MesoHOPS: Size-invariant scaling calculations of multi-excitation open quantum systems.

The photoexcitation dynamics of molecular materials on the 10-100 nm length scale depend on complex interactions between electronic and vibrational degrees of freedom, rendering exact calculations difficult or intractable. The adaptive Hierarchy of Pure States (adHOPS) is a formally exact method that leverages the locality imposed by interactions between thermal environments and electronic excitations to achieve size-invariant scaling calculations for single-excitation processes in systems described by a Frenkel-Holstein Hamiltonian. Here, we extend adHOPS to account for arbitrary couplings between thermal environments and vertical excitation energies, enabling formally exact, size-invariant calculations that involve multiple excitations or states with shared thermal environments. In addition, we introduce a low-temperature correction and an effective integration of the noise to reduce the computational expense of including ultrafast vibrational relaxation in Hierarchy of Pure States (HOPS) simulations. We present these advances in the latest version of the open-source MesoHOPS library and use MesoHOPS to characterize charge separation at a one-dimensional organic heterojunction when both the electron and hole are mobile.

Zero-Quantum-Defect Method and the Fundamental Vibrational Interval of H_{2}

The fundamental vibrational interval of H_{2}^{+} has been determined to be ΔG_{1/2}=2191.126 614(17) cm^{-1} by continuous-wave laser spectroscopy of Stark manifolds of Rydberg states of H_{2} with the H_{2}^{+} ion core in the ground and first vibrationally excited states. Extrapolation of the Stark shifts to zero field yields the zero-quantum-defect positions -R_{H_{2}}/n^{2}, from which ionization energies can be determined. Our new result represents a 4-order-of-magnitude improvement compared to earlier measurements. It agrees, within the experimental uncertainty, with the value of 2191.126 626 344(17)(100) cm^{-1} determined in nonrelativistic quantum electrodynamic calculations [V. Korobov, L. Hilico and J.-Ph. Karr, Phys. Rev. Lett. 118, 233001 (2017)PRLTAO0031-900710.1103/PhysRevLett.118.233001].

Simulating optical linear absorption for mesoscale molecular aggregates: An adaptive hierarchy of pure states approach.

In this paper, we present dyadic adaptive HOPS (DadHOPS), a new method for calculating linear absorption spectra for large molecular aggregates. This method combines the adaptive HOPS (adHOPS) framework, which uses locality to improve computational scaling, with the dyadic HOPS method previously developed to calculate linear and nonlinear spectroscopic signals. To construct a local representation of dyadic HOPS, we introduce an initial state decomposition that reconstructs the linear absorption spectra from a sum over locally excited initial conditions. We demonstrate the sum over initial conditions can be efficiently Monte Carlo sampled and that the corresponding calculations achieve size-invariant [i.e., O(1)] scaling for sufficiently large aggregates while trivially incorporating static disorder in the Hamiltonian. We present calculations on the photosystem I core complex to explore the behavior of the initial state decomposition in complex molecular aggregates as well as proof-of-concept DadHOPS calculations on an artificial molecular aggregate inspired by perylene bis-imide to demonstrate the size-invariance of the method.

Formally Exact Simulations of Mesoscale Exciton Diffusion in a Light-Harvesting 2 Antenna Nanoarray.

The photosynthetic apparatus of plants and bacteria combine atomically precise pigment-protein complexes with dynamic membrane architectures to control energy transfer on the 10-100 nm length scales. Recently, synthetic materials have integrated photosynthetic antenna proteins to enhance exciton transport, though the influence of artificial packing on the excited-state dynamics in these biohybrid materials is not fully understood. Here, we use the adaptive hierarchy of pure states (adHOPS) to perform a formally exact simulation of excitation energy transfer within artificial aggregates of light-harvesting complex 2 (LH2) with a range of packing densities. We find that LH2 aggregates support a remarkable exciton diffusion length ranging from 100 nm at a biological packing density to 300 nm at the densest packing previously suggested in an artificial aggregate. The unprecedented scale of these formally exact calculations also underscores the efficiency with which adHOPS simulates excited-state processes in molecular materials.

A comparison of harmonic and traditional sharp staphylectomy techniques in 15 brachycephalic dogs.

OBJECTIVES: The objective was to compare sharp staphylectomy and staphylectomy using harmonic focus shears, assess surgical time, intraoperative haemorrhage and outcome. Our hypothesis was that harmonic staphylectomy would result in reduced surgical time, decreased intraoperative haemorrhage and greater relative improvement. MATERIALS AND METHODS: Dogs that were presented to Highcroft Veterinary Referrals between July 2020 and September 2021 with brachycephalic obstructive airway syndrome and underwent surgical correction were prospectively enrolled. Surgical technique was randomised, and surgical time, staphylectomy time, intraoperative haemorrhage, hospitalisation and change in patients' Cambridge BOAS Grade at a 14-day recheck were recorded. RESULTS: Fifteen dogs were enrolled: seven dogs underwent sharp and eight underwent harmonic staphylectomy. Nine patients returned for follow-up, four of seven and five of eight, respectively. Harmonic staphylectomy was associated with less haemorrhage (0 versus 9 cotton buds) and a shorter average staphylectomy time (3 minutes 36 seconds versus 14 minutes 50 seconds). No statistically significant differences were observed in total surgery time, number of nights hospitalised, or change in Cambridge BOAS Grade. An average of 0.68 mm of thermal necrosis was seen at the cut edges of soft palates removed by harmonic staphylectomy. CLINICAL SIGNIFICANCE: Harmonic staphylectomy can result in a reduction in staphylectomy time and degree of intraoperative haemorrhage compared to sharp staphylectomy, with no deleterious impact on postoperative recovery or the long-term outcome of patients.

Calculating nonlinear response functions for multidimensional electronic spectroscopy using dyadic non-Markovian quantum state diffusion.

We present a methodology for simulating multidimensional electronic spectra of molecular aggregates with coupling of electronic excitation to a structured environment using the stochastic non-Markovian quantum state diffusion (NMQSD) method in combination with perturbation theory for the response functions. A crucial aspect of our approach is that we propagate the NMQSD equation in a doubled system Hilbert space but with the same noise. We demonstrate that our approach shows fast convergence with respect to the number of stochastic trajectories, providing a promising technique for numerical calculation of two-dimensional electronic spectra of large molecular aggregates.

Simulation of absorption spectra of molecular aggregates: A hierarchy of stochastic pure state approach.

Simulation of spectroscopic observables for molecular aggregates with strong and structured coupling of electronic excitation to vibrational degrees of freedom is an important but challenging task. The Hierarchy of Pure States (HOPS) provides a formally exact solution based on local, stochastic trajectories. Exploiting the localization of HOPS for the simulation of absorption spectra in large aggregates requires a formulation in terms of normalized trajectories. Here, we provide a normalized dyadic equation where the ket- and bra-states are propagated in different electronic Hilbert spaces. This work opens the door to applying adaptive HOPS methods for the simulation of absorption spectra.

Molecular origins of induction and loss of photoinhibition-related energy dissipation qI.

Photosynthesis fuels life on Earth using sunlight as energy source. However, light has a simultaneous detrimental effect on the enzyme triggering photosynthesis and producing oxygen, photosystem II (PSII). Photoinhibition, the light-dependent decrease of PSII activity, results in a major limitation to aquatic and land photosynthesis and occurs upon all environmental stress conditions. In this work, we investigated the molecular origins of photoinhibition focusing on the paradoxical energy dissipation process of unknown nature coinciding with PSII damage. Integrating spectroscopic, biochemical, and computational approaches, we demonstrate that the site of this quenching process is the PSII reaction center. We propose that the formation of quenching and the closure of PSII stem from the same event. We lastly reveal the heterogeneity of PSII upon photoinhibition using structure-function modeling of excitation energy transfer. This work unravels the functional details of the damage-induced energy dissipation at the heart of photosynthesis.

Formally exact simulations of mesoscale exciton dynamics in molecular materials.

Excited state carriers, such as excitons, can diffuse on the 100 nm to micron length scale in molecular materials but only delocalize over short length scales due to coupling between electronic and vibrational degrees-of-freedom. Here, we leverage the locality of excitons to adaptively solve the hierarchy of pure states equations (HOPS). We demonstrate that our adaptive HOPS (adHOPS) methodology provides a formally exact and size-invariant (i.e., ) scaling algorithm for simulating mesoscale quantum dynamics. Finally, we provide proof-of-principle calculations for exciton diffusion on linear chains containing up to 1000 molecules.

Directed kinetic transition network model.

Molecular dynamics simulations contain detailed kinetic information related to the functional states of proteins and macromolecules, but this information is obscured by the high dimensionality of configurational space. Markov state models and transition network models are widely applied to extract kinetic descriptors from equilibrium molecular dynamics simulations. In this study, we developed the Directed Kinetic Transition Network (DKTN)-a graph representation of a master equation which is appropriate for describing nonequilibrium kinetics. DKTN models the transition rate matrix among different states under detailed balance. Adopting the mixing time from the Markov chain, we use the half mixing time as the criterion to identify critical state transition regarding the protein conformational change. The similarity between the master equation and the Kolmogorov equation suggests that the DKTN model can be reformulated into the continuous-time Markov chain model, which is a general case of the Markov chain without a specific lag time. We selected a photo-sensitive protein, vivid, as a model system to illustrate the usage of the DKTN model. Overall, the DKTN model provides a graph representation of the master equation based on chemical kinetics to model the protein conformational change without the underlying assumption of the Markovian property.

Models and mechanisms of the rapidly reversible regulation of photosynthetic light harvesting.

The rapid response of photosynthetic organisms to fluctuations in ambient light intensity is incompletely understood at both the molecular and membrane levels. In this review, we describe research from our group over a 10-year period aimed at identifying the photophysical mechanisms used by plants, algae and mosses to control the efficiency of light harvesting by photosystem II on the seconds-to-minutes time scale. To complement the spectroscopic data, we describe three models capable of describing the measured response at a quantitative level. The review attempts to provide an integrated view that has emerged from our work, and briefly looks forward to future experimental and modelling efforts that will refine and expand our understanding of a process that significantly influences crop yields.

Canine urethral sphincter pressure profile under incremental inflation of an artificial cuff: a cadaver study.

OBJECTIVES: To determine whether artificial urethral sphincter filling volume is proportional to peak pressure exerted on the urethra. MATERIALS AND METHODS: Urethral pressure profilometry was performed in five female, medium-sized, mixed-breed canine cadavers following artificial urethral sphincter placement. Maximum urethral pressure was recorded following sequential incremental inflation of 0.15 mL and compared to baseline pressure and between dogs using two-way analysis of variance. RESULTS: Artificial urethral sphincter placement in cadavers was associated with an increase in urethral pressure, which was significantly correlated with inflation volume. The correlation was non-linear and demonstrated considerable individual variation. Maximum urethral pressures after artificial urethral sphincter placement exceeded those reported in conscious continent dogs within a narrow volume range, in which a 0.15 mL infusion more than doubled maximal urethral pressures. CLINICAL SIGNIFICANCE: Rapid increases in urethral pressure from the artificial urethral sphincter over a small range of filling volumes (0.15 mL increments) might explain why some clinical cases can become suddenly dysuric following incremental inflations. We suggest that smaller increments of filling (0.05 to 0.1 mL) may achieve finer pressure control.

Energy-dependent quenching adjusts the excitation diffusion length to regulate photosynthetic light harvesting.

An important determinant of crop yields is the regulation of photosystem II (PSII) light harvesting by energy-dependent quenching (qE). However, the molecular details of excitation quenching have not been quantitatively connected to the fraction of excitations converted to chemical energy by PSII reaction centers (PSII yield), which determines flux to downstream metabolism. Here, we incorporate excitation dissipation by qE into a pigment-scale model of excitation transfer and trapping for a 200 × 200-nm patch of the grana membrane. We show that excitation transport can be rigorously coarse grained to a 2D random walk with an excitation diffusion length determined by the extent of quenching. We present an alternative method for analyzing pulse amplitude-modulated chlorophyll fluorescence measurements that incorporates the effects of a variable excitation diffusion length during qE activation.

Mechanistic Regimes of Vibronic Transport in a Heterodimer and the Design Principle of Incoherent Vibronic Transport in Phycobiliproteins.

Following the observation of coherent oscillations in nonlinear spectra of photosynthetic pigment protein complexes, in particular, phycobilliproteins such as PC645, coherent vibronic transport has been suggested as a design principle for novel light-harvesting materials. Vibronic transport between energetically remote pigments is coherent when the presence of a vibration resonant with the electronic energy gap supports transient delocalization between the electronic excited states. We establish the mechanism of vibronic transport for a model heterodimer across a wide range of molecular parameter values. The resulting mechanistic map demonstrates that the molecular parameters of phycobiliproteins in fact support incoherent vibronic transport. This result points to an important design principle: Incoherent vibronic transport is more efficient than a coherent mechanism when energetic disorder exceeds the coupling between the donor and vibrationally excited acceptor states. Finally, our results suggest that the role of coherent vibronic transport in pigment protein complexes should be reevaluated.

Photochemical Control of Exciton Superradiance in Light-Harvesting Nanotubes.

Photosynthetic antennae and organic electronic materials use topological, structural, and molecular control of delocalized excitons to enhance and direct energy transfer. Interactions between the transition dipoles of individual chromophore units allow for coherent delocalization across multiple molecular sites. This delocalization, for specific geometries, greatly enhances the transition dipole moment of the lowest energy excitonic state relative to the chromophore and increases its radiative rate, a phenomenon known as superradiance. In this study, we show that ordered, self-assembled light-harvesting nanotubes (LHNs) display excitation-induced photobrightening and photodarkening. These changes in quantum yield arise due to changes in energetic disorder, which in turn increases/decreases excitonic superradiance. Through a combination of experiment and modeling, we show that intense illumination induces different types of chemical change in LHNs that reproducibly alter absorption and fluorescence properties, indicating control over excitonic delocalization. We also show that changes in spectral width and shift can be sensitive measures of system dimensionality, illustrating the mixed 1-2D nature of LHN excitons. Our results demonstrate a path forward for mastery of energetic disorder in an excitonic antenna, with implications for fundamental studies of coherent energy transport.

Local protein solvation drives direct down-conversion in phycobiliprotein PC645 via incoherent vibronic transport.

The mechanisms controlling excitation energy transport (EET) in light-harvesting complexes remain controversial. Following the observation of long-lived beats in 2D electronic spectroscopy of PC645, vibronic coherence, the delocalization of excited states between pigments supported by a resonant vibration, has been proposed to enable direct excitation transport from the highest-energy to the lowest-energy pigments, bypassing a collection of intermediate states. Here, we instead show that for phycobiliprotein PC645 an incoherent vibronic transport mechanism is at play. We quantify the solvation dynamics of individual pigments using ab initio quantum mechanics/molecular mechanics (QM/MM) nuclear dynamics. Our atomistic spectral densities reproduce experimental observations ranging from absorption and fluorescence spectra to the timescales and selectivity of down-conversion observed in transient absorption measurements. We construct a general model for vibronic dimers and establish the parameter regimes of coherent and incoherent vibronic transport. We demonstrate that direct down-conversion in PC645 proceeds incoherently, enhanced by large reorganization energies and a broad collection of high-frequency vibrations. We suggest that a similar incoherent mechanism is appropriate across phycobiliproteins and represents a potential design principle for nanoscale control of EET.

The incidence of surgical site dehiscence following full-thickness gastrointestinal biopsy in dogs and cats and associated risk factors.

OBJECTIVES: The objectives of this study were to: (1) document the incidence of surgical site dehiscence after full-thickness gastrointestinal biopsy in dogs and cats and (2) identify potential risk factors. METHODS: Data relating to dogs and cats undergoing full-thickness gastrointestinal biopsy were reviewed retrospectively following submission of a completed questionnaire by 12 referral institutions. Outcome measures were definite dehiscence, possible dehiscence (clinical records suggestive of dehiscence but not confirmed), suspected dehiscence (definite and possible combined) and death within 14 days. Logistic regression was planned for analysis of association of dehiscence with low preoperative serum albumin, biopsy through neoplastic tissue, biopsy alongside another major abdominal surgical procedure and biopsy of the colon. RESULTS: Of 172 cats, two (1·2%) had definite dehiscence, and four (2·3%) had possible dehiscence. Low preoperative serum albumin was significantly associated with definite dehiscence in univariable analysis and with suspected dehiscence and death within 14 days in univariable analysis, but all odds ratios had wide 95% confidence intervals. A histopathological diagnosis of neoplasia was significantly associated with death within 14 days in univariable analysis. Of 195 dogs, two (1·0%) had definite dehiscence, and three (1·5%) had possible dehiscence. In dogs, there was no association between any outcome measure and the putative risk factors. CLINICAL SIGNIFICANCE: Incidence of dehiscence following full-thickness gastrointestinal biopsy was low in this study. When determining the appropriateness of biopsy in individual cases, this information should be balanced against the potentially life-threatening consequences of dehiscence.