arXiv subjects

Sahin Buyukdagli

Publications and source records attributed to Sahin Buyukdagli.

At least 55 records · Page 3Linked to original sources

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↗

arXiv2014

Electrostatic correlations on the ionic selectivity of cylindrical membrane nanopores

We characterize the role of electrostatic fluctuations on the charge selectivity of cylindrical nanopores confining electrolyte mixtures. To this end, we develop an extended one-loop theory that can account for correlation effects induced by the surface charge, nanoconfinement of the electrolyte, and interfacial polarization charges associated with the low permittivity membrane. We validate the quantitative accuracy of the theory by comparisons with previously obtained Monte-Carlo simulation data from the literature, and scrutinize in detail the underlying forces driving the ionic selectivity of the nanopore. In the biologically relevant case of electrolytes with divalent cations such as CaCl2 in negatively charged nanopores, electrostatic correlations associated with the dense counterion layer in the channel result in an increase of the pore coion density with the surface charge. This peculiarity analogous to the charge inversion phenomenon remains intact for dielectrically inhomogeneous pores, which indicates that the effect should be observable in nanofiltration membranes or DNA-blocked nanopores characterized by a low membrane permittivity. Our results show that a quantitatively accurate consideration of correlation effects is necessary to determine the ionic selectivity of nanopores in the presence of electrolytes with multivalent counterions.

cond-mat.soft↗

arXiv2013

Microscopic formulation of non-local electrostatics in polar liquids embedding polarizable ions

Non-local electrostatic interactions associated with the finite solvent size and ion polarizability are investigated within the mean-field linear response theory. To this end, we introduce a field theoretic model of a polar liquid composed of linear multipole solvent molecules and embedding polarizable ions modeled as Drude oscillators. Unlike previous dipolar Poisson-Boltzmann formulations treating the solvent molecules as point dipoles, our model is able to qualitatively reproduce the non-local dielectric response behavior of polar liquids observed in Molecular Dynamics simulations and Atomic Force Microscope experiments for water solvent at charged interfaces. The present theory explains the formation of the associated interfacial hydration layers in terms of a cooperative dipolar response mechanism driven by the reaction of the solvent molecules to their own polarization field. We also incorporate into the theory the relative multipole/dipole moments of water molecules obtained from quantum mechanical calculations, and show that the multipolar contributions to the dielectric permittivity are largely dominated by the dipolar one. We find that this stems from the mutual cancellation of the first two interfacial hydration layers of opposite net charge for multipolar liquids. Within the same non-local dielectric response theory, we show that the induced ion polarizability reverses the interfacial ion density trends predicted by the Poisson-Boltzmann theory, resulting in a surface affinity of coions and exclusion of counterions. The results indicate that the consideration of the discrete charge composition of solvent molecules and ions is the key step towards a microscopic understanding of non-local electrostatic effects in polar solvents.

cond-mat.soft↗

arXiv2013

Alteration of gas phase ion polarizabilities upon hydration in high dielectric liquids

We investigate the modification of gas phase ion polarizabilities upon solvation in polar solvents and ionic liquids. To this aim, we develop a classical electrostatic theory of charged liquids composed of solvent molecules modeled as finite size dipoles, and embedding polarizable ions that consist of Drude oscillators. In qualitative agreement with ab-initio calculations of polar solvents and ionic liquids, the hydration energy of a polarizable ion in both type of dielectric liquid is shown to favor the expansion of its electronic cloud. Namely, the ion carrying no dipole moment in the gas phase acquires a dipole moment in the liquid environment, but its electron cloud also reaches an enhanced rigidity. We find that the overall effect is an increase of the gas phase polarizability upon hydration. In the specific case of ionic liquids, it is shown that this hydration process is driven by a collective solvation mechanism where the dipole moment of a polarizable ion induced by its interaction with surrounding ions self-consistently adds to the polarization of the liquid, thereby amplifying the dielectric permittivity of the medium in a substantial way. We propose this self-consistent hydration as the underlying mechanism behind the high dielectric permittivities of ionic liquids composed of small charges with negligible gas phase dipole moment. Hydration being a correlation effect, the emerging picture indicates that electrostatic correlations cannot be neglected in polarizable liquids.

cond-mat.soft↗

arXiv2012

Electrostatic correlations in inhomogeneous charged fluids beyond loop expansion

Electrostatic correlation effects in inhomogeneous symmetric electrolytes are investigated within a previously developed electrostatic self-consistent (SC) theory (R.R. Netz and H. Orland, Eur. Phys.J. E 11, 301 (2003)). To this aim, we introduce two computational approaches that allow to solve the SC equations beyond the loop expansion. Both approaches can handle the case of dielectrically discontinuous boundaries where the one-loop theory is known to fail. By comparing the theoretical results obtained from these schemes with the results of the MC simulations that we ran for ions at neutral single dielectric interfaces as well as with previous MC data for charged interfaces, we first show that the weak coupling (WC) Debye-Huckel (DH) theory remains quantitatively accurate up to the bulk ion density rhob=0.01 M, whereas the SC theory exhibits a good quantitative accuracy up to rhob=0.2 M. Then, we derive from the perturbative SC scheme the one-loop theory of asymmetrically partitioned salt systems around a dielectrically homogeneous charged surface. It is shown that correlation effects originate in these systems from a competition between the salt screening loss at the interface driving the ions to the bulk region, and the interfacial counterion screening excess attracting them towards the surface. In the case of weak surface charges, the interfacial salt screening loss is the dominant effect. As a result, correlations decrease the MF density of both coions and counterions. With increasing surface charge, the surface-attractive counterion screening excess starts to dominate, and correlation effects amplify in this regime the MF density of both type of ions. We also show that at a characteristic value of the electrostatic coupling parameter, electrostatic correlations result in a charge inversion effect.

cond-mat.soft↗

arXiv2012

Dipolar depletion effect on the differential capacitance of carbon based materials

The remarkably low experimental values of the capacitance data of carbon based materials in contact with water solvent needs to be explained from a microscopic theory in order to optimize the efficiency of these materials. We show that this experimental result can be explained by the dielectric screening deficiency of the electrostatic potential, which in turn results from the interfacial solvent depletion effect driven by image dipole interactions. We show this by deriving from the microscopic system Hamiltonian a non-mean-field dipolar Poisson-Boltzmann equation. This can account for the interaction of solvent molecules with their electrostatic image resulting from the dielectric discontinuity between the solvent medium and the substrate. The predictions of the extended dipolar Poisson-Boltzmann equation for the differential capacitance are compared with experimental data and good agreement is found without any fitting parameters.

cond-mat.soft↗

arXiv2012

Excluded volume effects in macromolecular forces and ion-interface interactions

A charged Yukawa liquid confined in a slit nanopore is studied in order to understand excluded volume effects in the interaction force between the pore walls. A previously developed self-consistent scheme (S. Buyukdagli el al., J. Stat. Mech. P05033 (2011)) and a new simpler variational procedure that self-consistently couple image forces, surface charge induced electric field and pore modified core interactions are used to this aim. For neutral pores, it is shown that with increasing pore size, the theory predicts a transition of the interplate pressure from an attractive to a strongly repulsive regime associated with an ionic packing state, an effect observed in previous Monte Carlo simulations for hard core charges. The role of the range of core interactions in the ionic rejection and interplate pressure is thoroughly analyzed. We show that the physics of the system can be split into two screening regimes. The ionic packing effect takes place in the regime of moderately screened core interactions characterized with the bare screening parameter of the Yukawa potential b<3/lB, where lB is the Bjerrum length. In the second regime of strongly screened core interactions b>3/lB, solvation forces associated with these interactions positively contribute to the ionic rejection driven by electrostatic forces and enhance the magnitude of the attractive pressure. The pronounced dependence of the interplate pressure and ionic partition coefficients on the magnitude and the range of core interactions indicates excluded volume effects as an important ion specificity and a non-negligible ingredient for the stability of macromolecules in electrolyte solutions.

cond-mat.soft↗

arXiv2011

Ion size effects at ionic exclusion from dielectric interfaces and slit nanopores

A previously developed field-theoretic model [R.D. Coalson et al., J. Chem. Phys. 102, 4584 (1995)] that treats core collisions and Coulomb interactions on the same footing is investigated in order to understand ion size effects on the partition of neutral and charged particles at planar interfaces and the ionic selectivity of slit nanopores. We introduce a variational scheme that can go beyond the mean-field (MF) regime and couple in a consistent way pore modified core interactions, steric effects, electrostatic solvation and image-charge forces, and surface charge induced electrostatic potential. We show that in the dilute limit, the MF and the variational theories agree well with MC simulation results, in contrast to a recent RPA method. The partition of charged Yukawa particles at a neutral dielectric interface (e.g air-water or protein-water interface) is investigated. It is shown that as a result of the competition between core collisions that push the ions towards the surface, and repulsive solvation and image forces that exclude them from the interface, a concentration peak of finite size ions sets in close to the dielectric interface. We also characterize the role played by the ion size on the ionic selectivity of neutral slit nanopores. We show that the complex interplay between electrostatic forces, excluded volume effects induced by core collisions and steric effects leads to an unexpected reversal in the ionic selectivity of the pore with varying pore size: while large pores exhibits a higher conductivity for large ions, narrow pores exclude large ions more efficiently than small ones.

cond-mat.soft↗

arXiv2011

Ionic exclusion phase transition in neutral and weakly charged cylindrical nanopores

A field theoretic variational approach is introduced to study ion penetration into water-filled cylindrical nanopores in equilibrium with a bulk reservoir. It is shown that (i) an ion located in a neutral pore undergoes two opposing mechanisms: the deformation of its surrounding ionic cloud of opposite charge, with respect to the reservoir, which increases the surface tension and tends to exclude ions form the pore, and (ii) the attractive contribution to the ion self-energy of the repulsive image forces associated with the dielectric jump between the solvent and the pore wall, which becomes more and more screened when ions enter the pore. For pore radii around 1 nm and bulk concentrations lower than 0.2 mol/L, this mechanism leads to a first-order phase transition, similar to capillary "evaporation", from an ionic-penetration state to an ionic-exclusion state. The discontinuous phase transition survives within the biological concentration range (~ 0.15 mol/L) for small enough membrane dielectric permittivities (< 5). In the case of a weakly charged pore, counterion penetration exhibits a non-monotonic behaviour and is characterized by two regimes: at low reservoir concentration or small pore radii, coions are excluded and the energy barrier for counterions is reduced but image forces remain strong enough, so that the counterion partition coefficient in the pore decreases with increasing reservoir concentration up to a characteristic value; for larger reservoir concentrations, image forces are screened and the partition coefficient of counterions increases with the reservoir electrolyte concentration.

cond-mat.soft↗

arXiv2010

Ionic Capillary Evaporation in Weakly Charged Nanopores

Using a variational field theory, we show that an electrolyte confined to a neutral cylindrical nanopore traversing a low dielectric membrane exhibits a first-order ionic liquid-vapor pseudo-phase-transition from an ionic-penetration "liquid" phase to an ionic-exclusion "vapor" phase, controlled by nanopore-modified ionic correlations and dielectric repulsion. For weakly charged nanopores, this pseudotransition survives and may shed light on the mechanism behind the rapid switching of nanopore conductivity observed in experiments.

cond-mat.soft↗

arXiv2010

Variational approach for electrolyte solutions: from dielectric interfaces to charged nanopores

A variational theory is developed to study electrolyte solutions, composed of interacting point-like ions in a solvent, in the presence of dielectric discontinuities and charges at the boundaries. Three important and non-linear electrostatic effects induced by these interfaces are taken into account: surface charge induced electrostatic field, solvation energies due to the ionic cloud, and image charge repulsion. Our variational equations thus go beyond the mean-field theory. The influence of salt concentration, ion valency, dielectric jumps, and surface charge is studied in two geometries. i) A single neutral air-water interface with an asymmetric electrolyte. A charge separation and thus an electrostatic field gets established due to the different image charge repulsions for coions and counterions. Both charge distributions and surface tension are computed and compared to previous approximate calculations. For symmetric electrolyte solutions close to a charged surface, two zones are characterized. In the first one, with size proportional to the logarithm of the coupling parameter, strong image forces impose a total ion exclusion, while in the second zone the mean-field approach applies. ii) A symmetric electrolyte confined between two dielectric interfaces as a simple model of ion rejection from nanopores. The competition between image charge repulsion and attraction of counterions by the membrane charge is studied. For small surface charge, the counterion partition coefficient decreases with increasing pore size up to a critical pore size, contrary to neutral membranes. For larger pore sizes, the whole system behaves like a neutral pore. The prediction of the variational method is also compared with MC simulations and a good agreement is observed.

cond-mat.soft↗

arXiv2010

Origin of negative differential thermal resistance in a chain of two weakly coupled nonlinear lattices

Negative differential resistance in electronic conduction has been extensively studied, but it is not the case for its thermal counterpart, namely, negative differential thermal resistance (NDTR). We present a classical Landauer formula in which the nonlinearity is incorporated by the self-consistent phonon theory in order to study the heat flux across a chain consisting of two weakly coupled lattices. Two typical nonlinear models of hard and soft on-site potentials are discussed, respectively. It is shown that the nonlinearity has strong impacts on the occurring of NDTR. As a result, a transition from the absence to the presence of NDTR is observed. The origin of NDTR consists in the competition between the temperature difference, which acts as an external field, and the temperature-dependent thermal boundary conductance. Finally, the onset of the transition is clearly illustrated for this model. Our analytical calculation agrees reasonably well with numerical simulations.

cond-mat.stat-mech↗

arXiv2010

Thermal conductivity of anharmonic lattices: Effective phonons and quantum corrections

We compare two effective phonon theories, which have both been applied recently to study heat conduction in anharmonic lattices. In particular, we study the temperature dependence of the thermal conductivity of the Fermi-Pasta-Ulam model via the Debye formula, showing the equivalence of both approaches. The temperature for the minimum of the thermal conductivity and the corresponding scaling behavior are analytically calculated, which agree well with the result obtained from nonequilibrium simulations. We also give quantum corrections for the thermal conductivity from quantum self-consistent phonon theory. The vanishing behavior at the low temperature regime and the existence of an umklapp peak are qualitatively consistent with experimental studies.

cond-mat.stat-mech↗

arXiv2010

On the application of Canonical Perturbation Theory up to the dissociation threshold

We investigate a model system consisting of a Morse oscillator strongly coupled to a doubly-degenerate bending degree of freedom and show that Canonical Perturbation Theory is able to provide a fairly precise, though not exact, approximation of the Hamiltonian up to the dissociation threshold. Quantum mechanical results and classical ones are discussed in this Letter.

physics.chem-ph↗

arXiv2010

Mapping between the order of thermal denaturation and the shape of the critical line of mechanical unzipping in 1-dimensional DNA models

In this Letter, we investigate the link between thermal denaturation and mechanical unzipping for two models of DNA, namely the Dauxois-Peyrard-Bishop model and a variant thereof we proposed recently. We show that the critical line that separates zipped from unzipped DNA sequences in mechanical unzipping experiments is a power-law in the temperature-force plane. We also prove that for the investigated models the corresponding critical exponent is proportional to the critical exponent alpha, which characterizes the behaviour of the specific heat in the neighbourhood of the critical temperature for thermal denaturation.

physics.bio-ph↗

arXiv2008

Computation of the temperature dependence of the heat capacity of complex molecular systems using random color noise

We propose a new method for computing the temperature dependence of the heat capacity in complex molecular systems. The proposed scheme is based on the use of the Langevin equation with low frequency color noise. We obtain the temperature dependence of the correlation time of random noises, which enables to model the partial thermalization of high-frequency vibrations, which is a pure quantum effect. By applying the method to carbon nanotubes, we show that the consideration of the color noise in the Langevin equation allows to reproduce the temperature evolution of the specific heat with good accuracy.

physics.comp-ph↗

arXiv2008

Statistical physics of the melting of inhomogeneous DNA

We studied how the inhomogeneity of a sequence affects the phase transition that takes place at DNA melting. Unlike previous works, which considered thermodynamic quantities averaged over many different inhomogeneous sequences, we focused on precise sequences and investigated the succession of local openings that lead to their dissociation. For this purpose, we performed Transfer Integral type calculations with two different dynamical models, namely the heterogeneous Dauxois-Peyrard-Bishop model and the model based on finite stacking enthalpies we recently proposed. It appears that, for both models, the essential effect of heterogeneity is to let different portions of the investigated sequences open at slightly different temperatures. Besides this macroscopic effect, the local aperture of each portion indeed turns out to be very similar to that of a homogeneous sequence with the same length. Rounding of each local opening transition is therefore merely a size effect. For the Dauxois-Peyrard-Bishop model, sequences with a few thousands base pairs are still far from the thermodynamic limit, so that it is inappropriate, for this model, to discuss the order of the transition associated with each local opening. In contrast, sequences with several hundreds to a few thousands base pairs are pretty close to the thermodynamic limit for the model we proposed. The temperature interval where power laws holds is consequently broad enough to enable the estimation of critical exponents. On the basis of the few examples we investigated, it seems that, for our model, disorder does not necessarily induce a decrease of the order of the transition.

physics.bio-ph↗

arXiv2007

1/f fluctuations of DNA temperature at thermal denaturation

We theoretically investigated the temperature fluctuations of DNA close to denaturation and observed a strong enhancement of these fluctuations at the critical temperature. Although in a much lower frequency range, such a sharp increase was also reported in the recent experimental work of Nagapriya et al [Phys. Rev. Lett. 96, 038102 (2006)]. We showed that there is instead no enhancement of temperature fluctuations when the dissipation coefficient in Langevin equations is assumed to be larger than a few tens of ps-1, and pointed out the possible role of the solvent in real experiments. We sought for a possible correlation between the growth of large bubbles and the enhancement of temperature fluctuations but found no direct evidence thereof. Finally, we showed that neither the enhancement of fluctuations nor the 1/f dependence are observed at the scale of a single base pair, while these properties show up when summing the contributions of a large number of base pairs. We therefore conclude that both effects result from collective motions that are facilitated by the divergence of the correlation length at denaturation.

physics.bio-ph↗