Search

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

In this paper we discuss a new formalism for producing an analytic coupled-cluster (CC) Green's function for an N-electron system by shifting the poles of similarity transformed Hamiltonians represented in N - 1 and N + 1 electron Hilbert spaces. Simple criteria are derived for the states in N - 1 and N + 1 electron spaces that are then corrected in the spectral resolution of the corresponding matrix representations of the similarity transformed Hamiltonian. The accurate description of excited state processes within a Green's function formalism would be of significant importance to a number of scientific communities ranging from physics and chemistry to engineering and the biological sciences. This is because the Green's function methodology provides a direct path for not only calculating properties whose underlying origins come from coupled many-body interactions but also provides a straightforward path for calculating electron transport, response, and correlation functions that allows for a direct link with experiment. As a special case of this general formulation, we discuss the application of this technique for Green's function defined by the CC with singles and doubles representation of the ground-state wave function. [ABSTRACT FROM AUTHOR]

Homeostatic regulation of neuronal activity is essential for robust computation; set-points, such as firing rate, are actively stabilized to compensate for perturbations. The disruption of brain function central to neurodegenerative disease likely arises from impairments of computationally essential set-points. Here, we systematically investigated the effects of tau-mediated neurodegeneration on all known set-points in neuronal activity. We continuously tracked hippocampal neuronal activity across the lifetime of a mouse model of tauopathy. We were unable to detect effects of disease in measures of single-neuron firing activity. By contrast, as tauopathy progressed, there was disruption of network-level neuronal activity, quantified by measuring neuronal pairwise interactions and criticality, a homeostatically controlled, ideal computational regime. Deviations in criticality correlated with symptoms, predicted underlying anatomical pathology, occurred in a sleep-wake-dependent manner, and could be used to reliably classify an animal's genotype. This work illustrates how neurodegeneration may disrupt the computational capacity of neurobiological systems., Competing Interests: Declaration of interests D.M.H. is on the scientific advisory board of C2N diagnostics and has equity. D.M.H. is on the scientific advisory board of Denali Therapeutics, Genentech, and Cajal Therapeutics and consults for Asteroid Therapeutics., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Diversity increases toward the tropics, but the strength of this pattern diverges with thermoregulatory strategy. Synthesizing over 30,000 species distributions, we quantified patterns of richness in terrestrial vertebrates, and present evidence for a latitudinal gradient of community composition. We observe a two orders of magnitude shift in comparative diversity with temperature, from endothermic mammal and avian dominance near the poles, toward ectothermic reptile and amphibian majority in the tropics. Next, we provide mechanistic support for a corresponding latitudinal gradient of predatory interactions. Using automated video tracking in >4500 trials, we show that differences in thermal sensitivity of locomotion in endothermic predators and ectothermic prey favors endotherms in colder environments and yields theoretically predicted foraging outcomes across thermal conditions, including the number of strikes, the distance traveled, and the time to capture prey. We also present evidence that endotherms use thermal cues to anticipate prey behavior, modulating the impact of temperature. Finally, we integrate theory and data to forecast future patterns of diversity, revealing that as the world get warmer, it will become increasingly reptilian. Overall, our results point toward a broad reorganization of vertebrate diversity with latitude, elevation, and temperature: from endotherm dominance in cold systems toward ectotherm dominance in warm.

Cell type is hypothesized to be a key determinant of a neuron's role within a circuit. Here, we examine whether a neuron's transcriptomic type influences the timing of its activity. We develop a deep-learning architecture that learns features of interevent intervals across timescales (ms to >30 min). We show that transcriptomic cell-class information is embedded in the timing of single neuron activity in the intact brain of behaving animals (calcium imaging and extracellular electrophysiology) as well as in a bio-realistic model of the visual cortex. Further, a subset of excitatory cell types are distinguishable but can be classified with higher accuracy when considering cortical layer and projection class. Finally, we show that computational fingerprints of cell types may be universalizable across structured stimuli and naturalistic movies. Our results indicate that transcriptomic class and type may be imprinted in the timing of single neuron activity across diverse stimuli., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

We study the vertical and adiabatic ionization potentials and electron affinities of bare and hydroxylated TiO 2 nanoclusters, as well as their fundamental gap and exciton binding energy values, to understand how the clusters' electronic properties change as a function of size and hydroxylation. In addition, we have employed a range of many-body methods; including G 0 W 0 , qsGW, EA/IP-EOM-CCSD, and DFT (B3LYP, PBE), to compare the performance and predictions of the different classes of methods. We demonstrate that, for bare clusters, all many-body methods predict the same trend with cluster size. The highest occupied and lowest unoccupied DFT orbitals follow the same trends as the electron affinity and ionization potentials predicted by the many-body methods, but are generally far too shallow and deep respectively in absolute terms. In contrast, the ΔDFT method is found to yield values in the correct energy window. However, its predictions depend upon the functional used and do not necessarily follow trends based on the many-body methods. Adiabatic potentials are predicted to be similar to their vertical counterparts and holes found to be trapped more strongly than excess electrons. The effect of hydroxylation on the clusters is to open up both the optical and fundamental gap. Finally, a simple microscopic explanation for the observed trends with cluster size and upon hydroxylation is proposed in terms of the onsite electrostatic potential.

Understanding how additives interact and segregate within bulk heterojunction (BHJ) thin films is critical for exercising control over structure at multiple length scales and delivering improvements in photovoltaic performance. The morphological evolution of poly(3-hexylthiophene) (P3HT) and phenyl-C61-butyric acid methyl ester (PCBM) blends that are commensurate with the size of a BHJ thin film is examined using petascale coarse-grained molecular dynamics simulations. Comparisons between two-component and three-component systems containing short P3HT chains as additives undergoing thermal annealing demonstrate that the short chains alter the morphology in apparently useful ways: they efficiently migrate to the P3HT/PCBM interface, increasing the P3HT domain size and interfacial area. Simulation results agree with depth profiles determined from neutron reflectometry measurements that reveal PCBM enrichment near substrate and air interfaces but a decrease in that PCBM enrichment when a small amount of short P3HT chains are integrated into the BHJ blend. Atomistic simulations of the P3HT/PCBM blend interfaces show a nonmonotonic dependence of the interfacial thickness as a function of number of repeat units in the oligomeric P3HT additive, and the thiophene rings orient parallel to the interfacial plane as they approach the PCBM domain. Using the nanoscale geometries of the P3HT oligomers, LUMO and HOMO energy levels calculated by density functional theory are found to be invariant across the donor/acceptor interface. These connections between additives, processing, and morphology at all length scales are generally useful for efforts to improve device performance.

In this paper, we report on the development of a parallel implementation of the coupled-cluster (CC) Green function formulation (GFCC) employing single and double excitations in the cluster operator (GFCCSD). A key aspect of this work is the determination of the frequency dependent self-energy, Σ(ω). The detailed description of the underlying algorithm is provided, including approximations used that preserve the pole structure of the full GFCCSD method, thereby reducing the computational costs while maintaining an accurate character of methodology. Furthermore, for systems with strong local correlation, our formulation reveals a diagonally dominate block structure where as the non-local correlation increases, the block size increases proportionally. To demonstrate the accuracy of our approach, several examples including calculations of ionization potentials for benchmark systems are presented and compared against experiment.

The Sign Learning Kink (SiLK) based Quantum Monte Carlo (QMC) method is used to calculate the ab initio ground state energies for multiple geometries of the H2O, N2, and F2 molecules. The method is based on Feynman's path integral formulation of quantum mechanics and has two stages. The first stage is called the learning stage and reduces the well-known QMC minus sign problem by optimizing the linear combinations of Slater determinants which are used in the second stage, a conventional QMC simulation. The method is tested using different vector spaces and compared to the results of other quantum chemical methods and to exact diagonalization. Our findings demonstrate that the SiLK method is accurate and reduces or eliminates the minus sign problem.

The photophysics of the Green Fluorescent Protein (GFP) chromophore is critically dependent on its local structure and on its environment. Despite extensive experimental and computational studies, there remain many open questions regarding the key fundamental variables that govern this process. One outstanding problem is the role of autoionization as a possible relaxation pathway of the excited state under different environmental conditions. This issue is considered in our work through combined experimental and theoretical studies of microsolvated clusters of the deprotonated p-hydroxybenzylidene-2,3-dimethylimidazolinone anion (HBDI(-)), an analog of the GFP chromophore. Through selective generation of microsolvated structures of predetermined size and subsequent analysis of experimental photoelectron spectra by high level ab initio methods, we are able to precisely identify the structure of the system, establish the accuracy of theoretical data, and provide reliable description of auto-ionization process as a function of hydrogen-bonding environment. Our study clearly illustrates the first few water molecules progressively stabilize the excited state of the chromophore anion against the autodetached neutral state, which should be an important trait for crystallographic water molecules in GFPs that has not been fully explored to date.

In this paper we discuss the application of novel parallel implementation of the coupled cluster (CC) and equation-of-motion coupled cluster methods (EOMCC) in calculations of excitation energies of triplet states in β-carotene. Calculated excitation energies are compared with experimental data, where available. We also provide a detailed description of the new parallel algorithms for iterative CC and EOMCC models involving singles and doubles excitations.

In both molecular and periodic solid-state systems there is a need for the accurate determination of the ionization potential and the electron affinity for systems ranging from light harvesting polymers and photocatalytic compounds to semiconductors. The development of a Green's function approach based on the coupled cluster (CC) formalism would be a valuable tool for addressing many properties involving many-body interactions along with their associated correlation functions. As a first step in this direction, we have developed an accurate and parallel efficient approach based on the equation of motion-CC technique. To demonstrate the high degree of accuracy and numerical efficiency of our approach we calculate the ionization potential and electron affinity for C60 and C70. Accurate predictions for these molecules are well beyond traditional molecular scale studies. We compare our results with experiments and both quantum Monte Carlo and GW calculations.

Enthalpies of formation for the ThX4 and UX4 (X = F, Cl, OH) species have been investigated with density functional theory and coupled-cluster methods. ThX4 molecules are all confirmed as tetrahedral, while all UX4 molecules are predicted to adopt D2d symmetry using density functional theory. Multireference coupled cluster approaches confirm the D2d symmetry for UF4. The bonding is mostly ionic, and predicted formation energies for the halogen species show good agreement with experiment. Our calculated hydration energy of UF4 (-54.0 kcal/mol) is in very good agreement with the experimental data (-54.8 kcal/mol). We predict CCSD(T) formation energies of ΔfG[U(OH)4(g)] = -286.3 kcal/mol and ΔfG[U(OH)4(aq)] = -318.7 kcal/mol. ΔfG[U(OH)4(aq)] is 21 kcal/mol less stable than the established experimental thermodynamic data.

The universal state selective (USS) multireference approach is used to construct new energy functionals which offer a possibility of bridging single and multireference coupled cluster theories (SR/MRCC). These functionals, which can be used to develop iterative and non-iterative approaches, utilize a special form of the trial wavefunctions, which assure additive separability (or size-consistency) of the USS energies in the non-interacting subsystem limit. When the USS formalism is combined with approximate SRCC theories, the resulting formalism can be viewed as a size-consistent version of the method of moments of coupled cluster equations employing a MRCC trial wavefunction. Special cases of the USS formulations, which utilize single reference state specific CC [V. V. Ivanov, D. I. Lyakh, and L. Adamowicz, Phys. Chem. Chem. Phys. 11, 2355 (2009)] and tailored CC [T. Kinoshita, O. Hino, and R. J. Bartlett, J. Chem. Phys. 123, 074106 (2005)] expansions are also discussed.

A novel parallel algorithm for noniterative multireference coupled cluster (MRCC) theories, which merges recently introduced reference-level parallelism (RLP) [Bhaskaran-Nair, K.; Brabec, J.; Aprà, E.; van Dam, H. J. J.; Pittner, J.; Kowalski, K. J. Chem. Phys.2012, 137, 094112] with the possibility of accelerating numerical calculations using graphics processing units (GPUs) is presented. We discuss the performance of this approach applied to the MRCCSD(T) method (iterative singles and doubles and perturbative triples), where the corrections due to triples are added to the diagonal elements of the MRCCSD effective Hamiltonian matrix. The performance of the combined RLP/GPU algorithm is illustrated on the example of the Brillouin-Wigner (BW) and Mukherjee (Mk) state-specific MRCCSD(T) formulations.

The concept of the model space underlying multireference coupled-cluster (MRCC) formulations is a powerful tool to deal with complex correlation effects for various electronic states. Here, we demonstrate that iterative state-specific MRCC methods (SS-MRCC) based on properly defined model spaces can be used to describe core-level excited states even when Hartree-Fock orbitals are utilized. We show that the SS-MRCC models with single and double excitations are comparable in accuracy to high-level single reference equation-of-motion coupled cluster (EOMCC) formalism.

In this paper we discuss the performance of the non-iterative state-specific multireference coupled cluster (SS-MRCC) methods accounting for the effect of triply excited cluster amplitudes. The corrections to the Brillouin-Wigner and Mukherjee's MRCC models based on the manifold of singly and doubly excited cluster amplitudes (BW-MRCCSD and Mk-MRCCSD, respectively) are tested and compared with exact full configuration interaction results for small systems (H(2)O, N(2), and Be(3)). For the larger systems (naphthyne isomers) the BW-MRCC and Mk-MRCC methods with iterative singles, doubles, and non-iterative triples (BW-MRCCSD(T) and Mk-MRCCSD(T)) are compared against the results obtained with single reference coupled cluster methods. We also report on the parallel performance of the non-iterative implementations based on the use of processor groups.

A new version of the multireference Mukherjee's coupled cluster method with perturbative triexcitations has been formulated, which is based on the uncoupled approximation applied to the triples equation. In contrast to the method developed by Evangelista et al. [J. Chem. Phys. 132, 074107 (2010)], the proposed approach does not require to solve the equation for T(3) amplitudes iteratively, yet yields results of essentially the same quality. The method, abbreviated as MR MkCCSD(Tu), has been implemented in the ACES II program package and its assessment has been performed on the BeH(2) model and on the tetramethyleneethane molecule.

We have developed the uncoupled version of multireference Mukherjee's coupled cluster method with connected triexcitations. The method has been implemented in ACES II program package. The agreement between the uncoupled and the standard version of Mukherjee's multireference coupled cluster method has been reported previously at the singles and doubles level by Das et al. [J. Mol. Struct.: THEOCHEM 79, 771 (2006); Chem. Phys. 349, 115 (2008)]. The aim of this article is to investigate this method further, in order to establish how its performance changes with the size of the basis set, size of the model space, multireference character of different molecules, and inclusion of connected triple excitations. Assessment of the new method has been performed on the singlet methylene, potential energy curve of fluorine molecule, and third b (1)Σ(g)(+) electronic state of oxygen molecule.

We have formulated the multireference Mukherjee's coupled clusters method with triexcitations (MR MkCCSDT) in the linked version and implemented it in the ACES II program package. The assessment of the new method has been performed on the first three electronic states of the oxygen molecule, on studies of singlet-triplet gap in methylene and twisted ethylene, where a comparison with other multireference CC treatments and with experimental data is available. The MR MkCCSDT results show accuracy comparable to which can be achieved with CCSDT in single reference cases. Comparison of the previously developed MkCCSD(T) method with MkCCSDT as a reference suggests, that MkCCSD(T) might be a promising candidate for an accurate treatment of systems where the static correlation plays an important role, at least for situations where small model spaces are sufficient.

We have formulated and implemented the multireference Mukherjee's coupled cluster method with connected singles, doubles, and perturbative triples [MR MkCCSD(T)] in the ACES II program package. Assessment of the new method has been performed on the first three electronic states of the oxygen molecule and on the automerization barrier of cyclobutadiene, where a comparison with other multireference CC treatments and with experimental data where available. The MR MkCCSD(T) method seems to be a promising candidate for an accurate, yet computationally tractable, treatment of systems where the static correlation plays an important role.