High resolution protein folding with a transferable potential

A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes graph-theoretical analysis of the ensemble of resulting folded conformations, was systematically applied and consistently produced structure predictions of approximately 3 Angstroms without any knowledge of the native state. To measure and understand the significance of the results, extensive control simulations were conducted. Graph theoretic analysis provides a means for systematically identifying the native fold and provides physical insight, conceptually linking the results to modern theoretical views of protein folding. In addition to presenting a method for prediction of structure and folding mechanism, our model suggests that a accurate all-atom amino acid representation coupled with a physically reasonable atomic interaction potential (that does not require optimization to the test set) and hydrogen bonding are essential features for a realistic protein model.Comment: submitted to PNAS 2005-03-1

Introduction: locating gentrification in the Global East

This special issue, a collection of papers presented and debated at an Urban Studies Foundation-funded workshop on Global Gentrification in London in 2012, attempts to problematise contemporary understandings of gentrification, which is all too often confined to the experiences of the so-called Global North, and sometimes too narrowly understood as classic gentrification. Instead of simply confirming the rise of gentrification in places outside of the usual suspects of North America and Western Europe, a more open-minded approach is advocated so as not to over-generalise distinctive urban processes under the label of gentrification, thus understanding gentrification as constitutive of diverse urban processes at work. This requires a careful attention to the complexity of property rights and tenure relations, and calls for a dialogue between gentrification and non-gentrification researchers to understand how gentrification communicates with other theories to capture the full dynamics of urban transformation. Papers in this special issue have made great strides towards these goals, namely theorising, distorting, mutating and bringing into question the concept of gentrification itself, as seen from the perspective of the Global East, a label that we have deliberately given in order to problematise the existing common practices of grouping all regions other than Western European and North American ones into the Global South

A topologically twisted index for three-dimensional supersymmetric theories

We provide a general formula for the partition function of three-dimensional (formula presented) gauge theories placed on S2 7S1 with a topological twist along S2, which can be interpreted as an index for chiral states of the theories immersed in background magnetic fields. The result is expressed as a sum over magnetic fluxes of the residues of a meromorphic form which is a function of the scalar zero-modes. The partition function depends on a collection of background magnetic fluxes and fugacities for the global symmetries. We illustrate our formula in many examples of 3d Yang-Mills-Chern-Simons theories with matter, including Aharony and Giveon-Kutasov dualities. Finally, our formula generalizes to \u3a9-backgrounds, as well as two-dimensional theories on S2 and four-dimensional theories on S2 7 T2. In particular this provides an alternative way to compute genus-zero A-model topological amplitudes and Gromov-Witten invariants

Self-trapping of excitons, violation of condon approximation, and efficient fluorescence in conjugated cycloparaphenylenes

Cycloparaphenylenes, the simplest structural unit of armchair carbon nanotubes, have unique optoelectronic properties counterintuitive in the class of conjugated organic materials. Our time-dependent density functional theory study and excited state dynamics simulations of cycloparaphenylene chromophores provide a simple and conceptually appealing physical picture explaining experimentally observed trends in optical properties in this family of molecules. Fully delocalized degenerate second and third excitonic states define linear absorption spectra. Self-trapping of the lowest excitonic state due to electron-phonon coupling leads to the formation of spatially localized excitation in large cycloparaphenylenes within 100 fs. This invalidates the commonly used Condon approximation and breaks optical selection rules, making these materials superior fluorophores. This process does not occur in the small molecules, which remain inefficient emitters. A complex interplay of symmetry, π-conjugation, conformational distortion and bending strain controls all photophysics of cycloparaphenylenes.Fil: Adamska, Lyudmyla. Los Alamos National Laboratory. Los Alamos; Estados UnidosFil: Nayyar, Iffat. Los Alamos National Laboratory. Los Alamos; Estados UnidosFil: Chen, Hang. Boston University; Estados UnidosFil: Swan, Anna K.. Boston University; Estados UnidosFil: Oldani, Andres Nicolas. Universidad Nacional de Quilmes; ArgentinaFil: Fernández Alberti, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes; ArgentinaFil: Golder, Matthew R.. University of Oregon; Estados UnidosFil: Jasti, Ramesh. University of Oregon; Estados UnidosFil: Doorn, Stephen K.. Los Alamos National Laboratory. Los Alamos; Estados UnidosFil: Tretiak, Sergei. Los Alamos National Laboratory. Los Alamos; Estados Unido