Following the aggregation of amyloid-forming peptides by computer simulations

There is experimental evidence suggesting that the toxicity of neurodegenerative diseases such as Alzheimer's disease may result from the soluble intermediate oligomers. It is therefore important to characterize extensively the early steps of oligomer formation at atomic level. As these structures are metastable and short lived, experimental data are difficult to obtain and they must be complemented with numerical simulations. In this work, we use the activation-relaxation technique coupled with a coarse-grained energy model to study in detail the mechanisms of aggregation of four lys-phe-phe-glu (KFFE) peptides. This is the shortest peptide known to form amyloid fibrils in vitro. Our simulations indicate that four KFFE peptides adopt a variety of oligomeric states (tetramers, trimers, and dimers) with various orientations of the chains in rapid equilibrium. This conformational distribution is consistent with all-atom molecular-dynamics simulations in explicit solvent and is sequence dependent; as seen experimentally, the lys-pro-gly-glu (KPGE) peptides adopt disordered structures in solution. Our unbiased simulations also indicate that the assembly process is much more complex than previously thought and point to intermediate structures which likely are kinetic traps for longer chains.     

Water motion in reverse micelles studied by quasielastic neutron scattering and molecular dynamics simulations

Motion of water molecules in Aerosol OT [sodium bis(2-ethylhexyl) sulfosuccinate, AOT] reverse micelles with water content w(0) ranging from 1 to 5 has been explored both experimentally through quasielastic neutron scattering (QENS) and with molecular dynamics (MD) simulations. The experiments were performed at the energy resolution of 85 microeV over the momentum transfer (Q) range of 0.36-2.53 A(-1) on samples in which the nonpolar phase (isooctane) and the AOT alkyl chains were deuterated, thereby suppressing their contribution to the QENS signal. QENS results were analyzed via a jump-diffusion/isotropic rotation model, which fits the results reasonably well despite the fact that confinement effects are not explicitly taken into account. This analysis indicates that in reverse micelles with low-water content (w(0)=1 and 2.5) translational diffusion rate is too slow to be detected, while for w(0)=5 the diffusion coefficient is much smaller than for bulk water. Rotational diffusion coefficients obtained from this analysis increase with w(0) and are smaller than for bulk water, but rotational mobility is less drastically reduced than translational mobility. Using the Faeder/Ladanyi model [J. Phys. Chem. B 104, 1033 (2000)] of reverse micelle interior, MD simulations were performed to calculate the self-intermediate scattering function F(S)(Q,t) for water hydrogens. Comparison of the time Fourier transform of this F(S)(Q,t) with the QENS dynamic structure factor S(Q,omega), shows good agreement between the model and experiment. Separate intermediate scattering functions F(S) (R)(Q,t) and F(S) (CM)(Q,t) were determined for rotational and translational motion. Consistent with the decoupling approximation used in the analysis of QENS data, the product of F(S) (R)(Q,t) and F(S) (CM)(Q,t) is a good approximation to the total F(S)(Q,t). We find that the decay of F(S) (CM)(Q,t) is nonexponential and our analysis of the MD data indicates that this behavior is due to lower water mobility close to the interface and to confinement-induced restrictions on the range of translational displacements. Rotational relaxation also exhibits nonexponential decay. However, rotational mobility of O-H bond vectors in the interfacial region remains fairly high due to the lower density of water-water hydrogen bonds in the vicinity of the interface.     

The effect of shear on colloidal aggregation and gelation studied using small-angle light scattering

In situ light scattering measurements were performed to investigate the effect of low shear rates (0.13-3.56 s(-1)) on an aggregating colloidal system made of 20 nm polystyrene particles. The aggregating system was subjected to a shear for a short period (ca. 33 s) and only once at various times after the onset of aggregation. The effect of shear (aggregation kinetics and morphology) was studied both in a cluster dilute and in a cluster dense regime (see introduction). Our results have shown that shear can enhance the aggregation and gelation. Shear induced growth can yield hybrid superaggregates when the system is dense.     

Probing amyloid fibril formation of the NFGAIL peptide by computer simulations

Amyloid fibril formation, as observed in Alzheimer's disease and type II diabetes, is currently described by a nucleation-condensation mechanism, but the details of the process preceding the formation of the nucleus are still lacking. In this study, using an activation-relaxation technique coupled to a generic energy model, we explore the aggregation pathways of 12 chains of the hexapeptide NFGAIL. The simulations show, starting from a preformed parallel dimer and ten disordered chains, that the peptides form essentially amorphous oligomers or more rarely ordered beta-sheet structures where the peptides adopt a parallel orientation within the sheets. Comparison between the simulations indicates that a dimer is not a sufficient seed for avoiding amorphous aggregates and that there is a critical threshold in the number of connections between the chains above which exploration of amorphous aggregates is preferred.     

Diffusive solvent dynamics in a polymer gel electrolyte studied by quasielastic neutron scattering

A quasielastic neutron scattering study has been performed on a polymer gel electrolyte consisting of lithium perchlorate dissolved in ethylene carbonate/propylene carbonate and stabilized with poly(methyl methacrylate). The dynamics of the solvent, which is crucial for the ion conduction in this system, was probed using the hydrogen/deuterium contrast variation method with nondeuterated solvent and a deuterated polymer matrix. Two relaxation processes of the solvent were studied in the 10-400 microeV range at different temperatures. From analysis of the momentum transfer dependence of the processes we conclude that the faster process ( approximately 100 microeV) is related to rotational diffusion of the solvent and the slower process ( approximately 10 microeV) to translational diffusion of the solvent. The translational diffusion is found to be similar to the diffusion in the corresponding liquid electrolyte at short distances, but geometrically constrained by the polymer matrix at distances beyond approximately 5 A. The study indicates that the hindered diffusion of the solvent on a length scale of the polymer network interchain distance ( approximately 5-20 A) is sufficient to explain the reduced macroscopic diffusivity and ion conductivity of the gel electrolyte compared to the liquid electrolyte.     

Morphology of bile salt micelles as studied by computer simulation methods

The relative arrangement of the neighboring bile ions and the shape of the hydrophobic and hydrogen-bonded primary micelles as well of the large secondary micelles formed by these ions are analyzed in detail on the basis of molecular dynamics computer simulations of 30 and 300 mM sodium cholate and sodium deoxycholate solutions. In the lower concentration considered, the systems only contain primary micelles, whereas in both of the 300 mM systems secondary micelles are also present. The simulations performed were long enough that the systems reached thermodynamic equilibrium. It is found that the neighboring cholate ions prefer alignments in which their quasi-planar tetracyclic ring systems are parallel with each other, whereas for deoxycholate an opening of the angle between these planes is observed. The shape of the micelles is characterized by the ratio of their three principal moments of inertia. The primary deoxycholate micelles are found to be rather spherical, whereas in the case of cholate somewhat flattened, disklike or oblate shaped ellipsoidal primary micelles are found, irrespective of whether these micelles are kept together by hydrogen bonds or are of hydrophobic origin. Finally, the secondary micelles are found to exhibit a large variety of shapes, ranging from flattened oblates to rodlike objects through various different irregular shapes, characterized by markedly different values of the three principal moments of inertia. The observed preferences of the relative arrangement of the neighboring ions and of the aggregate shapes as well as the differences observed in the behavior of the two bile ions studied in these respects are traced back to the molecular structure of these ions.     

Liquid-liquid phase transitions in supercooled water studied by computer simulations of various water models

Liquid-liquid and liquid-vapor coexistence regions of various water models were determined by Monte Carlo (MC) simulations of isotherms of density fluctuation-restricted systems and by Gibbs ensemble MC simulations. All studied water models show multiple liquid-liquid phase transitions in the supercooled region: we observe two transitions of the TIP4P, TIP5P, and SPCE models and three transitions of the ST2 model. The location of these phase transitions with respect to the liquid-vapor coexistence curve and the glass temperature is highly sensitive to the water model and its implementation. We suggest that the apparent thermodynamic singularity of real liquid water in the supercooled region at about 228 K is caused by an approach to the spinodal of the first (lowest density) liquid-liquid phase transition. The well-known density maximum of liquid water at 277 K is related to the second liquid-liquid phase transition, which is located at positive pressures with a critical point close to the maximum. A possible order parameter and the universality class of liquid-liquid phase transitions in one-component fluids are discussed.     

Self-organization and pattern formation of janus particles in two dimensions by computer simulations

The phase behavior and associated pattern formation of two-dimensional systems of hard disks decorated with amphiphilic coronae (Janus disks) are studied by means of Monte Carlo computer simulations. A primitive interaction potential that captures the essential interparticle interactions is introduced. Despite its simplicity, the system exhibits a very rich phase polymorphism. Apart from the isotropic phase and depending upon the coronal thickness, the simulated systems self-organize in a number of two-dimensional mesophases of various symmetries exhibiting a variety of novel patterns. The results of these simulations suggest that 2D Janus particles are promising candidates for bottom-up design of precise two-dimensional templates.     

Protein aggregation,particle formation,characterization & rheology

In this review, we attempt to give a concise overview of recent progress made in mechanistic understanding of protein aggregation, particulate formation and protein solution rheology. Recent advances in analytical techniques and methods for characterizing protein aggregation and the formed protein particles as well as advancements, technique limitations and controversies in the field of protein solution rheology are discussed. The focus of the review is primarily on biotherapeutics and proteins/antibodies that are relevant to that area. As per the remit of Current Opinion in Colloid and Interface Science, here we attempt to stimulate interest in areas of debate. While the field is certainly not mature enough that all problems may be considered resolved and accepted by consensus, we wish to highlight some areas of controversy and debate that need further attention from the scientific community.     

Thermodynamic considerations and computer simulations on the formation of core-shell nanoparticles under electrochemical conditions

We report on thermodynamic modeling and computer simulations on the electrochemical generation of metallic and bimetallic nanoparticles (NPs) by means of quenched molecular dynamics (QMD). The present results suggest that the spontaneous formation of core-shell NPs depends on several factors, i.e. size and shape of the core, chemical composition of the system, and under-/oversaturation conditions. Homo- and heteroatomic prototypical systems were considered. The former systems were Au and Pt. The latter were Ag(core)/Au(shell), Pt(core)/Au(shell), Au(core)/Ag(shell) and Au(core)/Pt(shell).     

Cluster-cluster aggregation kinetics and primary particle growth of soot nanoparticles in flame by light scattering and numerical simulations

The agglomeration kinetics of growing soot generated in a diffusion atmospheric flame are here studied in situ by light scattering technique to infer cluster morphology and size (fractal dimension D(f) and radius of gyration R(g)). SEM analysis is used as a standard reference to obtain primary particle size D(P) at different residence times. The number N(P) of primary particles per aggregate and the number concentration n(A) of clusters are evaluated on the basis of the measured angular patterns of the scattered light intensity. The major finding is that the kinetics of the coagulation process that yields to the formation of chain-like aggregates by soot primary particles (size 10 to 40 nm) can be described with a constant coagulation kernel beta(c,exp)=2.37x10(-9) cm3/s (coagulation constant tau(c) approximately = 0.28 ms). This result is in nice accord with the Smoluchowski coagulation equation in the free molecular regime, and, vice versa, it is in contrast with previous studies conducted by invasive (ex situ) techniques, which claimed the evidence in flames of coagulation rates much larger than the kinetic theory predictions. Thereafter, a number of numerical simulations is implemented to compare with the experimental results on primary particle growth rate and on the process of aggregate reshaping that is observed by light scattering at later residence times. The restructuring process is conjectured to occur, for not well understood reasons, as a direct consequence of the atomic rearrangement in the solid phase carbon due to the prolonged residence time within the flame. Thus, on one side, it is shown that the numerical simulations of primary size history compare well with the values of primary size from SEM experiment with a growth rate constant of primary diameter about 1 nm/s. On the other side, the evolution of aggregate morphology is found to be predictable by the numerical simulations when the onset of a first-order "thermal" restructuring mechanism is assumed to occur in the flame at about 20 ms residence time leading to aggregates with an asymptotic fractal dimension D(f,infinity) approximately = 2.5.     

Micelle formation in sodium hexadecyl sulfate surfactant solutions studied by small-angle neutron scattering

Micelle formation in aqueous sodium hexadecyl sulfate solutions is studied by small-angle neutron scattering. Measurements are carried out at different concentrations (1.1, 2.2, 3.2, 5.4, 10.9 and 32.8 mM/dm³) and at different temperatures (40°, 50°, and 60°C). The monotonous evolution of interparticle correlation can be observed on the measured scattering patterns. At high concentrations (10.9 and 32.8 mM/dm³) scattering patterns are described by interacting ellipsoids, but at low concentrations by non-interacting ellipsoids. Computation of the distance distribution function proved the ellipsoidal shape at 10.9 and 32.8 mM/dm³, but showed an unexpectedly large particle dimension and elongation of the micelles at lower concentrations.     

Supramolecular polymerization and gel formation of bis(merocyanine) dyes driven by dipolar aggregation

Two highly dipolar merocyanine dyes were tethered by a rigid tris(n-dodecyloxy)xylylene unit that preorganizes the dyes for a supramolecular polymerization process through intermolecular aggregation of the dyes. UV/vis spectroscopy revealed a solvent dependent equilibrium between monomeric dyes and two different types of dye aggregates that are characterized by hypsochromically shifted D- and H-type absorption bands. Taking into account the ditopic nature of the supramolecular building blocks, the occurrence of the D-band indicates the formation of an oligomeric/polymeric supramolecular chain whereas the observation of the H-band suggests a higher order assembly. For the H-aggregated dyes, intrinsic viscosities exceed 0.65 L g(-1) in methylcyclohexane, values typically found for macromolecular solutions. At higher concentration, further association of these aggregates takes place by entanglement of the alkyl groups leading to a substantial increase in viscosity and gelation. Rheology studies show linear viscoelastic behavior which was attributed to the formation of an entangled dynamic network. AFM and cryo-TEM studies of the gel reveal long and stiff rod-type assemblies. X-ray diffraction studies for a solid film show columnar mesomorphism. Based on these results, a structural model is proposed in which six helically preorganized strands of the supramolecular polymer intertwine to form a rod with a diameter of about 5 nm. Within these rods all dyes are tightly aggregated in a tubular fashion giving rise to delocalized excitonic states, and the pi-conjugated tube is jacketed by the tridodecyloxy groups.     

Scaling of the kinetics of slow aggregation and gel formation for a fluorinated polymer colloid

The aggregation and gelation kinetics in moderately concentrated (0.004 相似文献   

Monte Carlo computer simulations and electron microscopy of colloidal cluster formation via emulsion droplet evaporation

We consider a theoretical model for a binary mixture of colloidal particles and spherical emulsion droplets. The hard sphere colloids interact via additional short-ranged attraction and long-ranged repulsion. The droplet-colloid interaction is an attractive well at the droplet surface, which induces the Pickering effect. The droplet-droplet interaction is a hard-core interaction. The droplets shrink in time, which models the evaporation of the dispersed (oil) phase, and we use Monte Carlo simulations for the dynamics. In the experiments, polystyrene particles were assembled using toluene droplets as templates. The arrangement of the particles on the surface of the droplets was analyzed with cryogenic field emission scanning electron microscopy. Before evaporation of the oil, the particle distribution on the droplet surface was found to be disordered in experiments, and the simulations reproduce this effect. After complete evaporation, ordered colloidal clusters are formed that are stable against thermal fluctuations. Both in the simulations and with field emission scanning electron microscopy, we find stable packings that range from doublets, triplets, and tetrahedra to complex polyhedra of colloids. The simulated cluster structures and size distribution agree well with the experimental results. We also simulate hierarchical assembly in a mixture of tetrahedral clusters and droplets, and find supercluster structures with morphologies that are more complex than those of clusters of single particles.     

Triglyceride nanocrystal aggregation into polycrystalline colloidal networks: Ultra-small angle X-ray scattering,models and computer simulation

Triacylglycerols (TAGs) are the majority molecules present in edible fats and oils. Many of the functional characteristics of fat products depend on the colloidal fat crystal network present. Identifying the hierarchies of these colloidal networks and how they spontaneously self-assemble is important to understand their functionality and the oil binding capacity, and new insights into the nano- to meso-scale structure in these colloidal fat networks have been reported in recent years. Ultra small angle X-ray scattering (USAXS) is a technique new to the study of edible oil structures and, when combined with modelling and computer simulation, has enabled significant advances to be made in understanding the nano- to micro-scale crystalline structures of edible oils. In the four years since crystalline nanoplatelets (CNPs) were characterized, models have been made of these highly anisotropic nanoscale structures in which they were treated as the primary unit. In those models, CNPs were represented as close-packed rigid layers of spheres, so chosen because the van der Waals sphere–sphere interaction is known. The intent of the models was to predict the hierarchy of colloidal fat networks that would self-assemble from the components in edible oils. Initially, CNP aggregation was modelled under the assumption that all CNPs are present before aggregation begins and that their solubility in liquid oil is very low. The models successfully predicted the fractal dimensions subsequently measured using USAXS. This brief review reports on some of the latest models and simulations together with the results of USAXS experiments carried out on binary lipid systems, such as SSS in OOO, as well as certain complex systems that contain many different TAG molecules. The excellent agreement between the two approaches has established that USAXS is a powerful tool in the elucidation of the nano- to meso-length scales in fats and oils.     

Water properties and potential of mean force for hydrophobic interactions of methane and nanoscopic pockets studied by computer simulations

We consider model systems consisting of a methane molecule and hemispherical pockets of subnanometer radii whose walls are made of hydrophobic material. The potential of mean force for process of translocation of the methane molecule from bulk water into the pockets' interior is obtained, based on an explicit solvent molecular dynamics simulations. Accompanying changes in water density around the interacting objects and spatial distribution of solvent's potential energy are analyzed, allowing for interpretation of details of hydrophobic interactions in relation to hydrophobic hydration properties. Applicability of surface area-based models of hydrophobic effect for systems of interest is also investigated. A total work for the translocation process is not dependent on pocket's size, indicating that pocket desolvation has little contribution to free energy changes, which is consistent with the observation that solvent density is significantly reduced inside "unperturbed" pockets. Substantial solvent effects are shown to have a longer range than in case of a well investigated methane pair. A desolvation barrier is present in a smaller pocket system but disappears in the larger one, suggesting that a form of a "hydrophobic collapse" is observed.