TALEs from a spring -- superelasticity of Tal effector protein structures

A simple force-probe setup is employed to study the mechanical properties of transcription activator-like effector (TALE) proteins in computer experiments. It is shown that their spring-like arrangement benefits superelastic behaviour which is manifested by large-scale global conformational changes along the helical axis, thus linking structure and dynamics in TALE proteins. As evidenced from the measured force-extension curves the dHax3 and PthXo1 TALEs behave like linear springs, obeying Hooke's law, for moderate global structural changes. For larger deformations, however, the proteins exhibit nonlinearities and the structures become stiffer the more they are stretched. Flexibility is not homogeneously distributed over TALE structure, but instead soft spots which correspond to the RVD loop residues and present key agents in the transmission of conformational motions are identified.Comment: 6 pages, 4 figure

Magnetic screening in the hot gluon system

The gluon transverse self-energy of the pure Yang-Mills system at high-temperature is analysed in the static limit and at fourth order in the coupling. Possible contributions to this function are collected, seen to be gauge-fixing independent subsets and shown to vanish all, except those which are either regulators or constituents of the self-energy of Euklidean 3D Yang-Mills theory at zero temperature. The latter self-energy, in turn, is known from the non-perturbative analysis by Karabali and Nair.Comment: 11 pages, latex, correction of prefactor in (24

On the Gluon Plasmon Self-Energy at O(g)

The next-to-leading order contribution \d\P\omn (\o ,\vc q ) to the polarization function of the hot gluon system is analysed at non-zero wave vectors \vc q \,. Using Braaten-Pisarski resummation and general covariant gauges, \d\P\omn is found to be gauge-fixing independent and transverse on the longitudinal mass-shell. The real part of the longitudinal component \d\P_\ell is UV and IR stable (for real $q$). At imaginary $q$ it is IR singular, and at the point \o=0, $q^2=-3m^2$ it coincides with the result of Rebhan for next-to-leading order Debye screening. When $q$ approaches the lightcone, \d\P_\ell diverges like 1 / \wu {\o^2 - q^2} , reflecting the breakdown of the Braaten-Pisarski decomposition scheme in this limit.Comment: 14 pages, LaTe

Improved hard-thermal-loop effective action for hot QED and QCD

The conventional results for hard thermal loops, which are the building blocks of resummed perturbation theory in thermal field theories, have collinear singularities when external momenta are light-like. It is shown that by taking into account asymptotic thermal masses these singularities are removed. The thus improved hard thermal loops can be summarized by compact gauge-invariant effective actions, generalizing the ones found by Taylor and Wong, and by Braaten and Pisarski.Comment: 21 pages, LaTeX, requires elsart.sty and epsf.sty, 1 postscript figure, compressed and uuencoded, (new reference [9] added

A Case Study: Farrell Drilled Displacement Column Ground Improvement

The objective of this study is to document the ground improvement techniques employed by Farrell Design-Build Inc. to allow for the construction of the Emeryville Public Market. The market is a Mixed use building, housing tenants, a ground floor grocery, and parking structure. By showing the effectiveness of this system, it is the hope that other industry professionals will be more capable to undertake and solve complex soil issues. Ground improvement is a technical, and necessary part of construction, allowing for vertical construction to begin. Farrell’s technology has the ability to transform industry standards, and create new methods of dealing with poor soils. In this instance, on the Public Market, the land designated for construction had a history of being a dumping ground in the early 1900’s. Close to the San Francisco bay, all types of contaminants contributed to the degradation of the soil, from oil, to benzene, to asbestos. This created marsh-like, toxic soils, in which footings could not be easily excavated and poured. Farrell’s patented Drilled Displacement Column™ technique was of great use in this situation, and has the potential to be of equal use in other similar projects. Documenting this process is vital to the constant improvement of the construction industry, and the never ending push towards quality construction practice

Simple mechanics of protein machines

While belonging to the nanoscale, protein machines are so complex that tracing even a small fraction of their cycle requires weeks of calculations on supercomputers. Surprisingly, many aspects of their operation can be however already reproduced by using very simple mechanical models of elastic networks. The analysis suggests that, similar to other self-organized complex systems, functional collective dynamics in such proteins is effectively reduced to a low-dimensional attractive manifold