Wigner function approach to the quantum Brownian motion of a particle in a potential

Recent progress in our understanding of quantum effects on the Brownian motion in an external potential is reviewed. This problem is ubiquitous in physics and chemistry, particularly in the context of decay of metastable states, for example, the reversal of the magnetization of a single domain ferromagnetic particle, kinetics of a superconducting tunnelling junction, etc. Emphasis is laid on the establishment of master equations describing the diffusion process in phase space analogous to the classical Fokker-Planck equation. In particular, it is shown how Wigner's [E. P. Wigner, Phys. Rev., 1932, 40, 749] method of obtaining quantum corrections to the classical equilibrium Maxwell-Boltzmann distribution may be extended to the dissipative non-equilibrium dynamics governing the quantum Brownian motion in an external potential V(x), yielding a master equation for the Wigner distribution function W(x,p,t) in phase space (x,p). The explicit form of the master equation so obtained contains quantum correction terms up to o(h(4)) and in the classical limit, h --> 0, reduces to the classical Klein-Kramers equation. For a quantum oscillator, the method yields an evolution equation coinciding in all respects with that of Agarwal [G. S. Agarwal, Phys. Rev. A, 1971, 4, 739]. In the high dissipation limit, the master equation reduces to a semi-classical Smoluchowski equation describing non-inertial quantum diffusion in configuration space. The Wigner function formulation of quantum Brownian motion is further illustrated by finding quantum corrections to the Kramers escape rate, which, in appropriate limits, reduce to those yielded via quantum generalizations of reaction rate theory.     

A comparative study of the master equation approach and the discrete galerkin method for the simulation of free radical polymerization

The present article deals with the mathematical treatment of free radical polymerization reactions. As a typical example the synthesis of poly(methyl methacrylate) under realistic experimental conditions is investigated. Since the mathematical treatment of the kinetic rate equations raises severe numerical problems, alternative approaches are required. In this paper two of these methods, i.e. the discrete Galerkin method and the master equation approach, are compared. The discrete Galerkin method circumvents difficulties encountered by the direct integration of the kinetic rate equations but requires much a priori knowledge of the chemical reaction system. Within the framework of the master equation approach the polymerization reaction is regarded as a stochastic process. For the simulation of this stochastic process a modified algorithm is presented. The example of the polymerization of methyl methacrylate shows that the master equation approach is an efficient tool in the simulation of free radical polymerization reactions.     

Stochastic theory of direct simulation Monte Carlo method

A treatment of direct simulation Monte Carlo method as a Markov process with a master equation is given and the corresponding master equation is derived. A hierarchy of equations for the reduced probability distributions is derived from the master equation. An equation similar to the Boltzmann equation for single particle probability distribution is derived using assumption of molecular chaos. It is shown that starting from an uncorrelated state, the system remains uncorrelated always in the limit N→∞, where N is the number of particles. Simple applications of the formalism to direct simulation money games are given as examples to the formalism. The formalism is applied to the direct simulation of homogenous gases. It is shown that appropriately normalized single particle probability distribution satisfies the Boltzmann equation for simple gases and Wang Chang–Uhlenbeck equation for a mixture of molecular gases. As a consequence of this development we derive Birds no time counter algorithm. We extend the analysis to the inhomogeneous gases and define a new direct simulation algorithm for this case. We show that single particle probability distribution satisfies the Boltzmann equation in our algorithm in the limit N→∞, V _k →0, Δt→0 where V _k is the volume of kth cell. We also show that our algorithm and Bird’s algorithm approach each other in the limit N _k →∞ where N _k is the number of particles in the volume V _k .     

Stochastic simulation of catalytic surface reactions in the fast diffusion limit

The master equation of a lattice gas reaction tracks the probability of visiting all spatial configurations. The large number of unique spatial configurations on a lattice renders master equation simulations infeasible for even small lattices. In this work, a reduced master equation is derived for the probability distribution of the coverages in the infinite diffusion limit. This derivation justifies the widely used assumption that the adlayer is in equilibrium for the current coverages and temperature when all reactants are highly mobile. Given the reduced master equation, two novel and efficient simulation methods of lattice gas reactions in the infinite diffusion limit are derived. The first method involves solving the reduced master equation directly for small lattices, which is intractable in configuration space. The second method involves reducing the master equation further in the large lattice limit to a set of differential equations that tracks only the species coverages. Solution of the reduced master equation and differential equations requires information that can be obtained through short, diffusion-only kinetic Monte Carlo simulation runs at each coverage. These simulations need to be run only once because the data can be stored and used for simulations with any set of kinetic parameters, gas-phase concentrations, and initial conditions. An idealized CO oxidation reaction mechanism with strong lateral interactions is used as an example system for demonstrating the reduced master equation and deterministic simulation techniques.     

Recent developments in the kinetic theory of nucleation

A review of recent progress in the kinetics of nucleation is presented. In the conventional approach to the kinetic theory of nucleation, it is necessary to know the free energy of formation of a new-phase particle as a function of its independent variables at least for near-critical particles. Thus the conventional kinetic theory of nucleation is based on the thermodynamics of the process. The thermodynamics of nucleation can be examined by using various approaches, such as the capillarity approximation, density functional theory, and molecular simulation, each of which has its own advantages and drawbacks. Relatively recently a new approach to the kinetics of nucleation was proposed [Ruckenstein E, Nowakowski B. J Colloid Interface Sci 1990;137:583; Nowakowski B, Ruckenstein E. J Chem Phys 1991;94:8487], which is based on molecular interactions and does not employ the traditional thermodynamics, thus avoiding such a controversial notion as the surface tension of tiny clusters involved in nucleation. In the new kinetic theory the rate of emission of molecules by a new-phase particle is determined with the help of a mean first passage time analysis. This time is calculated by solving the single-molecule master equation for the probability distribution function of a surface layer molecule moving in a potential field created by the rest of the cluster. The new theory was developed for both liquid-to-solid and vapor-to-liquid phase transitions. In the former case the single-molecule master equation is the Fokker-Planck equation in the phase space which can be reduced to the Smoluchowski equation owing to the hierarchy of characteristic time scales. In the latter case, the starting master equation is a Fokker-Planck equation for the probability distribution function of a surface layer molecule with respect to both its energy and phase coordinates. Unlike the case of liquid-to-solid nucleation, this Fokker-Planck equation cannot be reduced to the Smoluchowski equation, but the hierarchy of time scales does allow one to reduce it to the Fokker-Plank equation in the energy space. The new theory provides an equation for the critical radius of a new-phase particle which in the limit of large clusters (low supersaturations) yields the Kelvin equation and hence an expression for the macroscopic surface tension. The theory was illustrated with numerical calculations for a molecular pair interaction potential combining the dispersive attraction with the hard-sphere repulsion. The results for the liquid-to-solid nucleation clearly show that at given supersaturation the nucleation rate depends on the cluster structure (for three cluster structures considered-amorphous, fcc, and icosahedral). For both the liquid-to-solid and vapor-to-liquid nucleation, the predictions of the theory are consistent with the results of classical nucleation theory (CNT) in the limit of large critical clusters (low supersaturations). For small critical clusters the new theory provides higher nucleation rates than CNT. This can be accounted for by the fact that CNT uses the macroscopic interfacial tension which presumably overpredicts the surface tension of small clusters, and hence underpredicts nucleation rates.     

Multiple‐Well,multiple‐path unimolecular reaction systems. I. MultiWell computer program suite

Unimolecular reaction systems in which multiple isomers undergo simultaneous reactions via multiple decomposition reactions and multiple isomerization reactions are of fundamental interest in chemical kinetics. The computer program suite described here can be used to treat such coupled systems, including the effects of collisional energy transfer (weak collisions). The program suite consists of MultiWell, which solves the internal energy master equation for complex unimolecular reactions systems; DenSum, which calculates sums and densities of states by an exact‐count method; MomInert, which calculates external principal moments of inertia and internal rotation reduced moments of inertia; and Thermo, which calculates equilibrium constants and other thermodynamics quantities. MultiWell utilizes a hybrid master equation approach, which performs like an energy‐grained master equation at low energies and a continuum master equation in the vibrational quasicontinuum. An adaptation of Gillespie's exact stochastic method is used for the solution. The codes are designed for ease of use. Details are presented of various methods for treating weak collisions with virtually any desired collision step‐size distribution and for utilizing RRKM theory for specific unimolecular rate constants. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 232–245, 2001     

Reducing a chemical master equation by invariant manifold methods

We study methods for reducing chemical master equations using the Michaelis-Menten mechanism as an example. The master equation consists of a set of linear ordinary differential equations whose variables are probabilities that the realizable states exist. For a master equation with s(0) initial substrate molecules and e(0) initial enzyme molecules, the manifold can be parametrized by s(0) of the probability variables. Fraser's functional iteration method is found to be difficult to use for master equations of high dimension. Building on the insights gained from Fraser's method, techniques are developed to produce s(0)-dimensional manifolds of larger systems directly from the eigenvectors. We also develop a simple, but surprisingly effective way to generate initial conditions for the reduced models.     

Generation of a library of particles having controlled sizes and shapes via the mechanical elongation of master templates

Herein we describe a versatile and readily scalable approach for the fabrication of particles with a variety of shapes and sizes from a single master template by augmenting the particle replication in nonwetting templates (PRINT) method with mechanical elongation. Repetition of the elongation steps in one direction leads to the fabrication of linear particles with high aspect ratio (AR), over 40 times greater than in the original master, while a range of particle shapes can be obtained by repeating the elongation procedure while changing the stretching direction, generating diamond, rectangular, curved parallelogram particles from a single cubic master.     

On equilibrium distributions and detailed balance relations in non-isothermal systems

The significance of the detailed balance principle and equilibrium solutions of the master equation is discussed from a thermodynamic point of view for isolated and isothermal systems. Starting from a master equation for all the time dependent degrees of freedom it is shown that the uniqueness of the equilibrium distribution as a stationary solution is ensured if the detailed rate constants are balanced with the aid of the distribution which maximizes the entropy subject to the thermodynamic constraints. This procedure should precede physical assumptions which simplify the original master equation, e.g. the assumption that rapidly relaxing modes can be described by canonical distribution functions.     

Wetting behavior of spherical nanoparticles at a vapor-liquid interface: a density functional theory study

The wetting behavior of spherical nanoparticles at a vapor-liquid interface is investigated by using density functional theory, and the line tension calculation method is modified by analyzing the total energy of the vapor-liquid-particle equilibrium. Compared with the direct measurement data from simulation, the results reveal that the thermodynamically consistent Young's equation for planar interfaces is still applicable for high curvature surfaces in predicting a wide range of contact angles. The effect of the line tension on the contact angle is further explored, showing that the contact angles given by the original and modified Young's equations are nearly the same within the region of 60° < θ < 120°. Whereas the effect is considerable when the contact angle deviates from the region. The wetting property of nanoparticles in terms of the fluid-particle interaction strength, particle size, and temperature is also discussed. It is found that, for a certain particle, a moderate fluid-particle interaction strength would keep the particle stable at the interface in a wide temperature range.     

Application of inverse iteration to 2-dimensional master equations

Recent developments in unimolecular theory have placed great emphasis on the role played by angular momentum in determining the details of the dependence of the rate coefficient on pressure and temperature. The natural way to investigate these dependencies is through the master equation formulation, where the rate coefficient is recovered as the eigenvalue of the smallest magnitude of the spatial operator. Except for very simple cases, the master equation must be solved with numerical methods. For the 2-dimensional master equation this leads to large sparse matrices and correspondingly lengthy computational times in order to determine the eigenvalue of the least magnitude. A reformulation of the problem in terms of a diffusion equation approximates the final matrix with a narrow banded matrix that can easily be factored using a variation of Gaussian elimination. The 2-dimensional master equation can then be solved with inverse iteration, which rapidly converges to the desired eigenpair. This method can be up to 10 times faster than conventional iterative algorithms for finding the desired eigenpair. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 :1004–1010, 1997     

Direct numerical simulation of electrokinetic translocation of a cylindrical particle through a nanopore using a Poisson-Boltzmann approach

Nanopore-based sensing of single molecules is based on a detectable change in the ionic current arising from the electrokinetic translocation of individual nanoparticles through a nanopore. In this study, we propose a continuum-based model to investigate the dynamic electrokinetic translocation of a cylindrical nanoparticle through a nanopore and the corresponding ionic current response. It is the first time to simultaneously solve the Poisson-Boltzmann equation for the ionic concentrations and the electric field contributed by the surface charges of the nanopore and the nanoparticle, the Laplace equation for the externally applied electric field, and the modified Stokes equations for the flow field using an arbitrary Lagrangian-Eulerian method. Current blockade due to the particle translocation is predicted when the electric double layers (EDLs) of the particle and the nanopore are not overlapped, which is in qualitative agreement with existing experimental observations. Effects due to the electric field intensity imposed, the EDL thickness, the nanopore's surface charge, the particle's initial orientation and lateral offset from the nanopore's centerline on the particle translocation including both translation and rotation, and the ionic current response are comprehensively investigated. Under a relatively low electric field imposed, the particle experiences a significant rotation and a lateral movement. However, the particle is aligned with its longest axis parallel to the local electric field very quickly due to the dielectrophoretic effect when the external electric field is relatively high.     

How to analyze the entropy and energy of interacting particles by simulating their stochastic disordering

The master equation describing single particle transitions is solved approximately, in terms of the population of “local states” for interacting particles. Without prior knowledge of forces this permits one to analyze the entropy, the partition function and hence the energy, of partially ordered particles, through a computer simulation of their disordering.     

Temperature dependence of hole growth kinetics in aluminum-phthalocyanine-tetrasulfonate in hyperquenched glassy water

The temperature (T) dependence of hole growth kinetics (HGK) data that span more than four decades of burn fluence are reported for aluminum-phthalocyanine tetrasulfonate (APT) in fresh and annealed hyperquenched glassy water (HGW) for temperatures between 5 and 20 K. The highly dispersive HGK data are modeled by using the "master" equation based on the two level system (TLS) model described in 2000 by Reinot and Small [J. Chem. Phys. 2000, 113, 10207]. We have demonstrated that thermal line broadening is not enough to account for temperature-dependent HGK for temperatures greater than 10 K. To overcome the discrepancy, the hole growth model must account for thermal hole filling (THF) processes. For the first time, the "master" equation used for HGK simulations is modified to take into account both the temperature dependence of the (single site) absorption spectrum and THF processes, effectively turning off those TLS which do not participate in the hole burning process at higher temperatures. A single set of parameters, some of which were determined directly from the hole spectra, was found to provide satisfactory fits to the HGK data for APT in fresh and annealed HGW for holes burned in the 679.7-676.9 nm range from the high to low energy sides of the Qx absorption band. Furthermore, we propose that HGK modeling at high burn fluences requires that the TLS model be further modified to take into account the existence of extrinsic multiple level systems.     

Rheological properties and particle behaviors of a non-dilute colloidal dispersion composed of ferromagnetic spherocylinder particles subjected to a simple shear flow (analysis by means of mean-field approximation)

We have investigated the rheological properties and the orientational distributions of particles of a non-dilute colloidal dispersion, which is composed of ferromagnetic spherocylinder particles, subject to a simple shear flow. The mean-field approximation is applied to take into account the interactions between spherocylinder particles. The basic equation of the orientational distribution function has been derived from the balance of the torques (including the term due to the mean field approximation) acting on the particle in an applied magnetic field; this is an integrodifferential equation. Then, the governing equation has been solved by means of the method of successive approximation and Galerkin's method. The results obtained here are summarized as follows. For the case of strong magnetic interactions between particles, the particle exhibits a sharp peak of the orientational distribution even for a weak applied magnetic field. In this case, the mean magnetic moment of the particle becomes large, which leads to strong interactions between the applied magnetic field and the particle. Thus, the particle tends to point to the magnetic filed direction under these situations. Also, in this case, a large increase in viscosity is obtained due to such a restriction concerning the particle orientation.     

How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?

The chemical Fokker-Planck equation and the corresponding chemical Langevin equation are commonly used approximations of the chemical master equation. These equations are derived from an uncontrolled, second-order truncation of the Kramers-Moyal expansion of the chemical master equation and hence their accuracy remains to be clarified. We use the system-size expansion to show that chemical Fokker-Planck estimates of the mean concentrations and of the variance of the concentration fluctuations about the mean are accurate to order Ω(-3∕2) for reaction systems which do not obey detailed balance and at least accurate to order Ω(-2) for systems obeying detailed balance, where Ω is the characteristic size of the system. Hence, the chemical Fokker-Planck equation turns out to be more accurate than the linear-noise approximation of the chemical master equation (the linear Fokker-Planck equation) which leads to mean concentration estimates accurate to order Ω(-1∕2) and variance estimates accurate to order Ω(-3∕2). This higher accuracy is particularly conspicuous for chemical systems realized in small volumes such as biochemical reactions inside cells. A formula is also obtained for the approximate size of the relative errors in the concentration and variance predictions of the chemical Fokker-Planck equation, where the relative error is defined as the difference between the predictions of the chemical Fokker-Planck equation and the master equation divided by the prediction of the master equation. For dimerization and enzyme-catalyzed reactions, the errors are typically less than few percent even when the steady-state is characterized by merely few tens of molecules.     

Computational aspects of master equation transformation in terms of moments

The master equation describing the temporal evolution of a gaseous system in contact with a heat bath can be transformed into a system of linear, constant-coefficient, first-order differential equations of moments of the population distribution. While it has the advantage that populations are obtained directly from observables (moments), this system of equations is not too well-conditioned and unless precautions are taken, unsurmountable numerical problems appear. These are principally associated with manipulations (inversion and taking the exponential of a matrix) involving slightly modified Vandermonde matrices whose elements span a very wide range of orders of magnitude. This article discusses ways to avoid these pitfalls which consist principally of a suitable matrix normalization.     

Simulating the proton transfer in gramicidin A by a sequential dynamical Monte Carlo method

The large interest in long-range proton transfer in biomolecules is triggered by its importance for many biochemical processes such as biological energy transduction and drug detoxification. Since long-range proton transfer occurs on a microsecond time scale, simulating this process on a molecular level is still a challenging task and not possible with standard simulation methods. In general, the dynamics of a reactive system can be described by a master equation. A natural way to describe long-range charge transfer in biomolecules is to decompose the process into elementary steps which are transitions between microstates. Each microstate has a defined protonation pattern. Although such a master equation can in principle be solved analytically, it is often too demanding to solve this equation because of the large number of microstates. In this paper, we describe a new method which solves the master equation by a sequential dynamical Monte Carlo algorithm. Starting from one microstate, the evolution of the system is simulated as a stochastic process. The energetic parameters required for these simulations are determined by continuum electrostatic calculations. We apply this method to simulate the proton transfer through gramicidin A, a transmembrane proton channel, in dependence on the applied membrane potential and the pH value of the solution. As elementary steps in our reaction, we consider proton uptake and release, proton transfer along a hydrogen bond, and rotations of water molecules that constitute a proton wire through the channel. A simulation of 8 mus length took about 5 min on an Intel Pentium 4 CPU with 3.2 GHz. We obtained good agreement with experimental data for the proton flux through gramicidin A over a wide range of pH values and membrane potentials. We find that proton desolvation as well as water rotations are equally important for the proton transfer through gramicidin A at physiological membrane potentials. Our method allows to simulate long-range charge transfer in biological systems at time scales, which are not accessible by other methods.     

Replication of a DNA microarray

A mechanical method for efficient replication of DNA microarrays is described. The approach consists of three steps. First, a master DNA microarray consisting of single-stranded DNA elements is exposed to a solution containing the biotin-functionalized complement of each array element. Following hybridization, a replica surface modified with streptavidin is brought into contact with the master. This results in linking of the biotin-functionalized complement with the replica surface. Next, the replica is separated from the master, and the complementary strands are transferred to the replica surface. The resulting complementary DNA microarray contains position-coded sequences that mirror the information contained on the master DNA microarray. Multiple replicas can be prepared from a single master, the replicas efficiently hybridize only their complement, and DNA not labeled with biotin is not transferred to the replica surface.