COMMUNICATIONS IN COMPUTATIONAL PHYSICS Vol. 6, No. 3, pp. 655-672 Commun. Comput. Phys. September 2009 Hydrophobic Effect in a Continuum Model of the Lipid Bilayer Phillip L. Wilson 1, ∗ , Huaxiong Huang 2 and Shu Takagi 3 1 Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand. 2 Department of Mathematics and Statistics, York University, Toronto, M3J 1P3, Canada. 3 Department of Mechanical Engineering, The University of Tokyo, Tokyo, Japan. Received 16 August 2008; Accepted (in revised version) 24 December 2008 Available online 19 February 2009 Abstract. We study a continuum paradigm of the lipid bilayer based on minimizing the free energy of a mixture of water and lipid molecules. This paper extends previ- ous work of Blom and Peletier [European J. Appl. Math., 15 (2004), pp. 487-508] in the following ways. (a) It formulates a more general model of the hydrophobic effect to facilitate connections with microscale simulations and first-principles analysis. (b) It clarifies the meaning and role of the model parameters. (c) It outlines a method for determining parameter values so that physically-realistic bilayer density profiles can be obtained, for example for use in macroscale simulations. Points (a)-(c) suggest that the model has potential to robustly connect some micro- and macroscale levels of mul- tiscale blood flow simulations. The mathematical modelling in point (a) is based upon a consideration of the underlying physics of inter-molecular forces. The governing equations thus obtained are minimized by gradient flows via a novel numerical ap- proach; this enables point (b). The numerical results are shown to behave physically in terms of the effect of background concentration, in contrast to the earlier model which is shown here to not display the expected behaviour. A “short-tail” approximation of the lipid molecules also gives an analytical tool which yields critical values of some pa- rameters under certain conditions. Point (c) involves the first quantitative comparison of the numerical data with physical experimental results. AMS subject classifications: 74G15, 74G65, 74K15, 74L15 Key words: Lipid bilayer, free energy, continuum model, numerical minimization. ∗ Corresponding author. Email addresses: p.wilson@math.canterbury.ac.nz (P. L. Wilson), hhuang@ mathstat.yorku.ca (H. Huang), takagi@mech.t.u-tokyo.ac.jp (S. Takagi) http://www.global-sci.com/ 655 c 2009 Global-Science Press