Unraveling the Pressure Effect on Nucleation Processes of Amyloidogenic Proteins

The influence of pressure on the nucleation rate of insulin under fibril‐forming conditions was studied and subsequently analysed using classical nucleation theory. The aim was a better understanding and quantification of the influence of pressure on protein aggregation/fibrillation reactions. The application of pressure has a drastic accelerating effect on the nucleation and growth process of insulin fibrils. We show that this effect arises from a volume decrease upon nucleus formation, due to formation of a less hydrated and more compact transition state that can be quantified extending nucleation theory by a pressure–volume term. Conversely, the absolute values of the lag time and the critical size of the nucleus cannot be satisfactorily described by the classical nucleation theory, which might be due to the presence of secondary effects, such as parallel aggregation pathways or fragmentation processes.     

Accounting for fluctuations in cluster parameters upon the description of nucleation in supersaturated vapor

A theory is proposed for stationary homogeneous nucleation in supersaturated vapor in which a modified expression for the rate of cluster evaporation was used to calculate the equilibrium distribution over the nucleus sizes and the rates of their formation. This rate was determined by the extrapolation to the region of small sizes of the corresponding expression for the macroscopic droplet derived according to thermodynamic notions that take fluctuations into account. Modified dependences of the size of critical nucleus and the rate of nucleation on the supersaturation and the temperature are determined and compared with the data of the classical theory of nucleation and experimental results.     

Melting dynamics of superheated argon: nucleation and growth

We investigate the microscopic melting process of a superheated argon solid using molecular dynamics simulations. We characterize the melting dynamics by following the temperature and time evolutions of liquid atoms and demonstrate the formation of a critical liquid nucleus via fluctuations and subsequent growth. The critical liquid nucleus size (about 120 atoms) obtained from our direct simulations is in accord with the prediction of the classical nucleation theory. The dynamic nucleation and growth of liquid also agree with the Johnson-Mehl-Avrami law, and the growth exponent n approximately 3 at the early stage followed by a substantial increase in n thereafter.     

Stresses inside critical nuclei

The usual derivation of classical nucleation theory is inappropriate for crystal nucleation. In particular, it leads to a seriously flawed estimate of the pressure inside a critical nucleus. This has consequences for the prediction of possible metastable phases during the nucleation process. In this paper, we reanalyze the theory for crystal nucleation based on the thermodynamics of small crystals suspended in a liquid, due to Mullins (J. Chem. Phys. 1984, 81, 1436). As an illustration of the difference between the classical picture and the present approach, we consider a numerical study of crystal nucleation in binary mixtures of hard spherical colloids with a size ratio of 1:10. The stable crystal phase of this system can be either dense or expanded. We find that, in the vicinity of the solid-solid critical point where the crystallites are highly compressible, small crystal nuclei are less dense than large nuclei. This phenomenon cannot be accounted for by either classical nucleation theory or by the Gibbsian droplet model.     

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.     

Crystal nucleation and the solid-liquid interfacial free energy

We present the results of molecular dynamics simulation of crystal nucleation in a supercooled Lennard-Jones liquid. Temperature and baric dependences of the nucleation rate, the Zeldovich factor, nucleus size diffusion coefficient, the radius, and the pressure in a critical crystal nucleus are defined in computer simulation. The data obtained have been used in the framework of classical nucleation theory to calculate the effective surface energy of crystal nuclei γ(e). It is shown that the value of γ(e) at T = const exceeds the value of the interfacial free energy at a flat crystal-liquid interface γ(∞) and γ(e) < γ(∞) at p = const.     

Distribution kinetics of polymer crystallization and the Avrami equation

Cluster distribution kinetics is adopted to explore the kinetics of polymer crystallization. Population balance equations based on crystal size distribution and concentration of amorphous polymer segments are solved numerically and the related dynamic moment equations are also solved. The model accounts for heterogeneous or homogeneous nucleation and crystal growth. Homogeneous nucleation rates follow the classical surface-energy nucleation theory. Different mass dependences of growth and dissociation rate coefficients are proposed to investigate the fundamental features of nucleation and crystal growth. A comparison of moment solutions with numerical solutions examines the validity of the model. The proposed distribution kinetics model provides a different interpretation of the familiar Avrami equation.     

Molecular Dynamics Studies of the Kinetics of Phase Changes in Clusters II: Crystal Nucleation from Molten (RbCl)256 and (RbCl)500 Clusters

Molecular dynamics computer simulations have been carried out to study the effects of cluster size and temperature on the nucleation rate of rubidium chloride clusters in the temperature range of 500-650 K. Clusters with 256 and 500 RbCl molecules have been studied and the results are compared with those obtained from 108 molecule clusters. The melting point (MP) of the clusters was observed to increase with the size of the clusters and can be described by a linear equation MP=997-405 N^−1/3, where N is the number of molecules in the cluster. The nucleation rate is found to decrease with increasing cluster size or increasing nucleation temperature. Both classical nucleation theory and diffuse interface theory are used to interpret our observed results.     

Tests of the homogeneous nucleation theory with molecular-dynamics simulations. I. Lennard-Jones molecules

Two kinds of the homogeneous nucleation theory exist at the present: the classical nucleation theory and the semiphenomenological model. To test them, we performed molecular-dynamics (MD) simulations of nucleation from vapor to liquid with 5000-20,000 Lennard-Jones-type molecules. Simulations were done for various values of supersaturation ratios (from 2 to 10) and temperatures (from 80 to 120 K). We compared the size distribution of clusters in MD simulations with those in the theoretical models because the number density of critical clusters governs the nucleation rate. We found that the semiphenomenological model achieves excellent agreements in size distributions of the clusters with all MD simulations we done. The classical theory underestimates the number density of the clusters in the temperature range of 80-100 K, but overestimates in 100-120 K. The semiphenomenological model also predicts well the nucleation rate in MD simulations, while the classical nucleation theory does not. Our results confirmed the validity of the semiphenomenological model for Lennard-Jones-type molecules.     

Nucleation near the spinodal: limitations of mean field density functional theory

We investigate the diverging size of the critical nucleus near the spinodal using the gradient theory (GT) of van der Waals and Cahn and Hilliard and mean field density functional theory (MFDFT). As is well known, GT predicts that at the spinodal the free energy barrier to nucleation vanishes while the radius of the critical fluctuation diverges. We show numerically that the scaling behavior found by Cahn and Hilliard for these quantities holds quantitatively for both GT and MFDFT. We also show that the excess number of molecules Deltag satisfies Cahn-Hilliard scaling near the spinodal and is consistent with the nucleation theorem. From the latter result, it is clear that the divergence of Deltag is due to the divergence of the mean field isothermal compressibility of the fluid at the spinodal. Finally, we develop a Ginzburg criterion for the validity of the mean field scaling relations. For real fluids with short-range attractive interactions, the near-spinodal scaling behavior occurs in a fluctuation dominated regime for which the mean field theory is invalid. Based on the nucleation theorem and on Wang's treatment of fluctuations near the spinodal in polymer blends, we infer a finite size for the critical nucleus at the pseudospinodal identified by Wang.     

The stage of nonisothermal nucleation of supercritical particles of a new phase under nonstationary conditions of particle diffusion growth and heat transfer to a medium

An analytical theory has been formulated for the stage of nonisothermal nucleation of supercritical particles in a metastable medium with instantaneously generated initial supersaturation. The theory takes into account the nonuniformities of metastable substance concentration and temperature, which result from the nonstationary diffusion of the substance to growing particles and the nonstationary transfer of the heat of the phase transition from the particles to the medium. The formulated theory extends the approach based on the concept of excluded volume that has recently been used in the theory of the stage of nucleation under isothermal conditions. This approach implies that the nucleation intensity of new particles is suppressed in spherical diffusion regions with certain sizes that surround previously nucleated supercritical particles and remaining unchanged in the rest of the medium. It has been shown that, when self-similar solutions are used for nonstationary equations of substance diffusion to particles and heat transfer from the particles, the ratio between the excluded volume and the particle volume is independent of particle size, thereby enabling one to analytically solve the integral equation for the excluded volume throughout a system as a time function at the stage of nucleation. The main characteristics of the phase transition have been found for the end of the stage of nucleation. Comparison has been carried out with the characteristics obtained in terms of the isothermal and nonisothermal nucleation theory upon uniform vapor consumption and heat dissipation (the mean-field approximation of vapor supersaturation and temperature).     

Determining the nucleation rate from the dimer growth probability

A new method is proposed for the determination of the stationary one-component nucleation rate J with the help of data for the growth probability P2 of a dimer which is the smallest cluster of the nucleating phase. The method is based on an exact formula relating J and P2, and is readily applicable to computer simulations of nucleation. Using the method, the dependence of J on the supersaturation s is determined by kinetic Monte Carlo simulations of two-dimensional (2D) nucleation of monolayers on the (100) face of Kossel crystal. The change of J over nearly 11 orders of magnitude is followed and it is found that the classical nucleation theory overestimates the simulation J values by an s-dependent factor. The 2D nucleus size evaluated via the nucleation theorem is described satisfactorily by the classical Gibbs-Thomson equation and its corrected version accounting for the spinodal limit of 2D nucleation.     

Steady-state nucleation rate and flux of composite nucleus at saddle point

The steady-state nucleation rate and flux of composite nucleus at the saddle point is studied by extending the theory of binary nucleation. The Fokker-Planck equation that describes the nucleation flux is derived using the Master equation for the growth of the composite nucleus, which consists of the core of the final stable phase surrounded by a wetting layer of the intermediate metastable phase nucleated from a metastable parent phase recently evaluated by Iwamatsu [J. Chem. Phys. 134, 164508 (2011)]. The Fokker-Planck equation is similar to that used in the theory of binary nucleation, but the non-diagonal elements exist in the reaction rate matrix. First, the general solution for the steady-state nucleation rate and the direction of nucleation flux is derived. Next, this information is then used to study the nucleation of composite nucleus at the saddle point. The dependence of steady-state nucleation rate as well as the direction of nucleation flux on the reaction rate in addition to the free-energy surface is studied using a model free-energy surface. The direction of nucleation current deviates from the steepest-descent direction of the free-energy surface. The results show the importance of two reaction rate constants: one from the metastable environment to the intermediate metastable phase and the other from the metastable intermediate phase to the stable new phase. On the other hand, the gradient of the potential Φ or the Kramers crossover function (the commitment or splitting probability) is relatively insensitive to reaction rates or free-energy surface.     

Test of classical nucleation theory via molecular-dynamics simulation

A direct test of classical nucleation theory (CNT) is made using molecular-dynamics simulations. The relation between critical nucleus size and undercooling temperature is extracted and the result yields the solid-liquid interfacial energy. It is shown that the CNT, within the assumptions made for spherical nucleus in supercooled liquid, is valid in the critical regime of nucleation for a large range of undercooling and nucleus size.     

Nonclassical nucleation kinetics in the crystallization of a supercooled melt

A molecular dynamics simulation of homogenous nucleation of a crystal in supercooled aluminum melt is performed. Nucleation rates at a temperature of 900 K in the range of pressures from 12 to 15 GPa are calculated. Analysis of the mean first-passage times of crystalline cluster sizes is performed. A stepwise dependence of the mean first-passage time on crystal nucleus size is observed, in contrast to the sigmoidal dependence that follows from classical nucleation theory. Based on the data from atomistic simulations, it is established that the form of the free energy barrier during nucleation differs significantly from the one assumed in classical nucleation theory for a spherically symmetric nucleus. It is supposed that the observed differences are apparently due to the complex structure of the crystalline nucleus.     

Nucleation rates in a new phenomenological model

In this paper we develop a new theory to evaluate the nucleation rate in the framework of the EMLD-DNT model. Beyond the model, our theory deals with cluster translation and exclusion, effects that have been virtually ignored in classical nucleation theory. We apply the model to the case of 1-pentanol, and compare the predictions with experimental results. We find an excellent agreement between the nucleation rate predicted by our theory and experimental data. The distinguishing feature of the model is its ability to predict successfully the rate of formation of the critical nucleus without the use of an intermolecular potential, employing only macroscopic thermodynamic properties.     

Molecular Dynamics Studies of the Kinetics of Phase Changes in Clusters IV： Crystal Nucleation from Molten （NaCl）256 and （NaCl）500 Clusters

Molecular dynamics computer simulation based on the Born-Mayer-Huggins potential function has been carried out to study the effects of duster size and temperature on the nucleation rate of sodium chloride dusters in the temperature range of 580 K to 630 K. Clusters with 256 and 500 NaCl molecules have been studied and the results have been compared with those obtained from 108 molecule dusters. The melting point (MP) of the clusters were observed to increase with the size of the clusters and can be well described by a linear equation MP =1107(37)-1229(23)N^-1/3(N is the number of molecules in the duster).The nucleation rate was found to decrease with increasing the duster size or temperature. Various nucleation theories have been used to interpret the nucleation rates obtained from this molecular dynamics simulation. It is possible to use a constant diffuse interface thickness to interpret the nucleation rate from the diffuse interface theory in the temperature range of this study. However, the interfacinl free energy estimated from classical nucleation theory and diffuse interface theory increases too fast with increasing the temperature while that from Gran-Gunton theory does not change with changing temperatures.The sizes of critical nuclei estimated from all the theories are smaller than those estimated from our simulations.     

Hit and miss of classical nucleation theory as revealed by a molecular simulation study of crystal nucleation in supercooled sulfur hexafluoride

Classical nucleation theory pictures the homogeneous nucleation of a crystal as the formation of a spherical crystalline embryo, possessing the properties of the macroscopic crystal, inside a parent supercooled liquid. In this work we study crystal nucleation in moderately supercooled sulfur hexafluoride by umbrella sampling simulations. The nucleation free energy evolves from 5.2kBT at T=170 K to 39.1kBT at T=195 K. The corresponding critical nucleus size ranges from 40 molecules at T=170 K to 266 molecules at T=195 K. Both nucleation free energy and critical nucleus size are shown to evolve with temperature according to the equations derived from the classical nucleation theory. Inspecting the obtained nuclei we show, however, that they present quite anisotropic shapes in opposition to the spherical assumption of the theory. Moreover, even though the critical nuclei possess the structure of the stable bcc plastic phase, the only mechanically stable crystal phase for SF6 in the temperature range investigated, they are shown to be less ordered than the corresponding macroscopic crystal. Their crystalline order is nevertheless shown to increase regularly with their size. This is confirmed by a study of a nucleus growth from a critical size to a size of the order of 10(4) molecules. Similarly to the fact that it does not affect the temperature dependence of the nucleation free energy and of the critical nucleus size, the ordering of the nucleus with size does not affect the growth rate of the nucleus.     

A novel method for evaluating the critical nucleus and the surface tension in systems with first order phase transition

We introduce a novel method for calculating the size of the critical nucleus and the value of the surface tension in systems with first order phase transition. The method is based on classical nucleation theory, and it consists in studying the thermodynamics of a sphere of given radius embedded in a frozen metastable surrounding. The frozen configuration creates a pinning field on the surface of the free sphere. The pinning field forces the sphere to stay in the metastable phase as long as its size is smaller than the critical nucleus. We test our method in two first order systems, both on a two-dimensional lattice: a system where the parameter tuning the transition is the magnetic field, and a second system where the tuning parameter is the temperature. In both cases the results are satisfying. Unlike previous techniques, our method does not require an infinite volume limit to compute the surface tension, and it therefore gives reliable estimates even by using relatively small systems. However, our method cannot be used at, or close to, the critical point, i.e., at coexistence, where the critical nucleus becomes infinitely large.