arXiv subjects

Rudolf Podgornik

Publications and source records attributed to Rudolf Podgornik.

At least 109 records · Page 6Linked to original sources

arXiv2013

Electrostatic stability and encapsidation of charged nano-droplets

We investigate electrostatic stability of charged droplets, modeled as permeable, charged spheres, and their encapsidation in thin, arbitrarily charged nano-shells, immersed in a neutralizing asymmetric electrolyte background. The latter consists of a small concentration of mobile multivalent counterions in a bathing solution of monovalent (positive and negative) ions. We use extensive Monte-Carlo simulations to investigate the spatial distribution of multivalent counterions and the electrostatic component of their osmotic pressure on the bounding surface of the spherical nano-shell. The osmotic pressure can be negative (inward pressure), positive (outward pressure) or zero, depending on the system parameters such as the charge density of the droplet, the charge density of the shell, and the electrolyte screening, which thus determine the stability of the nano-container. The counter-intuitive effects of multivalent counterions comprise the increased stability of the charged droplet with larger charge density, increased stability in the case of encapsidating shell of charge density of the same sign as the charged droplet, as well as the possibility to dispense altogether with the encapsidating shell, its confining effect taken over by the multivalent counterions. These dramatic effects are in stark contrast to the conventional mean-field picture, which in particular implies that a more highly charged spherical droplet should be electrostatically less stable because of its larger (repulsive) self-energy.

cond-mat.soft↗

arXiv2013

Interaction of a point charge with the surface of a uniaxial dielectric

We analyze the force on a point charge moving at relativistic speeds parallel to the surface of a uniaxial dielectric. Two cases are examined: a lossless dielectric with no dispersion and a dielectric with a plasma type response. The treatment focuses on the peculiarities of the strength and direction of the interaction force as compared to the isotropic case. We show that a plasma type dielectric can, under specific conditions, repel the point charge.

physics.class-ph↗

arXiv2013

Symmetry effects in electrostatic interactions between two arbitrarily charged spherical shells in the Debye-Hückel approximation

Inhomogeneous charge distributions have important repercussions on electrostatic interactions in systems of charged particles but are often difficult to examine theoretically. We investigate how electrostatic interactions are influenced by patchy charge distributions exhibiting certain point group symmetries. We derive a general form of the electrostatic interaction energy of two permeable, arbitrarily charged spherical shells in the Debye-Hückel approximation and apply it to the case of particles with icosahedral, octahedral, and tetrahedral inhomogeneous charge distributions. We analyze in detail how charge distribution symmetry modifies the interaction energy and find that local charge inhomogeneities reduce the repulsion of two overall equally charged particles, while sufficient orientational variation in the charge distribution can turn the minimum interaction energy into an attraction. Additionally we show that larger patches and thus lower symmetries and wave numbers result in bigger attraction given the same variation.

cond-mat.soft↗

arXiv2013

Statistical analysis of sizes and shapes of virus capsids and their resulting elastic properties

From the analysis of sizes of approximately 130 small icosahedral viruses we find that there is a typical structural capsid protein, having a mean diameter of 5 nm and a mean thickness of 3 nm, with more than two thirds of the analyzed capsid proteins having thicknesses between 2 nm and 4 nm. To investigate whether, in addition to the fairly conserved geometry, capsid proteins show similarities in the way they interact with one another, we examined the shapes of the capsids in detail. We classified them numerically according to their similarity to sphere and icosahedron and an interpolating set of shapes in between, all of them obtained from the theory of elasticity of shells. In order to make a unique and straightforward connection between an idealized, numerically calculated shape of an elastic shell and a capsid, we devised a special shape fitting procedure, the outcome of which is the idealized elastic shape fitting the capsid best. Using such a procedure we performed statistical analysis of a series of virus shapes and we found similarities between the capsid elastic properties of even very different viruses. As we explain in the paper, there are both structural and functional reasons for the convergence of protein sizes and capsid elastic properties. Our work presents a specific quantitative scheme to estimate relatedness between different proteins based on the details of the (quaternary) shape they form (capsid). As such, it may provide an information complementary to the one obtained from the studies of other types of protein similarity, such as the overall composition of structural elements, topology of the folded protein backbone, and sequence similarity.

physics.bio-ph↗

arXiv2012

Chirality-Dependent Properties of Carbon Nanotubes. Electronic Structure: Optical Dispersion Properties, Hamaker Coefficients and van der Waals - London dispersion interactions

Optical dispersion spectra at energies up to 30 eV play a vital role in understanding the chirality-dependent van der Waals London dispersion interactions of single wall carbon nanotubes (SWCNTs). We use one-electron theory based calculations to obtain the band structures and the frequency dependent dielectric response function from 0-30 eV for 64 SWCNTs differing in radius, electronic structure classification, and geometry. The resulting optical dispersion properties can be categorized over three distinct energy intervals (M, pi, and sigma, respectively representing 0-0.1, 0.1-5, and 5-30 eV regions) and over radii above or below the zone-folding limit of 0.7 nm. While pi peaks vary systematically with radius for a given electronic structure type, peaks are independent of tube radius above the zone folding limit and depend entirely on SWCNT geometry. Based on these calculated one-electron dielectric response functions we compute and review Van derWaals - London dispersion spectra, full spectral Hamaker coefficients, and van derWaals - London dispersion interaction energies for all calculated frequency dependent dielectric response functions. Our results are categorized using a new optical dielectric function classification scheme that groups the nanotubes according to observable trends and notable features (e.g. the metal paradox) in the 0-30 eV part of the optical dispersion spectra. While the trends in these spectra begin to break down at the zone folding diameter limit, the trends in the related van derWaals - London dispersion spectra tend to remain stable all the way down to the smallest single wall carbon nanotubes in a given class.

cond-mat.mes-hall↗

arXiv2012

Confined chiral polymer nematics: ordering and spontaneous condensation

We investigate condensation of a long confined chiral nematic polymer inside a spherical enclosure, mimicking condensation of DNA inside a viral capsid. The Landau-de Gennes nematic free energy {\sl Ansatz} appropriate for nematic polymers allows us to study the condensation process in detail with different boundary conditions at the enclosing wall that simulate repulsive and attractive polymer-surface interactions. Increasing the chirality, we observe a transformation of the toroidal condensate into a closed surface with an increasing genus, akin to the ordered domain formation observed in cryo-microscopy of bacteriophages.

cond-mat.soft↗

arXiv2012

Aspects of One-Dimensional Coulomb Gases

In this short review, we discuss recent advances in exact solutions of models based on a one- dimensional (1D) Coulomb gas by means of field-theoretic functional integral methods. The exact solutions can be used to assess the accuracy of various approximations such as the weak coupling Poisson-Boltzmann theory as well as the strong coupling theory of Coulomb gases. We consider three different 1D models: the Coulomb fluid configuration in the case of the soap film model consisting of positively and negatively charged particles between adsorbing boundaries, counterions between two charged surfaces, and an ionic liquid lattice capacitor with positively and negatively charged particles on a lattice between one positive and one negative bounding surface.

cond-mat.stat-mech↗

arXiv2012

Coulomb interactions between disordered charge distributions

We review some of the recent results in the context of the Coulomb interaction between dielectric surfaces which are randomly charged but remain net-neutral on the average. Such surfaces are found to interact in vacuum with attractive long-range normal forces due to the presence of the quenched charge disorder which can compete with the standard Casimir-Van der Waals forces. They can also interact with random lateral forces and torques, which exhibit zero mean values but finite and long-range root-mean-square values. These effects can play an important role in Casimir experiments as well as in the interaction between solid surfaces as well as biomolecular surfaces that are often covered by disordered charge distributions.

cond-mat.soft↗

arXiv2012

One dimensional Potts model with many-body interactions and the Generalized Model of Polypeptide Chain for the helix-coil transition

Helix-coil transition in polypeptides is an example of a spin model with a preferred spin direction, in the sense that a theoretical formulation of this problem requires to assign a preferred value of spin to the helical conformation in order to account for different symmetries of the helical {\sl vs.} the coil states. This leads to the spin Hamiltonian of the {\sl Generalized Model of Polypeptide Chain} (GMPC) variety as opposed to the Potts model variety, both with many-body interactions. We compare the explicit solution of the Potts model and the solution of the GMPC within the transfer-matrix formalism. Comparison of both secular equations reveals that the largest eigenvalue of the Potts model with $Δ$ many-body interactions is identical to the largest eigenvalue of the GMPC model with $Δ-1$ many-body interactions, indicating the equivalence of both free energies. In distinction, the second largest eigenvalues do not coincide, leading to different thermal behavior of the spatial correlation length, related to the helix-coil transition interval. Spin models with built-in spin anisotropy thus engender different physical properties in the thermodynamic limit that we explore in detail.

cond-mat.stat-mech↗

arXiv2012

Electrostatic interactions mediated by polarizable counterions: weak and strong coupling limits

We investigate the statistical mechanics of an inhomogeneous Coulomb fluid composed of charged particles with static polarizability. We derive the weak- and the strong-coupling approximations and evaluate the partition function in a planar dielectric slab geometry with charged boundaries. We investigate the density profiles and the disjoining pressure for both approximations. Comparison to the case of non-polarizable counterions shows that polarizability brings important differences in the counterion density distribution as well as the counterion mediated electrostatic interactions between charged dielectric interfaces.

cond-mat.soft↗

arXiv2012

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.

cond-mat.soft↗

arXiv2012

Attraction between Neutral Dielectrics Mediated by Multivalent Ions in an Asymmetric Ionic Fluid

We study the interaction between two neutral plane-parallel dielectric bodies in the presence of a highly asymmetric ionic fluid, containing multivalent as well as monovalent (salt) ions. Image charge interactions, due to dielectric discontinuities at the boundaries, as well as effects from ion confinement in the slit region between the surfaces are taken fully into account, leading to image-generated depletion attraction, ion correlation attraction and steric-like repulsive interactions. We investigate these effects by employing a combination of methods including explicit-ion and implicit-ion Monte-Carlo simulations, as well as an effective interaction potential analytical theory. The latter incorporates strong ion-image charge correlations, which develop in the presence of high valency ions in the mixture. We show that the implicit-ion simulations and the proposed analytical theory can describe the explicit simulation results on a qualitative level, while excellent quantitative agreement can be obtained for sufficiently large monovalent salt concentrations. The resultant attractive interaction between the neutral surfaces is shown to be significant, as compared with the usual van der Waals interactions between semi-infinite dielectrics, and can thus play a significant role at the nano scale.

cond-mat.soft↗

arXiv2012

Sample-to-sample torque fluctuations in a system of coaxial randomly charged surfaces

Polarizable randomly charged dielectric objects have been recently shown to exhibit long-range lateral and normal interaction forces even when they are effectively net neutral. These forces stem from an interplay between the quenched statistics of random charges and the induced dielectric image charges. This type of interaction has recently been evoked to interpret measurements of Casimir forces in vacuo, where a precise analysis of such disorder-induced effects appears to be necessary. Here we consider the torque acting on a randomly charged dielectric surface (or a sphere) mounted on a central axle next to another randomly charged surface and show that although the resultant mean torque is zero, its sample-to-sample fluctuation exhibits a long-range behavior with the separation distance between the juxtaposed surfaces and that, in particular, its root-mean-square value scales with the total area of the surfaces. Therefore, the disorder-induced torque between two randomly charged surfaces is expected to be much more pronounced than the disorder-induced lateral force and may provide an effective way to determine possible disorder effects in experiments, in a manner that is independent of the usual normal force measurement.

cond-mat.soft↗

arXiv2012

Electromagnetic fluctuation-induced interactions in randomly charged slabs

Randomly charged net-neutral dielectric slabs are shown to interact across a featureless dielectric continuum with long-range electrostatic forces that scale with the statistical variance of their quenched random charge distribution and inversely with the distance between their bounding surfaces. By accounting for the whole spectrum of electromagnetic field fluctuations, we show that this long-range disorder-generated interaction extends well into the retarded regime where higher-order Matsubara frequencies contribute significantly. This occurs even for highly clean samples with only a trace amount of charge disorder and shows that disorder effects can be important down to the nano scale. As a result, the previously predicted non-monotonic behavior for the total force between dissimilar slabs as a function of their separation distance is substantially modified by higher-order contributions, and in almost all cases of interest, we find that the equilibrium inter-surface separation is shifted to substantially larger values compared to predictions based solely on the zero-frequency component. This suggests that the ensuing non-monotonic interaction is more easily amenable to experimental detection. The presence of charge disorder in the intervening dielectric medium between the two slabs is shown to lead to an additional force that can be repulsive or attractive depending on the system parameters and can, for instance, wash out the non-monotonic behavior of the total force when the intervening slab contains a sufficiently large amount of disorder charges.

cond-mat.soft↗

arXiv2012

Wrapping Transition and Wrapping-Mediated Interactions for Discrete Binding along an Elastic Filament: An Exact Solution

The wrapping equilibria of one and two adsorbing cylinders are studied along a semi-flexible filament (polymer) due to the interplay between elastic rigidity and short-range adhesive energy between the cylinder and the filament. We show that statistical mechanics of the system can be solved exactly using a path integral formalism which gives access to the full effect of thermal fluctuations, going thus beyond the usual Gaussian approximations which take into account only the contributions from the minimal energy configuration and small fluctuations about this minimal energy solution. We obtain the free energy of the wrapping-unwrapping transition of the filament around the cylinders as well as the effective interaction between two wrapped cylinders due to thermal fluctuations of the elastic filament. A change of entropy due to wrapping of the filament around the adsorbing cylinders as they move closer together is identified as an additional source of interactions between them. Such entropic wrapping effects should be distinguished from the usual entropic configuration effects in semi-flexible polymers. Our results may be applicable to the problem of adsorption of proteins as well as synthetic nano-particles on semi-flexible polymers such as DNA.

cond-mat.soft↗

arXiv2012

How simple can a model of an empty viral capsid be? Charge distributions in viral capsids

We investigate and quantify salient features of the charge distributions on viral capsids. Our analysis combines the experimentally determined capsid geometry with simple models for ionization of amino acids, thus yielding the detailed description of spatial distribution for positive and negative charge across the capsid wall. The obtained data is processed in order to extract the mean radii of distributions, surface charge densities and dipole moment densities. The results are evaluated and examined in light of previously proposed models of capsid charge distributions, which are shown to have to some extent limited value when applied to real viruses.

physics.bio-ph↗

arXiv2012

The one dimensional Coulomb lattice fluid capacitor

The one dimensional Coulomb lattice fluid in a capacitor configuration is studied. The model is formally exactly soluble via a transfer operator method within a field theoretic representation of the model. The only interactions present in the model are the one dimensional Coulomb interaction between cations and anions and the steric interaction imposed by restricting the maximal occupancy at any lattice site to one particle. Despite the simplicity of the model, a wide range of intriguing physical phenomena arise, some of which are strongly reminiscent of those seen in experiments and numerical simulations of three dimensional ionic liquid based capacitors. Notably we find regimes where over-screening and density oscillations are seen near the capacitor plates. The capacitance is also shown to exhibit strong oscillations as a function of applied voltage. It is also shown that the corresponding mean field theory misses most of these effects. The analytical results are confirmed by extensive numerical simulations.

cond-mat.soft↗

arXiv2012

Osmotic pressure induced coupling between cooperativity and stability of a helix-coil transition

Most helix-coil transition theories can be characterized by a set of three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to the helical state formation; and geometric, indicating how many repeating units are affected by the formation of one helical state. Depending on their effect on the helix-coil transition, solvents or co-solutes can be classified with respect to their action on these parameters. Solvent interactions that alter the entropic cost of helix formation by their osmotic action can affect both the stability (transition temperature) and the cooperativity (transition interval) of the helix-coil transition. A consistent inclusion of osmotic pressure effects in a description of helix-coil transition for poly(L-glutamic acid) in solution with polyethylene glycol can offer an explanation of the experimentally observed linear dependence of transition temperature on osmotic pressure as well as the concurrent changes in the cooperativity of the transition.

q-bio.BM↗