785 research outputs found
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
C720
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 , 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 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.
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