Fidelity enhancement by logical qubit encoding

We demonstrate coherent control of two logical qubits encoded in a decoherence free subspace (DFS) of four dipolar-coupled protons in an NMR quantum information processor. A pseudo-pure fiducial state is created in the DFS, and a unitary logical qubit entangling operator evolves the system to a logical Bell state. The four-spin molecule is partially aligned by a liquid crystal solvent, which introduces strong dipolar couplings among the spins. Although the system Hamiltonian is never fully specified, we demonstrate high fidelity control over the logical degrees of freedom. In fact, the DFS encoding leads to higher fidelity control than is available in the full four-spin Hilbert space.Comment: 10 pages, 2 figure

Similarities and differences between molecular order in the nematic and twist-bend nematic phases of a symmetric liquid crystal dimer

The order parameter, Szz, where z is the para axis of the difluoroterphenyl groups in DTC5C9, have been obtained from chemical shift anisotropies measured by ¹³C – {¹1H} NMR experiments at temperatures throughout the nematic, NU, and twist-bend nematic, NTB, phases shown by this compound. The order parameter temperature profiles are unusual in having a maximum value in the NU phase and then decreasing until the NTB phase is reached. There is a small discontinuity (~2%) in Szz at T_(NN_TB )and then a gradual decrease until a new phase appears. This behaviour is interpreted as revealing a temperature-dependent tilting of local directors in both phases away from the applied magnetic field direction. In the enantiomorphic twist-bend phase this tilt is consistent with the structure of the phase as a helical arrangement of local directors, whilst in the high-temperature non-chiral nematic the tilt must involve a non-chiral arrangement. It is proposed that in both phases the tilting of directors has a common origin in the bent shape of the molecules

Structure of a bacterial cell surface decaheme electron conduit

Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along “nanowire” appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split ß-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface

UV-induced ligand exchange in MHC class I protein crystals

High-throughput structure determination of protein−ligand complexes is central in drug development and structural proteomics. To facilitate such high-throughput structure determination we designed an induced replacement strategy. Crystals of a protein complex bound to a photosensitive ligand are exposed to UV light, inducing the departure of the bound ligand, allowing a new ligand to soak in. We exemplify the approach for a class of protein complexes that is especially recalcitrant to high-throughput strategies: the MHC class I proteins. We developed a UV-sensitive, “conditional”, peptide ligand whose UV-induced cleavage in the crystals leads to the exchange of the low-affinity lytic fragments for full-length peptides introduced in the crystallant solution. This “in crystallo” exchange is monitored by the loss of seleno-methionine anomalous diffraction signal of the conditional peptide compared to the signal of labeled MHC β2m subunit. This method has the potential to facilitate high-throughput crystallography in various protein families

Thermodynamic aspects of materials' hardness: prediction of novel superhard high-pressure phases

In the present work we have proposed the method that allows one to easily estimate hardness and bulk modulus of known or hypothetical solid phases from the data on Gibbs energy of atomization of the elements and corresponding covalent radii. It has been shown that hardness and bulk moduli of compounds strongly correlate with their thermodynamic and structural properties. The proposed method may be used for a large number of compounds with various types of chemical bonding and structures; moreover, the temperature dependence of hardness may be calculated, that has been performed for diamond and cubic boron nitride. The correctness of this approach has been shown for the recently synthesized superhard diamond-like BC5. It has been predicted that the hypothetical forms of B2O3, diamond-like boron, BCx and COx, which could be synthesized at high pressures and temperatures, should have extreme hardness

Spontaneous formation and stability of small GaP fullerenes

We report the spontaneous formation of a GaP fullerene cage in ab-initio Molecular Dynamics simulations starting from a bulk fragment. A systematic study of the geometric and electronic properties of neutral and ionized GaP clusters suggests the stability of hetero-fullerenes formed by a compound with zincblend bulk structure. We find that GaP fullerenes up to 28 atoms have high symmetry, closed electronic shells, large HOMO-LUMO energy gaps and do not dissociate when ionized. We compare our results for GaP with those obtained by other groups for the corresponding BN clusters.Comment: To appear on PRL, 4 pages, 1 figure, Late

Class I major histocompatibility complexes loaded by a periodate trigger

Class I major histocompatibility complexes (MHCs) present peptide ligands on the cell surface for recognition by appropriate cytotoxic T cells. The unstable nature of unliganded MHC necessitates the production of recombinant class I complexes through in vitro refolding reactions in the presence of an added excess of peptides. This strategy is not amenable to high-throughput production of vast collections of class I complexes. To address this issue, we recently designed photocaged MHC ligands that can be cleaved by a UV light trigger in the MHC bound state under conditions that do not affect the integrity of the MHC structure. The results obtained with photocaged MHC ligands demonstrate that conditional MHC ligands can form a generally applicable concept for the creation of defined peptide−MHCs. However, the use of UV exposure to mediate ligand exchange is unsuited for a number of applications, due to the lack of UV penetration through cell culture systems and due to the transfer of heat upon UV irradiation, which can induce evaporation. To overcome these limitations, here, we provide proof-of-concept for the generation of defined peptide−MHCs by chemical trigger-induced ligand exchange. The crystal structure of the MHC with the novel chemosensitive ligand showcases that the ligand occupies the expected binding site, in a conformation where the hydroxyl groups should be reactive to periodate. We proceed to validate this technology by producing peptide−MHCs that can be used for T cell detection. The methodology that we describe here should allow loading of MHCs with defined peptides in cell culture devices, thereby permitting antigen-specific T cell expansion and purification for cell therapy. In addition, this technology will be useful to develop miniaturized assay systems for performing high-throughput screens for natural and unnatural MHC ligands