Stochastic approach to irreversible thermodynamics.

An extension of classical irreversible thermodynamics pioneered by Ilya Prigogine is developed, in which fluctuations of macroscopic observables accounting for microscopic-scale processes are incorporated. The contribution of the fluctuations to the entropy production is derived from a generalized entropy balance equation and expressed in terms of the fluctuating variables, via an extended local equilibrium Ansatz and in terms of the probability distributions of these variables. The approach is illustrated on reactive systems involving linear and nonlinear steps, and the role of the distance from equilibrium and of the nonlinearities is assessed.

Stochastic thermodynamics of reactive systems: An extended local equilibrium approach.

The recently developed extended local equilibrium approach to stochastic thermodynamics is applied to reactive systems. The properties of the fluctuating entropy and entropy production are analyzed for general linear and for prototypical nonlinear kinetic processes. It is shown that nonlinear kinetics typically induces deviations of the mean entropy production from its value in the deterministic (mean-field) limit.

Mechanism for the stabilization of protein clusters above the solubility curve.

Pan, Vekilov and Lubchenko [J. Phys. Chem.

Kinetics of intermediate-mediated self-assembly in nanosized materials: a generic model.

We propose in this paper a generic model of a nonstandard aggregation mechanism for self-assembly processes of a class of materials involving the mediation of intermediates consisting of a polydisperse population of nanosized particles. The model accounts for a long induction period in the process. The proposed mechanism also gives insight on future experiments aiming at a more comprehensive picture of the role of self-organization in self-assembly processes.

Kinetic rougheninglike transition with finite nucleation barrier.

Recent observations of the growth of protein crystals have identified two different growth regimes. At low supersaturation, the surface of the crystal is smooth and increasing in size due to the nucleation of steps at defects and the subsequent growth of the steps. At high supersaturation, nucleation occurs at many places simultaneously, the crystal surface becomes rough, and the growth velocity increases more rapidly with increasing supersaturation than in the smooth regime.

Kinetics of docking in postnucleation stages of self-assembly.

In a previous study, the early stages of self-assembly in nanophase materials were explored by coupling a kinetic mean-field analysis with a lattice-based stochastic theory [J. J. Kozak et al.

Theoretical evidence for a dense fluid precursor to crystallization.

We present classical density functional theory calculations of the free-energy landscape for fluids below their triple point as a function of density and crystallinity. We find that, both for a model globular protein and for a simple atomic fluid modeled with a Lennard-Jones interaction, it is free-energetically easier to crystallize by passing through a metastable dense fluid in accord with the Ostwald rule of stages but in contrast to the alternative of ordering and densifying at once as assumed in the classical picture of crystallization.

The effect of the range of interaction on the phase diagram of a globular protein.

Thermodynamic perturbation theory is applied to the model of globular proteins studied by ten Wolde and Frenkel [P. R. ten Wolde and D.

Pattern formation and fluctuation-induced transitions in protein crystallization.

A kinetic model of protein crystallization accounting for the nucleation stage, the growth and competition of solid particles and the formation of macroscopic patterns is developed. Different versions are considered corresponding successively, to a continuous one-dimensional crystallization reactor, a coarse grained two-box model and a model describing the evolution of the space averaged values of fluid and solid material. The analysis brings out the high multiplicity of the patterns.