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Electronic spins provide an additional degree of freedom that can be used in modern spin-based electronic devices. Some benefits of spintronic devices include nonvolatility, energy efficiency, high endurance, and CMOS compatibility, which can be leveraged for data processing and storage applications in today's digital era. To implement such functionalities, controlling and manipulating electron spins is of prime interest. One of the efficient ways of achieving this in spintronics is to use the electric field to control electron spin or magnetism through the voltage-controlled magnetic anisotropy (VCMA) effect. VCMA avoids the movement of charges and significantly reduces the Ohmic loss. This article reviews VCMA-based spintronic devices for magnetic memory applications. First, we briefly discuss the VCMA effect and various mechanisms explaining its physical origin. We then mention various challenges in VCMA that impede it for practical VCMA-based magnetic memory. We review various techniques to address them, such as field-free switching operation, write error rate improvement, widening the operation window, enhancing the VCMA coefficient, and ensuring fast-read operation with low read disturbance. Finally, we draw conclusions outlining the future perspectives. [ABSTRACT FROM AUTHOR]

The use of cavities to impact molecular structure and dynamics has become popular. As cavities, in particular plasmonic nanocavities, are lossy and the lifetime of their modes can be very short, their lossy nature must be incorporated into the calculations. The Lindblad master equation is commonly considered an appropriate tool to describe this lossy nature. This approach requires the dynamics of the density operator and is thus substantially more costly than approaches employing the Schrödinger equation for the quantum wave function when several or many nuclear degrees of freedom are involved. In this work, we compare numerically the Lindblad and Schrödinger descriptions discussed in the literature for a molecular example where the cavity is pumped by a laser. The laser and cavity properties are varied over a range of parameters. It is found that the Schrödinger description adequately describes the dynamics of the polaritons and emission signal as long as the laser intensity is moderate and the pump time is not much longer than the lifetime of the cavity mode. Otherwise, it is demonstrated that the Schrödinger description gradually fails. We also show that the failure of the Schrödinger description can often be remedied by renormalizing the wave function at every step of time propagation. The results are discussed and analyzed. [ABSTRACT FROM AUTHOR]

We optimize the internuclear geometry and electronic structure of a model chiral system to achieve a maximal photoelectron circular dichroism (PECD) in its one-photon ionization by circularly polarized light. The electronic structure calculations are performed by the single center method, while the optimization is done using quantum alchemy employing a Taylor series expansion. Thereby, the effect of bond lengths and uncompensated charge distributions on the chiral response of the model is investigated theoretically in some detail. It is demonstrated that manipulating a chiral asymmetry of the ionic potential may enhance the dichroic parameter (i.e., the PECD) of the randomly oriented model system well beyond β1 = 25%. Furthermore, we demonstrate that quantum alchemy is applicable to PECD despite the unusually strong coupling of spatial and electronic degrees of freedom and discuss the relative impact of the individual degrees of freedom in this model system. We define the necessary conditions for the computational design of PECD for real (non-model) chiral molecules using our approach. [ABSTRACT FROM AUTHOR]

We present a general and practical theoretical framework to investigate how energy is dissipated in open quantum system dynamics. This is performed by quantifying the contributions of individual bath components to the overall dissipation of the system. The framework is based on the Nakajima–Zwanzig projection operator technique, which allows us to express the rate of energy dissipation into a specific bath degree of freedom by using traces of operator products. The approach captures system-bath interactions to all orders, but is based on second-order perturbation theory on the off-diagonal subsystem's couplings and a Markovian description of the bath. The usefulness of our theory is demonstrated by applying it to various models of open quantum systems involving harmonic oscillators or spin baths and connecting the outcomes to existing results such as our previously reported formula derived for locally coupled harmonic baths [Kim and Franco, J. Chem. Phys. 154, 084109 (2021)]. We also prove that the dissipation calculated by our theory rigorously satisfies thermodynamic principles such as energy conservation and detailed balance. Overall, the strategy can be used to develop the theory and simulation of dissipation pathways to interpret and engineer the dynamics of open quantum systems. [ABSTRACT FROM AUTHOR]

Microgels exhibit the ability to undergo reversible swelling in response to shifts in environmental factors that include variations in temperature, concentration, and pH. While several models have been put forward to elucidate specific aspects of microgel swelling and its impact on bulk behavior, a consistent theoretical description that chains throughout the microscopic degrees of freedom with suspension properties and deepens into the full implications of swelling remains a challenge yet to be met. In this work, we extend the mean-field swelling model of microgels from Denton and Tang [J. Chem. Phys. 145, 164901 (2016)] to include the finite extensibility of the polymer chains. The elastic contribution to swelling in the original work is formulated for Gaussian chains. By using the Langevin chain model, we modify this elastic contribution in order to account for finite extensibility effects, which become prominent for microgels containing highly charged polyelectrolytes and short polymer chains. We assess the performance of both elastic models, namely for Gaussian and Langevin chains, comparing against coarse-grained bead–spring simulations of ionic microgels with explicit electrostatic interactions. We examine the applicability scope of the models under a variation of parameters, such as ionization degree, microgel concentration, and salt concentration. The models are also tested against experimental results. This work broadens the applicability of the microgel swelling model toward a more realistic description, which brings advantages when describing the suspensions of nanogels and weak-polyelectrolyte micro-/nanogels. [ABSTRACT FROM AUTHOR]

In molecular dynamics simulations, dynamically consistent coarse-grained (CG) models commonly use stochastic thermostats to model friction and fluctuations that are lost in a CG description. While Markovian, i.e., time-local, formulations of such thermostats allow for an accurate representation of diffusivities/long-time dynamics, a correct description of the dynamics on all time scales generally requires non-Markovian, i.e., non-time-local, thermostats. These thermostats typically take the form of a Generalized Langevin Equation (GLE) determined by a memory kernel. In this work, we use a Markovian embedded formulation of a position-independent GLE thermostat acting independently on each CG degree of freedom. Extracting the memory kernel of this CG model from atomistic reference data requires several approximations. Therefore, this task is best understood as an inverse problem. While our recently proposed approximate Newton scheme allows for the iterative optimization of memory kernels (IOMK), Markovian embedding remained potentially error-prone and computationally expensive. In this work, we present an IOMK-Gauss–Newton scheme (IOMK-GN) based on IOMK that allows for the direct parameterization of a Markovian embedded model. [ABSTRACT FROM AUTHOR]

In this paper, we present a combined experimental and theoretical study that explored the initial sticking of water on cooled surfaces. Specifically, these ultra-high vacuum gas–surface scattering experiments utilized supersonic molecular beam techniques in conjunction with a cryogenically cooled highly oriented pyrolytic graphite crystal, giving control over incident kinematic conditions. The D2O translational energy spanning 300–750 meV, the relative D2O flux, and the incident angle could all be varied independently. Three different experimental measurements were made. One involved measuring the total amount of D2O scattering as a function of surface temperature to determine the onset of sticking under non-equilibrium gas–surface collision conditions. Another measurement used He specular scattering to assess structural and coverage information for the interface during D2O adsorption. Finally, we used time-of-flight (TOF) measurements of the scattered D2O to determine how energy is exchanged with the graphite surface at surface temperatures above and near the conditions needed for gaseous condensation. For comparison and elaboration of the roles that internal degrees of freedom play in this process, we also did similar TOF measurements using another mass 20 incident particle, atomic neon. Enriching this study are precise molecular dynamics simulations that elaborate on gas–surface energy transfer and the roles of molecular degrees of freedom in gas–surface collisional energy exchange processes. This study furthers our fundamental understanding of energy exchange and the onset of sticking and ultimately gaseous condensation for gas–surface encounters occurring under high-velocity flows. [ABSTRACT FROM AUTHOR]

Porous, stacked two-dimensional covalent organic frameworks (2D COFs) bearing semiconducting linkers can support directional charge transfer across adjacent layers of the COF. To better inform the current and possible future design rules for enhancing electron and hole transport in such materials, an understanding of how linker selection and functionalization affects interlayer electronic couplings is essential. We report electronic structure simulation and analysis of electronic couplings across adjacent linker units and to encapsulated species in functionalized electroactive 2D COFs. The detailed dependence of these electronic couplings on interlayer interactions is examined through scans along key interlayer degrees of freedom and through configurational sampling from equilibrium molecular dynamics on semiempirical potential energy surfaces. Beyond affirming the sensitivity of the electronic coupling to interlayer distance and orientation, these studies offer guidance toward linker functionalization strategies for enhancing charge carrier transport in electroactive 2D COFs. [ABSTRACT FROM AUTHOR]

A novel mixed quantum–classical approach to simulating nonadiabatic dynamics of molecules at metal surfaces is presented. The method combines the numerically exact hierarchical equations of motion approach for the quantum electronic degrees of freedom with Langevin dynamics for the classical degrees of freedom, namely, low-frequency vibrational modes within the molecule. The approach extends previous mixed quantum–classical methods based on Langevin equations to models containing strong electron–electron or quantum electronic–vibrational interactions, while maintaining a nonperturbative and non-Markovian treatment of the molecule–metal coupling. To demonstrate the approach, nonequilibrium transport observables are calculated for a molecular nanojunction containing strong interactions. [ABSTRACT FROM AUTHOR]

Deposition of Mo S 2 on Au(111) alters the electronic properties of Mo S 2 . In this study, we investigate the free-standing MoS 2 monolayer and the MoS 2 /Au(111) heterostructure, with and without strain, as well as defects of interest in memristive and neuromorphic applications. We focus on the so-called atomristor devices based on monolayer materials that achieve resistive switching characteristics with the adsorption and desorption of metal adatoms. Our study confirms that the formation of midgap states is the primary mechanism behind the resistive switching. Our results show that strain lowers the adsorption/desorption energies of Au+defect structures of interest, leading to more favorable switching energies, but simultaneously reduces the switching ratio between states of differing conductivities. The presence of the Au(111) substrate additionally introduces non-uniform amounts of strain and charge transfer to the MoS 2 monolayer. We propose that the induced strain contributes to the experimentally observed n - to p -type transition and Ohmic to Schottky transition in the MoS 2 monolayer. The charge transfer leads to a permanent polarization at the interface, which can be tuned by strain. Our study has important implications on the role of the electrode as being a source of the observed variability in memristive devices and as an additional degree of freedom for tuning the switching characteristics of the memristor device. [ABSTRACT FROM AUTHOR]

Two computational approaches for computing the rates of internal conversions in molecular systems where a large set of nuclear degrees of freedom plays a role are discussed and compared. One approach is based on the numerical solution of the time-dependent Schrödinger equation and allows us to include almost the whole set of vibrational coordinates, thanks to the employment of effective procedures for selecting those elements of the Hilbert space which play a significant role in dynamics. The other approach, based on the time-dependent perturbation theory and limited to the use of the harmonic approximation, allows us to include the whole Hilbert space spanned by the vibrational states of the system. The two approaches are applied to the photophysics of azulene, whose anti-Kasha behavior caused by anomalous internal conversion rates is well assessed. The calculated rates for the decays of the first two excited singlet states are in very good agreement with experimental data, indicating the reliability of both methodologies. [ABSTRACT FROM AUTHOR]

Coarse-grained (CG) molecular models greatly reduce the computational cost of simulations allowing for longer and larger simulations, but come with an artificially increased acceleration of the dynamics when compared to the parent atomistic (AA) simulation. This impedes their use for the quantitative study of dynamical properties. During coarse-graining, grouping several atoms into one CG bead not only reduces the number of degrees of freedom but also reduces the roughness on the molecular surfaces, leading to the acceleration of dynamics. The RoughMob approach [M. K. Meinel and F. Müller-Plathe, J. Phys. Chem. B 126(20), 3737–3747 (2022)] quantifies this change in geometry and correlates it to the acceleration by making use of four so-called roughness volumes. This method was developed using simple one-bead CG models of a set of hydrocarbon liquids. Potentials for pure components are derived by the structure-based iterative Boltzmann inversion. In this paper, we find that, for binary mixtures of simple hydrocarbons, it is sufficient to use simple averaging rules to calculate the roughness volumes in mixtures from the roughness volumes of pure components and add a correction term quadratic in the concentration without the need to perform any calculation on AA or CG trajectories of the mixtures themselves. The acceleration factors of binary diffusion coefficients and both self-diffusion coefficients show a large dependence on the overall acceleration of the system and can be predicted a priori without the need for any AA simulations within a percentage error margin, which is comparable to routine measurement accuracies. Only if a qualitatively accurate description of the concentration dependence of the binary diffusion coefficient is desired, very few additional simulations of the pure components and the equimolar mixture are required. [ABSTRACT FROM AUTHOR]

Enhanced sampling algorithms are indispensable when working with highly disconnected multimodal distributions. An important application of these is the conformational exploration of particular internal degrees of freedom of molecular systems. However, despite the existence of many commonly used enhanced sampling algorithms to explore these internal motions, they often rely on system-dependent parameters, which negatively impact efficiency and reproducibility. Here, we present fully adaptive simulated tempering (FAST), a variation of the irreversible simulated tempering algorithm, which continuously optimizes the number, parameters, and weights of intermediate distributions to achieve maximally fast traversal over a space defined by the change in a predefined thermodynamic control variable such as temperature or an alchemical smoothing parameter. This work builds on a number of previously published methods, such as sequential Monte Carlo, and introduces a novel parameter optimization procedure that can, in principle, be used in any expanded ensemble algorithms. This method is validated by being applied on a number of different molecular systems with high torsional kinetic barriers. We also consider two different soft-core potentials during the interpolation procedure and compare their performance. We conclude that FAST is a highly efficient algorithm, which improves simulation reproducibility and can be successfully used in a variety of settings with the same initial hyperparameters. [ABSTRACT FROM AUTHOR]

Among lattice configurations of densely packed hard ellipses, Monte Carlo simulations are used to identify the so-called parallel and diagonal lattices as the two favorable states. The free energies of these two states are computed for several system sizes employing the Einstein crystal method. An accurate calculation of the free energy difference between the two states reveals the parallel lattice as the state with the lowest free energy. The origin of the entropic difference between the two states is further elucidated by assessing the roles of the translational and rotational degrees of freedom. [ABSTRACT FROM AUTHOR]

Entangled two-photon absorption (ETPA) could form the basis of nonlinear quantum spectroscopy at very low photon fluxes, since, at sufficiently low photon fluxes, ETPA scales linearly with the photon flux. When different pairs start to overlap temporally, accidental coincidences are thought to give rise to a "classical" quadratic scaling that dominates the signal at large photon fluxes and, thus, recovers a supposedly classical regime, where any quantum advantage is thought to be lost. Here, we scrutinize this assumption and demonstrate that quantum-enhanced absorption cross sections can persist even for very large photon numbers. To this end, we use a minimal model for quantum light, which can interpolate continuously between the entangled pair and a high-photon-flux limit, to analytically derive ETPA cross sections and the intensity crossover regime. We investigate the interplay between spectral and spatial degrees of freedom and how linewidth broadening of the sample impacts the experimentally achievable enhancement. [ABSTRACT FROM AUTHOR]

Two-dimensional (2D) transition metal dichalcogenides have emerged as promising quantum functional blocks benefitting from their unique combination of spin, valley, and layer degrees of freedom, particularly for the tremendous flexibility of moiré superlattices formed by van der Waals stacking. These degrees of freedom coupled with the enhanced Coulomb interaction in 2D structures allow excitons to serve as on-chip information carriers. However, excitons are spatially circumscribed due to their low mobility and limited lifetime. One way to overcome these limitations is through the coupling of excitons with surface plasmon polaritons (SPPs), which facilitates an interaction between remote quantum states. Here, we showcase the successful coupling of SPPs with interlayer excitons in molybdenum diselenide/tungsten diselenide heterobilayers. Our results indicate that the valley polarization can be efficiently transferred to SPPs, enabling preservation of polarization information even after propagating tens of micrometers. [ABSTRACT FROM AUTHOR]

We evaluate depletion forces in molecular dynamics simulation of a binary mixture of spheres (depleted particles) and rods (depletant particles) for a wide range of densities for both species. This evaluation was carried out using a recently proposed least squares fitting algorithm. We found that the restriction of the rods' rotational degrees of freedom, when the distance between two spheres is less than the rods length, creates a shallow, and apparently linear, attractive force ramp. For intersphere distances smaller than the rods' diameter, a much stronger attractive force is found, and a large repulsive barrier appears between these aforementioned regimes, roughly at the distance of the rods' thickness. The evaluated forces are validated via a comparison of the pairwise correlation functions obtained from molecular dynamics simulation of a mono-disperse sphere fluid, using the evaluated effective forces, against the original (full system) pairwise correlation functions. Agreement is excellent. We also record the angular pairwise correlation function, using the P2(x) Legendre polynomial, and find that for high densities of both species, a local nematic ordering starts to appear. This nematic order may be a factor in the small differences found between original and effective pairwise correlation functions at high densities of rods. [ABSTRACT FROM AUTHOR]

The vibronic structure and nuclear dynamics in the first five excited singlet electronic states of bithiophene (2T) are investigated here. Specifically, considerations are given to comprehend the first two structureless and broad electronic absorption bands and the role of nonadiabatic coupling in the excited state relaxation mechanism of 2T in the gas phase. Associated potential energy surfaces (PESs) are established by constructing a model vibronic coupling Hamiltonian using 18 vibrational degrees of freedom and extensive ab initio electronic structure calculations. The topographies of these PESs are critically examined, and multiple conical intersections are established. The nuclear dynamics calculations are performed by propagating wave packets on the coupled electronic manifold. The present theoretical results are in good agreement with the experimental observations. It is found that strong nonadiabatic coupling between the S1–S4 and S1–S5 states along totally symmetric modes is predominantly responsible for the structureless and broad first absorption band, and overlapping S2, S3, S4, and S5 states form the second absorption band. Photorelaxation from the highly excited S5 to the lowest S1 state takes place through a cascade of diabatic population transfers among the S1–S4–S5 electronic manifold within the first ∼100 fs. Totally symmetric C=C stretching, C–S stretching, C–H wagging, ring puckering, and inter-ring bending modes collectively drive such relaxation dynamics. [ABSTRACT FROM AUTHOR]

We report high-level calculations of the excited states of [2,2]-paracyclophane (PCP), which was recently investigated experimentally by ultrafast pump–probe experiments on oriented single crystals [Haggag et al., ChemPhotoChem 6 e202200181 (2022)]. PCP, in which the orientation of the two benzene rings and their range of motion are constrained, serves as a model for studying benzene excimer formation. The character of the excimer state and the state responsible for the brightest transition are similar to those of the benzene dimer. The constrained structure of PCP allows one to focus on the most important degree of freedom, the inter-ring distance. The calculations explain the main features of the transient absorption spectral evolution. This brightest transition of the excimer is polarized along the inter-fragment axis. The absorption of the light polarized in the plane of the rings reveals the presence of other absorbing states of Rydberg character, with much weaker intensities. We also report new transient absorption data obtained by a broadband 8 fs pump, which time-resolve strong modulations of the excimer absorption. The combination of theory and experiment provides a detailed picture of the evolution of the electronic structure of the PCP excimer in the course of a single molecular vibration. [ABSTRACT FROM AUTHOR]

We report the nonlinear dielectric properties of three triple-perovskite ruthenates: Ba 3 CoRu 2 O 9 , Ba 3 BiRu 2 O 9 , and Sr 3 CaRu 2 O 9. These compounds exhibit notable correlations among their spin, charge, lattice, and polar degrees of freedom. Ba 3 CoRu 2 O 9 displays a pronounced frequency-dependent relaxation in χ 2 , 3 just above the magnetoelastic transition, occurring around 100 K, followed by an abrupt loss of polarization within the ordered phase. In Ba 3 BiRu 2 O 9 , we encounter the possibility of multiple coexisting relaxation behaviors, indicating a complex phase strongly influenced by the spin-gap opening at 175 K. Lastly, Sr 3 CaRu 2 O 9 displays anomalies with strong dispersion effects close to its magnetic transitions, indicating a robust coupling between magnetic and dipolar orders in the system. These measurements highlight the significance of higher-order (hyper-)susceptibilities in providing profound insight into the dynamics of a system, offering information otherwise inaccessible through the linear polarization response alone. [ABSTRACT FROM AUTHOR]

We introduce a generalized micro–macro Markov chain Monte Carlo (mM-MCMC) method with pseudo-marginal approximation to the free energy that is able to accelerate sampling of the microscopic Gibbs distributions when there is a time-scale separation between the macroscopic dynamics of a reaction coordinate and the remaining microscopic degrees of freedom. The mM-MCMC method attains this efficiency by iterating four steps: (i) propose a new value of the reaction coordinate, (ii) accept or reject the macroscopic sample, (iii) run a biased simulation that creates a microscopic molecular instance that lies close to the newly sampled macroscopic reaction coordinate value, and (iv) microscopic accept/reject step for the new microscopic sample. In the present paper, we eliminate the main computational bottleneck of earlier versions of this method: the necessity to have an accurate approximation of free energy. We show that the introduction of a pseudo-marginal approximation significantly reduces the computational cost of the microscopic accept/reject step while still providing unbiased samples. We illustrate the method's behavior on several molecular systems with low-dimensional reaction coordinates. [ABSTRACT FROM AUTHOR]

The light-harvesting excitonic properties of poly(phenylene ethynylene) (PPE) extended dendrimers (tree-like π-conjugated macromolecules) involve a directional cascade of local excitation energy transfer (EET) processes occurring from the "leaves" (shortest branches) to the "trunk" (longest branch), which can be viewed from a vibronic perspective as a sequence of internal conversions occurring among a connected graph of nonadiabatically coupled locally excited electronic states via conical intersections. The smallest PPE building block that is able to exhibit EET, the asymmetrically meta-substituted PPE oligomer with one acetylenic bond on one side and two parallel ones on the other side (hence, 2-ring and 3-ring para-substituted pseudo-fragments), is a prototype and the focus of the present work. From linear-response time-dependent density functional theory electronic-structure calculations of the molecule as regards its first two nonadiabatically coupled, optically active, singlet excited states, we built a (1 + 2)-state-8-dimensional vibronic-coupling Hamiltonian model for running subsequent multiconfiguration time-dependent Hartree wavepacket relaxations and propagations, yielding both steady-state absorption and emission spectra as well as real-time dynamics. The EET process from the shortest branch to the longest one occurs quite efficiently (about 80% quantum yield) within the first 25 fs after light excitation and is mediated vibrationally through acetylenic and quinoidal bond-stretching modes together with a particular role given to the central-ring anti-quinoidal rock-bending mode. Electronic and vibrational energy relaxations, together with redistributions of quantum populations and coherences, are interpreted herein through the lens of a nonadiabatic perspective, showing some interesting segregation among the foremost photoactive degrees of freedom as regards spectroscopy and reactivity. [ABSTRACT FROM AUTHOR]

We propose a quantum tomography (QT) approach to retrieve the temporally evolving reduced density matrix in electronic state basis, where the populations and coherence between the ground state and excited state are reconstructed from the ultrafast electron diffraction signal. In order to showcase the capability of the proposed QT approach, we simulate the nuclear wavepacket dynamics and ultrafast electron diffraction of photoexcited pyrrole molecules using the ab initio quantum chemical CASSCF method. From the simulated time-resolved diffraction data, we retrieve the evolving density matrix in a crude diabatic representation basis and reveal the symmetry of the excited pyrrole wavepacket. Our QT approach opens the route to make a quantum version of "molecular movie" that covers the electronic degree of freedom and equips ultrafast electron diffraction with the power to reveal the coherence between electronic states, relaxation, and dynamics of population transfer. [ABSTRACT FROM AUTHOR]

The observation that materials can change their properties when placed inside or near an optical resonator has sparked a fervid interest in understanding the effects of strong light–matter coupling on molecular dynamics, and several approaches have been proposed to extend the methods of computational chemistry into this regime. Whereas the majority of these approaches have focused on modeling a single molecule coupled to a single cavity mode, changes to chemistry have so far only been observed experimentally when very many molecules are coupled collectively to multiple modes with short lifetimes. While atomistic simulations of many molecules coupled to multiple cavity modes have been performed with semi-classical molecular dynamics, an explicit description of cavity losses has so far been restricted to simulations in which only a very few molecular degrees of freedom were considered. Here, we have implemented an effective non-Hermitian Hamiltonian to explicitly treat cavity losses in large-scale semi-classical molecular dynamics simulations of organic polaritons and used it to perform both mean-field and surface hopping simulations of polariton relaxation, propagation, and energy transfer. [ABSTRACT FROM AUTHOR]

The time-dependent relaxation of a dynamical system may exhibit a power-law behavior that is superimposed by log-periodic oscillations. D. Sornette [Phys. Rep. 297, 239 (1998)] showed that this behavior can be explained by a discrete scale invariance of the system, which is associated with discrete and equidistant timescales on a logarithmic scale. Examples include such diverse fields as financial crashes, random diffusion, and quantum topological materials. Recent time-resolved experiments and molecular dynamics simulations suggest that discrete scale invariance may also apply to hierarchical dynamics in proteins, where several fast local conformational changes are a prerequisite for a slow global transition to occur. Employing entropy-based timescale analysis and Markov state modeling to a simple one-dimensional hierarchical model and biomolecular simulation data, it is found that hierarchical systems quite generally give rise to logarithmically spaced discrete timescales. By introducing a one-dimensional reaction coordinate that collectively accounts for the hierarchically coupled degrees of freedom, the free energy landscape exhibits a characteristic staircase shape with two metastable end states, which causes the log-periodic time evolution of the system. The period of the log-oscillations reflects the effective roughness of the energy landscape and can, in simple cases, be interpreted in terms of the barriers of the staircase landscape. [ABSTRACT FROM AUTHOR]

We show that standard Ehrenfest dynamics does not conserve linear and angular momentum when using a basis of truncated adiabatic states. However, we also show that previously proposed effective Ehrenfest equations of motion [M. Amano and K. Takatsuka, "Quantum fluctuation of electronic wave-packet dynamics coupled with classical nuclear motions," J. Chem. Phys. 122, 084113 (2005) and V. Krishna, "Path integral formulation for quantum nonadiabatic dynamics and the mixed quantum classical limit," J. Chem. Phys. 126, 134107 (2007)] involving the non-Abelian Berry force do maintain momentum conservation. As a numerical example, we investigate the Kramers doublet of the methoxy radical using generalized Hartree–Fock with spin–orbit coupling and confirm that angular momentum is conserved with the proper equations of motion. Our work makes clear some of the limitations of the Born–Oppenheimer approximation when using ab initio electronic structure theory to treat systems with unpaired electronic spin degrees of freedom, and we demonstrate that Ehrenfest dynamics can offer much improved, qualitatively correct results. [ABSTRACT FROM AUTHOR]

We explore theoretically the effects of external potentials on the spatial distribution of particle properties in a liquid of explicitly responsive macromolecules. In particular, we focus on the bistable particle size as a coarse-grained internal degree of freedom (DoF, or "property"), σ, that moves in a bimodal energy landscape, in order to model the response of a state-switching (big-to-small) macromolecular liquid to external stimuli. We employ a mean-field density functional theory (DFT) that provides the full inhomogeneous equilibrium distributions of a one-component model system of responsive colloids (RCs) interacting with a Gaussian pair potential. For systems confined between two parallel hard walls, we observe and rationalize a significant localization of the big particle state close to the walls, with pressures described by an exact RC wall theorem. Application of more complex external potentials, such as linear (gravitational), osmotic, and Hamaker potentials, promotes even stronger particle size segregation, in which macromolecules of different size are localized in different spatial regions. Importantly, we demonstrate how the degree of responsiveness of the particle size and its coupling to the external potential tune the position-dependent size distribution. The DFT predictions are corroborated by Brownian dynamics simulations. Our study highlights the fact that particle responsiveness can be used to localize liquid properties and therefore helps to control the property- and position-dependent function of macromolecules, e.g., in biomedical applications. [ABSTRACT FROM AUTHOR]

Organic molecular solids can exhibit rich phase diagrams. In addition to structurally unique phases, translational and rotational degrees of freedom can melt at different state points, giving rise to partially disordered solid phases. The structural and dynamic disorder in these materials can have a significant impact on the physical properties of the organic solid, necessitating a thorough understanding of disorder at the atomic scale. When these disordered phases form at low temperatures, especially in crystals with light nuclei, the prediction of material properties can be complicated by the importance of nuclear quantum effects. As an example, we investigate nuclear quantum effects on the structure and dynamics of the orientationally disordered, translationally ordered plastic phase of the acetylene:ammonia (1:1) co-crystal that is expected to exist on the surface of Saturn's moon Titan. Titan's low surface temperature (∼90 K) suggests that the quantum mechanical behavior of nuclei may be important in this and other molecular solids in these environments. By using neural network potentials combined with ring polymer molecular dynamics simulations, we show that nuclear quantum effects increase orientational disorder and rotational dynamics within the acetylene:ammonia (1:1) co-crystal by weakening hydrogen bonds. Our results suggest that nuclear quantum effects are important to accurately model molecular solids and their physical properties in low-temperature environments. [ABSTRACT FROM AUTHOR]

We demonstrate that, for systems with spin–orbit coupling and an odd number of electrons, the standard fewest switches surface hopping algorithm does not conserve the total linear or angular momentum. This lack of conservation arises not so much from the hopping direction (which is easily adjusted) but more generally from propagating adiabatic dynamics along surfaces that are not time reversible. We show that one solution to this problem is to run along eigenvalues of phase-space electronic Hamiltonians H(R, P) (i.e., electronic Hamiltonians that depend on both nuclear position and momentum) with an electronic–nuclear coupling Γ · P [see Eq. (25)], and we delineate the conditions that must be satisfied by the operator Γ. The present results should be extremely useful as far as developing new semiclassical approaches that can treat systems where the nuclear, electronic orbital, and electronic spin degrees of freedom altogether are all coupled together, hopefully including systems displaying the chiral-induced spin selectivity effect. [ABSTRACT FROM AUTHOR]

The network structure within polymers significantly influences their mechanical properties, including their strength, toughness, and fatigue resistance. All-atom molecular dynamics (AAMD) simulations offer a method to investigate the energy dissipation mechanism within polymers during deformation and fracture; Such an approach is, however, computationally inefficient when used to analyze polymers with complex network structures, such as the common chemically double-networked hydrogels. Alternatively, coarse-grained molecular dynamics (CGMD) models, which reduce the computational degrees of freedom by concentrating a set of adjacent atoms into a coarse-grained bead, can be employed. In CGMD simulations, a coarse-grained force field (CGFF) is a critical factor affecting the simulation accuracy. In this paper, we proposed a data-based method for predicting the CGFF parameters to improve the simulation efficiency of complex cross-linked network in polymers. Here, we utilized a typical chemically double-networked hydrogel as an example. An artificial neural network was selected, and it was trained with the tensile stress–strain data from the CGMD simulations using different CGFF parameters. The CGMD simulations using the predicted CGFF parameters show good agreement with the AAMD simulations and are almost fifty times faster. The data-inspired CGMD model presented here broadens the applicability of molecular dynamics simulations to cross-linked polymers and has the potential to provide insights that will aid the design of polymers with desirable mechanical properties. [ABSTRACT FROM AUTHOR]

Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in a solution, where the molecule(s) and the solvent dynamics need to be integrated, rendering the simulations computationally costly and often unfeasible for physically/biologically relevant time scales. Standard coarse graining approaches can reproduce equilibrium distributions and structural features but do not properly include the dynamics. In this work, we develop a general data-driven coarse-graining methodology inspired by the Mori–Zwanzig formalism, which shows that macroscopic systems with a large number of degrees of freedom can be described by a few relevant variables and additional noise and memory terms. Our coarse-graining method consists of numerical integrators for the distinguished components, where the noise and interaction terms with other system components are substituted by a random variable sampled from a data-driven model. The model is parameterized using data from multiple short-time full-system simulations, and then, it is used to run long-time simulations. Applying our methodology to three systems—a distinguished particle under a harmonic and a bistable potential and a dimer with two metastable configurations—the resulting coarse-grained models are capable of reproducing not only the equilibrium distributions but also the dynamic behavior due to temporal correlations and memory effects. Remarkably, our method even reproduces the transition dynamics between metastable states, which is challenging to capture correctly. Our approach is not constrained to specific dynamics and can be extended to systems beyond Langevin dynamics, and, in principle, even to non-equilibrium dynamics. [ABSTRACT FROM AUTHOR]

Bottom-up methods for coarse-grained (CG) molecular modeling are critically needed to establish rigorous links between atomistic reference data and reduced molecular representations. For a target molecule, the ideal reduced CG representation is a function of both the conformational ensemble of the system and the target physical observable(s) to be reproduced at the CG resolution. However, there is an absence of algorithms for selecting CG representations of molecules from which complex properties, including molecular electronic structure, can be accurately modeled. We introduce continuously gated message passing (CGMP), a graph neural network (GNN) method for atomically decomposing molecular electronic structure sampled over conformational ensembles. CGMP integrates 3D-invariant GNNs and a novel gated message passing system to continuously reduce the atomic degrees of freedom accessible for electronic predictions, resulting in a one-shot importance ranking of atoms contributing to a target molecular property. Moreover, CGMP provides the first approach by which to quantify the degeneracy of "good" CG representations conditioned on specific prediction targets, facilitating the development of more transferable CG representations. We further show how CGMP can be used to highlight multiatom correlations, illuminating a path to developing CG electronic Hamiltonians in terms of interpretable collective variables for arbitrarily complex molecules. [ABSTRACT FROM AUTHOR]

Arising from the harmonic approximation in solving the vibrational Schrödinger equation, normal modes dissect molecular vibrations into distinct degrees of freedom. Normal modes are widely used as they give rise to descriptive vibrational notations and are convenient for expanding anharmonic potential energy surfaces as an alternative to higher-order Taylor series representations. Usually, normal modes are expressed in Cartesian coordinates, which bears drawbacks that can be overcome by switching to internal coordinates. Considering vibrational notations, normal modes with delocalized characters are difficult to denote, but internal coordinates offer a route to clearer notations. Based on the Hessian, normal mode decomposition schemes for a given set of internal coordinates can describe a normal mode by its contributions from internal coordinates. However, choosing a set of internal coordinates is not straightforward. While the Hessian provides unique sets of normal modes, various internal coordinate sets are possible for a given system. In the present work, we employ a normal mode decomposition scheme to choose an optimal set. Therefore, we screen reasonable sets based on topology and symmetry considerations and rely on a metric that minimizes coupling between internal coordinates. Ultimately, the Nomodeco toolkit presented here generates internal coordinate sets to find an optimal set for representing molecular vibrations. The resulting contribution tables can be used to clarify vibrational notations. We test our scheme on small to mid-sized molecules, showing how the space of definable internal coordinate sets can significantly be reduced. [ABSTRACT FROM AUTHOR]

Chemical and photochemical reactivity, as well as supramolecular organization and several other molecular properties, can be modified by strong interactions between light and matter. Theoretical studies of these phenomena require the separation of the Schrödinger equation into different degrees of freedom as in the Born–Oppenheimer approximation. In this paper, we analyze the electron–photon Hamiltonian within the cavity Born–Oppenheimer approximation (CBOA), where the electronic problem is solved for fixed nuclear positions and photonic parameters. In particular, we focus on intermolecular interactions in representative dimer complexes. The CBOA potential energy surfaces are compared with those obtained using a polaritonic approach, where the photonic and electronic degrees of freedom are treated at the same level. This allows us to assess the role of electron–photon correlation and the accuracy of CBOA. [ABSTRACT FROM AUTHOR]

We introduce a generalization of the σ-SCF method to approximate noncollinear spin ground and excited single-reference electronic states by minimizing the Hamiltonian variance. The new method is based on the σ-SCF method, originally proposed by Ye et al. [J. Chem. Phys. 147, 214104 (2017)], and provides a prescription to determine ground and excited noncollinear spin states on an equal footing. Our implementation was carried out utilizing an initial simulated annealing stage followed by a mean-field iterative self-consistent approach to simplify the cumbersome search introduced by generalizing the spin degrees of freedom. The simulated annealing stage ensures a broad exploration of the Hilbert space spanned by the generalized spin single-reference states with random complex element-wise rotations of the generalized density matrix elements in the simulated annealing stage. The mean-field iterative self-consistent stage employs an effective Fockian derived from the variance, which is utilized to converge tightly to the solutions. This process helps us to easily find complex spin structures, avoiding manipulating the initial guess. As proof-of-concept tests, we present results for Hn (n = 3–7) planar rings and polyhedral clusters with geometrical spin frustration. We show that most of these systems have noncollinear spin excited states that can be interpreted in terms of geometric spin frustration. These states are not directly targeted by energy minimization methods, which are meant to converge to the ground state. This stresses the capability of the σ-SCF methodology to find approximate noncollinear spin structures as mean-field excited states. [ABSTRACT FROM AUTHOR]

As the main merits, self-stabilization and no magnetic resistance make the high-temperature superconducting (HTS) magnetic levitation technology a crucial area for high-speed magnetic levitation development. To guarantee a stable operation of superconducting magnetic levitation systems, the dynamic characteristics of superconducting bulk materials occupy a significant place. However, in the previous research, there is still a lack of a simulation method that can describe 6 degree of freedom (DOF) motion of the superconductor. In this paper, an electromagnetic–thermal–dynamic coupling calculation model was established first. Then, the damping characteristics of 5-DOF superconducting levitation were experimentally tested, and the response analysis of the superconductor under 1–20 Hz excitation was carried out to explore the coupled motion relationship between the various degrees of freedom of the superconductor. In addition to the above, the operating conditions and primary resonance intervals that should be avoided by the HTS maglev system were identified. Additionally, a numerical simulation was conducted to investigate the dynamic response of the HTS maglev system under impact loads. All in all, this study explored the temperature rise conditions of superconducting bulk materials under excitation force through magnetic-thermal-force multi-physics coupling research. This 6-DOF model can provide a comprehensive simulation method for superconducting maglev systems in superconductor's motion behavior, attitude, and thermal state monitoring. [ABSTRACT FROM AUTHOR]

Charge-stabilized colloidal suspensions display a rich variety of microstructural and thermodynamic properties, which are determined by electro-steric interactions between all ionic species. The large size asymmetry between molecular-scale microions and colloidal macroions allows the microion degrees of freedom to be integrated out, leading to an effective one-component model of microion-dressed colloidal quasi-particles. For highly charged colloids with strong macroion–microion correlations, nonlinear effects can be incorporated into effective interactions by means of charge renormalization methods. Here, we compare and partially extend several practical mean-field methods of calculating renormalized colloidal interaction parameters, including effective charges and screening constants, as functions of concentration and ionic strength. Within the one-component description, we compute structural and thermodynamic properties from the effective interactions and assess the accuracy of the different methods by comparing predictions with elaborate primitive-model simulations [P. Linse, J. Chem. Phys. 113, 4359 (2000)]. We also compare various prescriptions for the osmotic pressure of suspensions in Donnan equilibrium with a salt ion reservoir and analyze instances where the macroion effective charge becomes larger than the bare one. The methods assessed include single-center cell, jellium, and multi-center mean-field theories. The strengths and weaknesses of the various methods are critically assessed, with the aim of guiding optimal and accurate implementations. [ABSTRACT FROM AUTHOR]

The computation of the nuclear quantum dynamics of molecules is challenging, requiring both accuracy and efficiency to be applicable to systems of interest. Recently, theories have been developed for employing time-dependent basis functions (denoted modals) with vibrational coupled cluster theory (TDMVCC). The TDMVCC method was introduced along with a pilot implementation, which illustrated good accuracy in benchmark computations. In this paper, we report an efficient implementation of TDMVCC, covering the case where the wave function and Hamiltonian contain up to two-mode couplings. After a careful regrouping of terms, the wave function can be propagated with a cubic computational scaling with respect to the number of degrees of freedom. We discuss the use of a restricted set of active one-mode basis functions for each mode, as well as two interesting limits: (i) the use of a full active basis where the variational modal determination amounts essentially to the variational determination of a time-dependent reference state for the cluster expansion; and (ii) the use of a single function as an active basis for some degrees of freedom. The latter case defines a hybrid TDMVCC/TDH (time-dependent Hartree) approach that can obtain even lower computational scaling. The resulting computational scaling for hybrid and full TDMVCC[2] is illustrated for polyaromatic hydrocarbons with up to 264 modes. Finally, computations on the internal vibrational redistribution of benzoic acid (39 modes) are used to show the faster convergence of TDMVCC/TDH hybrid computations towards TDMVCC compared to simple neglect of some degrees of freedom. [ABSTRACT FROM AUTHOR]

Site-selective probing of iodine 4d orbitals at 13.1 nm was used to characterize the photolysis of CH2I2 and CH2BrI initiated at 202.5 nm. Time-dependent fragment ion momenta were recorded using Coulomb explosion imaging mass spectrometry and used to determine the structural dynamics of the dissociating molecules. Correlations between these fragment momenta, as well as the onset times of electron transfer reactions between them, indicate that each molecule can undergo neutral three-body photolysis. For CH2I2, the structural evolution of the neutral molecule was simultaneously characterized along the C–I and I–C–I coordinates, demonstrating the sensitivity of these measurements to nuclear motion along multiple degrees of freedom. [ABSTRACT FROM AUTHOR]

For a system without spin–orbit coupling, the (i) nuclear plus electronic linear momentum and (ii) nuclear plus orbital electronic angular momentum are good quantum numbers. Thus, when a molecular system undergoes a nonadiabatic transition, there should be no change in the total linear or angular momentum. Now, the standard surface hopping algorithm ignores the electronic momentum and indirectly equates the momentum of the nuclear degrees of freedom to the total momentum. However, even with this simplification, the algorithm still does not conserve either the nuclear linear or the nuclear angular momenta. Here, we show that one way to address these failures is to dress the derivative couplings (i.e., the hopping directions) in two ways: (i) we disallow changes in the nuclear linear momentum by working in a translating basis (which is well known and leads to electron translation factors) and (ii) we disallow changes in the nuclear angular momentum by working in a basis that rotates around the center of mass [which is not well-known and leads to a novel, rotationally removable component of the derivative coupling that we will call electron rotation factors below, cf. Eq. (96)]. The present findings should be helpful in the short term as far as interpreting surface hopping calculations for singlet systems (without spin) and then developing the new surface hopping algorithm in the long term for systems where one cannot ignore the electronic orbital and/or spin angular momentum. [ABSTRACT FROM AUTHOR]

Micromagnetic simulations require the numerically challenging preservation of the Euclidean norm during the whole simulation. This can be accomplished by applying a priori length preserving methods, renormalization algorithms, or penalization strategies. The latter one includes both the penalty method and the Lagrangian multiplier. The penalty method requires the definition of a penalty parameter during the initiation of the simulation which, depending on its size, can lead to an unsatisfied constraint or stiff and difficult to solve systems of equations. The Lagrange multiplier always penalizes in problem-dependent intensity, hence, an additional degree of freedom is added to the system of equations to the drawback of higher computational costs. This paper proposes a method that utilizes a perturbed Lagrangian multiplier and an element level static condensation to condensate the additional degree of freedom. This guarantees fast simulations, and no parameter fitting in advance. Suitable numerical examples are conducted to prove the workability of the outlined scheme and to highlight the efficiency compared to the non-condensed formulation. [ABSTRACT FROM AUTHOR]

Metal–water interfaces are central to understanding aqueous-phase heterogeneous catalytic processes. However, the explicit modeling of the interface is still challenging as it necessitates extensive sampling of the interfaces' degrees of freedom. Herein, we use ab initio molecular dynamics (AIMD) simulations to study the adsorption of furfural, a platform biomass chemical on several catalytically relevant metal–water interfaces (Pt, Rh, Pd, Cu, and Au) at low coverages. We find that furfural adsorption is destabilized on all the metal–water interfaces compared to the metal–gas interfaces considered in this work. This destabilization is a result of the energetic penalty associated with the displacement of water molecules near the surface upon adsorption of furfural, further evidenced by a linear correlation between solvation energy and the change in surface water coverage. To predict solvation energies without the need for computationally expensive AIMD simulations, we demonstrate OH binding energy as a good descriptor to estimate the solvation energies of furfural. Using microkinetic modeling, we further explain the origin of the activity for furfural hydrogenation on intrinsically strong-binding metals under aqueous conditions, i.e., the endothermic solvation energies for furfural adsorption prevent surface poisoning. Our work sheds light on the development of active aqueous-phase catalytic systems via rationally tuning the solvation energies of reaction intermediates. [ABSTRACT FROM AUTHOR]

A non-slip constraint between a particle and a wall is applied at the microscopic level of collision dynamics using the rough sphere model. We analyze the consequences of the translation–rotation coupling of a rough sphere confined between two parallel planar walls and establish that shearing the walls past each other (i) preferentially deposits energy into the rotational degree of freedom and (ii) results in a bounded oscillation of the energy of the confined particle. [ABSTRACT FROM AUTHOR]

The computation of entropy in liquids and liquid crystal (LC) phases is a big challenge in statistical physics. In this work, we extend the two-phase thermodynamic model (2PT) to shape anisotropic soft repulsive spherocylinders (SRSs) and report the absolute values of entropy for different LC phases for a range of aspect ratios L/D = 2 − 5. We calculate the density of states for different LC phases and decompose it into contributions arising from translational and rotational degrees of freedom. The translational and rotational modes are further partitioned into diffusive, gas-like, and non-diffusive, solid-like components using a fluidicity factor. In the dilute limit, the entropy values obtained from the 2PT method match exactly those of an ideal rigid rotor. We find that, for a given packing fraction, the magnitude of the total entropy is roughly equal regardless of the different LC phases associated with different aspect ratios. We also compute the excess entropy (for L/D = 5) and compare those with the values obtained using the standard integration approach of MD or Monte Carlo equation of state of SRS. The values obtained using both approaches match very well. The rotational and translational fluidicity factors are further used to determine the phase boundaries of different LC phases. [ABSTRACT FROM AUTHOR]

Hydrogen atom scattering on metal surfaces is investigated based on a simplified Newns–Anderson model. Both the nuclear and electronic degrees of freedom are treated quantum mechanically. By partitioning all the surface electronic states as the bath, the hierarchical equations of motion method for the fermionic bath is employed to simulate the scattering dynamics. It is found that, with a reasonable set of parameters, the main features of the recent experimental studies of hydrogen atom scattering on metal surfaces can be reproduced. Vibrational states on the chemisorption state whose energies are close to the incident energy are found to play an important role, and the scattering process is dominated by a single-pass electronic transition forth and back between the diabatic physisorption and chemisorption states. Further study on the effects of the atom-surface coupling strength reveals that, upon increasing the atom-surface coupling strength, the scattering mechanism changes from typical nonadiabatic transitions to dynamics in the electronic friction regime. [ABSTRACT FROM AUTHOR]

Transport properties are essential for the understanding and modeling of electrochemical cells, in particular complex systems like lithium-ion batteries. In this study, we demonstrate how a certain degree of freedom in the choice of variables allows us to efficiently determine a complete set of transport properties. We apply the entropy production invariance condition to different sets of electrolyte variables and obtain a general set of formulas. We demonstrate the application of these formulas to an electrolyte typical for lithium-ion batteries, 1M lithium hexafluoro-phosphate in a 1:1 wt. % mixture of ethylene and diethyl carbonates. While simplifications can be introduced, they provide inadequate predictions of conductivity and transport numbers, and we argue that a full matrix of Onsager coefficients is needed for adequate property predictions. Our findings highlight the importance of a complete set of transport coefficients for accurate modeling of complex electrochemical systems and the need for careful consideration of the choice of variables used to determine these properties. [ABSTRACT FROM AUTHOR]

Electron transfer (ET) is a fundamental process in chemistry and biochemistry, and electronic coupling is an important determinant of the rate of ET. However, the electronic coupling is sensitive to many nuclear degrees of freedom, particularly those involved in intermolecular movements, making its characterization challenging. As a result, dynamic disorder in electron transfer coupling has rarely been investigated, hindering our understanding of charge transport dynamics in complex chemical and biological systems. In this work, we employed molecular dynamic simulations and machine-learning models to study dynamic disorder in the coupling of hole transfer between neighboring ethylene and naphthalene dimer. Our results reveal that low-frequency modes dominate these dynamics, resulting primarily from intermolecular movements such as rotation and translation. Interestingly, we observed an increasing contribution of translational motion as temperature increased. Moreover, we found that coupling is sub-Ohmic in its spectral density character, with cut-off frequencies in the range of 102 cm−1. Machine-learning models allow direct study of dynamics of electronic coupling in charge transport with sufficient ensemble trajectories, providing further new insights into charge transporting dynamics. [ABSTRACT FROM AUTHOR]

Determining collective variables (CVs) for conformational transitions is crucial to understanding their dynamics and targeting them in enhanced sampling simulations. Often, CVs are proposed based on intuition or prior knowledge of a system. However, the problem of systematically determining a proper reaction coordinate (RC) for a specific process in terms of a set of putative CVs can be achieved using committor analysis (CA). Identifying essential degrees of freedom that govern such transitions using CA remains elusive because of the high dimensionality of the conformational space. Various schemes exist to leverage the power of machine learning (ML) to extract an RC from CA. Here, we extend these studies and compare the ability of 17 different ML schemes to identify accurate RCs associated with conformational transitions. We tested these methods on an alanine dipeptide in vacuum and on a sarcosine dipeptoid in an implicit solvent. Our comparison revealed that the light gradient boosting machine method outperforms other methods. In order to extract key features from the models, we employed Shapley Additive exPlanations analysis and compared its interpretation with the "feature importance" approach. For the alanine dipeptide, our methodology identifies ϕ and θ dihedrals as essential degrees of freedom in the C7ax to C7eq transition. For the sarcosine dipeptoid system, the dihedrals ψ and ω are the most important for the cisαD to transαD transition. We further argue that analysis of the full dynamical pathway, and not just endpoint states, is essential for identifying key degrees of freedom governing transitions. [ABSTRACT FROM AUTHOR]

A theoretical framework is presented for the computation of the rovibrational polaritonic states of a molecule in a lossless infrared (IR) microcavity. In the proposed approach, the quantum treatment of the rotational and vibrational motions of the molecule can be formulated using arbitrary approximations. The cavity-induced changes in electronic structure are treated perturbatively, which allows using the existing polished tools of standard quantum chemistry for determining electronic molecular properties. As a case study, the rovibrational polaritons and related thermodynamic properties of H2O in an IR microcavity are computed for varying cavity parameters, applying various approximations to describe the molecular degrees of freedom. The self-dipole interaction is significant for nearly all light–matter coupling strengths investigated, and the molecular polarizability proved important for the correct qualitative behavior of the energy level shifts induced by the cavity. On the other hand, the magnitude of polarization remains small, justifying the perturbative approach for the cavity-induced changes in electronic structure. Comparing results obtained using a high-accuracy variational molecular model with those obtained utilizing the rigid rotor and harmonic oscillator approximations revealed that as long as the rovibrational model is appropriate for describing the field-free molecule, the computed rovibropolaritonic properties can be expected to be accurate as well. Strong light–matter coupling between the radiation mode of an IR cavity and the rovibrational states of H2O leads to minor changes in the thermodynamic properties of the system, and these changes seem to be dominated by non-resonant interactions between the quantum light and matter. [ABSTRACT FROM AUTHOR]

Understanding dynamics in complex systems is challenging because there are many degrees of freedom, and those that are most important for describing events of interest are often not obvious. The leading eigenfunctions of the transition operator are useful for visualization, and they can provide an efficient basis for computing statistics, such as the likelihood and average time of events (predictions). Here, we develop inexact iterative linear algebra methods for computing these eigenfunctions (spectral estimation) and making predictions from a dataset of short trajectories sampled at finite intervals. We demonstrate the methods on a low-dimensional model that facilitates visualization and a high-dimensional model of a biomolecular system. Implications for the prediction problem in reinforcement learning are discussed. [ABSTRACT FROM AUTHOR]