Kinetic theory of nucleation based on a first passage time analysis: improvement by the density-functional theory

A recent kinetic theory of nucleation [see, e.g., E. Ruckenstein and B. Nowakowski, J. Colloid Interface Sci. 137, 583 (1990)] is based on molecular interactions and avoids the traditional thermodynamics. The rate of emission of molecules from a cluster is found via a first passage time analysis. This time is calculated by solving the single-molecule master equation for the probability distribution function of a surface molecule located in the potential field created by the cluster. The liquid cluster was assumed to have sharp boundaries and uniform density. In the present paper, this assumption is removed by using the density-functional theory to find the density profiles. Thus, more accurate calculations of the potential field created by the cluster, its emission rate, and nucleation rate are obtained. The modified theory is illustrated by numerical calculations for a molecular pair interaction potential combining the dispersive attraction with the hard-sphere repulsion.     

Kinetic model for binary homogeneous nucleation in the H2O-H2SO4 system: comparison with experiments and classical theory of nucleation

A kinetic model to predict nucleation rates in the sulfuric acid-water system is presented. It allows calculating steady-state nucleation rates and the corresponding time lag, using a direct solution of a system of kinetic equations that describe the populations of sub- and near-critical clusters. This kinetic model takes into account cluster-cluster collisions and decay of clusters into smaller clusters. The model results are compared with some predictions obtained with the classical nucleation theory (CNT) and also with available measurement data obtained in smog chambers or flow tubes. It is shown that in the case of slow nucleation processes, the kinetic model and the CNT as used by Shugard et al. [J. Chem. Phys. 75, 5298 (1974)] give the same results. However, in the case of intensive nucleation, a large part of the nucleation flux is due to cluster-cluster collisions and the CNT underestimates the nucleation rates.     

Dynamical integration of a Markovian web: a first passage time approach

In this work we address the dynamics of Markovian systems by tracking the evolution of the probability distribution, utilizing mean first passage time theory to augment the set of states considered. The method is validated on a lattice system and is applied, in conjunction with landscape analysis (saddle point searches) and multidimensional transition-state theory, to an atomistic model of glassy atactic polystyrene, in order to follow its time evolution over more than ten orders of magnitude on the time scale, from less than 10(-15) up to 10(-5) s. Frequencies extracted from the eigenvalues of the rate constant matrix are in favorable agreement with experimental measurements of subglass relaxation transitions at 250 K.     

Water diffusion through a membrane protein channel: a first passage time approach

Water diffusion through OmpF, a porin in the outer membrane of Escherichia coli, is studied by molecular dynamics simulation. A first passage time approach allows characterizing the diffusive properties of a well-defined region of this channel. A carbon nanotube, which is considerably more homogeneous, serves as a model to validate the methodology. Here we find, in addition to the expected regular behavior, a gradient of the diffusion coefficient at the channel ends, witness of the transition from confinement in the channel to bulk behavior in the connected reservoirs. Moreover, we observe the effect of a kinetic boundary layer, which is the counterpart of the initial ballistic regime in a mean square displacement analysis. The overall diffusive behavior of water in OmpF shows remarkable similarity with that in a homogeneous channel. However, a small fraction of the water molecules appears to be trapped by the protein wall for considerable lengths of time. The distribution of trapping times exhibits a broad power law distribution psi(tau) approximately tau (-2.4), up to tau=10 ns, a bound set by the length of the simulation run. We discuss the effect of this distribution on the dynamic properties of water in OmpF in terms of incomplete sampling of phase space.     

Calculation of the mean first passage time tested on simple two-dimensional models

A particle diffusing in a two-dimensional (2D) container, shaped as a simplified configuration space of two passing 2D circular particles in a flat channel, is considered. The mean first passage time through one absorbing boundary is calculated using the one-dimensional Fick-Jacobs equation and its modification; both derived by mapping the 2D diffusion equation onto the longitudinal ("reaction") coordinate. The obtained results are compared with the hopping time, defined as the inverted lowest eigenvalue of the full 2D problem. The comparison shows that the mapped equations give reliable results, in contrast to predictions of the simplest concept of the transition state theory.     

Multicomponent dynamical nucleation theory and sensitivity analysis

Vapor to liquid multicomponent nucleation is a dynamical process governed by a delicate interplay between condensation and evaporation. Since the population of the vapor phase is dominated by monomers at reasonable supersaturations, the formation of clusters is governed by monomer association and dissociation reactions. Although there is no intrinsic barrier in the interaction potential along the minimum energy path for the association process, the formation of a cluster is impeded by a free energy barrier. Dynamical nucleation theory provides a framework in which equilibrium evaporation rate constants can be calculated and the corresponding condensation rate constants determined from detailed balance. The nucleation rate can then be obtained by solving the kinetic equations. The rate constants governing the multistep kinetics of multicomponent nucleation including sensitivity analysis and the potential influence of contaminants will be presented and discussed.     

Mean first passage time for the contact between the ends of a chain polymer

We investigate the first passage times for the contact between the ends of a Rouse chain, whose initial separation is greater than a predefined contact distance, sigma, and equilibrium-distributed. An approximate analytic expression for the mean first passage time is obtained and compared with the results of previous theories and Brownian dynamics simulations. We find that the results of the present theory are in better agreement with Brownian dynamics simulation results than those of previously reported theories.     

Kinetic theory of heterogeneous nucleation; effect of nonuniform density in the nuclei

The heterogeneous nucleation of a liquid from a vapor in contact with a planar solid surface or a solid surface with cavities is examined on the basis of the kinetic theory of nucleation developed by Nowakowski and Ruckenstein [J. Phys. Chem. 96 (1992) 2313] which is extended to nonuniform fluid density distribution (FDD) in the nucleus. The latter is determined under the assumption that at each moment the FDD in the nucleus is provided by the density functional theory (DFT) for a nanodrop. As a result of this assumption, the theory does not require to consider that the contact angle which the nucleus makes with the solid surface and the density of the nucleus are independent parameters since they are provided by the DFT. For all considered cases, the nucleation rate is higher in the cavities than on a planar surface and increases with increasing strength of the fluid-solid interactions and decreasing cavity radius. The difference is small at high supersaturations (small critical nuclei), but becomes larger at low supersaturations when the critical nucleus has a size comparable with the size of the cavity. The nonuniformity of the FDD in the nucleus decreases the nucleation rate when compared to the uniform FDD.     

Kinetic model of electrochemical nucleation

The process of electrochemical nucleation is analyzed in terms of stochastic formation of clusters of different size over the electrode surface. It is shown that the ground equation of the atomistic theory of nucleation can be derived without resort to the thermodynamic approach, in particular, the concept of the nucleus energy and its dependence on the nucleus size.     

Calculation of solid-liquid interfacial free energy: a classical nucleation theory based approach

We present a simple approach to calculate the solid-liquid interfacial free energy. This new method is based on the classical nucleation theory. Using the molecular dynamics simulation, we employ spherical crystal nuclei embedded in the supercooled liquids to create an ideal model of a homogeneous nucleation. The interfacial free energy is extracted by fitting the relation between the critical nucleus size and the reciprocal of the critical undercooling temperature. The orientationally averaged interfacial free energy is found to be 0.302+/-0.002 (in standard LJ unit). The temperature dependence of the interfacial free energy is also obtained in this work. We find that the interfacial free energy increases slightly with increasing temperature. The positive temperature coefficient of the interfacial free energy is in qualitative agreement with Spaepen's analysis [Solid State Phys. 47, FS181 (1994)] and Turnbull's empirical estimation [J. Appl. Phys. 21, 1022 (1950)].     

Approximate first passage time distribution for barrier crossing in a double well under fractional Gaussian noise

The distribution of waiting times, f(t), between successive turnovers in the catalytic action of single molecules of the enzyme beta-galactosidase has recently been determined in closed form by Chaudhury and Cherayil [J. Chem. Phys. 125, 024904 (2006)] using a one-dimensional generalized Langevin equation (GLE) formalism in combination with Kramers' flux-over-population approach to barrier crossing dynamics. The present paper provides an alternative derivation of f(t) that eschews this approach, which is strictly applicable only under conditions of local equilibrium. In this alternative derivation, a double well potential is incorporated into the GLE, along with a colored noise term representing protein conformational fluctuations, and the resulting equation transformed approximately to a Smoluchowski-type equation. f(t) is identified with the first passage time distribution for a particle to reach the barrier top starting from an equilibrium distribution of initial points, and is determined from the solution of the above equation using local boundary conditions. The use of such boundary conditions is necessitated by the absence of definite information about the precise nature of the boundary conditions applicable to stochastic processes governed by non-Markovian dynamics. f(t) calculated in this way is found to have the same analytic structure as the distribution calculated by the flux-over-population method.     

Kinetic Monte Carlo study of nucleation processes on patterned surfaces

The properties of template-directed nucleation are studied in the transition region where full nucleation control is lost and additional nucleation beyond the prepatterned structure is observed. To get deeper insight into the microscopic mechanisms, Monte Carlo simulations were performed. In this context, the previously used continuous algorithm [F. Kalischewski, J. Zhu, and A. Heuer, Phys. Rev. B 77, 155401, (2008)] was replaced by a discrete one to reduce simulation time and to allow more detailed calculations. The applied method is based on the assumption that the molecules on the surface occupy the sites of a simple fcc lattice. It is shown that a careful mapping of the continuous Monte Carlo technique onto the discrete algorithm leads to a good reproduction of the former results by means of the latter method. Furthermore, the new method facilitates the calculation of the spatial distribution of nuclei on the surface. This provides a detailed comparison with experimental data.     

On the rate of nucleation in binary systems

The technique used by many authors for finding a saddle point on the free energy surface in a binary system has been criticized recently. It is shown that the new approach proposed in two recent articles does not lead to any better agreement between theory and experiment than the previous method, especially for mixtures presenting strong surface enrichment effects.     

Suppression of binary nucleation in amorphous La-Fe-Sb mixtures

The nucleation energy of a series of La(x)Fe(y)Sb(z) modulated elemental reactants was measured as a function of the Fe/Sb ratio over a large composition range while holding the La content constant. The nucleation energy of the ternary compound La(0.5)Fe(4)Sb(12) with the skutterudite crystal structure was found to depend very strongly on the Fe/Sb ratio in the modulated elemental reactant, with a higher nucleation energy as the Fe/Sb ratio is moved away from the 1:3 stoichiometric value. When the results of this study are compared with those from Fe(y)Sb(z) modulated reactants, the addition of lanthanum was found to suppress the nucleation of FeSb(2), thereby broadening the Fe/Sb composition range in which the ternary skutterudite compound La(x)Fe(4)Sb(12) nucleates. This suppression of nucleation of a binary phase on addition of a ternary component to an amorphous intermediate is in agreement with theoretical arguments. The observed suppression of nucleation also provides rational for the observed nucleation of metastable ternary and higher-order compounds from homogeneous amorphous reactants.     

Kinetic patterns for thermal oxidation of binary and ternary blends based on polylactide and polyethylene

Russian Chemical Bulletin - The effect of introduced aged low density polyethylene (LDPE-A) on structure and properties of mixed blends based on polylactide (PLA) and low density polyethylene...     

Efficient computation of the first passage time distribution of the generalized master equation by steady-state relaxation

The generalized master equation or the equivalent continuous time random walk equations can be used to compute the macroscopic first passage time distribution (FPTD) of a complex stochastic system from short-term microscopic simulation data. The computation of the mean first passage time and additional low-order FPTD moments can be simplified by directly relating the FPTD moment generating function to the moments of the local FPTD matrix. This relationship can be physically interpreted in terms of steady-state relaxation, an extension of steady-state flow. Moreover, it is amenable to a statistical error analysis that can be used to significantly increase computational efficiency. The efficiency improvement can be extended to the FPTD itself by modelling it using a gamma distribution or rational function approximation to its Laplace transform.     

Atomistic theory of amyloid fibril nucleation

We consider the nucleation of amyloid fibrils at the molecular level when the process takes place by a direct polymerization of peptides or protein segments into β-sheets. Employing the atomistic nucleation theory (ANT), we derive a general expression for the work to form a nanosized amyloid fibril (protofilament) composed of successively layered β-sheets. The application of this expression to a recently studied peptide system allows us to determine the size of the fibril nucleus, the fibril nucleation work, and the fibril nucleation rate as functions of the supersaturation of the protein solution. Our analysis illustrates the unique feature of ANT that the size of the fibril nucleus is a constant integer in a given supersaturation range. We obtain the ANT nucleation rate and compare it with the rates determined previously in the scope of the classical nucleation theory (CNT) and the corrected classical nucleation theory (CCNT). We find that while the CNT nucleation rate is orders of magnitude greater than the ANT one, the CCNT and ANT nucleation rates are in very good quantitative agreement. The results obtained are applicable to homogeneous nucleation, which occurs when the protein solution is sufficiently pure and/or strongly supersaturated.