arXiv subjects

Rudolf Podgornik

Publications and source records attributed to Rudolf Podgornik.

At least 91 records · Page 5Linked to original sources

arXiv2015

Effective interactions between fluid membranes

A self-consistent theory is proposed for the general problem of interacting undulating fluid membranes subject to the constraint that they do not interpenetrate. We implement the steric constraint via an exact functional integral representation, and through the use of a saddle-point approximation transform it into a novel effective steric potential. The steric potential is found to consist of two contributions: one generated by zero mode fluctuations of the membranes, and the other by thermal bending fluctuations. For membranes of cross-sectional area $S$, we find that the bending fluctuation part scales with the inter-membrane separation $d$ as $d^{-2}$ for $d \ll \sqrt{S}$, but crosses over to $d^{-4}$ scaling for $d \gg \sqrt{S}$, whereas the zero mode part of the steric potential always scales as $d^{-2}$. For membranes interacting exclusively via the steric potential, we obtain closed-form expressions for the effective interaction potential and for the rms undulation amplitude $σ$, which becomes small at low temperatures $T$ and/or large bending stiffnesses $κ$. Moreover, $σ$ scales as $d$ for $d \ll \sqrt{S}$, but saturates at $\sqrt{k_{\rm B} T S/κ}$ for $d \gg \sqrt{S}$. In addition, using variational Gaussian theory, we apply our self-consistent treatment to study inter-membrane interactions subject to three different types of potential: (i)~the Moreira-Netz potential for a pair of strongly charged membranes with an intervening solution of multivalent counterions, (ii)~an attractive square well, (iii)~the Morse potential, and (iv)~a combination of hydration and van der Waals interactions.

cond-mat.soft↗

arXiv2015

Solvent Effects in the Helix-Coil Transition Model can explain the Unusual Biophysics of Intrinsically Disordered Proteins

We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible states to the number corresponding to a helical conformation. The resulting transition phase diagram is then juxtaposed with the unusual behavior of the secondary structures in Intrinsically Disordered Proteins (IDPs) and a number of similarities are observed, even if the protein folding is a more complex transition than the helix-coil transition. In fact, the deficit in bulky and hydrophobic amino acids observed in IDPs, translated into larger values of phase space volume, allows us to locate the region in parameter space of the helix-coil transition that would correspond to the secondary structure transformations that are intrinsic to conformational transitions in IDPs and that is characterized by a modified phase diagram when compared to globular proteins. Here, we argue how the nature of this modified phase diagram, obtained from a model of the helix-coil transition in a solvent, would illuminate the turned-out response of IDPs to the changes in the environment conditions that follow straightforwardly from the re-entrant (cold denaturation) branch in their folding phase diagram.

q-bio.BM↗

arXiv2015

Bending rigidities and interdomain forces in membranes with coexisting lipid domains

In order to precisely quantify the fundamental interactions between heterogeneous lipid membranes with coexisting liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed detailed osmotic stress SAXS experiments by exploiting the domain alignment in raft-mimicking lipid multibilayers. Performing a Monte Carlo (MC) based analysis allowed us to determine with high reliability the magnitude and functional dependence of interdomain forces concurrently with the bending elasticity moduli. In contrast to previous methodologies, this approach enabled us to consider the entropic undulation repulsions on a fundamental level, without having to take recourse to crudely justified mean-field like additivity assumptions. Our detailed Hamaker coefficient calculations indicated only small differences in the van der Waals attractions of coexisting Lo and Ld phases. In contrast, the repulsive hydration and undulation interactions differed significantly, with the latter dominating the overall repulsions in the Ld phase. Therefore, alignment of like domains in multibilayers appears to originate from both, hydration and undulation repulsions.

cond-mat.soft↗

arXiv2015

Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities

We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van der Waals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel $r^{-5}$ scaling behavior of the van der Waals interaction energy for small inter-polymer separation $r$, in contradistinction to the $r^{-4}$ scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently aligned identical polymers. Such behavior can assist the molecular recognition between polymers.

cond-mat.soft↗

arXiv2015

Differential capacitance of the electric double layer: The interplay between ion finite size and dielectric decrement

We study the electric double layer by combining the effects of ion finite size and dielectric decrement. At high surface potential, both mechanisms can cause saturation of the counter-ion concentration near a charged surface. The modified Grahame equation and differential capacitance are derived analytically for a general expression of a permittivity epsilon(n) that depends on the local ion concentration, n, and under the assumption that the co-ions are fully depleted from the surface. The concentration at counter-ion saturation is found for any epsilon(n), and a criterion predicting which of the two mechanisms (steric vs. dielectric decrement) is the dominant one is obtained. At low salinity, the differential capacitance as function of surface potential has two peaks (so-called camel-shape). Each of these two peaks is connected to a saturation of counter-ion concentration caused either by dielectric decrement or by their finite size. Because these effects depend mainly on the counter-ion concentration at the surface proximity, for opposite surface-potential polarity either the cations or anions play the role of counter-ions, resulting in an asymmetric camel-shape. At high salinity, we obtain and analyze the crossover in the differential capacitance from a double-peak shape to a uni-modal one. Finally, several nonlinear models of the permittivity decrement are considered, and we predict that the concentration at dielectrophoretic saturation shifts to higher concentration than those obtained by the linear decrement model.

cond-mat.soft↗

arXiv2014

Strong coupling electrostatics for randomly charged surfaces: Antifragility and effective interactions

We study the effective interaction mediated by strongly coupled Coulomb fluids between dielectric surfaces carrying quenched, random monopolar charges with equal mean and variance, both when the Coulomb fluid consists only of mobile multivalent counterions and when it consists of an asymmetric ionic mixture containing multivalent and monovalent (salt) ions in equilibrium with an aqueous bulk reservoir. We analyze the consequences that follow from the interplay between surface charge disorder, dielectric and salt image effects, and the strong electrostatic coupling that results from multivalent counterions on the distribution of these ions and the effective interaction pressure they mediate between the surfaces. In a dielectrically homogeneous system, we show that the multivalent counterions are attracted towards the surfaces with a singular, disorder-induced potential that diverges logarithmically on approach to the surfaces, creating a singular counterion density profile with an algebraic divergence at the surfaces. This effect drives the system towards a state of lower thermal "disorder", one that can be described by a renormalized temperature, exhibiting thus a remarkable antifragility. The interaction pressure acting on the surfaces displays in general a highly non-monotonic behavior as a function of the inter-surface separation with a prominent regime of attraction at small to intermediate separations. This attraction is caused directly by the combined effects from charge disorder and strong coupling electrostatics of multivalent counterions, which can be quite significant even with a small degree of surface charge disorder relative to the mean surface charge. The strong coupling, disorder-induced attraction is typically far more stronger than the van der Waals interaction between the surfaces, especially within a range of several nanometers for the inter-surface separation.

cond-mat.soft↗

arXiv2014

Charge regulation in ionic solutions: thermal fluctuations and Kirkwood-Schumaker interaction

We study the behavior of two macroions with dissociable charge groups, regulated by local variables such as pH and electrostatic potential, immersed in a mono-valent salt solution, considering cases where the net charge can either change sign or remain of the same sign depending on these local parameters. The charge regulation, in both cases, is described with the proper free energy function for each of the macroions, while the coupling between the charges is evaluated on the approximate Debye-Hückel level. The charge correlation functions and the ensuing charge fluctuation forces are calculated analytically and numerically. Strong attraction between like-charged macroions is found close to the point of zero charge, specifically due to asymmetric, anticorrelated charge fluctuations of the macroion charges. The general theory is then implemented for a system of two protein-like macroions, generalizing the form and magnitude of the Kirkwood-Schumaker interaction.

physics.chem-ph↗

arXiv2014

Asymmetric Coulomb fluids at randomly charged dielectric interfaces: Anti-fragility, overcharging and charge inversion

We study the distribution of multivalent counterions next to a dielectric slab, bearing a quenched, random distribution of charges on one of its solution interfaces, with a given mean and variance, both in the absence and in the presence of a bathing monovalent salt solution. We use the previously derived approach based on the dressed multivalent-ion theory that combines aspects of the strong and weak coupling of multivalent and monovalent ions in a single framework. The presence of quenched charge disorder on the charged surface of the dielectric slab is shown to substantially increase the density of multivalent counterions in its vicinity. In the counterion-only model (with no monovalent salt ions), the surface disorder generates an additional logarithmic attraction potential and thus an algebraically singular counterion density profile at the surface. This behavior persists also in the presence of a monovalent salt bath and results in significant violation of the contact-value theorem, reflecting the anti-fragility effects of the disorder that drive the system towards a more ordered state. In the presence of an interfacial dielectric discontinuity, depleting the counterion layer at the surface, the charge disorder still generates a much enhanced counterion density further away from the surface. Likewise, the charge inversion and/or overcharging of the surface occur more strongly and at smaller bulk concentrations of multivalent counterions when the surface carries quenched charge disorder. Overall, the presence of quenched surface charge disorder leads to sizable effects in the distribution of multivalent counterions in a wide range of realistic parameters and typically within a distance of a few nanometers from the charged surface.

cond-mat.soft↗

arXiv2014

Fluctuation-induced interactions in nematics with disordered anchoring energy

We examine fluctuation-induced (pseudo-Casimir) interactions in nematic liquid-crystalline films confined between two surfaces, where one of the surfaces imposes a strong homeotropic anchoring (ensuring a uniform mean director profile), while the other one is assumed to be a chemically disordered substrate exhibiting an annealed, random distribution of anchoring energies. We employ a saddle-point approximation to evaluate the free energy of interaction mediated between the two surfaces and investigate how the interaction force is influenced by the presence of disordered surface anchoring energy. It is shown that the disorder results in a renormalization of the effective surface anchoring parameter in a way that it leads to quantitative and qualitative changes (including a change of sign at intermediate inter-surface separations) in the pseudo-Casimir interaction force when compared with the interaction force in the absence of disorder.

cond-mat.soft↗

arXiv2014

Field theoretic description of charge regulation interaction

In order to find the exact form of the electrostatic interaction between two proteins with dissociable charge groups in aqueous solution, we have studied a model system composed of two macroscopic surfaces with charge dissociation sites immersed in a counterion-only ionic solution. Field-theoretic representation of the grand canonical partition function is derived and evaluated within the mean-field approximation, giving the Poisson-Boltzmann theory with the Ninham-Parsegian boundary condition. Gaussian fluctuations around the mean-field are then analyzed in the lowest order correction that we calculate analytically and exactly, using the path integral representation for the partition function of a harmonic oscillator with time-dependent frequency. The first order (one loop) free energy correction gives the interaction free energy that reduces to the zero-frequency van der Waals form in the appropriate limit but in general gives rise to a mono-polar fluctuation term due to charge fluctuation at the dissociation sites. Our formulation opens up the possibility to investigate the Kirkwood-Shumaker interaction in more general contexts where their original derivation fails.

physics.chem-ph↗

arXiv2014

Relaxation of the thermal Casimir force between net neutral plates containing Brownian charges

We investigate the dynamics of thermal Casimir interactions between plates described within a living conductor model, with embedded mobile anions and cations, whose density field obeys a stochastic partial differential equation which can be derived starting from the Langevin equations of the individual particles. This model describes the thermal Casimir interaction in the same way that the fluctuating dipole model describes van der Waals interactions. The model is analytically solved in a Debye-Hückel-like approximation. We identify several limiting dynamical regimes where the time dependence of the thermal Casimir interactions can be obtained explicitly. Most notably we find a regime with diffusive scaling, even though the charges are confined to the plates and do not diffuse into the intervening space, which makes the diffusive scaling difficult to anticipate and quite unexpected on physical grounds.

cond-mat.stat-mech↗

arXiv2014

From toroidal to rod-like condensates of semiflexible polymers

The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring molecules, using analytical theory supported by Monte Carlo simulations. Both conformations considered are characterized by a local nematic order with hexagonal packing symmetry of neighboring DNA molecules, but differ in global configuration of the chain and the distribution of its curvature as it wraps around to form a condensate. The long-range interactions driving the DNA condensation are assumed to be of the form pertaining to the attractive depletion potential as well as the attractive counterion induced soft potential. In the stiffness-length plane we find a transition between rod-like to toroid condensate for increasing stiffness at a fixed chain length $L$. Strikingly, the transition line is found to have a $L^{1/3}$ dependence irrespective of the details of the long-range interactions between neighboring molecules. When realistic DNA parameters are used, our description reproduces rather well some of the experimental features observed in DNA condensates.

cond-mat.soft↗

arXiv2014

Kirkwood-Shumaker interactions and general thermal fluctuation forces

We present an extension of the Kirkwood-Shumaker (KS) theory of proton-fluctuation interactions to situations where the perturbation theory, usually invoked to derive these interactions, fails. In order to do that we formulate a generalized theory of fluctuation interactions with non-linear macroion (surface) free energy term that naturally leads to the long-range KS interactions, but can also be straightforwardly generalized to situations where the perturbation expansion ceases to be valid. It also allows for other surface free energy terms to be treated within the same formalism, enabling us to derive the complete fluctuation interaction with monopolar and dipolar fluctuations included, leading to the KS theory as a limiting form.

physics.bio-ph↗

arXiv2014

A unified description of solvent effects in the helix-coil transition

We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer hydrogen bonds that can compete with the intrinsic intra-polymer hydrogen bonded configurations (competing interactions) and implicit solvent action, where the solvent-polymer interactions tune biopolymer configurations by changing the activity of the solvent (non-competing interactions). The overall spin Hamiltonian is comprised of three terms: the background \emph{in vacuo} Hamiltonian of the "Generalized Model of Polypeptide Chain" type and two additive terms that account for the two above mechanisms of solvent action. We show that on this level the solvent degrees of freedom can be {\sl explicitly} and {\sl exactly} traced over, the ensuing effective partition function combining all the solvent effects in a unified framework. In this way we are able to address helix-coil transitions for polypeptides, proteins, and DNA, with different buffers and different external constraints. Our spin-based effective Hamiltonian is applicable for treatment of such diverse phenomena as cold denaturation, effects of osmotic pressure on the cold and warm denaturation, complicated temperature dependence of the hydrophobic effect as well as providing a conceptual base for understanding the behavior of Intrinsically Disordered Proteins and their analogues.

q-bio.BM↗

arXiv2013

Tensorial conservation law for nematic polymers

We derive the "conservation law" for nematic polymers in tensorial form valid for quadrupolar orientational order in contradistinction to the conservation law in the case of polar orientational order. Due to microscopic differences in the coupling between the orientational field deformations and the density variations for polar and quadrupolar order, we find that respective order parameters satisfy fundamentally distinct constraints. Being necessarily scalar in its form, the tensorial conservation law is obtained straightforwardly from the gradients of the polymer nematic tensor field and connects the spatial variation of this tensor field with density variations. We analyze the differences between the polar and the tensorial forms of the conservation law, present some explicit orientational fields that satisfy this new constraint and discuss the role of singular "hairpins", which do not affect local quadrupolar order of polymer nematics, but nevertheless influence its gradients.

cond-mat.soft↗

arXiv2013

Pseudo-Casimir interactions across nematic films with disordered anchoring axis

We consider the effective pseudo-Casimir interaction forces mediated by a nematic liquid-crystalline film bounded by two planar surfaces, one of which imposes a random (disordered) distribution of the preferred anchoring axis in the so-called easy direction. We consider both the case of a quenched as well as an annealed disorder for the easy direction on the disordered surface and analyze the resultant fluctuation-induced interaction between the surfaces. In the case of quenched disorder, we show that the disorder effects appear additively in the total interaction and are dominant at intermediate inter-surface separations. Disorder effects are shown to be unimportant at both very small and very large separations. In the case of annealed disorder its effects are non-additive in the total inter-surface interaction and can be rationalized in terms of a renormalized extrapolation length.

cond-mat.soft↗

arXiv2013

Perspective: Coulomb fluids -- weak coupling, strong coupling, in between and beyond

We present a personal view on the current state of statistical mechanics of Coulomb fluids with special emphasis on the interactions between macromolecular surfaces, concentrating on the weak and the strong coupling limits. Both are introduced for a (primitive) counterion-only system in the presence of macroscopic, uniformly charged boundaries, where they can be derived systematically. Later we show how this formalism can be generalized to the cases with additional characteristic length scales that introduce new coupling parameters into the problem. These cases most notably include asymmetric ionic mixtures with mono- and multivalent ions that couple differently to charged surfaces, ions with internal charge (multipolar) structure and finite static polarizability, where weak and strong coupling limits can be constructed by analogy with the counterion-only case and lead to important new insights into their properties that can not be derived by any other means.

cond-mat.soft↗

arXiv2013

Multivalent ion effects on electrostatic stability of virus-like nano-shells

Electrostatic properties and stability of charged virus-like nano-shells are examined in ionic solutions with monovalent and multivalent ions. A theoretical model based on a thin charged spherical shell and multivalent ions within the "dressed multivalent ion" approximation, yielding their distribution across the shell and the corresponding electrostatic (osmotic) pressure acting on the shell, is compared with extensive implicit Monte-Carlo simulations. It is found to be accurate for positive or low negative surface charge densities of the shell and for sufficiently high (low) monovalent (multivalent) salt concentrations. Phase diagrams involving electrostatic pressure exhibit positive and negative values, corresponding to an outward and an inward facing force on the shell, respectively. This provides an explanation for the high sensitivity of viral shell stability and self-assembly of viral capsid shells on the ionic environment.

cond-mat.soft↗