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Multiple ERI (Electron Repulsion Integral) tensor contractions (METC) with several matrices are ubiquitous in quantum chemistry. In response theories, the contraction operation, rather than ERI computations, can be the major bottleneck, as its computational demands are proportional to the multiplicatively combined contributions of the number of excited states and the kernel pre-factors. This paper presents several high-performance strategies for METC. Optimal approaches involve either the data layout reformations of interim density and Fock matrices, the introduction of intermediate ERI quartet buffer, and loop-reordering optimization for a higher cache hit rate. The combined strategies remarkably improve the performance of the MRSF (mixed reference spin flip)-TDDFT (time-dependent density functional theory) by nearly 300%. The results of this study are not limited to the MRSF-TDDFT method and can be applied to other METC scenarios. [ABSTRACT FROM AUTHOR]

In this paper, we outline a physically motivated framework for describing spin-selective recombination processes in chiral systems, from which we derive spin-selective reaction operators for recombination reactions of donor–bridge–acceptor molecules, where the electron transfer is mediated by chirality and spin–orbit coupling. In general, the recombination process is selective only for spin-coherence between singlet and triplet states, and it is not, in general, selective for spin polarization. We find that spin polarization selectivity only arises in hopping-mediated electron transfer. We describe how this effective spin-polarization selectivity is a consequence of spin-polarization generated transiently in the intermediate state. The recombination process also augments the coherent spin dynamics of the charge separated state, which is found to have a significant effect on the recombination dynamics and to destroy any long-lived spin polarization. Although we only consider a simple donor–bridge–acceptor system, the framework we present here can be straightforwardly extended to describe spin-selective recombination processes in more complex systems. [ABSTRACT FROM AUTHOR]

In this paper, the solubility of carbon dioxide (CO2) in water along the isobar of 400 bar is determined by computer simulations using the well-known TIP4P/Ice force field for water and the TraPPE model for CO2. In particular, the solubility of CO2 in water when in contact with the CO2 liquid phase and the solubility of CO2 in water when in contact with the hydrate have been determined. The solubility of CO2 in a liquid–liquid system decreases as the temperature increases. The solubility of CO2 in a hydrate–liquid system increases with temperature. The two curves intersect at a certain temperature that determines the dissociation temperature of the hydrate at 400 bar (T3). We compare the predictions with T3 obtained using the direct coexistence technique in a previous work. The results of both methods agree, and we suggest 290(2) K as the value of T3 for this system using the same cutoff distance for dispersive interactions. We also propose a novel and alternative route to evaluate the change in chemical potential for the formation of hydrates along the isobar. The new approach is based on the use of the solubility curve of CO2 when the aqueous solution is in contact with the hydrate phase. It considers rigorously the non-ideality of the aqueous solution of CO2, providing reliable values for the driving force for nucleation of hydrates in good agreement with other thermodynamic routes used. It is shown that the driving force for hydrate nucleation at 400 bar is larger for the methane hydrate than for the carbon dioxide hydrate when compared at the same supercooling. We have also analyzed and discussed the effect of the cutoff distance of dispersive interactions and the occupancy of CO2 on the driving force for nucleation of the hydrate. [ABSTRACT FROM AUTHOR]

The development of multireference coupled cluster (MRCC) techniques has remained an open area of study in electronic structure theory for decades due to the inherent complexity of expressing a multiconfigurational wavefunction in the fundamentally single-reference coupled cluster framework. The recently developed multireference-coupled cluster Monte Carlo (mrCCMC) technique uses the formal simplicity of the Monte Carlo approach to Hilbert space quantum chemistry to avoid some of the complexities of conventional MRCC, but there is room for improvement in terms of accuracy and, particularly, computational cost. In this paper, we explore the potential of incorporating ideas from conventional MRCC—namely, the treatment of the strongly correlated space in a configuration interaction formalism—to the mrCCMC framework, leading to a series of methods with increasing relaxation of the reference space in the presence of external amplitudes. These techniques offer new balances of stability and cost against accuracy, as well as a means to better explore and better understand the structure of solutions to the mrCCMC equations. [ABSTRACT FROM AUTHOR]

In this paper, we present a new module to predict the potential surface reconstruction configurations of given surface structures in the framework of our machine learning and graph theory assisted universal structure searcher. In addition to random structures generated with specific lattice symmetry, we made full use of bulk materials to obtain a better distribution of population energy, namely, randomly appending atoms to a surface cleaved from bulk structures or moving/removing some of the atoms on the surface, which is inspired by natural surface reconstruction processes. In addition, we borrowed ideas from cluster predictions to spread structures better between different compositions, considering that surface models of different atom numbers usually have some building blocks in common. To validate this newly developed module, we tested it with studies on the surface reconstructions of Si (100), Si (111), and 4H–SiC (1 1 ̄ 02) − c (2 × 2) , respectively. We successfully gave the known ground states, as well as a new SiC surface model, in an extremely Si-rich environment. [ABSTRACT FROM AUTHOR]

In this paper, we present a covariant approach that utilizes Noether's second theorem to derive a symmetric stress tensor from the grand thermodynamic potential functional. We focus on the practical case where the density of the grand thermodynamic potential is dependent on the first and second coordinate derivatives of the scalar order parameters. Our approach is applied to several models of inhomogeneous ionic liquids that consider electrostatic correlations of ions or short-range correlations related to packing effects. Specifically, we derive analytical expressions for the symmetric stress tensors of the Cahn–Hilliard-like model, Bazant–Storey–Kornyshev model, and Maggs–Podgornik–Blossey model. All of these expressions are found to be consistent with respective self-consistent field equations. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Semiflexible slender filaments are ubiquitous in nature and cell biology, including in the cytoskeleton, where reorganization of actin filaments allows the cell to move and divide. Most methods for simulating semiflexible inextensible fibers/polymers are based on discrete (bead-link or blob-link) models, which become prohibitively expensive in the slender limit when hydrodynamics is accounted for. In this paper, we develop a novel coarse-grained approach for simulating fluctuating slender filaments with hydrodynamic interactions. Our approach is tailored to relatively stiff fibers whose persistence length is comparable to or larger than their length and is based on three major contributions. First, we discretize the filament centerline using a coarse non-uniform Chebyshev grid, on which we formulate a discrete constrained Gibbs–Boltzmann (GB) equilibrium distribution and overdamped Langevin equation for the evolution of unit-length tangent vectors. Second, we define the hydrodynamic mobility at each point on the filament as an integral of the Rotne–Prager–Yamakawa kernel along the centerline and apply a spectrally accurate "slender-body" quadrature to accurately resolve the hydrodynamics. Third, we propose a novel midpoint temporal integrator, which can correctly capture the Ito drift terms that arise in the overdamped Langevin equation. For two separate examples, we verify that the equilibrium distribution for the Chebyshev grid is a good approximation of the blob-link one and that our temporal integrator for overdamped Langevin dynamics samples the equilibrium GB distribution for sufficiently small time step sizes. We also study the dynamics of relaxation of an initially straight filament and find that as few as 12 Chebyshev nodes provide a good approximation to the dynamics while allowing a time step size two orders of magnitude larger than a resolved blob-link simulation. We conclude by applying our approach to a suspension of cross-linked semiflexible fibers (neglecting hydrodynamic interactions between fibers), where we study how semiflexible fluctuations affect bundling dynamics. We find that semiflexible filaments bundle faster than rigid filaments even when the persistence length is large, but show that semiflexible bending fluctuations only further accelerate agglomeration when the persistence length and fiber length are of the same order. [ABSTRACT FROM AUTHOR]

Second-order N-electron valence state perturbation theory (NEVPT2) is an exactly size-consistent and intruder-state-free multi-reference theory. To accelerate the NEVPT2 computation, Guo and Neese combined it with the local pair-natural orbital (PNO) method using the projected atomic orbitals (PAOs) as the underlying local basis [Guo et al., J. Chem. Phys. 144, 094111 (2016)]. In this paper, we report the further development of the PNO-NEVPT2 method using the orthonormal and non-redundant localized virtual molecular orbitals (LVMOs) instead of PAOs. The LVMOs were previously considered to perform relatively poor compared to PAOs because the resulting orbital domains were unacceptably large. Our prior work, however, showed that this drawback can be remedied by re-forming the domain construction scheme using differential overlap integrals [Saitow et al., J. Chem. Phys. 157, 084101 (2022)]. In this work, we develop further refinements to enhance the feasibility of using LVMOs. We first developed a two-level semi-local approach for screening out so-called weak-pairs to select or truncate the pairs for PNO constructions more flexibly. As a refinement specific to the Pipek–Mezey localization for LVMOs, we introduced an iterative scheme to truncate the Givens rotations using varying thresholds. We assessed the LVMO-based PNO-NEVPT2 method through benchmark calculations for linear phenyl alkanes, which demonstrate that it performs comparably well relative to the PAO-based approach. In addition, we evaluated the Co–C bond dissociation energies for the cobalamin derivatives composed of 200 or more atoms, which confirms that the LVMO-based method can recover more than 99.85% of the canonical NEVPT2 correlation energy. [ABSTRACT FROM AUTHOR]

In two recent papers [A. D. Becke, J. Chem. Phys. 156, 214101 (2022) and A. D. Becke, J. Chem. Phys. 157, 234102 (2022)], we compared two Kohn–Sham density functionals based on physical modeling and theory with the best density-functional power-series fits in the literature. The best error statistics reported to date for a hybrid functional on the general main-group thermochemistry, kinetics, and noncovalent interactions (GMTKN55) chemical database of Goerigk et al. [Phys. Chem. Chem. Phys. 19, 32184 (2017)] were obtained. In the present work, additional second-order perturbation-theory terms are considered. The result is a 12-parameter double-hybrid density functional with the lowest GMTKN55 WTMAD2 "weighted total mean absolute deviation" error (1.76 kcal/mol) yet seen for any hybrid or double-hybrid density-functional approximation. We call it "DH23." [ABSTRACT FROM AUTHOR]

Metal oxide nanoparticle (NP) supports of both good conductivity and stability have the potential to enhance both the reaction activity and stability of the loaded electrocatalysts. In this paper, a facile two-step approach to disperse Pt nanoparticles on the surface of an IrO2 NP support (Pt/IrO2) was developed. Physical characterization by x-ray diffraction spectroscopy and transmission/scanning electron microscopy suggests a good dispersion of the Pt NPs. The temperature effect (from 293 to 353 K) of oxygen reduction reaction on Pt/IrO2 was studied by using a rotating ring disk electrode The results show that although the kinetic current density on Pt/IrO2 is close to that on commercial Pt/C at room temperature, the apparent activation energy (Ea,app) in the former case is much lower, suggesting a much higher activity at elevated temperatures. The superiority in Ea,app is attributed to the electron interaction between Pt and the IrO2 support, as supported by the change of surface chemical state given by x-ray photo-electron spectroscopy. [ABSTRACT FROM AUTHOR]

This paper aims at the theoretical study of the CO2 magnetic-dipole ν2 + ν3 rovibrational absorption band that was recently detected in the Martian atmosphere. Specific characteristics of the magnetic dipole operator are carefully examined. Our evaluation of the magnetic-dipole line intensities is based on the variational calculations and the use of molecular properties is determined through specially performed ab initio quantum chemical calculations. The comparison of our simulated magnetic-dipole spectrum with available laboratory taken data also requires the knowledge of line intensities in the quadrupole band, which partially overlaps with that magnetic-dipole. Quadrupole intensities, once reconsidered, are permitted to correct previously reported values of the integrated intensity as well as the intensity of selected branches. The sum of our calculated magnetic-dipole and quadrupole rovibrational lines is shown to be in good agreement with both sets of presently available data from FTIR and OFCEAS laboratory observations. [ABSTRACT FROM AUTHOR]

In Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], we presented the ring-polymer instanton with explicit friction (RPI-EF) method and showed how it can be connected to the ab initio electronic friction formalism. This framework allows for the calculation of tunneling reaction rates that incorporate the quantum nature of the nuclei and certain types of non-adiabatic effects (NAEs) present in metals. In this paper, we analyze the performance of RPI-EF on model potentials and apply it to realistic systems. For a 1D double-well model, we benchmark the method against numerically exact results obtained from multi-layer multi-configuration time-dependent Hartree calculations. We demonstrate that RPI-EF is accurate for medium and high friction strengths and less accurate for extremely low friction values. We also show quantitatively how the inclusion of NAEs lowers the crossover temperature into the deep tunneling regime, reduces the tunneling rates, and, in certain regimes, steers the quantum dynamics by modifying the tunneling pathways. As a showcase of the efficiency of this method, we present a study of hydrogen and deuterium hopping between neighboring interstitial sites in selected bulk metals. The results show that multidimensional vibrational coupling and nuclear quantum effects have a larger impact than NAEs on the tunneling rates of diffusion in metals. Together with Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], these results advance the calculations of dissipative tunneling rates from first principles. [ABSTRACT FROM AUTHOR]

A Brownian bridge is a continuous random walk conditioned to end in a given region by adding an effective drift to guide paths toward the desired region of phase space. This idea has many applications in chemical science where one wants to control the endpoint of a stochastic process—e.g., polymer physics, chemical reaction pathways, heat/mass transfer, and Brownian dynamics simulations. Despite its broad applicability, the biggest limitation of the Brownian bridge technique is that it is often difficult to determine the effective drift as it comes from a solution of a Backward Fokker–Planck (BFP) equation that is infeasible to compute for complex or high-dimensional systems. This paper introduces a fast approximation method to generate a Brownian bridge process without solving the BFP equation explicitly. Specifically, this paper uses the asymptotic properties of the BFP equation to generate an approximate drift and determine ways to correct (i.e., re-weight) any errors incurred from this approximation. Because such a procedure avoids the solution of the BFP equation, we show that it drastically accelerates the generation of conditioned random walks. We also show that this approach offers reasonable improvement compared to other sampling approaches using simple bias potentials. [ABSTRACT FROM AUTHOR]

Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and refold has important implications for biology. This paper reports a theoretical model and computer simulation of the ab initio folding of DNA inverted repeat sequences. The formulation is based on an all-atom conformational model of the sugar-phosphate backbone via chain closure, and it incorporates three major molecular-level driving forces—base stacking, counterion-induced backbone self-interactions, and base pairing—via separate analytical theories designed to capture and reproduce the effects of the solvent without requiring explicit water and ions in the simulation. To accelerate computational throughput, a mixed numerical/analytical algorithm for the calculation of the backbone conformational volume is incorporated into the Monte Carlo simulation, and special stochastic sampling techniques were employed to achieve the computational efficiency needed to fold nucleic acids from scratch. This paper describes implementation details, benchmark results, and the advantages and technical challenges with this approach. [ABSTRACT FROM AUTHOR]

The rotationally resolved infrared (IR) spectrum of the He– H 3 + complex has been measured in a cryogenic ion trap experiment at a nominal temperature of 4 K. Predissociation of the stored complex has been invoked by excitation of the degenerate ν2 mode of the H 3 + sub-unit using a pulsed optical parametric oscillator system. An assignment of the experimental spectrum became possible through one-to-one correlations with bands of the spectrum theoretically predicted in Paper I [Harding et al., J. Chem. Phys. 156, 144307 (2022)]. 19 bands have been assigned and analyzed, and the energy term diagram of the lower states of this floppy molecular complex has been derived from combination differences (CDs) in the experimental spectrum. Ground state combination differences (GSCDs) reveal a large part of the energy term diagram for the He– H 3 + complex in its vibrational ground state, v = 0. Experimental and theoretical term energies agree within experimental accuracy for the rotational fine structure associated with the total angular momentum quantum number J and the parity e/f as well as for the coarse spacing of the lowest K states of the complex. This favorable comparison shows that the potential energy surface (PES) calculated in Paper I is accurate. The barriers between the three equivalent global minima in this PES are relatively low and the He– H 3 + complex is extremely floppy, with nearly unhindered internal rotation of the H 3 + sub-unit. The resulting Coriolis interactions couple the internal and end-over-end rotation of the complex and contribute significantly to the energy terms. They are observed both in experiment and theory and are, e.g., the origin of different rotational constants for states of e and f parity. Also in this respect, experiment and theory agree very well. Despite the assignment and analysis of many bands of the extremely rich IR spectrum of He– H 3 + , higher levels of excitation, including the complex stretching mode, need further attention. [ABSTRACT FROM AUTHOR]

Comparing a discrete molecular spectrum to a continuous molecular spectrum in a quantitative manner is a challenging problem, for example, when attempting to fit a theoretical stick spectrum to a continuous spectrum. In this paper, the use of computational optimal transport is investigated for such a problem. In the optimal transport literature, the comparison of a discrete and a continuous spectrum is referred to as semi-discrete optimal transport and is a situation where a metric such as least-squares may be difficult to define except under special conditions. The merits of an optimal transport approach for this problem are investigated using the transport distance defined for the semi-discrete case. A tutorial on semi-discrete optimal transport for molecular spectra is included in this paper, and several well-chosen synthetic spectra are investigated to demonstrate the utility of computational optimal transport for the semi-discrete case. Among several types of investigations, we include calculations showing how the frequency resolution of the continuous spectrum affects the transport distance between a discrete and a continuous spectrum. We also use the transport distance to measure the distance between a continuous experimental electronic absorption spectrum of SO2 and a theoretical stick spectrum for the same system. The comparison of the theoretical and experimental SO2 spectra also allows us to suggest a theoretical value for the band origin that is closer to the observed band origin than previous theoretical values. [ABSTRACT FROM AUTHOR]

Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute–solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies. [ABSTRACT FROM AUTHOR]

In this paper, we perform the exact diagonalization of a light–matter strongly coupled system taking into account arbitrary losses via both energy dissipation in the optically active material and photon escape out of the resonator. This allows us to naturally treat the cases of couplings with structured reservoirs, which can strongly impact the polaritonic response via frequency-dependent losses or discrete-to-continuum strong coupling. We discuss the emergent gauge freedom of the resulting theory and provide analytical expressions for all the gauge-invariant observables in both the Power–Zienau–Woolley and the Coulomb representations. In order to exemplify the results, the theory is finally specialized to two specific cases. In the first one, both light and matter resonances are characterized by Lorentzian linewidths, and in the second one, a fixed absorption band is also present. The analytical expressions derived in this paper can be used to predict, fit, and interpret results from polaritonic experiments with arbitrary values of the light–matter coupling and with losses of arbitrary intensity and spectral shape in both the light and matter channels. A Matlab code implementing our results is provided. [ABSTRACT FROM AUTHOR]

Transient absorption (TA) and time-resolved photoluminescence (PL) spectroscopies have been used to elucidate the hole tunneling and Auger dynamics in biexcitons and negative trions in high-quality InP/ZnSe/ZnS quantum dots (QDs). In a previous paper [Nguyen et al., J. Phys. Chem. C 125, 15405–15414 (2021)], we showed that under high-intensity photoexcitation, two types of biexcitons are formed: those having two conduction band electrons and two valence band holes (designated as an XX state) and those having two conduction band electrons, one valence band hole, and an additional trapped hole (designated as an XT state). In the present paper, we show that both types of biexcitons can undergo Auger processes, with those of the XT state being a factor of four to five slower than those of the XX state. In addition, the trapped holes can undergo tunneling into the valence band, converting an XT state to an XX state. The relative amplitudes of the fast (XX) and slow (XT) components are different in the TA and PL kinetics, and these differences can be quantitatively understood in terms of oscillator strengths and electron–hole overlap integrals of each state. XT to XX hole tunneling rates are obtained from the comparison of the XT state lifetimes with those of the negative trions. This comparison shows that the tunneling times decrease with decreasing core size and shell thickness. These times are about 2 ns for the thinnest shell red-emitting QDs and decrease to 330 ps for QDs that luminesce in the yellow. [ABSTRACT FROM AUTHOR]

This paper reports the energies and charge and spin distributions of both the vertically excited and fully relaxed GR1 states of the neutral singlet vacancy in diamond obtained from direct Δ-SCF calculations used previously to describe the low-lying excited states in AFII NiO and α-Al2O3. The calculations are based on the B3LYP functional in its standard form, with a C basis set that is identical to that which was used previously in numerous calculations of the ground state properties of defective diamond. Both the vertically excited and thermally relaxed GR1 states are predicted to be excitonic and insulating, with extensive re-distribution of charge and spin density and back-donation to the donor site. The present calculations suggest that the triplet state makes no contribution to the GR1 excitation. The predicted energy of the zero phonon line (1.57 eV) compares with the observed value of 1.67 eV, which also suggests that the GR1 state is neutral. The bandgaps lead to an estimate of the next higher (GR2) excited state energy, which is close to that found in the observed spectra. Similar calculations are used to predict the energies of the higher gap states at (5.0–5.5) eV, including the bulk value of 7.3 eV, which compares with the experimental value of (7.3–7.4) eV. An explanation is suggested as to why only the GR1 luminescence is observed. This paper also suggests an alternative channel for the recovery of the ground state in photoluminescence studies. [ABSTRACT FROM AUTHOR]

It is well-known experimentally that the positively charged muon and the muonium atom may bind to molecules and solids, and through muon's magnetic interaction with unpaired electrons, valuable information on the local environment surrounding the muon is deduced. Theoretical understanding of the structure and properties of resulting muonic species requires accurate and efficient quantum mechanical computational methodologies. In this paper, the two-component density functional theory (TC-DFT), as a first principles method, which treats electrons and the positive muon on an equal footing as quantum particles, is introduced and implemented computationally. The main ingredient of this theory, apart from the electronic exchange–correlation functional, is the electron–positive muon correlation functional that is foreign to the purely electronic DFT. A Wigner-type local electron–positive muon correlation functional, termed eμc-1, is proposed in this paper and its capability is demonstrated through its computational application to a benchmark set of muonic organic molecules. The TC-DFT equations containing eμc-1 are not only capable of predicting the muon's binding site correctly, but they also reproduce muon's zero-point vibrational energies and the muonic densities much more accurately than the TC-DFT equations lacking eμc-1. Thus, this study sets the stage for developing accurate electron–positive muon functionals, which can be used within the context of the TC-DFT to elucidate the intricate interaction of the positive muon with complex molecular systems. [ABSTRACT FROM AUTHOR]

We report further investigations to aid the development of a Laplace MP2 (second-order Møller Plesset) method with a range separated Coulomb potential partitioned into short- and long-range parts. The implementation of the method extensively uses sparse matrix algebra, density fitting techniques for the short-range part, and a Fourier transformation in spherical coordinates for the long-range part of the potential. Localized molecular orbitals are employed for the occupied space, whereas virtual space is described by orbital specific virtual orbitals (OSVs) associated with localized molecular orbitals. The Fourier transform is deficient for very large distances between localized occupied orbitals, and a multipole expansion for widely separated pairs is introduced for the direct MP2 contribution, which is applicable also to non-Coulombic potentials that do not satisfy the Laplace equation. For the exchange contribution, an efficient screening of contributing localized occupied pairs is employed, which is discussed more completely here. To mitigate errors due to the truncation of OSVs, a simple and efficient extrapolation procedure is used to obtain results close to MP2 for the full basis set of atomic orbitals Using a suitable set of default parameters, the accuracy of the approach is demonstrated. The current implementation of the approach is not very efficient, and the aim of this paper is to introduce and critically discuss ideas that can have more general applicability beyond MP2 calculations for large molecules. [ABSTRACT FROM AUTHOR]

The complexity of mathematical models in biology has rendered model reduction an essential tool in the quantitative biologist's toolkit. For stochastic reaction networks described using the Chemical Master Equation, commonly used methods include time-scale separation, Linear Mapping Approximation, and state-space lumping. Despite the success of these techniques, they appear to be rather disparate, and at present, no general-purpose approach to model reduction for stochastic reaction networks is known. In this paper, we show that most common model reduction approaches for the Chemical Master Equation can be seen as minimizing a well-known information-theoretic quantity between the full model and its reduction, the Kullback–Leibler divergence defined on the space of trajectories. This allows us to recast the task of model reduction as a variational problem that can be tackled using standard numerical optimization approaches. In addition, we derive general expressions for propensities of a reduced system that generalize those found using classical methods. We show that the Kullback–Leibler divergence is a useful metric to assess model discrepancy and to compare different model reduction techniques using three examples from the literature: an autoregulatory feedback loop, the Michaelis–Menten enzyme system, and a genetic oscillator. [ABSTRACT FROM AUTHOR]

This paper concerns the representation of angular momentum operators in the Born–Oppenheimer theory of polyatomic molecules and the various forms of the associated conservation laws. Topics addressed include the question of whether these conservation laws are exactly equivalent or only to some order of the Born–Oppenheimer parameter κ = (m/M)1/4 and what the correlation is between angular momentum quantum numbers in the various representations. These questions are addressed in both problems involving a single potential energy surface and those with multiple, strongly coupled surfaces and in both the electrostatic model and those for which fine structure and electron spin are important. The analysis leads to an examination of the transformation laws under rotations of the electronic Hamiltonian; of the basis states, both adiabatic and diabatic, along with their phase conventions; of the potential energy matrix; and of the derivative couplings. These transformation laws are placed in the geometrical context of the structures in the nuclear configuration space that are induced by rotations, which include the rotational orbits or fibers, the surfaces upon which the orientation of the molecule changes but not its shape, and the section, an initial value surface that cuts transversally through the fibers. Finally, it is suggested that the usual Born–Oppenheimer approximation can be replaced by a dressing transformation, that is, a sequence of unitary transformations that block-diagonalize the Hamiltonian. When the dressing transformation is carried out, we find that the angular momentum operator does not change. This is a part of a system of exact equivalences among various representations of angular momentum operators in Born–Oppenheimer theory. Our analysis accommodates large-amplitude motions and is not dependent on small-amplitude expansions about an equilibrium position. Our analysis applies to noncollinear configurations of a polyatomic molecule; this covers all but a subset of measure zero (the collinear configurations) in the nuclear configuration space. [ABSTRACT FROM AUTHOR]

Lithium–ion batteries are key elements of electric vehicles and energy storage systems, and their accurate State of Charge (SOC) estimation is momentous for battery energy management, safe operation, and extended service life. In this paper, the Multi-Kernel Relevance Vector Machine (MKRVM) and Whale Optimization Algorithm (WOA) are used to estimate the SOC of lithium–ion batteries under different operating conditions. In order to better learn and estimate the battery SOC, MKRVM is used to establish a model to estimate lithium–ion battery SOC. WOA is used to automatically adjust and optimize weights and kernel parameters of MKRVM to improve estimation accuracy. The proposed model is validated with three lithium–ion batteries under different operating conditions. In contrast to other optimization algorithms, WOA has a better optimization effect and can estimate the SOC more accurately. In contrast to the single kernel function, the proposed multi-kernel function greatly improves the precision of the SOC estimation model. In contrast to the traditional method, the WOA-MKRVM has a higher precision of SOC estimation. [ABSTRACT FROM AUTHOR]

The interactions between molecules and electrode surfaces play a key role in electrochemical processes and are a subject of extensive research, both experimental and theoretical. In this paper, we address the water dissociation reaction on a Pd(111) electrode surface, modeled as a slab embedded in an external electric field. We aim at unraveling the relationship between surface charge and zero-point energy in aiding or hindering this reaction. We calculate the energy barriers with dispersion-corrected density-functional theory and an efficient parallel implementation of the nudged-elastic-band method. We show that the lowest dissociation barrier and consequently the highest reaction rate take place when the field reaches a strength where two different geometries of the water molecule in the reactant state are equally stable. The zero-point energy contributions to this reaction, on the other hand, remain nearly constant across a wide range of electric field strengths, despite significant changes in the reactant state. Interestingly, we show that the application of electric fields that induce a negative charge on the surface can make nuclear tunneling more significant for these reactions. [ABSTRACT FROM AUTHOR]

Anti-freeze proteins (AFPs) protect organisms at freezing conditions by attaching to the ice surface and arresting its growth. Each adsorbed AFP locally pins the ice surface, resulting in a metastable dimple for which the interfacial forces counteract the driving force for growth. As supercooling increases, these metastable dimples become deeper, until metastability is lost in an engulfment event where the ice irreversibly swallows the AFP. Engulfment resembles nucleation in some respects, and this paper develops a model for the "critical profile" and free energy barrier for the engulfment process. Specifically, we variationally optimize the ice–water interface and estimate the free energy barrier as a function of the supercooling, the AFP footprint size, and the distance to neighboring AFPs on the ice surface. Finally, we use symbolic regression to derive a simple closed-form expression for the free energy barrier as a function of two physically interpretable, dimensionless parameters. [ABSTRACT FROM AUTHOR]

Trapping diffusive particles at surfaces is a key step in many systems in chemical and biological physics. Trapping often occurs via reactive patches on the surface and/or the particle. The theory of boundary homogenization has been used in many prior works to estimate the effective trapping rate for such a system in the case that either (i) the surface is patchy and the particle is uniformly reactive or (ii) the particle is patchy and the surface is uniformly reactive. In this paper, we estimate the trapping rate for the case that the surface and the particle are both patchy. In particular, the particle diffuses translationally and rotationally and reacts with the surface when a patch on the particle contacts a patch on the surface. We first formulate a stochastic model and derive a five-dimensional partial differential equation describing the reaction time. We then use matched asymptotic analysis to derive the effective trapping rate, assuming that the patches are roughly evenly distributed and occupy a small fraction of the surface and the particle. This trapping rate involves the electrostatic capacitance of a four-dimensional duocylinder, which we compute using a kinetic Monte Carlo algorithm. We further use Brownian local time theory to derive a simple heuristic estimate of the trapping rate and show that it is remarkably close to the asymptotic estimate. Finally, we develop a kinetic Monte Carlo algorithm to simulate the full stochastic system and then use these simulations to confirm the accuracy of our trapping rate estimates and homogenization theory. [ABSTRACT FROM AUTHOR]

Due to the ubiquity and importance of water, water dimer has been intensively studied. Computing the (ro-)vibrational spectrum of water dimer is challenging. The potential has eight wells separated by low barriers, which makes harmonic approximations of limited utility. A variational approach is imperative, but difficult because there are 12 coupled vibrational coordinates. In this paper, we use a product contracted basis whose functions are products of intramolecular and intermolecular functions computed using an iterative eigensolver. An intermediate matrix F facilitates calculating matrix elements. Using F, it is possible to do calculations on a general potential without storing the potential on the full quadrature grid. We find that surprisingly many intermolecular functions are required. This is due to the importance of coupling between inter- and intra-molecular coordinates. The full G16 symmetry of water dimer is exploited. We calculate, for the first time, monomer excited stretch states and compare P(1) transition frequencies with their experimental counterparts. We also compare with experimental vibrational shifts and tunneling splittings. Surprisingly, we find that the largest tunneling splitting, which does not involve the interchange of the two monomers, is smaller in the asymmetric stretch excited state than in the ground state. Differences between levels we compute and those obtained with a [6+6]D adiabatic approximation [Leforestier et al. J. Chem. Phys. 137 014305 (2012)] are ∼ 0.6 cm−1 for states without monomer excitation, ∼ 4 cm−1 for monomer excited bend states, and as large as ∼ 10 cm−1 for monomer excited stretch states. [ABSTRACT FROM AUTHOR]

In this paper, we propose to compute the electronic circular dichroism (ECD) spectra of chiral molecules using a real-time propagation of the time-dependent Schrödinger equation (TDSE) in the space of electronic field-free eigenstates, by coupling TDSE with a given treatment of the electronic structure of the target. The time-dependent induced magnetic moment is used to compute the ECD spectrum from an explicit electric perturbation. The full matrix representing the transition magnetic moment in the space of electronic states is generated from that among pairs of molecular orbitals. In the present work, we show the ECD spectra of methyloxirane, of several conformers of L-alanine, and of the Λ-Co(acac)3 complex, computed from a singly excited ansatz of time-dependent density functional theory eigenstates. The time-domain ECD spectra properly reproduce the frequency-domain ones obtained in the linear-response regime and quantitatively agree with the available experimental data. Moreover, the time-domain approach to ECD allows us to naturally go beyond the ground-state rotationally averaged ECD spectrum, which is the standard outcome of the linear-response theory, e.g., by computing the ECD spectra from electronic excited states. [ABSTRACT FROM AUTHOR]

In this paper, we present a comprehensive account of quantum dissipation theories with the quadratic environment couplings. The theoretical development includes the Brownian solvation mode embedded hierarchical quantum master equations, a core-system hierarchy construction that verifies the extended dissipaton equation of motion (DEOM) formalism [R. X. Xu et al., J. Chem. Phys. 148, 114103 (2018)]. Developed are also the quadratic imaginary-time DEOM for equilibrium and the λ(t)-DEOM for nonequilibrium thermodynamics problems. Both the celebrated Jarzynski equality and Crooks relation are accurately reproduced, which, in turn, confirms the rigorousness of the extended DEOM theories. While the extended DEOM is more numerically efficient, the core-system hierarchy quantum master equation is favorable for "visualizing" the correlated solvation dynamics. [ABSTRACT FROM AUTHOR]

The electrical manipulation of magnetization is appealing to the relevant experiment and spintronic device. In this paper, we focus on the electrical and magnetic properties of a thin film cleaved from the nonmagnetic half-Heusler compound CoTiSb. By means of the first-principles calculations, we find that the surface of TiSb termination possesses ferrimagnetism with a magnetic moment of 0.35 (0.49) μB per unit cell without (with) Hubbard U, which can persist below the Curie temperature of 48 (54) K. What is more, such a surface magnetism can be tuned to nonmagnetism by gate-induced hole doping with a concentration of 2.83 × 1014 (3.55 × 1014) cm−2. This magnetic tunability of the CoTiSb slab provides a platform to realize the pseudo-spin valve with both the magnetic electrodes and nonmagnetic space layer made of the same material without hetero-interfaces. [ABSTRACT FROM AUTHOR]

With an ever-increasing interest in water properties, many intermolecular force fields have been proposed to describe the behavior of water. Unfortunately, good models for liquid water usually cannot provide simultaneously an accurate melting point for ice. For this reason, the TIP4P/Ice model was developed for targeting the melting point and has become the preferred choice for simulating ice at coexistence. Unfortunately, available data for its dynamic properties in the liquid state are scarce. Therefore, we demonstrate a series of simulations aimed at the calculation of transport coefficients for the TIP4P/Ice model over a large range of thermodynamic conditions, ranging from T = 245 K to T = 350 K, for the temperature, and from p = 0 to p = 500 MPa, for the pressure. We have found that the self-diffusion (shear viscosity) exhibits smaller (increased) values than TIP4P/2005 and experiments. However, rescaling the temperature with respect to the triple point temperature, as in a corresponding states plot, we find that TIP4P/Ice compares very well with TIP4P/2005 and experiment. Such observations allow us to infer that despite the different original purposes of these two models examined here, one can benefit from a vast number of reports regarding the behavior of transport coefficients for the TIP4P/2005 model and utilize them following the routine described in this paper. [ABSTRACT FROM AUTHOR]

Superionic (SI) water ices—high-temperature, high-pressure phases of water in which oxygen ions occupy a regular crystal lattice whereas the protons flow in a liquid-like manner—have attracted a growing amount of attention over the past few years, in particular due to their possible role in the magnetic anomalies of the ice giants Neptune and Uranus. In this paper, we consider the calculation of the free energies of such phases, exploring hybrid reference systems consisting of a combination of an Einstein solid for the oxygen ions occupying a crystal lattice and a Uhlenbeck-Ford potential for the protonic fluid that avoids irregularities associated with possible particle overlaps. Applying this approach to a recent neural-network potential-energy landscape for SI water ice, we compute Gibbs free energies as a function of temperature for the SI fcc and liquid phases to determine the melting temperature Tm at 340 GPa. The results are consistent with previous estimates and indicate that the entropy difference between both phases is comparatively small, in particular due to the large amplitude of vibration of the oxygen ions in the fcc phase at the melting temperature. [ABSTRACT FROM AUTHOR]

Until quite recently, in almost all papers on crystal nucleation in glass-forming substances, it was assumed that nucleation proceeds in a completely relaxed supercooled liquid and, hence, at constant values of the critical parameters determining the nucleation rate for any given set of temperature, pressure, and composition. Here, we analyze the validity of this hypothesis for a model system by studying nucleation in a lithium silicate glass treated for very long times (up to 250 days) in deeply supercooled states, reaching 60 K below the laboratory glass transition temperature, Tg. At all temperatures in the considered range, T < Tg, we observed an enormous difference between the experimental number of nucleated crystals, N(t), and its theoretically expected value computed by assuming the metastable state of the relaxing glass has been reached. Analyzing the origin of this discrepancy, we confirmed that the key parameters determining the nucleation rates change with time as a result of the glass relaxation process. Finally, we demonstrate that, for temperatures below 683 K, this particular glass almost fully crystallizes prior to reaching the ultimate steady-state nucleation regime (e.g., at 663 K, it would take 176 years for the glass to reach 99% crystallization, while 2600 years would be needed for complete relaxation). This comprehensive study proves that structural relaxation strongly affects crystal nucleation in deeply supercooled states at temperatures well below Tg; hence, this phenomenon has to be accounted for in any crystal nucleation model. [ABSTRACT FROM AUTHOR]

The excitation energy transfer (EET) process for photosynthetic antenna complexes consisting of subunits, each comprised of multiple chromophores, remains challenging to describe. The multichromophoric Förster resonance energy transfer theory is a popular method to describe the EET process in such systems. This paper presents a new time-domain method for calculating energy transfer based on the combination of multichromophoric Förster resonance energy transfer theory and the Numerical Integration of the Schrödinger Equation method. After validating the method on simple model systems, we apply it to the Light-Harvesting antenna 2 (LH2) complex, a light harvesting antenna found in purple bacteria. We use a simple model combining the overdamped Brownian oscillators to describe the dynamic disorder originating from the environmental fluctuations and the transition charge from the electrostatic potential coupling model to determine the interactions between chromophores. We demonstrate that with this model, both the calculated spectra and the EET rates between the two rings within the LH2 complex agree well with experimental results. We further find that the transfer between the strongly coupled rings of neighboring LH2 complexes can also be well described with our method. We conclude that our new method accurately describes the EET rate for biologically relevant multichromophoric systems, which are similar to the LH2 complex. Computationally, the new method is very tractable, especially for slow processes. We foresee that the method can be applied to efficiently calculate transfer in artificial systems as well and may pave the way for calculating multidimensional spectra of extensive multichromophoric systems in the future. [ABSTRACT FROM AUTHOR]

Utilizing localized orbitals, local correlation theory can reduce the unphysically high system-size scaling of post-Hartree–Fock (post-HF) methods to linear scaling in insulating molecules. The sparsity of the four-index electron repulsion integral (ERI) tensor is central to achieving this reduction. For second-order Møller–Plesset theory (MP2), one of the simplest post-HF methods, only the (ia|jb) ERIs are needed, coupling occupied orbitals i, j and virtuals a, b. In this paper, we compare the numerical sparsity (called the "ragged list") and two other approaches revealing the low-rank sparsity of the ERI. The ragged list requires only one set of (localized) virtual orbitals, and we find that the orthogonal valence virtual-hard virtual set of virtuals originally proposed by Subotnik et al. gives the sparsest ERI tensor. To further compress the ERI tensor, the pair natural orbital (PNO) type representation uses different sets of virtual orbitals for different occupied orbital pairs, while the occupied-specific virtual (OSV) approach uses different virtuals for each occupied orbital. Our results indicate that while the low-rank PNO representation achieves significant rank reduction, it also requires more memory than the ragged list. The OSV approach requires similar memory to that of the ragged list, but it involves greater algorithmic complexity. An approximation (called the "fixed sparsity pattern") for solving the local MP2 equations using the numerically sparse ERI tensor is proposed and tested to be sufficiently accurate and to have highly controllable error. A low-scaling local MP2 algorithm based on the ragged list and the fixed sparsity pattern is therefore promising. [ABSTRACT FROM AUTHOR]

Over the last century, quantum theories have revolutionized our understanding of material properties. One of the most striking quantum phenomena occurring in heterogeneous media is the quantum tunneling effect, where carriers can tunnel through potential barriers even if the barrier height exceeds the carrier energy. Interestingly, the tunneling process can be accompanied by the absorption or emission of light. In most tunneling junctions made of noble metal electrodes, these optical phenomena are governed by plasmonic modes, i.e., light-driven collective oscillations of surface electrons. In the emission process, plasmon excitation via inelastic tunneling electrons can improve the efficiency of photon generation, resulting in bright nanoscale optical sources. On the other hand, the incident light can affect the tunneling behavior of plasmonic junctions as well, leading to phenomena such as optical rectification and induced photocurrent. Thus, plasmonic tunneling junctions provide a rich platform for investigating light–matter interactions, paving the way for various applications, including nanoscale light sources, sensors, and chemical reactors. In this paper, we will introduce recent research progress and promising applications based on plasmonic tunneling junctions. [ABSTRACT FROM AUTHOR]

Introducing nanorods into a polymeric matrix can enhance the physical and mechanical properties of the resulting material. In this paper, we focus on understanding the dispersion and orientation patterns of nanorods in an unentangled polymer melt, particularly as a function of nanorod concentration, using molecular dynamics simulations. The system is comprised of flexible polymer chains and multi-thread nanorods that are equilibrated in the NPT ensemble. All interactions are purely repulsive except for those between polymers and rods. Results with attractive vs repulsive polymer–rod interactions are compared and contrasted. The concentration of rods has a direct impact on the phase behavior of the system. At lower concentrations, rods phase separate into nematic clusters, whereas at higher concentrations more isotropic and less structured rod configurations are observed. A detailed examination of the conformation of the polymer chains near the rod surface shows extension of the chains along the director of the rods (especially within clusters). The dispersion and orientation of the nanorods are a result of the competition between depletion entropic forces responsible for the formation of rod clusters, the enthalpic effects that improve mixing of rods and polymer, and entropic losses of polymers interpenetrating rod clusters. [ABSTRACT FROM AUTHOR]

Many phase change materials (PCMs) are found to crystallize without exhibiting a glass transition endotherm upon reheating. In this paper, we review experimental evidence revealing that these PCMs and likely other hyperquenched molecular and metallic systems can crystallize from the glassy state when reheated at a standard rate. Among these evidences, PCMs annealed below the glass transition temperature Tg exhibit slower crystallization kinetics despite an increase in the number of sub-critical nuclei that should promote the crystallization speed. Flash calorimetry uncovers the glass transition endotherm hidden by crystallization and reveals a distinct change in kinetics when crystallization switches from the glassy to the supercooled liquid state. The resulting Tg value also rationalizes the presence of the pre-Tg relaxation exotherm ubiquitous of hyperquenched systems. Finally, the shift in crystallization temperature during annealing exhibits a non-exponential decay that is characteristic of structural relaxation in the glass. Modeling using a modified Turnbull equation for nucleation rate supports the existence of sub-Tg fast crystallization and emphasizes the benefit of a fragile-to-strong transition for PCM applications due to a reduction in crystallization at low temperature (improved data retention) and increasing its speed at high temperature (faster computing). [ABSTRACT FROM AUTHOR]

Fewest-switches surface hopping (FSSH) has emerged as one of the leading methods for modeling the quantum dynamics of molecular systems. While its original formulation was limited to adiabatic populations, the growing interest in the application of FSSH to coherent phenomena prompts the question of how one should construct a complete density matrix based on FSSH trajectories. A straightforward solution is to define adiabatic coherences based on wavefunction coefficients. In this paper, we demonstrate that inconsistencies introduced in the density matrix through such treatment may lead to a violation of positivity. We furthermore show that a recently proposed coherent generalization of FSSH results in density matrices that satisfy positivity while yielding improved accuracy throughout much (but not all) of parameter space. [ABSTRACT FROM AUTHOR]

Electrochemical impedance spectroscopy (EIS) is a powerful characterization technique for the in-depth investigation of kinetic/transport parameters detection, reaction mechanism understanding, and degradation effects exploration in lithium-ion battery (LIB) systems. However, due to the lack of standardized criterion/paradigm, severe misinterpretations occur frequently during an EIS measurement. In this paper, the significance of instrumental accuracy is described and the character/principle of selection on the simulation model is illuminated/proposed, showing that an adequate precision device and an appropriate fitting model are a prerequisite for a correct EIS analysis. Moreover, the drawbacks of conventional two-electrode EIS experiments for typical coin-type cells are rigorously pointed out by comparison with the ideal three-electrode configuration, where the real impedance information of the cathode would be masked by the sum of both the anode film resistance response and the unavoidable inductive loop signal. The three-electrode case enables efficient accurate observations on individual electrodes, thus facilitating abundant and useful information acquisition. Consequently, devices with a sufficient accuracy, rational simulation models, and advanced three-electrode cells are distinctly illustrated as standardized criterion/paradigm for EIS characterizations, which are essentially important for electrode and interface modifications in LIBs. [ABSTRACT FROM AUTHOR]

The transport of particles through channels is of paramount importance in physics, chemistry, and surface science due to its broad real world applications. Much insight can be gained by observing the transition paths of a particle through a channel and collecting statistics on the lifetimes in the channel or the escape probabilities from the channel. In this paper, we consider the diffusive transport through a narrow conical channel of a Brownian particle subject to intermittent dynamics, namely, stochastic resetting. As such, resetting brings the particle back to a desired location from where it resumes its diffusive phase. To this end, we extend the Fick–Jacobs theory of channel-facilitated diffusive transport to resetting-induced transport. Exact expressions for the conditional mean first passage times, escape probabilities, and the total average lifetime in the channel are obtained, and their behavior as a function of the resetting rate is highlighted. It is shown that resetting can expedite the transport through the channel—rigorous constraints for such conditions are then illustrated. Furthermore, we observe that a carefully chosen resetting rate can render the average lifetime of the particle inside the channel minimal. Interestingly, the optimal rate undergoes continuous and discontinuous transitions as some relevant system parameters are varied. The validity of our one-dimensional analysis and the corresponding theoretical predictions is supported by three-dimensional Brownian dynamics simulations. We thus believe that resetting can be useful to facilitate particle transport across biological membranes—a phenomenon that can spearhead further theoretical and experimental studies. [ABSTRACT FROM AUTHOR]

Using an approach based on the diffusion analog of the Cattaneo–Vernotte differential model, we find the exact analytical solution to the corresponding time-dependent linear hyperbolic initial boundary value problem, describing irreversible diffusion-controlled reactions under Smoluchowski's boundary condition on a spherical sink. By means of this solution, we extend exact analytical calculations for the time-dependent classical Smoluchowski rate coefficient to the case that includes the so-called inertial effects, occurring in the host media with finite relaxation times. We also present a brief survey of Smoluchowski's theory and its various subsequent refinements, including works devoted to the description of the short-time behavior of Brownian particles. In this paper, we managed to show that a known Rice's formula, commonly recognized earlier as an exact reaction rate coefficient for the case of hyperbolic diffusion, turned out to be only its approximation being a uniform upper bound of the exact value. Here, the obtained formula seems to be of great significance for bridging a known gap between an analytically estimated rate coefficient on the one hand and molecular dynamics simulations together with experimentally observed results for the short times regime on the other hand. A particular emphasis has been placed on the rigorous mathematical treatment and important properties of the relevant initial boundary value problems in parabolic and hyperbolic diffusion theories. [ABSTRACT FROM AUTHOR]

In this paper, we investigate prenucleation and heterogeneous nucleation in the liquid Pb/solid Al system as an example of systems with large lattice misfit using molecular dynamics simulation. Solid Pb and Al have a large positive lattice misfit (f) of 18.2% along the densely packed [110] direction. This study reveals that prenucleation occurs at 600 K (an undercooling of 15 K), and a 2-dimensional (2D) ordered structure forms at the interface with a coincidence site lattice (CSL) between the first Pb and first Al layers. The CSL accommodates the major part of the f, and only a small residual lattice misfit (fr) of 1.9% remains. The formation of the CSL transforms the original substrate into a considerably potent nucleant, where the first Pb layer becomes the new surface layer of the substrate. At an undercooling of about 22 K, nucleation proceeds by merging 2D ordered structure through structural templating: the second Pb layer is epitaxial to the CSL Pb layer, the third Pb layer largely accommodates the fr, and the fourth Pb layer is a nearly perfect crystalline plane. Further analysis indicates that the interface with the CSL has a lower interfacial energy than with a cube-to-cube orientation relationship. For the first time, we established that the CSL was an effective mechanism to accommodate the f for systems with a large positive misfits. Heterogeneous nucleation is governed not by a single mechanism (misfit dislocations in Turnbull's model), but instead by various mechanisms depending on f. This study sheds new light on the atomistic mechanism of heterogeneous nucleation. [ABSTRACT FROM AUTHOR]

Coarse-grained (CG) models facilitate an efficient exploration of complex systems by reducing the unnecessary degrees of freedom of the fine-grained (FG) system while recapitulating major structural correlations. Unlike structural properties, assessing dynamic properties in CG modeling is often unfeasible due to the accelerated dynamics of the CG models, which allows for more efficient structural sampling. Therefore, the ultimate goal of the present series of articles is to establish a better correspondence between the FG and CG dynamics. To assess and compare dynamical properties in the FG and the corresponding CG models, we utilize the excess entropy scaling relationship. For Paper I of this series, we provide evidence that the FG and the corresponding CG counterpart follow the same universal scaling relationship. By carefully reviewing and examining the literature, we develop a new theory to calculate excess entropies for the FG and CG systems while accounting for entropy representability. We demonstrate that the excess entropy scaling idea can be readily applied to liquid water and methanol systems at both the FG and CG resolutions. For both liquids, we reveal that the scaling exponents remain unchanged from the coarse-graining process, indicating that the scaling behavior is universal for the same underlying molecular systems. Combining this finding with the concept of mapping entropy in CG models, we show that the missing entropy plays an important role in accelerating the CG dynamics. [ABSTRACT FROM AUTHOR]

For many laser-based methods of material characterization and analysis, a tensor formulation of theory is necessary, especially in techniques that exploit nonlinear or chiral optics. The fundamental interactions that underpin such methods offer various levels of approach to theory, but the most rigorous often lead to equations of considerable complexity. To compute the values for individual material parameters frequently demands making assumptions of extreme simplicity, overly dependent on calculational method, yet still providing unsatisfactory results. A pragmatic and entirely rigorous symmetry-based approach to the irreducible tensorial structures circumvents many of these problems, securing reliable results and guiding the pathway to applications. Instead of focusing on individual tensor components, such an approach can rapidly determine the number of linearly independent quantities—and hence the number of operationally different setups necessary for full characterization. By such means, one can directly ascertain how variations of optical polarization and beam geometry can reliably capture the response of any material system. The use of an irreducible tensor method operates independently of any means that might be chosen to calculate material properties. It removes the need for common simplifying assumptions, such as the approximation of tensorial structure by a scalar representation, adoption of a two-state model, or disregarding near-resonance damping. It also obviates any dependence on a choice of simulation package or quantum-calculational software. In this paper, the principles are set down and illustrated by application to experiments of varying degrees of complexity, including interactions of growing significance in the realm of chiral nonlinear optics. Limitations of this approach are also critically assessed. [ABSTRACT FROM AUTHOR]

Efficient energy transport in photosynthetic antenna is a long-standing source of inspiration for artificial light harvesting materials. However, characterizing the excited states of the constituent chromophores poses a considerable challenge to mainstream quantum chemical and semiempirical excited state methods due to their size and complexity and the accuracy required to describe small but functionally important changes in their properties. In this paper, we explore an alternative approach to calculating the excited states of large biochromophores, exemplified by a specific method for calculating the Qy transition of bacteriochlorophyll a, which we name Chl-xTB. Using a diagonally dominant approximation to the Casida equation and a bespoke parameterization scheme, Chl-xTB can match time-dependent density functional theory's accuracy and semiempirical speed for calculating the potential energy surfaces and absorption spectra of chlorophylls. We demonstrate that Chl-xTB (and other prospective realizations of our protocol) can be integrated into multiscale models, including concurrent excitonic and point-charge embedding frameworks, enabling the analysis of biochromophore networks in a native environment. We exploit this capability to probe the low-frequency spectral densities of excitonic energies and interchromophore interactions in the light harvesting antenna protein LH2 (light harvesting complex 2). The impact of low-frequency protein motion on interchromophore coupling and exciton transport has routinely been ignored due to the prohibitive costs of including it in simulations. Our results provide a more rigorous basis for continued use of this approximation by demonstrating that exciton transition energies are unaffected by low-frequency vibrational coupling to exciton interaction energies. [ABSTRACT FROM AUTHOR]

Simulating the unitary dynamics of a quantum system is a fundamental problem of quantum mechanics, in which quantum computers are believed to have significant advantage over their classical counterparts. One prominent such instance is the simulation of electronic dynamics, which plays an essential role in chemical reactions, non-equilibrium dynamics, and material design. These systems are time-dependent, which requires that the corresponding simulation algorithm can be successfully concatenated with itself over different time intervals to reproduce the overall coherent quantum dynamics of the system. In this paper, we quantify such simulation algorithms by the property of being fully-coherent: the algorithm succeeds with arbitrarily high success probability 1 − δ while only requiring a single copy of the initial state. We subsequently develop fully-coherent simulation algorithms based on quantum signal processing (QSP), including a novel algorithm that circumvents the use of amplitude amplification while also achieving a query complexity additive in time t, ln(1/δ), and ln(1/ϵ) for error tolerance ϵ: Θ ‖ H ‖ | t | + ln (1 / ϵ) + ln (1 / δ) . Furthermore, we numerically analyze these algorithms by applying them to the simulation of the spin dynamics of the Heisenberg model and the correlated electronic dynamics of an H2 molecule. Since any electronic Hamiltonian can be mapped to a spin Hamiltonian, our algorithm can efficiently simulate time-dependent ab initio electronic dynamics in the circuit model of quantum computation. Accordingly, it is also our hope that the present work serves as a bridge between QSP-based quantum algorithms and chemical dynamics, stimulating a cross-fertilization between these exciting fields. [ABSTRACT FROM AUTHOR]