Swelling of two-dimensional polymer rings by trapped particles

The mean area of a two-dimensional Gaussian ring of $N$ monomers is known to diverge when the ring is subject to a critical pressure differential, $p_c \sim N^{-1}$. In a recent publication [Eur. Phys. J. E 19, 461 (2006)] we have shown that for an inextensible freely jointed ring this divergence turns into a second-order transition from a crumpled state, where the mean area scales as $\sim N$, to a smooth state with $\sim N^2$. In the current work we extend these two models to the case where the swelling of the ring is caused by trapped ideal-gas particles. The Gaussian model is solved exactly, and the freely jointed one is treated using a Flory argument, mean-field theory, and Monte Carlo simulations. For fixed number $Q$ of trapped particles the criticality disappears in both models through an unusual mechanism, arising from the absence of an area constraint. In the Gaussian case the ring swells to such a mean area, $\sim NQ$, that the pressure exerted by the particles is at $p_c$ for any $Q$. In the freely jointed model the mean area is such that the particle pressure is always higher than $p_c$, and $$ consequently follows a single scaling law, $\sim N^2 f(Q/N)$, for any $Q$. By contrast, when the particles are in contact with a reservoir of fixed chemical potential, the criticality is retained. Thus, the two ensembles are manifestly inequivalent in these systems.Comment: 8 page

Law of corresponding states for osmotic swelling of vesicles

As solute molecules permeate into a vesicle due to a concentration difference across its membrane, the vesicle swells through osmosis. The swelling can be divided into two stages: (a) an "ironing" stage, where the volume-to-area ratio of the vesicle increases without a significant change in its area; (b) a stretching stage, where the vesicle grows while remaining essentially spherical, until it ruptures. We show that the crossover between these two stages can be represented as a broadened continuous phase transition. Consequently, the swelling curves for different vesicles and different permeating solutes can be rescaled into a single, theoretically predicted, universal curve. Such a data collapse is demonstrated for giant unilamellar POPC vesicles, osmotically swollen due to the permeation of urea, glycerol, or ethylene glycol. We thereby gain a sensitive measurement of the solutes' membrane permeability coefficients, finding a concentration-independent coefficient for urea, while those of glycerol and ethylene glycol are found to increase with solute concentration. In addition, we use the width of the transition, as extracted from the data collapse, to infer the number of independent bending modes that affect the thermodynamics of the vesicle in the transition region.Comment: 10 page

Swelling of particle-encapsulating random manifolds

We study the statistical mechanics of a closed random manifold of fixed area and fluctuating volume, encapsulating a fixed number of noninteracting particles. Scaling analysis yields a unified description of such swollen manifolds, according to which the mean volume gradually increases with particle number, following a single scaling law. This is markedly different from the swelling under fixed pressure difference, where certain models exhibit criticality. We thereby indicate when the swelling due to encapsulated particles is thermodynamically inequivalent to that caused by fixed pressure. The general predictions are supported by Monte Carlo simulations of two particle-encapsulating model systems -- a two-dimensional self-avoiding ring and a three-dimensional self-avoiding fluid vesicle. In the former the particle-induced swelling is thermodynamically equivalent to the pressure-induced one whereas in the latter it is not.Comment: 8 pages, 6 figure

Critical swelling of particle-encapsulating vesicles

We consider a ubiquitous scenario where a fluctuating, semipermeable vesicle is embedded in solution while enclosing a fixed number of solute particles. The swelling with increasing number of particles or decreasing concentration of the outer solution exhibits a continuous phase transition from a fluctuating state to the maximum-volume configuration, whereupon appreciable pressure difference and surface tension build up. This criticality is unique to particle-encapsulating vesicles, whose volume and inner pressure both fluctuate. It implies a universal swelling behavior of such vesicles as they approach their limiting volume and osmotic lysis.Comment: 4 pages, 1 figur

Increased Concentration of Polyvalent Phospholipids in the Adsorption Domain of a Charged Protein

We studied the adsorption of a charged protein onto an oppositely charged membrane, composed of mobile phospholipids of differing valence, using a statistical-thermodynamical approach. A two-block model was employed, one block corresponding to the protein-affected region on the membrane, referred to as the adsorption domain, and the other to the unaffected remainder of the membrane. We calculated the protein-induced lipid rearrangement in the adsorption domain as arising from the interplay between the electrostatic interactions in the system and the mixing entropy of the lipids. Equating the electrochemical potentials of the lipids in the two blocks yields an expression for the relations among the various lipid fractions in the adsorption domain, indicating a sensitive dependence of lipid fraction on valence. This expression is a result of the two-block picture but does not depend on further details of the protein-membrane interaction. We subsequently calculated the lipid fractions themselves using the Poisson-Boltzmann theory. We examined the dependence of lipid enrichment, i.e., the ratio between the lipid fractions inside and outside the adsorption domain, on various parameters such as ionic strength and lipid valence. Maximum enrichment was found for lipid valence of about (-3) to (-4) in physiological conditions. Our results are in qualitative agreement with recent experimental studies on the interactions between peptides having a domain of basic residues and membranes containing a small fraction of the polyvalent phosphatidylinositol 4,5-bisphosphate (PIP2). This study provides theoretical support for the suggestion that proteins adsorbed onto membranes through a cluster of basic residues may sequester PIP2 and other polyvalent lipids.Comment: 25 pages, 12 figure

Algorithms for Molecular Biology Fall Semester, 2001

Introduction 12.1.1 Background Proteins are long chains of Amino Acids (AA). There are 20 di#erent AAs that serve as building blocks for proteins. Each AA has a specific chemical structure which contains a carbon backbone similar to all amino acids and a residue which varies between the AAs. The length of a protein chain can range from 50 to 1000-3000 AA (200 on the average). Proteins are known to have many important functions in the cell, such as enzymatic activity, storage and transport of material, signal transduction, antibodies and more. An important property of a protein is the length and composition of the AA chain. The series can be obtained automatically from the gene that encodes for the protein. Another interesting property is the unique folding. The AA composition of a protein will usually uniquely determine (on specific environment conditions) the 3D structure of the protein (e.g., two proteins with the same AA sequence will have the same 3D structure in natural conditi