We present an interferometrie technique allowing reliable measurements of bending modulus κ, membrane tension Σ and adhesion energy W of cells crawling on substrates. All three parameters are important for cell locomotion and reflect the local balance of attractive and repulsive forces between cell and substratum as well as the internal coupling of cell membrane and the underlying cytoskeleton. Mutants of the Dictyostelium ameba lacking an important cytoskeletal protein, Cortexillin, exhibited a markedly reduced bending modulus and adhesion energy as compared to wild type Dictyostelium. In addition, experiments with model membrane systems suggest that the combination of attractive and repulsive forces results in a local clustering of receptors mediating cell adhesion.

We describe a new, high-resolution technique for determining the local viscoelastic response of polymer gels on a micrometer scale. This is done by monitoring thermal fluctuations of embedded probe particles. We derive the relationship between the amplitude of fluctuations and the low-frequency storage modulus G′, as well as the relationship between the fluctuation power spectrum, measured between 0.1 Hz and 25kHz, and the complex shear modulus G((ω). For both, semiflexible F-actin solutions and flexible polyacrylamide (PAAm) gels we observe high-frequency power-law dependence in the spectra, which reflects the behavior of the shear modulus. However, we observe distinctly different scaling exponents for G((ω) in F-actin and PAAm gels—presumably due to the semiflexible nature of the actin filaments.

We present a method that uses two- and three-particle correlation functions between solute atoms and water molecules to approximate the density profile of water surrounding biomolecules. The method is based on a potential of mean force expansion and uses X-ray crystallography, NMR, or modeling structural input information on the biomolecule. For small hydrophobic solutes, we have calculated entropies of hydration using the predicted water densities that are in good agreement with experimental results. We have also predicted the hydration of the catabolite activator protein-DNA complex. The method is extremely efficient and makes possible the study of hydration of large biomolecules within CPU minutes.

The DNA double helix is a semi-flexible polymer with twist rigidity. Its bending elasticity gives rise to entropie polymer elasticity, which can be precisely studied in single-molecule experiments. DNA's twist rigidity causes it to wrap around itself, or ‘supercoil’, when it is sufficiently twisted; thermal fluctuations destabilize supercoiling for DNAs twisted fewer than once per twist persistence length. Twisted DNAs under tension, braided DNAs, and the internal dynamics of supercoiled DNAs are discussed. The interplay between braiding and supercoiling free energy is argued to be important for the decatenation of duplicated DNAs in prokaryote cells.

The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this important material parameter. We extract its value from a recent experiment of Strick et al. and find rough agreement with an independent experimental estimate recently given by Marko. We also present a very simple microscopic theory predicting a value comparable to the one observed.

Distearyldimethylammonium (DSDMA) X (X− = OH, H2PO4) interact with double stranded T4 DNA (166 kilobase pairs) below and above the CMC (1.5×10−6). Below the CMC of either DSDMA X where the cationic double-chained surfactants are in the monomeric state, T4 DNA and DSDMA+form a compact complex where all surfactant molecules are bound. Close to the CMC, particularly for DSDMA OH but also in the presence of , T4 DNA exhibits a condensed (globule) conformation, though some DNA molecules are in the more extended DNA conformation. Above the CMC of DSDMA X a plateau is reached (up to 3.0 × 10−6 M surfactant) revealing a penetration of DSDMA molecules into the DNA globules resulting in a loosening of the tightened state of DNA. The various stages of the transition from the condensed coil to the extended state of T4 DNA with changing DSDMA X concentrations was monitored by static and inelastic light scattering experiments which were supplemented by small-angle X-ray scattering measurements.

We present a new method for electrophoretic separation of DNA, Ferro fluid Array Electrophoresis (FAE). The method uses a stabilized suspension of an hydrophobic ferrofluid in aqueous buffer as the separating medium. When this suspension is placed in a slab cell and submitted to a magnetic field perpendicular to the slab plane, it organizes into a regular array of columns with micron-sized spacing. DNA migrating in this maze leads to size-fractionation. Resolution of lambda phage (48.5 kbp) and T4 (140 kbp) DNA molecules in 30 mn is achieved. The motion of individual DNA molecules during FAE is observed using fluorescence videomicroscopy, and the molecular mechanisms responsible for separation are discussed in the light of recent computer simulations. During migration, large DNA molecules temporarily wrap around the impenetrable ferrofluid columns. They disengage by slippage, like a rope on a pulley, and the dependence of the disengagement time upon DNA size is responsible for the size-fractionation.

The conformation change of DNA fragments due to divalent counterion condensation onto DNA was investigated by pulse gel electrophoresis, and interpreted by gel models (Reptation and Henry model) and Manning's counterion condensation theory. The measured mobility reductions μ/μ0 of λ-DNA-Hind III fragments, ranging from 23.13 to 2.027 kilobase pairs, due to interaction with divalent cation Mg2+ (1–400 μμ), and Ca2+(0–40 μM) in tris-borate buffer were well fit by Manning's Counterion Condensation (CC) theory. We observed the normalized mobility reduction to be shifted by a small amount Δ(μ/μ0) relative to the CC prediction value. Δ(μ/μ0) is a function of DNA length, and the ion environment (divalent concentration C2 and ionic strength). The ‘shift’ phenomena only occurred close to where C2 began dominating the counterion binding, a condition described by the monovalent/divalent cation isocompetition point. Combining our observation with theoretical considerations, we conclude that the divalent counterion condensation changes the DNA fragments' conformation, resulting in an end-to-end distance decrease which is molecular weight dependent. The effect was enhanced by an increase of divalent ion concentration and a decrease of the ionic strength.

Alignment algorithms are commonly used to detect and quantify similarities between DNA sequences. We study these algorithms in the framework of a recent theory viewing similarity detection as a geometrical critical phenomenon of directed random walks. We show that the roughness of these random walks governs the fidelity of an alignment, i.e., its ability to capture the correlations between the sequences compared. Criteria for the optimization of alignment algorithms emerge from this theory.

Recent work on flexible membranes such as lipid bilayers with anchored polymers is briefly reviewed. These polymers exert bending moments onto the membranes and, thus, lead to a polymer–induced curvature. From the theoretical point of view, this curvature depends (i) on the membrane–polymer interactions; (ii) on the size of the polymers; and (iii) on the polymer coverage. Experimentally, these curvature effects can be deduced from systematic studies of polymer–decorated vesicles in which one monitors the vesicle shape with varying solvent conditions.

Macroscopically, phase changes (induced due to change of curvature) were observed on the introduction of PEG (polyethyleneglycol) grafted on lipids (anchored polymers) in the Winsor phases of microemulsion. Replacing some of the surfactant in the monolayers of the micro-emulsion with polymer grafted lipids changes the interaction between droplets of micro- emulsion and a greater increase in the percentage of anchored polymer in the monolayer might even bring about structural changes. The results on winsor phases, droplet microemulsions and bicontinous phases with anchored polymers as studied by Small Angle Neutron Scattering (SANS) are reported below, together with the contrast variation techniques used to characterize average curvature in the system.

The rich phase behaviour displayed by phospholipid bilayers and their structural relationship to biological membranes have made them fascinating objects of study. Despite being one of the most often examined of these model membrane systems, dipalmitoylphosphatidylcholine (DPPC) continues to be a source of interest for scientists. In particular, the ripple phase, Pβ′, of fully hydrated DPPC has generated a great deal of attention over the years as scientists have tried to understand the structural details of this novel phase1–5.

We investigate nonequilibrium behavior of a polydisperse ensemble of fluid membrane vesicles by means of a diffusive Boltzmann transport equation which, incorporates vesicle diffusion and the reactions between vesicles. This approach is used to study the time evolution of the size distribution of an initially monodisperse vesicle ensemble and its interesting properties such as the internal aqueous, encapsulated volume. We investigate various nonequilibrium paths such ensembles may follow during the equilibration process.

In this study we investigate the equilibrium conformational properties and dynamic relaxation behavior of polymer loops grafted at an interface using the discontinuous molecular dynamics simulation technique. Differences and similarities between the structural and dynamic properties of polymer loops and tails are identified. The conformational properties of mixtures of polymers loops and tails are also studied using the bond-fluctuation method. The effect of mixture composition on the conformational properties of the individual components in the mixture is discussed.

A detailed physical analysis of data obtained from static light and dynamic light scattering experiments with polymer-like distearyldimethylammonium OH (DSDMA X) micelles has been undertaken at dilute and semidilute concentrations, and compared with those in the presence of racemic and enantiomeric anions, e.g. S-(+)-lactate or the R-(-)-enantiomer.

The interfaces between the water-rich, oil-rich and disordered phases of a balanced ternary mixture of oil, water and amphiphile are studied, on the basis of a vector lattice model, by means of an exact partial integration and a local mean field approximation. The phase diagram exhibits a water/oil-rich phase, structured (ordered bicontinuous and lamellar) phases and a disordered phase with a microemulsion region. The interfacial tension and profiles at oil/water/disordered phase coexistence are calculated and the possibility of a wetting transition is discussed.

Self-assembling protein filaments are important components of a cell's superstructure. Among these, actin filaments form the backbone of protrusions and extensions such as pseudopodia. The rates at which these structures extend cover a startlingly wide range: the acrosomal process of the sea cucumber may extend 90 μm in 10 seconds, which is more than 20 times the speed at which an epithelial goldfish keratocyte crawls. We seek to explain this range by examining the delivery of actin monomers to the growing filament ends. We show that the diffusive flux of actin monomers is adequate for fueling the slower movement of crawling cells, but is insufficient to propel the quicker acrosomal process of the sea cucumber. By introducing bulk fluid flow in response to the diffusive movement of water through the cell membrane, actin delivery can be enhanced. We compare the calculated speeds to experimental observations and discuss future refinements to the model.

The effects of soft repulsions on hard particle systems are calculated using an avoidance model which improves upon the simple mean field approximation. The method not only yields a better free energy, but also gives an estimate for the short-range positional order induced by soft repulsions. The results indicate little short-range order for isotropically oriented rods. However, for parallel rods short-range order increases to significant levels as the particle axial ratio increases.

Situations where a polymeric material is exposed to a solvent mixture so that the different components within the mixture can diffuse into the polymer are common both in industrial applications and in biological processes. Often one of the components is taken up preferentially and its presence affects the diffusion properties of the remaining components. The problem of accounting for processes of this type has not been dealt with in a systematic way. This may in part be due to the difficulty of characterizing experimentally the separate diffusion behavior of the various components: data of this kind are now becoming available for simple binary mixtures. In order to model this class of problems, a lattice model involving a polymer matrix (M) and two diffusing components (A and B) has been introduced. The Monte Carlo evolution of the system has been examined for different values of the local A–M, B–M and A–B interactions. These results shed light on the microscopic origin of selective uptake.

High resolution melting curves of total nuclear Dictyostelium discoideum DNA (A×3 strain) are compared to theoretical melting calculated from GENBANK sequences(1.74 % of total) by the statistical thermodynamics program MELTSIM, parameterized for long DNA sequences(1,2). The lower and upper limits of simulated melting agree quantitatively with the experimental melting of total DNA. Calculated melting of coding, intron and flanking regions indicate that intron and flanking DNAs are extremely (A+T)-rich and account for the earliest melting DNA. There is no temperature overlap of these regions with coding DNA. A theoretical denaturation map of DNA containing the ribosomal DNA genes showed excellent agreement with subtransition positions of these genes in experimental curves. Agreement between these calculated and experimental melting data demonstrates our ability to accurately simulate DNA melting in complex eukaryotic genomes. This has important consequences for the understanding of sequence dependent energetic properties of nucleic acids and their potential use as biomaterials.