Solutions to the time-dependent,forced quantum oscillator equation in the coordinate representation

Time-dependent creation and annihilation operators are derived which are used to obtain exact solutions, in the coordinate representation, to the time-dependent, forced quantum oscillator equation. The solutions are used to obtain a general formula for the transition probabilities, valid for any time-dependent force.     

Exact quantum master equation via the calculus on path integrals

An exact quantum master equation formalism is constructed for the efficient evaluation of quantum non-Markovian dissipation beyond the weak system-bath interaction regime in the presence of time-dependent external field. A novel truncation scheme is further proposed and compared with other approaches to close the resulting hierarchically coupled equations of motion. The interplay between system-bath interaction strength, non-Markovian property, and required level of hierarchy is also demonstrated with the aid of simple spin-boson systems.     

Properties of the generalized master equation: Green's functions and probability density functions in the path representation

The Green's function for the master equation and the generalized master equation in path representation is an infinite sum over the length of path probability density functions (PDFs). In this paper, the properties of path PDFs are studied both qualitatively and quantitatively. The results are used in building efficient approximations for Green's function in 1D, and are relevant in modeling and in data analysis.     

Theory of multichromophoric coherent resonance energy transfer: a polaronic quantum master equation approach

The approach of second order time local quantum master equation in the polaron picture, which has been employed for a theory of coherent resonance energy transfer, is extended for general multichromophore systems. Explicit expressions for all the kernel and inhomogeneous terms are derived, which can be calculated by any standard numerical procedure. The theory is then applied to a model of donor-bridge-acceptor system moderately coupled to bosonic bath. The results are compared with those based on the theory of Fo?rster's resonance energy transfer. It is shown that coherently coupled multichromophores can speed up the transfer of energy substantially and in a way insensitive to the disorder.     

Revision of a multiparameter equation of state to improve the representation in the critical region: application to water

We have developed a crossover formalism for the thermodynamic surface of pure fluids, which can be applied to any multiparameter equation of state. This procedure has been used to incorporate scaling law behavior into a representation of the thermodynamic properties of water and steam developed by Pruss and Wagner (PW EOS) and adopted recently by the International Association for the Properties of Water and Steam. Our revision to this equation retains most of the functional form and coefficients of the PW EOS, but replaces two of the terms with a crossover representation of scaling law behavior. In order to develop this model, we first developed a new crossover formulation for steam in the critical region, and second, we have incorporated universal crossover functions into the original PW EOS. In the modified form, the PW equation of state reproduces the scaling laws down to dimensionless temperatures τ=10⁻⁷. Far from the critical point the equations practically coincide.     

Time autocorrelation function analysis of master equation and its application to atomic clusters

We derive the energy fluctuation Delta(2)E, and the time autocorrelation kappa(tau) and its Fourier transformation--the fluctuation spectra S(omega)--of the master-equation transition matrix. The contribution from each eigenmode of the transition matrix to these fluctuation quantities reveals the relevant importance of the individual mode in the relaxation processes. The time scales associated with these relaxation processes are determined by the corresponding eigenvalues. Unlike traditional time evolution analysis, the autocorrelation function and fluctuation spectra analysis does not involve an arbitrary initial population. It is also more suitable for analyzing the underlying dynamic, kinetic behavior near the equilibrium and the behavior of the long-time-scale rare events. We utilize our technique to analyze the solid-liquid phase coexistence of the 13-atom Morse cluster and the fcc-to-icosahedral structure transition of the 38-atom Lennard-Jones cluster. For the processes studied, the fluctuation spectra from the master equation simplify the analysis of the transition matrix, and the important relaxation modes are easily extracted.     

The Dirac equation in quantum chemistry: strategies to overcome the current computational problems

A perspective on the use of the relativistic Dirac equation in quantum chemistry is given. It is demonstrated that many of the computational problems that plague the current implementations of the different electronic structure methods can be overcome by utilizing the locality of the small component wave function and density. Possible applications of such new and more efficient formulations are discussed.     

Reaction of phenyl radicals with acetylene: quantum chemical investigation of the mechanism and master equation analysis of the kinetics

The mechanism of the C(6)H(5) + C(2)H(2) reaction has been investigated by various quantum chemical methods. Electrophilic addition to the CC triple bond is found to be the only important mode of phenyl radical attack on acetylene. The initially formed chemically activated C(6)H(5)C(2)H(2) adducts may follow several isomerization pathways in competition with collisional stabilization and H-elimination. Thermochemistry of various decomposition and isomerization channels is evaluated by the G2M method. For key intermediates, the following standard enthalpies of formation have been deduced from isodesmic reactions: 94.2 +/- 2.0 kcal/mol (C(6)H(5)CHCH), 86.4 +/- 2.0 kcal/mol (C(6)H(5)CCH(2)), and 95.5 +/- 1.8 kcal/ mol (o-C(6)H(4)C(2)H(3)). The accuracy of theoretical predictions was examined through extensive comparisons with available experimental and theoretical data. The kinetics and product branching of the C(6)H(5) + C(2)H(2) reaction have been evaluated by weak collision master equation/Rice-Ramsperger-Kassel-Marcus (RRKM) analysis of the truncated kinetic model including only kinetically important transformations of the isomeric C(8)H(7) radicals. Available experimental kinetic data can be quantitatively reproduced by calculation with a minor adjustment of the C(6)H(5) addition barrier from 3.7 to 4.1 kcal/mol. Our predicted total rate constant, k(R1) = (1.29 x 10(10))T(0.834) exp(-2320/T) cm(3) mol(-)(1) s(-)(1), is weakly dependent on P and corresponds to the phenylation process under combustion conditions (T > 1000 K).     

A master equation for S(q,ω) leading to the hydrodynamic regime for simple fluids

A master equation relating the coherent and incoherent dynamical structure factors S(q, ω) and S_S(q, ω) is introduced on the basis of physical arguments suggested by previous theories. It is shown that, once S_S(q, ω) and the first six moments of S(q, ω) are known, the resulting expression for S(q, ω) contains the correct hydrodynamic regime as well as the free particle behaviour. The relationships thus introduced between the transport coefficients and the molecular quantities are compared to the experimental data for liquid argon. Molecular dynamics data are also well reproduced.     

Quantum master equation method based on the broken-symmetry time-dependent density functional theory: application to dynamic polarizability of open-shell molecular systems

A novel method for the calculation of the dynamic polarizability (α) of open-shell molecular systems is developed based on the quantum master equation combined with the broken-symmetry (BS) time-dependent density functional theory within the Tamm-Dancoff approximation, referred to as the BS-DFTQME method. We investigate the dynamic α density distribution obtained from BS-DFTQME calculations in order to analyze the spatial contributions of electrons to the field-induced polarization and clarify the contributions of the frontier orbital pair to α and its density. To demonstrate the performance of this method, we examine the real part of dynamic α of singlet 1,3-dipole systems having a variety of diradical characters (y). The frequency dispersion of α, in particular in the resonant region, is shown to strongly depend on the exchange-correlation functional as well as on the diradical character. Under sufficiently off-resonant condition, the dynamic α is found to decrease with increasing y and/or the fraction of Hartree-Fock exchange in the exchange-correlation functional, which enhances the spin polarization, due to the decrease in the delocalization effects of π-diradical electrons in the frontier orbital pair. The BS-DFTQME method with the BHandHLYP exchange-correlation functional also turns out to semiquantitatively reproduce the α spectra calculated by a strongly correlated ab initio molecular orbital method, i.e., the spin-unrestricted coupled-cluster singles and doubles.     

Energy transfer in master equation simulations: A new approach

Collisional energy transfer plays a key role in recombination, unimolecular, and chemical activation reactions. For master equation simulations of such reaction systems, it is conventionally assumed that the rate constant for inelastic energy transfer collisions is independent of the excitation energy. However, numerical instabilities and nonphysical results are encountered when normalizing the collision step‐size distribution in the sparse density of states regime at low energies. It is argued here that the conventional assumption is not correct, and it is shown that the numerical problems and nonphysical results are eliminated by making a plausible assumption about the energy dependence of the rate coefficient for inelastic collisions. The new assumption produces a model that is more physically realistic for any reasonable choice of collision step‐size distribution, but more work remains to be done. The resulting numerical algorithm is stable and noniterative. Testing shows that overall accuracy in master equation simulations is better with this new approach than with the conventional one. This new approach is appropriate for all energy‐grained master equation formulations. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 748–763, 2009     

Exciton migration dynamics in a dendritic molecule: quantum master equation approach using ab initio molecular orbital configuration interaction method

We investigate the exciton migration dynamics in a dendritic molecular model composed of pi-conjugation linear-leg units (acetylenes and diacetylene) and a benzene ring (branching point) using the quantum master equation approach with the ab initio molecular orbital (MO) configuration interaction (CI) method. The efficient migration of exciton from short-length linear legs (acetylenes) to long-length linear leg (diacetylene) via a benzene ring is observed. As predicted in previous studies, the exciton (electron and hole) distributions are relatively well localized in each generation segmented by the meta-branching point (meta-substituted benzene ring) though the electron and hole distributions are delocalized and are somewhat spatially different from each other within each generation. It is found that the excitons localized in the generation composed of short linear legs occupy in higher-lying exciton states, while those in the generation composed of long linear legs do in lower-lying ones. These features suggest the decoupling of pi-conjugation at the meta-branching point. On the other hand, the relaxation effect between exciton states is found to be caused by the exciton-phonon coupling, in which the existence of common configurations (electron-hole pairs) in CI wave functions between adjacent exciton states (having primary distributions on short and long linear-leg regions, respectively) is important for the relaxation between their exciton states. This feature indicates the importance of partial penetration of pi-conjugation through the meta-substituted benzene ring in excited states for such exciton migration.     

Core molecule dependence of energy migration in phenylacetylene nanostar dendrimers: Ab initio molecular orbital-configuration interaction based quantum master equation study

The core molecule dependence of energy (exciton) migration in phenylacetylene nanostar dendrimers is investigated using the ab initio molecular orbital (MO)-configuration interaction based quantum master equation approach. We examine three kinds of core molecular species, i.e., benzene, anthracene, and pentacene, with different highest occupied MO-lowest unoccupied MO (HOMO-LUMO) gaps, which lead to different orbital interactions between the dendron parts and the core molecule. The nanostars bearing anthracene and pentacene cores are characterized by multistep exciton states with spatially well-segmented distributions: The exciton distributions of high-lying exciton states are spatially localized well in the periphery region, whereas those of low-lying exciton states are done in the core region. On the other hand, for the nanostar bearing benzene core, which also has multistep exciton states, the spatial exciton distributions of low-lying exciton states are delocalized over the dendron and the core regions. It is found that the former nanostars exhibit nearly complete exciton migration from the periphery to the core molecule in contrast to the latter one, in which significant exciton distribution remains in the dendron parts attached to the core after the exciton relaxation, although all these dendrimers exhibit fast exciton relaxation from the initially populated states. It is predicted from the analysis based on the MO correlation diagrams and the relative relaxation factor that the complete exciton migration to the core occurs not only when the HOMO-LUMO gap of the core molecule is nearly equal to that of the dendron parts attached to the core (anthracene case) but also when fairly smaller than that (pentacene case), whereas the complete migration is not achieved when the HOMO-LUMO gap of the core is larger than that of the dendron parts (benzene case). These results suggest that the fast and complete exciton migration of real dendrimers could be realized by adjusting the HOMO-LUMO gap of the core molecule to be smaller than that of dendron parts, although there exist more complicated relaxation processes as compared to simple dendritic aggregate models studied so far.     

Laguerre polynomial solutions to master equation for vibrational energy relaxation in gases

Collisional energy transfer between highly vibrationally excited molecules and a bath gas is considered as a stochastic process occurring in energy space. An exact solution to master equation for the conditional probability is given in terms of simple analytical formulas for weak and strong collisions. The strong collisions are shown to manifest themselves in the distribution pattern composed of maxima and minima in the energy dependence of conditional probability. This effect is explained in detail on physical grounds.     

Bistability in the chemical master equation for dual phosphorylation cycles

Dual phospho/dephosphorylation cycles, as well as covalent enzymatic-catalyzed modifications of substrates are widely diffused within cellular systems and are crucial for the control of complex responses such as learning, memory, and cellular fate determination. Despite the large body of deterministic studies and the increasing work aimed at elucidating the effect of noise in such systems, some aspects remain unclear. Here we study the stationary distribution provided by the two-dimensional chemical master equation for a well-known model of a two step phospho/dephosphorylation cycle using the quasi-steady state approximation of enzymatic kinetics. Our aim is to analyze the role of fluctuations and the molecules distribution properties in the transition to a bistable regime. When detailed balance conditions are satisfied it is possible to compute equilibrium distributions in a closed and explicit form. When detailed balance is not satisfied, the stationary non-equilibrium state is strongly influenced by the chemical fluxes. In the last case, we show how the external field derived from the generation and recombination transition rates, can be decomposed by the Helmholtz theorem, into a conservative and a rotational (irreversible) part. Moreover, this decomposition allows to compute the stationary distribution via a perturbative approach. For a finite number of molecules there exists diffusion dynamics in a macroscopic region of the state space where a relevant transition rate between the two critical points is observed. Further, the stationary distribution function can be approximated by the solution of a Fokker-Planck equation. We illustrate the theoretical results using several numerical simulations.     

Extended diffusion in a double well potential: Transition from classical to quantum regime

The transition between the classical and quantum regimes in the diffusion of a particle in a 2-4 double-well potential is treated via the strong collision model in the high-temperature limit. Both the classical and semiclassical position correlation functions, their spectra, and correlation times are evaluated using the memory function formalism. It is shown that even in the high temperature limit, marked classical-quantum transition effects appear in the observables when collisions are rare.     

The finite state projection algorithm for the solution of the chemical master equation

This article introduces the finite state projection (FSP) method for use in the stochastic analysis of chemically reacting systems. One can describe the chemical populations of such systems with probability density vectors that evolve according to a set of linear ordinary differential equations known as the chemical master equation (CME). Unlike Monte Carlo methods such as the stochastic simulation algorithm (SSA) or tau leaping, the FSP directly solves or approximates the solution of the CME. If the CME describes a system that has a finite number of distinct population vectors, the FSP method provides an exact analytical solution. When an infinite or extremely large number of population variations is possible, the state space can be truncated, and the FSP method provides a certificate of accuracy for how closely the truncated space approximation matches the true solution. The proposed FSP algorithm systematically increases the projection space in order to meet prespecified tolerance in the total probability density error. For any system in which a sufficiently accurate FSP exists, the FSP algorithm is shown to converge in a finite number of steps. The FSP is utilized to solve two examples taken from the field of systems biology, and comparisons are made between the FSP, the SSA, and tau leaping algorithms. In both examples, the FSP outperforms the SSA in terms of accuracy as well as computational efficiency. Furthermore, due to very small molecular counts in these particular examples, the FSP also performs far more effectively than tau leaping methods.