Gating-like Motions and Wall Porosity in a DNA Nanopore Scaffold Revealed by Molecular Simulations

Recently developed synthetic membrane pores composed of folded DNA enrich the current range of natural and engineered protein pores and of nonbiogenic channels. Here we report all-atom molecular dynamics simulations of a DNA nanotube (DNT) pore scaffold to gain fundamental insight into its atomic structure, dynamics, and interactions with ions and water. Our multiple simulations of models of DNTs that are composed of a six-duplex bundle lead to a coherent description. The central tube lumen adopts a cylindrical shape while the mouth regions at the two DNT openings undergo gating-like motions which provide a possible molecular explanation of a lower conductance state observed in our previous experimental study on a membrane-spanning version of the DNT (ACS Nano 2015, 9, 1117-26). Similarly, the central nanotube lumen is filled with water and ions characterized by bulk diffusion coefficients while the gating regions exhibit temporal fluctuations in their aqueous volume. We furthermore observe that the porous nature of the walls allows lateral leakage of ions and water. This study will benefit rational design of DNA nanopores of enhanced stability of relevance for sensing applications, of nanodevices with tunable gating properties that mimic gated ion channels, or of nanopores featuring defined permeation behavior

NSTX Report on FES Joint Facilities Research Milestone 2010

Annual Target: Conduct experiments on major fusion facilities to improve understanding of the heat transport in the tokamak scrape-off layer (SOL) plasma, strengthening the basis for projecting divertor conditions in ITER. The divertor heat flux profiles and plasma characteristics in the tokamak scrape-off layer will be measured in multiple devices to investigate the underlying thermal transport processes. The unique characteristics of C-Mod, DIII-D, and NSTX will enable collection of data over a broad range of SOL and divertor parameters (e.g., collisionality ν*, beta β, parallel heat flux q||, and divertor geometry). Coordinated experiments using common analysis methods will generate a data set that will be compared with theory and simulation

Impact of the Wall Conditioning Program on Plasma Performance in NSTX

High performance operating regimes have been achieved on NSTX (National Spherical Torus Experiment) through impurity control and wall-conditioning techniques. These techniques include HeGDC-aided boronization using deuterated trimethylboron, inter-discharge HeGDC, 350 C PFC bake-out followed by D2 and HeGDC, and experiments to test fueling discharges with either a He-trimethylboron mixture or pure trimethylboron. The impact of this impurity and density control program on recent advances in NSTX plasma performance is discussed

Local and global Fokker-Planck neoclassical calculations showing flow and bootstrap current modification in a pedestal

In transport barriers, particularly H-mode edge pedestals, radial scale lengths can become comparable to the ion orbit width, causing neoclassical physics to become radially nonlocal. In this work, the resulting changes to neoclassical flow and current are examined both analytically and numerically. Steep density gradients are considered, with scale lengths comparable to the poloidal ion gyroradius, together with strong radial electric fields sufficient to electrostatically confine the ions. Attention is restricted to relatively weak ion temperature gradients (but permitting arbitrary electron temperature gradients), since in this limit a delta-f (small departures from a Maxwellian distribution) rather than full-f approach is justified. This assumption is in fact consistent with measured inter-ELM H-Mode edge pedestal density and ion temperature profiles in many present experiments, and is expected to be increasingly valid in future lower collisionality experiments. In the numerical analysis, the distribution function and Rosenbluth potentials are solved for simultaneously, allowing use of the exact field term in the linearized Fokker-Planck collision operator. In the pedestal, the parallel and poloidal flows are found to deviate strongly from the best available conventional neoclassical prediction, with large poloidal variation of a different form than in the local theory. These predicted effects may be observable experimentally. In the local limit, the Sauter bootstrap current formulae appear accurate at low collisionality, but they can overestimate the bootstrap current near the plateau regime. In the pedestal ordering, ion contributions to the bootstrap and Pfirsch-Schluter currents are also modified

Enhanced energy confinement and performance in a low-recycling tokamak,

ABSTRACT Extensive lithium wall coatings and liquid lithium plasma-limiting surfaces reduce recycling, with dramatic improvements in ohmic plasma discharges in the Current Drive eXperimentUpgrade (CDX-U). Global energy confinement times increase by up to 6×. These results exceed confinement scalings such as ITER98P(y,1) by 2-3×, and represent the largest increase in confinement ever observed for an ohmic tokamak plasma

Practical computational toolkits for dendrimers and dendrons structure design

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface (GUI) toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.Peer reviewe