Excited state mean-field theory without automatic differentiation.

We present a formulation of excited state mean-field theory in which the derivatives with respect to the wave function parameters needed for wave function optimization (not to be confused with nuclear derivatives) are expressed analytically in terms of a collection of Fock-like matrices. By avoiding the use of automatic differentiation and grouping Fock builds together, we find that the number of times we must access the memory-intensive two-electron integrals can be greatly reduced. Furthermore, the new formulation allows the theory to exploit the existing strategies for efficient Fock matrix construction. We demonstrate this advantage explicitly via the shell-pair screening strategy with which we achieve a cubic overall cost scaling. Using this more efficient implementation, we also examine the theory's ability to predict charge redistribution during charge transfer excitations. Using the coupled cluster as a benchmark, we find that by capturing orbital relaxation effects and avoiding self-interaction errors, excited state mean field theory out-performs other low-cost methods when predicting the charge density changes of charge transfer excitations.

Nuclear-electronic orbital Ehrenfest dynamics.

The recently developed real-time nuclear-electronic orbital (RT-NEO) approach provides an elegant framework for treating electrons and selected nuclei, typically protons, quantum mechanically in nonequilibrium dynamical processes. However, the RT-NEO approach neglects the motion of the other nuclei, preventing a complete description of the coupled nuclear-electronic dynamics and spectroscopy. In this work, the dynamical interactions between the other nuclei and the electron-proton subsystem are described with the mixed quantum-classical Ehrenfest dynamics method. The NEO-Ehrenfest approach propagates the electrons and quantum protons in a time-dependent variational framework, while the remaining nuclei move classically on the corresponding average electron-proton vibronic surface. This approach includes the non-Born-Oppenheimer effects between the electrons and the quantum protons with RT-NEO and between the classical nuclei and the electron-proton subsystem with Ehrenfest dynamics. Spectral features for vibrational modes involving both quantum and classical nuclei are resolved from the time-dependent dipole moments. This work shows that the NEO-Ehrenfest method is a powerful tool to study dynamical processes with coupled electronic and nuclear degrees of freedom.

QMCPACK: Advances in the development, efficiency, and application of auxiliary field and real-space variational and diffusion quantum Monte Carlo.

We review recent advances in the capabilities of the open source ab initio Quantum Monte Carlo (QMC) package QMCPACK and the workflow tool Nexus used for greater efficiency and reproducibility. The auxiliary field QMC (AFQMC) implementation has been greatly expanded to include k-point symmetries, tensor-hypercontraction, and accelerated graphical processing unit (GPU) support. These scaling and memory reductions greatly increase the number of orbitals that can practically be included in AFQMC calculations, increasing the accuracy. Advances in real space methods include techniques for accurate computation of bandgaps and for systematically improving the nodal surface of ground state wavefunctions. Results of these calculations can be used to validate application of more approximate electronic structure methods, including GW and density functional based techniques. To provide an improved foundation for these calculations, we utilize a new set of correlation-consistent effective core potentials (pseudopotentials) that are more accurate than previous sets; these can also be applied in quantum-chemical and other many-body applications, not only QMC. These advances increase the efficiency, accuracy, and range of properties that can be studied in both molecules and materials with QMC and QMCPACK.

Variational Excitations in Real Solids: Optical Gaps and Insights into Many-Body Perturbation Theory.

We present an approach to studying optical band gaps in real solids in which quantum Monte Carlo methods allow for the application of a rigorous variational principle to both ground and excited state wave functions. In tests that include small, medium, and large band gap materials, optical gaps are predicted with a mean absolute deviation of 3.5% against experiment, less than half the equivalent errors for typical many-body perturbation theories. The approach is designed to be insensitive to the choice of density functional, a property we exploit in order to provide insight into how far different functionals are from satisfying the assumptions of many-body perturbation theory. We explore this question most deeply in the challenging case of ZnO, where we show that, although many commonly used functionals have shortcomings, there does exist a one-particle basis in which perturbation theory's zeroth-order picture is sound. Insights of this nature should be useful in guiding the future application and improvement of these widely used techniques.

Resveratrol ameliorates cardiac dysfunction induced by pressure overload in rats via structural protection and modulation of Ca(2+) cycling proteins.

BACKGROUND: Cardiac hypertrophy is a compensatory stage of the heart in response to stress such as pressure overload (PO), which can develop into heart failure (HF) if left untreated. Resveratrol has been reported to prevent the development of hypertrophy and contractile dysfunction induced by PO. However, other studies found that resveratrol treatment for a longer period of time failed to regress cardiac hypertrophy. The aim of this study is to determine the timing of resveratrol treatment to achieve antihypertrophic effect and investigate whether resveratrol prevents the development of HF through preservation of myocardium structure and modulation of Ca(2+) handling proteins. METHODS: To generate rats with cardiac hypertrophy, male Sprague-Dawley rats were subjected to PO (aortic banding procedure) for 4 weeks. Sham-operated animals served as controls. Rats with cardiac hypertrophy were given resveratrol (4 mg/kg/day) for 4, 6, and 8 weeks, respectively. Histological and echocardiographic analysis and transmission electron microscopy were performed to assess cardiac structure and function. The levels of Ca(2+) handling proteins were measured by western blot analysis. RESULTS: Histological analysis showed that resveratrol treatment regressed developed cardiac hypertrophy at 8 and 10 weeks postsurgery, but not at 12 weeks. However, resveratrol strongly and continuously prevented the development of cardiac dysfunction and dilation of cardiac chamber as evaluated by echocardiography and H&E staining of heart cross-sections. In addition, PO-induced cardiac fibrosis was completely inhibited by resveratrol treatment. Resveratrol markedly prevented the disrupted myocardium but partially rescued mitochondrial abnormality in banded rats. Moreover, resveratrol prevented the alteration of Ca(2+) handling proteins induced by aortic banding, including downregulation of sarcoplasmic reticulum Ca(2+) ATPase 2 (SERCA2) and ryanodine receptor 2 (RyR2), hypophosphorylated phospholamban (PLB), upregulation of Na(+)/Ca(2+)-exchangers (NCX1) and increased expression and phosphorylation of Ca(2+)/calmodulin -dependent protein kinase II (CaMKII). Moreover, resveratrol alleviated the decreased SERCA activity induced by aortic banding. CONCLUSIONS: Resveratrol effectively prevented the transition from compensatory to decompensatory stage of cardiac hypertrophy induced by PO, but this effect is dependent on the timing of treatment. We suggest that resveratrol may exert beneficial effects on cardiac hypertrophy through protection of cardiac structure and modulation of Ca(2+) handling proteins.

Alterations in cardiac structure and function in a modified rat model of myocardial hypertrophy.

This study was aimed to establish a stable animal model of left ventricular hypertrophy (LVH) to provide theoretical and experimental basis for understanding the development of LVH. The abdominal aorta of male Wistar rats (80-100 g) was constricted to a diameter of 0.55 mm between the branches of the celiac and anterior mesenteric arteries. Echocardiography using a linear phased array probe was performed as well as pathological examination and plasma B-type natriuretic peptide (BNP) measurement at 3, 4 and 6 weeks after abdominal aortic constriction (AAC). The results showed that the acute mortality rate (within 24 h) of this modified rat model was 8%. Animals who underwent AAC demonstrated significantly increased interventricular septal (IVS), LV posterior wall (LVPWd), LV mass index (LVMI), cross-sectional area (CSA) of myocytes, and perivascular fibrosis; the ejection fraction (EF), fractional shortening (FS), and cardiac output (CO) were consistently lower at each time point after AAC. Notably, differences in these parameters between AAC group and sham group were significant by 3 weeks and reached peaks at 4th week. Following AAC, the plasma BNP was gradually elevated compared with the sham group at 3rd and 6th week. It was concluded that this modified AAC model can develop LVH, both stably and safely, by week four post-surgery; echocardiography is able to assess changes in chamber dimensions and systolic properties accurately in rats with LVH.

Chitosan inhibits Penicillium expansum possibly by binding to DNA and triggering apoptosis.

Chitosan is a natural polysaccharide that is abundant, biocompatible and exhibits effective antifungal activity against various pathogenic fungi. However, the potential intracellular targets of chitosan in pathogenic fungi and the way of activity of chitosan are far from well known. The present work demonstrated that chitosan could inhibit Penicillium expansum, the principal causal agent of postharvest blue mold decay on apple fruits, by binding to DNA and triggering apoptosis. UV-visible spectroscopy, fluorescence spectroscopy and electrophoretic mobility assay proved the interaction between chitosan and DNA, while atomic force microscope (AFM) observation revealed the binding morphology of chitosan to DNA. Chitosan could inhibit in vitro DNA replication, and cell cycle analysis employing flow cytometry demonstrated that cell cycle was retarded by chitosan treatment. Furthermore, the reactive oxygen species (ROS) assay and membrane potential analysis showed that apoptosis was induced in P. expansum cells after exposure to chitosan. In conclusion, our results confirmed that chitosan interacts with DNA and induces apoptosis. These findings are expected to provide a feasible theoretical basis and practical direction for the promoting and implementing of chitosan in plant protection and further illuminate the possible antifungal mechanisms of chitosan against fungal pathogens.

Endoglucanase H from Aspergillus westerdijkiae Plays an Important Role in the Virulence on Pear Fruits.

Aspergillus westerdijkiae can infect many agricultural products including cereals, grapes, and pear. Pathogenic fungi secrete diverse effectors as invasive weapons for successful invasion the host plant. During the pathogen-host interaction, 4486 differentially expressed genes were observed in A. westerdijkiae with 2773 up-regulated and 1713 down-regulated, whereas 8456 differentially expressed genes were detected in pear fruits with 4777 up-regulated and 3679 down-regulated. A total of 309 effector candidate genes were identified from the up-regulated genes in A. westerdijkiae. Endoglucanase H (AwEGH) was significantly induced during the pathogen-host interaction. Deletion of AwEGH resulted in altered fungal growth and morphology and reduced conidia production and germination compared to the wild-type. Further experiments demonstrated that AwEGH plays a role in cell wall integrity. Importantly, disruption of AwEGH significantly reduced the fungal virulence on pear fruits, and this defect can be partly explained by the impaired ability of A. westerdijkiae to penetrate host plants.

MicroRNA-26 was decreased in rat cardiac hypertrophy model and may be a promising therapeutic target.

MicroRNA (miR)-26 was found to be downregulated in cardiac diseases. In this study, the critical role of miR-26 in myocardial hypertrophy in both in vivo and in vitro was investigated. Sixteen male Wistar rats that underwent sham or transverse abdominal aortic constriction (TAAC) surgery were divided into control or TAAC group. Cardiomyocytes were isolated from neonatal Sprague-Dawley rats. Our study demonstrated that miR-26a/b was downregulated in both TAAC rat model and cardiomyocytes. The results of luciferase assays also suggested that glycogen synthase kinase 3ß (GSK3ß) may be a direct target of miR-26. The overexpression of miR-26 attenuated GSK3ß expression and inhibited myocardial hypertrophy. The downregulation of miR-26 reversed these effects. Furthermore, silence of GSK3ß gene phenocopied the anti-hypertrophy effects of miR-26, whereas overexpression of this protein attenuated the effects of miR-26. Taken together, these data suggest that miR-26 regulates pathological structural changes in the rat heart, which may be associated with suppression of the GSK3ß signaling pathway, and implicate the potential application of miR-26 in diagnosis and therapy of cardiac hypertrophy.

Transcriptome Analysis and Functional Characterization Reveal That Peclg Gene Contributes to the Virulence of Penicillium expansum on Apple Fruits.

Penicillium expansum is the causal agent of blue mold decay on apple fruits and is also known to be the major producer of patulin, a mycotoxin that represents serious hazard to human health. Several mechanisms have been suggested to explain the pathogenesis of P. expansum in host plants. Secreted effector proteins are vital for the pathogenicity of many fungal pathogens through manipulating their hosts for efficient colonization. In this study, we performed a RNA-Seq analysis followed by computational prediction of effector proteins from P. expansum during infection of the host apple fruits, and a total of 212 and 268 candidate effector protein genes were identified at 6 and 9 h after inoculation (hai), respectively. One of the candidate effector protein genes was identified as a concanavalin A-like lectin/glucanase (Peclg), which was dramatically induced during the pathogen-host interaction. Targeted knockout of Peclg resulted in significant reduction in conidial production and germination relative to the wild type. Further studies showed that in addition to salt stress, the mutant was much more sensitive to SDS and Congo red, suggesting a defect in cell wall integrity. Pathogenicity assays revealed that the ΔPeclg mutant showed significant decrease in virulence and infectious growth on apple fruits. All these results suggest that Peclg is required for fungal growth, stress response, and the virulence of P. expansum.

Solvated Nuclear-Electronic Orbital Structure and Dynamics.

Nonadiabatic dynamical processes such as proton-coupled electron transfer and excited state intramolecular proton transfer have been the subject of much research. One of the promising theoretical methods to describe these processes is the nuclear-electronic orbital (NEO) approach. This approach inherently accounts for nuclear quantum effects within quantum chemistry calculations, and it has recently been extended to directly simulate nonadiabatic processes with the development of real-time NEO methods. These processes can also be significantly dependent on the surrounding chemical environment, however, and capturing the effects of the environment is often necessary for analyzing experimentally relevant systems. This work couples the NEO density functional theory and real-time time-dependent density functional theory approaches with solvation through the polarizable continuum model. The effects of this coupling are investigated for ground state properties, solvent-dependent vibrational frequencies, and direct excited state intramolecular proton transfer dynamics.

Screening of Bacillus velezensis E2 and the Inhibitory Effect of Its Antifungal Substances on Aspergillus flavus.

Aspergilus flavus is the main pathogenic fungus that causes food mold. Effective control of A. flavus contamination is essential to ensure food safety. The lipopeptides (LPs) produced by Bacillus strains have been shown to have an obvious antifungal effect on molds. In this study, an antagonist strain of Bacillus velezensis with obvious antifungal activity against A. flavus was isolated from the surface of healthy rice. Using HPLC-MS analysis, the main components of LPs produced by strain E2 were identified as fengycin and iturins. Further investigations showed that LPs could inhibit the spore germination, and even cause abnormal expansion of hyphae and cell rupture. Transcriptomic analyses showed that some genes, involved in ribosome biogenesis in eukaryotes (NOG1, KRE33) and aflatoxin biosynthesis (aflK, aflR, veA, omtA) pathways in A. flavus were significantly down-regulated by LPs. In conclusion, this study provides novel insights into the cellular and molecular antifungal mechanisms of LPs against grain A. flavus contamination.

Excited State Intramolecular Proton Transfer with Nuclear-Electronic Orbital Ehrenfest Dynamics.

The recent development of the Ehrenfest dynamics approach in the nuclear-electronic orbital (NEO) framework provides a promising way to simulate coupled nuclear-electronic dynamics. Our previous study showed that the NEO-Ehrenfest approach with a semiclassical traveling proton basis method yields accurate predictions of molecular vibrational frequencies. In this work, we provide a more thorough analysis of the semiclassical traveling proton basis method to elucidate its validity and convergence behavior. We also conduct NEO-Ehrenfest dynamics simulations to study an excited state intramolecular proton transfer process. These simulations reveal that nuclear quantum effects influence the predictions of proton transfer reaction rates and kinetic isotope effects due to the intrinsic delocalized nature of the quantum nuclear wave function. This work illustrates the importance of nuclear quantum effects in coupled nuclear-electronic dynamical processes and shows that the NEO-Ehrenfest approach can be a powerful tool for providing insights and predictions for these processes.

Density Functional Extension to Excited-State Mean-Field Theory.

We investigate an extension of excited-state mean-field theory in which the energy expression is augmented with density functional components in an effort to include the effects of weak electron correlations. The approach remains variational and entirely time independent, allowing it to avoid some of the difficulties associated with linear response and the adiabatic approximation. In particular, all of the electrons' orbitals are relaxed state specifically, and there is no reliance on Kohn-Sham orbital energy differences, both of which are important features in the context of charge transfer. Preliminary testing shows clear advantages for single-component charge transfer states, but the method, at least in its current form, is less reliable for states in which multiple particle-hole transitions contribute significantly.

Frequency and Time Domain Nuclear-Electronic Orbital Equation-of-Motion Coupled Cluster Methods: Combination Bands and Electronic-Protonic Double Excitations.

The accurate description of excited vibronic states is important for modeling a wide range of photoinduced processes. The nuclear-electronic orbital (NEO) approach, which treats specified protons on the same level as the electrons, can describe excited electronic-protonic states. Herein the multicomponent equation-of-motion coupled cluster with singles and doubles (NEO-EOM-CCSD) method and its time-domain counterpart, TD-NEO-EOM-CCSD, are developed and implemented. The application of these methods to the HCN molecule highlights their capabilities. These methods predict qualitatively reasonable energies and intensities for a combination band corresponding to simultaneous excitation of two vibrational modes, as well as an overtone. These methods also describe states with double excitation character, such as excited electronic-protonic states corresponding to the simultaneous excitation of an electron and a proton. The ability of the NEO-EOM-CCSD method and its time-dependent counterpart to describe combination bands, overtones, and double excitations will enable a wide range of photochemical applications.

Real-Time Time-Dependent Nuclear-Electronic Orbital Approach: Dynamics beyond the Born-Oppenheimer Approximation.

The quantum mechanical treatment of both electrons and nuclei is crucial in nonadiabatic dynamical processes such as proton-coupled electron transfer. The nuclear-electronic orbital (NEO) method provides an elegant framework for including nuclear quantum effects beyond the Born-Oppenheimer approximation. To enable the study of nonequilibrium properties, we derive and implement a real-time NEO (RT-NEO) approach based on time-dependent Hatree-Fock or density functional theory, in which the electronic and nuclear degrees of freedom are propagated in a time-dependent variational framework. Nuclear and electronic spectral features can be resolved from the time-dependent dipole moment computed using the RT-NEO method. The test cases show the dynamical interplay between the quantum nuclei and the electrons through vibronic coupling. Moreover, vibrational excitation in the RT-NEO approach is demonstrated by applying a resonant driving field, and electronic excitation is demonstrated by simulating excited state intramolecular proton transfer. This work shows that the RT-NEO approach is a promising tool to study nonadiabatic quantum dynamical processes within a time-dependent variational description for the coupled electronic and nuclear degrees of freedom.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids.

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

A Blocked Linear Method for Optimizing Large Parameter Sets in Variational Monte Carlo.

We present a modification to variational Monte Carlo's linear method optimization scheme that addresses a critical memory bottleneck while maintaining compatibility with both the traditional ground state variational principle and our recently introduced variational principle for excited states. For wave function ansatzes with tens of thousands of variables, our modification reduces the required memory per parallel process from tens of gigabytes to hundreds of megabytes, making the methodology a much better fit for modern supercomputer architectures in which data communication and per-process memory consumption are primary concerns. We verify the efficacy of the new optimization scheme in small molecule tests involving both the Hilbert space Jastrow antisymmetric geminal power ansatz and real space multi-Slater Jastrow expansions. Satisfied with its performance, we have added the optimizer to the QMCPACK software package, with which we test a systematically convergent, nonperturbative approach to excitation energies on the example of a Mott-insulating hydrogen ring.

Equation of Motion Theory for Excited States in Variational Monte Carlo and the Jastrow Antisymmetric Geminal Power in Hilbert Space.

An equation of motion formalism for excited states in variational Monte Carlo is derived, and a pilot implementation for the Jastrow-modified antisymmetric geminal power is tested. In single excitations across a range of small molecules, this combination is shown to be intermediate in accuracy between configuration interaction singles and equation of motion coupled cluster with singles and doubles. For double excitations, energy errors are found to be similar to those for coupled cluster.