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An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles for chemical reactions in a solvent or macromolecular environment.
High throughput discovery of amorphous bioresorbable alloys. Top: combinatorial sputtering setup. Bottom: composition of libraries deposited on silicon (Si) wafers for (a) magnesium (Mg)–zinc (Zn)–calcium (Ca) and the (b) iron (Fe)–Mg–Zn systems.
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A case performance study of a planar field emission cathode (FEC) based on nitrogen-incorporated ultrananocrystalline diamond, (N)UNCD, was carried out in an RF 1.3 GHz electron gun. The FEC was a 100 nm (N)UNCD film grown on a 20 mm diameter stainless steel disk with a Mo buffer layer. At surface gradients 45–65 MV/m, peak currents of 1–80 mA (equivalent to 0.3–25 mA/cm{sup 2}) were achieved. Imaging with two YAG screens confirmed emission from the (N)UNCD surface with (1) the beam emittance of 1.5 mm × mrad/mm-rms and (2) longitudinal FWHM and rms widths of non-Gaussian energy spread of 0.7% and 11% at an electron energy of 2 MeV. Current stability was tested over the course of 36 × 10{sup 3} RF pulses (equivalent to 288 × 10{sup 6 }GHz oscillations)
A 3-dimensional particle-in-cell/Monte Carlo collision simulation that is fully implemented on a graphics processing unit (GPU) is described and used to determine low-temperature plasma characteristics at high reduced electric field, E/n, in nitrogen gas. Details of implementation on the GPU using the NVIDIA Compute Unified Device Architecture framework are discussed with respect to efficient code execution. The software is capable of tracking around 10 × 10{sup 6} particles with dynamic weighting and a total mesh size larger than 10{sup 8} cells. Verification of the simulation is performed by comparing the electron energy distribution function and plasma transport parameters to known Boltzmann Equation (BE) solvers. Under the assumption of a uniform electric field and neglecting the build-up of positive ion space charge, the simulation agrees well with the BE solvers. The model is utilized to calculate plasma characteristics of a pulsed, parallel plate discharge. A photoionization model provides the simulation with additional electrons after the initial seeded electron density has drifted towards the anode. Comparison of the performance benefits between the GPU-implementation versus a CPU-implementation is considered, and a speed-up factor of 13 for a 3D relaxation Poisson solver is obtained. Furthermore, a factor 60 speed-up is realized for parallelization of the electron processes.
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Abstract Background Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cycles (TICs) causing unbounded metabolic flux ranges are often encountered. TICs satisfy the mass balance and directionality constraints but violate the second law of thermodynamics. Current practices involve implementing additional constraints to ensure not only optimal but also loopless flux distributions. However, the mixed integer linear programming problems required to solve become computationally intractable for genome-scale metabolic models. Results We aimed to identify the fewest needed constraints sufficient for optimality under the loopless requirement. We found that loopless constraints are required only for the reactions that share elementary flux modes representing TICs with reactions that are part of the objective function. We put forth the concept of localized loopless constraints (LLCs) to enforce this minimal required set of loopless constraints. By combining with a novel procedure for minimal null-space calculation, the computational time for loopless flux variability analysis (ll-FVA) is reduced by a factor of 10–150 compared to the original loopless constraints and by 4–20 times compared to the current fastest method Fast-SNP with the percent improvement increasing with model size. Importantly, LLCs offer a scalable strategy for loopless flux calculations for multi-compartment/multi-organism models of large sizes, for example, shortening the CPU time for ll-FVA from 35 h to less than 2 h for a model with more than104 reactions. Availability and implementation Matlab functions are available in the Supplementary Material or at https://github.com/maranasgroup/lll-FVA Supplementary information Supplementary data are available at Bioinformatics online.
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Optimization of electron coupling into small solid angles is of extreme importance to applications, such as Fast Ignition, that require maximum electron energy deposition within a small volume. To optimize this coupling, we use the ultra-high-contrast Trident laser, which remains below intensity of 10 11 W/cm 2 until < 0.1 ns before the main pulse, while still attaining high-energy, 75 J, and peak intensity of 5 x 10 19 W/cm 2 . Using a cone-wire target, we find that the coupling into the 40 μm diameter wire is increased by a factor of 2.7x over the low-contrast Titan laser at similar peak intensity. Full-scale simulations are used to model the laser interaction and quantitatively reproduce the experimental results. These show that increase in coupling is due to both a closer interaction, as well as the reduction of laser filamentation and self-focusing.
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