Wall conditions in ORMAK

From surface effects in controlled thermonuclear fusion devices and reactors meeting; Argonne, Illnois, USA (10 Jan 1974). ORMAK is a diffuse toroidal pinch with typical plasma currents of 100 kA, electron temperatures of 800 eV, and ion temperatures of 300 eV. The walls of the plasma region are made of stainless steel coated with an intermediate layer of platinum 0.05 mu thick and an outer 1 to 2 mu layer of gold. Tests with an Ion Microprobe Mass Analyzer have shown that the platinum acts to decrease diffusion of impurities from the stalnless steel to the surface. Gold was chosen to inhibit the surface chemical adsorption of gases. Studies with a movable limiter indicate that electron energy is lost at the plasma edge mainly via line radiation and cooling on ions, while ions are lost from the plasma by charge exchange. Thus the walls are bombarded by energetic neutrals, line radiation and, in addition, bremsstrahlung x-rays. The flux of energetic neutrals is measured by a charge exchange analyzer. Wall bombardment by such neutrals should cause sputtering, and gold has been observed spectroscopically near the limiter, increasing with time during a shot, However, analysis of impurities coated on a window by the discharge indicated very little gold sputtering and re-deposition. To measure the sputterirg rate, a wall sample was coated with 105 A of radioactive gold and bombarded with neutrals from ORMAK during a day's run. No measurable sputtering was found within the counting statistics of the measurement, but surface carbon contamination of the sample prevented any final conclusions. (auth

Calculation of the Free Energy and Cooperativity of Protein Folding

Calculation of the free energy of protein folding and delineation of its pre-organization are of foremost importance for understanding, predicting and designing biological macromolecules. Here, we introduce an energy smoothing variant of parallel tempering replica exchange Monte Carlo (REMS) that allows for efficient configurational sampling of flexible solutes under the conditions of molecular hydration. Its usage to calculate the thermal stability of a model globular protein, Trp cage TC5b, achieves excellent agreement with experimental measurements. We find that the stability of TC5b is attained through the coupled formation of local and non-local interactions. Remarkably, many of these structures persist at high temperature, concomitant with the origin of native-like configurations and mesostates in an otherwise macroscopically disordered unfolded state. Graph manifold learning reveals that the conversion of these mesostates to the native state is structurally heterogeneous, and that the cooperativity of their formation is encoded largely by the unfolded state ensemble. In all, these studies establish the extent of thermodynamic and structural pre-organization of folding of this model globular protein, and achieve the calculation of macromolecular stability ab initio, as required for ab initio structure prediction, genome annotation, and drug design

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins. Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For the Trp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap. Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at of 4.4 Å from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the and chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data

Multiscale Coarse-Graining of the Protein Energy Landscape

A variety of coarse-grained (CG) models exists for simulation of proteins. An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields. In the present work, atomistic simulations of peptide folding and aggregation equilibria are force-matched using multiscale coarse-graining to develop and test a CG interaction potential of general utility for the simulation of proteins of arbitrary sequence. The reduced representation relies on multiple interaction sites to maintain the anisotropic packing and polarity of individual sidechains. CG energy landscapes computed from replica exchange simulations of the folding of Trpzip, Trp-cage and adenylate kinase resemble those of other reduced representations; non-native structures are observed with energies similar to those of the native state. The artifactual stabilization of misfolded states implies that non-native interactions play a deciding role in deviations from ideal funnel-like cooperative folding. The role of surface tension, backbone hydrogen bonding and the smooth pairwise CG landscape is discussed. Ab initio folding aside, the improved treatment of sidechain rotamers results in stability of the native state in constant temperature simulations of Trpzip, Trp-cage, and the open to closed conformational transition of adenylate kinase, illustrating the potential value of the CG force field for simulating protein complexes and transitions between well-defined structural states

Oak Ridge National Laboratory Report CF-61-2-57

Oscillations have been observed in a magnetically supported cylindrical rod of plasma. This rod of plasma can be the discharge occurring in the defining aperture of a Mode II, pressure gradient arc. Similar oscillations can also occur in the column of a Mode I arc. These oscillations appear to be the mechanism that drives the Mode II blowup phenomena