Defect-induced fracture topologies in Al₂O₃ ceramic-graphene nanocomposites

Models of ceramic-graphene nanocomposites are used to study how the manufacturing process-dependent arrangement of reduced graphene oxide (rGO) inclusions governs nano-crack network development. The work builds upon recent studies of such composites where a novel combinatorial approach was used to investigate the effect of rGO arrangements on electrical conductivity and porosity. This approach considers explicitly the discrete structure of the composite and represents it as a collection of entities of different dimensions - grains, grain boundaries, triple junctions, and quadruple points. Here, the combinatorial approach is developed further by considering the effects of rGO agglomerations, stress concentrators and adhesion energies on intergranular cracking. The results show that the fracture networks can be effectively controlled by the local ordering of rGO inclusions to allow for a concurrent increase in the strength and conductivity of the ceramic composites. It is shown that the ratio of local stress concentrators related to rGO inclusions and cracks is the most significant factor affecting the nano-crack network topology. The local spatial arrangement of rGO inclusions becomes an effective tool for controlling nano-crack network topology only when this ratio approaches one. It is anticipated that these results will inform future design of toughness-enhanced composites

Dynamics of electron emission in double photoionization processes near the Krypton 3d threshold

Two electron emission following photoabsorption near the Kr 3d threshold is investigated both experimentally and theoretically. On the experimental side, electron/electron coincidences using a magnetic bottle time of flight spectrometer allow us to observe the complete Double Photo Ionisation (DPI) continua of selected Kr2+ final states, and to see how these continua are affected by resonant processes in the vicinity of the Kr 3d threshold. The analysis is based on a quantum mechanical approach that takes into account the contribution of three different processes: A) Auger decay of the inner 3d vacancy with the associated post collision interaction (PCI) effects, B) capture of slow photoelectrons into discrete states followed by valence multiplet decay (VMD) of the excited ionic states and C) valence shell DPI. The dominant process for each Kr2+(4p-2) final state is the photoionization of the inner shell followed by Auger decay of the 3d vacancies. Moreover, for the 4p2(3P) and 4p-2(1D) final ionic states an important contribution comes from the processes of slow photoelectron capture followed by VMD as well as from double ionization of the outer shell involving also VMD

Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse

The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core. This view integrates water expulsion effects into the funnel energy landscape theory of protein folding. Comparisons to experimental results are shown for the SH3 protein. After the folding transition, a near-native intermediate with partially solvated hydrophobic core is found. This transition is followed by a final step that cooperatively squeezes out water molecules from the partially hydrated protein core.Comment: Proceedings of the National Academy of Science, 2002, Vol.99. 685-69

Investigation of routes and funnels in protein folding by free energy functional methods

We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can lower the free energy barrier to folding. Correlating stronger contact energies with entropically likely contacts of a given native structure lowers the barrier, and anticorrelating the energies has the reverse effect. Designing in relatively mild energetic heterogeneity can eliminate the barrier completely at the transition temperature. Sequences with native energies tuned to fold uniformly, as well as sequences tuned to fold by a single or a few routes, are rare. Sequences with weak native energetic heterogeneity are more common; their folding kinetics is more strongly determined by properties of the native structure. Sequences with different distributions of stability throughout the protein may still be good folders to the same structure. A measure of folding route narrowness is introduced which correlates with rate, and which can give information about the intrinsic biases in ordering due to native topology. This theoretical framework allows us to systematically investigate the coupled effects of energy and topology in protein folding, and to interpret recent experiments which investigate these effects.Comment: 12 pages, 1 figure, to appear in Proc. Natl. Acad. Sc

Postcollision interaction effects in KLL Auger spectra following argon 1s photoionization

Postcollision interaction effects on the Auger decay of a deep core hole are studied both experimentally and theoretically. KL2,3L2,3 decay spectra of the Ar 1s vacancy are measured with high-energy resolution with excess photon energies ranging from 0 to 200 eV above the ionization threshold. Interaction of the Auger electron with the photoelectron and the ion field manifests itself in the Auger spectra as a distortion of the energy distribution of the Auger electron close to threshold. Moreover, recapture of the photoelectron due to energy exchange is dominating in the low-photon-energy range above threshold. The experimental results are compared with calculations based on the semiclassical approach to the postcollision interaction. The energies of the discrete levels and individual recapture cross sections are computed in the Hartree-Fock approximation. Good agreement is found between the calculated and experimental spectra, validating the model used

Prediction of the 3D Structure and Dynamics of Human DP G-Protein Coupled Receptor Bound to an Agonist and an Antagonist

Prostanoids play important physiological roles in the cardiovascular and immune systems and in pain sensation in peripheral systems through their interactions with eight G-protein coupled receptors. These receptors are important drug targets, but development of subtype specific agonists and antagonists has been hampered by the lack of 3D structures for these receptors. We report here the 3D structure for the human DP G-protein coupled receptor (GPCR) predicted by the MembStruk computational method. To validate this structure, we use the HierDock computational method to predict the binding mode for the endogenous agonist (PGD2) to DP. Based on our structure, we predicted the binding of different antagonists and optimized them. We find that PGD2 binds vertically to DP in the TM1237 region with the α chain toward the extracellular (EC) region and the ω chain toward the middle of the membrane. This structure explains the selectivity of the DP receptor and the residues involved in the predicted binding site correlate very well with available mutation experiments on DP, IP, TP, FP, and EP subtypes. We report molecular dynamics of DP in explicit lipid and water and find that the binding of the PGD2 agonist leads to correlated rotations of helices of TM3 and TM7, whereas binding of antagonist leads to no such rotations. Thus, these motions may be related to the mechanism of activation

KFC Server: interactive forecasting of protein interaction hot spots

The KFC Server is a web-based implementation of the KFC (Knowledge-based FADE and Contacts) model—a machine learning approach for the prediction of binding hot spots, or the subset of residues that account for most of a protein interface's; binding free energy. The server facilitates the automated analysis of a user submitted protein–protein or protein–DNA interface and the visualization of its hot spot predictions. For each residue in the interface, the KFC Server characterizes its local structural environment, compares that environment to the environments of experimentally determined hot spots and predicts if the interface residue is a hot spot. After the computational analysis, the user can visualize the results using an interactive job viewer able to quickly highlight predicted hot spots and surrounding structural features within the protein structure. The KFC Server is accessible at http://kfc.mitchell-lab.org