Spin resonance with trapped ions

Abstract

A modified ion trap is described where experiments (in particular related to quantum information processing) that usually require optical radiation can be carried out using microwave or radio frequency electromagnetic fields. Instead of applying the usual methods for coherent manipulation of trapped ions, a string of ions in such a modified trap can be treated like a molecule in nuclear magnetic resonance experiments taking advantage of spin-spin coupling. The collection of trapped ions can be viewed as an N-qubit molecule with adjustable spin-spin coupling constants. Given N identically prepared quantum mechanical two-level systems (qubits), the optimal strategy to estimate their quantum state requires collective measurements. Using the ground state hyperfine levels of electrodynamically trapped 171 Yb + , we have implemented an adaptive algorithm for state estimation involving sequential measurements on arbitrary qubit states.

A pH-dependent computational approach to the effect of mutations on protein stability

“…which is similar to M1K, appears in the most stabilizing quadruple mutation, M1R/E3K/K65I/E66L, found by the direct evolution method. [25] The quadruple mutation increases T m to above 858C, which is comparable with the midpoints of thermal denaturation of hyper-thermostable proteins. Unlike the mutation M1K, we were unable to find any experimental data about S11K or S11R.…”

“…[16] While most of them reveal the key mutations leading to the improved thermostability of Bc-Csp, it is interesting that in a number of studies based on Proside method of direct evolution, the authors successfully found mutants that are quite different from the native thermophile, but have comparable, even improved thermostability with a melting temperature (T m ) up to 828C [24] and 858C. [25] Those temperatures are above the midpoint temperature of thermal unfolding of Bc-Csp (768C) and comparable to the midpoint of denaturation of the hyperthermostable analog from Thermotoga maritima.…”

“…The high stabilizing effect of the E3 and E66 mutations is consistent with the key role of eliminating the negative charge of one or both of these residues in raising the T m from around 568C for the mesophilic protein to a T m of 768C for the thermophilic Bc-Csp. [23] Furthermore, the experimental [25] DDG mut 5 23.4 kcal/mol for the double mutation E3R/E66L clearly shows that among the 12 different sites between Bs-CspB and Bc-Csp, these two sites have the biggest effect on protein stability. Although the two residues are far apart in sequence, they are relatively close (about 7 Å apart) in the Bs-CspB structure.…”

“…In the study by Wunderlich et al [25] on stabilizing the cold shock protein by evolutionary optimization of electrostatic interactions, the authors carried out a Proside [26] search for stable variants of Bs-CspB by targeting nine surface residues, 5, 10, 12, 19, 20, 22, 43, 46, and 48, that are remote from the binding site of the protein. The respective codons were replaced by triplets coding at least one acidic, basic, polar, and non-polar residue.…”

“…The tests include both large numbers of single point, double, and triple mutations. As a case study to test the combinatorial mutagenesis functionality of the computational protocol, we used our method to suggest possible mutations which can change the mesophilic cold shock protein to a thermophilic variant by mimicking the experimental studies of Schmid and coworkers [23][24][25] based on the Proside method of direct evolution [26] and site-directed mutagenesis in the search of stabilizing mutations. For this purpose, we used combination of single point scanning mutagenesis and multiple sites combinatorial mutations and provide a comparison to Proside results to assess the accuracy and reliability of the predictions and to demonstrate how the computational protocol can be used to guide a real experimental work.…”