Publications by authors named "Jonathan J Foley"

Experimental demonstrations of modified chemical structure and reactivity under strong light-matter coupling have spurred theoretical and computational efforts to uncover underlying mechanisms. Ab initio cavity quantum electrodynamics (QED) combines quantum chemistry with cavity QED to investigate these phenomena in detail. Unitary transformations of ab initio cavity QED Hamiltonians have been used to make them more computationally tractable.

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Molecules under strong or ultra-strong light-matter coupling present an intriguing route to modify chemical structure, properties, and reactivity. A rigorous theoretical treatment of such systems requires handling matter and photon degrees of freedom on an equal quantum mechanical footing. In the regime of molecular electronic strong or ultra-strong coupling to one or a few molecules, it is desirable to treat the molecular electronic degrees of freedom using the tools of ab initio quantum chemistry, yielding an approach referred to as ab initio cavity quantum electrodynamics (ai-QED), where the photon degrees of freedom are treated at the level of cavity QED.

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The emerging field of polaritonic chemistry explores the behavior of molecules under strong coupling with cavity modes. Despite recent developments in polaritonic methods for simulating polaritonic chemistry under electronic strong coupling, their capabilities are limited, especially in cases where the molecule also features strong electronic correlation. To bridge this gap, we have developed a novel method for cavity QED calculations utilizing the Density Matrix Renormalization Group (DMRG) algorithm in conjunction with the Pauli-Fierz Hamiltonian.

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We calculate, using time-dependent density functional theory, absorption and circular dichroism (CD) spectra for a series of small helical gold nanorod structures with a width of 0.6 nm and length increasing from 0.7 nm for Au to 1.

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Polariton chemistry has attracted great attention as a potential route to modify chemical structure, properties, and reactivity through strong interactions among molecular electronic, vibrational, or rovibrational degrees of freedom. A rigorous theoretical treatment of molecular polaritons requires the treatment of matter and photon degrees of freedom on equal quantum mechanical footing. In the limit of molecular electronic strong or ultrastrong coupling to one or a few molecules, it is desirable to treat the molecular electronic degrees of freedom using the tools of quantum chemistry, yielding an approach we refer to as cavity quantum electrodynamics, where the photon degrees of freedom are treated at the level of cavity quantum electrodynamics.

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There is a growing demand for new fluorescent small molecule dyes for solid state applications in the photonics and optoelectronics industry. Thiazolo[5,4-]thiazole (TTz) is an organic heterocycle moiety which has previously shown remarkable properties as a conjugated polymer and in solution-based studies. For TTz-based small molecules to be incorporated in solid-state fluorescence-based optical devices, a thorough elucidation of their structure-photophysical properties needs to be established.

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We combine ab initio molecular electronic Hamiltonians with a cavity quantum electrodynamics model for dissipative photonic modes and apply mean-field theories to the ground- and excited-states of resulting polaritonic systems. In particular, we develop a non-Hermitian configuration interaction singles theory for mean-field ground- and excited-states of the molecular system strongly interacting with a photonic mode and apply these methods to elucidating the phenomenology of paradigmatic polaritonic systems. We leverage the Psi4Numpy framework to yield open-source and accessible reference implementations of these methods.

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The influence of external dielectric environments is well understood for 2D semiconductor materials but overlooked for colloidally grown II-VI nanoplatelets (NPLs). In this work, we synthesize MX (M = Cd, Hg; X = Se, Te) NPLs of varying thicknesses and apply the Elliott model to extract exciton binding energies-reporting values in good agreement with prior methods and extending to less studied cadmium telluride and mercury chalcogenide NPLs. We find that the exciton binding energy is modulated both by the relative effect of internal vs external dielectric and by the thickness of the semiconductor material.

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We present a non-Hermitian formulation of the polaritonic structure of azobenzene strongly coupled to a photonic mode that explicitly accounts for the fleeting nature of the photon-molecule interaction. This formalism reveals that the polaritonic nonadiabatic couplings that facilitate cis-trans isomerization can be dramatically modified by photonic dissipation. We perform Fewest-Switches Surface Hopping dynamics on the surfaces that derive from our non-Hermitian formalism and find that the polaritonic isomerization yields are strongly suppressed for moderate dissipation rates and that cavity-free isomerization dynamics are recovered under large dissipation rates.

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The efficiency of a thermophotovoltaic (TPV) system depends critically upon the spectral selectivity and stability of an emitter, which may operate most effectively at temperatures in excess of 1000 °C. We computationally design and experimentally demonstrate a novel selective emitter design based on multilayer nanostructures, robust to off-normal emission angles. A computational search of the material and temperature compatibility space of simple emitter designs motivates new material classes and identifies several promising multilayer nanostructure designs for both TPV absorber and emitter applications.

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Balancing gene expression is a fundamental challenge of all cell types. To properly regulate transcription on a genome-wide level, there are myriad mechanisms employed by the cell. One layer to this regulation is through spatial positioning, with particular chromosomal loci exerting an influence on transcription throughout a region.

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It is essential that cells orchestrate gene expression for the specific niche that they occupy, and this often requires coordination of the expression of large sets of genes. There are multiple regulatory systems that exist for modulation of gene expression, including the adjacent-gene coregulation of the rRNA and ribosome biogenesis and ribosomal protein families. Both gene families exhibit a nonrandom genomic distribution, often clustered directly adjacent to another member of the same family, which results in a tighter transcriptional coordination among adjacent paired genes than that of the unpaired genes within each regulon and can result in a shared promoter that coordinates expression of the pairs.

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We report a class of thermophotovoltaic emitter structures built upon planar films that support resonant modes, known as perfectly-absorbing modes, that facilitate an exceptional optical response for selective emission. These planar structures have several key advantages over previously-proposed designs for TPV applications: they are simple to fabricate, are stable across a range of temperatures and conditions, and are capable of achieving some of the highest spectral efficiencies reported of any class of emitter structure. Utilization of these emitters leads to exceptionally high device efficiencies under low operating temperature conditions, which should open new opportunities for waste heat management.

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Switchable surface redox chemistry is demonstrated in gold@iron/iron oxide core-shell nanoparticles with ambient oxidation and plasmon-mediated reduction to modulate the oxidation state of shell layers. The iron shell can be oxidized to iron oxide through ambient oxidation, leading to an enhancement and red-shift of the gold surface plasmon resonance (SPR). This enhanced gold SPR can drive reduction of the iron oxide shell under broadband illumination to reversibly blue-shift and significantly dampen gold SPR absorption.

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Synthesis of nanoparticle dimers made of asymmetric compositions is very challenging because of the difficulty in manipulating the nanoparticles' surface chemistries in order to control the assembly and/or growth of different nanoparticles. In this Letter, we report a seed-mediated, surface-confined epitaxial overgrowth strategy that enables the synthesis of high-quality interfaced Au-Ag heterodimers in the quantum size regime (diameters <10 nm). Au and Ag share a common face-centered cubic lattice and have nearly identical lattice constants, which facilitates epitaxial overgrowth and allows direct contact between the Au and Ag domains.

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Recent experiments show that the cage isomer of the water hexamer is lower in energy than the prism isomer near 0 K, and yet state-of-the-art electronic structure calculations predict the prism to be lower in energy than the cage at 0 K. Here, we study the relative energies of the water hexamers from the parametric two-electron reduced density matrix (2-RDM) method in which the 2-RDM rather than the wave function is the basic variable of the calculations. In agreement with experiment and in contrast with traditional wave function methods, the 2-RDM calculations predict the cage to be more stable than the prism after vibrational zero-point correction.

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Photoexcited radical reactions are critical to processes in both nature and materials, and yet they can be challenging for electronic structure methods due to the presence of strong electron correlation. Reduced-density-matrix (RDM) methods, based on solving the anti-Hermitian contracted Schrödinger equation (ACSE) for the two-electron RDM (2-RDM), are examined for studying the strongly correlated mechanisms of these reactions with application to the electrocyclic interconversion of allyl and cyclopropyl radicals. We combine recent extensions of the ACSE to excited states [G.

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A conical intersection in triplet excited states of methylene is computed through the direct calculation of two-electron reduced density matrices (2-RDMs) from solutions of the anti-Hermitian contracted Schrodinger equation (ACSE). The study synthesizes recent extensions of the ACSE method for the treatment of excited states [G. Gidofalvi and D.

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The hydrogen [1,3]-sigmatropic shift in propene is predicted by the Woodward-Hoffman rules to occur by an antarafacial pathway, yet the lack of experimental evidence suggests that this pathway is not favorable. Two natural questions arise: (i) can the [1,3]-shift be made more favorable by a symmetry-forbidden multistep pathway, and (ii) can the energetics be influenced by a substituent on propene? As in many chemical reactions, describing the energetics of these reactions requires a balanced treatment of both single-reference and multireference electron correlations, and yet traditional wave function methods often excel in treating only one kind of correlation. An equitable description of correlation effects, however, can be achieved, at a cost similar to efficient single-reference methods, by computing the two-electron reduced density matrix (2-RDM) from the anti-Hermitian part of the contracted Schrödinger equation (ACSE) [D.

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