Electric-field screening

In physics, screening is the damping of electric fields caused by the presence of mobile charge carriers. It is an important part of the behavior of charge-carrying fluids, such as ionized gases (classical plasmas), electrolytes, and charge carriers in electronic conductors (semiconductors, metals). In a fluid, with a given permittivity ε, composed of electrically charged constituent particles, each pair of particles (with charges q1 and q2) interact through the Coulomb force as \mathbf{F} = \frac{q_1 q_2}{4\pi\varepsilon \left|\mathbf{r}\right|^2}\hat{\mathbf{r}}, where the vector r is the relative position between the charges. This interaction complicates the theoretical treatment of the fluid. For example, a naive quantum mechanical calculation of the ground-state energy density yields infinity, which is unreasonable. The difficulty lies in the fact that even though the Coulomb force diminishes with distance as 1/r2, the average

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Thermodynamics of Writhe in DNA Minicircles from Molecular Dynamics Simulations

Jonathan Mitchell

DNA supercoiling plays a role in genetic control by imposing torsional stress. This can induce writhe, which changes the global shape of the DNA. We have used atomistic molecular dynamics simulations to partition the free energy changes driving the writhing and unwrithing transitions in supercoiled minicircle DNA. The calculations show that while writhing is energetically driven, the unwrithing transition occurs because the circular state has a higher configurational entropy than the plectoneme. Writhing improves the van der Waals interactions between stacked bases, but can be suppressed by electrostatic repulsion within the negatively charged backbone strands in low salt conditions where electrostatic screening is poor. The free energy difference between circular and plectonemic DNA is determined by such a delicate balance of opposing thermodynamic terms that any perturbation in the environment, such as a change in salt concentration, can be sufficient to convert between these two states. This switchable behavior provides a mechanism for supercoiled DNA to store and communicate biological information physically as well as chemically. DOI: 10.1103/PhysRevLett.110.148105

Amer Physical Soc2013

Heavy impurity transport in tokamaks with plasma flows and saturated 3D perturbations

Wilfred Anthony Cooper, Jonathan Graves, Samuel Lanthaler, Eduardo José Lascas Neto, Madhusudan Raghunathan, Cristian Sommariva

Observations in JET hybrid scenarios show that early termination of the plasma can be caused by tungsten accumulation events, sometimes preceded by large living MHD perturbations [1]. Only recent investigations have been made into understanding the effects of 3D background rotation profiles and 3D MHD equilibria on the transport of heavy impurities. The VENUS- LEVIS PIC code [2] has been used to follow heavy impurities in the presence of a 1/1 kink saturated 3D MHD equilibrium and strong toroidal rotation [3]. In the present work, a now self- consistent treatment of the same problem is pursued. An implementation of the 3D centrifugal effects and 3D electrostatic potential correction on the VENUS-LEVIS code, based on the neo- classical 3D flow theory in [4] and the guiding center theory in [5], is presented. The code is used to follow heavy impurities on a 3D magnetic geommetry with 3D centrifugal effects, in order to understand how these 3D neoclassical effects will affect the overall neoclassical trans- port of heavy impurities. In particular, we focus our study on a saturated 1/1 internal kink mode as it has been seen in experiments that a correlation between this 3D magnetic structure and the inward flux of heavy impurities may exist. Simulations are performed to study this phenomena in both high (Pfirsch-Schlüter) and low (banana) collisionality regimes for the background ions in order to understand the impact of the saturated 1/1 internal kink mode on the peaking of tungsten distributions in JET hybrid scenarios exhibiting continuous 1/1 activity.

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Influence of Subsurface Layers on the Adsorption of Large Organic Molecules on Close-Packed Metal Surfaces

Klaus Kern

The asymmetric molecule 4-[trans-2-(pyrid-4-yl-vinyl)] benzoic acid (PVBA) adsorbed on Cu(111) is characterized by scanning tunneling microscopy (STM) and density functional theory (DFT) to determine the influence of subsurface atomic layers on the adsorption. In contrast to the 6-fold symmetry of the first atomic layer of close-packed surfaces, we find that the arrangement of the isolated molecules follows predominantly a 3-fold symmetry. This reduction in symmetry, where the molecule selects a specific orientation along the axes, reveals the contribution of lower-lying Cu layers to the molecular arrangement, Our calculations rationalize the interaction of the substrate with the molecule in terms of electrostatic screening and local relaxation phenomena.

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