Energy landscapes hold the key to understanding a wide range of molecular phenomena. The problem of how a denatured protein re-folds to its active state (Levinthal's paradox 1 ) has been addressed in terms of the underlying energy landscape 2±7 , as has the widely used`strong' and`fragile' classi®cation of liquids 8,9 . Here we show how three archetypal energy landscapes for clusters of atoms or molecules can be characterized in terms of the disconnectivity graphs 10 of their energy minimaÐthat is, in terms of the pathways that connect minima at different threshold energies. First we consider a cluster of 38 Lennard±Jones particles, whose energy landscape is a`double funnel' on which relaxation to the global minimum is diverted into a set of competing structures. Then we characterize the energy landscape associated with the annealing of C 60 cages to buckministerfullerene, and show that it provides experimentally accessible clues to the relaxation pathway. Finally we show a very different landscape morphology, that of a model water cluster (H 2 O) 20 , and show how it exhibits features expected for a`strong' liquid. These three examples do not exhaust the possibilities, and might constitute substructures of still more complex landscapes.We use disconnectivity graphs 10 to visualize the energy landscapes, based upon samples of pathways linking local minima via transition states. At any given total energy we elucidate which of the local minima in our sample are connected by pathways that lie below the energy threshold. At ®nite energy the minima are divided into disconnected sets of mutually accessible structures, separated by insurmountable barriers. The resulting graphs are clearest when we present the results as the total energy increases in regular steps along the vertical axis. Each line begins from a different local minimum at a vertical height determined by the potential energy at the bottom of the corresponding well. A node joins lines at the lowest energy for which the minima become mutually accessible. We are free to choose the horizontal displacements to give the most helpful representation of the resulting graph.Graphs such as these, which are connected but contain no cycles, are known as`trees' for reasons which should be clear from Fig. 1. The gentle`funnel' with high barriers in Fig. 1a produces a graph which looks like a weeping willow. The graph for the ef®cient funnel with lower barriers in Fig. 1b reminds us of a palm tree, whilst the graph for the rough landscape in Fig. 1c resembles a banyan tree with its branches planted into the ground.We ®rst focus on a cluster of 38 atoms bound by the Lennard± Jones potential, represented here by (LJ) 38 . The lowest-energy icosahedral minimum lies signi®cantly above the truncated octahedron 11 , and the two minima are well separated in con®gura-tion space. Relaxation to the global minimum is hampered because the vast majority of local minima are associated with the liquidlike state of the cluster and have polytetrahedral character 11 . Minima based upon ic...
Photoresponsive molecules that incorporate peptides capable of material-specific recognition provide a basis for biomolecule-mediated control of the nucleation, growth, organization, and activation of hybrid inorganic/organic nanostructures. These hybrid molecules interact with the inorganic surface through multiple noncovalent interactions which allow reconfiguration in response to optical stimuli. Here, we quantify the binding of azobenzene-peptide conjugates that exhibit optically triggered cis-trans isomerization on Ag surfaces and compare to their behavior on Au. These results demonstrate differences in binding and switching behavior between the Au and Ag surfaces. These molecules can also produce and stabilize Au and Ag nanoparticles in aqueous media where the biointerface can be reproducibly and reversibly switched by optically triggered azobenzene isomerization. Comparisons of switching rates and reversibility on the nanoparticles reveal differences that depend upon whether the azobenzene is attached at the peptide N- or C-terminus, its isomerization state, and the nanoparticle composition. Our integrated experimental and computational investigation shows that the number of ligand anchor sites strongly influences the nanoparticle size. As predicted by our molecular simulations, weaker contact between the hybrid biomolecules and the Ag surface, with fewer anchor residues compared with Au, gives rise to differences in switching kinetics on Ag versus Au. Our findings provide a pathway toward achieving new remotely actuatable nanomaterials for multiple applications from a single system, which remains difficult to achieve using conventional approaches.
There still exists some confusion in the literature concerning the definition of a minimum energy pathway and the coordinate system in which it is calculated. Here we compare steepest-descent and eigenvector-following pathways, both with and without a mass-weighted metric. The systems studied are disilane and the water trimer, and we employ various basis sets at the SCF level of theory. We find that paths calculated using eigenvector-following and steepestdescent are practically the same, at least in terms of the reaction mechanism. We find that for the mass-weighted metric the pathways are similar, although in principle they do not have to be identical. Finally, we verify that the geometrical symmetry selection rules hold for a pathway mediated by a recently discovered transition state of the disilane system.
Librarians can replace or supplement traditional in-class instruction with course-specific online tutorials. The literature demonstrates how tutorials customized for specific courses are more beneficial than tutorials on basic research skills. Many authors discuss creating online tutorials but do not design one devoted to a specific course. With increasing demand for instruction services, online tutorials can ease staffing concerns prevalent at many libraries and otherwise enhance the quality of instruction and its application to varied learning styles. Using the Blackboard course management system, the authors created an online tutorial tailored to the required World Civilizations course at the University at Buffalo. The tutorial incorporated elements of successful online tutorials described in the literature: clear terminology, a quiz for self-assessment, opportunities for active learning, and individual e-mail feedback between students and librarians, and applied them to a specific course. The authors discuss student and librarian reaction to the tutorial and make recommendations for how the tutorial can be improved and implemented in everyday instruction services.
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