| 1. |
- Abel, I, et al.
(författare)
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Overview of the JET results with the ITER-like wall
- 2013
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 53:10, s. 104002-
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Tidskriftsartikel (refereegranskat)abstract
- Following the completion in May 2011 of the shutdown for the installation of the beryllium wall and the tungsten divertor, the first set of JET campaigns have addressed the investigation of the retention properties and the development of operational scenarios with the new plasma-facing materials. The large reduction in the carbon content (more than a factor ten) led to a much lower Z(eff) (1.2-1.4) during L- and H-mode plasmas, and radiation during the burn-through phase of the plasma initiation with the consequence that breakdown failures are almost absent. Gas balance experiments have shown that the fuel retention rate with the new wall is substantially reduced with respect to the C wall. The re-establishment of the baseline H-mode and hybrid scenarios compatible with the new wall has required an optimization of the control of metallic impurity sources and heat loads. Stable type-I ELMy H-mode regimes with H-98,H-y2 close to 1 and beta(N) similar to 1.6 have been achieved using gas injection. ELM frequency is a key factor for the control of the metallic impurity accumulation. Pedestal temperatures tend to be lower with the new wall, leading to reduced confinement, but nitrogen seeding restores high pedestal temperatures and confinement. Compared with the carbon wall, major disruptions with the new wall show a lower radiated power and a slower current quench. The higher heat loads on Be wall plasma-facing components due to lower radiation made the routine use of massive gas injection for disruption mitigation essential.
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| 2. |
- Romanelli, F, et al.
(författare)
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Overview of the JET results
- 2011
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 51:9
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Tidskriftsartikel (refereegranskat)abstract
- Since the last IAEA Conference JET has been in operation for one year with a programmatic focus on the qualification of ITER operating scenarios, the consolidation of ITER design choices and preparation for plasma operation with the ITER-like wall presently being installed in JET. Good progress has been achieved, including stationary ELMy H-mode operation at 4.5 MA. The high confinement hybrid scenario has been extended to high triangularity, lower ρ*and to pulse lengths comparable to the resistive time. The steady-state scenario has also been extended to lower ρ*and ν*and optimized to simultaneously achieve, under stationary conditions, ITER-like values of all other relevant normalized parameters. A dedicated helium campaign has allowed key aspects of plasma control and H-mode operation for the ITER non-activated phase to be evaluated. Effective sawtooth control by fast ions has been demonstrated with3He minority ICRH, a scenario with negligible minority current drive. Edge localized mode (ELM) control studies using external n = 1 and n = 2 perturbation fields have found a resonance effect in ELM frequency for specific q95values. Complete ELM suppression has, however, not been observed, even with an edge Chirikov parameter larger than 1. Pellet ELM pacing has been demonstrated and the minimum pellet size needed to trigger an ELM has been estimated. For both natural and mitigated ELMs a broadening of the divertor ELM-wetted area with increasing ELM size has been found. In disruption studies with massive gas injection up to 50% of the thermal energy could be radiated before, and 20% during, the thermal quench. Halo currents could be reduced by 60% and, using argon/deuterium and neon/deuterium gas mixtures, runaway electron generation could be avoided. Most objectives of the ITER-like ICRH antenna have been demonstrated; matching with closely packed straps, ELM resilience, scattering matrix arc detection and operation at high power density (6.2 MW m-2) and antenna strap voltages (42 kV). Coupling measurements are in very good agreement with TOPICA modelling. © 2011 IAEA, Vienna.
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| 3. |
- Berk, H. L., et al.
(författare)
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Explanation of the JET n=0 chirping mode
- 2006
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Ingår i: Nuclear Fusion. - 0029-5515 .- 1741-4326. ; 46:10, s. S888-S897
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Tidskriftsartikel (refereegranskat)abstract
- Persistent rapid up and down frequency chirping modes with a toroidal mode number of zero (n = 0) are observed in the JET tokamak when energetic ions, in the range of several hundred keV, are created by high field side ion cyclotron resonance frequency heating. Fokker-Planck calculations demonstrate that the heating method enables the formation of an energetically inverted ion distribution which supplies the free energy for the ions to excite a mode related to the geodesic acoustic mode. The large frequency shifts of this mode are attributed to the formation of phase space structures whose frequencies, which are locked to an ion orbit bounce resonance frequency, are forced to continually shift so that energetic particle energy can be released to counterbalance the energy dissipation present in the background plasma.
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| 4. |
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| 5. |
- Fasoli, A., et al.
(författare)
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Chapter 5 : Physics of energetic ions
- 2007
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 47:6, s. S264-S284
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Forskningsöversikt (refereegranskat)abstract
- This chapter reviews the progress accomplished since the redaction of the first ITER Physics Basis (1999 Nucl. Fusion 39 2137-664) in the field of energetic ion physics and its possible impact on burning plasma regimes. New schemes to create energetic ions simulating the fusion-produced alphas are introduced, accessing experimental conditions of direct relevance for burning plasmas, in terms of the Alfvenic Mach number and of the normalised pressure gradient of the energetic ions, though orbit characteristics and size cannot always match those of ITER. Based on the experimental and theoretical knowledge of the effects of the toroidal magnetic field ripple on direct fast ion losses, ferritic inserts in ITER are expected to provide a significant reduction of ripple alpha losses in reversed shear configurations. The nonlinear fast ion interaction with kink and tearing modes is qualitatively understood, but quantitative predictions are missing, particularly for the stabilisation of sawteeth by fast particles that can trigger neoclassical tearing modes. A large database on the linear stability properties of the modes interacting with energetic ions, such as the Alfven eigenmode has been constructed. Comparisons between theoretical predictions and experimental measurements of mode structures and drive/damping rates approach a satisfactory degree of consistency, though systematic measurements and theory comparisons of damping and drive of intermediate and high mode numbers, the most relevant for ITER, still need to be performed. The nonlinear behaviour of Alfven eigenmodes close to marginal stability is well characterized theoretically and experimentally, which gives the opportunity to extract some information on the particle phase space distribution from the measured instability spectral features. Much less data exists for strongly unstable scenarios, characterised by nonlinear dynamical processes leading to energetic ion redistribution and losses, and identified in nonlinear numerical simulations of Alfven eigenmodes and energetic particle modes. Comparisons with theoretical and numerical analyses are needed to assess the potential implications of these regimes on burning plasma scenarios, including in the presence of a large number of modes simultaneously driven unstable by the fast ions.
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| 6. |
- Ghiringhelli, Luca M, et al.
(författare)
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Competing adsorption between hydrated peptides and water onto metal surfaces : from electronic to conformational properties
- 2008
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 130:40, s. 13460-13464
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Tidskriftsartikel (refereegranskat)abstract
- Inorganic-(bio)organic interfaces are of central importance in many fields of current research. Theoretical and computational tools face the difficult problem of the different time and length scales that are involved and linked in a nontrivial way. In this work, a recently proposed hierarchical quantum-classical scale-bridging approach is further developed to study large flexible molecules. The approach is then applied to study the adsorption of oligopeptides on a hydrophilic Pt(111) surface under complete wetting conditions. We examine histidine sequences, which are well known for their binding affinity to metal surfaces. Based on a comparison with phenylalanine, which binds as strong as histidine under high vacuum conditions but, as we show, has no surface affinity under wet conditions, we illustrate the mediating effects of near-surface water molecules. These contribute significantly to the mechanism and strength of peptide binding. In addition to providing physical-chemical insights in the mechanism of surface binding, our computational approach provides future opportunities for surface-specific sequence design.
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| 7. |
- Kasson, Peter M., et al.
(författare)
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Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions
- 2013
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Ingår i: Chemistry and Physics of Lipids. - : Elsevier BV. - 0009-3084 .- 1873-2941. ; 169, s. 106-112
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Tidskriftsartikel (refereegranskat)abstract
- Cellular lipid membranes are spatially inhomogeneous soft materials. Materials properties such as pressure and surface tension thus show important microscopic-scale variation that is critical to many biological functions. We present a means to calculate pressure and surface tension in a 3D-resolved manner within molecular-dynamics simulations and show how such measurements can yield important insight. We also present the first corrections to local virial and pressure fields to account for the constraints typically used in lipid simulations that otherwise cause problems in highly oriented systems such as bilayers. Based on simulations of an asymmetric bacterial ion channel in a POPC bilayer, we demonstrate how 3D-resolved pressure can probe for both short-range and long-range effects from the protein on the membrane environment. We also show how surface tension is a sensitive metric for inter-leaflet equilibrium and can be used to detect even subtle imbalances between bilayer leaflets in a membrane-protein simulation. Since surface tension is known to modulate the function of many proteins, this effect is an important consideration for predictions of ion channel function. We outline a strategy by which our local pressure measurements, which we make available within a version of the GROMACS simulation package, may be used to design optimally equilibrated membrane-protein simulations.
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| 8. |
- Lundborg, M., et al.
(författare)
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The accelerated weight histogram method for alchemical free energy calculations
- 2021
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 154:20
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Tidskriftsartikel (refereegranskat)abstract
- The accelerated weight histogram method is an enhanced sampling technique used to explore free energy landscapes by applying an adaptive bias. The method is general and easy to extend. Herein, we show how it can be used to efficiently sample alchemical transformations, commonly used for, e.g., solvation and binding free energy calculations. We present calculations and convergence of the hydration free energy of testosterone, representing drug-like molecules. We also include methane and ethanol to validate the results. The protocol is easy to use, does not require a careful choice of parameters, and scales well to accessible resources, and the results converge at least as quickly as when using conventional methods. One benefit of the method is that it can easily be combined with other reaction coordinates, such as intermolecular distances.
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| 9. |
- Pronk, Sander, et al.
(författare)
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GROMACS 4.5 : a high-throughput and highly parallel open source molecular simulation toolkit
- 2013
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 29:7, s. 845-854
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.
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| 10. |
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