Search

This paper presents the molecular dynamics simulation of 1 mol kg−1 LiPF6 in a binary solvent of ethylene carbonate (EC) and dimethylcarbonate, which is a representative electrolyte solution for lithium-ion batteries. The simulation successfully reproduced the diffusion coefficient, ionic conductivity, and shear viscosity as functions of EC content at 300 K, which had been experimentally determined in our previous study. The Yukawa potential was adopted to model intercharge interactions to reduce computational costs, which consequently allowed us to precisely calculate the conductivity and viscosity by directly integrating time-correlation functions without explicitly modeling the molecular polarization. Breaking down microscopic current correlation functions into components revealed that, whereas the cation–anion attractive interaction dominantly impedes the conduction when the EC content is low, it is the cation–cation and anion–anion repulsive interactions that reduce the conductivity at a high EC content. An analysis of the pressure correlations revealed that all components positively contribute to the viscosity in the binary solvent without the electrolyte. On the other hand, negative terms are observed in five out of six cross correlations in the presence of the electrolyte, implying that these correlations negatively contribute to the shear stress and entropy production, both of which are net positive. [ABSTRACT FROM AUTHOR]

This paper presents a comprehensive study of the theory of entangled two-photon emission/absorption (E2P-EA) between a many-level cascade donor and a many-level acceptor (which could be quantum dots or molecules) using second-order perturbation theory and where the donor–acceptor pair is in a homogeneous but dispersive medium. To understand the mechanism of E2P-EA, we analyze how dipole orientation, radiative lifetime, energy detuning between intermediate states, separation distance, and entanglement time impact the E2P-EA rate. Our study shows that there are quantum interference effects in the E2P-EA rate expression that lead to oscillations in the rate as a function of entanglement time. Furthermore, we find that the E2P-EA rate for a representative system consisting of two quantum dots can be comparable to one-photon emission/absorption (OP-EA) when donor and acceptor are within a few nm. However, the E2P-EA rate falls off much more quickly with separation distance than does OP-EA. [ABSTRACT FROM AUTHOR]

Many state-of-the art machine learning (ML) interatomic potentials are based on a local or semi-local (message-passing) representation of chemical environments. They, therefore, lack a description of long-range electrostatic interactions and non-local charge transfer. In this context, there has been much interest in developing ML-based charge equilibration models, which allow the rigorous calculation of long-range electrostatic interactions and the energetic response of molecules and materials to external fields. The recently reported kQEq method achieves this by predicting local atomic electronegativities using Kernel ML. This paper describes the q-pac Python package, which implements several algorithmic and methodological advances to kQEq and provides an extendable framework for the development of ML charge equilibration models. [ABSTRACT FROM AUTHOR]

As biomolecules vibrate and rotate in the terahertz band, the biological effects of terahertz electromagnetic fields have drawn considerable attention from the physiological and medical communities. Ion channels are the basis of biological electrical signals, so studying the effect of terahertz electromagnetic fields on ion channels is significant. In this paper, the effect of a terahertz electromagnetic field with three different frequencies, 6, 15, and 25 THz, on the Kv1.2 potassium ion channel was investigated by molecular dynamics simulations. The results show that an electromagnetic field with a 15 THz frequency can significantly enhance the permeability of the Kv1.2 potassium ion channel, which is 1.7 times higher than without an applied electric field. By analyzing the behavior of water molecules, it is found that the electromagnetic field with the 15 THz frequency shortens the duration of frozen and relaxation processes when potassium ions pass through the channel, increases the proportion of the direct knock-on mode, and, thus, enhances the permeability of the Kv1.2 potassium ion channel. [ABSTRACT FROM AUTHOR]

The collective coupling of an ensemble of molecules to a light field is commonly described by the Tavis–Cummings model. This model includes numerous eigenstates that are optically decoupled from the optically bright polariton states. Accessing these dark states requires breaking the symmetry in the corresponding Hamiltonian. In this paper, we investigate the influence of non-unitary processes on the dark state dynamics in the molecular Tavis–Cummings model. The system is modeled with a Lindblad equation that includes pure dephasing, as it would be caused by weak interactions with an environment, and photon decay. Our simulations show that the rate of pure dephasing, as well as the number of two-level systems, has a significant influence on the dark state population. [ABSTRACT FROM AUTHOR]

The MACE architecture represents the state of the art in the field of machine learning force fields for a variety of in-domain, extrapolation, and low-data regime tasks. In this paper, we further evaluate MACE by fitting models for published benchmark datasets. We show that MACE generally outperforms alternatives for a wide range of systems, from amorphous carbon, universal materials modeling, and general small molecule organic chemistry to large molecules and liquid water. We demonstrate the capabilities of the model on tasks ranging from constrained geometry optimization to molecular dynamics simulations and find excellent performance across all tested domains. We show that MACE is very data efficient and can reproduce experimental molecular vibrational spectra when trained on as few as 50 randomly selected reference configurations. We further demonstrate that the strictly local atom-centered model is sufficient for such tasks even in the case of large molecules and weakly interacting molecular assemblies. [ABSTRACT FROM AUTHOR]

Electronic structure calculations have the potential to predict key matter transformations for applications of strategic technological importance, from drug discovery to material science and catalysis. However, a predictive physicochemical characterization of these processes often requires accurate quantum chemical modeling of complex molecular systems with hundreds to thousands of atoms. Due to the computationally demanding nature of electronic structure calculations and the complexity of modern high-performance computing hardware, quantum chemistry software has historically failed to operate at such large molecular scales with accuracy and speed that are useful in practice. In this paper, novel algorithms and software are presented that enable extreme-scale quantum chemistry capabilities with particular emphasis on exascale calculations. This includes the development and application of the multi-Graphics Processing Unit (GPU) library LibCChem 2.0 as part of the General Atomic and Molecular Electronic Structure System package and of the standalone Extreme-scale Electronic Structure System (EXESS), designed from the ground up for scaling on thousands of GPUs to perform high-performance accurate quantum chemistry calculations at unprecedented speed and molecular scales. Among various results, we report that the EXESS implementation enables Hartree–Fock/cc-pVDZ plus RI-MP2/cc-pVDZ/cc-pVDZ-RIFIT calculations on an ionic liquid system with 623 016 electrons and 146 592 atoms in less than 45 min using 27 600 GPUs on the Summit supercomputer with a 94.6% parallel efficiency. [ABSTRACT FROM AUTHOR]

Inferring transient molecular structural dynamics from diffraction data is an ambiguous task that often requires different approximation methods. In this paper, we present an attempt to tackle this problem using machine learning. Although most recent applications of machine learning for the analysis of diffraction images apply only a single neural network to an experimental dataset and train it on the task of prediction, our approach utilizes an additional generator network trained on both synthetic and experimental data. Our network converts experimental data into idealized diffraction patterns from which information is extracted via a convolutional neural network trained on synthetic data only. We validate this approach on ultrafast electron diffraction data of bismuth samples undergoing thermalization upon excitation via 800 nm laser pulses. The network was able to predict transient temperatures with a deviation of less than 6% from analytically estimated values. Notably, this performance was achieved on a dataset of 408 images only. We believe that employing this network in experimental settings where high volumes of visual data are collected, such as beam lines, could provide insights into the structural dynamics of different samples. [ABSTRACT FROM AUTHOR]

Salt solubility is generally determined under isotropic stress conditions. Yet, in the context of salt weathering of porous media, mechanical constraints on the in-pore growth of salt crystals are likely to be orientation-dependent, resulting in an anisotropic stress state on the crystal. In this paper, we determine by molecular simulation the solubility of NaCl in water when the crystal is subjected to anisotropic stress. Such anisotropy causes the chemical potential of the crystal to be orientation-dependent, and proper thermodynamic formulation requires describing the chemical potential as a tensor. The solute and crystal chemical potentials are computed from free energy calculations using Hamiltonian thermodynamic integration, and the usual condition of solubility is reformulated to account for the tensorial nature of the crystal chemical potential. We investigate in detail how the uniaxial compression of the crystal affects its solubility. The molecular simulation results led to revisiting the Correns law under anisotropic stress. Regarding the solute, the non-ideal behavior of the liquid phase is captured using Pitzer's ion interaction approach up to high concentrations of interest for in-pore crystallization and beyond the concentrations addressed in the existing literature. Regarding NaCl crystals, the validity of the generalized Gibbs–Duhem equation for a tensorial chemical potential is carefully verified, and it is found that crystallization progresses almost orthogonally to the crystal surface even under high shear stresses. Comparing uniaxial and isotropic compression highlights the major differences in solubility caused by stress anisotropy, and the revisited Correns law offers an appropriate framework to capture this phenomenon. [ABSTRACT FROM AUTHOR]

The present paper reformulates and improves a previously proposed determinant-based second-order multi-reference perturbative formalism. Through a rather simple modification of the energy denominators, this formalism takes into account the interactions between the model space determinants, which are repeated in outer space. The method has been shown to be size-consistent when the model space is a complete active space, which is a severe limit. It is shown here that the completeness of the model space is not necessary to keep this property, provided that the zero-order function satisfies some conditions. For instance, size consistency may be obtained from truncated complete active spaces. It may even be satisfied from Singles and Doubles Configuration Interactions, provided that a coupled electron pair approximation is used in the definition of the model space wave function. The physical content of the method is illustrated by a series of model problems, showing its robustness. A major benefit of the fact that the perturbers are single determinants is the possibility to revise with full flexibility the model-space component of the wave function, i.e., to treat the feedback effect of the dynamic correlation on the valence component of the wave function. [ABSTRACT FROM AUTHOR]

Tensor algebra operations such as contractions in computational chemistry consume a significant fraction of the computing time on large-scale computing platforms. The widespread use of tensor contractions between large multi-dimensional tensors in describing electronic structure theory has motivated the development of multiple tensor algebra frameworks targeting heterogeneous computing platforms. In this paper, we present Tensor Algebra for Many-body Methods (TAMM), a framework for productive and performance-portable development of scalable computational chemistry methods. TAMM decouples the specification of the computation from the execution of these operations on available high-performance computing systems. With this design choice, the scientific application developers (domain scientists) can focus on the algorithmic requirements using the tensor algebra interface provided by TAMM, whereas high-performance computing developers can direct their attention to various optimizations on the underlying constructs, such as efficient data distribution, optimized scheduling algorithms, and efficient use of intra-node resources (e.g., graphics processing units). The modular structure of TAMM allows it to support different hardware architectures and incorporate new algorithmic advances. We describe the TAMM framework and our approach to the sustainable development of scalable ground- and excited-state electronic structure methods. We present case studies highlighting the ease of use, including the performance and productivity gains compared to other frameworks. [ABSTRACT FROM AUTHOR]

In this paper, we present a continuation of our research on modeling electrolyte solutions within charged pores. We make use of the model developed by Blossey et al. [Phys. Rev. E 95, 060602 (2017)], which takes into account the structural interactions between ions through a bilinear form over the gradients of local ionic concentrations in the grand thermodynamic potential, as well as their steric interactions through the lattice gas model. The structural interactions may describe the effects of the molecular structure of ions at a phenomenological level. For example, these effects include steric effects due to non-spherical shapes of ions, their conformational lability, and solvent effects. In addition, we explore their specific interactions with the pore walls by incorporating external attractive potentials. Our primary focus is on observing the behavior of ionic concentration profiles and the disjoining pressure as the pore width changes. By starting with the local mechanical equilibrium condition, we derive a general expression for the disjoining pressure. Our findings indicate that considering the structural interactions of ions leads to a pronounced minimum on the disjoining pressure profiles at small pore widths. We attribute this minimum to the formation of electric double layers on the electrified surfaces of the pore. In addition, our results demonstrate that the inclusion of the attractive interactions of ions with the pore walls enhances this minimum and shifts it to smaller pore thicknesses. Our theoretical discoveries may be useful for those involved in supercapacitor electrochemical engineering, particularly when working with porous electrodes that have been infused with concentrated electrolyte solutions. [ABSTRACT FROM AUTHOR]

In this paper, we present an extended dissipaton equation of motion for studying the dynamics of electronic impurity systems. Compared with the original theoretical formalism, the quadratic couplings are introduced into the Hamiltonian accounting for the interaction between the impurity and its surrounding environment. By exploiting the quadratic fermionic dissipaton algebra, the proposed extended dissipaton equation of motion offers a powerful tool for studying the dynamical behaviors of electronic impurity systems, particularly in situations where nonequilibrium and strongly correlated effects play significant roles. Numerical demonstrations are carried out to investigate the temperature dependence of the Kondo resonance in the Kondo impurity model. [ABSTRACT FROM AUTHOR]

The dual exponential coupled cluster theory proposed by Tribedi et al.[J. Chem. Theory Comput. 16, 10, 6317–6328 (2020)] performs significantly better for a wide range of weakly correlated systems than the coupled cluster theory with singles and doubles excitations due to the implicit inclusion of high-rank excitations. The high-rank excitations are included through the action of a set of vacuum annihilating scattering operators that act non-trivially on certain correlated wavefunctions and are determined via a set of local denominators involving the energy difference between certain excited states. This often leads the theory to be prone to instabilities. In this paper, we show that restricting the correlated wavefunction, on which the scattering operators act, to be spanned by only the singlet-paired determinants can avoid catastrophic breakdown. For the first time, we present two nonequivalent approaches to arrive at the working equations, viz., the projective approach with sufficiency conditions and the amplitude form with many-body expansion. Although the effect of the triple excitation is quite small around molecular equilibrium geometry, this scheme leads to a better qualitative description of the energetics in the regions of strong correlation. With many pilot numerical applications, we have demonstrated the performance of the dual-exponential scheme with both the proposed solution strategies while restricting the excitation subspaces coupled to the corresponding lowest spin channels. [ABSTRACT FROM AUTHOR]

We investigate, in this paper, the Gaussian (G) function with odd powers of r, rxaybzc exp(−αr2), called the r-Gaussian or simply the rG function. The reason we investigate this function here is that it is generated as the elements of the complement functions (cf's) when we apply the free complement (FC) theory for solving the Schrödinger equation to the initial functions composed of the Gaussian functions. This means that without the rG functions, the Gaussian set of functions cannot produce the exact solutions of the Schrödinger equation, showing the absolute importance of the rG functions in quantum chemistry. Actually, the rG functions drastically improve the wave function near the cusp region. This was shown by the applications of the present theory to the hydrogen and helium atoms. When we use the FC-sij theory, in which the inter-electron function rij is replaced with its square s i j = r i j 2 that is integrable, we need only one- and two-electron integrals for the G and rG functions. The one-center one- and two-electron integrals of the rG functions are always available in a closed form. To calculate the integrals of the multi-centered rG functions, we proposed the rG-NG expansion method, in which an rG function is expanded by a linear combination of the G functions. The optimal exponents and coefficients of this expansion were given for N = 2, 3, 4, 5, 6, and 9. To show the accuracy and the usefulness of the rG-NG method, we applied the FC-sij theory to the hydrogen molecule. [ABSTRACT FROM AUTHOR]

The diffusion of small molecular penetrants through polymeric materials represents an important fundamental problem, relevant to the design of materials for applications such as coatings and membranes. Polymer networks hold promise in these applications because dramatic differences in molecular diffusion can result from subtle changes in the network structure. In this paper, we use molecular simulation to understand the role that cross-linked network polymers have in governing the molecular motion of penetrants. By considering the local, activated alpha relaxation time of the penetrant and its long-time diffusive dynamics, we can determine the relative importance of activated glassy dynamics on penetrants at the segmental scale vs entropic mesh confinement on penetrant diffusion. We vary several parameters, such as the cross-linking density, temperature, and penetrant size, to show that cross-links primarily affect molecular diffusion through the modification of the matrix glass transition, with local penetrant hopping at least partially coupled to the segmental relaxation of the polymer network. This coupling is very sensitive to the local activated segmental dynamics of the surrounding matrix, and we also show that penetrant transport is affected by dynamic heterogeneity at low temperatures. To contrast, only at high temperatures and for large penetrants or when the dynamic heterogeneity effect is weak, does the effect of mesh confinement become significant, even though penetrant diffusion more broadly empirically follows similar trends as established models of mesh confinement-based transport. [ABSTRACT FROM AUTHOR]

In this paper, a broadband metamaterial absorber consisting of the doped silicon substrate and the square array of doped silicon covered by a SU-8 layer is presented. The target structure achieves an average absorption of 94.42% in the studied frequency range (0.5–8 THz). In particular, the structure exceeds 90% absorption in the frequency range of 1.44–8 THz, which is a significant increase in bandwidth relative to reported devices of the same type. Next, the near-perfect absorption of the target structure is verified by the impedance matching principle. Furthermore, through the analysis of the electric field distribution inside the structure, the physical mechanism of its broadband absorption is investigated and explained. Finally, the impact of fluctuations in the incident angle, polarization angle, and structural parameters on the absorption efficiency is examined at length. The analysis shows that the structure has characteristics, such as polarization insensitivity, wide-angle absorption, and good process tolerance. The proposed structure is advantageous for applications in THz shielding, cloaking, sensing, and energy harvesting. [ABSTRACT FROM AUTHOR]

Cation exchange is a versatile post-synthetic method to explore a wide range of nanoparticle compositions, phases, and morphologies. Recently, several studies have expanded the scope of cation exchange to magic-size clusters (MSCs). Mechanistic studies indicated that MSC cation exchange undergoes a two-stage reaction pathway instead of the continuous diffusion-controlled mechanism found in nanoparticle cation exchange reactions. The cation exchange intermediate, however, has not been well-identified despite it being the key to understanding the reaction mechanism. Only indirect evidence, such as exciton peak shifts and powder x-ray diffraction, has been used to indicate the formation of the cation exchange intermediate. In this paper, we investigate the unusual nature of cation exchange in nanoclusters using our previously reported CdS MSC. High-resolution mass spectra reveal two cation exchanged reaction intermediates [Ag2Cd32S33(L) and AgCd33S33(L), L: oleic acid] as well as the fully exchanged Ag2S cluster. Crystal and electronic structure characterizations also confirm the two-stage reaction mechanism. Additionally, we investigate the Cu/CdS MSC cation exchange reaction and find a similar two-stage reaction mechanism. Our study shows that the formation of dilutely exchanged intermediate clusters can be generally found in the first stage of the MSC cation exchange reaction. By exchanging different cations, these intermediate clusters can access varying properties compared to their unexchanged counterparts. [ABSTRACT FROM AUTHOR]

A novel chiroptical sensing technique was recently introduced that utilized the helical phase of the structured light as a chiral reagent instead of polarization of light to differentiate enantiopure chiral liquids. The unique advantage of this non-resonant, nonlinear technique is that the chiral signal can be scaled and tuned. In this paper, we extend this technique to enantiopure powders of alanine and camphor by dissolving them in solvents of varying concentrations. We show the differential absorbance of helical light to be an order of magnitude higher relative to conventional resonant linear techniques and is comparable to nonlinear techniques that use circularly polarized light. The origin of helicity dependent absorption is discussed in terms of induced multipole moments in nonlinear light–matter interaction. These results opens up new opportunities in using helical light as a primary chiral reagent in nonlinear spectroscopic techniques. [ABSTRACT FROM AUTHOR]

In this paper, we announce the public release of a massively parallel, graphics processing unit (GPU)-accelerated software, which is the first to combine both coarse-grained particle simulations and field-theoretic simulations in one simulation package. MATILDA.FT (Mesoscale, Accelerated, Theoretically Informed, Langevin, Dissipative particle dynamics, and Field Theory) was designed from the ground-up to run on CUDA-enabled GPUs with Thrust library acceleration, enabling it to harness the possibility of massive parallelism to efficiently simulate systems on a mesoscopic scale. It has been used to model a variety of systems, from polymer solutions and nanoparticle-polymer interfaces to coarse-grained peptide models and liquid crystals. MATILDA.FT is written in CUDA/C++ and is object oriented, making its source-code easy to understand and extend. Here, we present an overview of the currently available features, and the logic of parallel algorithms and methods. We provide the necessary theoretical background and present examples of systems simulated using MATILDA.FT as the simulation engine. The source code, along with the documentation, additional tools, and examples, can be found on the GitHub MATILDA.FT repository. [ABSTRACT FROM AUTHOR]

Several new variants of the locally-renormalized coupled-cluster (CC) approaches that account for the effect of triples (LR-CCSD(T)) have been formulated and implemented for arbitrary reference states using the TENSOR CONTRACTION ENGINE functionality, enabling the automatic generation of an efficient parallel code. Deeply rooted in the recently derived numerator–denominator-connected (NDC) expansion for the ground-state energy [K. Kowalski and P. Piecuch, J. Chem. Phys. 122, 074107 (2005)], LR-CCSD(T) approximations use, in analogy to the completely renormalized CCSD(T) (CR-CCSD(T)) approach, the three-body moments in constructing the noniterative corrections to the energies obtained in CC calculations with singles and doubles (CCSD). In contrast to the CR-CCSD(T) method, the LR-CCSD(T) approaches discussed in this paper employ local denominators, which assure the additive separability of the energies in the noninteracting system limit when the localized occupied spin-orbitals are employed in the CCSD and LR-CCSD(T) calculations. As clearly demonstrated on several challenging examples, including breaking the bonds of the F2, N2, and CN molecules, the LR-CCSD(T) approaches are capable of providing a highly accurate description of the entire potential-energy surface (PES), while maintaining the characteristic N7scaling of the ubiquitous CCSD(T) approach. Moreover, as illustrated numerically for the ozone molecule, the LR-CCSD(T) approaches yield highly competitive values for a number of equilibrium properties including bond lengths, angles, and harmonic frequencies. [ABSTRACT FROM AUTHOR]

This paper reports the derivation and implementation of the electric dipole-magnetic dipole and electric dipole-electric quadrupole polarizability tensors at the density functional theory level with periodic boundary conditions (DFT-PBC). These tensors are combined to evaluate the Buckingham/Dunn tensor that describes the optical rotation (OR) in oriented chiral systems. We describe several aspects of the derivation of the equations and present test calculations that verify the correctness of the tensor formulation and their implementation. The results show that the full OR tensor is completely origin invariant as for molecules and that PBC calculations match molecular cluster calculations on 1D chains. A preliminary investigation on the choice of density functional, basis set, and gauge indicates a similar dependence as for molecules: the functional is the primary factor that determines the OR magnitude, followed by the basis set and to a much smaller extent the choice of gauge. However, diffuse functions may be problematic for PBC calculations even if they are necessary for the molecular case. A comparison with experimental data of OR for the tartaric acid crystal shows reasonable agreement given the level of theory employed. The development presented in this paper offers the opportunity to simulate the OR of chiral crystalline materials with general-purpose DFT-PBC methods, which, in turn, may help to understand the role of intermolecular interactions on this sensitive electronic property. [ABSTRACT FROM AUTHOR]

The article discusses the debate surrounding the mechanism of sum frequency generation (SFG) signals emitted by liquid benzene. The authors argue that the main signal comes from local modes generated by symmetry breaking, while another paper challenges this view and suggests that the dominant mechanism is the interfacial electric quadrupole. The authors refute this argument, stating that their previous paper considered both symmetry breaking and the electric quadrupole in their calculations, while the opposing paper did not properly examine the effect of symmetry breaking. The authors present evidence of symmetry breaking through computational evaluations and the reversal of symmetry breaking at the silica-benzene interface. They recommend that the opposing authors consider these evidences before drawing their conclusion. [Extracted from the article]

Density-functional-theory-based chemical reactivity indicators are formulated for degenerate and near-degenerate ground states. For degenerate states, the functional derivatives of the energy with respect to the external potential do not exist, and must be replaced by the weaker concept of functional variation. The resultant reactivity indicators depend on the specific perturbation. Because it is sometimes impractical to compute reactivity indicators for a specific perturbation, we consider two special cases: point-charge perturbations and Dirac delta function perturbations. The Dirac delta function perturbations provide upper bounds on the chemical reactivity. Reactivity indicators using the common used 'average of degenerate states approximation' for degenerate states provide a lower bound on the chemical reactivity. Unfortunately, this lower bound is often extremely weak. Approximate formulas for the reactivity indicators within the frontier-molecular-orbital approximation and special cases (two or three degenerate spatial orbitals) are presented in the supplementary material. One remarkable feature that arises in the frontier molecular orbital approximation, and presumably also in the exact theory, is that removing electrons sometimes causes the electron density to increase at the location of a negative (attractive) Dirac delta function perturbation. That is, the energetic response to a reduction in the external potential can increase even when the number of electrons decreases. [ABSTRACT FROM AUTHOR]

This paper proposes the first linear scaling implementation for the domain decomposition approach of the polarizable continuum model (ddPCM) for the computation of the solvation energy and forces. The ddPCM-equation consists of a (non-local) integral equation on the van der Waals or solvent accessible surface of the solute's cavity resulting in a dense solution matrix, and, in turn, one matrix–vector multiplication has a quadratic arithmetic complexity with respect to the number of atoms of the solute molecule. The use of spherical harmonics as basis functions makes it natural to employ the fast multipole method (FMM) in order to provide an asymptotically linear scaling method. In this paper, we employ the FMM in a non-uniform manner with a clusterization based on a recursive inertial bisection. We present some numerical tests illustrating the accuracy and scaling of our implementation. [ABSTRACT FROM AUTHOR]

Ninety years ago, Wigner derived the leading order expansion term in ℏ2 for the tunneling rate through a symmetric barrier. His derivation included two contributions: one came from the parabolic barrier, but a second term involved the fourth-order derivative of the potential at the barrier top. He left us with a challenge, which is answered in this paper, to derive the same but for an asymmetric barrier. A crucial element of the derivation is obtaining the ℏ2 expansion term for the projection operator, which appears in the flux-side expression for the rate. It is also reassuring that an analytical calculation of semiclassical transition state theory (TST) reproduces the anharmonic corrections to the leading order of ℏ2. The efficacy of the resulting expression is demonstrated for an Eckart barrier, leading to the conclusion that especially when considering heavy atom tunneling, one should use the expansion derived in this paper, rather than the parabolic barrier approximation. The rate expression derived here reveals how the classical TST limit is approached as a function of ℏ and, thus, provides critical insights to understand the validity of popular approximate theories, such as the classical Wigner, centroid molecular dynamics, and ring polymer molecular dynamics methods. [ABSTRACT FROM AUTHOR]

We have analyzed the effects of the spreads in experimental parameters on the reliability of speeds and angular distributions extracted from a generic surface-scattering experiment based on planar laser-induced fluorescence detection. The numerical model assumes a pulsed beam of projectile molecules is directed at a surface. The spatial distribution of the scattered products is detected by imaging the laser-induced fluorescence excited by a thin, pulsed sheet of laser light. Monte Carlo sampling is used to select from realistic distributions of the experimental parameters. The key parameter is found to be the molecular-beam diameter, expressed as a ratio to the measurement distance from the point of impact. Measured angular distributions are negligibly distorted when this ratio is <∼10%. Measured most-probable speeds are more tolerant, being undistorted when it is <∼20%. In contrast, the spread of speeds or of corresponding arrival times in the incident molecular beam has only very minor systematic effects. The thickness of the laser sheet is also unimportant within realistic practical limits. These conclusions are broadly applicable to experiments of this general type. In addition, we have analyzed the specific set of parameters designed to match the experiments on OH scattering from a liquid perfluoropolyether (PFPE) surface in the Paper I [Roman et al., J. Chem. Phys. 158, 244704 (2023)]. This reveals that the detailed form of the molecular-beam profile is important, particularly on apparent angular distributions, for geometric reasons that we explain. Empirical factors have been derived to correct for these effects. [ABSTRACT FROM AUTHOR]

Inelastic collisions of OH with an inert liquid perfluoropolyether (PFPE) surface have been studied experimentally. A pulsed molecular beam of OH with a kinetic energy distribution peaking at 35 kJ mol−1 was directed at a continually refreshed PFPE surface. OH molecules were detected state-selectively with spatial and temporal resolution by pulsed, planar laser-induced fluorescence. The scattered speed distributions were confirmed to be strongly superthermal, regardless of the incidence angle (0° or 45°). Angular scattering distributions were measured for the first time; their reliability was confirmed through extensive Monte Carlo simulations of experimental averaging effects, described in Paper II [A. G. Knight et al., J. Chem. Phys. 158, 244705 (2023)]. The distributions depend markedly on the incidence angle and are correlated with scattered OH speed, consistent with predominantly impulsive scattering. For 45° incidence, the angular distributions are distinctly asymmetric to the specular side but peak at sub-specular angles. This, along with the breadth of the distributions, is incompatible with scattering from a surface that is flat on a molecular scale. New molecular dynamics simulations corroborate the roughness of the PFPE surface. A subtle but unexpected systematic dependence of the angular distribution on the OH rotational state was found, which may be dynamical in origin. The OH angular distributions are similar to those for kinematically similar Ne scattering from PFPE and hence not strongly perturbed by OH being a linear rotor. The results here are broadly compatible with prior predictions from independent quasiclassical trajectory simulations of OH scattering from a model-fluorinated self-assembled monolayer surface. [ABSTRACT FROM AUTHOR]

The research presented in the paper concerns the elastic properties of struvite. The article combines theoretical and experimental research. Experimental studies were carried out on struvite single crystals grown in sodium metasilicate gel by single diffusion. This unique method leads to obtaining crystals of sufficiently large size to conduct, for the first time, experimental measurement of elastic properties of monocrystalline struvite. Using the nanoindentation method, the Ez = 29.1 ± 0.7 GPa value of the component of Young's modulus was determined for a struvite single crystal. In addition, the elastic constants C11, C22, and C33 were determined using micro-Brillouin spectroscopy. Theoretical calculations of the abovementioned properties have been carried out by employing density functional theory methods. Scaling of the theoretical elastic constants leads to obtaining good agreement with the experimental values. Values of the Ex and Ey components of the Young's modulus, not available from the experimental nanoindentation technique, have been determined theoretically as 23 GPa and 27 GPa, respectively. Differences in the values of elastic components and Young's modulus components are related to the layered crystal structure of struvite and directional character of the hydrogen-bonding pattern. [ABSTRACT FROM AUTHOR]

With increasing demand and environmental concerns, researchers are exploring new materials that can perform as well or better than traditional materials while reducing environmental impact. The BAMline, a real-life sample materials research beamline, provides unique insights into materials' electronic and chemical structure at different time and length scales. The beamline specializes in x-ray absorption spectroscopy, x-ray fluorescence spectroscopy, and tomography experiments. This enables real-time optimization of material properties and performance for various applications, such as energy transfer, energy storage, catalysis, and corrosion resistance. This paper gives an overview of the analytical methods and sample environments of the BAMline, which cover non-destructive testing experiments in materials science, chemistry, biology, medicine, and cultural heritage. We also present our own synthesis methods, processes, and equipment developed specifically for the BAMline, and we give examples of synthesized materials and their potential applications. Finally, this article discusses the future perspectives of the BAMline and its potential for further advances in sustainable materials research. [ABSTRACT FROM AUTHOR]

We present the computational methodology, which for the first time allows rigorous twelve-dimensional (12D) quantum calculations of the coupled intramolecular and intermolecular vibrational states of hydrogen-bonded trimers of flexible diatomic molecules. Its starting point is the approach that we introduced recently for fully coupled 9D quantum calculations of the intermolecular vibrational states of noncovalently bound trimers comprised of diatomics treated as rigid. In this paper, it is extended to include the intramolecular stretching coordinates of the three diatomic monomers. The cornerstone of our 12D methodology is the partitioning of the full vibrational Hamiltonian of the trimer into two reduced-dimension Hamiltonians, one in 9D for the intermolecular degrees of freedom (DOFs) and another in 3D for the intramolecular vibrations of the trimer, and a remainder term. These two Hamiltonians are diagonalized separately, and a fraction of their respective 9D and 3D eigenstates is included in the 12D product contracted basis for both the intra- and intermolecular DOFs, in which the matrix of the full 12D vibrational Hamiltonian of the trimer is diagonalized. This methodology is implemented in the 12D quantum calculations of the coupled intra- and intermolecular vibrational states of the hydrogen-bonded HF trimer on an ab initio calculated potential energy surface (PES). The calculations encompass the one- and two-quanta intramolecular HF-stretch excited vibrational states of the trimer and low-energy intermolecular vibrational states in the intramolecular vibrational manifolds of interest. They reveal several interesting manifestations of significant coupling between the intra- and intermolecular vibrational modes of (HF)3. The 12D calculations also show that the frequencies of the v = 1, 2 HF stretching states of the HF trimer are strongly redshifted in comparison to those of the isolated HF monomer. Moreover, the magnitudes of these trimer redshifts are much larger than that of the redshift for the stretching fundamental of the donor-HF moiety in (HF)2, most likely due to the cooperative hydrogen bonding in (HF)3. The agreement between the 12D results and the limited spectroscopic data for the HF trimer, while satisfactory, leaves room for improvement and points to the need for a more accurate PES. [ABSTRACT FROM AUTHOR]

This paper reports the release of PathSum, a new software suite of state-of-the-art path integral methods for studying the dynamics of single or extended systems coupled to harmonic environments. The package includes two modules, suitable for system–bath problems and extended systems comprising many coupled system–bath units, and is offered in C++ and Fortran implementations. The system–bath module offers the recently developed small matrix path integral (SMatPI) and the well-established iterative quasi-adiabatic propagator path integral (i-QuAPI) method for iteration of the reduced density matrix of the system. In the SMatPI module, the dynamics within the entanglement interval can be computed using QuAPI, the blip sum, time evolving matrix product operators, or the quantum–classical path integral method. These methods have distinct convergence characteristics and their combination allows a user to access a variety of regimes. The extended system module provides the user with two algorithms of the modular path integral method, applicable to quantum spin chains or excitonic molecular aggregates. An overview of the methods and code structure is provided, along with guidance on method selection and representative examples. [ABSTRACT FROM AUTHOR]

With the development of modern industry, the discharge of dye wastewater is increasing year by year, and the damage caused by this wastewater to the ecosystem is often irreversible. Therefore, the research on the harmless treatment of dyes has attracted much attention in recent years. In this paper, commercial titanium dioxide (anatase nanometer titanium dioxide) was heat treated with anhydrous ethanol to synthesize titanium carbide (C/TiO2). Its maximum adsorption capacity for cationic dyes methylene blue (MB) and Rhodamine B is 27.3 and 124.6 mg g−1, respectively, which is much higher than that of pure TiO2. The adsorption kinetics and isotherm model of C/TiO2 were studied and characterized by Brunauer–Emmett–Teller, x-ray photoelectron spectroscopy, x-ray diffraction, Fourier transform infrared spectroscopy, and other methods. The results show that the carbon layer on the surface of C/TiO2 promotes the increase in surface hydroxyl groups, which is the main reason for the increase in MB adsorption. Compared with other adsorbents, C/TiO2 showed excellent reusability. The experimental results of adsorbent regeneration showed that the adsorption rate R% of MB was almost unchanged after three cycles. During the recovery of C/TiO2, the dyes adsorbed on its surface are removed, which solves the problem that the adsorbent cannot degrade dyes simply by adsorption. Additionally, C/TiO2 has a stable adsorption effect, is insensitive to the pH value, has a simple preparation process, and has relatively low raw material prices, making it suitable for large-scale operation. Therefore, it has good commercial prospects in the organic dye industry wastewater treatment. [ABSTRACT FROM AUTHOR]

Some chemical reactions proceed on multiple potential energy surfaces and are often accompanied by a change in spin multiplicity, being called spin-forbidden reactions, where the spin–orbit coupling (SOC) effects play a crucial role. In order to efficiently investigate spin-forbidden reactions with two spin states, Yang et al. [Phys. Chem. Chem. Phys. 20, 4129–4136 (2018)] proposed a two-state spin-mixing (TSSM) model, where the SOC effects between the two spin states are simulated by a geometry-independent constant. Inspired by the TSSM model, we suggest a multiple-state spin-mixing (MSSM) model in this paper for the general case with any number of spin states, and its analytic first and second derivatives have been developed for locating stationary points on the mixed-spin potential energy surface and estimating thermochemical energies. To demonstrate the performance of the MSSM model, some spin-forbidden reactions involving 5d transition elements are calculated using the density functional theory (DFT), and the results are compared with the two-component relativistic ones. It is found that MSSM DFT and two-component DFT calculations may provide very similar stationary-point information on the lowest mixed-spin/spinor energy surface, including structures, vibrational frequencies, and zero-point energies. For the reactions containing saturated 5d elements, the reaction energies by MSSM DFT and two-component DFT agree very well within 3 kcal/mol. As for the two reactions OsO+ + CH4 → OOs(CH2)+ + H2 and W + CH4 → WCH2 + H2 involving unsaturated 5d elements, MSSM DFT may also yield good reaction energies of similar accuracy but with some counterexamples. Nevertheless, the energies may be remarkably improved by a posteriori single point energy calculations using two-component DFT at the MSSM DFT optimized geometries, and the maximum error of about 1 kcal/mol is almost independent of the SOC constant used. The MSSM method as well as the developed computer program provides an effective utility for studying spin-forbidden reactions. [ABSTRACT FROM AUTHOR]

In modern electronics and power systems, good-performance dielectric capacitors have an essential function. Polymer-based dielectrics are widely used in the field of dielectric capacitors because of their large dielectric constant, flexibility, low density, and ease of processing. At present, ferroelectric polymers suffer from low breakdown field strength and high dielectric losses. How to improve the performance of dielectric materials in capacitors is still a promising research. This paper chooses the ferroelectric polymer poly(vinylidene fluoride) (PVDF) that worked as the matrix, and the linear polymers polyimide, cyanoethyl pullulan (CR-S), polyethersulfone, and cyanoethylated cellulose served as fillers. This all-organic dielectric composite produced as films working in electrostatic energy storage devices is prepared by using a casting method. Analyzing the test results, the composite film exhibited excellent electrical properties when the CR-S doping content was 5 wt. %. The organic composite dielectric based on CR-S/PVDF has a breakdown field strength of 450 MV/m, a discharge energy storage density (Ue) of 10.3 J/cm3, a high dielectric constant of 10.9, and a low dielectric loss of 0.004 at 1 kHz, which is a significant improvement compared with other dielectric composites. This all-organic dielectric composite strategy offers a new approach to achieve better-performance dielectric energy storage materials. [ABSTRACT FROM AUTHOR]

Observations of a high spin selectivity in various helical structures, which is called the chirality-induced spin selectivity, suggest a common mechanism originating from the helical geometry. In this paper, we consider a helical chain of atomic p± orbitals having the tangential angular momentum l = ±1. We show in this model that the coupling of l and the spin gives rise to spin-velocity locking, i.e., directions of spin and group velocity are parallel or antiparallel depending on the chirality of the helix, and consequently, an almost perfect spin selectivity in a specific energy region in a wide range of the curvature and the torsion of the helix. We find that the present spin-velocity locking originates from the helical symmetry in which the Hamiltonian is invariant with respect to a combined operation of the rotation around the helix axis and the translation along the helix axis. Therefore, we expect that spin-velocity locking occurs in a wide variety of helical structures. [ABSTRACT FROM AUTHOR]

Transient bonds between fast linkers and slower particles are widespread in physical and biological systems. Despite their diverse structure and function, a commonality is that the linkers diffuse on timescales much faster compared to the overall motion of the particles they bind to. This limits numerical and theoretical approaches that need to resolve these diverse timescales with high accuracy. Many models, therefore, resort to effective, yet ad hoc, dynamics, where linker motion is only accounted for when bound. This paper provides a mathematical justification for such coarse-grained dynamics that preserves detailed balance at equilibrium. Our derivation is based on multiscale averaging techniques and is broadly applicable. We verify our results with simulations on a minimal model of fast linker binding to a slow particle. We show how our framework can be applied to various systems, including those with multiple linkers, stiffening linkers upon binding, or slip bonds with force-dependent unbinding. Importantly, the preservation of detailed balance only sets the ratio of the binding to the unbinding rates, but it does not constrain the detailed expression of binding kinetics. We conclude by discussing how various choices of binding kinetics may affect macroscopic dynamics. [ABSTRACT FROM AUTHOR]

In this paper, we use the previously introduced Canonical Polyadic (CP)-Multiple Shift Block Inverse Iteration (MSBII) eigensolver [S. D. Kallullathil and T. Carrington, J. Chem. Phys. 155, 234105 (2021)] in conjunction with a contraction tree to compute vibrational spectra. The CP-MSBII eigensolver uses the CP format. The memory cost scales linearly with the number of coordinates. A tensor in CP format represents a wavefunction constrained to be a sum of products (SOP). An SOP wavefunction can be made more accurate by increasing the number of terms, the rank. When the required rank is large, the runtime of a calculation in CP format is long, although the memory cost is small. To make the method more efficient, we break the full problem into pieces using a contraction tree. The required rank for each of the sub-problems is small. To demonstrate the effectiveness of the ideas, we computed vibrational energy levels of acetonitrile (12-D) and ethylene oxide (15-D). [ABSTRACT FROM AUTHOR]

A photovoltaic device fabricated with conventional zincblende materials can use the Type-II quantum well structure, which spatially separates electrons and holes, to reduce their recombination rate. In order to obtain higher power conversion efficiency, it is desirable to preserve more energetic carriers by engineering a phonon "bottleneck," a mismatch between the gaps in the well and barrier phonon structure. Such a mismatch leads to poor phonon transport and therefore prevents energy from leaving the system in the form of heat. In this paper, we perform a superlattice phonon calculation to verify the "bottleneck" effect and build on this a model to predict the steady state of the hot electrons under photoexcitation. We describe the electrons and phonons with a coupled Boltzmann equation system and numerically integrate it to get the steady state. We find that inhibited phonon relaxation does lead to a more out-of-equilibrium electron distribution and discuss how this might be enhanced. We examine the different behaviors obtained for various combinations of recombination and relaxation rates and their experimental signatures. [ABSTRACT FROM AUTHOR]

Simulations of exciton and charge hopping in amorphous organic materials involve numerous physical parameters. Each of these parameters must be computed from costly ab initio calculations before the simulation can commence, resulting in a significant computational overhead for studying exciton diffusion, especially in large and complex material datasets. While the idea of using machine learning to quickly predict these parameters has been explored previously, typical machine learning models require long training times, which ultimately contribute to simulation overheads. In this paper, we present a new machine learning architecture for building predictive models for intermolecular exciton coupling parameters. Our architecture is designed in such a way that the total training time is reduced compared to ordinary Gaussian process regression or kernel ridge regression models. Based on this architecture, we build a predictive model and use it to estimate the coupling parameters which enter into an exciton hopping simulation in amorphous pentacene. We show that this hopping simulation is able to achieve excellent predictions for exciton diffusion tensor elements and other properties as compared to a simulation using coupling parameters computed entirely from density functional theory. This result, along with the short training times afforded by our architecture, shows how machine learning can be used to reduce the high computational overheads associated with exciton and charge diffusion simulations in amorphous organic materials. [ABSTRACT FROM AUTHOR]

The self-consistent phonon (SCP) method allows one to include anharmonic effects when treating a many-body quantum system at thermal equilibrium. The system is then described by an effective temperature-dependent harmonic Hamiltonian, which can be used to estimate its various dynamic and static properties. In this paper, we combine SCP with ab initio (AI) potential energy evaluation in which case the numerical bottleneck of AI-SCP is the evaluation of Gaussian averages of the AI potential energy and its derivatives. These averages are computed efficiently by the quasi-Monte Carlo method utilizing low-discrepancy sequences leading to a fast convergence with respect to the number, S, of the AI energy evaluations. Moreover, a further substantial (an-order-of-magnitude) improvement in efficiency is achieved once a numerically cheap approximation of the AI potential is available. This is based on using a perturbation theory-like (the two-grid) approach in which it is the average of the difference between the AI and the approximate potential that is computed. The corresponding codes and scripts are provided. [ABSTRACT FROM AUTHOR]

A large number of force fields have been proposed for describing the behavior of liquid water within classical atomistic simulations, particularly molecular dynamics. In the past two decades, models that incorporate molecular polarizability and even charge transfer have become more prevalent, in attempts to develop more accurate descriptions. These are frequently parameterized to reproduce the measured thermodynamics, phase behavior, and structure of water. On the other hand, the dynamics of water is rarely considered in the construction of these models, despite its importance in their ultimate applications. In this paper, we explore the structure and dynamics of polarizable and charge-transfer water models, with a focus on timescales that directly or indirectly relate to hydrogen bond (H-bond) making and breaking. Moreover, we use the recently developed fluctuation theory for dynamics to determine the temperature dependence of these properties to shed light on the driving forces. This approach provides key insight into the timescale activation energies through a rigorous decomposition into contributions from the different interactions, including polarization and charge transfer. The results show that charge transfer effects have a negligible effect on the activation energies. Furthermore, the same tension between electrostatic and van der Waals interactions that is found in fixed-charge water models also governs the behavior of polarizable models. The models are found to involve significant energy–entropy compensation, pointing to the importance of developing water models that accurately describe the temperature dependence of water structure and dynamics. [ABSTRACT FROM AUTHOR]

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 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 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 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]