The low-density/high-density liquid phase transition for model globular proteins

The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and finite temperature classical Density Functional Theory calculations. We use a parametrized potential that can vary smoothly from the standard Lennard-Jones interaction characteristic of simple fluids, to the ten Wolde-Frenkel model for the effective interaction of globular proteins in solution. We find that the large excluded volume characteristic of large macromolecules such as proteins is the dominant effect in determining the liquid-vapor surface tension and nucleation properties. The variation of the range of the potential only appears important in the case of small excluded volumes such as for simple fluids. The DFT calculations are then used to study homogeneous nucleation of the high-density phase from the low-density phase including the nucleation barriers, nucleation pathways and the rate. It is found that the nucleation barriers are typically only a few $k_{B}T$ and that the nucleation rates substantially higher than would be predicted by Classical Nucleation Theory.Comment: To appear in Langmui

Quantitative plane-resolved crystal growth and dissolution kinetics by coupling in situ optical microscopy and diffusion models : the case of salicylic acid in aqueous solution

The growth and dissolution kinetics of salicylic acid crystals are investigated in situ by focusing on individual microscale crystals. From a combination of optical microscopy and finite element method (FEM) modeling, it was possible to obtain a detailed quantitative picture of dissolution and growth dynamics for individual crystal faces. The approach uses real-time in situ growth and dissolution data (crystal size and shape as a function of time) to parametrize a FEM model incorporating surface kinetics and bulk to surface diffusion, from which concentration distributions and fluxes are obtained directly. It was found that the (001) face showed strong mass transport (diffusion) controlled behavior with an average surface concentration close to the solubility value during growth and dissolution over a wide range of bulk saturation levels. The (1̅10) and (110) faces exhibited mixed mass transport/surface controlled behavior, but with a strong diffusive component. As crystals became relatively large, they tended to exhibit peculiar hollow structures in the end (001) face, observed by interferometry and optical microscopy. Such features have been reported in a number of crystals, but there has not been a satisfactory explanation for their origin. The mass transport simulations indicate that there is a large difference in flux across the crystal surface, with high values at the edge of the (001) face compared to the center, and this flux has to be redistributed across the (001) surface. As the crystal grows, the redistribution process evidently can not be maintained so that the edges grow at the expense of the center, ultimately creating high index internal structures. At later times, we postulate that these high energy faces, starved of material from solution, dissolve and the extra flux of salicylic acid causes the voids to close

Multifractal analysis of the electronic states in the Fibonacci superlattice under weak electric fields

Influence of the weak electric field on the electronic structure of the Fibonacci superlattice is considered. The electric field produces a nonlinear dynamics of the energy spectrum of the aperiodic superlattice. Mechanism of the nonlinearity is explained in terms of energy levels anticrossings. The multifractal formalism is applied to investigate the effect of weak electric field on the statistical properties of electronic eigenfunctions. It is shown that the applied electric field does not remove the multifractal character of the electronic eigenfunctions, and that the singularity spectrum remains non-parabolic, however with a modified shape. Changes of the distances between energy levels of neighbouring eigenstates lead to the changes of the inverse participation ratio of the corresponding eigenfunctions in the weak electric field. It is demonstrated, that the local minima of the inverse participation ratio in the vicinity of the anticrossings correspond to discontinuity of the first derivative of the difference between marginal values of the singularity strength. Analysis of the generalized dimension as a function of the electric field shows that the electric field correlates spatial fluctuations of the neighbouring electronic eigenfunction amplitudes in the vicinity of anticrossings, and the nonlinear character of the scaling exponent confirms multifractality of the corresponding electronic eigenfunctions.Comment: 10 pages, 9 figure

Conversion of self-assembled monolayers into nanocrystalline graphene: Structure and electric transport

Graphene-based materials have been suggested for applications ranging from nanoelectronics to nanobiotechnology. However, the realization of graphene-based technologies will require large quantities of free-standing two-dimensional (2D) carbon materials with tuneable physical and chemical properties. Bottom-up approaches via molecular self-assembly have great potential to fulfil this demand. Here, we report on the fabrication and characterization of graphene made by electron-radiation induced cross-linking of aromatic self-assembled monolayers (SAMs) and their subsequent annealing. In this process, the SAM is converted into a nanocrystalline graphene sheet with well defined thickness and arbitrary dimensions. Electric transport data demonstrate that this transformation is accompanied by an insulator to metal transition that can be utilized to control electrical properties such as conductivity, electron mobility and ambipolar electric field effect of the fabricated graphene sheets. The suggested route opens broad prospects towards the engineering of free-standing 2D carbon materials with tuneable properties on various solid substrates and on holey substrates as suspended membranes.Comment: 30 pages, 5 figure

Role of water in Protein Aggregation and Amyloid Polymorphism

A variety of neurodegenerative diseases are associated with the formation of amyloid plaques. Our incomplete understanding of this process underscores the need to decipher the principles governing protein aggregation. Most experimental and simulation studies have been interpreted largely from the perspective of proteins: the role of solvent has been relatively overlooked. In this Account, we provide a perspective on how interactions with water affect folding landscapes of A$\beta$ monomers, A$\beta_{16-22}$ oligomer formation, and protofilament formation in a Sup35 peptide. Simulations show that the formation of aggregation-prone structures (N$^*$) similar to the structure in the fibril requires overcoming high desolvation barrier. The mechanism of protofilament formation in a polar Sup35 peptide fragment illustrates that water dramatically slows down self-assembly. Release of water trapped in the pores as water wires creates protofilament with a dry interface. Similarly, one of the main driving force for addition of a solvated monomer to a preformed fibril is the entropy gain of released water. We conclude by postulating that two-step model for protein crystallization must also hold for higher order amyloid structure formation starting from N$^*$. Multiple N$^*$ structures with varying water content results in a number of distinct water-laden polymorphic structures. In predominantly hydrophobic sequences, water accelerates fibril formation. In contrast, water-stabilized metastable intermediates dramatically slow down fibril growth rates in hydrophilic sequences.Comment: 27 pages, 4 figures; Accounts of Chemical Research, 201

Monitoring and Scoring Counter-Diffusion Protein Crystallization Experiments in Capillaries by in situ Dynamic Light Scattering

In this paper, we demonstrate the feasibility of using in situ Dynamic Light Scattering (DLS) to monitor counter-diffusion crystallization experiments in capillaries. Firstly, we have validated the quality of the DLS signal in thin capillaries, which is comparable to that obtained in standard quartz cuvettes. Then, we have carried out DLS measurements of a counter-diffusion crystallization experiment of glucose isomerase in capillaries of different diameters (0.1, 0.2 and 0.3 mm) in order to follow the temporal evolution of protein supersaturation. Finally, we have compared DLS data with optical recordings of the progression of the crystallization front and with a simulation model of counter-diffusion in 1D