Onsager’s variational principle in soft matter : introduction and application to the dynamics of adsorption of proteins onto fluid membranes

This book is the first collection of lipid-membrane research conducted by leading mechanicians and experts in continuum mechanics. It brings the overall intellectual framework afforded by modern continuum mechanics to bear on a host of challenging problems in lipid membrane physics. These include unique and authoritative treatments of differential geometry, shape elasticity, surface flow and diffusion, interleaf membrane friction, phase transitions, electroelasticity and flexoelectricity, and computational modelling. [Chapter] Lipid bilayers are unique soft materials operating in general in the low Reynolds limit. While their shape is predominantly dominated by curvature elasticity as in a solid shell, their in-plane behavior is that of a largely inextensible viscous fluid. Furthermore, lipid membranes are extremely responsive to chemical stimuli. Because in their biological context they are continuously brought out-of-equilibrium mechanically or chemically, it is important to understand their dynamics. Here, we introduce Onsager’s variational principle as a general and transparent modeling tool for lipid bilayer dynamics. We introduce this principle with elementary examples, and then use it to study the sorption of curved proteins on lipid membranes.Peer ReviewedPostprint (author's final draft

Mobility Measurements Probe Conformational Changes in Membrane Proteins due to Tension

The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such proteins cause local deformations in the membrane, which induce an extra hydrodynamic drag on the protein. Using membrane tension to control the magnitude of the deformations and hence the drag, measurements of diffusivity can be used to infer--- via an elastic model of the protein--- how conformation is changed by tension. Motivated by recent experimental results [Quemeneur et al., Proc. Natl. Acad. Sci. USA, 111 5083 (2014)] we focus on KvAP, a voltage-gated potassium channel. The conformation of KvAP is found to change considerably due to tension, with its `walls', where the protein meets the membrane, undergoing significant angular strains. The torsional stiffness is determined to be 26.8 kT at room temperature. This has implications for both the structure and function of such proteins in the environment of a tension-bearing membrane.Comment: Manuscript: 4 pages, 4 figures. Supplementary Material: 8 pages, 1 figur

Hydrodynamic Flows on Curved Surfaces: Spectral Numerical Methods for Radial Manifold Shapes

We formulate hydrodynamic equations and spectrally accurate numerical methods for investigating the role of geometry in flows within two-dimensional fluid interfaces. To achieve numerical approximations having high precision and level of symmetry for radial manifold shapes, we develop spectral Galerkin methods based on hyperinterpolation with Lebedev quadratures for $L^2$-projection to spherical harmonics. We demonstrate our methods by investigating hydrodynamic responses as the surface geometry is varied. Relative to the case of a sphere, we find significant changes can occur in the observed hydrodynamic flow responses as exhibited by quantitative and topological transitions in the structure of the flow. We present numerical results based on the Rayleigh-Dissipation principle to gain further insights into these flow responses. We investigate the roles played by the geometry especially concerning the positive and negative Gaussian curvature of the interface. We provide general approaches for taking geometric effects into account for investigations of hydrodynamic phenomena within curved fluid interfaces.Comment: 14 figure

Chetaev vs. vakonomic prescriptions in constrained field theories with parametrized variational calculus

Starting from a characterization of admissible Cheataev and vakonomic variations in a field theory with constraints we show how the so called parametrized variational calculus can help to derive the vakonomic and the non-holonomic field equations. We present an example in field theory where the non-holonomic method proved to be unphysical

Aeroacoustic and aerodynamic applications of the theory of nonequilibrium thermodynamics

Recent developments in the field of nonequilibrium thermodynamics associated with viscous flows are examined and related to developments to the understanding of specific phenomena in aerodynamics and aeroacoustics. A key element of the nonequilibrium theory is the principle of minimum entropy production rate for steady dissipative processes near equilibrium, and variational calculus is used to apply this principle to several examples of viscous flow. A review of nonequilibrium thermodynamics and its role in fluid motion are presented. Several formulations are presented of the local entropy production rate and the local energy dissipation rate, two quantities that are of central importance to the theory. These expressions and the principle of minimum entropy production rate for steady viscous flows are used to identify parallel-wall channel flow and irrotational flow as having minimally dissipative velocity distributions. Features of irrotational, steady, viscous flow near an airfoil, such as the effect of trailing-edge radius on circulation, are also found to be compatible with the minimum principle. Finally, the minimum principle is used to interpret the stability of infinitesimal and finite amplitude disturbances in an initially laminar, parallel shear flow, with results that are consistent with experiment and linearized hydrodynamic stability theory. These results suggest that a thermodynamic approach may be useful in unifying the understanding of many diverse phenomena in aerodynamics and aeroacoustics

Theory of optimum shapes in free-surface flows. Part 2. Minimum drag profiles in infinite cavity flow

The problem considered here is to determine the shape of a symmetric two-dimensional plate so that the drag of this plate in infinite cavity flow is a minimum. With the flow assumed steady and irrotational, and the effects due to gravity ignored, the drag of the plate is minimized under the constraints that the frontal width and wetted arc-length of the plate are fixed. The extremization process yields, by analogy with the classical Euler differential equation, a pair of coupled nonlinear singular integral equations. Although analytical and numerical attempts to solve these equations prove to be unsuccessful, it is shown that the optimal plate shapes must have blunt noses. This problem is next formulated by a method using finite Fourier series expansions, and optimal shapes are obtained for various ratios of plate arc-length to plate width