Dynamics of a molecular glass former: Energy landscapes for diffusion in ortho-terphenyl.

Relaxation times and transport processes of many glass-forming supercooled liquids exhibit a super-Arrhenius temperature dependence. We examine this phenomenon by computer simulation of the Lewis-Wahnström model for ortho-terphenyl. We propose a microscopic definition for a single-molecule cage-breaking transition and show that, when correlation behaviour is taken into account, these rearrangements are sufficient to reproduce the correct translational diffusion constants over an intermediate temperature range in the supercooled regime. We show that super-Arrhenius behaviour can be attributed to increasing negative correlation in particle movement at lower temperatures and relate this to the cage-breaking description. Finally, we sample the potential energy landscape of the model and show that it displays hierarchical ordering. Substructures in the landscape, which may correspond to metabasins, have boundaries defined by cage-breaking transitions. The cage-breaking formulation provides a direct link between the potential energy landscape and macroscopic diffusion behaviour.This work was supported by the University of Cambridge through a CHSS studentship to S.P.N., and by the European Research Council.This is the author accepted manuscript. The final version is available at http://dx.doi.org/10.1063/1.4954324

Exploiting the potential energy landscape to sample free energy

We review a number of recently developed strategies for enhanced sampling of complex systems based on knowledge of the potential energy landscape. We describe four approaches, replica exchange, Kirkwood sampling, superposition-enhanced nested sampling, and basin sampling, and show how each of them can exploit information for low-lying potential energy minima obtained using basin-hopping global optimization. Characterizing these minima is generally much faster than equilibrium thermodynamic sampling, because large steps in configuration space between local minima can be used without concern for maintaining detailed balance.The authors gratefully acknowledge financial support from the EPSRC and the ERC. S.M acknowledges financial support from the Gates Cambridge Scholarship.This is the accepted manuscript. The final published version is available at http://onlinelibrary.wiley.com/doi/10.1002/wcms.1217/abstract

The HATNet and HATSouth Exoplanet Surveys

The Hungarian-made Automated Telescope Network (HATNet) has been in operation since 2003, with the key science goal being the discovery and accurate characterization of transiting extrasolar planets (TEPs) around bright stars. Using six small, 11\,cm\ aperture, fully automated telescopes in Arizona and Hawaii, as of 2017 March, it has discovered and accurately characterized 67 such objects. The HATSouth network of telescopes has been in operation since 2009, using slightly larger, 18\,cm diameter optical tubes. It was the first global network of telescopes using identical instrumentation. With three premier sites spread out in longitude (Chile, Namibia, Australia), the HATSouth network permits round-the-clock observations of a 128 square arcdegree swath of the sky at any given time, weather permitting. As of this writing, HATSouth has discovered 36 transiting exoplanets. Many of the altogether ~100 HAT and HATSouth exoplanets were the first of their kind. They have been important contributors to the rapidly developing field of exoplanets, motivating and influencing observational techniques, theoretical studies, and also actively shaping future instrumentation for the detection and characterization of such objects.Comment: Invited review chapter, accepted for publication in "Handbook of Exoplanets", edited by H.J. Deeg and J.A. Belmonte, Springer Reference Work

Superposition enhanced nested sampling

The theoretical analysis of many problems in physics, astronomy and applied mathematics requires an efficient numerical exploration of multimodal parameter spaces that exhibit broken ergodicity. Monte Carlo methods are widely used to deal with these classes of problems, but such simulations suffer from a ubiquitous sampling problem: the probability of sampling a particular state is proportional to its entropic weight. Devising an algorithm capable of sampling efficiently the full phase space is a long-standing problem. Here we report a new hybrid method for the exploration of multimodal parameter spaces exhibiting broken ergodicity. Superposition enhanced nested sampling (SENS) combines the strengths of global optimization with the unbiased/athermal sampling of nested sampling, greatly enhancing its efficiency with no additional parameters. We report extensive tests of this new approach for atomic clusters that are known to have energy landscapes for which conventional sampling schemes suffer from broken ergodicity. We also introduce a novel parallelization algorithm for nested sampling

Defining and quantifying frustration in the energy landscape: Applications to atomic and molecular clusters, biomolecules, jammed and glassy systems

The emergence of observable properties from the organisation of the underlying potential energy landscape is analysed, spanning a full range of complexity from self-organising to glassy and jammed systems. The examples include atomic and molecular clusters, a β-barrel protein, the GNNQQNY peptide dimer, and models of condensed matter that exhibit structural glass formation and jamming. We have considered measures based on several different properties, namely, the Shannon entropy, an equilibrium thermodynamic measure that uses a sample of local minima, and indices that require additional information about the connections between local minima in the form of transition states. A frustration index is defined that correlates directly with key properties that distinguish relaxation behaviour within this diverse set. The index uses the ratio of the energy barrier to the energy difference with reference to the global minimum. The contributions for each local minimum are weighted by the equilibrium occupation probabilities. Hence we obtain fundamental insight into the connections and distinctions between systems that cover the continuum from efficient structure-seekers to landscapes that exhibit broken ergodicity and rare event dynamics.We acknowledge the Engineering and Physical Sciences Research Council, UK (EPSRC) for funding under Programme Grant No. EP/I001352/1 and the European Research Council (ERC)

Non-monotonic temperature evolution of dynamic correlations in glass-forming liquids

The viscosity of glass-forming liquids increases by many orders of magnitude if their temperature is lowered by a mere factor of 2-3 [1,2]. Recent studies suggest that this widespread phenomenon is accompanied by spatially heterogeneous dynamics [3,4], and a growing dynamic correlation length quantifying the extent of correlated particle motion [5-7]. Here we use a novel numerical method to detect and quantify spatial correlations which reveal a surprising non-monotonic temperature evolution of spatial dynamical correlations, accompanied by a second length scale that grows monotonically and has a very different nature. Our results directly unveil a dramatic qualitative change in atomic motions near the mode-coupling crossover temperature [8] which involves no fitting or indirect theoretical interpretation. Our results impose severe new constraints on the theoretical description of the glass transition, and open several research perspectives, in particular for experiments, to confirm and quantify our observations in real materials.Comment: 7 page

Soil organic matter and litter chemistry response to experimental N deposition in northern temperate deciduous forest ecosystems

The effects of atmospheric nitrogen (N) deposition on organic matter decomposition vary with the biochemical characteristics of plant litter. At the ecosystem-scale, net effects are difficult to predict because various soil organic matter (SOM) fractions may respond differentially. We investigated the relationship between SOM chemistry and microbial activity in three northern deciduous forest ecosystems that have been subjected to experimental N addition for 2 years. Extractable dissolved organic carbon (DOC), DOC aromaticity, C : N ratio, and functional group distribution, measured by Fourier transform infrared spectra (FTIR), were analyzed for litter and SOM. The largest biochemical changes were found in the sugar maple–basswood (SMBW) and black oak–white oak (BOWO) ecosystems. SMBW litter from the N addition treatment had less aromaticity, higher C : N ratios, and lower saturated carbon, lower carbonyl carbon, and higher carboxylates than controls; BOWO litter showed opposite trends, except for carbonyl and carboxylate contents. Litter from the sugar maple–red oak (SMRO) ecosystem had a lower C : N ratio, but no change in DOC aromaticity. For SOM, the C : N ratio increased with N addition in SMBW and SMRO ecosystems, but decreased in BOWO; N addition did not affect the aromaticity of DOC extracted from mineral soil. All ecosystems showed increases in extractable DOC from both litter and soil in response to N treatment. The biochemical changes are consistent with the divergent microbial responses observed in these systems. Extracellular oxidative enzyme activity has declined in the BOWO and SMRO ecosystems while activity in the SMBW ecosystem, particularly in the litter horizon, has increased. In all systems, enzyme activities associated with the hydrolysis and oxidation of polysaccharides have increased. At the ecosystem scale, the biochemical characteristics of the dominant litter appear to modulate the effects of N deposition on organic matter dynamics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72320/1/j.1365-2486.2005.01001.x.pd

The Shapes of Cooperatively Rearranging Regions in Glass Forming Liquids

The shapes of cooperatively rearranging regions in glassy liquids change from being compact at low temperatures to fractal or ``stringy'' as the dynamical crossover temperature from activated to collisional transport is approached from below. We present a quantitative microscopic treatment of this change of morphology within the framework of the random first order transition theory of glasses. We predict a correlation of the ratio of the dynamical crossover temperature to the laboratory glass transition temperature, and the heat capacity discontinuity at the glass transition, Delta C_p. The predicted correlation agrees with experimental results for the 21 materials compiled by Novikov and Sokolov.Comment: 9 pages, 6 figure

GlyGly-CTERM and Rhombosortase: A C-Terminal Protein Processing Signal in a Many-to-One Pairing with a Rhomboid Family Intramembrane Serine Protease

The rhomboid family of serine proteases occurs in all domains of life. Its members contain at least six hydrophobic membrane-spanning helices, with an active site serine located deep within the hydrophobic interior of the plasma membrane. The model member GlpG from Escherichia coli is heavily studied through engineered mutant forms, varied model substrates, and multiple X-ray crystal studies, yet its relationship to endogenous substrates is not well understood. Here we describe an apparent membrane anchoring C-terminal homology domain that appears in numerous genera including Shewanella, Vibrio, Acinetobacter, and Ralstonia, but excluding Escherichia and Haemophilus. Individual genomes encode up to thirteen members, usually homologous to each other only in this C-terminal region. The domain's tripartite architecture consists of motif, transmembrane helix, and cluster of basic residues at the protein C-terminus, as also seen with the LPXTG recognition sequence for sortase A and the PEP-CTERM recognition sequence for exosortase. Partial Phylogenetic Profiling identifies a distinctive rhomboid-like protease subfamily almost perfectly co-distributed with this recognition sequence. This protease subfamily and its putative target domain are hereby renamed rhombosortase and GlyGly-CTERM, respectively. The protease and target are encoded by consecutive genes in most genomes with just a single target, but far apart otherwise. The signature motif of the Rhombo-CTERM domain, often SGGS, only partially resembles known cleavage sites of rhomboid protease family model substrates. Some protein families that have several members with C-terminal GlyGly-CTERM domains also have additional members with LPXTG or PEP-CTERM domains instead, suggesting there may be common themes to the post-translational processing of these proteins by three different membrane protein superfamilies