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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]

Developing fluorescence-encoded infrared (FEIR) vibrational spectroscopy for single-molecule applications requires a detailed understanding of how the molecular response and external experimental parameters manifest in the detected signals. In Paper I [L. Whaley-Mayda, A. Guha, and A. Tokmakoff, J. Chem. Phys. 159, 194201 (2023)] we introduced a nonlinear response function theory to describe vibrational dynamics, vibronic coupling, and transition dipole orientation in FEIR experiments with ultrashort pulses. In this second paper, we apply the theory to investigate the role of intermode vibrational coherence, the orientation of vibrational and electronic transition dipoles, and the effects of finite pulse durations in experimental measurements. We focus on measurements at early encoding delays—where signal sizes are largest and therefore of most value for single-molecule experiments, but where many of these phenomena are most pronounced and can complicate the appearance of data. We compare experiments on coumarin dyes with finite-pulse response function simulations to explain the time-dependent behavior of FEIR spectra. The role of the orientational response is explored by analyzing polarization-dependent experiments and their ability to resolve relative dipole angles in the molecular frame. This work serves to demonstrate the molecular information content of FEIR experiments, and develop insight and guidelines for their interpretation. [ABSTRACT FROM AUTHOR]

This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). While Paper II successfully captured translational motions in CG systems using a hard sphere mapping, the absence of rotational motions in single-site CG models introduces differences between FG and CG dynamics. In this third paper, our objective is to faithfully recover atomistic diffusion coefficients from CG dynamics by incorporating rotational dynamics. By extracting FG rotational diffusion, we unravel, for the first time reported to our knowledge, a universality in excess entropy scaling between the rotational and translational diffusion. Once the missing rotational dynamics are integrated into the CG translational dynamics, an effective translation-rotation coupling becomes essential. We propose two different approaches for estimating this coupling parameter: the rough hard sphere theory with acentric factor (temperature-independent) or the rough Lennard-Jones model with CG attractions (temperature-dependent). Altogether, we demonstrate that FG diffusion coefficients can be recovered from CG diffusion coefficients by (1) incorporating "entropy-free" rotational diffusion with translation-rotation coupling and (2) recapturing the missing entropy. Our findings shed light on the fundamental relationship between FG and CG dynamics in molecular fluids. [ABSTRACT FROM AUTHOR]

In a recent paper, Di Lisio et al. [J. Chem. Phys. 159, 064505 (2023)] analyzed a series of temperature down-jumps using the single-parameter aging (SPA) ansatz combined with a specific assumption about density scaling in the out-of-equilibrium system and did not find a good prediction for the largest down-jumps. In this paper, we show that SPA in its original form does work for all their data, including large jumps of ΔT > 20 K. Furthermore, we discuss different approaches to the extension of the density scaling concept to out-of-equilibrium systems. [ABSTRACT FROM AUTHOR]

In this paper, we investigate the role of electron correlation in predicting the S1–S0 and T1–S0 excitation energies and, hence, the singlet–triplet gap (ΔEST) in a set of cyclazines, which act as templates for potential candidates for fifth generation organic light emitting diode materials. This issue has recently garnered much interest with the focus being on the inversion of the ΔEST, although experiments have indicated near degenerate levels with both positive and negative being within the experimental error bar [J. Am. Chem. Soc. 102, 6068 (1980), J. Am. Chem. Soc. 108, 17(1986)]. We have carried out a systematic and exhaustive study of various excited state electronic structure methodologies and identified the strengths and shortcomings of the various approaches and approximations in view of this challenging case. We have found that near degeneracy can be achieved either with a proper balance of static and dynamic correlation in multireference theories or with state-specific orbital corrections, including its coupling with correlation. The role of spin contamination is also discussed. Eventually, this paper seeks to produce benchmark numbers for establishing cost-effective theories, which can then be used for screening derivatives of these templates with desirable optical and structural properties. Additionally, we would like to point out that the use of domain-based local pair natural orbital-similarity transformed EOM-coupled cluster singles and doubles as the benchmark for ΔEST [as used in J. Phys. Chem. A 126(8), 1378 (2022), Chem. Phys. Lett. 779, 138827 (2021)] is not a suitable benchmark for these classes of molecules. [ABSTRACT FROM AUTHOR]

Thermal energy storage and utilization has been widely concerned due to the intermittency, renewability, and economy of renewable energy. In this paper, the potential energy function of binary Na2CO3–K2CO3 salt was first constructed using the Deep Potential GENerator (DPGEN) enhanced sampling method. Deep potential molecular dynamics simulations were performed to calculate the thermal properties and structural evolution of binary carbonates. The results show that as the temperature increases from 1073 to 1273 K, the viscosity and thermal conductivity decrease from 5.011 mPa s and 0.502 W/(m K) to 2.526 mPa s and 0.481 W/(m K), respectively. The decrease in viscosity is related to the distance and interaction between the molten salt ions. In addition, the diffusion coefficients, energy barriers, ionic radius, angular distribution function, and coordination number of molten salt were calculated and analyzed. The CO32− exhibits a stable planar triangular structure. The ionic radius of Na+ is smaller than that of K+, which makes Na+ suffer less spatial hindrance during motion and has a higher diffusion coefficient. The energy barriers that Na+ needs to overcome to escape the Coulomb force is greater than that of K+ ions, so molten salt containing Na+ may possess greater heat storage potential. We believe that the potential function constructed with DPGEN enhanced sampling strategy can provide more convincing results for predicting the thermal properties of molten salts. This paper aims to provide a technical route to develop the novel complex molten salt phase change material for thermal energy storage. [ABSTRACT FROM AUTHOR]

Diffusion in complex heterogeneous media, such as biological tissues or porous materials, typically involves constrained displacements in tortuous structures and sticky environments. Therefore, diffusing particles experience both entropic (excluded-volume) forces and the presence of complex energy landscapes. In this situation, one may describe transport through an effective diffusion coefficient. In this paper, we examine comb structures with finite-length 1D and finite-area 2D fingers, which act as purely diffusive traps. We find that there exists a critical width of 2D fingers, above which the effective diffusion along the backbone is faster than for an equivalent arrangement of 1D fingers. Moreover, we show that the effective diffusion coefficient is described by a general analytical form for both 1D and 2D fingers, provided the correct scaling variable is identified as a function of the structural parameters. Interestingly, this formula corresponds to the well-known general situation of diffusion in a medium with fast reversible adsorption. Finally, we show that the same formula describes diffusion in the presence of dilute potential energy traps, e.g., through a landscape of square wells. While diffusion is ultimately always the result of microscopic interactions (with particles in the fluid, other solutes, and the environment), effective representations are often of great practical use. The results reported in this paper help clarify the microscopic origins and the applicability of global, integrated descriptions of diffusion in complex media. [ABSTRACT FROM AUTHOR]

This paper focuses on phase and aggregation behavior for linear chains composed of blocks of hydrophilic and hydrophobic segments. Phase and conformational transitions of patterned chains are relevant for understanding liquid–liquid separation of biomolecular condensates, which play a prominent role in cellular biophysics and for surfactant and polymer applications. Previous studies of simple models for multiblock chains have shown that, depending on the sequence pattern and chain length, such systems can fall into one of two categories: displaying either phase separation or aggregation into finite-size clusters. The key new result of this paper is that both formation of finite-size aggregates and phase separation can be observed for certain chain architectures at appropriate conditions of temperature and concentration. For such systems, a bulk dense liquid condenses from a dilute phase that already contains multi-chain finite-size aggregates. The computational approach used in this study involves several distinct steps using histogram-reweighting grand canonical Monte Carlo simulations, which are described in some level of detail. [ABSTRACT FROM AUTHOR]

The Wigner phase space formulation of quantum mechanics is a complete framework for quantum dynamic calculations that elegantly highlights connections with classical dynamics. In this series of two articles, building upon previous efforts, we derive the full hierarchy of approximate semiclassical (SC) dynamic methods for adiabatic and non-adiabatic problems in Wigner phase space. In Paper I, focusing on adiabatic single surface processes, we derive the well-known double Herman–Kluk (DHK) approximation for real-time correlation functions in Wigner phase space and connect it to the linearized SC (LSC) approximation through a stationary phase approximation. We exploit this relationship to introduce a new hybrid SC method, termed Adiabatic Hybrid Wigner Dynamics (AHWD) that allows for a few important "system" degrees of freedom (dofs) to be treated at the DHK level, while treating the rest of the dofs (the "bath") at the LSC level. AHWD is shown to accurately capture quantum interference effects in models of coupled oscillators and the decoherence of vibrational probability density of a model I2 Morse oscillator coupled to an Ohmic thermal bath. We show that AHWD significantly mitigates the sign problem and employs reduced dimensional prefactors bringing calculations of complex system–bath problems within the reach of SC methods. Paper II focuses on extending this hybrid SC dynamics to nonadiabatic processes. [ABSTRACT FROM AUTHOR]

The Journal of Chemical Physics has released a special issue focused on software for atomistic machine learning. This issue aims to address the lack of journals dedicated to publishing scientific software papers. The collection of papers in this issue provides insight into the tools and goals of software implementations in the field of atomistic machine learning. The articles cover a range of topics, including machine-learning interatomic potentials, sampling, dataset repositories, workflows, and auxiliary tooling and analysis. The article concludes by emphasizing the importance of software implementations in the field and encourages further submissions on relevant topics. [Extracted from the article]

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence. [ABSTRACT FROM AUTHOR]

A preceding paper [M. Dhar, J. A. Dickinson, and M. A. Berg, J. Chem. Phys. 159, 054110 (2023)] shows how to remove additive noise from an experimental time series, allowing both the equilibrium distribution of the system and its Green's function to be recovered. The approach is based on nonlinear-correlation functions and is fully nonparametric: no initial model of the system or of the noise is needed. However, single-molecule spectroscopy often produces time series with either photon or photon-counting noise. Unlike additive noise, photon noise is signal-size correlated and quantized. Photon counting adds the potential for bias. This paper extends noise-corrected-correlation methods to these cases and tests them on synthetic datasets. Neither signal-size correlation nor quantization is a significant complication. Analysis of the sampling error yields guidelines for the data quality needed to recover the properties of a system with a given complexity. We show that bias in photon-counting data can be corrected, even at the high count rates needed to optimize the time resolution. Using all these results, we discuss the factors that limit the time resolution of single-molecule spectroscopy and the conditions that would be needed to push measurements into the submicrosecond region. [ABSTRACT FROM AUTHOR]

Two-dimensional transition metal dichalcogenides and semiconductor metal oxides have shown great potential in photocatalysis. However, their stability and efficiency need to be further improved. In this paper, porous ZnO nanorods with high specific surface area were prepared from metal-organic framework ZIF-8 by a simple hydrothermal method. A MoS2/ZnO composite was constructed by loading MoS2 onto the surface of porous ZnO nanorods. Compared with ZnO materials prepared by other methods, MoS2/ZnO prepared in this paper exhibits superior photocatalytic performance. The enhanced photocatalytic activity of the MoS2/ZnO composite can be attributed to the formation of heterojunctions and strong interaction between them, which greatly facilitate the separation of electrons and holes at the contact interface. In addition, due to the wide absorption region of the visible spectrum, MoS2 can greatly broaden the light absorption range of the material after the formation of the composite material, increase the utilization rate of visible light, and reduce the combination of electrons and holes. This study provides a new way to prepare cheap and efficient photocatalysts. [ABSTRACT FROM AUTHOR]

Fluorescence-encoded infrared (FEIR) spectroscopy is an emerging technique for performing vibrational spectroscopy in solution with detection sensitivity down to single molecules. FEIR experiments use ultrashort pulses to excite a fluorescent molecule's vibrational and electronic transitions in a sequential, time-resolved manner, and are therefore sensitive to intervening vibrational dynamics on the ground state, vibronic coupling, and the relative orientation of vibrational and electronic transition dipole moments. This series of papers presents a theoretical treatment of FEIR spectroscopy that describes these phenomena and examines their manifestation in experimental data. This first paper develops a nonlinear response function description of Fourier-transform FEIR experiments for a two-level electronic system coupled to multiple vibrations, which is then applied to interpret experimental measurements in the second paper [L. Whaley-Mayda et al., J. Chem. Phys. 159, 194202 (2023)]. Vibrational coherence between pairs of modes produce oscillatory features that interfere with the vibrations' population response in a manner dependent on the relative signs of their respective Franck–Condon wavefunction overlaps, leading to time-dependent distortions in FEIR spectra. The orientational response of population and coherence contributions are analyzed and the ability of polarization-dependent experiments to extract relative transition dipole angles is discussed. Overall, this work presents a framework for understanding the full spectroscopic information content of FEIR measurements to aid data interpretation and inform optimal experimental design. [ABSTRACT FROM AUTHOR]

Double Resonance is a powerful spectroscopic method that unambiguously assigns the rigorous quantum numbers of one state of a transition. However, there is often ambiguity as to the branch (ΔJ) of that transition. Spectroscopists have resolved this ambiguity by using the dependence of the double resonance intensity on the relative polarization directions of pump and probe radiation. However, published theoretical predictions for this ratio are based upon a weak (i.e., non-saturating) field approximation. This paper presents theoretical predictions for these intensity ratios for cases where the pump field is strongly saturating in the two limits of transitions dominated by homogeneous or of inhomogeneous broadening. Saturation reduces but does not eliminate the magnitude of the polarization effect (driving the intensity ratio closer to unity) even with strong pump saturation. For the case of an inhomogeneously broadened line, such as when Doppler broadened linewidth dominates over the power-broadened homogeneous line width, a large fraction of the low pump power polarization anisotropy remains. This paper reports predicted polarization ratios for both linear and circular pump and probe field polarizations. The present predictions are compared with experimental measurements on CH4 ground state → ν3 → 3ν3 transitions recently reported by de Oliveira et al.63 and these are in better agreement than with the weak field predictions. [ABSTRACT FROM AUTHOR]

This paper presents an exploration of a specific type of a generalized multicomponent solution model, which appears to be first given by Saulov in the current explicit form. The assumptions of the underlying theory and a brief derivation of the main equation have been provided preliminarily for completeness and notational consistency. The resulting formulae for the Gibbs free energy of mixing and the chemical potentials are multivariate polynomials with physically meaningful coefficients and the mole fractions of the components as variables. With one additional assumption about the relative magnitudes of the solvent–solute and solute–solute interaction exchange energies, combining rules were obtained that express the mixed coefficients of the polynomial in terms of its pure coefficients. This was done by exploiting the mathematical structure of the asymmetric form of the solvent chemical potential equation. The combining rules allow one to calculate the thermodynamic properties of the solvent with multiple solutes from binary mixture data only (i.e., each solute with the solvent), and hence, are of practical importance. Furthermore, a connection was established between the osmotic virial coefficients derived in this work and the original osmotic virial coefficients of Hill found by employing a different procedure, illustrating the equivalency of what appears to be two different theories. A validation of the combining rules derived here has been provided in a separate paper where they were successfully used to predict the freezing points of ternary salt solutions of water. [ABSTRACT FROM AUTHOR]

Solvation dynamics in ionic liquids show features that are often associated with supercooled liquids, including "stretched" nonexponential relaxation. To better understand the mechanism behind the stretching, the nonlinear mode-correlation methods proposed in Paper I [S. R. Hodge and M. A. Berg, J. Chem. Phys. 155, 024122 (2021)] are applied to a simulation of a prototypical ionic liquid. A full Green's function is recovered. In addition, specific tests for non-Gaussian dynamics are made. No deviations from Gaussian dynamics are found. This finding is incompatible with rate heterogeneity as a cause of the nonexponential relaxation and appears to be in conflict with an earlier multidimensional analysis of the same data. Although this conflict is not resolved here, this work does demonstrate the practicality of mode-correlation analysis in the face of finite datasets and calculations. [ABSTRACT FROM AUTHOR]

This article is a response to a comment made by Professor Liu regarding a previously published paper. The response addresses questions raised by Professor Liu and focuses on three key aspects of the validity of the paper. It explains the use of different contractions in the construction of the QED Hamiltonians and clarifies the commutation relations used in the calculations. The article also highlights that the formulation of the molecular orbital method described in the paper is independent of the ordering of the operators and can derive expressions for various perturbation theories. The response concludes by stating that alternative criteria for the QED Hamiltonians are not ruled out and could be explored in future research. [Extracted from the article]

In continuation with Paper I [S. R. Reddy et al., J. Chem. Phys. 151, 054303 (2019)], the vibronic structure and dynamics of the 1 Σ u + electronic state of C15, C17, C19, and C21 chains in the coupled manifold of 1 Σ u + –1Πg–1Πu– 1 Σ g + electronic states have been investigated in this paper. The model vibronic Hamiltonian developed through extensive ab initio quantum chemistry calculations in Paper I is employed, and first principles nuclear dynamics calculations are carried out to obtain the photoabsorption band of the 1 Σ u + electronic state. Both time-independent and time-dependent quantum mechanical calculations are carried out to precisely locate the vibrational levels, assign them with the progression of vibrational modes, and elucidate the impact of both Renner-Teller and pseudo-Renner-Teller couplings on them. The nonradiative decay of the 1 Σ u + electronic state is studied, and it is found that the decay rate is comparable with the prediction made for them to be qualified as a carrier of diffuse interstellar bands in the literature. The theoretical results are found to be in good accord with the available experimental results. [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]

This work follows a companion article, which will be referred to as Paper I [Campeggio et al., J. Chem. Phys. 158, 244104 (2023)] in which a quantum-stochastic Liouville equation for the description of the quantum–classical dynamics of a molecule in a dissipative bath has been formulated in curvilinear internal coordinates. In such an approach, the coordinates of the system are separated into three subsets: the quantum coordinates, the classical relevant nuclear degrees of freedom, and the classical irrelevant (bath) coordinates. The equation has been derived in natural internal coordinates, which are bond lengths, bond angles, and dihedral angles. The resulting equation needs to be parameterized. In particular, one needs to compute the potential energy surfaces, the friction tensor, and the rate constants for the nonradiative jumps among the quantum states. While standard methods exist for the calculation of energy and dissipative properties, an efficient evaluation of the transition rates needs to be developed. In this paper, an approximated treatment is introduced, which leads to a simple explicit formula with a single adjustable parameter. Such an approximated expression is compared with the exact calculation of transition rates obtained via molecular dynamics simulations. To make such a comparison possible, a simple sandbox system has been used, with two quantum states and a single internal coordinate (together with its conjugate momentum). Results show that the adjustable parameter, which is an effective decoherence time, can be parameterized from the effective relaxation times of the autocorrelation functions of the conjugated momenta of the relevant nuclear coordinates. [ABSTRACT FROM AUTHOR]

The study and modeling of water exchange in complex media using different applications of diffusion and relaxation magnetic resonance (MR) have been of interest in recent years. Most models attempt to describe this process using a first order kinetics expression, which is appropriate to describe chemical exchange; however, it may not be suitable to describe diffusion-driven exchange since it has no direct relationship to diffusion dynamics of water molecules. In this paper, these limitations are addressed through a more general exchange expression that does consider such important properties. This exchange fraction expression features a multi-exponential recovery at short times and a mono-exponential decay at long times, both of which are not captured by the first order kinetics expression. Furthermore, simplified exchange expressions containing partial information of the analyzed system's diffusion and relaxation processes and geometry are proposed, which can potentially be employed in already established estimation protocols. Finally, exchange fractions estimated from simulated MR data and derived here were compared, showing qualitative similarities but quantitative differences, suggesting that the features of the derived exchange fraction in this paper can be partially recovered by employing an existing estimation framework. [ABSTRACT FROM AUTHOR]

Biased and accelerated molecular simulations (BAMS) are widely used tools to observe relevant molecular phenomena occurring on time scales inaccessible to standard molecular dynamics, but evaluation of the physical time scales involved in the processes is not directly possible from them. For this reason, the problem of recovering dynamics from such kinds of simulations is the object of very active research due to the relevant theoretical and practical implications of dynamics on the properties of both natural and synthetic molecular systems. In a recent paper [A. Rapallo et al., J. Comput. Chem. 42, 586–599 (2021)], it has been shown how the coupling of BAMS (which destroys the dynamics but allows to calculate average properties) with Extended Diffusion Theory (EDT) (which requires input appropriate equilibrium averages calculated over the BAMS trajectories) allows to effectively use the Smoluchowski equation to calculate the orientational time correlation function of the head–tail unit vector defined over a peptide in water solution. Orientational relaxation of this vector is the result of the coupling of internal molecular motions with overall molecular rotation, and it was very well described by correlation functions expressed in terms of weighted sums of suitable time-exponentially decaying functions, in agreement with a Brownian diffusive regime. However, situations occur where exponentially decaying functions are no longer appropriate to capture the actual dynamical behavior, which exhibits persistent long time correlations, compatible with the so called subdiffusive regimes. In this paper, a generalization of EDT will be given, exploiting a fractional Smoluchowski equation (FEDT) to capture the non-exponential character observed in the relaxation of intramolecular distances and molecular radius of gyration, whose dynamics depend on internal molecular motions only. The calculation methods, proper to EDT, are adapted to implement the generalization of the theory, and the resulting algorithm confirms FEDT as a tool of practical value in recovering dynamics from BAMS, to be used in general situations, involving both regular and anomalous diffusion regimes. [ABSTRACT FROM AUTHOR]

Despite the importance of rhodium complexes in catalysis, and the favorable 100% natural abundance of the spin-1/2 103Rh nucleus, there are few reports of 103Rh nuclear magnetic resonance (NMR) parameters in the literature. In part, this is the consequence of the very low gyromagnetic ratio of 103Rh and its dismal NMR sensitivity. In a previous paper [Harbor-Collins et al., J. Chem. Phys. 159, 104 307 (2023)], we demonstrated an NMR methodology for 1H-enhanced 103Rh NMR and demonstrated an application to the 103Rh NMR of the dirhodium formate paddlewheel complex. In this paper, we employ selective 18O labeling to break the magnetic equivalence of the 103Rh spin pair of dirhodium formate. This allows the estimation of the 103Rh–103Rh spin–spin coupling and provides access to the 103Rh singlet state. We present the first measurement of a 18O-induced 103Rh secondary isotope shift as well as the first instance of singlet order generated in a 103Rh spin pair. The field-dependence of 103Rh singlet relaxation is measured by field-cycling NMR experiments. [ABSTRACT FROM AUTHOR]

Protein folding in confined media has attracted wide attention over the past 15 years due to its importance to both in vivo and in vitro applications. It is generally believed that protein stability increases by decreasing the size of the confining medium, if the medium’s walls are repulsive, and that the maximum folding temperature in confinement is in a pore whose size D0 is only slightly larger than the smallest dimension of a protein’s folded state. Until recently, the stability of proteins in pores with a size very close to that of the folded state has not received the attention it deserves. In a previous paper [L. Javidpour and M. Sahimi, J. Chem. Phys. 135, 125101 (2011)], we showed that, contrary to the current theoretical predictions, the maximum folding temperature occurs in larger pores for smaller α-helices. Moreover, in very tight pores, the free energy surface becomes rough, giving rise to a new barrier for protein folding close to the unfolded state. In contrast to unbounded domains, in small nanopores proteins with an α-helical native state that contain the β structures are entropically stabilized implying that folding rates decrease notably and that the free energy surface becomes rougher. In view of the potential significance of such results to interpretation of many sets of experimental data that could not be explained by the current theories, particularly the reported anomalously low rates of folding and the importance of entropic effects on proteins’ misfolded states in highly confined environments, we address the following question in the present paper: To what extent the geometry of a confined medium affects the stability and folding rates of proteins? Using millisecond-long molecular dynamics simulations, we study the problem in three types of confining media, namely, cylindrical and slit pores and spherical cavities. Most importantly, we find that the prediction of the previous theories that the dependence of the maximum folding temperature Tf on the size D of a confined medium occurs in larger media for larger proteins is correct only in spherical geometry, whereas the opposite is true in the two other geometries that we study. Also studied is the effect of the strength of the interaction between the confined media’s walls and the proteins. If the walls are only weakly or moderately attractive, a complex behavior emerges that depends on the size of the confining medium. [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]

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]

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 first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of the scaling relationship was not possible due to the semi-empirical nature. In this second paper, an analytical excess entropy scaling relation is derived for bottom-up CG systems. At the single-site CG resolution, effective hard sphere systems are constructed that yield near-identical dynamical properties as the target CG systems by taking advantage of how hard sphere dynamics and excess entropy can be analytically expressed in terms of the liquid packing fraction. Inspired by classical equilibrium perturbation theories and recent advances in constructing hard sphere models for predicting activated dynamics of supercooled liquids, we propose a new approach for understanding the diffusion of molecular liquids in the normal regime using hard sphere reference fluids. The proposed "fluctuation matching" is designed to have the same amplitude of long wavelength density fluctuations (dimensionless compressibility) as the CG system. Utilizing the Enskog theory to derive an expression for hard sphere diffusion coefficients, a bridge between the CG dynamics and excess entropy is then established. The CG diffusion coefficient can be roughly estimated using various equations of the state, and an accurate prediction of accelerated CG dynamics at different temperatures is also possible in advance of running any CG simulation. By introducing another layer of coarsening, these findings provide a more rigorous method to assess excess entropy scaling and understand the accelerated CG dynamics of molecular fluids. [ABSTRACT FROM AUTHOR]

Jiang and co-workers use high resolution STM to investigate the reaction and self-assembly of (3,6-dibromo-9,10-phenanthrenequinone, or DBPQ) molecules on Ag (100) and Ag (110) surfaces in order to understand the mechanism of bottom-up assembly on surfaces.[31] They show that, through the inclusion of multiple functional groups within a precursor molecule, it becomes possible to fabricate new low-dimensional materials with unique chemical, physical, and electronic properties. Herbst and Fransson consider the core-valence separation approximation that is often used in the calculation of core-level spectra.[5] They show how to quantify the errors in this approximation, thereby opening the door to error-quantified predictions relevant to x-ray spectroscopy. 153(16), 164108 (2020).10.1063/5.0019557 5 M. F. Herbst and T. Fransson, "Quantifying the error of the core-valence separation approximation", J. Chem. Phys. Zhu and co-workers tackle this problem for a model system containing a 2D semiconductor heterojunction and show convincingly the efficient hot electron transfer from photoexcited MoTe SB 2 sb to WS SB 2 sb .[30] This finding provides important insight into the competition between hot electron cooling and transfer at 2D semiconductor interfaces and suggests an intriguing possibility for the exploration of hot electron devices. [Extracted from the article]

Spontaneous self-assembly of hard convex polyhedra is known to form orientationally disordered crystalline phases, where particle orientations do not follow the same pattern as the positional arrangement of the crystal. A distinct type of orientational phase with discrete rotational mobility has been reported in hard particle systems. In this paper, we present a new analysis method for characterizing the orientational phase of a crystal, which is based on algorithmic detection of unique orientations. Using this method, we collected complete statistics of discrete orientations along the Monte Carlo simulation trajectories and observed that particles were equally partitioned among them, with specific values of pairwise orientational differences. These features remained constant across the pressure range and did not depend on rotational mobility. The discrete mobility was characteristic of a distinct equilibrium thermodynamic phase, qualitatively different from the freely rotating plastic phase with continuous orientations. The high pressure behavior with frozen particle orientations was part of that same description and not a non-equilibrium arrested state. We introduced a precise notion of orientational order and demonstrated that the system was maximally disordered at the level of a unit cell, even though individual particles could only take a few discrete orientations. We report the existence of this phase in five polyhedral shapes and in systematically curated shape families constructed around two of them. The symmetry mismatch between the particle and the crystallographic point groups was found to be a predictive indicator for the occurrence of this phase. [ABSTRACT FROM AUTHOR]

When we place conducting bodies in electrolyte solutions, their surface potential Φs appears to be much smaller in magnitude than the applied one Φ0 and normally does not obey the classical electrostatic boundary condition of a constant potential expected for conductors. In this paper, we demonstrate that an explanation of these observations can be obtained by postulating that diffuse ions condense at the "wall" due to the reduced permittivity of a solvent. For small values of Φ0, the surface potential responds linearly. On increasing Φ0 further, Φs augments nonlinearly and then saturates to a constant value. Analytical approximations for Φs derived for these three distinct modes show that it always adjusts to salt concentration, which is equivalent to a violation of the constant potential condition. The latter would be appropriate for highly dilute solutions but only if Φ0 is small. Surprisingly, when the plateau with high Φs is reached, the conductor surface switches to a constant charge density condition normally expected for insulators. Our results are directly relevant for conducting electrodes, mercury drops, colloidal metallic particles, and more. [ABSTRACT FROM AUTHOR]

Proteins can form droplets via liquid–liquid phase separation (LLPS) in cells. Recent experiments demonstrate that LLPS is qualitatively different on two-dimensional (2D) surfaces compared to three-dimensional (3D) solutions. In this paper, we use mathematical modeling to investigate the causes of the discrepancies between LLPS in 2D and 3D. We model the number of proteins and droplets inducing LLPS by continuous-time Markov chains and use chemical reaction network theory to analyze the model. To reflect the influence of space dimension, droplet formation and dissociation rates are determined using the first hitting times of diffusing proteins. We first show that our stochastic model reproduces the appropriate phase diagram and is consistent with the relevant thermodynamic constraints. After further analyzing the model, we find that it predicts that the space dimension induces qualitatively different features of LLPS, which are consistent with recent experiments. While it has been claimed that the differences between 2D and 3D LLPS stem mainly from different diffusion coefficients, our analysis is independent of the diffusion coefficients of the proteins since we use the stationary model behavior. Our results thus give new hypotheses about how space dimension affects LLPS. [ABSTRACT FROM AUTHOR]

The introduction of machine learned potentials (MLPs) has greatly expanded the space available for studying Nuclear Quantum Effects computationally with ab initio path integral (PI) accuracy, with the MLPs' promise of an accuracy comparable to that of ab initio at a fraction of the cost. One of the challenges in development of MLPs is the need for a large and diverse training set calculated by ab initio methods. This dataset should ideally cover the entire phase space, while not searching this space using ab initio methods, as this would be counterproductive and generally intractable with respect to computational time. In this paper, we present the self-learning PI hybrid Monte Carlo Method using a mixed ab initio and ML potential (SL-PIHMC-MIX), where the mixed potential allows for the study of larger systems and the extension of the original SL-HMC method [Nagai et al., Phys. Rev. B 102, 041124 (2020)] to PI methods and larger systems. While the MLPs generated by this method can be directly applied to run long-time ML-PIMD simulations, we demonstrate that using PIHMC-MIX with the trained MLPs allows for an exact reproduction of the structure obtained from ab initio PIMD. Specifically, we find that the PIHMC-MIX simulations require only 5000 evaluations of the 32-bead structure, compared to the 100 000 evaluations needed for the ab initio PIMD result. [ABSTRACT FROM AUTHOR]

In this paper, we analyze the properties of the recently proposed real-time equation-of-motion coupled-cluster (RT-EOM-CC) cumulant Green's function approach [Rehr et al., J. Chem. Phys. 152, 174113 (2020)]. We specifically focus on identifying the limitations of the original time-dependent coupled cluster (TDCC) ansatz and propose an enhanced double TDCC ansatz, ensuring the exactness in the expansion limit. In addition, we introduce a practical cluster-analysis-based approach for characterizing the peaks in the computed spectral function from the RT-EOM-CC cumulant Green's function approach, which is particularly useful for the assignments of satellite peaks when many-body effects dominate the spectra. Our preliminary numerical tests focus on reproducing, approximating, and characterizing the exact impurity Green's function of the three-site and four-site single impurity Anderson models using the RT-EOM-CC cumulant Green's function approach. The numerical tests allow us to have a direct comparison between the RT-EOM-CC cumulant Green's function approach and other Green's function approaches in the numerical exact limit. [ABSTRACT FROM AUTHOR]

Singlet fission (SF) is a charge carrier multiplication process that has potential for improving the performance of (opto)electronic devices from the conversion of one singlet exciton S1 into two triplet excitons T1 via a spin-entangled triplet pair state 1(TT). This process depends highly on molecular packing and morphology, both for the generation and dissociation of 1(TT) states. Many benchmark SF materials, such as acenes, are also prone to photodegradation reactions, such as endoperoxide (EPO) formation and photodimerization, which inhibit realization of SF devices. In this paper, we compare functionalized tetracenes R–Tc with two packing motifs: "slip-stack" packing in R = TES, TMS, and tBu and "gamma" packing in R = TBDMS to determine the effects of morphology on SF as well as on photodegradation using a combination of temperature and magnetic field dependent spectroscopy, kinetic modeling, and time-dependent density functional theory. We find that both "slip-stack" and "gamma" packing support SF with high T1 yield at room temperature (up to 191% and 181%, respectively), but "slip-stack" is considerably more advantageous at low temperatures (< 150 K). In addition, each packing structure has a distinct emissive relaxation pathway competitive to SF, while the states involved in the SF itself are dark. The "gamma" packing has superior photostability, both in regards to EPO formation and photodimerization. The results indicate that the trade-off between SF efficiency and photostability can be overcome with material design, emphasize the importance of considering both photophysical and photochemical properties, and inform efforts to develop optimal SF materials for (opto)electronic applications. [ABSTRACT FROM AUTHOR]

We theoretically demonstrated that helical-photon-dressed states determine the rotational directions of the π-electrons of aromatic ring molecules formed by a circularly polarized or an elliptically polarized laser. This theory was verified using a minimal three-electronic-state model under the frozen nuclei condition. The model consists of the ground state and either a doubly degenerate electronic excited state or two quasi-degenerate excited states. Three helical-photon-dressed states were derived by solving the time-dependent Schrödinger equation within the semi-classical treatment of light–molecule interactions and rotating wave approximation. The angular momenta of the two helical-photon-dressed states represent the classical rotational direction, and that of the remaining state represents the opposite rotation, that is, non-classical rotation. Classical rotation means that π-electrons have the same rotational direction as that of a given helical electric field vector and obeys the classical equations of motion. Non-classical rotation indicates that the rotational direction is opposite to that of the helical electric field vector. Non-classical rotation is forbidden in an aromatic ring molecule with high symmetry formed by a circularly polarized laser but is allowed in a low symmetric aromatic ring molecule. The sum of the angular momenta of the three dressed states is zero. This is called the sum law for the angular momentum components in this paper. Benzene (D6h) and toluene (CS) were adopted as typical aromatic ring molecules of high and low symmetries, respectively. Finally, considering the effects of nuclear vibrations in the adiabatic approximation, an expression for the π-electron angular momentum was derived and applied to toluene. [ABSTRACT FROM AUTHOR]

Recent 15N R1ρ-relaxation studies have shown that proteins in the solid state undergo slow, low amplitude global motion in the sub-millisecond time range. This range is at the edge of the time window for R1ρ experiments and, therefore, the motional parameters obtained by this method are not precise or reliable. In this paper, we present a 2H stimulated echo study of this type of molecular dynamics. The 2H stimulated echo experiments on a static sample allow for direct measurement of the correlation function in the time range of 10−6–10−1 s, making them well suited to study this type of molecular mobility. We have conducted a detailed analytical and numerical comparison of the correlation functions obtained from the relaxation and stimulated echo experiments, which are generally different. We have identified conditions and algorithms that enable a direct comparison of the relaxation and stimulated echo experimental results. Using the protein GB1 in the form of a lyophilized powder, we have demonstrated that 15N R1ρ-relaxation and 2H stimulated echo experiments yield essentially the same slow-motion correlation function. Surprisingly, this type of motion is observed not only in the protein sample but also in the tripeptide and single amino acid solid samples. The comparison of data measured in these three samples at different temperatures led us to conclude that this slow motion is, in fact, ultrasonic phonons, which seem to be inherent to all rigid biological solids. [ABSTRACT FROM AUTHOR]

In a companion paper, we put forth a thermodynamic model for complex formation via a chemical reaction involving multiple macromolecular species, which may subsequently undergo liquid–liquid phase separation and a further transition into a gel-like state. In the present work, we formulate a thermodynamically consistent kinetic framework to study the interplay between phase separation, chemical reaction, and aging in spatially inhomogeneous macromolecular mixtures. A numerical algorithm is also proposed to simulate domain growth from collisions of liquid and gel domains via passive Brownian motion in both two and three spatial dimensions. Our results show that the coarsening behavior is significantly influenced by the degree of gelation and Brownian motion. The presence of a gel phase inside condensates strongly limits the diffusive transport processes, and Brownian motion coalescence controls the coarsening process in systems with high area/volume fractions of gel-like condensates, leading to the formation of interconnected domains with atypical domain growth rates controlled by size-dependent translational and rotational diffusivities. [ABSTRACT FROM AUTHOR]

Instanton theory relates the rate constant for tunneling through a barrier to the periodic classical trajectory on the upturned potential energy surface, whose period is τ = ℏ/(kBT). Unfortunately, the standard theory is only applicable below the "crossover temperature," where the periodic orbit first appears. This paper presents a rigorous semiclassical (ℏ → 0) theory for the rate that is valid at any temperature. The theory is derived by combining Bleistein's method for generating uniform asymptotic expansions with a real-time modification of Richardson's flux-correlation function derivation of instanton theory. The resulting theory smoothly connects the instanton result at low temperature to the parabolic correction to Eyring transition state theory at high-temperature. Although the derivation involves real time, the final theory only involves imaginary-time (thermal) properties, consistent with the standard version of instanton theory. Therefore, it is no more difficult to compute than the standard theory. The theory is illustrated with application to model systems, where it is shown to give excellent numerical results. Finally, the first-principles approach taken here results in a number of advantages over previous attempts to extend the imaginary free-energy formulation of instanton theory. In addition to producing a theory that is a smooth (continuously differentiable) function of temperature, the derivation also naturally incorporates hyperasymptotic (i.e., multi-orbit) terms and provides a framework for further extensions of the theory. [ABSTRACT FROM AUTHOR]

This paper presents a mean field theory of electrolyte solutions, extending the classical Debye–Hückel–Onsager theory to provide a detailed description of the electrical conductivity in strong electrolyte solutions. The theory systematically incorporates the effects of ion specificity, such as steric interactions, hydration of ions, and their spatial charge distributions, into the mean-field framework. This allows for the calculation of ion mobility and electrical conductivity, while accounting for relaxation and hydrodynamic phenomena. At low concentrations, the model reproduces the well-known Kohlrausch's limiting law. Using the exponential (Slater-type) charge distribution function for solvated ions, we demonstrate that experimental data on the electrical conductivity of aqueous 1:1, 2:1, and 3:1 electrolyte solutions can be approximated over a broad concentration range by adjusting a single free parameter representing the spatial scale of the nonlocal ion charge distribution. Using the fitted value of this parameter at 298.15 K, we obtain good agreement with the available experimental data when calculating electrical conductivity across different temperatures. We also analyze the effects of temperature and electrolyte concentration on the relaxation and electrophoretic contributions to total electrical conductivity, explaining the underlying physical mechanisms responsible for the observed behavior. [ABSTRACT FROM AUTHOR]

Aqueous interfaces containing organic/inorganic molecules are important in various biological, industrial, and atmospheric processes. So far, the study on the dynamics of interfacial molecules has been carried out with time-resolved vibrational sum-frequency generation (TR-VSFG) and time-resolved electronic sum-frequency generation (TR-ESFG) techniques. Although the ESFG probe is powerful for investigating interfacial photochemical dynamics of solute molecules by monitoring the electronic transition of transients or photoproducts at the interface, heterodyne detection is highly desirable for obtaining straightforward information, particularly in time-resolved measurements. So far, heterodyne detection has been realized only for TR-VSFG measurements but not for TR-ESFG measurements. In this paper, we report on femtosecond time-resolved heterodyne-detected ESFG (TR-HD-ESFG) spectroscopy for the first time. With TR-HD-ESFG developed, we measured the time-resolved electronic ΔImχ(2) spectra (pump-induced changes in the imaginary part of the second-order susceptibility) of a prototype dye, malachite green (MG), at the air/water interface. The obtained ΔImχ(2) spectra clearly show not only the ground-state bleach but also the excited-state band of MG at the air/water interface, demonstrating the high potential of TR-HD-ESFG as a new powerful tool to investigate ultrafast reaction dynamics at the interface. [ABSTRACT FROM AUTHOR]

Signaling in cells is full of noise and, hence, described with stochastic biochemical models. Thus, an efficient computation algorithm for these fluctuating reactions is much needed. Apart from the very popular Monte Carlo simulation, methods based on probability distributions are frequently desired due to their analytical tractability and possible numerical advantages in diverse circumstances, among which the variational approach is the most notable. In this paper, new basis functions are proposed to better depict possibly complex distribution profiles, and an extra regularization scheme is supplied to the variational equation to remove occasional degeneracy-induced singularities during the evolution. The new extension is applied to four typical biochemical reaction models and restores the Gillespie results accurately but with greatly reduced simulation time. This modified variational approach is expected to work in a wide range of cell signaling networks. [ABSTRACT FROM AUTHOR]

In 2012, the molecular structure of a new, broad class of ice-binding proteins, classified as "domain of unknown function" (DUF) 3494, was described for the first time. These proteins have a common tertiary structure and are characterized by a very wide spectrum of antifreeze activity (from weakly active to hyperactive). The ice-binding surface (IBS) region of these molecules differs significantly in its structure from the IBS of previously known antifreeze proteins (AFPs), showing a complete lack of regularity and high hydrophilicity. The presence of a regular, repeating structural motif in the IBS region of hitherto known AFP molecules, combined with the hydrophobic nature of this surface, promotes the formation of an ice-like ordering of the solvation water layer and, as a result, facilitates the process of transformation of this water layer into ice. It is, therefore, surprising that the newly discovered DUF3494 class of proteins clearly breaks out of this characteristic. In this paper, using molecular dynamics simulations, we analyze the solvation water structure of the IBS region of both DUF3494 family molecules and AFPs. As we show, although the IBS of DUF3494 molecules does not form an ice-like water structure in the solvation layer, this is compensated by the formation of the equivalent of "anchored clathrate water," in the form of a relatively large number of water molecules bound to the surface of the protein molecule and providing potential binding sites for it to the ice surface. [ABSTRACT FROM AUTHOR]

The generalized quantum master equation (GQME) approach provides a powerful general-purpose framework for simulating the inherently quantum mechanical dynamics of a subset of electronic reduced density matrix elements of interest in complex molecular systems. Previous studies have found that combining the GQME approach with quasiclassical mapping Hamiltonian (QC/MH) methods can dramatically improve the accuracy of electronic populations obtained via those methods. In this paper, we perform a complimentary study of the advantages offered by the GQME approach for simulating the dynamics of electronic coherences, which play a central role in optical spectroscopy, quantum information science, and quantum technology. To this end, we focus on cases where the electronic coherences predicted for the spin-boson benchmark model by direct application of various QC/MH methods are inaccurate. We find that similar to the case of electronic populations, combining the QC/MH methods with the GQME approach can dramatically improve the accuracy of the electronic coherences obtained via those methods. We also provide a comprehensive analysis of how the performance of GQMEs depends on the choice of projection operator and electronic basis and show that the accuracy and feasibility of the GQME approach can benefit from casting the GQME in terms of the eigen-basis of the observable of interest. [ABSTRACT FROM AUTHOR]

ipie is a Python-based auxiliary-field quantum Monte Carlo (AFQMC) package that has undergone substantial improvements since its initial release [Malone et al., J. Chem. Theory Comput. 19(1), 109–121 (2023)]. This paper outlines the improved modularity and new capabilities implemented in ipie. We highlight the ease of incorporating different trial and walker types and the seamless integration of ipie with external libraries. We enable distributed Hamiltonian simulations of large systems that otherwise would not fit on a single central processing unit node or graphics processing unit (GPU) card. This development enabled us to compute the interaction energy of a benzene dimer with 84 electrons and 1512 orbitals with multi-GPUs. Using CUDA and cupy for NVIDIA GPUs, ipie supports GPU-accelerated multi-slater determinant trial wavefunctions [Huang et al. arXiv:2406.08314 (2024)] to enable efficient and highly accurate simulations of large-scale systems. This allows for near-exact ground state energies of multi-reference clusters, [Cu2O2]2+ and [Fe2S2(SCH3)4]2−. We also describe implementations of free projection AFQMC, finite temperature AFQMC, AFQMC for electron–phonon systems, and automatic differentiation in AFQMC for calculating physical properties. These advancements position ipie as a leading platform for AFQMC research in quantum chemistry, facilitating more complex and ambitious computational method development and their applications. [ABSTRACT FROM AUTHOR]

Transport and dispersion of active particles in structured environments, such as corrugated channels and porous media, are important for the understanding of both natural and engineered active systems. Owing to their continuous self-propulsion, active particles exhibit rectified transport under spatially asymmetric confinement. While progress has been made in experiments and particle-based simulations, a theoretical understanding of the effective long-time transport dynamics in spatially periodic geometries remains less developed. In this paper, we apply generalized Taylor dispersion theory to analyze the long-time effective transport dynamics of active Brownian particles (ABPs) in periodic channels and fields. We show that the long-time transport behavior is governed by an effective advection–diffusion equation. The derived macrotransport equations allow us to characterize the average drift and effective dispersion coefficient. For the case of ABPs subject to a no-flux boundary condition at the channel wall, we show that regardless of activity, the average drift is given by the net diffusive flux along the channel. For ABPs, their activity is the driving mechanism that sustains a density gradient, which ultimately leads to rectified motion along the channel. Our continuum theory is validated against direct Brownian dynamics simulations of the Langevin equations governing the motion of each ABP. [ABSTRACT FROM AUTHOR]

The transformative impact of modern computational paradigms and technologies, such as high-performance computing (HPC), quantum computing, and cloud computing, has opened up profound new opportunities for scientific simulations. Scalable computational chemistry is one beneficiary of this technological progress. The main focus of this paper is on the performance of various quantum chemical formulations, ranging from low-order methods to high-accuracy approaches, implemented in different computational chemistry packages and libraries, such as NWChem, NWChemEx, Scalable Predictive Methods for Excitations and Correlated Phenomena, ExaChem, and Fermi–Löwdin orbital self-interaction correction on Azure Quantum Elements, Microsoft's cloud services platform for scientific discovery. We pay particular attention to the intricate workflows for performing complex chemistry simulations, associated data curation, and mechanisms for accuracy assessment, which is demonstrated with the Arrows automated workflow for high throughput simulations. Finally, we provide a perspective on the role of cloud computing in supporting the mission of leadership computational facilities. [ABSTRACT FROM AUTHOR]

A central paradigm of polymer physics states that chains in melts behave like random walks as intra- and interchain interactions effectively cancel each other out. Likewise, θ-chains, i.e., chains at the transition from a swollen coil to a globular phase, are also thought to behave like ideal chains, as attractive forces are counterbalanced by repulsive entropic contributions. While the simple mapping to an equivalent Kuhn chain works rather well in most scenarios with corrections to scaling, random walks do not accurately capture the topology and knots, particularly for flexible chains. In this paper, we demonstrate with Monte Carlo and molecular dynamics simulations that chains in polymer melts and θ-chains not only agree on a structural level for a range of stiffnesses but also topologically. They exhibit similar knotting probabilities and knot sizes, both of which are not captured by ideal chain representations. This discrepancy comes from the suppression of small knots in real chains, which is strongest for very flexible chains because excluded volume effects are still active locally and become weaker with increasing semiflexibility. Our findings suggest that corrections to ideal behavior are indeed similar for the two scenarios of real chains and that the structure and topology of a chain in a melt can be approximately reproduced by a corresponding θ-chain. [ABSTRACT FROM AUTHOR]