Persistent effects of inertia on diffusion-influenced reactions: Theoretical methods and applications.

The Cattaneo-Vernotte model has been widely studied to take momentum relaxation into account in transport equations. Yet, the effect of reactions on the Cattaneo-Vernotte model has not been fully elucidated. At present, it is unclear how the current density associated with reactions can be expressed in the Cattaneo-Vernotte model. Herein, we derive a modified Cattaneo-Vernotte model by applying the projection operator method to the Fokker-Planck-Kramers equation with a reaction sink. The same modified Cattaneo-Vernotte model can be derived by a Grad procedure. We show that the inertial effect influences the reaction rate coefficient differently depending on whether the intrinsic reaction rate constant in the reaction sink term depends on the solute relative velocity or not. The momentum relaxation effect can be expressed by a modified Smoluchowski equation including a memory kernel using the Cattaneo-Vernotte model. When the intrinsic reaction rate constant is independent of the reactant velocity and is localized, the modified Smoluchowski equation should be generalized to include a reaction term without a memory kernel. When the intrinsic reaction rate constant depends on the relative velocity of reactants, an additional reaction term with a memory kernel is required because of competition between the current density associated with the reaction and the diffusive flux during momentum relaxation. The competition effect influences even the long-time reaction rate coefficient.

Inertial dynamic effects on diffusion-influenced reactions: Approach based on the diffusive Cattaneo system.

We investigate the inertial dynamic effects on the kinetics of diffusion-influenced reactions by solving the linear diffusive Cattaneo system with the reaction sink term. Previous analytical studies on the inertial dynamic effects were limited to the bulk recombination reaction with infinite intrinsic reactivity. In the present work, we investigate the combined effects of inertial dynamics and finite reactivity on both bulk and geminate recombination rates. We obtain explicit analytical expressions for the rates, which show that both bulk and geminate recombination rates are retarded appreciably at short times due to the inertial dynamics. In particular, we find a distinctive feature of the inertial dynamic effect on the survival probability of a geminate pair at short times, which can be manifested in experimental observations.

Interplay of reactive interference and crowding effects in the diffusion-influenced reaction kinetics.

We investigate the interplay of reactive interference and crowding effects in the irreversible diffusion-influenced bimolecular reactions of the type A+B→P+B by using the Brownian dynamics simulation method. It is known that the presence of nonreactive crowding agents retards the reaction rate when the volume fraction of the crowding agents is large enough. On the other hand, a high concentration of B is known to increase the reaction rate more than expected from the mass action law, although the B's may also act as crowders. Therefore, it would be interesting to see which effect dominates when the number density of B as well as the number density of the crowders increases. We will present an approximate theory that provides a reasonable account for the Brownian dynamics simulation results.

Green's function of the Smoluchowski equation with reaction sink: Application to geminate and bulk recombination reactions.

By applying a recently developed solution method for the Fredholm integral equation of the second kind, we obtain an expression for Green's function of the Smoluchowski equation with a reaction sink. The result is applied to obtain accurate analytical expressions for the time-dependent survival probability of a geminate reactant pair and the rate coefficient of the bulk recombination between reactants undergoing diffusive motions under strong Coulomb interactions. The effects of both repulsive and attractive interactions are considered, and the results are compared with the numerical results obtained by solving the equation for the survival probability and the nonequilibrium pair correlation function. It is shown that the solutions are accurate enough for most reasonable parameter values.

Transport dynamics of complex fluids.

Thermal motion in complex fluids is a complicated stochastic process but ubiquitously exhibits initial ballistic, intermediate subdiffusive, and long-time diffusive motion, unless interrupted. Despite its relevance to numerous dynamical processes of interest in modern science, a unified, quantitative understanding of thermal motion in complex fluids remains a challenging problem. Here, we present a transport equation and its solutions, which yield a unified quantitative explanation of the mean-square displacement (MSD), the non-Gaussian parameter (NGP), and the displacement distribution of complex fluids. In our approach, the environment-coupled diffusion kernel and its time correlation function (TCF) are the essential quantities that determine transport dynamics and characterize mobility fluctuation of complex fluids; their time profiles are directly extractable from a model-free analysis of the MSD and NGP or, with greater computational expense, from the two-point and four-point velocity autocorrelation functions. We construct a general, explicit model of the diffusion kernel, comprising one unbound-mode and multiple bound-mode components, which provides an excellent approximate description of transport dynamics of various complex fluidic systems such as supercooled water, colloidal beads diffusing on lipid tubes, and dense hard disk fluid. We also introduce the concepts of intrinsic disorder and extrinsic disorder that have distinct effects on transport dynamics and different dependencies on temperature and density. This work presents an unexplored direction for quantitative understanding of transport and transport-coupled processes in complex disordered media.

Time-dependent electron transfer rate between geminate ions with strong Coulomb interaction and distance-dependent reactivity.

Previous analytic expressions for the time-dependent rate of diffusion-influenced electron-transfer between geminate ions were obtained for the case when the reaction occurs at a contact separation. By applying a recently developed solution method for the Fredholm integral equation of the second kind, we obtain an accurate analytic expression for the time-dependent electron-transfer rate with the account of the distance-dependent reactivity. We also consider the dependence of the rate on the initial separation between the geminate ions. We check the accuracy of the solution against numerical results obtained by solving the equation for the survival probability. The solution is found to be accurate enough for most reasonable parameter values.

Efficient implementations of analytic energy gradient for mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT).

Analytic energy gradients of individual singlet and triplet states with respect to nuclear coordinates are derived and implemented for the collinear mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT), which eliminates the problematic spin-contamination of SF-TDDFT. Dimensional-transformation matrices for the singlet and triplet response spaces are introduced, simplifying the subsequent derivations. These matrices enable the general forms of MRSF-TDDFT equations to be similar to those of SF-TDDFT, suggesting that the computational overhead of singlet or triplet states for MRSF-TDDFT is nearly identical to that of SF-TDDFT. In test calculations, the new MRSF-TDDFT yields quite different optimized structures and energies as compared to SF-TDDFT. These differences turned out to mainly come from the spin-contamination of SF-TDDFT, which are largely cured by MRSF-TDDFT. In addition, it was demonstrated that the clear separation of singlet states from triplets dramatically simplifies the location of minimum energy conical intersection. As a result, it is clear that the MRSF-TDDFT has advantages over SF-TDDFT in terms of both accuracy and practicality. Therefore, it can be a preferred method, which is readily applied to other "black-box" type applications, such as the minimum-energy optimization, reaction path following, and molecular dynamics simulations.

New Method for Constant- NPT Molecular Dynamics.

The well-established molecular dynamics simulation methods for constant- NPT ensemble systems such as the Andersen-Nosé-Hoover method and their variants may alter the dynamic properties of the molecules under consideration, because their equations of motion are modified by the coupling with thermostat or barostat. To circumvent this artifact, we propose a new molecular dynamics simulation algorithm, by which only the molecules near the wall of the simulation box are coupled to the thermostat and barostat and the molecules of interest placed in the inner part of the simulation box remain intact. We test the efficiency of our algorithm in attaining the target temperature and pressure and the conformity of the calculated equilibrium and dynamic properties to those of a constant- NPT ensemble system.

Fast Overlap Evaluations for Nonadiabatic Molecular Dynamics Simulations: Applications to SF-TDDFT and TDDFT.

Fast overlap integral algorithms for the spin-flip time-dependent density functional theory (SF-TDDFT) and the linear response (LR)-TDDFT were proposed on the basis of determinant factorization (DF) and the truncated Leibnitz formula (TLF). These in turn allow efficient computation of nonadiabatic coupling terms (NACTs) in nonadiabatic molecular dynamics simulations. The TLF(0), TLF(1), and TLF(2) were proposed according to the truncation order. The DF and TLF(1) or TLF(2) provide a four order combined performance improvement to the conventional method without introducing additional errors in the finite difference approximation. On the other hand, the DF and TLF(0) provide a five orders performance improvement making it the most efficient algorithm for NACT calculations so far with errors slightly larger than those of the finite difference approximation. The same techniques can be also applicable to other determinantal wave functions.

Eliminating spin-contamination of spin-flip time dependent density functional theory within linear response formalism by the use of zeroth-order mixed-reference (MR) reduced density matrix.

The use of the mixed reference (MR) reduced density matrix, which combines reduced density matrices of the MS = +1 and -1 triplet-ground states, is proposed in the context of the collinear spin-flip-time-dependent density functional theory (SF-TDDFT) methodology. The time-dependent Kohn-Sham equation with the mixed state is solved by the use of spinor-like open-shell orbitals within the linear response formalism, which enables to generate additional configurations in the realm of TD-DFT. The resulting MR-SF-TDDFT computational scheme has several advantages before the conventional collinear SF-TDDFT. The spin-contamination of the response states of SF-TDDFT is nearly removed. This considerably simplifies the identification of the excited states, especially in the "black-box" type applications, such as the automatic geometry optimization, reaction path following, or molecular dynamics simulations. With the new methodology, the accuracy of the description of the excited states is improved as compared to the collinear SF-TDDFT. Several test examples, which include systems typified by strong non-dynamic correlation, orbital (near) degeneracy, and conical intersections, are given to illustrate the performance of the new method.

Effects of external electric field and anisotropic long-range reactivity on charge separation probability.

We consider the effects of external electric field and anisotropic long-range reactivity on the recombination dynamics of a geminate charge pair. A closed-form analytic expression for the ultimate separation probability of the pair is presented. In previous theories, analytic expressions for the separation probability were obtained only for the case where the recombination reaction can be assumed to occur at a contact separation. For this case, Noolandi and Hong obtained an exact solution, but their expression for the separation probability was too complicated to evaluate. Hence an approximate analytic expression proposed by Braun has been widely used. However, Braun's expression overestimates the separation probability when the electric field is large. In this work, we present an approximate analytic expression that is accurate enough for all parameter values. In addition, the expression is also applicable when the interaction between the geminate charge pair is described by screened Coulombic potential, and the recombination reaction has an anisotropic and long-range reactivity. We also provide the expression for the separation probability when the initial separation between the geminate charge pair is larger than the contact distance.

Concentration effects on the rates of irreversible diffusion-influenced reactions.

We formulate a new theory of the effects of like-particle interactions on the irreversible diffusion-influenced bimolecular reactions of the type A + B → P + B by considering the evolution equation of the triplet ABB number density field explicitly. The solution to the evolution equation is aided by a recently proposed method for solving the Fredholm integral equation of the second kind. We evaluate the theory by comparing its predictions with the results of extensive computer simulations. The present theory provides a reasonable explanation of the simulation results.

An accurate expression for the rates of diffusion-influenced bimolecular reactions with long-range reactivity.

By using the recently developed method for solving the Fredholm integral equations of the second kind, we derive a very accurate expression for the steady-state rate constant of diffusion-influenced bimolecular reactions involving long-range reactivity. We consider the general case in which the reactants interact via an arbitrary central potential and hydrodynamic interaction. The rate expression becomes exact in the two opposite limits of small and large reactivity, and also performs very well in the intermediate regime.

Internal Diffusion-Controlled Enzyme Reaction: The Acetylcholinesterase Kinetics.

Acetylcholinesterase is an enzyme with a very high turnover rate; it quenches the neurotransmitter, acetylcholine, at the synapse. We have investigated the kinetics of the enzyme reaction by calculating the diffusion rate of the substrate molecule along an active site channel inside the enzyme from atomic-level molecular dynamics simulations. In contrast to the previous works, we have found that the internal substrate diffusion is the determinant of the acetylcholinesterase kinetics in the low substrate concentration limit. Our estimate of the overall bimolecular reaction rate constant for the enzyme is in good agreement with the experimental data. In addition, the present calculation provides a reasonable explanation for the effects of the ionic strength of solution and the mutation of surface residues of the enzyme. The study suggests that internal diffusion of the substrate could be a key factor in understanding the kinetics of enzymes of similar characteristics.

Effects of the interaction potential and hydrodynamic interaction on the diffusion-influenced reaction rates.

Recently, we proposed an accurate analytic expression for the diffusive propagator of a pair of particles under a central interaction potential and hydrodynamic interaction, and derived the rate expressions for fully diffusion-controlled geminate and bimolecular reactions. In this work, we present a still more accurate propagator expression, and extend the theory to the partially diffusion-controlled cases with various types of interaction potentials, including the screened Coulomb potential and the potential of mean force due to solvation. We evaluate the accuracies of our theory and other competing theories against exact numerical results. It is shown that the improved rate expressions provide near exact results for most types of interaction potentials.

Zwanzig-Mori equation for the time-dependent pair distribution function.

We develop a microscopic theoretical framework for the time-dependent pair distribution function starting from the Liouville equation. An exact Zwanzig-Mori equation of motion for the time-dependent pair distribution function is derived based on the projection-operator formalism. It is demonstrated that, under the Markovian approximation, our equation reduces to the so-called telegraph equation that includes the potential of mean force acting between the pair particles. With the additional approximation neglecting the inertia term, our equation takes the form of Smoluchowski's equation, which has been previously introduced with intuitive arguments and shown to satisfactorily reproduce the simulation results of the particle-pair dynamics.

Communication: Propagator for diffusive dynamics of an interacting molecular pair.

We introduce a new method of solution for the Fredholm integral equations of the second kind. The method would be useful when the direct iterative approach leads to a divergent perturbation series solution. By using the method, we obtain an accurate expression of the propagator for diffusive dynamics of a pair of particles interacting via an arbitrary central potential and hydrodynamic interaction. We test the accuracy of the propagator expression by calculating the diffusion-controlled geminate and bimolecular reaction rates. It is shown that our propagator expression provides very accurate results for the whole time region.

Kinetics of collision-induced reactions between hard-sphere reactants.

We investigate the reaction kinetics of hard-sphere reactants that undergo reaction upon collision. When the reaction probability at a given collision is unity, the Noyes rate theory provides an exact expression of the rate coefficient. For the general case with the reaction probability less than unity, Noyes assumed that successive recollision times between a tagged pair of reactants are decorrelated. We show that with this renewal assumption, the rate theory of Wilemski and Fixman yields the same rate coefficient expression as the Noyes theory. To evaluate the validity of the renewal assumption, we carry out molecular dynamics simulations. Contrary to the usual expectation, we find that the renewal assumption works better at higher particle densities. The present study shows that the rate coefficient for collision-induced hard-sphere reactions can be estimated with great accuracy by using the first recollision time distribution alone, regardless of the magnitude of the reaction probability at a given collision.

A rigorous foundation of the diffusion-influenced bimolecular reaction kinetics.

We formulate a general theory of the diffusion-influenced kinetics of irreversible bimolecular reactions occurring in the low concentration limit. Starting from the classical Liouville equation for the reactants and explicit solvent molecules, a formally exact expression for the bimolecular reaction rate coefficient is derived; the structures of reactant molecules and the sink functions may be arbitrarily complicated. The present theoretical formulation shows clearly how the well-known Noyes and Wilemski-Fixman rate theories are related and can be improved in a systematic manner. The general properties of the rate coefficient such as the long-time behavior and the upper and the lower bounds are analyzed. When the reaction can occur at a range of distance, the non-Markovianity of repeated encounter events between a reactant pair becomes significant and either the Noyes theory or the Wilemski-Fixman theory fails. The present theory provides a practical method for calculating the rate expression for such reactions, which improves significantly on the Wilemski-Fixman theory.

Diffusion-influenced reactions involving a reactant with two active sites.

We consider the kinetics of diffusion-influenced reactions which involve a reactant species that can be modeled as a sphere with two reactive patches located on its surface at an arbitrary angular distance. An approximate analytic expression for the rate coefficient is derived based on the Wilemski-Fixman-Weiss decoupling approximation and a multivariable Padé approximation. The accuracy of the rate expression is evaluated against computer simulations as well as an exact analytic expression available for a special case. The present theory provides accurate estimates for the magnitude of diffusive interference effects between the two reactive patches. We also present an efficient Brownian dynamics method for calculating the time-dependent rate coefficient, which is applicable when the reactants involve multiple active sites.