Similarities between protein folding and granular jamming.

Grains and glasses, widely different materials, arrest their motions upon decreasing temperature and external load, respectively, in common ways, leading to a universal jamming phase diagram conjecture. However, unified theories are lacking, mainly because of the disparate nature of the particle interactions. Here we demonstrate that folded proteins exhibit signatures common to both glassiness and jamming by using temperature- and force-unfolding molecular dynamics simulations. Upon folding, proteins develop a peak in the interatomic force distributions that falls on a universal curve with experimentally measured forces on jammed grains and droplets. Dynamical signatures are found as a dramatic slowdown of stress relaxation upon folding. Together with granular similarities, folding is tied not just to the jamming transition, but a more nuanced picture of anisotropy, preparation protocol and internal interactions emerges. Results have implications for designing stable polymers and can open avenues to link protein folding to jamming theory

Rotating magnetic field actuation of a multicilia configuration

This paper was presented at the 2nd Micro and Nano Flows Conference (MNF2009), which was held at Brunel University, West London, UK. The conference was organised by Brunel University and supported by the Institution of Mechanical Engineers, IPEM, the Italian Union of Thermofluid dynamics, the Process Intensification Network, HEXAG - the Heat Exchange Action Group and the Institute of Mathematics and its Applications.The current paper continues the analysis of a completely novel method of fluid manipulation technology in micro-fluidics systems, inspired by nature, namely by the mechanisms found in ciliates. More information on this subject can be found at http://www.hitech-projects.com/euprojects/artic/. In order to simulate the drag forces acting on an array of artificial cilia, we have developed a computer code that is based on fundamental solutions of Stokes flow in a semi-infinite domain. The actuation mechanism consists of a bi-directional rotating excitation magnetic field. The magnetization induced by the magnetic field was calculated in a separate routine based on the Integral Nonlinear Equations Approach with 1D discretization of wire (cilium). Time averaged x-coordinate mass flow rates are computed for several cilium configurations resulting. The outcome and originality of this paper consist on assessing magnetic actuation as a practical tool for obtaining a consistent one-directional fluid flow.This work has been supported through grant ARTIC FP6-2004-NMP-TI4

Fluctuation-Driven Molecular Transport in an Asymmetric Membrane Channel

Channel proteins, that selectively conduct molecules across cell membranes, often exhibit an asymmetric structure. By means of a stochastic model, we argue that channel asymmetry in the presence of non-equilibrium fluctuations, fueled by the cell's metabolism as observed recently, can dramatically influence the transport through such channels by a ratchet-like mechanism. For an aquaglyceroporin that conducts water and glycerol we show that a previously determined asymmetric glycerol potential leads to enhanced inward transport of glycerol, but for unfavorably high glycerol concentrations also to enhanced outward transport that protects a cell against poisoning.Comment: REVTeX4, 4 pages, 3 figures; Accepted for publication in Phys. Rev. Let

On a method to calculate conductance by means of the Wigner function: two critical tests

We have implemented the linear response approximation of a method proposed to compute the electron transport through correlated molecules based on the time-independent Wigner function [P. Delaney and J. C. Greer, \prl {\bf 93}, 36805 (2004)]. The results thus obtained for the zero-bias conductance through quantum dot both without and with correlations demonstrate that this method is either quantitatively nor qualitatively able to provide a correct physical escription of the electric transport through nanosystems. We present an analysis indicating that the failure is due to the manner of imposing the boundary conditions, and that it cannot be simply remedied.Comment: 22 pages, 7 figur