A model for ionic solutions with an attractive short-range pair interaction between the ions is presented. The short-range interaction is accounted for by adding a quadratic nonlocal term to the Poisson-Boltzmann free energy. The model is used to study solvent effects in a planar electric double layer. The counterion density is found to increase near the charged surface, as compared with the Po...

In vertebrates, the mineralocorticoid receptor (MR) is a steroid-activated nuclear (NR) that plays essential roles in water-electrolyte balance and blood pressure homeostasis. It belongs to group of oxo-steroidian NRs, together with glucocorticoid (GR), progesterone (PR), androgen (AR) receptors. Classically, these NRs homodimerize bind specific genomic sequences activate gene expression. are m...

In this study, we have mapped the surface charge of wool fibers using chemically specific high-resolution force spectroscopy in order to better understand the dispersion of amino acids in relation to fiber morphology. The inter-surface forces between standard atomic force microscopy (AFM) probe tips (tip radius ~ 50 nm) functionalized with COOH and NH(3) terminated alkanethiol self assembling m...

A widely used electrostatics model in the biomolecular modeling community, the nonlinear Poisson–Boltzmann equation, along with its finite element approximation, are analyzed in this paper. A regularized Poisson–Boltzmann equation is introduced as an auxiliary problem, making it possible to study the original nonlinear equation with delta distribution sources. A priori error estimates for the f...

In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide an understanding of the interactions involved that goes beyond, and is an important complement to, experimental studies. Poisson-Boltzmann electrostatic models provide a faster ...

The Polo-Like Kinase 1 (PLK1) acts as a central regulator of mitosis and is over-expressed in a wide range of human tumours where high levels of expression correlate with a poor prognosis. PLK1 comprises two structural elements, a kinase domain and a polo-box domain (PBD). The PBD binds phosphorylated substrates to control substrate phosphorylation by the kinase domain. Although the PBD prefere...

where ρ is the mass density, S is the entropy density, and p is the pressure. It was shown in Morrison and Greene [1980] that this system, as well as its magnetohydrodynamic extension, admit a noncanonical Poisson formulation, that is, equation (1.1) can be written as ḟ = {f, h}, relative to a Hamiltonian function h. The study of the relativistic case was initiated in Bia lynicki-Birula, Hubbar...

Developing chemicals that inhibit checkpoint kinase 1 (Chk1) is a promising adjuvant therapeutic to improve the efficacy and selectivity of DNA-targeting agents. Reliable prediction of binding-free energy and binding affinity of Chk1 inhibitors can provide a guide for rational drug design. In this study, multiple docking strategies and Prime/Molecular Mechanics Generalized Born Surface Area (Pr...

On the local systems Hamiltonian in the weakly nonlocal Poisson brackets. Abstract We study in this work the important class of nonlocal Poisson Brackets (PB) which we call weakly nonlocal. They appeared recently in some investigations in the Soliton Theory. However there was no theory of such brackets except very special first order case. Even in this case the theory was not developed enough. ...

We construct the noncanonical Poisson bracket associated with the phase space of first order moments of the velocity field and quadratic moments of the density of a fluid with a free-boundary, constrained by the condition of incompressibility. Two methods are used to obtain the bracket, both based on Dirac’s procedure for incorporating constraints. First, the Poisson bracket of moments of the u...