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Ali Nadim

Publications and source records attributed to Ali Nadim.

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Musings on the Riemann Hypothesis

We present a few ideas on the Riemann Hypothesis based on properties of analytic functions in the complex plane. In particular, we focus on the real and imaginary parts of the Riemann xi ($\xi$) function whose zeros coincide with those of the zeta ($\zeta$) function within the critical strip. We discuss the forms of the zero contour lines of the two conjugate harmonic functions (the real and imaginary parts of xi) and consider where their intersections could conceivably occur. Those intersections would be the roots of both $\xi$ and $\zeta$ functions. The question of whether a zero could occur away from the critical line becomes equivalent to whether the solutions of a pair of Laplace's equations with well-defined boundary conditions in some semi-infinite strip can possess zero contour lines that intersect within that strip.

math.AP

Modeling Ion-Specific Effects in Polyelectrolyte Brushes: A Modified Poisson-Nernst-Planck Model

Polyelectrolyte brushes consist of a set of charged linear macromolecules each tethered at one end to a surface. An example is the glycocalyx which refers to hair-like negatively charged sugar molecules that coat the outside membrane of all cells. We consider the transport and equilibrium distribution of ions, and the resulting electrical potential, when such a brush is immersed in a salt buffer containing monovalent cations (sodium and/or potassium). The Gouy-Chapman model for ion screening at a charged surface captures the effects of the Coulombic force that drives ion electrophoresis and diffusion, but neglects non-Coulombic forces and ion pairing. By including the distinct binding affinities of these counter-ions with the brush, and their so-called Born radii, which account for Born forces acting on them when the permittivity is non-uniform, we propose modified Poisson-Nernst-Planck continuum models that show the distinct profiles that may result depending on those ion-specific properties.

physics.bio-ph

Mathematical Modeling of Microscale Biology: Ion Pairing, Dielectric Decrement, and Born Energy in Glycosaminoglycan Brushes

Biological macromolecules including nucleic acids, proteins, and glycosaminoglycans are typically anionic and can span domains of up to hundreds of nanometers and even micron length scales. The structures exist in crowded environments that are dominated by weak multivalent electrostatic interactions that can be modeled using mean field continuum approaches that represent underlying molecular nanoscale biophysics. We develop such models for glycosaminoglycan brushes using both steady state modified Poisson-Boltzmann models and transient Poisson-Nernst-Planck models that incorporate important ion-specific (Hofmeister) effects. The results quantify how electroneutrality is attained through ion electrophoresis, dielectric decrement hydration forces, and ion-specific pairing. Brush-Salt interfacial profiles of the electrostatic potential as well as bound and unbound ions are characterized for imposed jump conditions across the interface. The models should be applicable to many intrinsically-disordered biophysical environments and are anticipated to provide insight into the design and development of therapeutics and drug-delivery vehicles to improve human health.

physics.bio-ph

Thin liquid film resulting from a distributed source on a vertical wall

We examine the dynamics of a thin film formed by a distributed liquid source on a vertical solid wall. The model is derived using the lubrication approximation and includes the effects of gravity, upward airflow and surface tension. When surface tension is neglected, a critical source strength is found below which the film flows entirely upward due to the airflow, and above which some of the flow is carried downward by gravity. In both cases, a steady state is established over the region where the finite source is located. Shock waves that propagate in both directions away from the source region are analyzed. Numerical simulations are included to validate the analytical results. For models including surface tension, numerical simulations are carried out. The presence of surface tension, even when small, causes a dramatic change in the film profiles and the speed and structure of the shock waves. These are studied in more detail by examining the traveling wave solutions away from the source region.

physics.flu-dyn

Marangoni effects on a thin liquid film coating a sphere with axial or radial thermal gradients

We study the time evolution of a thin liquid film coating the outer surface of a sphere in the presence of gravity, surface tension and thermal gradients. We derive the fourth-order nonlinear partial differential equation that models the thin film dynamics, including Marangoni terms arising from the dependence of surface tension on temperature. We consider two different imposed temperature distributions with axial or radial thermal gradients. We analyze the stability of a uniform coating under small perturbations and carry out numerical simulations in COMSOL for a range of parameter values. In the case of an axial temperature gradient, we find steady states with either uniform film thickness, or with the fluid accumulating at the bottom or near the top of the sphere, depending on the total volume of liquid in the film, dictating whether gravity or Marangoni effects dominate. In the case of a radial temperature gradient, a stability analysis reveals the most unstable non-axisymmetric modes on an initially uniform coating film.

cond-mat.soft

A p53 Oscillator Model of DNA Break Repair Control

The transcription factor p53 is an important regulator of cell fate. Mutations in p53 gene are associated with many cancers. In response to signals such as DNA damage, p53 controls the transcription of a series of genes that cause cell cycle arrest during which DNA damage is repaired, or triggers programmed cell death that eliminates possibly cancerous cells wherein DNA damage might have remained unrepaired. Previous experiments showed oscillations in p53 level in response to DNA damage, but the mechanism of oscillation remained unclear. Here we examine a model where the concentrations of p53 isoforms are regulated by Mdm22, Arf, Siah, and beta-catenin. The extent of DNA damage is signalled through the switch-like activity of a DNA damage sensor, the DNA-dependent protein kinase Atm. This switch is responsible for initiating and terminating oscillations in p53 concentration. The strength of the DNA damage signal modulates the number of oscillatory waves of p53 and Mdm22 but not the frequency or amplitude of oscillations{a result that recapitulates experimental findings. A critical fnding was that the phosphorylated form of Nbs11, a member of the DNA break repair complex Mre11-Rad50-Nbs11 (MRN), must augment the activity of Atm kinase. While there is in vitro support for this assumption, this activity appears essential for p53 dynamics. The model provides several predictions concerning, among others, degradation of the phosphorylated form of p53, the rate of DNA repair as a function of DNA damage, the sensitivity of p53 oscillation to transcription rates of SIAH, beta-CATENIN and ARF, and the hysteretic behavior of active Atm kinase levels with respect to the DNA damage signal

q-bio.MN

On acoustic cavitation of slightly subcritical bubbles

The classical Blake threshold indicates the onset of quasistatic evolution leading to cavitation for gas bubbles in liquids. When the mean pressure in the liquid is reduced to a value below the vapor pressure, the Blake analysis identifies a critical radius which separates quasistatically stable bubbles from those which would cavitate. In this work, we analyze the cavitation threshold for radially symmetric bubbles whose radii are slightly less than the Blake critical radius, in the presence of time-periodic acoustic pressure fields. A distinguished limit equation is derived that predicts the threshold for cavitation for a wide range of liquid viscosities and forcing frequencies. This equation also yields frequency-amplitude response curves. Moreover, for fixed liquid viscosity, our study identifies the frequency that yields the minimal forcing amplitude sufficient to initiate cavitation. Numerical simulations of the full Rayleigh-Plesset equation confirm the accuracy of these predictions. Finally, the implications of these findings for acoustic pressure fields that consist of two frequencies will be discussed.

physics.flu-dyn