arXiv subjects

Rudolf Podgornik

Publications and source records attributed to Rudolf Podgornik.

At least 73 records · Page 4Linked to original sources

arXiv2018

Spontaneous symmetry breaking of charge-regulated surfaces

The interaction between two chemically identical charge-regulated surfaces is studied using the classical density functional theory. In contrast to common expectations and assumptions, under certain realistic conditions we find a spontaneous emergence of disparate charge densities on the two surfaces. The surface charge densities can differ not only in their magnitude, but quite unexpectedly, even in their sign, implying that the electrostatic interaction between the two chemically identical surfaces can be attractive instead of repulsive. Moreover, an initial symmetry with equal charge densities on both surfaces can also be broken spontaneously upon decreasing the separation between the two surfaces. The origin of this phenomenon is a competition between the adsorption of ions from the solution to the surface and the interaction between the adsorbed ions already on the surface.These findings are fundamental for the understanding of the forces between colloidal objects and, in particular, they are bound to strongly influence the present picture of protein interaction.

cond-mat.soft↗

arXiv2017

Varieties of charge distributions in coat proteins of ssRNA+ viruses

A major part of the interactions involved in the assembly and stability of icosahedral, positive-sense single-stranded RNA (ssRNA+) viruses is electrostatic in nature, as can be inferred from the strong $pH$- and salt-dependence of their assembly phase diagrams. Electrostatic interactions do not act only between the capsid coat proteins (CPs), but just as often provide a significant contribution to the interactions of the CPs with the genomic RNA, mediated to a large extent by positively charged, flexible N-terminal tails of the CPs. In this work, we provide two clear and complementary definitions of an N-terminal tail of a protein, and use them to extract the tail sequences of a large number of CPs of ssRNA+ viruses. We examine the $pH$-dependent interplay of charge on both tails and CPs alike, and show that -- in contrast to the charge on the CPs -- the net positive charge on the N-tails persists even to very basic $pH$ values. In addition, we note a limit to the length of the wild-type genomes of those viruses which utilize positively charged tails, when compared to viruses without charged tails and similar capsid size. At the same time, we observe no clear connection between the charge on the N-tails and the genome lengths of the viruses included in our study.

physics.bio-ph↗

arXiv2017

pH dependence of charge multipole moments in proteins

Electrostatic interactions play a fundamental role in the structure and function of proteins. Due to ionizable amino acid residues present on the solvent-exposed surfaces of proteins, the protein charge is not constant but varies with the changes in the environment -- most notably, the pH of the surrounding solution. We study the effects of pH on the charge of four globular proteins by expanding their surface charge distributions in terms of multipoles. The detailed representation of the charges on the proteins is in this way replaced by the magnitudes and orientations of the multipole moments of varying order. Focusing on the three lowest-order multipoles -- the total charge, dipole, and quadrupole moment -- we show that the value of pH influences not only their magnitudes, but more notably and importantly also the spatial orientation of their principal axes. Our findings imply important consequences for the study of protein-protein interactions and the assembly of both proteinaceous shells and patchy colloids with dissociable charge groups.

physics.bio-ph↗

arXiv2017

Interactions between Charged Particles with bathing Multivalent Counterions: Experiments {\it vs} Dressed Ion Theory

We compare the recent experimentally measured forces between charged colloidal particles, as well as their effective surface potentials (surface charge) in the presence of multivalent counterions in a bathing monovalent salt solution, with the predictions of the dressed ion theory of strongly charged colloidal systems. The benchmark for comparison is provided by the DLVO theory and the deviations from its predictions at small separations are taken as an indication of the additional non-DLVO attractions that can be fitted by an additional phenomenological exponential term. The parameters characterizing this non-DLVO exponential term as well as the dependencies of the effective potential on the counterion concentration and valency predicted by the dressed ion theory are well within the experimental values. This suggests that the deviations from the DLVO theory are probably caused by ion correlations as formalized within the dressed ion theory.

cond-mat.soft↗

arXiv2016

Modulation of elasticity and interactions in charged lipid multibilayers: monovalent salt solutions

We have studied the electrostatic screening effect of NaCl solutions on the interactions between anionic lipid bilayers in the fluid lamellar phase using a Poisson-Boltzmann based mean-field approach with constant charge and constant potential limiting charge regulation boundary conditions. The full DLVO potential, including the electrostatic, hydration and van der Waals interactions, was coupled to thermal bending fluctuations of the membranes via a variational Gaussian Ansatz. This allowed us to analyze the coupling between the osmotic pressure and the fluctuation amplitudes and compare them both simultaneously with the measured dependence on the bilayer separation, determined by the small-angle X-ray scattering experiments. High-structural resolution analysis of the scattering data revealed no significant changes of membrane structure as a function of salt concentration. Parsimonious description of our results is consistent with the constant charge limit of the general charge regulation phenomenology, with fully dissociated lipid charge groups, together with a four-fold reduction of the membranes' bending rigidity upon increasing NaCl concentration.

cond-mat.soft↗

arXiv2016

Effects of RNA branching on the electrostatic stabilization of viruses

Many single-stranded (ss) RNA viruses self assemble from capsid protein subunits and the nucleic acid to form an infectious virion. It is believed that the electrostatic interactions between the negatively charged RNA and the positively charged viral capsid proteins drive the encapsidation, although there is growing evidence that the sequence of the viral RNA also plays a role in packaging. In particular the sequence will determine the possible secondary structures that the ssRNA will take in solution. In this work, we use a mean field theory to investigate how the secondary structure of the RNA combined with electrostatic interactions affects the efficiency of assembly and stability of the assembled virions. We show that the secondary structure of RNA may result in negative osmotic pressures while a linear polymer causes positive osmotic pressures for the same conditions. This may suggest that the branched structure makes the RNA more effectively packaged and the virion more stable.

physics.bio-ph↗

arXiv2016

Van der Waals torque and force between dielectrically anisotropic layered media

We analyse van der Waals interactions between a pair of dielectrically anisotropic plane-layered media interacting across a dielectrically isotropic solvent medium. We develop a general formalism based on transfer matrices to investigate the van der Waals torque and force in the limit of weak birefringence and dielectric matching between the ordinary axes of the anisotropic layers and the solvent. We apply this formalism to study the following systems: (i) a pair of single anisotropic layers, (ii) a single anisotropic layer interacting with a multilayered slab consisting of alternating anisotropic and isotropic layers, and (iii) a pair of multilayered slabs each consisting of alternating anisotropic and isotropic layers, looking at the cases where the optic axes lie parallel and/or perpendicular to the plane of the layers. For the first case, the optic axes of the oppositely facing anisotropic layers of the two interacting slabs generally possess an angular mismatch, and within each multilayered slab the optic axes may either be the same, or undergo constant angular increments across the anisotropic layers. In particular, we examine how the behaviors of the van der Waals torque and force can be "tuned" by adjusting the layer thicknesses, the relative angular increment within each slab, and the angular mismatch between the slabs.

cond-mat.soft↗

arXiv2016

Chirality modifies the interaction between knots

In this study we consider an idealization of a typical optical tweezers experiment involving a semiflexible double-knotted polymer, with steric hindrance and persistence length matching those of dsDNA in high salt concentration, under strong stretching. Using exhaustive Molecular Dynamics simulations we show that not only does a double-knotted dsDNA filament under tension possess a free energy minimum when the two knots are intertwined, but also that the depth of this minimum depends on the relative chirality of the two knots. We rationalize this dependence of the effective interaction on the chirality in terms of a competition between chain entropy and bending energy.

cond-mat.soft↗

arXiv2016

Nonequilibrium Tuning of the Thermal Casimir Effect

In net-neutral systems correlations between charge fluctuations generate strong attractive thermal Casimir forces and engineering these forces to optimize nanodevice performance is an important challenge. We show how the normal and lateral thermal Casimir forces between two plates containing Brownian charges can be modulated by decorrelating the system through the application of an electric field, which generates a nonequilibrium steady state with a constant current in one or both plates, reducing the ensuing fluctuation-generated normal force while at the same time generating a lateral drag force. This hypothesis is confirmed by detailed numerical simulations as well as an analytical approach based on stochastic density functional theory.

cond-mat.stat-mech↗

arXiv2016

Pseudo-Casimir stresses and elasticity of a confined elastomer film

Investigations of the elastic behavior of bulk elastomers have traditionally proceeded on the basis of classical rubber elasticity, which regards chains as thermally fluctuating but disregards the thermal fluctuations of the cross-links. Here, we consider an incompressible and flat elastomer film of an axisymmetric shape confined between two large hard co-planar substrates, with the axis of the film perpendicular to the substrates. We address the impact that thermal fluctuations of the cross-links have on the free energy of elastic deformation of the system, subject to the requirement that the fluctuating elastomer cannot detach from the substrates. We examine the behavior of the deformation free energy for one case where a rigid pinning boundary condition is applied to a class of elastic fluctuations at the confining surfaces, and another case where the same elastic fluctuations are subjected to soft "gluing" potentials. We find that there can be significant departures (both quantitative and qualitative) from the prediction of classical rubber elasticity theory when elastic fluctuations are included. Finally, we compare the character of the attractive part of the elastic fluctuation-induced, or pseudo-Casimir, stress with the standard thermal Casimir stress in confined but non-elastomeric systems, finding the same power law decay behavior when a rigid pinning boundary condition is applied, for the case of the gluing potential, we find that the leading order correction to the attractive part of the fluctuation stress decays inversely with the inter-substrate separation.

cond-mat.soft↗

arXiv2016

From polymers to proteins: effect of side chains and broken symmetry in the formation of secondary structures within a Wang-Landau approach

We study the equilibrium properties of a single flexible homopolymers where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well potential. To this aim, we use both replica exchange canonical simulations and micro-canonical Wang-Landau techniques. We perform a close comparative analysis of the corresponding results, and find perfect agreement between the two methods as well as the past results. The model is then refined in two different directions. By allowing partial overlapping between consecutive beads, we break the spherical symmetry and thus provide a severe constraint on the possible conformations of the chain. This leads to a single helix or a double helix ground state, depending on the range of the interactions. Alternatively, we introduce additional spherical beads at specific positions to represent the steric hindrance of the side chains in real proteins. The ground state in this case is found to be again a globule, thus showing that contrary to some recent suggestions, side chains alone are not sufficient to insure a protein-like structure. Finally, we show that a combination of the above two effects increases the stability of the obtaining secondary structures, in agreement with previous results. The fundamental role played by the range of the square-well attraction is highlighted, and it is shown that they play a role similar to that found in simple liquids and polymers. Perspectives in terms of protein folding are finally discussed.

cond-mat.soft↗

arXiv2016

Titratable Macroions in Multivalent Electrolyte Solutions: Strong Coupling Dressed Ion Approach

We present a theoretical description of the effect of polyvalent ions on the interaction between titratable macro-ions. The model system consists of two point-like macro-ions with dissociable sites, immersed in an asymmetric ionic mixture of monovalent and polyvalent salts. We formulate a {\em dressed ion strong coupling theory}, based on the decomposition of the asymmetric ionic mixture into a weakly electrostatically coupled monovalent salt, and into polyvalent ions that are strongly electrostatically coupled to the titratable macro-ions. The charge of the macroions is not considered as fixed, but is allowed to respond to local bathing solution parameters (electrostatic potential, $pH$ of the solution, salt concentration) through a simple {\em charge regulation} model. The approach presented, yielding an effective polyvalent-ion mediated interaction between charge-regulated macro-ions at various solution conditions, describes the strong coupling equivalent of the Kirkwood-Schumaker interaction.

physics.bio-ph↗

arXiv2016

RNA topology remolds electrostatic stabilization of viruses

Simple RNA viruses efficiently encapsulate their genome into a nano-sized protein shell: the capsid. Spontaneous co-assembly of the genome and the capsid proteins is driven predominantly by electrostatic interactions between the negatively charged RNA and the positively charged inner capsid wall. Using field theoretic formulation we show that the inherently branched RNA secondary structure allows viruses to maximize the amount of encapsulated genome and make assembly more efficient, allowing viral RNAs to out-compete cellular RNAs during replication in infected host cells.

physics.bio-ph↗

arXiv2015

Phase diagram of the ground states of DNA condensates

Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting compaction. $x=1$ corresponds to the worm-like chain model. Surprisingly, the phase diagram as well as the transition lines between the ground states are found to be a function of $x$. The model provides a simple explanation for the results of prior experimental and computational studies and makes predictions for the specific geometries of the ground states. The results underscore the impact of the form of the microscopic bending energy at macroscopic observable scales.

q-bio.BM↗

arXiv2015

Van der Waals interaction between polymers with sequence-specific polarizabilities: Stiff polymers and flexible Gaussian coils

We consider the van der Waals interaction between a pair of polymers with quenched heterogeneous sequences of local polarizabilities along their backbones, and study the effective pairwise interaction energy for both stiff polymers and flexible Gaussian coils. In particular, we focus on the cases where the pair of polarizability sequences are (i)~distinct and (ii)~identical. We find that the pairwise interaction energies of distinct and identical Gaussian coils are both isotropic and exhibit the same decay behavior for separations larger than the gyration radius, in contradistinction to the orientationally anisotropic interaction energies of distinct and identical stiff polymers. For both Gaussian coils and stiff polymers, the attractive interaction between identical polymers is enhanced if the polarizability sequence is more heterogeneous.

cond-mat.soft↗

arXiv2015

Repulsive Casimir interaction: Boyer oscillators at nanoscale

We study the effect of temperature on the repulsive Casimir interaction between an ideally permeable and an ideally polarizable plate {\it in vacuo}. At small separations or for low temperatures the quantum fluctuations of the electromagnetic field give the main contribution to the interaction, while at large separations or for high temperatures the interaction is dominated by the classical thermal fluctuations of the field. At intermediate separations or finite temperatures both the quantum and thermal fluctuations contribute. For a system composed of one infinitely permeable plate between two ideal conductors at a finite temperature, we identify a {\it stable mechanical equilibrium} state, if the infinitely permeable plate is located in the middle of the cavity. For small displacements the restoring force of this {\it Boyer oscillator} is linear in the deviation from the equilibrium position, with a spring constant that depends inversely on the separation between the two conducting plates and linearly on temperature. Furthermore, an array of such oscillators presents an ideal Einsteinian crystal that displays a fluctuation force between its outer boundaries stemming from the displacement fluctuations of the Boyer oscillators.

cond-mat.stat-mech↗

arXiv2015

Correlation functions of main-chain polymer nematics constrained by tensorial and vectorial conservation laws

We present and analyze correlation functions of a main-chain polymer nematic in a continuum worm-like chain description for two types of constraints formalized by the tensorial and vectorial conservation laws, both originating in the microscopic chain integrity, i.e., the conectivity of the polymer chains. In particular, our aim is to identify the features of the correlation functions that are most susceptible to the differences between the two constraints. Besides the density and director autocorrelations in both the tensorial and vectorial cases, we calculate also the density -- director correlation functions, the latter being a direct signature of the presence of a specific constraint. Its amplitude is connected to the strength of the constraint and is zero if none of the constraints is present, i.e., for a standard non-polymeric nematic. Generally, the correlation functions with the constraints differ substantially from the correlation functions in the non-polymeric case, if the constraints are strong which in practice requires long chains. Moreover, for the tensorial conservation law to be well distinguishable from the vectorial one, the chain persistence length should be much smaller than the total length of the chain, so that hairpins (chain backfolding) are numerous and the polar order is small.

cond-mat.soft↗

arXiv2015

Ion-mediated interactions between net-neutral slabs: Weak and strong disorder effects

We investigate the effective interaction between two randomly charged but otherwise net-neutral, planar dielectric slabs immersed in an asymmetric Coulomb fluid containing a mixture of mobile monovalent and multivalent ions. The presence of charge disorder on the apposed bounding surfaces of the slabs leads to substantial qualitative changes in the way they interact, as compared with the standard picture provided by the van der Waals and image-induced, ion-depletion interactions. While, the latter predict purely attractive interactions between strictly neutral slabs, we show that the combined effects from surface charge disorder, image depletion, Debye (or salt) screening and also, in particular, their coupling with multivalent ions, give rise to a more diverse behavior for the effective interaction between net-neutral slabs. Disorder effects show large variation depending on the properly quantified strength of disorder, leading either to non-monotonic effective interaction with both repulsive and attractive branches when the surface charges are weakly disordered (small disorder variance) or to a dominating attractive interaction that is larger both in its range and magnitude than what is predicted from the van der Waals and image-induced, ion-depletion interactions, when the surfaces are strongly disordered (large disorder variance).

cond-mat.soft↗