Kenley Pelzer - Academia.edu (original) (raw)

Papers by Kenley Pelzer

American Journal of Transplantation, 2021

The Organ Procurement and Transplant Network (OPTN) implemented a new heart allocation policy on ... more The Organ Procurement and Transplant Network (OPTN) implemented a new heart allocation policy on October 18, 2018. Published estimates of lower post-transplant survival under the new policy in cohorts with limited follow-up may be biased by informative censoring. Using the Scientific Registry of Transplant Recipients, we used the Kaplan-Meier method to estimate 1-year post-transplant survival for pre-policy (November 1, 2016, to October 31, 2017) and post-policy cohorts (November 1, 2018, to October 31, 2019) with follow-up through March 2, 2021. We adjusted for changes in recipient population over time with a multivariable Cox proportional hazards model. To demonstrate the effect of inadequate follow-up on post-policy survival estimates, we repeated the analysis but only included follow-up through October 31, 2019. Transplant programs transplanted 2594 patients in the pre-policy cohort and 2761 patients in the post-policy cohort. With follow-up through March 2, 2021, unadjusted 1-year post-transplant survival was 90.6% (89.5% - 91.8%) in the pre-policy cohort and 90.8% (89.7% - 91.9%) in the post-policy cohort (adjusted HR = 0.93 [0.77-1.12]). Ignoring follow-up after October 31, 2019, the post-policy estimate was biased downward (1-year: 82.2%). When estimated with adequate follow-up, 1-year post-transplant survival under the new heart allocation policy was not significantly different.

Journal of Applied Crystallography, 2021

Bragg coherent diffraction imaging (BCDI) provides a powerful tool for obtaining high-resolution ... more Bragg coherent diffraction imaging (BCDI) provides a powerful tool for obtaining high-resolution structural information from nanocrystalline materials. Here a BCDI sample consisting of a large number of randomly oriented nanoscale crystals is considered. Ideally, only one crystal is oriented to produce a Bragg peak on the detector. However, diffraction from other crystals often produces additional signals on the detector. Before the measured diffraction patterns can be processed into structural images, scientists routinely need to manually identify and remove the `alien' intensities from sources other than the intended crystal. With the development of modern high-coherence storage rings, such as the upgraded Advanced Photon Source (APS), the already slow process of manual preprocessing will be untenable for the large volumes of data that will be produced. An automated method of identifying and deleting alien intensities is proposed. This method exploits the fact that BCDI of a p...

The Journal of Physical Chemistry C, 2017

Recent experimental studies revealed that charge carriers harvested by bulk heterojunction organi... more Recent experimental studies revealed that charge carriers harvested by bulk heterojunction organic photovoltaics can be collected on ultrafast time scales. To investigate ultrafast exciton mobility, we construct simple, nonatomistic models of a common polymeric electron donor material. We first explore the relationship between the magnitude of energetic noise in the model Hamiltonian and the spatial extent of resulting eigenstates. We then employ a quantum master equation approach to simulate migration of chromophore-localized initial excited states. Excitons initially localized on a single chromophore at the center of the model delocalize down polymer chains and across pi-stacked chromophores through a coherent, wavelike mechanism during the first few tens of femtoseconds. We explore the dependence of this coherent delocalization on coupling strength and on the magnitude of energetic noise. At longer times we observe continued migration toward a uniform population distribution that proceeds through an incoherent, diffusive mechanism. A series of simulations modeling exciton harvesting in domains of varying size demonstrates that smaller domains enhance ultrafast exciton harvesting yield. Our nonatomistic model falls short of quantitative accuracy but demonstrates that excitons are mobile within electron donor domains on ultrafast time scales and that coherent exciton transport can enhance ultrafast exciton harvesting.

Molecular Systems Design & Engineering, 2016

One of the most important factors in determining organic photovoltaic device performance is the e... more One of the most important factors in determining organic photovoltaic device performance is the efficiency of exciton dissociation and charge separation at donor/acceptor heterojunctions. This review discusses theoretical and computational approaches to modeling this crucial process of charge generation.

The Journal of Physical Chemistry C, 2017

Non-aqueous redox flow batteries have attracted recent attention with their potential for high el... more Non-aqueous redox flow batteries have attracted recent attention with their potential for high electrochemical storage capacity, with organic electrolytes serving as solvents with a wide electrochemical stability window. Organic molecules can also serve as electroactive species, where molecules with low reduction potentials or high oxidation potentials can provide substantial chemical energy. To identify promising electrolytes in a vast chemical space, high-throughput screening (HTS) of candidate molecules plays an important role, where HTS is used to calculate properties of thousands of molecules and identify a few organic molecules worthy of further attention in battery research. Here, we present reduction and oxidation potentials obtained from HTS of 4178 molecules. The molecules are composed of base groups of five or six-membered rings with one or two functional groups attached, with the set of possible functional groups including both electron-withdrawing and electron-donating groups. In addition to observing the trends in potentials that result from differences in organic base groups and functional groups, we analyze the effects of molecular characteristics such as multiple bonds, Hammett parameters, and functional group position. This work provides useful guidance in determining how the identities of the base groups and functional groups are correlated with desirable reduction and oxidation potentials.

Chemical Science, 2017

Using ab initio calculations of charges in PCBM fullerenes, a multiscale approach applies classic... more Using ab initio calculations of charges in PCBM fullerenes, a multiscale approach applies classical molecular dynamics to model charge transfer.

The Journal of chemical physics, Jan 14, 2015

Two-dimensional nanoplatelets (NPLs) are an exciting class of materials with promising optical an... more Two-dimensional nanoplatelets (NPLs) are an exciting class of materials with promising optical and energy transport properties. The possibility of efficient energy transport between nanoplatelets raises questions regarding the nature of energy transfer in these thin, laterally extended systems. A challenge in understanding exciton transport is the uncertainty regarding the size of the exciton. Depending on the material and defects in the nanoplatelet, an exciton could plausibly extend over an entire plate or localize to a small region. The variation in possible exciton sizes raises the question how exciton size impacts the efficiency of transport between nanoplatelet structures. Here, we explore this issue using a quantum master equation approach. This method goes beyond the assumptions of Förster theory to allow for quantum mechanical effects that could increase energy transfer efficiency. The model is extremely flexible in describing different systems, allowing us to test the effe...

The Journal of Physical Chemistry C, 2014

ABSTRACT Organic semiconductors offer a low-cost alternative to inorganic semiconductors. However... more ABSTRACT Organic semiconductors offer a low-cost alternative to inorganic semiconductors. However, their usefulness is limited by a relatively low mobility of polaron charge carriers. Past research indicates a positive correlation between charge density and charge mobility in organic semiconductors. This relationship is usually attributed to the phenomenon of excess charges filling traps. Here, we explore whether charge density may also affect mobility via influence on intermolecular couplings. Density functional theory (DFT) with a long-range corrected (LC-BLYP) functional is used to calculate charge densities and electronic couplings of negative charges on C-70 fullerenes in the presence of nearby negative point charges, which provides an upper limit calculation of the influence of nearby polarons. We find that in C-70 systems with relatively low couplings, the presence of additional charges has an effect of maximizing intermolecular couplings and hence transport. This effect drops off quickly with distance, suggesting that it is relevant only at extremely high charge densities that are an unlikely event in current C-70 devices. The effect of charge density on couplings may be useful in understanding transport in very limited regions of C-70 materials where the local charge density is high; however, it is unlikely to affect overall device performance.

Science (New York, N.Y.), Jan 5, 2014

The ability to predict the pressure dependence of chemical reaction rates would be a great boon t... more The ability to predict the pressure dependence of chemical reaction rates would be a great boon to kinetic modeling of processes such as combustion and atmospheric chemistry. This pressure dependence is intimately related to the rate of collision-induced transitions in energy E and angular momentum J. We present a scheme for predicting this pressure dependence based on coupling trajectory-based determinations of moments of the E,J-resolved collisional transfer rates with the two-dimensional master equation. This completely a priori procedure provides a means for proceeding beyond the empiricism of prior work. The requisite microcanonical dissociation rates are obtained from ab initio transition state theory. Predictions for the CH4 = CH3 + H and C2H3 = C2H2 + H reaction systems are in excellent agreement with experiment.

The Journal of Physical Chemistry B, 2014

Long-lived coherences have been observed in photosynthetic complexes after laser excitation, insp... more Long-lived coherences have been observed in photosynthetic complexes after laser excitation, inspiring new theories regarding the extreme quantum efficiency of photosynthetic energy transfer. Whether coherent (ballistic) transport occurs in nature and whether it improves photosynthetic efficiency remain topics of debate. Here, we use a nonequilibrium Green's function analysis to model exciton transport after excitation from an incoherent source (as opposed to coherent laser excitation). We find that even with an incoherent source, the rate of environmental dephasing strongly affects exciton transport efficiency, suggesting that the relationship between dephasing and efficiency is not an artifact of coherent excitation. The Green's function analysis provides a clear view of both the pattern of excitonic fluxes among chromophores and the multidirectionality of energy transfer that is a feature of coherent transport. We see that even in the presence of an incoherent source, transport occurs by qualitatively different mechanisms as dephasing increases. Our approach can be generalized to complex synthetic systems and may provide a new tool for optimizing synthetic light harvesting materials.

The Journal of Physical Chemistry A, 2011

Polyaromatic hydrocarbons (PAHs) are a class of organic molecules with importance in several bran... more Polyaromatic hydrocarbons (PAHs) are a class of organic molecules with importance in several branches of science, including medicine, combustion chemistry, and materials science. The delocalized π-orbital systems in PAHs require highly accurate electronic structure methods to capture strong electron correlation. Treating correlation in PAHs has been challenging because (i) traditional wave function methods for strong correlation have not been applicable since they scale exponentially in the number of strongly correlated orbitals, and (ii) alternative methods such as the density-matrix renormalization group and variational twoelectron reduced density matrix (2-RDM) methods have not been applied beyond linear acene chains. In this paper we extend the earlier results from active-space variational 2-RDM theory [Gidofalvi, G.; Mazziotti, D. A. J. Chem. Phys. 2008, 129, 134108] to the more general two-dimensional arrangement of rings-acene sheets-to study the relationship between geometry and electron correlation in PAHs. The acene-sheet calculations, if performed with conventional wave function methods, would require wave function expansions with as many as 1.5 Â 10 17 configuration state functions. To measure electron correlation, we employ several RDM-based metrics: (i) natural-orbital occupation numbers, (ii) the 1-RDM von Neumann entropy, (iii) the correlation energy per carbon atom, and (iv) the squared Frobenius norm of the cumulant 2-RDM. The results confirm a trend of increasing polyradical character with increasing molecular size previously observed in linear PAHs and reveal a corresponding trend in two-dimensional (arch-shaped) PAHs. Furthermore, in PAHs of similar size they show significant variations in correlation with geometry. PAHs with the strictly linear geometry (chains) exhibit more electron correlation than PAHs with nonlinear geometries (sheets).

New Journal of Physics, 2013

The role of noise in the transport properties of quantum excitations is a topic of great importan... more The role of noise in the transport properties of quantum excitations is a topic of great importance in many fields, from organic semiconductors for technological applications to light-harvesting complexes in photosynthesis. In this paper we study a semi-classical model where a tight-binding Hamiltonian is fully coupled to an underlying spatially extended nonlinear chain of atoms. We show that the transport properties of a quantum excitation are subtly modulated by (i) the specific type (local versus non-local) of exciton-phonon coupling and by (ii) nonlinear effects of the underlying lattice. We report a non-monotonic dependence of the exciton diffusion coefficient on temperature, in agreement with earlier predictions, as a direct consequence of the lattice-induced fluctuations in the hopping rates due to long-wavelength vibrational modes. A standard measure of transport efficiency confirms that both nonlinearity in the underlying lattice and off-diagonal exciton-phonon coupling promote transport efficiency at high temperatures, preventing the Zeno-like quench observed in other models lacking an explicit noise-providing dynamical system.

The Journal of Chemical Physics, 2012

An open question at the forefront of modern physical sciences is what role, if any, quantum effec... more An open question at the forefront of modern physical sciences is what role, if any, quantum effects may play in biological sensing and energy transport mechanisms. One area of such research concerns the possibility of coherent energy transport in photosynthetic systems. Spectroscopic evidence of long-lived quantum coherence in photosynthetic light-harvesting pigment protein complexes (PPCs), along with theoretical modeling of PPCs, has indicated that coherent energy transport might boost efficiency of energy transport in photosynthesis. Accurate assessment of coherence lifetimes is crucial for modeling the extent to which quantum effects participate in this energy transfer, because such quantum effects can only contribute to mechanisms proceeding on timescales over which the coherences persist. While spectroscopy is a useful way to measure coherence lifetimes, inhomogeneity in the transition energies across the measured ensemble may lead to underestimation of coherence lifetimes from spectroscopic experiments. Theoretical models of antenna complexes generally model a single system, and direct comparison of single system models to ensemble averaged experimental data may lead to systematic underestimation of coherence lifetimes, distorting much of the current discussion. In this study, we use simulations of the Fenna-Matthews-Olson complex to model single complexes as well as averaged ensembles to demonstrate and roughly quantify the effect of averaging over an inhomogeneous ensemble on measured coherence lifetimes. We choose to model the Fenna-Matthews-Olson complex because that system has been a focus for much of the recent discussion of quantum effects in biology, and use an early version of the well known environment-assisted quantum transport model to facilitate straightforward comparison between the current model and past work. Although ensemble inhomogeneity is known to lead to shorter lifetimes of observed oscillations (simply inhomogeneous spectral broadening in the time domain), this important fact has been left out of recent discussions of spectroscopic measurements of energy transport in photosynthesis. In general, these discussions have compared single-system theoretical models to whole-ensemble laboratory measurements without addressing the effect of inhomogeneous dephasing. Our work addresses this distinction between single system and ensemble averaged observations, and shows that the ensemble averaging inherent in many experiments leads to an underestimation of coherence lifetimes in individual systems.

ABSTRACTDuring Chicago’s initial COVID-19 vaccine rollout, the city disproportionately allocated ... more ABSTRACTDuring Chicago’s initial COVID-19 vaccine rollout, the city disproportionately allocated vaccines to zip codes with high incomes and predominantly White populations. However, the impact of this inequitable distribution on COVID-19 outcomes is unknown. This observational study determined the association between zip-code level vaccination rate and COVID-19 mortality in residents of 52 Chicago zip codes. After controlling for age distribution and recovery from infection, a 10% higher vaccination rate by March 28, 2021, was associated with a 39% lower relative risk of death during the peak of the spring wave of COVID-19. Using a difference-in-difference analysis, Chicago could have prevented an estimated 72% of deaths in the least vaccinated quartile of the city (vaccination rates of 17.8 – 26.9%) if it had had the same vaccination rate as the most vaccinated quartile (39.9 – 49.3%). Inequitable vaccine allocation in Chicago likely exacerbated existing racial disparities in COVI...

American Journal of Transplantation, 2021

The Organ Procurement and Transplant Network (OPTN) implemented a new heart allocation policy on ... more The Organ Procurement and Transplant Network (OPTN) implemented a new heart allocation policy on October 18, 2018. Published estimates of lower post-transplant survival under the new policy in cohorts with limited follow-up may be biased by informative censoring. Using the Scientific Registry of Transplant Recipients, we used the Kaplan-Meier method to estimate 1-year post-transplant survival for pre-policy (November 1, 2016, to October 31, 2017) and post-policy cohorts (November 1, 2018, to October 31, 2019) with follow-up through March 2, 2021. We adjusted for changes in recipient population over time with a multivariable Cox proportional hazards model. To demonstrate the effect of inadequate follow-up on post-policy survival estimates, we repeated the analysis but only included follow-up through October 31, 2019. Transplant programs transplanted 2594 patients in the pre-policy cohort and 2761 patients in the post-policy cohort. With follow-up through March 2, 2021, unadjusted 1-year post-transplant survival was 90.6% (89.5% - 91.8%) in the pre-policy cohort and 90.8% (89.7% - 91.9%) in the post-policy cohort (adjusted HR = 0.93 [0.77-1.12]). Ignoring follow-up after October 31, 2019, the post-policy estimate was biased downward (1-year: 82.2%). When estimated with adequate follow-up, 1-year post-transplant survival under the new heart allocation policy was not significantly different.

Journal of Applied Crystallography, 2021

Bragg coherent diffraction imaging (BCDI) provides a powerful tool for obtaining high-resolution ... more Bragg coherent diffraction imaging (BCDI) provides a powerful tool for obtaining high-resolution structural information from nanocrystalline materials. Here a BCDI sample consisting of a large number of randomly oriented nanoscale crystals is considered. Ideally, only one crystal is oriented to produce a Bragg peak on the detector. However, diffraction from other crystals often produces additional signals on the detector. Before the measured diffraction patterns can be processed into structural images, scientists routinely need to manually identify and remove the `alien' intensities from sources other than the intended crystal. With the development of modern high-coherence storage rings, such as the upgraded Advanced Photon Source (APS), the already slow process of manual preprocessing will be untenable for the large volumes of data that will be produced. An automated method of identifying and deleting alien intensities is proposed. This method exploits the fact that BCDI of a p...

The Journal of Physical Chemistry C, 2017

Recent experimental studies revealed that charge carriers harvested by bulk heterojunction organi... more Recent experimental studies revealed that charge carriers harvested by bulk heterojunction organic photovoltaics can be collected on ultrafast time scales. To investigate ultrafast exciton mobility, we construct simple, nonatomistic models of a common polymeric electron donor material. We first explore the relationship between the magnitude of energetic noise in the model Hamiltonian and the spatial extent of resulting eigenstates. We then employ a quantum master equation approach to simulate migration of chromophore-localized initial excited states. Excitons initially localized on a single chromophore at the center of the model delocalize down polymer chains and across pi-stacked chromophores through a coherent, wavelike mechanism during the first few tens of femtoseconds. We explore the dependence of this coherent delocalization on coupling strength and on the magnitude of energetic noise. At longer times we observe continued migration toward a uniform population distribution that proceeds through an incoherent, diffusive mechanism. A series of simulations modeling exciton harvesting in domains of varying size demonstrates that smaller domains enhance ultrafast exciton harvesting yield. Our nonatomistic model falls short of quantitative accuracy but demonstrates that excitons are mobile within electron donor domains on ultrafast time scales and that coherent exciton transport can enhance ultrafast exciton harvesting.

Molecular Systems Design & Engineering, 2016

One of the most important factors in determining organic photovoltaic device performance is the e... more One of the most important factors in determining organic photovoltaic device performance is the efficiency of exciton dissociation and charge separation at donor/acceptor heterojunctions. This review discusses theoretical and computational approaches to modeling this crucial process of charge generation.

The Journal of Physical Chemistry C, 2017

Non-aqueous redox flow batteries have attracted recent attention with their potential for high el... more Non-aqueous redox flow batteries have attracted recent attention with their potential for high electrochemical storage capacity, with organic electrolytes serving as solvents with a wide electrochemical stability window. Organic molecules can also serve as electroactive species, where molecules with low reduction potentials or high oxidation potentials can provide substantial chemical energy. To identify promising electrolytes in a vast chemical space, high-throughput screening (HTS) of candidate molecules plays an important role, where HTS is used to calculate properties of thousands of molecules and identify a few organic molecules worthy of further attention in battery research. Here, we present reduction and oxidation potentials obtained from HTS of 4178 molecules. The molecules are composed of base groups of five or six-membered rings with one or two functional groups attached, with the set of possible functional groups including both electron-withdrawing and electron-donating groups. In addition to observing the trends in potentials that result from differences in organic base groups and functional groups, we analyze the effects of molecular characteristics such as multiple bonds, Hammett parameters, and functional group position. This work provides useful guidance in determining how the identities of the base groups and functional groups are correlated with desirable reduction and oxidation potentials.

Chemical Science, 2017

Using ab initio calculations of charges in PCBM fullerenes, a multiscale approach applies classic... more Using ab initio calculations of charges in PCBM fullerenes, a multiscale approach applies classical molecular dynamics to model charge transfer.

The Journal of chemical physics, Jan 14, 2015

Two-dimensional nanoplatelets (NPLs) are an exciting class of materials with promising optical an... more Two-dimensional nanoplatelets (NPLs) are an exciting class of materials with promising optical and energy transport properties. The possibility of efficient energy transport between nanoplatelets raises questions regarding the nature of energy transfer in these thin, laterally extended systems. A challenge in understanding exciton transport is the uncertainty regarding the size of the exciton. Depending on the material and defects in the nanoplatelet, an exciton could plausibly extend over an entire plate or localize to a small region. The variation in possible exciton sizes raises the question how exciton size impacts the efficiency of transport between nanoplatelet structures. Here, we explore this issue using a quantum master equation approach. This method goes beyond the assumptions of Förster theory to allow for quantum mechanical effects that could increase energy transfer efficiency. The model is extremely flexible in describing different systems, allowing us to test the effe...

The Journal of Physical Chemistry C, 2014

ABSTRACT Organic semiconductors offer a low-cost alternative to inorganic semiconductors. However... more ABSTRACT Organic semiconductors offer a low-cost alternative to inorganic semiconductors. However, their usefulness is limited by a relatively low mobility of polaron charge carriers. Past research indicates a positive correlation between charge density and charge mobility in organic semiconductors. This relationship is usually attributed to the phenomenon of excess charges filling traps. Here, we explore whether charge density may also affect mobility via influence on intermolecular couplings. Density functional theory (DFT) with a long-range corrected (LC-BLYP) functional is used to calculate charge densities and electronic couplings of negative charges on C-70 fullerenes in the presence of nearby negative point charges, which provides an upper limit calculation of the influence of nearby polarons. We find that in C-70 systems with relatively low couplings, the presence of additional charges has an effect of maximizing intermolecular couplings and hence transport. This effect drops off quickly with distance, suggesting that it is relevant only at extremely high charge densities that are an unlikely event in current C-70 devices. The effect of charge density on couplings may be useful in understanding transport in very limited regions of C-70 materials where the local charge density is high; however, it is unlikely to affect overall device performance.

Science (New York, N.Y.), Jan 5, 2014

The ability to predict the pressure dependence of chemical reaction rates would be a great boon t... more The ability to predict the pressure dependence of chemical reaction rates would be a great boon to kinetic modeling of processes such as combustion and atmospheric chemistry. This pressure dependence is intimately related to the rate of collision-induced transitions in energy E and angular momentum J. We present a scheme for predicting this pressure dependence based on coupling trajectory-based determinations of moments of the E,J-resolved collisional transfer rates with the two-dimensional master equation. This completely a priori procedure provides a means for proceeding beyond the empiricism of prior work. The requisite microcanonical dissociation rates are obtained from ab initio transition state theory. Predictions for the CH4 = CH3 + H and C2H3 = C2H2 + H reaction systems are in excellent agreement with experiment.

The Journal of Physical Chemistry B, 2014

Long-lived coherences have been observed in photosynthetic complexes after laser excitation, insp... more Long-lived coherences have been observed in photosynthetic complexes after laser excitation, inspiring new theories regarding the extreme quantum efficiency of photosynthetic energy transfer. Whether coherent (ballistic) transport occurs in nature and whether it improves photosynthetic efficiency remain topics of debate. Here, we use a nonequilibrium Green's function analysis to model exciton transport after excitation from an incoherent source (as opposed to coherent laser excitation). We find that even with an incoherent source, the rate of environmental dephasing strongly affects exciton transport efficiency, suggesting that the relationship between dephasing and efficiency is not an artifact of coherent excitation. The Green's function analysis provides a clear view of both the pattern of excitonic fluxes among chromophores and the multidirectionality of energy transfer that is a feature of coherent transport. We see that even in the presence of an incoherent source, transport occurs by qualitatively different mechanisms as dephasing increases. Our approach can be generalized to complex synthetic systems and may provide a new tool for optimizing synthetic light harvesting materials.

The Journal of Physical Chemistry A, 2011

Polyaromatic hydrocarbons (PAHs) are a class of organic molecules with importance in several bran... more Polyaromatic hydrocarbons (PAHs) are a class of organic molecules with importance in several branches of science, including medicine, combustion chemistry, and materials science. The delocalized π-orbital systems in PAHs require highly accurate electronic structure methods to capture strong electron correlation. Treating correlation in PAHs has been challenging because (i) traditional wave function methods for strong correlation have not been applicable since they scale exponentially in the number of strongly correlated orbitals, and (ii) alternative methods such as the density-matrix renormalization group and variational twoelectron reduced density matrix (2-RDM) methods have not been applied beyond linear acene chains. In this paper we extend the earlier results from active-space variational 2-RDM theory [Gidofalvi, G.; Mazziotti, D. A. J. Chem. Phys. 2008, 129, 134108] to the more general two-dimensional arrangement of rings-acene sheets-to study the relationship between geometry and electron correlation in PAHs. The acene-sheet calculations, if performed with conventional wave function methods, would require wave function expansions with as many as 1.5 Â 10 17 configuration state functions. To measure electron correlation, we employ several RDM-based metrics: (i) natural-orbital occupation numbers, (ii) the 1-RDM von Neumann entropy, (iii) the correlation energy per carbon atom, and (iv) the squared Frobenius norm of the cumulant 2-RDM. The results confirm a trend of increasing polyradical character with increasing molecular size previously observed in linear PAHs and reveal a corresponding trend in two-dimensional (arch-shaped) PAHs. Furthermore, in PAHs of similar size they show significant variations in correlation with geometry. PAHs with the strictly linear geometry (chains) exhibit more electron correlation than PAHs with nonlinear geometries (sheets).

New Journal of Physics, 2013

The role of noise in the transport properties of quantum excitations is a topic of great importan... more The role of noise in the transport properties of quantum excitations is a topic of great importance in many fields, from organic semiconductors for technological applications to light-harvesting complexes in photosynthesis. In this paper we study a semi-classical model where a tight-binding Hamiltonian is fully coupled to an underlying spatially extended nonlinear chain of atoms. We show that the transport properties of a quantum excitation are subtly modulated by (i) the specific type (local versus non-local) of exciton-phonon coupling and by (ii) nonlinear effects of the underlying lattice. We report a non-monotonic dependence of the exciton diffusion coefficient on temperature, in agreement with earlier predictions, as a direct consequence of the lattice-induced fluctuations in the hopping rates due to long-wavelength vibrational modes. A standard measure of transport efficiency confirms that both nonlinearity in the underlying lattice and off-diagonal exciton-phonon coupling promote transport efficiency at high temperatures, preventing the Zeno-like quench observed in other models lacking an explicit noise-providing dynamical system.

The Journal of Chemical Physics, 2012

An open question at the forefront of modern physical sciences is what role, if any, quantum effec... more An open question at the forefront of modern physical sciences is what role, if any, quantum effects may play in biological sensing and energy transport mechanisms. One area of such research concerns the possibility of coherent energy transport in photosynthetic systems. Spectroscopic evidence of long-lived quantum coherence in photosynthetic light-harvesting pigment protein complexes (PPCs), along with theoretical modeling of PPCs, has indicated that coherent energy transport might boost efficiency of energy transport in photosynthesis. Accurate assessment of coherence lifetimes is crucial for modeling the extent to which quantum effects participate in this energy transfer, because such quantum effects can only contribute to mechanisms proceeding on timescales over which the coherences persist. While spectroscopy is a useful way to measure coherence lifetimes, inhomogeneity in the transition energies across the measured ensemble may lead to underestimation of coherence lifetimes from spectroscopic experiments. Theoretical models of antenna complexes generally model a single system, and direct comparison of single system models to ensemble averaged experimental data may lead to systematic underestimation of coherence lifetimes, distorting much of the current discussion. In this study, we use simulations of the Fenna-Matthews-Olson complex to model single complexes as well as averaged ensembles to demonstrate and roughly quantify the effect of averaging over an inhomogeneous ensemble on measured coherence lifetimes. We choose to model the Fenna-Matthews-Olson complex because that system has been a focus for much of the recent discussion of quantum effects in biology, and use an early version of the well known environment-assisted quantum transport model to facilitate straightforward comparison between the current model and past work. Although ensemble inhomogeneity is known to lead to shorter lifetimes of observed oscillations (simply inhomogeneous spectral broadening in the time domain), this important fact has been left out of recent discussions of spectroscopic measurements of energy transport in photosynthesis. In general, these discussions have compared single-system theoretical models to whole-ensemble laboratory measurements without addressing the effect of inhomogeneous dephasing. Our work addresses this distinction between single system and ensemble averaged observations, and shows that the ensemble averaging inherent in many experiments leads to an underestimation of coherence lifetimes in individual systems.

ABSTRACTDuring Chicago’s initial COVID-19 vaccine rollout, the city disproportionately allocated ... more ABSTRACTDuring Chicago’s initial COVID-19 vaccine rollout, the city disproportionately allocated vaccines to zip codes with high incomes and predominantly White populations. However, the impact of this inequitable distribution on COVID-19 outcomes is unknown. This observational study determined the association between zip-code level vaccination rate and COVID-19 mortality in residents of 52 Chicago zip codes. After controlling for age distribution and recovery from infection, a 10% higher vaccination rate by March 28, 2021, was associated with a 39% lower relative risk of death during the peak of the spring wave of COVID-19. Using a difference-in-difference analysis, Chicago could have prevented an estimated 72% of deaths in the least vaccinated quartile of the city (vaccination rates of 17.8 – 26.9%) if it had had the same vaccination rate as the most vaccinated quartile (39.9 – 49.3%). Inequitable vaccine allocation in Chicago likely exacerbated existing racial disparities in COVI...