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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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

An important class of methods for modeling dynamics in open quantum systems is based on the well-known influence functional (IF) approach to solving path-integral equations of motion. Within this paradigm, path-filtering schemes based on the removal of IF elements that fall below a certain threshold aim to reduce the effort needed to calculate and store the influence functional, making very challenging simulations possible. A filtering protocol of this type is considered acceptable as long as the simulation remains mathematically stable. This, however, does not guarantee that the approximated dynamics preserve the physics of the simulated process. In this paper, we explore the possibility of training Generative Flow Networks (GFlowNets) to produce filtering protocols while optimizing for mathematical stability and for physical accuracy. Trained using the trajectory balance objective, the model produces sets of paths to be added to a truncated initial set; it is rewarded if the combined set of paths gives rise to solutions in which the trace of the density matrix is conserved, the populations remain real, and the dynamics approach the exact reference. Using a simple two-level system coupled to a dissipative reservoir, we perform proof-of-concept simulations and demonstrate the elegant and surprising filtering solutions proposed by the GFlowNet., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

This paper investigates the dynamic behavior of EthylChlorophyllide A (EChlideA) molecules in a methanol solution confined within a 4 nm silica nanoslit, using molecular dynamics simulations over a duration of 1 ms. Three systems, containing 1, 2, and 4 solutes, were studied at 298 K. The results demonstrate that EChlideA molecules predominantly adsorb onto the silica surfaces, driven by specific interactions between chlorin ring's methyl group and the hydroxyl groups of the silica. This adsorption leads to stable binding, particularly in less crowded environments, as indicated by the potential of mean force analysis. Higher molecular concentrations, such as those with four EChlideA molecules, introduce variation in binding strength due to molecular aggregation and complex interactions. The orientation analysis reveals that the chlorin ring tends to align parallel to the surface, requiring rotational adjustments during surface diffusion. In addition, solvent coordination around the Mg ion remains consistent under bulk conditions, although with some variation in higher concentrations. This study also highlights a decrease in linear diffusion and an increase in rotational relaxation times for EChlideA molecules within the confined nanoslit, reflecting the influence of molecular concentration and arrangement on their dynamics. These findings provide valuable insights into the role of surface interactions, molecular orientation, and solvent coordination in confined environments, offering implications for the design of nanoscale systems., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The first-principles quantum chemical computations often scale as Nk (N = basis sets; k = 1-4 for linear scaling, Hartree-Fock or density functional theory methods), which makes the development of accurate pseudopotentials and efficient basis sets necessary ingredients in modeling of heavy elements such as lanthanides and actinides. Recently, we have developed 4f-in-core norm-conserving pseudopotentials and associated basis sets for the trivalent lanthanides [Lu et al., J. Chem. Theory Comput. 19, 82-96 (2023)]. In the present paper, we present a unified approach to optimize high-quality Gaussian basis sets for modeling and simulations of condensed-phase systems. The newly generated basis sets not only capture the low total energy and fairly reasonable condition number of overlap matrix of lanthanide-containing systems, but also exhibit good transferability and reproducibility. These advantages ensure the accuracy of the basis sets while avoiding linear dependency concern of atom-centered basis sets. The performance of the basis sets is further illustrated in lanthanide molecular and condensed-phase systems by using Gaussian-plane wave density functional approach of CP2K. These new basis sets can be of particular interest to model structurally complicated lanthanide molecules, clusters, solutions, and solid systems., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The Atomic, Molecular, and Optical Science (AMOS) Gateway is a comprehensive cyberinfrastructure for research and educational activities in computational AMO science. The B-Spline atomic R-Matrix (BSR) suite of programs is one of several computer programs currently available on the gateway. It is an excellent example of the gateway's potential to increase the scientific productivity of AMOS users. While the suite is available to be used in batch mode, its complexity does not make it well-suited to the approach taken in the gateway's default setup. The complexity originates from the need to execute many different computations and to construct generally complex workflows, requiring numerous input files that must be used in a specific sequence. The BSR graphical user interface described in this paper was developed to considerably simplify employing the BSR codes on the gateway, making BSR available to a large group of researchers and students interested in AMO science., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Action spectroscopies use a readout created by the action of light on the molecules or material rather than optical absorption. Ultrafast 2D photocurrent and 2D fluorescence spectroscopies are two such action spectroscopies. Despite their utility, multidimensional action spectroscopies suffer from a background created by incoherent population mixing. These backgrounds appear when the action of one molecule impacts that of another, creating a signal that mimics a fourth-order population response but is really just the convolution of two linear responses. The background created by incoherent mixing is often much larger than the desired foreground signals. In this paper, we describe the physical mechanisms that give rise to the incoherent signals, drawing Feynman paths for each. There are three variations of incoherent signals, differing by their pulse ordering. They all have the same phase dependence as the desired fourth-order population signals and so cannot be removed by standard phase cycling, but they do differ in their polarization responses and dephasing times. We propose, and implement, a spectrometer design that eliminates the background signals for isotropically oriented samples, leaving only the desired fourth-order 2D action spectra. Our spectrometer utilizes a TWINS interferometer and a pulse shaper interferometer, each driven with a different white-light source so that the pulse pairs within each interferometer are phase stable, but not between the two. The lack of phase stability between the two interferometers eliminates two of the three incoherent responses. The third incoherent response is eliminated with the polarization scheme ⟨0, π/2, π/4, π/4⟩. Our spectrometer also enables both 2D photocurrent and 2D white-light spectra to be collected simultaneously, thereby enabling a direct comparison between action and optical detection under identical conditions and at the exact same position on the sample. Using this spectrometer and photovoltaic devices made from thin films of semiconducting carbon nanotubes, we demonstrate 2D photocurrent spectra free of incoherent background., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The homogeneous electron gas is a system that has many applications in chemistry and physics. However, its infinite nature makes studies at the many-body level complicated due to long computational run times. Because it is size extensive, coupled cluster theory is capable of studying the homogeneous electron gas, but it still poses a large computational challenge as the time needed for precise calculations increases in a polynomial manner with the number of particles and single-particle states. Consequently, achieving convergence in energy calculations becomes challenging, if not prohibited, due to long computational run times and high computational resource requirements. This paper develops the sequential regression extrapolation (SRE) to predict the coupled cluster energies of the homogeneous electron gas in the complete basis limit using Bayesian ridge regression and many-body perturbation theory correlation energies to the second order to make predictions from calculations at truncated basis sizes. Using the SRE method, we were able to predict the coupled cluster double energies for the electron gas across a variety of values of N and rs, for a total of 70 predictions, with an average error of 5.20 × 10-4 hartree while saving 88.9 h of computational time. The SRE method can accurately extrapolate electron gas energies to the complete basis limit, saving both computational time and resources. Additionally, the SRE is a general method that can be applied to a variety of systems, many-body methods, and extrapolations., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In a well-known paper, Jeremy England derived a bound on the free energy dissipated by a self-replicating system [J. L. England, "Statistical physics of self-replication," J. Chem. Phys. 139, 121923 (2013)]. This bound is usually interpreted as a universal relationship that connects thermodynamic dissipation to replicator per-capita decay and growth rates. We argue from basic thermodynamic principles against this interpretation. In fact, we suggest that such a relationship cannot exist in principle, because it is impossible for a thermodynamically consistent replicator to undergo both per-capita growth and per-capita decay back into reactants. Instead, replicator may decay into separate waste products, but in that case, replication and decay are two independent physical processes, and there is no universal relationship that connects their thermodynamic and dynamical properties., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Designing coatings and films that can protect surfaces is important in a wide variety of applications from corrosion prevention to anti-fouling. These systems are challenging from a modeling perspective because they are invariably multicomponent, which quickly leads to an expansive design space. At a minimum, the system has a substrate, a film (often composed of a polymeric material), a ubiquitous carrier solvent, which may be either a vapor or liquid phase, and one or more contaminants. Each component has an impact on the effectiveness of coating. This paper focuses on films that are used as a barrier to surface contamination, but the results also extend to surface coatings that are designed to extract a low density species from the fluid phase as in liquid chromatography. A coarse-grained model is developed using Yukawa potentials that encompasses both repulsive and attractive interactions among the species. Classical density functional theory calculations are presented to show how contaminant adsorption is controlled by the molecular forces in the system. Two specific vectors through the parameter space are considered to address likely experimental manipulations that change either the solvent or the polymer in a system. We find that all the adsorption results can be unified by considering an appropriate combination of molecular parameters. As a result, these calculations provide a link between molecular interactions and film performance and may serve to guide the rational design of films., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The calculation of molecular excited states is critically important to decipher a plethora of molecular properties. In this paper, we develop an equation of motion formalism on top of a bi-exponentially parameterized ground state wavefunction toward the determination of excited states. While the ground state bi-exponential parameterization ensures an accurate description of the wavefunction through the inclusion of high-rank correlation effects, the excited state is parameterized by a novel linear response operator with an effective excitation rank beyond two. To treat the ground and excited states in the same footings, in addition to the conventional one- and two-body response operators, we introduced certain two-body "generalized" response operators with an effective excitation rank of one. We introduce a projective formulation for determining the perturbed amplitudes for the set of "generalized" operators. Our formulation entails a significantly small number of unknown parameters and is shown to be highly accurate compared to allied methods for several difficult chemical systems., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Heterojunction catalysts in the field of hydrogen evolution reaction (HER) from electrocatalytic water splitting have recently become a hot research topic. In this paper, we systematically calculated the HER catalytic performance of a MoS2/CoS2 heterojunction for the first time, considering the effect of edge sites regulation, strain and electric field. The results indicate that the MoS2/CoS2 heterojunction exhibits synergistic catalytic performance compared to MoS2 and CoS2, the HER catalytic activity of which can be improved by exposing more edge sites or regulating the S content on the edges, with an optimized ratio of 25%. Surprisingly, applying strain has a slight effect on the catalytic activity of the edge, however, an obvious effect on the basal plane. For example, applying 2% tensile strain on the MoS2/CoS2 heterojunction can improve the edge catalytic performance by 13%, and for the basal plane, this value can reach 92%. In this case, the catalytic performance of the basal plane is better than that of the edge with 2% and without strain. Since the basal plane accounts for the majority of the two-dimensional catalysts, the catalytic performance of the basal plane is generally much lower than that of the edge. This discovery is of great significance, which means by adjusting strain, the catalytic performance of the heterojunction catalyst is likely to be improved by orders of magnitude. Moreover, considering the actual experimental process, we also calculated the effect of the electric field and found that 0.7 V/Å electric field can enhance the HER catalytic activity of the MoS2/CoS2 heterojunction by 23%., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Liquid-liquid phase transitions hold a unique and profound significance within condensed matter physics. These transitions, while conceptually intriguing, often pose formidable computational challenges. However, recent advances in neural network (NN) potentials offer a promising avenue to effectively address these challenges. In this paper, we delve into the structural transitions of liquid CdTe, CdS, and their alloy systems using molecular dynamics simulations, harnessing the power of an NN potential named LaspNN. Our investigations encompass both pressure and temperature effects. Through our simulations, we uncover three primary liquid structures around melting points that emerge as pressure increases: tetrahedral, rock salt, and close-packed structures, which greatly resemble those of solid states. In the high-temperature regime, we observe the formation of Te chains and S dimers, providing a deeper understanding of the liquid's atomic arrangements. When examining CdSxTe1-x alloys, our findings indicate that a small substitution of S by Te atoms for S-rich alloys (x > 0.5) exhibits a structural transition much different from CdS, while a large substitution of Te by S atoms for Te-rich alloys (x < 0.5) barely exhibits a structural transition similar to CdTe. We construct a schematic diagram for liquid alloys that considers both temperature and pressure, providing a comprehensive overview of the alloy system's behavior. The local aggregation of Te atoms demonstrates a linear relationship with alloy composition x, whereas that of S atoms exhibits a nonlinear one, shedding light on the composition-dependent structural changes., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In this paper, we investigate the Feshbach resonances of high partial waves and the influence of spin-spin (S-S) interaction on ultracold scattering processes. Taking the Na23- Rb87 system as an example, we plot the variations of weakly bound state energy and elastic scattering cross section with magnetic field and with collision energy. We find that the number of splittings in high partial wave Feshbach resonances does not strictly conform to the expected l + 1 (l is rotational angular momentum), and the deviation is attributed to the influence of bound states in other channels coupled by S-S interaction. For different ml (the projection of l on the external magnetic field direction), the effects of S-S interaction lead to different scattering patterns in the incident channels. These results reveal the complex features of ultracold scattering processes in high partial waves caused by S-S interaction., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Strong light-matter coupling within an optical cavity leverages the collective interactions of molecules and confined electromagnetic fields, giving rise to the possibilities of modifying chemical reactivity and molecular properties. While collective optical responses, such as enhanced Rabi splitting, are often observed, the overall effect of the cavity on molecular systems remains ambiguous for a large number of molecules. In this paper, we investigate the non-adiabatic electron transfer process in electron donor-acceptor pairs influenced by collective excitation and local molecular dynamics. Using the timescale difference between reorganization and thermal fluctuations, we derive analytical formulas for the electron transfer rate constant and the polariton relaxation rate. These formulas apply to any number of molecules (N) and account for the collective effect as induced by cavity photon coupling. Our findings reveal a non-monotonic dependence of the rate constant on N, which can be understood by the interplay between electron transfer and polariton relaxation. As a result, the cavity-induced quantum yield increases linearly with N for small N (as predicted by a simple Dicke model) but shows a turnover and suppression for large N. We also interrelate the thermal bath frequency and the number of molecules, suggesting the optimal number for maximizing enhancement. The analysis provides an analytical insight for understanding the collective excitation of light and electron transfer, helping to predict the optimal condition for effective cavity-controlled chemical reactivity., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Understanding how external electric fields (EFs) impact the properties of aqueous molecules is crucial for various applications in chemistry, biology, and engineering. In this paper, we present a study utilizing molecular dynamics simulation to explore how direct-current (DC) and alternative-current (AC) EFs affect hydrophobic (n-triacontane) and hydrophilic (PEG-10) oligomer chains. Through a machine learning approach, we extract a 2-dimensional free energy (FE) landscape of these molecules, revealing that electric fields modulate the FE landscape to favor stretched configurations and enhance the alignment of the chain with the electric field. Our observations indicate that DC EFs have a more prominent impact on modulation compared to AC EFs and that EFs have a stronger effect on hydrophobic chains than on hydrophilic oligomers. We analyze the orientation of water dipole moments and hydrogen bonds, finding that EFs align water molecules and induce more directional hydrogen bond networks, forming 1D water structures. This favors the stretched configuration and alignment of the studied oligomers simultaneously, as it minimizes the disruption of 1D structures. This research deepens our understanding of the mechanisms by which electric fields modulate molecular properties and could guide the broader application of EFs to control other aqueous molecules, such as proteins or biomolecules., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The high resolution Rydberg absorption spectrum of 2-butyne C4H6 recorded previously at the SOLEIL synchrotron facility has been interpreted using multichannel quantum defect theory (MQDT). The calculations are based on the continuum scattering calculations of Xu et al., J. Chem. Phys. 136, 154303 (2012) and of Jacovella et al., J. Phys. Chem. A 119, 12339 (2015) pertaining to the dipole-allowed excited state symmetries in absorption from the ground state. In contrast to the traditional approach of calculating low-lying electronic states first and then attempting to extend the calculations to ever higher energy, here the analysis proceeds through the extension of these detailed calculations of the electronic continuum scattering down into the discrete region of the spectrum. The continuum reaction matrices and dipole transition moments are adapted to the discrete Rydberg region via the use of an energy-modified formulation of MQDT theory and associated energy dependences of the quantum defects. The analysis reproduces more than 40 Rydberg states from n ≈ 10 down to the 3d and 4s levels with an rms error of better than 20 cm-1. These belong to five Rydberg series with three different molecular symmetries. While the approach predicts many additional series, most of these are calculated and observed to carry only little oscillator strength. The analysis shows that the Rydberg spectrum is dominated by the excitation of an e″ symmetry electron of fδ and gπ type, in line with what previous studies of the above-threshold shape resonance of 2-butyne have shown. The present study is intended to serve as an example showing how first principles continuum calculations may be useful for the interpretation of highly bound discrete states in a range that poses problems for the standard ab initio techniques. The quantitative treatment of the dipole absorption cross sections is deferred to a future paper., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

This second paper in a series of two describes the chirped-pulse ice apparatus that permits the detection of buffer gas cooled molecules desorbed from an energetically processed ice using broadband mm-wave rotational spectroscopy. Here, we detail the lower ice stage developed to generate ices at 4 K, which can then undergo energetic processing via UV/VUV photons or high-energy electrons and which ultimately enter the gas phase via temperature-programmed desorption (TPD). Over the course of TPD, the lower ice stage is interfaced with a buffer gas cooling cell that allows for sensitive detection via chirped-pulse rotational spectroscopy in the 60-90 GHz regime. In addition to a detailed description of the ice component of this apparatus, we show proof-of-principle experiments demonstrating the detection of H2CO products formed through irradiation of neat methanol ices or 1:1 CO + CH4 mixed ices., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In this paper, we explored the resistivity behavior of Sb7Se3 thin films on flexible mica. The films maintained their resistance characteristics through various thicknesses and bending cycles. With increasing bends, resistivity and phase transition temperature of both amorphous and crystalline states rose, while the resistance drift coefficient gradually increased. Raman and near infrared experiments confirmed the internal structural changes and bandgap enhancement after bending. Transmission electron microscopy showed enhanced crystallization and uniform element distribution after annealing. Atomic force microscopy observed cracks, explaining the property changes. Additionally, we developed a flexible Sb7Se3 thin-film resistive device with swift reversibility (∼10 ns) regardless of bending, opening new avenues for flexible information storage., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Biphasic interfaces are complex but fascinating regimes that display a number of properties distinct from those of the bulk. The CO2-H2O interface, in particular, has been the subject of a number of studies on account of its importance for the carbon life cycle as well as carbon capture and sequestration schemes. Despite this attention, there remain a number of open questions on the nature of the CO2-H2O interface, particularly concerning the interfacial tension and phase behavior of CO2 at the interface. In this paper, we seek to address these ambiguities using ab initio-quality simulations. Harnessing the benefits of machine-learned potentials and enhanced statistical sampling methods, we present an ab initio-level description of the CO2-H2O interface. Interfacial tensions are predicted from 1 to 500 bars and found to be in close agreement with experiment at pressures for which experimental data are available. Structural analyses indicate the buildup of an adsorbed, saturated CO2 film forming at a low pressure (20 bars) with properties similar to those of the bulk liquid, but preferential perpendicular alignment with respect to the interface. The CO2 monolayer buildup coincides with a reduced structuring of water molecules close to the interface. This study highlights the predictive nature of machine-learned potentials for complex macroscopic properties of biphasic interfaces, and the mechanistic insight obtained into carbon dioxide aggregation at the water interface is of high relevance for geoscience, climate research, and materials science., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).)

In the study of stochastic systems, the committor function describes the probability that a system starting from an initial configuration x will reach a set B before a set A. This paper introduces an efficient and interpretable algorithm for approximating the committor, called the "fast committor machine" (FCM). The FCM uses simulated trajectory data to build a kernel-based model of the committor. The kernel function is constructed to emphasize low-dimensional subspaces that optimally describe the A to B transitions. The coefficients in the kernel model are determined using randomized linear algebra, leading to a runtime that scales linearly with the number of data points. In numerical experiments involving a triple-well potential and alanine dipeptide, the FCM yields higher accuracy and trains more quickly than a neural network with the same number of parameters. The FCM is also more interpretable than the neural net., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Motivated by the various applications of the trapping diffusion-influenced reaction theory in physics, chemistry, and biology, this paper deals with irreducible Cartesian tensor (ICT) technique within the scope of the generalized method of separation of variables (GMSV). We provide a survey from the basic concepts of the theory and highlight the distinctive features of our approach in contrast to similar techniques documented in the literature. The solution to the stationary diffusion equation under appropriate boundary conditions is represented as a series in terms of ICT. By means of proved translational addition theorem, we straightforwardly reduce the general boundary value diffusion problem for N spherical sinks to the corresponding resolving infinite set of linear algebraic equations with respect to the unknown tensor coefficients. These coefficients exhibit an explicit dependence on the arbitrary three-dimensional configurations of N sinks with different radii and surface reactivities. Our research contains all relevant mathematical details such as terminology, definitions, and geometrical structure, along with a step by step description of the GMSV algorithm with the ICT technique to solve the general diffusion boundary value problem within the scope of Smoluchowski's trapping model., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In this paper, an exact analytical solution is presented for achieving coherent population transfer and creating arbitrary coherent superposition states in a five-state chainwise system by a train of coincident pulses. We show that the solution of a five-state chainwise system can be reduced to an equivalent three-state Λ-type one with the simplest resonant coupling under the assumption of adiabatic elimination together with a requirement of the relation among the four coincident pulses. In this method, the four coincident pulses at each step all have the same time dependence, but with specific magnitudes. The results show that, by using a train of appropriately coincident pulses, this technique not only enables complete population transfer, but also creates any desired coherent superposition between the initial and final states, while the population in all intermediate states is effectively suppressed. Furthermore, this technique can also exhibit a one-way population transfer behavior. The results are of potential interest in applications where high-fidelity multi-state quantum control is essential, e.g., quantum information, atom optics, formation of ultracold molecules, cavity QED, nuclear coherent population transfer, and light transfer in waveguide arrays., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

CuGBasis is a free and open-source CUDA®/Python library for efficient computation of scalar, vector, and matrix quantities crucial for the post-processing of electronic structure calculations. CuGBasis integrates high-performance Graphical Processing Unit (GPU) computing with the ease and flexibility of Python programming, making it compatible with a vast ecosystem of libraries. We showcase its utility as a Python library and demonstrate its seamless interoperability with existing Python software to gain chemical insight from quantum chemistry calculations. Leveraging GPU-accelerated code, cuGBasis exhibits remarkable performance, making it highly applicable to larger systems or large databases. Our benchmarks reveal a 100-fold performance gain compared to alternative software packages, including serial/multi-threaded Central Processing Unit and GPU implementations. This paper outlines various features and computational strategies that lead to cuGBasis's enhanced performance, guiding developers of GPU-accelerated code., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The description of quantum transport in the strong system-reservoir coupling regime poses a significant theoretical and computational challenge that demands specialized tools for accurate analysis. RealTimeTransport is a new open-source C++ library that enables the computation of both stationary and transient transport observables for generic quantum systems connected to metallic reservoirs. It computes the Nakajima-Zwanzig memory kernels for both dynamics and transport in real-time, going beyond traditional expansions in the bare system-reservoir couplings. Currently, several methods are available as follows: (i) A renormalized perturbation theory in leading and next-to-leading order, which avoids the low-temperature breakdown that limits the traditional theory. (ii) Starting from this well-behaved reference solution, a two- and three-loop, self-consistent renormalization-group transformation of the memory kernels is implemented. This allows refined quantitative predictions even in the presence of many body resonances, such as the Kondo enhancement of cotunneling. This paper provides an overview of the theory, the architecture of RealTimeTransport, and practical demonstrations of the currently implemented methods. In particular, we analyze the stationary transport through a serial double quantum dot and showcase for the T = 0 interacting Anderson model the complete time-development of single-electron tunneling (SET), cotunneling-assisted SET, and inelastic cotunneling resonances throughout the entire gate-bias stability diagram. We discuss the range of applicability of the implemented methods and benchmark them against other advanced approaches., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).)

In this paper, we report a new algorithm for creating an adaptive basis set in the Multiconfigurational Ehrenfest (MCE) method, which is termed Full Cloning (FC), and test it together with the existing Multiple Cloning (MC) using the spin-boson model at zero-temperature as a benchmark. The zero-temperature spin-boson regime is a common hurdle in the development of methods that seek to model quantum dynamics. Two versions of MCE exist. We demonstrate that MC is vital for the convergence of MCE version 2 (MCEv2). The first version (MCEv1) converges much better than MCEv2, but FC improves its convergence in a few cases where it is hard to converge it with the help of a reasonably small size of the basis set., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

Forte is an open-source library specialized in multireference electronic structure theories for molecular systems and the rapid prototyping of new methods. This paper gives an overview of the capabilities of Forte, its software architecture, and examples of applications enabled by the methods it implements., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International (CC BY-NC-ND) license (https://creativecommons.org/licenses/by-nc-nd/4.0/).)

In this paper, we consider the problem of numerical investigation of the counting statistics for a class of one-dimensional systems. Importance sampling, the cornerstone technique usually implemented for such problems, critically hinges on selecting an appropriate biased distribution. While an exponential tilt in the observable stands as the conventional choice for various problems, its efficiency in the context of counting statistics may be significantly hindered by the genuine discreteness of the observable. To address this challenge, we propose an alternative strategy, which we call importance sampling with the local tilt. We demonstrate the efficiency of the proposed approach through the analysis of three prototypical examples: a set of independent Gaussian random variables, Dyson gas, and symmetric simple exclusion process with a steplike initial condition., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Quantum dynamics simulation and computational spectroscopy serve as indispensable tools for the theoretical understanding of various fundamental physical and chemical processes, ranging from charge transfer to photochemical reactions. When simulating realistic systems, the primary challenge stems from the overwhelming number of degrees of freedom and the pronounced many-body correlations. Here, we present Kylin-V, an innovative quantum dynamics package designed for accurate and efficient simulations of dynamics and spectroscopic properties of vibronic Hamiltonians for molecular systems and their aggregates. Kylin-V supports various quantum dynamics and computational spectroscopy methods, such as time-dependent density matrix renormalization group and our recently proposed single-site and hierarchical mapping approaches, as well as vibrational heat-bath configuration interaction. In this paper, we introduce the methodologies implemented in Kylin-V and illustrate their performances through a diverse collection of numerical examples., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In this work, we determine the dissociation line of the nitrogen (N2) hydrate by computer simulation using the TIP4P/Ice model for water and the TraPPE force field for N2. This work is the natural extension of Paper I, in which the dissociation temperature of the N2 hydrate has been obtained at 500, 1000, and 1500 bar [Algaba et al., J. Chem. Phys. 159, 224707 (2023)] using the solubility method and assuming single occupancy. We extend our previous study and determine the dissociation temperature of the N2 hydrate at different pressures, from 500 to 4500 bar, taking into account the single and double occupancy of the N2 molecules in the hydrate structure. We calculate the solubility of N2 in the aqueous solution as a function of temperature when it is in contact with a N2-rich liquid phase and when in contact with the hydrate phase with single and double occupancy via planar interfaces. Both curves intersect at a certain temperature that determines the dissociation temperature at a given pressure. We observe a negligible effect of occupancy on the dissociation temperature. Our findings are in very good agreement with the experimental data taken from the literature. We have also obtained the driving force for the nucleation of the hydrate as a function of temperature and occupancy at several pressures. As in the case of the dissociation line, the effect of occupancy on the driving force for nucleation is negligible. To the best of our knowledge, this is the first time that the effect of the occupancy on the driving force for nucleation of a hydrate that exhibits sII crystallographic structure is studied from computer simulation., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In this paper, we use nested tensor-train contractions to compute vibrational and ro-vibrational energy levels of molecules with five and six atoms. At each step, we fully exploit symmetry by using symmetry adapted basis functions obtained from an irreducible tensor method. Contracted basis functions are determined by diagonalizing reduced dimensional Hamiltonian matrices. The size of matrices of eigenvectors, used to account for coupling between groups of coordinates, is reduced by discarding rows and columns. The size of the matrices that must be diagonalized is thus substantially reduced, making it possible to use direct eigensolvers, even for molecules with five and six atoms. The symmetry-adapted contracted vibrational basis functions have been used to compute J = 0 energy levels of the CH3CN (C3v) and J > 0 levels of CH4., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique "fingerprint" of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. We demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Recently, Theophilou [J. Chem. Phys. 149, 074104 (2018)] proposed a peculiar version of the density functional theory by showing that the set of spherical averages of the density around the nuclei determines uniquely the external potential in atoms, molecules, and solids. Here, this novel theory is extended to individual excited states. The generalization is based on the method developed in the series of papers by Ayers, Levy, and Nagy [Phys. Rev. A 85, 042518 (2012)]. Generalized Hohenberg-Kohn theorems are proved to the set of spherically symmetric densities using constrained search. A universal variational functional for the sum of the kinetic and electron-electron repulsion energies is constructed. The functional is appropriate for the ground state and all bound excited states. Euler equations and Kohn-Sham equations for the set are derived. The Euler equations can be rewritten as Schrödinger-like equations for the square root of the radial densities, and the effective potentials in them can be expressed in terms of wave function expectation values. The Hartree plus exchange-correlation potentials can be given by the difference of the interacting and the non-interacting effective potentials., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

This paper explores the use of deoxyribonucleic acid (DNA) origami structures as nanorobot components. Investigating the functional properties of DNA origami structures can facilitate the fabrication of DNA origami-based nanorobots. The wireframe structure stands out as one of the most interesting DNA origami structures. Hence, the present study aims to employ these structures to create DNA origami nanoactuators. The research delves into the design of DNA origami structures with the aim of opening under specific temperature conditions. Short DNA strands (staples) are one of the crucial parts of DNA origami structures, and the appropriate design of these strands can lead to the creation of structures with different properties. Thus, the components of the DNA origami nanoactuator are tailored to enable intentional opening at specific temperatures while maintaining stability at lower temperatures. This structural modification showcases the functional property of the DNA origami structure. The engineered DNA origami nanoactuator holds potential applications in medicine. By carrying drugs under specific temperature conditions and releasing them under different temperature conditions, it can serve as a platform for smart drug delivery purposes., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Neural network interatomic potentials (NNPs) have recently proven to be powerful tools to accurately model complex molecular systems while bypassing the high numerical cost of ab initio molecular dynamics simulations. In recent years, numerous advances in model architectures as well as the development of hybrid models combining machine-learning (ML) with more traditional, physically motivated, force-field interactions have considerably increased the design space of ML potentials. In this paper, we present FeNNol, a new library for building, training, and running force-field-enhanced neural network potentials. It provides a flexible and modular system for building hybrid models, allowing us to easily combine state-of-the-art embeddings with ML-parameterized physical interaction terms without the need for explicit programming. Furthermore, FeNNol leverages the automatic differentiation and just-in-time compilation features of the Jax Python library to enable fast evaluation of NNPs, shrinking the performance gap between ML potentials and standard force-fields. This is demonstrated with the popular ANI-2x model reaching simulation speeds nearly on par with the AMOEBA polarizable force-field on commodity GPUs (graphics processing units). We hope that FeNNol will facilitate the development and application of new hybrid NNP architectures for a wide range of molecular simulation problems., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)