Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways

Diverse classes of proteins function through large-scale conformational changes; sophisticated enhanced sampling methods have been proposed to generate these macromolecular transition paths. As such paths are curves in a high-dimensional space, they have been difficult to compare quantitatively, a prerequisite to, for instance, assess the quality of different sampling algorithms. The Path Similarity Analysis (PSA) approach alleviates these difficulties by utilizing the full information in 3N-dimensional trajectories in configuration space. PSA employs the Hausdorff or Fr\'echet path metrics---adopted from computational geometry---enabling us to quantify path (dis)similarity, while the new concept of a Hausdorff-pair map permits the extraction of atomic-scale determinants responsible for path differences. Combined with clustering techniques, PSA facilitates the comparison of many paths, including collections of transition ensembles. We use the closed-to-open transition of the enzyme adenylate kinase (AdK)---a commonly used testbed for the assessment enhanced sampling algorithms---to examine multiple microsecond equilibrium molecular dynamics (MD) transitions of AdK in its substrate-free form alongside transition ensembles from the MD-based dynamic importance sampling (DIMS-MD) and targeted MD (TMD) methods, and a geometrical targeting algorithm (FRODA). A Hausdorff pairs analysis of these ensembles revealed, for instance, that differences in DIMS-MD and FRODA paths were mediated by a set of conserved salt bridges whose charge-charge interactions are fully modeled in DIMS-MD but not in FRODA. We also demonstrate how existing trajectory analysis methods relying on pre-defined collective variables, such as native contacts or geometric quantities, can be used synergistically with PSA, as well as the application of PSA to more complex systems such as membrane transporter proteins.Comment: 9 figures, 3 tables in the main manuscript; supplementary information includes 7 texts (S1 Text - S7 Text) and 11 figures (S1 Fig - S11 Fig) (also available from journal site

Biogeochemical control on the temporal variability of trace element concentrations in the Oubangui river (Central African Republic)

Dissolved Ba, Cd, Co, Mn, Mo, Ni, Rb, Sb, Sr, U and V were measured in the Oubangui river (Central African Republic) during a complete flood period. The dissolved concentrations vary by factors ranging from 1.4 to 8.2 as a function of river discharge : Sr, Ba, Rb and Mo concentrations decrease with rising stage ; Ni, U, Sb, Cd, V and Mn concentrations increase with rising stage. These distributions are explained by a mixing of quick flow, mostly surface runoff with delayed flow, mostly groundwater. The dual origin of stream waters is demonstrated by the major element ratios, which are close to a silicate end-member during the high-flow period and trend towards a carbonate end-member during the low-flow period. Moreover, geological heterogeneities in the Oubangui basin may play a role in the variation of concentrations observed at the basin outlet. The previously indicated presence of a subsurface carbonate sequence in the lower part of the basin is confirmed. Cd, V, Mn and Co show peak concentrations during decreasing stage. We suggest that biological processes such as release from phytoplanktonic material and dissolution of oxides or carbonate phases may explain this maximum. (Résumé d'auteur

The asymptotic quasi-stationary states of the two-dimensional magnetically confined plasma and of the planetary atmosphere

We derive the differential equation governing the asymptotic quasi-stationary states of the two dimensional plasma immersed in a strong confining magnetic field and of the planetary atmosphere. These two systems are related by the property that there is an intrinsic constant length: the Larmor radius and respectively the Rossby radius and a condensate of the vorticity field in the unperturbed state related to the cyclotronic gyration and respectively to the Coriolis frequency. Although the closest physical model is the Charney-Hasegawa-Mima (CHM) equation, our model is more general and is related to the system consisting of a discrete set of point-like vortices interacting in plane by a short range potential. A field-theoretical formalism is developed for describing the continuous version of this system. The action functional can be written in the Bogomolnyi form (emphasizing the role of Self-Duality of the asymptotic states) but the minimum energy is no more topological and the asymptotic structures appear to be non-stationary, which is a major difference with respect to traditional topological vortex solutions. Versions of this field theory are discussed and we find arguments in favor of a particular form of the equation. We comment upon the significant difference between the CHM fluid/plasma and the Euler fluid and respectively the Abelian-Higgs vortex models.Comment: Latex 126 pages, 7 eps figures included. Discussion on various forms of the equatio

Transport and Boundary Scattering in Confined Geometries: Analytical Results

We utilize a geometric argument to determine the effects of boundary scattering on the carrier mean-free path in samples of various cross sections. Analytic expressions for samples with rectangular and circular cross sections are obtained. We also outline a method for incorporating these results into calculations of the thermal conductivity.Comment: 35 pages, Late

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F. Robert Henderson et al., Increasing Eastern Bluebirds in Kansas, Kansas State University, November 1990

Discerning autotrophy, mixotrophy and heterotrophyin marine TACK archaea from the North Atlantic

DNA stable isotope probing (SIP) was used to track the uptake of organic and inorganic carbon sources for TACK archaea(Thaumarchaeota/Aigarchaeota/Crenarchaeota/Korarchaeota) on a cruise of opportunity in the North Atlantic. Due to water limitations, duplicate samples from the deep photic (60–115 m), the mesopelagic zones (local oxygen minimum; 215–835 m)and the bathypelagic zone (2085–2835 m) were amended with various combinations of12C- or13C-acetate/urea/bicarbonate to assess cellular carbon acquisition. The SIP results indicated the majority of TACK archaeal operational taxonomic units(OTUs) incorporated13C from acetate and/or urea into newly synthesized DNA within 48 h. A small fraction (16%) of the OTUs, often representing the most dominant members of the archaeal community, were able to incorporate bicarbonate in addition to organic substrates. Only two TACK archaeal OTUs were found to incorporate bicarbonate but not urea or acetate.These results further demonstrate the utility of SIP to elucidate the metabolic capability of mesothermal archaea in distinct oceanic settings and suggest that TACK archaea play a role in organic carbon recycling in the mid-depth to deep ocea

Surface freshwater storage variations in the Orinoco floodplains using multi-satellite observations

Variations in surface water extent and storage are poorly characterized from regional to global scales. In this study, a multi-satellite approach is proposed to estimate the water stored in the floodplains of the Orinoco Basin at a monthly time-scale using remotely-sensed observations of surface water from the Global Inundation Extent Multi-Satellite (GIEMS) and stages from Envisat radar altimetry. Surface water storage variations over 2003-2007 exhibit large interannual variability and a strong seasonal signal, peaking during summer, and associated with the flood pulse. The volume of surface water storage in the Orinoco Basin was highly correlated with the river discharge at Ciudad Bolivar (R = 0.95), the closest station to the mouth where discharge was estimated, although discharge lagged one month behind storage. The correlation remained high (R = 0.73) after removing seasonal effects. Mean annual variations in surface water volume represented similar to 170 km(3), contributing to similar to 45% of the Gravity Recovery and Climate Experiment (GRACE)-derived total water storage variations and representing similar to 13% of the total volume of water that flowed out of the Orinoco Basin to the Atlantic Ocean

Control of Dephasing and Phonon Emission in Coupled Quantum Dots

We predict that phonon subband quantization can be detected in the non-linear electron current through double quantum dot qubits embedded into nano-size semiconductor slabs, acting as phonon cavities. For particular values of the dot level splitting $\Delta$, piezo-electric or deformation potential scattering is either drastically reduced as compared to the bulk case, or strongly enhanced due to phonon van Hove singularities. By tuning $\Delta$ via gate voltages, one can either control dephasing, or strongly increase emission into phonon modes with characteristic angular distributions.Comment: 4 pages, 3 figures, accepted for publication as Rapid Comm. in Phys. Rev.

An outbreak of viral gastroenteritis linked to municipal water supply, Lombardy, Italy, June 2009

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