1,187 research outputs found
Phase-stabilized, 1.5-W frequency comb at 2.8 to 4.8 micron
We present a high-power optical parametric oscillator-based frequency comb in
the mid-infrared wavelength region using periodically poled lithium niobate.
The system is synchronously pumped by a 10-W femtosecond Yb:fiber laser
centered at 1.07 um and is singly resonant for the signal. The idler (signal)
wavelength can be continuously tuned from 2.8 to 4.8 um (1.76 to 1.37 um) with
a simultaneous bandwidth as high as 0.3 um and a maximum average idler output
power of 1.50 W. We also demonstrate the performance of the stabilized comb by
recording the heterodyne beat with a narrow-linewidth diode laser. This OPO is
an ideal source for frequency comb spectroscopy in the mid-IR.Comment: 4 figure
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
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