Predictions of structural elements for the binding of Hin recombinase with the hix site of DNA

Molecular dynamics simulations were coupled with experimental data from biochemistry and genetics to generate a theoretical structure for the binding domain of Hin recombinase complexed with the hix site of DNA. The theoretical model explains the observed sequence specificity of Hin recombinase and leads to a number of testable predictions concerning altered sequence selectivity for various mutants of protein and DNA. Combining molecular dynamics simulations with constraints based on current knowledge of protein structure leads to a theoretical structure of the binding domain of Hin recombinase with the hix site of DNA. The model offers a mechanistic explanation of the presently known characteristics of Hin and predicts the effects of specific mutations of both protein and DNA. The predictions can be tested by currently feasible experiments that should lead to refinements in and improvements on the current theoretical model. Because current experimental and theoretical methods are all limited to providing only partial information about protein-DNA interactions, we believe that this approach of basing molecular simulations on experimental knowledge and using the results of these simulations to design new, more precise experimental tests will be of general utility. These results provide additional evidence for the generality of the helix-turn-helix motif in DNA recognition and stabilization of proteins on DNA

What do indigenous communities think of the CSR practices of mining companies?

This paper examines how one indigenous community in the Western Province of Papua New Guinea (PNG) views the social responsibility initiatives of OK Tedi Mining Ltd (OTML). This mining operation has been controversial since its inception, and various operators of the mine have sought to engage the community and to undertake a number of CSR-related projects. Insights gained from four focus groups amongst the Ok Tedi River indigenous communities show that while some members of the community are satisfied with the company’s efforts at the macro level, many have reservations about the effectiveness of the programs at the micro level on the village and family unit. The implementation of CSR activities are slow and in many instances do not effectively address stakeholder concerns

An Unusual Hydrogen Migration/C−H Activation Reaction with Group 3 Metals

A novel hydrogen migration from the phenyl ring to the pyridine ring of an yttrium pyridyl complex supported by a 1,1′-ferrocene diamide ligand is reported. Density functional theory calculations were instrumental in probing the mechanism for this transformation

Versions of confinement: Melville's bodies and the psychology of conquest

This thesis explores aspects of Melville’s presentation of both the whale and the human bodies in Moby-Dick and human bodies in other important novels. It argues that Melville uses his presentation of bodies to explore some of the versions of confinement those bodies experience, and by doing so, analyses the psychology which subtends that confinement. Throughout Melville’s works bodies are confined, both within literal spatial limits and by the psychology which creates and/or accepts these spatial limits. The thesis argues that perhaps the most important version of bodily confinement Melville addresses is the impulse to conquer bodies, both that of the other and one’s own. It adopts a largely psychoanalytic approach to interpreting bodies and their impulse to conquer, so that the body is seen to figure both in its actions and its external appearance the operations of the inner psyche. The figure of the body is equally prevalent in Melville’s exploration of nationalist conquest, where, as with Manifest Destiny and antebellum expansionism, the psychological and physical lack experienced by characters can be read as motivating factors in the ideology of conquest. A final important strand of the thesis is its argument in favour of a gradual shift in Melville’s interpretation of the value and possibility of genuine communion between human beings and between humans and the whale. One may read Typee as an attempt by Melville to explore the possibility of a this-worldly utopia in which human beings can return to a version of primitive interconnectedness. This exploration may be seen to be extended in Moby-Dick, particularly in Ishmael’s attempts to find communion with others and in some moments of encounter with the whales. The thesis uses phenomenology as a theory to interpret what Melville is trying to suggest in these moments of encounter. However, it argues, finally, that such encounter, or ‘intersubjectivity’ is eventually jettisoned, especially in the works after Moby-Dick. By the end of Melville’s life and work, any hope of an intersubjective utopia he may have harboured as a younger man have been removed in favour of a refusal actually to assert any final ‘truth’ about social, political or even religious experience. Billy Budd, his last body, is hanged, and his final word is silence

Reaction of Group III Biheterocyclic Complexes

Group III alkyl complexes supported by a ferrocene diamide ligand (1,1′-fc(NSitBuMe_2)_2) have been found to be reactive toward aromatic N-heterocycles such as 1-methylimidazole and pyridines. These reactions were investigated experimentally and computationally. An initial C−H activation event is followed by a coupling reaction to form biheterocyclic complexes, in which one of the rings is dearomatized. In the case of 1-methylimidazole, the biheterocyclic compound could not be isolated and further led to an imidazole ring-opened product; in the case of pyridines, it transformed into an isomer with extended conjugation of double bonds. Mechanisms for both reactions are proposed on the basis of experimental and computational results. DFT calculations were also used to show that an energetically accessible pathway for the ring-opening of pyridines exists

An et al. Reply

Our Letter reported high-resolution transmission electron microscopy on commercial quality boron showing that ∼2=3 of the grains exhibit smooth microstructure, leading to an x-ray diffraction pattern of well-known beta boron [1]. The other 1=3 grains exhibit a uniform zigzag pattern that extends across the entire grain and exhibits a very regular twinlike symmetry on every other lattice plane. This second phase gives diffraction patterns that are different from beta

New Ground-State Crystal Structure of Elemental Boron

Elemental boron exhibits many polymorphs in nature based mostly on an icosahedral shell motif, involving stabilization of 13 strong multicenter intraicosahedral bonds. It is commonly accepted that the most thermodynamic stable structure of elemental boron at atmospheric pressure is the β rhombohedral boron (β−B). Surprisingly, using high-resolution transmission electron microscopy, we found that pure boron powder contains grains of two different types, the previously identified β−B containing a number of randomly spaced twins and what appears to be a fully transformed twinlike structure. This fully transformed structure, denoted here as τ−B, is based on the Cmcm orthorhombic space group. Quantum mechanics predicts that the newly identified τ−B structure is 13.8  meV/B more stable than β−B. The τ−B structure allows 6% more charge transfer from B_(57) units to nearby B_(12) units, making the net charge 6% closer to the ideal expected from Wade’s rules. Thus, we predict the τ−B structure to be the ground state structure for elemental boron at atmospheric pressure

Nucleation of amorphous shear bands at nanotwins in boron suboxide

The roles of grain boundaries and twin boundaries in mechanical properties are well understood for metals and alloys. However, for covalent solids, their roles in deformation response to applied stress are not established. Here we characterize the nanotwins in boron suboxide (B_6O) with twin boundaries along the {0111} planes using both scanning transmission electron microscopy and quantum mechanics. Then, we use quantum mechanics to determine the deformation mechanism for perfect and twinned B_6O crystals for both pure shear and biaxial shear deformations. Quantum mechanics suggests that amorphous bands nucleate preferentially at the twin boundaries in B_6O because the twinned structure has a lower maximum shear strength by 7.5% compared with perfect structure. These results, which are supported by experimental observations of the coordinated existence of nanotwins and amorphous shear bands in B_6O, provide a plausible atomistic explanation for the influence of nanotwins on the deformation behaviour of superhard ceramics