Proteins in solution: Fractal surfaces in solutions

The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly. Molecular dynamics simulation, as an appropriate computational tool for studying the hydration shell of proteins, is also discussed. The concept of protein surfaces with fractal dimensions is elaborated. We finish by exposing an experimental (using small angle X-ray scattering) and a computer simulation case study, which are meant as demonstrations of the possibilities we have at hand for investigating the delicate interfaces that connect (and divide) protein molecules and the neighboring electrolyte solution.Comment: 8 pages, 5 figure

An independent, general method for checking consistency between diffraction data and partial radial distribution functions derived from them: the example of liquid water

There are various routes for deriving partial radial distribution functions of disordered systems from experimental diffraction (and/or EXAFS) data. Due to limitations and errors of experimental data, as well as to imperfections of the evaluation procedures, it is of primary importance to confirm that the end result (partial radial distribution functions) and the primary information (diffraction data) are consistent with each other. We introduce a simple approach, based on Reverse Monte Carlo modelling, that is capable of assessing this dilemma. As a demonstration, we use the most frequently cited set of "experimental" partial radial distribution functions on liquid water and investigate whether the 3 partials (O-O, O-H and H-H) are consistent with the total structure factor of pure liquid D_2O from neutron diffraction and that of H_2O from X-ray diffraction. We find that while neutron diffraction on heavy water is in full agreement with all the 3 partials, the addition of X-ray diffraction data clearly shows problems with the O-O partial radial distribution function. We suggest that the approach introduced here may also be used to establish whether partial radial distribution functions obtained from statistical theories of the liquid state are consistent with the measured structure factors.Comment: 6 pages, 3 figure

Local order and orientational correlations in liquid and crystalline phases of carbon tetrabromide from neutron powder diffraction measurements

The liquid, plastic crystalline and ordered crystalline phases of CBr$_4$ were studied using neutron powder diffraction. The measured total scattering differential cross-sections were modelled by Reverse Monte Carlo simulation techniques (RMC++ and RMCPOW). Following successful simulations, the single crystal diffraction pattern of the plastic phase, as well as partial radial distribution functions and orientational correlations for all the three phases have been calculated from the atomic coordinates ('particle configurations'). The single crystal pattern, calculated from a configuration that had been obtained from modelling the powder pattern, shows identical behavior to the recent single crystal data of Folmer et al. (Phys. Rev. {\bf B77}, 144205 (2008)). The BrBr partial radial distribution functions of the liquid and plastic crystalline phases are almost the same, while CC correlations clearly display long range ordering in the latter phase. Orientational correlations also suggest strong similarities between liquid and plastic crystalline phases, whereas the monoclinic phase behaves very differently. Orientations of the molecules are distinct in the ordered phase, whereas in the plastic crystal their distribution seems to be isotropic.Comment: 19 pages, 7 figures, accepted for publication in Physical Review B (http://prb.aps.org/

Generalized spin Sutherland systems revisited

We present generalizations of the spin Sutherland systems obtained earlier by Blom and Langmann and by Polychronakos in two different ways: from SU(n) Yang--Mills theory on the cylinder and by constraining geodesic motion on the N-fold direct product of SU(n) with itself, for any N>1. Our systems are in correspondence with the Dynkin diagram automorphisms of arbitrary connected and simply connected compact simple Lie groups. We give a finite-dimensional as well as an infinite-dimensional derivation and shed light on the mechanism whereby they lead to the same classical integrable systems. The infinite-dimensional approach, based on twisted current algebras (alias Yang--Mills with twisted boundary conditions), was inspired by the derivation of the spinless Sutherland model due to Gorsky and Nekrasov. The finite-dimensional method relies on Hamiltonian reduction under twisted conjugations of N-fold direct product groups, linking the quantum mechanics of the reduced systems to representation theory similarly as was explored previously in the N=1 case.Comment: 21 page

Derivations of the trigonometric BC(n) Sutherland model by quantum Hamiltonian reduction

The BC(n) Sutherland Hamiltonian with coupling constants parametrized by three arbitrary integers is derived by reductions of the Laplace operator of the group U(N). The reductions are obtained by applying the Laplace operator on spaces of certain vector valued functions equivariant under suitable symmetric subgroups of U(N)\times U(N). Three different reduction schemes are considered, the simplest one being the compact real form of the reduction of the Laplacian of GL(2n,C) to the complex BC(n) Sutherland Hamiltonian previously studied by Oblomkov.Comment: 30 pages, LateX; v2: final version with minor stylistic modification

Phase field approach to heterogeneous crystal nucleation in alloys

We extend the phase field model of heterogeneous crystal nucleation developed recently [L. Gránásy, T. Pusztai, D. Saylor, and J. A. Warren, Phys. Rev. Lett. 98, 035703 (2007)] to binary alloys. Three approaches are considered to incorporate foreign walls of tunable wetting properties into phase field simulations: a continuum realization of the classical spherical cap model (called Model A herein), a non-classical approach (Model B) that leads to ordering of the liquid at the wall, and to the appearance of a surface spinodal, and a non-classical model (Model C) that allows for the appearance of local states at the wall that are accessible in the bulk phases only via thermal fluctuations. We illustrate the potential of the presented phase field methods for describing complex polycrystalline solidification morphologies including the shish-kebab structure, columnar to equiaxed transition, and front-particle interaction in binary alloys