Methods for enzyme library creation: which one will you choose? A guide for novices and experts to introduce genetic diversity

Enzyme engineering allows to explore sequence diversity in search for new properties. The scientific literature is populated with methods to create enzyme libraries for engineering purposes, however, choosing a suitable method for the creation of mutant libraries can be daunting, in particular for the novices. Here, we address both novices and experts: how can one enter the arena of enzyme library design and what guidelines can advanced users apply to select strategies best suited to their purpose? Section I is dedicated to the novices and presents an overview of established and standard methods for library creation, as well as available commercial solutions. The expert will discover an up-to-date tool to freshen up their repertoire (Section I) and learn of the newest methods that are likely to become a mainstay (Section II). We focus primarily on in vitro methods, presenting the advantages of each method. Our ultimate aim is to offer a selection of methods/strategies that we believe to be most useful to the enzyme engineer, whether a first-timer or a seasoned user

Continuous Plasma density measurement in TJ-II infrared interferometer-Advanced signal processing based on FPGAs

This work presents the behavioral simulation in an FPGA of a novel processing system for measuring line average electronic density in the TJ-II stellarator diagnostic, Infra-Red Two-Color Interferometer. Line average electronic density is proportional to phase difference between probing and reference signals of the interferometer, as the Appleton–Hartree cold plasma model states. The novelty of the approach is the development of a real time measuring system where research work has been carried out in two ways: a new interpolation algorithm and the implementation of a new specific processor on an FPGA. The main goal of this new system is to measure line plasma electronic density for several channels in real time, also it will be useful to eliminate intermediate mixing frequency stages (the output signals coming from the interferometer are going to be directly sampled) and finally to generate real time density signals for control purposes in TJ-II and in other diagnostics. This device is intended to be the new data acquisition-processing system for the future six channel infrared interferometer that requires at least 14 input signals. The knowledge acquired could be useful in the design of W7-X and ITER IR-interferometer data acquisition and processing systems

Electron Bernstein waves emission in the TJ-II Stellarator

Taking advantage of the electron Bernstein waves heating (EBWH) system of the TJ-II stellarator, an electron Bernstein emission (EBE) diagnostic was installed. Its purpose is to investigate the B-X-O radiation properties in the zone where optimum theoretical EBW coupling is predicted. An internal movable mirror shared by both systems allows us to collect the EBE radiation along the same line of sight that is used for EBW heating. The theoretical EBE has been calculated for different orientations of the internal mirror using the TRUBA code as ray tracer. A comparison with experimental data obtained in NBI discharges is carried out. The results provide a valuable information regarding the experimental O-X mode conversion window expected in the EBW heating experiments. Furthermore, the characterization of the radiation polarization shows evidence of the underlying B-X-O conversion process.Comment: 21 pages, 14 figure

Study of the neoclassical radial electric field of the TJ-II flexible heliac

Calculations of the monoenergetic radial diffusion coefficients are presented for several configurations of the TJ-II stellarator usually explored in operation. The neoclassical radial fluxes and the ambipolar electric field for the standard configuration are then studied for three different collisionality regimes, obtaining precise results in all cases

Calculation of the bootstrap current profile for the TJ-II stellarator

Calculations of the bootstrap current for the TJ-II stellarator are presented. DKES and NEO-MC codes are employed; the latter has allowed, for the first time, the precise computation of the bootstrap transport coefficient in the long mean free path regime of this device. The low error bars allow a precise convolution of the monoenergetic coefficients, which is confirmed by error analysis. The radial profile of the bootstrap current is presented for the first time for the 100_44_64 configuration of TJ-II for three different collisionality regimes. The bootstrap coefficient is then compared to that of other configurations of TJ-II regularly operated. The results show qualitative agreement with toroidal current measurements; precise comparison with real discharges is ongoing

Latest physics results of TJ-II flexible heliac

This paper is devoted to the presentation of the most relevant recent Physics results obtained in the TJ-II flexible heliac. Firstly ECRH modulation and plasma breakdown studies are summarised; then the particle control techniques used to obtain reproducible discharges with density under control are presented. Transport studies show internal heat transport barriers that reduce heat conductivity to neoclassical values, and ELM-like transport events, similar to those observed in tokamaks and in other stellarators before and during H mode transition. Evidence of ExB sheared has been observed both in the proximity of rational surfaces. Finally, a high resolution Thomsom Scattering system has shown Te and ne profile structures

Perturbative transport experiments on TJ-II Flexible Heliac

Transport properties of TJ-II are explored performing perturbative experiments and taking advantage of TJ-II flexibility. Rotational transform can be varied in a wide range, which allows one to introduce low order rationals and to study their effect on transport. On the other hand, confinement properties can be studied at very different rotational transform values and for different values of magnetic shear: Experiments on influence of the magnetic shear on confinement are reported. In these cases a Ohmic current has been induced in TJ-II plasma to modify magnetic shear and to evaluate itsd effect on confinement, showing that negative shear improves the confinement. Heat transport is also reduced by locating a low order rational near the power deposition profile. Plasma potential profiles have been recently measured in some configurations up to the plasma core with the Heavy Ion Beam Probe (HIBP) diagnostic and the electric field values measured in low-density plasmas are consistent with neoclassical calculations near the plasma core. Plasma edge turbulent transport has been studied in configurations that are marginally stable due to decreased magnetic well. Results show a dynamical coupling between gradients and turbulent transport. Finally, cold pulse propagation has been studied showing ballistic non diffusive propagation

Effect of the aspect ratio on the stability limits of TJ-II-like stellarators

The four-field-period device TJ-II has a major radius of 1.5 m and an average plasma radius of 0.10--0.25 m, with a typical plasma aspect ratio A{sub P} of 10. In the infinite aspect ratio, helically symmetric limit, the region of the stability to low-n modes has been shown to extend to average betas of at least 40%, for a relatively highly indented plasma. It is possible to approximate the helically symmetric limit from the actual TJ-II parameters increasing the number of toroidal periods N{sub T} and choosing the major radius R{sub O} such as to obtain a constant helical pitch h = N{sub T}/R{sub O}. In this way the aspect ratio per period is fixed. In this work we analyze a shear-less TJ-II configuration with a rotational transform per period of 0.36 and a vacuum magnetic well of 3.5%. By taking for N{sub T} the values N{sub T} = 3, 4, 5, 8, 10, 11, 12, 19 and 100 a sequence of equilibria is generated. These equilibria are calculated with the fixed boundary version of the VMEC code. The Mercier stability properties are then analyzed