Lagrangian descriptors of driven chemical reaction manifolds

Using Lagrangian descriptors to calculate the Maslov index of periodic orbits

The Maslov index of a periodic orbit is an important piece in the semiclassical quantization of nonintegrable systems, while almost all existing techniques that lead to a rigorous calculation of this index are elaborate and mathematically demanding. In this paper, we describe a straightforward technique, for systems with two degrees of freedom, based on the Lagrangian descriptors. Our method is illustrated by applying it to the two-dimensional coupled quartic oscillator.

Lagrangian descriptors: The shearless curve and the shearless attractor

Hamiltonian systems with a nonmonotonic frequency profile are called nontwist. One of the key properties of such systems, depending on adjustable parameters, is the presence of a robust transport barrier in the phase space called the shearless curve, which becomes the equally robust shearless attractor when dissipation is introduced. We consider the standard nontwist map with and without dissipation. We derive analytical expressions for the Lagrangian descriptor (LD) for the unperturbed map and show how they are related to the rotation number profile. We show how the LDs can reconstruct finite segments of the invariant manifolds for the perturbed map. In the conservative case, we demonstrate how the LDs distinguish the chaotic seas from regular structures. The LDs also provide a remarkable tool to identify when the shearless curve is destroyed: we present a fractal boundary, in the parameter space, for the existence or not of the shearless torus. In the dissipative case, we show how the LDs can be used to localize point attractors and the shearless attractor and distinguish their basins of attraction.

Energy transport between heat baths with oscillating temperatures

Energy transport is a fundamental physical process that plays a prominent role in the function and performance of myriad systems and technologies. Recent experimental measurements have shown that subjecting a macroscale system to a time-periodic temperature gradient can increase thermal conductivity in comparison to a static temperature gradient. Here, we theoretically examine this mechanism in a nanoscale model by applying a stochastic Langevin framework to describe the energy transport properties of a particle connecting two heat baths with different temperatures, where the temperature difference between baths is oscillating in time. Analytical expressions for the energy flux of each heat bath and for the system itself are derived for the case of a free particle and a particle in a harmonic potential. We find that dynamical effects in the energy flux induced by temperature oscillations give rise to complex energy transport hysteresis effects. The presented results suggest that applying time-periodic temperature modulations is a potential route to control energy storage and release in molecular devices and nanosystems.

Quantifying chaos using Lagrangian descriptors

We present and validate simple and efficient methods to estimate the chaoticity of orbits in low-dimensional conservative dynamical systems, namely, autonomous Hamiltonian systems and area-preserving symplectic maps, from computations of Lagrangian descriptors (LDs) on short time scales. Two quantities are proposed for determining the chaotic or regular nature of orbits in a system's phase space, which are based on the values of the LDs of these orbits and of nearby ones: The difference and ratio of neighboring orbits' LDs. Using as generic test models the prototypical two degree of freedom Hénon-Heiles system and the two-dimensional standard map, we find that these indicators are able to correctly characterize the chaotic or regular nature of orbits to better than 90% agreement with results obtained by implementing the Smaller Alignment Index (SALI) method, which is a well-established chaos detection technique. Further investigating the performance of the two introduced quantities, we discuss the effects of the total integration time and of the spacing between the used neighboring orbits on the accuracy of the methods, finding that even typical short time, coarse-grid LD computations are sufficient to provide reliable quantification of the systems' chaotic component, using less CPU time than the SALI. In addition to quantifying chaos, the introduced indicators have the ability to reveal details about the systems' local and global chaotic phase space structure. Our findings clearly suggest that LDs can also be used to quantify and investigate chaos in continuous and discrete low-dimensional conservative dynamical systems.

Phase space geometry of isolated to condensed chemical reactions

The complexity of gas and condensed phase chemical reactions has generally been uncovered either approximately through transition state theories or exactly through (analytic or computational) integration of trajectories. These approaches can be improved by recognizing that the dynamics and associated geometric structures exist in phase space, ensuring that the propagator is symplectic as in velocity-Verlet integrators and by extending the space of dividing surfaces to optimize the rate variationally, respectively. The dividing surface can be analytically or variationally optimized in phase space, not just over configuration space, to obtain more accurate rates. Thus, a phase space perspective is of primary importance in creating a deeper understanding of the geometric structure of chemical reactions. A key contribution from dynamical systems theory is the generalization of the transition state (TS) in terms of the normally hyperbolic invariant manifold (NHIM) whose geometric phase-space structure persists under perturbation. The NHIM can be regarded as an anchor of a dividing surface in phase space and it gives rise to an exact non-recrossing TS theory rate in reactions that are dominated by a single bottleneck. Here, we review recent advances of phase space geometrical structures of particular relevance to chemical reactions in the condensed phase. We also provide conjectures on the promise of these techniques toward the design and control of chemical reactions.

Thermal decay rates of an activated complex in a driven model chemical reaction

Recent work has shown that in a nonthermal, multidimensional system, the trajectories in the activated complex possess different instantaneous and time-averaged reactant decay rates. Under dissipative dynamics, it is known that these trajectories, which are bound on the normally hyperbolic invariant manifold (NHIM), converge to a single trajectory over time. By subjecting these dissipative systems to thermal noise, we find fluctuations in the saddle-bound trajectories and their instantaneous decay rates. Averaging over these instantaneous rates results in the decay rate of the activated complex in a thermal system. We find that the temperature dependence of the activated complex decay in a thermal system can be linked to the distribution of the phase space resolved decay rates on the NHIM in the nondissipative case. By adjusting the external driving of the reaction, we show that it is possible to influence how the decay rate of the activated complex changes with rising temperature.

Detecting reactive islands in a system-bath model of isomerization

In this article, we study the conformational isomerization in a solvent using a system-bath model where the phase space structures relevant for the reaction dynamics are revealed. These phase space structures are an integral part of understanding the reaction mechanism, that is the pathways that reactive trajectories undertake, in the presence of a solvent. Our approach involves detecting the analogs of the reactive islands first discussed in the works by Davis, Marston, De Leon, Berne and coauthors in the system-bath model using Lagrangian descriptors. We first present the structure of the reactive islands for the two degrees of freedom system modelling isomerization in the absence of the bath using direct computation of cylindrical (tube) manifolds and verify the Lagrangian descriptor method for detecting the reactive islands. The hierarchy of the reactive islands as indicated in the recent work by Patra and Keshavamurthy is shown to be related to the temporal features in committor probabilities. Next, we investigate the influence of the solvent on the reactive islands that we previously revealed for the two degrees of freedom system and discuss the use of the Lagrangian descriptor in the high-dimensional phase space of the system-bath model.

Phase space analysis of the dynamics on a potential energy surface with an entrance channel and two potential wells

In this paper, we unveil the geometrical template of phase space structures that governs transport in a Hamiltonian system described by a potential energy surface with an entrance/exit channel and two wells separated by an index-1 saddle. For the analysis of the nonlinear dynamics mechanisms, we apply the method of Lagrangian descriptors, a trajectory-based scalar diagnostic tool that is capable of providing a detailed phase space tomography of the interplay between the invariant manifolds of the system. Our analysis reveals that the stable and unstable manifolds of the two families of unstable periodic orbits (UPOs) that exist in the regions of the wells are responsible for controlling access to the potential wells of the trajectories that enter the system through the entrance/exit channel. We demonstrate that the heteroclinic and homoclinic connections that arise in the system between the manifolds of the families of UPOs characterize the branching ratio, a relevant quantity used to measure product distributions in chemical reaction dynamics.

Finding normally hyperbolic invariant manifolds in two and three degrees of freedom with Hénon-Heiles-type potential

We present a method based on a Lagrangian descriptor for revealing the high-dimensional phase space structures that are of interest in nonlinear Hamiltonian systems with index-1 saddle. These phase space structures include a normally hyperbolic invariant manifold and its stable and unstable manifolds, which act as codimension-1 barriers to phase space transport. In this article, finding the invariant manifolds in high-dimensional phase space will constitute identifying coordinates on these invariant manifolds. The method of Lagrangian descriptor is demonstrated by applying to classical two and three degrees of freedom Hamiltonian systems which have implications for myriad applications in chemistry, engineering, and physics.

Effects of temperature and mass conservation on the typical chemical sequences of hydrogen oxidation

Macroscopic properties of reacting mixtures are necessary to design synthetic strategies, determine yield, and improve the energy and atom efficiency of many chemical processes. The set of time-ordered sequences of chemical species are one representation of the evolution from reactants to products. However, only a fraction of the possible sequences is typical, having the majority of the joint probability and characterizing the succession of chemical nonequilibrium states. Here, we extend a variational measure of typicality and apply it to atomistic simulations of a model for hydrogen oxidation over a range of temperatures. We demonstrate an information-theoretic methodology to identify typical sequences under the constraints of mass conservation. Including these constraints leads to an improved ability to learn the chemical sequence mechanism from experimentally accessible data. From these typical sequences, we show that two quantities defining the variational typical set of sequences-the joint entropy rate and the topological entropy rate-increase linearly with temperature. These results suggest that, away from explosion limits, data over a narrow range of thermodynamic parameters could be sufficient to extrapolate these typical features of combustion chemistry to other conditions.

Upside/Downside statistical mechanics of nonequilibrium Brownian motion. I. Distributions, moments, and correlation functions of a free particle

Statistical properties of Brownian motion that arise by analyzing, separately, trajectories over which the system energy increases (upside) or decreases (downside) with respect to a threshold energy level are derived. This selective analysis is applied to examine transport properties of a nonequilibrium Brownian process that is coupled to multiple thermal sources characterized by different temperatures. Distributions, moments, and correlation functions of a free particle that occur during upside and downside events are investigated for energy activation and energy relaxation processes and also for positive and negative energy fluctuations from the average energy. The presented results are sufficiently general and can be applied without modification to the standard Brownian motion. This article focuses on the mathematical basis of this selective analysis. In subsequent articles in this series, we apply this general formalism to processes in which heat transfer between thermal reservoirs is mediated by activated rate processes that take place in a system bridging them.

Nonexponential kinetics of ion pair dissociation in electrofreezing water

Temporally- or spatially-heterogeneous environments can participate in many kinetic processes, from chemical reactions and self-assembly to the forced dissociation of biomolecules. Here, we simulate the molecular dynamics of a model ion pair forced to dissociate in an explicit, aqueous solution. Triggering dissociation with an external electric field causes the surrounding water to electrofreeze and the ion pair population to decay nonexponentially. To further probe the role of the aqueous environment in the kinetics, we also simulate dissociation events under a purely mechanical force on the ion pair. In this case, regardless of whether the surrounding water is a liquid or already electrofrozen, the ion pair population decays exponentially with a well-defined rate constant that is specific to the medium and applied force. These simulation data, and the rate parameters we extract, suggest the disordered kinetics in an electrofreezing medium are a result of the comparable time scales of two concurrent processes, electrofreezing and dissociation.