Detection Limit for Optically Sensing Specific Protein Interactions in Free-solution

Optical molecular sensing techniques are often limited by the refractive index change associated with the probed interactions. In this work, we present a closed form analytical model to estimate the magnitude of optical refractive index change arising from protein-protein interactions. The model, based on the Maxwell Garnett effective medium theory and first order chemical kinetics serves as a general framework for estimating the detection limits of optical sensing of molecular interactions. The model is applicable to situations where one interacting species is immobilized to a surface, as commonly done, or to emerging techniques such as Back-Scattering Interferometry (BSI) where both interacting species are un-tethered. Our findings from this model point to the strong role of as yet unidentified factors in the origin of the BSI signal resulting in significant deviation from linear optical response.Comment: 7 Page Manuscript + 14 Page Supplementary Informatio

The smooth cut-off Hierarchical Reference Theory of fluids

We provide a comprehensive presentation of the Hierarchical Reference Theory (HRT) in the smooth cut-off formulation. A simple and self-consistent derivation of the hierarchy of differential equations is supplemented by a comparison with the known sharp cut-off HRT. Then, the theory is applied to a hard core Yukawa fluid (HCYF): a closure, based on a mean spherical approximation ansatz, is studied in detail and its intriguing relationship to the self consistent Ornstein-Zernike approximation is discussed. The asymptotic properties, close to the critical point are investigated and compared to the renormalization group results both above and below the critical temperature. The HRT free energy is always a convex function of the density, leading to flat isotherms in the two-phase region with a finite compressibility at coexistence. This makes HRT the sole liquid-state theory able to obtain directly fluid-fluid phase equilibrium without resorting to the Maxwell construction. The way the mean field free energy is modified due to the inclusion of density fluctuations suggests how to identify the spinodal curve. Thermodynamic properties and correlation functions of the HCYF are investigated for three values of the inverse Yukawa range: z=1.8, z=4 and z=7 where Monte Carlo simulations are available. The stability of the liquid-vapor critical point with respect to freezing is also studied.Comment: 23 pages, 15 figures, 1 tabl

Partitioning a macroscopic system into independent subsystems

We discuss the problem of partitioning a macroscopic system into a collection of independent subsystems. The partitioning of a system into replica-like subsystems is nowadays a subject of major interest in several field of theoretical and applied physics, and the thermodynamic approach currently favoured by practitioners is based on a phenomenological definition of an interface energy associated with the partition, due to a lack of easily computable expressions for a microscopic (i.e.~particle-based) interface energy. In this article, we outline a general approach to derive sharp and computable bounds for the interface free energy in terms of microscopic statistical quantities. We discuss potential applications in nanothermodynamics and outline possible future directions.Comment: This is an author-created, un-copyedited version of an article accepted for publication in JSTA

Diffusion of multiple species with excluded-volume effects

Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing Brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results

Fourier's Law in a Generalized Piston Model

A simplified, but non trivial, mechanical model -- gas of $N$ particles of mass $m$ in a box partitioned by $n$ mobile adiabatic walls of mass $M$ -- interacting with two thermal baths at different temperatures, is discussed in the framework of kinetic theory. Following an approach due to Smoluchowski, from an analysis of the collisions particles/walls, we derive the values of the main thermodynamic quantities for the stationary non-equilibrium states. The results are compared with extensive numerical simulations; in the limit of large $n$, $mN/M\gg 1$ and $m/M \ll 1$, we find a good approximation of Fourier's law.Comment: 14 pages, 5 figure