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We investigate the nonlinear dynamics of a damped Peyrard-Bishop DNA model taking into account long-range interactions with distance dependence |l|^-s on the elastic coupling constant between different DNA base pairs. Considering both…

Biological Physics · Physics 2017-07-12 J. Brizar Okaly , Alain Mvogo , R. Laure Woulaché , T. Crépin Kofané

A molecular model is proposed of a bilayer consisting of fully saturated DPPC and mono unsaturated DOPC. The model not only encompasses the constant density within the hydrophobic core of the bilayer, but also the tendency of chain segments…

Biological Physics · Physics 2009-11-10 R. Elliott , K. Katsov , M. Schick , I. Szleifer

A Poisson-Boltzmann approach is used to determine the double-layer integral and differential capacitances in a finite-length situation for an electrolytic cell. By means of simple analytical calculations, it is shown how these quantities…

Statistical Mechanics · Physics 2012-04-03 Roberta Rarumy Ribeiro de Almeida , Luiz Roberto Evangelista , Giovanni Barbero

Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…

We propose a model for the liquid-liquid phase transition observed in osmotic pressure measurements of certain charged lamellae-forming amphiphiles. The model free energy combines mean-field electrostatic and phenomenological…

Soft Condensed Matter · Physics 2012-01-31 Daniel Harries , Rudi Podgornik , V. Adrian Parsegian , Etay Mar-Or , David Andelman

We propose a very simple but 'realistic' model of amphiphilic bilayers,simple enough to be able to include a large number of molecules in the sample, but nevertheless detailed enough to include molecular charge distributions, flexible…

Soft Condensed Matter · Physics 2009-11-13 Z. Gamba

Swollen stacks of finite-size disc-like Laponite clay platelets are investigated within a Wigner-Seitz cell model. Each cell is a cylinder containing a coaxial platelet at its centre, together with an overall charge-neutral distribution of…

Soft Condensed Matter · Physics 2009-10-31 R. J. F. Leote de Carvalho , E. Trizac , J. -P. Hansen

The response of a semiflexible polyelectrolyte chain to stretching in the regimes of moderate and weak screening is studied theoretically, with a special focus on DNA experiments. By using the nonlinear Poisson--Boltzmann description of…

Soft Condensed Matter · Physics 2007-05-23 Alexei V. Tkachenko

A nonlinear response theory is developed and applied to electrostatic interactions between spherical macroions, screened by surrounding microions, in charge-stabilized colloidal suspensions. The theory describes leading-order nonlinear…

Soft Condensed Matter · Physics 2009-11-10 A. R. Denton

The Poisson Boltzmann equation is known for its success in describing the Debye layer that arises from the charge separation phenomenon at the silica/water interface. However, by treating only the mobile ionic charges in the liquid, the…

Soft Condensed Matter · Physics 2019-07-30 Maijia Liao , Li Wan , Shixin Xu , Chun Liu , Ping Sheng

A model of a finite cylindrical ion channel through a phospholipid membrane of width $L$ separating two electrolyte reservoirs is studied. Analytical solution of the Poisson equation is obtained for an arbitrary distribution of ions inside…

Soft Condensed Matter · Physics 2009-11-11 Yan Levin

Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have…

Soft Condensed Matter · Physics 2026-05-13 Gabrielle R. Abraham , Tianhao Li , Anna Nguyen , William M. Jacobs , Omar A. Saleh

The electrophoretic behaviour of flexible polyelectrolyte chains ranging from single monomers up to long fragments of hundred repeat units is studied by a mesoscopic simulation approach. Abstracting from the atomistic details of the…

Soft Condensed Matter · Physics 2015-05-13 Kai Grass , Christian Holm

We devise a soft, solvent-free, coarse-grained model for lipid bilayer membranes. The non-bonded interactions take the form of a weighted-density functional which allows us to describe the thermodynamics of self-assembly and packing effects…

Soft Condensed Matter · Physics 2010-06-09 Martin Hömberg , Marcus Müller

We develop a dielectric matrix and analyze plasmon dispersion in strongly coupled charged-particle bilayers in the quantum domain. The formulation is based on the classical quasi-localized charge approximation (QLCA) and extends the QLCA…

Other Condensed Matter · Physics 2009-11-10 Kenneth I. Golden , Hania Mahassen , Gabor J. Kalman , Gaetano Senatore , F. Rapisarda

The electric double layer structure in an electrolyte close to a solid substrate near the three-phase contact line is approximated by considering the linearized Poisson-Boltzmann equation in a wedge geometry. The mathematical approach…

Soft Condensed Matter · Physics 2012-09-03 Aaron Dörr , Steffen Hardt

In this chapter we review the electrostatic properties of charged membranes in aqueous solutions, with or without added salt, employing simple physical models. The equilibrium ionic profiles close to the membrane are governed by the…

Soft Condensed Matter · Physics 2023-01-05 Tomer Markovich , David Andelman , Rudi Podgornik

Dynamic lateral transport of lipids, proteins, and self-assembled structures in biomembranes plays crucial roles in diverse cellular processes. In this study, we perform a coarse-grained molecular dynamics simulation on a vesicle composed…

Soft Condensed Matter · Physics 2023-11-27 Hiroaki Ito , Naofumi Shimokawa , Yuji Higuchi

We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic…

Soft Condensed Matter · Physics 2009-11-07 M. Patra , M. Karttunen , M. Hyvonen , E. Falck , P. Lindqvist , I. Vattulainen

Fusion of lipid bilayers in membranes is important in processes from vesicle-cell interactions (as in drug delivery) to exosome-cell signaling, while transient transmembrane electric fields are known to occur spontaneously. Two contacting…

Soft Condensed Matter · Physics 2024-04-09 Yu Zhang , Di Jin , Jacob Klein