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.     

Nucleation rate isotherms of argon from molecular dynamics simulations

We report six nucleation rate isotherms of vapor-liquid nucleation of Lennard-Jones argon from molecular dynamics simulations. The isotherms span three orders of magnitude in nucleation rates, 10(23)相似文献   

Homogeneous nucleation rates of higher n-alcohols measured in a laminar flow diffusion chamber

Nucleation rate isotherms of n-butanol, n-pentanol, n-hexanol, n-heptanol, and n-octanol were measured in a laminar flow diffusion chamber using helium as carrier gas. The measurements were made at 250-310 K, corresponding to reduced temperatures of 0.43-0.50, and at atmospheric pressure. Experimental nucleation rate range was from 10(3) to 10(7) cm(-3) s(-1). The expression and accuracy of thermodynamic parameters, in particular equilibrium vapor pressure, were found to have a significant effect on calculated nucleation rates. The results were compared to the classical nucleation theory (CNT), the self-consistency corrected classical theory (SCC) and the Hale's scaled model of the CNT. The average ratio between the experimental and theoretical nucleation rates for all alcohols used was 1.5x10(3) when the CNT was used, and 0.2x10(-1) when the SCC was used and 0.7x10(-1) when the Hale's scaled theory was used. The average values represent all the alcohols used at the same reduced temperatures. The average ratio was about the same throughout the temperature range, although J(exp)/J(the) calculated with the Hale's scaled theory increased slightly with increasing temperature. The saturation ratio dependency was predicted closest to experiment with the classical nucleation theory. The nucleation rates were compared to those found in the literature. The measurements were in reasonable agreement with each other. The molecular content of critical alcohol clusters was between 35 and 80 molecules. At a fixed reduced temperature, the number of molecules in a critical cluster decreased as a function of alcohol carbon chain length. The number of molecules in critical clusters was compared to those predicted by the Kelvin equation. The theory predicted the critical cluster sizes well.     

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.     

Test of classical nucleation theory on deeply supercooled high-pressure simulated silica

We test classical nucleation theory (CNT) in the case of simulations of deeply supercooled, high density liquid silica, as modeled by the van Beest-Kramer-van Santen potential. We find that at density rho=4.38 gcm(3), spontaneous nucleation of crystalline stishovite occurs in conventional molecular dynamics simulations at temperature T=3000 K, and we evaluate the nucleation rate J directly at this T via "brute force" sampling of nucleation events in numerous independent runs. We then use parallel, constrained Monte Carlo simulations to evaluate DeltaG(n), the free energy to form a crystalline embryo containing n silicon atoms, at T=3000, 3100, 3200, and 3300 K. By comparing the form of DeltaG(n) to CNT, we test the ability of CNT to reproduce the observed behavior as we approach the regime where spontaneous nucleation occurs on simulation time scales. We find that the prediction of CNT for the n dependence of DeltaG(n) fits reasonably well to the data at all T studied. Deltamu, the chemical potential difference between bulk liquid and stishovite, is evaluated as a fit parameter in our analysis of the form of DeltaG(n). Compared to directly determined values of Deltamu extracted from previous work, the fitted values agree only at T=3300 K; at lower T the fitted values increasingly overestimate Deltamu as T decreases. We find that n(*), the size of the critical nucleus, is approximately ten silicon atoms at T=3300 K. At 3000 K, n(*) decreases to approximately 3, and at such small sizes methodological challenges arise in the evaluation of DeltaG(n) when using standard techniques; indeed even the thermodynamic stability of the supercooled liquid comes into question under these conditions. We therefore present a modified approach that permits an estimation of DeltaG(n) at 3000 K. Finally, we directly evaluate at T=3000 K the kinetic prefactors in the CNT expression for J, and find physically reasonable values; e.g., the diffusion length that Si atoms must travel in order to move from the liquid to the crystal embryo is approximately 0.2 nm. We are thereby able to compare the results for J at 3000 K obtained both directly and based on CNT, and find that they agree within an order of magnitude. In sum, our work quantifies how certain predictions of CNT (e.g., for Deltamu) break down in this deeply supercooled limit, while others [the n dependence of DeltaG(n)] are not as adversely affected.     

Homogeneous nucleation in supersaturated vapors of methane, ethane, and carbon dioxide predicted by brute force molecular dynamics

Molecular dynamics (MD) simulation is applied to the condensation process of supersaturated vapors of methane, ethane, and carbon dioxide. Simulations of systems with up to a 10(6) particles were conducted with a massively parallel MD program. This leads to reliable statistics and makes nucleation rates down to the order of 10(30) m(-3) s(-1) accessible to the direct simulation approach. Simulation results are compared to the classical nucleation theory (CNT) as well as the modification of Laaksonen, Ford, and Kulmala (LFK) which introduces a size dependence of the specific surface energy. CNT describes the nucleation of ethane and carbon dioxide excellently over the entire studied temperature range, whereas LFK provides a better approach to methane at low temperatures.     

Homogeneous nucleation of water between 200 and 240 K: new wave tube data and estimation of the Tolman length

We have measured homogeneous nucleation rates of water at 200-240 K in the carrier gas helium, in the range of 10(13) - 10(17) m(-3) s(-1) using an expansion wave tube. The rates agree well with the results of Wolk and Strey [J. Phys. Chem. B 105, 11683 (2001)] in the range of overlap (220-240 K), and are summarized by the empirical fit J = S exp[4.6 + 0.244T-(906.8 - 2.914T)(ln S)(2)], with J the nucleation rate in m(-3) s(-1), S the supersaturation, and T the temperature in K. We find that the supersaturation dependence of both our rates and those of Wolk and Strey is lower than classical theory predicts, and that the critical cluster is smaller than the classical critical size. These deviations are explained in the framework of the Tolman theory for surface tension, and the "Tolman length" is estimated from our experimental results. We find a positive Tolman length that increases with decreasing temperature, from about 0.1 Angstrom at 260 K to (0.6 +/- 0.4) Angstroms at 200 K. We present a nucleation rate expression that takes the Tolman length into account and show that both the supersaturation and temperature dependence are improved, compared to the classical theory.     

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.     

Nucleation in electrochemical growth of the Ag(100) crystal face: determining the nucleus size via the nucleation theorem

We employ the nucleation theorem for a model-independent determination of the size of the two-dimensional (2D) Ag nucleus with the aid of experimental data for the nucleation-mediated electrochemical growth of the Ag(100) crystal face in aqueous solution of AgNO(3) at 318 K. These data are for the stationary rate of 2D nucleation, for the initial portion of the potentiostatic current transient pertaining to atomically smooth face, and for the galvanostatic current corresponding to stationary growth of the face. It turns out that the 2D nucleus is constituted of 17-64 Ag atoms when the overpotential is in the range of 12-22.4 mV. Upon expressing the overpotential in terms of supersaturation, it is found that the experimental data for the size of the 2D Ag nucleus are in conformity with existing simulation data for the size of the 2D nucleus on the (100) face of Kossel crystal (the simulation nucleus contains 1-30 atoms). It is found as well that the Gibbs-Thomson equation of the classical theory of 2D nucleation describes very well the supersaturation dependence of the size of both the Ag and the simulation nucleus.     

Analysis of the dielectric permittivity of suspensions by means of the logarithmic derivative of its real part

Measurement of the dielectric permittivity of colloidal suspensions in the kilohertz frequency range (the so-called low-frequency dielectric dispersion) is a promising tool for the electrokinetic characterization of colloids. However, this technique is less used than would be desirable because of the difficulties associated with the measurements, the most important of which is the electrode polarization (EP). Recently (M. Wübbenhorst and J. Van Turnhout, Dielectrics Newsl. November (2000)) a method was proposed that appears capable of separating the unwanted electrode effects from the double-layer relaxation that we are interested in. The method, based on the logarithmic derivative of raw epsilon'(omega) data (epsilon'(omega) is the real part of the permittivity of the suspension for a frequency omega of the applied AC field), is first checked against the well-known theory of the AC permittivity of colloidal suspensions developed by DeLacey and White (E. H. B. DeLacey and L. R. White, J. Chem. Soc. Faraday Trans. 277, 2007 (1981)). We show that the derivative epsilon'(D)(omega)=-(pi/2)(partial differential epsilon'/partial differential ln omega) gives an excellent representation of the true imaginary part of the permittivity, epsilon'(omega). The technique is then applied to experimental data of the dielectric constant of polystyrene and ethylcellulose suspensions. We found that epsilon'(D) displays two separated behaviors when plotted against log omega in the frequency range 100 Hz-1 MHz: a monotonous decrease (associated with EP) followed by an absorption peak (associated with the double-layer relaxation, or alpha-relaxation). Interestingly, they are separated enough to make it possible to easily find the characteristic frequency of the alpha-relaxation. Fitting a relaxation function to epsilon'(D)(omega) after eliminating the part due to EP, we could calculate the real part epsilon'(omega) and compare it to the DeLacey and White (DW) theoretical predictions. A significantly better agreement between DW calculations and experimental epsilon'(omega) data is obtained when the logarithmic derivative method is used, as compared to the classical electrode-separation techniques.     

Simple correction to the classical theory of homogeneous nucleation

Formation of the new disperse phase via homogeneous nucleation plays a fundamental role wherever the first-order phase transitions occur. Inconsistent temperature dependence of the nucleation rates and poor agreement of theoretical critical supersaturations with experimental data for a number of substances are fundamental problems of the classical nucleation theory (CNT). Here we show that these problems can be solved with a simple empirical correction to CNT. Despite its simplicity, the corrected CNT (CCNT) accurately predicts temperature dependences and absolute values of the critical supersaturations for both organic and inorganic substances with widely varying properties at different ambient conditions and it works surprisingly well in a wide size range down to few molecules. The difference in predictions of CCNT and other versions of the classical nucleation theory commonly used in analyzing experimental data is discussed. It has been found that CCNT consistently gives better agreement with experimental data than other versions of classical nucleation theory.     

Homogeneous nucleation of n-propanol, n-butanol, and n-pentanol in a supersonic nozzle

We have measured the nucleation conditions of n-propanol, n-butanol, and n-pentanol in a supersonic Laval nozzle, and estimated that the maximum nucleation rate J is 5 x 10(16) cm(-3) s(-1) with an uncertainty factor of 2. Plotting the vapor pressures p(J(max) ) and temperatures T(J(max) ) corresponding to the maximum nucleation rate as ln(p) versus 1T, produces a series of well separated straight lines. When these values are scaled by their respective critical parameters, p(c) and T(c), the data lie close to a single straight line. Comparing the experimental data to the predictions of classical nucleation theory reveals much higher experimental rates, and the deviation increases with increasing alcohol chain length and decreasing temperature. A scaling analysis in terms of Hale's scaled nucleation model [Phys. Rev. A 33, 4156 (1986); Metall. Trans. A 23, 1863 (1992)], clearly shows that our data are consistent with experimental nucleation rates measured using other devices that have characteristic rates many orders of magnitude lower.     

Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain.

A 7.6 ns molecular dynamics trajectory of the betaARK1 PH domain in explicit water with appropriate ions was calculated at 300 K. Spectral densities at omega = 0, omega(N), and 0.87omega(H) and the model-free parameters were evaluated from the experimental as well as the simulated data, taking the anisotropic overall motion of the protein into account. Experimental and simulated spectral densities are in reasonable general agreement for NH bond vectors, where the corresponding motions have converged within the simulation time. A sufficient sampling of the motions for NH bonds within flexible parts of the protein requires a longer simulation time. The simulated spectral densities J(0) and J(omega(N)) are, on average, 4.5% and 16% lower than the experimental data; the corresponding numbers for the core residues are about 6%; the high-frequency spectral densities J(0.87omega(H)) are lower by, on average, 16% (21% for the core). The simulated order parameters, S(2), are also lower, although the overall disagreement between the simulation and experiment is less pronounced: 1% for all residues and 6% for the core. The observed systematic decrease of simulated spectral density and the order parameters compared to the experimental data can be partially attributed to the ultrafast librational motion of the NH bonds with respect to their peptide plane, which was analyzed in detail. This systematic difference is most pronounced for J(0.87omega(H)), which appears to be most sensitive to the slow, subnanosecond time scale of internal motion, whereas J(0) and J(omega(N)) are dominated by the overall rotational tumbling of the protein. Similar discrepancies are observed between the experimentally measured (15)N relaxation parameters (R(1), R(2), NOE) and their values calculated from the simulated spectral densities. The analysis of spectral densities provides additional information regarding the comparison of the simulated and experimental data, not available from the model-free analysis.     

Homogeneous nucleation of n-nonane and n-propanol mixtures: a comparison of classical nucleation theory and experiments

The homogeneous nucleation rates for n-nonane-n-propanol vapor mixtures have been calculated as a function of vapor-phase activities at 230 K using the classical nucleation theory (CNT) with both rigorous and approximate kinetic prefactors and compared to previously reported experimental data. The predicted nucleation rates resemble qualitatively the experimental results for low n-nonane gas phase activity. On the high nonane activity side the theoretical nucleation rates are about three orders of magnitude lower than the experimental data when using the CNT with the approximate kinetics. The accurate kinetics improves the situation by reducing the difference between theory and experiments to two orders of magnitude. Besides the nucleation rate comparison and the experimental and predicted onset activities, the critical cluster composition is presented. The total number of molecules is approximated by CNT with reasonable accuracy. Overall, the classical nucleation theory with rigorous kinetic prefactor seems to perform better. The thermodynamic parameters needed to calculate the nucleation rates are revised extensively. Up-to-date estimates of liquid phase activities using universal functional activity coefficient Dortmund method are presented together with the experimental values of surface tensions obtained in the present study.     

A linear comprehensive adsorption model of hydrogen on super activated carbon under supercritical conditions

The adsorption isotherms of hydrogen on super activated carbon were measured systematically, covering a temperature range of 93-293 K at 20 K intervals and pressures up to 7 MPa. All the experimental data were linearized by adopting the coordinates ln ln(n) vs 1/(ln P). The results indicate that the adsorption limit (P(lim), n(lim)) exists virtually at high pressure and has a certain physical meaning. Based on the adsorption limit, further analyses were carried out by modeling the adsorption isotherms in the coordinates ln(n(lim)/n) vs ln(RT(ln(P(lim)/P) and a linear comprehensive adsorption model was proposed in the form n (lim)=n.exp(psi T+lambda/T-c/) (beta).[RT ln( P (lim)P )] (b) which can predict the adsorption isotherm of hydrogen on activated carbon in supercritical conditions.     

Crystallization kinetics study of poly(L‐lactic acid)/carbon nanotubes nanocomposites

Effects of carbon nanotubes (CNT) on the isothermal crystallization kinetics of poly(L ‐lactic acid) (PLLA) were quantitatively investigated using the Avrami equation and the secondary nucleation theory of Lauritzen and Hoffman. CNT via grafting modification with PLLA could well disperse in the PLLA matrix and give significantly enhanced crystallization rate and crystallinity of PLLA as analyzed by differential scanning calorimetry and polarized optical microscopy. Analysis of isothermal crystallization kinetics using the Avrami equation demonstrated that CNT significantly enhanced the bulk crystallization of PLLA. Analysis of spherulite growth kinetics using the secondary nucleation theory of Lauritzen and Hoffman found that CNT could expand the temperature range of the crystallization regime III of PLLA. Values of the nucleation constant (K_g) in crystallization regimes III and II of PLLA both increased with increasing CNT contents. The K_g III/K_g II ratios were found to be close to the theoretical value 2 but were not clearly found to depend on the CNT contents. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 983–989, 2010     

Temperature dependence of homogeneous nucleation rates for water: near equivalence of the empirical fit of Wölk and Strey, and the scaled nucleation model

It is pointed out that the temperature fitting function of W?lk and Strey [J. Phys. Chem. 105, 11683 (2001)], recently shown to convert the Becker-D?ring [Ann. Phys. (Leipzig) 24, 719 (1935)] nucleation rate into an expression in agreement with much of the experimental water nucleation rate data, also converts the Becker-D?ring rate into a form nearly equivalent with the scaled nucleation rate model, J(scaled)=J(oc) exp[-16piOmega(3)(T(c)T-1)(3)3(ln S)(2)]. In the latter expression J(oc) is the inverse thermal wavelength cubed/sec, evaluated at T(c).     

Explosive cavitation in superheated liquid argon

The kinetics of explosive boiling-up of liquid argon has been investigated at negative pressures created by the reflection of a compression pulse 3-5 mus long from the free surface of a liquid by the method of liquid pulse heating on a thin platinum wire (with a rate of temperature increase of about 1 Kmus). The limiting superheats T(*) (stretches p(*)), the effective nucleation rate J(*), and the derivative G(T)=(d ln JdT)(T=T(*) ) have been determined by experimental data on the thermal perturbation of a wire probe and the results of solution of the problem on the initial stage of explosive boiling-up of a liquid. The experimental data are compared with homogeneous nucleation theory.     

纳米粒子相变的分子动力学研究：Cu453的性质、结构与结晶成核

Molecular dynamics （MD） computer simulations have been carried out to study the structures, properties and crystal nucleation of nanoparticles with 453 Cu atoms. Structure information was analyzed from the MD simulations, while properties of nanoparticles of Cu453, such as melting point, freezing temperature, heat capacity and mo- lar volumes, have been estimated. The face center cubic （FCC） phase and icosahedron （Ih） phase were observed during the quenching process, and nucleation rates of crystallization to FCC crystal of Cu453 at temperatures of 650, 700, 750, and 800 K were analyzed. Both classical nucleation theory （CNT） and diffuse interface theory （DIT） were used to interpret our observed nucleation rates. The free energy and diffuse interface thickness between the liquid and the FCC crystal phases were estimated by the CNT and DIT respectively, and the results show that the DIT does not work properly to the system.