arXiv subjects

Ralf Blossey

Publications and source records attributed to Ralf Blossey.

31 records · Page 2Linked to original sources

arXiv2018

Comment on "Nonlocal statistical field theory of dipolar particles in electrolyte solutions" by Y.A. Budkov

The article by Budkov introduces a nonlocal field-theoretic model of solvent-explicit electrostatics. Despite giving a detailed introduction to the early literature on the topic, the article misses out on a series of articles that we published several years ago. Consequently, the manuscript essentially rederives without mention several results that were derived by us for the first time.

cond-mat.soft↗

arXiv2016

Correlation-induced DNA adsorption on like-charged membranes

The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates for further analysis, e.g., by force microscopy, or the pulling of polyelectrolytes into membrane nanopores, as in sequencing applications. In this paper, we present a theoretical analysis of such scenarios based on the self-consistent field theory approach, which allows us to address the important effect of charge correlations. We calculate the grand potential of a stiff polyelectrolyte immersed in an electrolyte in contact with a negatively charged dielectric membrane. For the sake of conciseness, we neglect conformational polymer fluctuations and model the molecule as a rigid charged line. At strongly charged membranes, the adsorbed counterions enhance the screening ability of the interfacial region. In the presence of highly charged polymers such as double-stranded DNA molecules close to the membrane, this enhanced interfacial screening dominates the mean-field level DNA-membrane repulsion and results in the adsorption of the DNA molecule to the surface. This picture provides a simple explanation for the recently observed DNA binding onto similarly charged substrates [G. L.-Caballero et al., Soft Matter 10, 2805 (2014)] and points out charge correlations as a non-negligible ingredient of polymer-surface interactions.

cond-mat.soft↗

arXiv2016

Beyond Poisson-Boltzmann: fluctuations and fluid structure in a self-consistent theory

Poisson-Boltzmann (PB) theory is the classic approach to soft matter electrostatics which has been applied to numerous problems of physical chemistry and biophysics. Its essential limitations are the neglect of correlation effects and of fluid structure. Recently, several theoretical insights have allowed the formulation of approaches that go beyond PB theory in a systematic way. In this topical review we provide an update on the developments achieved in self-consistent formulations of correlation-corrected Poisson-Boltzmann theory. We introduce the corresponding system of coupled nonlinear equations for both continuum electrostatics with a uniform dielectric constant and a structured solvent, a dipolar Coulomb fluid, including nonlocal effects. While the approach is only approximate and also limited to corrections in the so-called weak fluctuation regime, it allows to include physically relevant effects, as we show for a range of applications of these equations.

cond-mat.soft↗

arXiv2015

Ionic current inversion in pressure-driven polymer translocation through nanopores

We predict streaming current inversion with multivalent counterions in hydrodynamically driven polymer translocation events from a correlation-corrected charge transport theory including charge fluctuations around mean-field electrostatics. In the presence of multivalent counterions, electrostatic many-body effects result in the reversal of the DNA charge. The attraction of anions to the charge-inverted DNA molecule reverses the sign of the ionic current through the pore. Our theory allows for a comprehensive understanding of the complex features of the resulting streaming currents. The underlying mechanism is an efficient way to detect DNA charge reversal in pressure-driven translocation experiments with multivalent cations.

cond-mat.soft↗

arXiv2014

Dipolar correlations in structured solvents under nanoconfinement

We study electrostatic correlations in structured solvents confined to nanoscale systems. We derive variational equations of Netz-Orland type for a model liquid composed of finite size dipoles. These equations are solved for both dilute solvents and solvents at physiological concentrations in a slit nanopore geometry. Correlation effects are of major importance for the dielectric reduction and anisotropy of the solvent resulting from dipole image interactions and also lead to a reduction of van der Waals attractions between low dielectric bodies. Finally, by comparison with other recently developed self-consistent theories and experiments, we scrutinize the effect of solvent-membrane interactions on the differential capacitance of the charged liquid in contact with low dielectric substrates. The interfacial solvent depletion driven by solvent-image interactions plays the major role in the observed low values of the experimental capacitance data, while non-locality associated with the extended charge structure of solvent molecules only brings a minor contribution.

cond-mat.soft↗

arXiv2014

Nonlocal and nonlinear electrostatics of a dipolar Coulomb fluid

We study a model Coulomb fluid consisting of dipolar solvent molecules of finite extent generalizing the point-like Dipolar Poisson-Boltzmann model (DPB) previously introduced by Coalson and Duncan (J. Phys. Chem 100, 2612 (1996)) and Abrashkin et al. (Phys. Rev. Lett. 99, 077801 (2007)). We formulate a nonlocal Poisson-Boltzmann equation (NLPB) and study both linear and nonlinear dielectric response in this model for the case of a single plane geometry. Our results shed light on the relevance of nonlocal vs nonlinear effects in continuum models of material electrostatics.

cond-mat.soft↗

arXiv2013

Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.

physics.bio-ph↗

arXiv2008

Spinodal dewetting of thin films with large interfacial slip: implications from the dispersion relation

We compare the dispersion relations for spinodally dewetting thin liquid films for increasing magnitude of interfacial slip length in the lubrication limit. While the shape of the dispersion relation, in particular the position of the maximum, are equal for no-slip up to moderate slip lengths, the position of the maximum shifts to much larger wavelengths for large slip lengths. Here, we discuss the implications of this fact for recently developed methods to assess the disjoining pressure in spinodally unstable thin films by measuring the shape of the roughness power spectrum. For PS films on OTS covered Si wafers (with slip length b approx. 1 mum) we predict a 20% shift of the position of the maximum of the power spectrum which should be detectable in experiments.

cond-mat.soft↗

arXiv2008

Kinetic proofreading of gene activation by chromatin remodeling

Gene activation in eukaryotes involves the concerted action of histone tail modifiers, chromatin remodellers and transcription factors, whose precise coordination is currently unknown. We demonstrate that the experimentally observed interactions of the molecules are in accord with a kinetic proofreading scheme. Our finding could provide a basis for the development of quantitative models for gene regulation in eukaryotes based on the combinatorical interactions of chromatin modifiers.

q-bio.MN↗

arXiv2006

Slip vs viscoelasticity in dewetting thin films

Ultrathin polymer films on non-wettable substrates display dynamic features which have been attributed to either viscoelastic or slip effects. Here we show that in the weak and strong slip regime effects of viscoelastic relaxation are either absent or not distinguishable from slip effects. Strong-slip modifies the fastest unstable mode in a rupturing thin film, which questions the standard approach to reconstruct the effective interface potential from dewetting experiments.

cond-mat.soft↗

arXiv2005

Exons, introns and DNA thermodynamics

The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from the genomic DNA by removing all introns. A clear correspondence is observed between exons and melting domains. This finding may provide new insights in the physical mechanisms underlying the evolution of genes.

q-bio.BM↗

arXiv2004

Reparametrizing loop entropy weights: Effect on DNA melting curves

Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior loop melting. So far, in the modeling of DNA melting, the entropy of denaturated loops has been estimated from the number of configurations of a closed self-avoiding walk. It is well understood now that a loop embedded in a chain is characterized by a loop closure exponent c which is higher than that of an isolated loop. Here we report an analysis of DNA melting curves for sequences of a broad range of lengths (from 10 to 10^6 base pairs) calculated with a program based on the algorithms underlying MELTSIM. Using the embedded loop exponent we find that the cooperativity parameter is one order of magnitude bigger than current estimates. We argue that in the melting region the double helix persistence length is greatly reduced compared to its room temperature value, so that the use of the embedded loop closure exponent for real DNA sequences is justified.

cond-mat.stat-mech↗

arXiv2003

Individualistic networks and networking individuals in Tango Argentino

We have performed a simulation study of the social network arising from dancing partner selection in Tango Argentino. Tango Argentino is a famous intellectual dance which combines individualistic behaviour with consensual social rules, generating complex patterns of network behaviour in time. We quantify these patterns by time-dependent degree distributions and clustering coefficients for the network structure, and by monitoring the evolution of the individual dancers skill. In particular, we have investigated how successful new dancers are in entering the network under the promotion of established network members. Our approach allows us to predict the success of mentoring in a social network.

cond-mat.soft↗