pH-induced morphological changes of proteinaceous viral shells.

Changes in environmental pH can induce morphological changes in empty proteinaceous shells of bacteriophages in vitro that are very similar to changes occurring in viral capsids in vivo after encapsidation of DNA. These changes in capsid shape and size cannot be explained with a simple elastic model alone. We propose a new theoretical framework that combines the elasticity of thin icosahedral shells with the pH dependence of capsid charge distribution. Minimization of the sum of elastic and electrostatic free energies leads to equilibrium shapes of viral shells that depend on a single elastic parameter and the detailed configuration of the imbedded protein charges. Based on the in vitro shell reconstructions of bacteriophage HK97 we elucidate the details of how the reversible transition between Prohead II and Expansion Intermediate II states of the HK97 procapsid is induced by pH changes, as well as some other features of the bacteriophage maturation.

Structural interactions in ionic liquids linked to higher-order Poisson-Boltzmann equations.

We present a derivation of generalized Poisson-Boltzmann equations starting from classical theories of binary fluid mixtures, employing an approach based on the Legendre transform as recently applied to the case of local descriptions of the fluid free energy. Under specific symmetry assumptions, and in the linearized regime, the Poisson-Boltzmann equation reduces to a phenomenological equation introduced by Bazant et al. [Phys. Rev. Lett. 106, 046102 (2011)]PRLTAO0031-900710.1103/PhysRevLett.106.046102, whereby the structuring near the surface is determined by bulk coefficients.

General theory of asymmetric steric interactions in electrostatic double layers.

We study the mean-field Poisson-Boltzmann equation in the context of dense ionic liquids where steric effects become important. We generalise lattice gas theory by introducing a Flory-Huggins entropy for ions of differing volumes and then compare the effective free energy density to other existing lattice gas approximations, not based on the Flory-Huggins Ansatz. Within the methodology presented we also invoke more realistic equations of state, such as the Carnahan-Starling approximation, that are not based on the lattice gas approximation and lead to thermodynamic functions and properties that differ strongly from the lattice gas case. We solve the Carnahan-Starling model in the high density limit, and demonstrate a slow, power-law convergence at high potentials. We elucidate how equivalent convex free energy functions can be constructed that describe steric effects in a manner which is more convenient for numerical minimisation.

Quantitative nanoscale electrostatics of viruses.

Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed ϕ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material.

Antipolar and Anticlinic Mesophase Order in Chromatin Induced by Nucleosome Polarity and Chirality Correlations.

Contrary to the usual "rigid supermolecular assembly" paradigm of chromatin structure, we propose to analyze its eventual ordered state in terms of symmetry properties of individual nucleosomes that give rise to mesophase order parameters, like in many other soft-matter systems. Basing our approach on the Landau-de Gennes phenomenology, we describe the mesoscale order in chromatin by antipolar and anticlinic correlations of chiral individual nucleosomes. This approach leads to a unifying physical picture of a whole series of soft locally ordered states with different apparent structures, including the recently observed heteromorphic chromatin, stemming from the antipolar arrangement of nucleosomes complemented by their chiral twisting. Properties of these states under an external force field can reconcile apparently contradictory results of single-molecule experiments.

Effect of magnesium ions on dielectric relaxation in semidilute DNA aqueous solutions.

The effect of magnesium ion Mg(2+) on the dielectric relaxation of semidilute DNA aqueous solutions has been studied by means of dielectric spectroscopy in the 100 Hz-100 MHz frequency range. de Gennes-Pfeuty-Dobrynin semidilute solution correlation length is the pertinent fundamental length scale for sufficiently low concentration of added salt, describing the collective properties of Mg-DNA solutions. No relaxation fingerprint of the DNA denaturation bubbles, leading to exposed hydrophobic core scaling, was detected at low DNA concentrations, thus indicating an increased stability of the double-stranded conformation in Mg-DNA solutions as compared to the case of Na-DNA solutions. Some changes are detected in the behavior of the fundamental length scale pertaining to the single molecule DNA properties, reflecting modified electrostatic screening effects of the Odijk-Skolnick-Fixman type. All results consistently demonstrate that Mg(2+) ions interact with DNA in a similar way as Na(1+) ions do, their effect being mostly describable through an enhanced screening.

Polymers pushing Polymers: Polymer Mixtures in Thermodynamic Equilibrium with a Pore.

We investigate polymer partitioning from polymer mixtures into nanometer size cavities by formulating an equation of state for a binary polymer mixture assuming that only one (smaller) of the two polymer components can penetrate the cavity. Deriving the partitioning equilibrium equations and solving them numerically allows us to introduce the concept of "polymers-pushing-polymers" for the action of non-penetrating polymers on the partitioning of the penetrating polymers. Polymer partitioning into a pore even within a very simple model of a binary polymer mixture is shown to depend in a complicated way on the composition of the polymer mixture and/or the pore-penetration penalty. This can lead to enhanced as well as diminished partitioning, due to two separate energy scales that we analyse in detail.

Structure and dynamics of hyaluronic acid semidilute solutions: a dielectric spectroscopy study.

Dielectric spectroscopy is used to investigate fundamental length scales describing the structure of hyaluronic acid sodium salt (Na-HA) semidilute aqueous solutions. In salt-free regime, the length scale of the relaxation mode detected in MHz range scales with HA concentration as c(HA)(-0.5) and corresponds to the de Gennes-Pfeuty-Dobrynin correlation length of polyelectrolytes in semidilute solution. The same scaling was observed for the case of long, genomic DNA. Conversely, the length scale of the mode detected in kilohertz range also varies with HA concentration as c(HA)(-0.5) which differs from the case of DNA (c(DNA)(-0.25)). The observed behavior suggests that the relaxation in the kilohertz range reveals the de Gennes-Dobrynin renormalized Debye screening length, and not the average size of the chain, as the pertinent length scale. Similarly, with increasing added salt the electrostatic contribution to the HA persistence length is observed to scale as the Debye length, contrary to scaling pertinent to the Odijk-Skolnick-Fixman electrostatic persistence length observed in the case of DNA. We argue that the observed features of the kilohertz range relaxation are due to much weaker electrostatic interactions that lead to the absence of Manning condensation as well as a rather high flexibility of HA as compared to DNA.

Viscous compressible hydrodynamics at planes, spheres and cylinders with finite surface slip.

We consider the linearized time-dependent Navier-Stokes equation including finite compressibility and viscosity. We first constitute the Green's function, from which we derive the flow profiles and response functions for a plane, a sphere and a cylinder for arbitrary surface slip length. For high driving frequency the flow pattern is dominated by the diffusion of vorticity and compression, for low frequency compression propagates in the form of sound waves which are exponentially damped at a screening length larger than the sound wave length. The crossover between the diffusive and propagative compression regimes occurs at the fluid's intrinsic frequency omega approximately c2rho0/eta, with c the speed of sound, rho0 the fluid density and eta the viscosity. In the propagative regime the hydrodynamic response function of spheres and cylinders exhibits a high-frequency resonance when the particle size is of the order of the sound wave length. A distinct low-frequency resonance occurs at the boundary between the propagative and diffusive regimes. Those resonant features should be detectable experimentally by tracking the diffusion of particles, as well as by measuring the fluctuation spectrum or the response spectrum of trapped particles. Since the response function depends sensitively on the slip length, in principle the slip length can be deduced from an experimentally measured response function.

Optically anisotropic infinite cylinder above an optically anisotropic half space: Dispersion interaction of a single-walled carbon nanotube with a substrate.

A complete form of the van der Waals dispersion interaction between an infinitely long anisotropic semiconducting/insulating thin cylinder and an anisotropic half space is derived for all separations between the cylinder and the half space. The derivation proceeds from the theory of dispersion interactions between two anisotropic infinite half spaces as formulated in Phys. Rev. A 71, 042102 (2005). The approach is valid in the retarded as well as nonretarded regimes of the interaction and is coupled with the recently evaluated ab initio dielectric response functions of various semiconducting/insulating single wall carbon nanotubes, enables the authors to evaluate the strength of the van der Waals dispersion interaction for all orientation angles and separations between a thin cylindrical nanotube and the half space. The possibility of repulsive and/or nonmonotonic dispersion interactions is examined in detail.

A phenomenological one-parameter equation of state for osmotic pressures of PEG and other neutral flexible polymers in good solvents.

We present a phenomenological one-parameter scaling equation of state that accurately represents osmotic pressures of neutral flexible polymers in good solvents from the dilute through the semidilute regime. The equation comprises a sum of scaled van't Hoff and des Cloizeaux terms including a fitted parameter alpha, the "crossover index", which encapsulates all chemical specificity and determines the relevant prefactors. Strikingly different values of alpha are found for the two very different systems poly(ethyleneglycol)/water (PEG) and poly(alpha-methylstyrene)/toluene (PAMS). Alpha-dependent rescaling collapses both data sets to a simple one-parameter scaling function. The fact that the anomalous system PEG/water and the canonical system PAMS/toluene can both be described by the same equation of state attests to the robustness of the polymer-scaling concepts introduced by de Gennes.

The role of multipoles in counterion-mediated interactions between charged surfaces: strong and weak coupling.

We present general arguments for the importance, or lack thereof, of structure in the charge distribution of counterions for counterion-mediated interactions between bounding symmetrically charged surfaces. We show that on the mean field or weak coupling level, the charge quadrupole contributes the lowest order modification to the contact value theorem and thus to the intersurface electrostatic interactions. The image effects are non-existent on the mean field level even with multipoles. On the strong coupling level the quadrupoles and higher order multipoles contribute additional terms to the interaction free energy only in the presence of dielectric inhomogeneities. Without them, the monopole is the only multipole that contributes to the strong coupling electrostatics. We explore the consequences of these statements in all their generality.

Strong-coupling electrostatics in the presence of dielectric inhomogeneities.

We study the strong-coupling (SC) interaction between two like-charged membranes of finite thickness embedded in a medium of higher dielectric constant. A generalized SC theory is applied along with extensive Monte Carlo simulations to study the image charge effects induced by multiple dielectric discontinuities in this system. These effects lead to strong counterion crowding in the central region of the intersurface space upon increasing the solvent-membrane dielectric mismatch and change the membrane interactions from attractive to repulsive at small separations. These features agree quantitatively with the SC theory at elevated couplings or dielectric mismatch where the correlation hole around counterions is larger than the thickness of the central counterion layer.

Packing nanomechanics of viral genomes.

We investigate the osmotic equilibrium between a bulk polyethylene glycol (PEG) solution and DNA tightly packed in a spherical capsid. We base our analysis on the equations of thermodynamic equilibrium in terms of osmotic pressure. The equality between external osmotic pressure of PEG and osmotic pressure of tightly packed DNA gives us the DNA encapsidation curves. In this way we directly connect the wealth of existing osmotic pressure data for DNA in the bulk with the DNA encapsidation curves within small viral capsids. Specific calculations are made for a monovalent salt, Na(+) -DNA and a divalent salt, Mn(2+) -DNA that have quite different DNA encapsidation behaviors. The main conclusion of our work is that bending energy of DNA is of minor importance regarding the encapsidated DNA length, but has a non-negligible influence on the density distribution of DNA within the capsid.

Weak- and strong-coupling electrostatic interactions between asymmetrically charged planar surfaces.

We compare weak- and strong-coupling theory of counterion-mediated electrostatic interactions between two asymmetrically charged plates with extensive Monte Carlo simulations. Analytical results in both weak- and strong-coupling limits compare excellently with simulations in their respective regimes of validity. The system shows a surprisingly rich structure in terms of interactions between the surfaces as well as fundamental qualitative differences in behavior in the weak- and the strong-coupling limits.

Electrostatic image effects for counterions between charged planar walls.

We study the effect of dielectric inhomogeneities on the interaction between two planparallel charged surfaces with oppositely charged mobile charges in between. The dielectric constant between the surfaces is assumed to be different from the dielectric constant of the two semi-infinite regions bounded by the surfaces, giving rise to electrostatic image interactions. We show that on the weak-coupling level the image charge effects are generally small, making their mark only in the second-order fluctuation term. However, in the strong-coupling limit, the image effects are large and fundamental. They modify the interactions between the two surfaces in an essential way. Our calculations are particularly useful in the regime of parameters where computer simulations would be difficult and extremely time consuming due to the complicated nature of the long-range image potentials.

The boundary element approach to Van der Waals interactions.

We develop a boundary element method to calculate Van der Waals interactions for systems composed of domains of spatially constant dielectric response of a general boundary shape. We achieve this by rewriting the interaction energy expression presented in Phys. Rev. B, 62 (2000) 6997 exclusively in terms of surface integrals of surface operators. We validate this approach in the Lifshitz case and give numerical results for the interaction of two spheres as well as the van der Waals self-interaction of a uniaxial ellipsoid. Our method is simple to implement and is particularly suitable for a full, non-perturbative numerical evaluation of non-retarded van der Waals interactions between objects of a completely general shape.

Screwlike order, macroscopic chirality, and elastic distortions in high-density DNA mesophases.

We investigate a new screwlike liquid-crystalline ordering in solutions of helical biopolymers and its influence on the state of individual molecules. In the resulting mesophase translational and rotational motions of molecules are coupled in screw fluctuations. We show that in contrast to the case of conventional chiral liquid crystals the elastic distortion does not twist the screw order but leads to overwinding of individual helical molecules. This explains the peculiarities of high-density DNA mesophases.

Dielectric relaxation of DNA aqueous solutions.

We report on a detailed characterization of complex dielectric response of Na-DNA aqueous solutions by means of low-frequency dielectric spectroscopy (40 Hz-110 MHz). Results reveal two broad relaxation modes of strength 20

Screening and fundamental length scales in semidilute Na-DNA aqueous solutions.

The fundamental length scales in semidilute Na-DNA aqueous solutions have been investigated by dielectric spectroscopy. The low- and the high-frequency relaxation modes are studied in detail. The length scale of the high-frequency relaxation mode at high DNA concentrations can be identified with the de Gennes-Pfeuty-Dobrynin correlation length of polyelectrolytes in semidilute solution, whereas at low DNA concentrations and in the low added salt limit the length scale shows an unusual exponent reminiscent of semidilute polyelectrolyte chains with hydrophobic backbone. The length scale of the low-frequency relaxation mode corresponds to a Gaussian chain composed of correlation blobs in the low added salt limit, and to the Odijk-Skolnick-Fixman value of the single chain persistence length in the high added salt limit.