chapter describes the use of statistical learning to prognose if an anti-angiogenic drug (Bevacizumab) would successfully treat a glioblastoma multiforme tumor. This was conducted by first measuring protein levels from 92 blood samples using the DNA-encoded antibody library platform. This allowed the measure of 35 different proteins per sample, with comparable sensitivity to ELISA. Two statistical learning models were developed in order to predict whether the treatment would succeed. The first, logistic regression, predicted with 85% accuracy and an AUC of 0.901 using a five protein panel. These five proteins were statistically significant predictors and gave insight into the mechanism behind anti-angiogenic success/failure. The second model, an ensemble model of logistic regression, kNN, and random forest, predicted with a slightly higher accuracy of 87%.

The third chapter details the development of a photocleavable conjugate that multiplexed cell surface detection in microfluidic devices. The method successfully detected streptavidin on coated beads with 92% positive predictive rate. Furthermore, chambers with 0, 1, 2, and 3+ beads were statistically distinguishable. The method was then used to detect CD3 on Jurkat T cells, yielding a positive predictive rate of 49% and false positive rate of 0%.

The fourth chapter talks about the use of measuring T cell polyfunctionality in order to predict whether a patient will succeed an adoptive T cells transfer therapy. In 15 patients, we measured 10 proteins from individual T cells (~300 cells per patient). The polyfunctional strength index was calculated, which was then correlated with the patient's progress free survival (PFS) time. 52 other parameters measured in the single cell test were correlated with the PFS. No statistical correlator has been determined, however, and more data is necessary to reach a conclusion.

Finally, the fifth chapter talks about the interactions between T cells and how that affects their protein secretion. It was observed that T cells in direct contact selectively enhance their protein secretion, in some cases by over 5 fold. This occurred for Granzyme B, Perforin, CCL4, TNFa, and IFNg. IL- 10 was shown to decrease slightly upon contact. This phenomenon held true for T cells from all patients tested (n=8). Using single cell data, the theoretical protein secretion frequency was calculated for two cells and then compared to the observed rate of secretion for both two cells not in contact, and two cells in contact. In over 90% of cases, the theoretical protein secretion rate matched that of two cells not in contact.

1. Ultrasonic studies of binary liquid structure in the critical region. Theory and experiment for the 2,6-lutidine/water system. 2. Hartree-Fock calculations of electric polarizabilities of some simple atoms and molecules, and their practicality. 3. Calculation of vibrational transition probabilities in collinear atom-diatom and diatom-diatom collisions with Lennard-Jones interaction

Part 1. Many interesting visual and mechanical phenomena occur in the critical region of fluids, both for the gas-liquid and liquid-liquid transitions. The precise thermodynamic and transport behavior here has some broad consequences for the molecular theory of liquids. Previous studies in this laboratory on a liquid-liquid critical mixture via ultrasonics supported a basically classical analysis of fluid behavior by M. Fixman (e. g., the free energy is assumed analytic in intensive variables in the thermodynamics)--at least when the fluid is not too close to critical. A breakdown in classical concepts is evidenced close to critical, in some well-defined ways. We have studied herein a liquid-liquid critical system of complementary nature (possessing a lower critical mixing or consolute temperature) to all previous mixtures, to look for new qualitative critical behavior. We did not find such new behavior in the ultrasonic absorption ascribable to the critical fluctuations, but we did find extra absorption due to chemical processes (yet these are related to the mixing behavior generating the lower consolute point). We rederived, corrected, and extended Fixman's analysis to interpret our experimental results in these more complex circumstances. The entire account of theory and experiment is prefaced by an extensive introduction recounting the general status of liquid state theory. The introduction provides a context for our present work, and also points out problems deserving attention. Interest in these problems was stimulated by this work but also by work in Part 3.

Part 2. Among variational theories of electronic structure, the Hartree-Fock theory has proved particularly valuable for a practical understanding of such properties as chemical binding, electric multipole moments, and X-ray scattering intensity. It also provides the most tractable method of calculating first-order properties under external or internal one-electron perturbations, either developed explicitly in orders of perturbation theory or in the fully self-consistent method. The accuracy and consistency of first-order properties are poorer than those of zero-order properties, but this is most often due to the use of explicit approximations in solving the perturbed equations, or to inadequacy of the variational basis in size or composition. We have calculated the electric polarizabilities of H₂, He, Li, Be, LiH, and N₂ by Hartree-Fock theory, using exact perturbation theory or the fully self-consistent method, as dictated by convenience. By careful studies on total basis set composition, we obtained good approximations to limiting Hartree-Fock values of polarizabilities with bases of reasonable size. The values for all species, and for each direction in the molecular cases, are within 8% of experiment, or of best theoretical values in the absence of the former. Our results support the use of unadorned Hartree-Pock theory for static polarizabilities needed in interpreting electron-molecule scattering data, collision-induced light scattering experiments, and other phenomena involving experimentally inaccessible polarizabilities.

Part 3. Numerical integration of the close-coupled scattering equations has been carried out to obtain vibrational transition probabilities for some models of the electronically adiabatic H₂-H₂ collision. All the models use a Lennard-Jones interaction potential between nearest atoms in the collision partners. We have analyzed the results for some insight into the vibrational excitation process in its dependence on the energy of collision, the nature of the vibrational binding potential, and other factors. We conclude also that replacement of earlier, simpler models of the interaction potential by the Lennard-Jones form adds very little realism for all the complication it introduces. A brief introduction precedes the presentation of our work and places it in the context of attempts to understand the collisional activation process in chemical reactions as well as some other chemical dynamics.