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We study fractal measures on Euclidean space through the dynamics of "zooming in" on typical points. The resulting family of measures (the "scenery"), can be interpreted as an orbit in an appropriate dynamical system which often…
Preliminary results are presented for the kinetics of phase separation in three distinct models of protein aggregation. The first is a model of the formation of spherical microcrystals of insulin via an initial formation of fractal clusters…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…
We present and discuss a novel approach to the direct and inverse protein folding problem. The proposed strategy is based on a variational approach that allows the simultaneous extraction of amino acid interactions and the low-temperature…
We outline a strategy for quantitatively evaluating the conformational characteristics of self-assembled structures using the techniques of contrast variation small angle neutron scattering. By means of basis function expansion, a case…
This work thoroughly examines several analytical tools, each possessing a different level of mathematical intricacy, for the purpose of characterizing the orientation distribution function of elongated objects under flow. Our investigation…
Continuum or hybrid modeling of bilayer membrane morphological dynamics induced by embedded proteins necessitates the identification of protein-membrane interfaces and coupling of deformations of two surfaces. In this article we developed…
Soft interfaces can mediate interactions between particles bound to them. The force transmitted through the surface geometry on a particle may be expressed as a closed line integral of the surface stress tensor around that particle. This…
Interactive molecular graphics applications facilitate analysis of three dimensional protein structures. Naturally, non-interactive 2-D snapshots of the protein structures do not convey the same level of geometric detail. Several 2-D…
Thin film processing by means of sputter deposition inherently depends on the interaction of energetic particles with a target surface and the subsequent particle transport. The length and time scales of the underlying physical phenomena…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
In molecular physics, it is often necessary to average over the orientation of molecules when calculating observables, in particular when modelling experiments in the liquid or gas phase. Evaluated in terms of Euler angles, this is closely…
Small-angle neutron scattering experiments and molecular dynamics simulations combined with an application of concepts from soft matter physics to complex protein mixtures provide new insight into the stability of eye lens protein mixtures.…
An accurate modeling of reactive flows in fractured porous media is a key ingredient to obtain reliable numerical simulations of several industrial and environmental applications. For some values of the physical parameters we can observe…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
We study the electrical double layer at the interface between a protein crystal and a salt solution or a dilute solution of protein, and estimate the double layer's contribution to the interfacial tension of this interface. This…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
We present a flexible discretization technique for computational models of thin tubular networks embedded in a bulk domain, for example a porous medium. These systems occur in the simulation of fluid flow in vascularized biological tissue,…
We report theoretical and simulation studies of phase coexistence in model globular protein solutions, based on short-range, central, pair potential representations of the interaction among macro-particles. After reviewing our previous…