512 research outputs found
Helical states of nonlocally interacting molecules and their linear stability: geometric approach
The equations for strands of rigid charge configurations interacting
nonlocally are formulated on the special Euclidean group, SE(3), which
naturally generates helical conformations. Helical stationary shapes are found
by minimizing the energy for rigid charge configurations positioned along an
infinitely long molecule with charges that are off-axis. The classical energy
landscape for such a molecule is complex with a large number of energy minima,
even when limited to helical shapes. The question of linear stability and
selection of stationary shapes is studied using an SE(3) method that naturally
accounts for the helical geometry. We investigate the linear stability of a
general helical polymer that possesses torque-inducing non-local
self-interactions and find the exact dispersion relation for the stability of
the helical shapes with an arbitrary interaction potential. We explicitly
determine the linearization operators and compute the numerical stability for
the particular example of a linear polymer comprising a flexible rod with a
repeated configuration of two equal and opposite off-axis charges, thereby
showing that even in this simple case the non-local terms can induce
instability that leads to the rod assuming helical shapes.Comment: 34 pages, 9 figure
A systematically coarse-grained model for DNA, and its predictions for persistence length, stacking, twist, and chirality
We introduce a coarse-grained model of DNA with bases modeled as rigid-body
ellipsoids to capture their anisotropic stereochemistry. Interaction potentials
are all physicochemical and generated from all-atom simulation/parameterization
with minimal phenomenology. Persistence length, degree of stacking, and twist
are studied by molecular dynamics simulation as functions of temperature, salt
concentration, sequence, interaction potential strength, and local position
along the chain, for both single- and double-stranded DNA where appropriate.
The model of DNA shows several phase transitions and crossover regimes in
addition to dehybridization, including unstacking, untwisting, and collapse
which affect mechanical properties such as rigidity and persistence length. The
model also exhibits chirality with a stable right-handed and metastable
left-handed helix.Comment: 30 pages, 20 figures, Supplementary Material available at
http://www.physics.ubc.ca/~steve/publications.htm
LSST Classifier
The LSST (Large Synoptic Survey Telescope) Space Image Classifier Team built an application that uses crowd sourcing and machine learning to classify space objects in LSST image data. This project aims to work towards LSST science outreach goals.https://pilotscholars.up.edu/egr_project/1003/thumbnail.jp
Reflections on designing and implementing a task-based unit using gamebooks
A small scale action-research project was designed to explore the effectiveness of using interactive narratives to facilitate L2 output in a communicative English class. A four-week unit of instruction was implemented across five classes comprised of non-English major students at a university in Japan. Using graded reader gamebooks from the Atama-ii series, activities were designed to simultaneously engage students in English reading while also promoting active discussion in English. Data was collected in the form of instructor field logs and student surveys. Researchers concluded that although the activities did not facilitate in-class L2 communicative output, the gamebooks did serve to increase students’ willingness to engage in English activities
Hierarchical Chain Model of Spider Capture Silk Elasticity
Spider capture silk is a biomaterial with both high strength and high
elasticity, but the structural design principle underlying these remarkable
properties is still unknown. It was revealed recently by atomic force
microscopy that, an exponential force--extension relationship holds both for
capture silk mesostructures and for intact capture silk fibers [N. Becker et
al., Nature Materials 2, 278 (2003)]. In this Letter a simple hierarchical
chain model was proposed to understand and reproduce this striking observation.
In the hierarchical chain model, a polymer is composed of many structural
motifs which organize into structural modules and supra-modules in a
hierarchical manner. Each module in this hierarchy has its own characteristic
force. The repetitive patterns in the amino acid sequence of the major
flagelliform protein of spider capture silk is in support of this model.Comment: 4 pages, 3 figures. Will be formally published in PR
Measurement of the electric dipole moments for transitions to rubidium Rydberg states via Autler-Townes splitting
We present the direct measurements of electric-dipole moments for
transitions with for Rubidium atoms. The
measurements were performed in an ultracold sample via observation of the
Autler-Townes splitting in a three-level ladder scheme, commonly used for
2-photon excitation of Rydberg states. To the best of our knowledge, this is
the first systematic measurement of the electric dipole moments for transitions
from low excited states of rubidium to Rydberg states. Due to its simplicity
and versatility, this method can be easily extended to other transitions and
other atomic species with little constraints. Good agreement of the
experimental results with theory proves the reliability of the measurement
method.Comment: 12 pages, 6 figures; figure 6 replaced with correct versio
Robust Myco-Composites as a Platform for Versatile Hybrid-Living Structural Materials
Fungal mycelium, a living network of filamentous threads, thrives on
lignocellulosic waste and exhibits rapid growth, hydrophobicity, and intrinsic
regeneration, offering a potential means to create next-generation sustainable
and functional composites. However, existing hybrid-living mycelium composites
(myco-composites) are tremendously constrained by conventional mold-based
manufacturing processes, which are only compatible with simple geometries and
coarse biomass substrates that enable gas exchange. Here we introduce a class
of structural myco-composites manufactured with a novel platform that harnesses
high-resolution biocomposite additive manufacturing and robust mycelium
colonization with indirect inoculation. We leverage principles of hierarchical
composite design and selective nutritional provision to create a robust
myco-composite that is scalable, tunable, and compatible with complex
geometries. To illustrate the versatility of this platform, we characterize the
impact of mycelium colonization on mechanical and surface properties of the
composite, finding that it yields the strongest mycelium composite reported to
date, and demonstrate fabrication of unique foldable bio-welded containers and
flexible mycelium textiles. This study bridges the gap between biocomposite and
hybrid-living materials research, opening the door to advanced structural
mycelium applications and demonstrating a novel platform for development of
diverse hybrid-living materials
Glassy transition in a disordered model for the RNA secondary structure
We numerically study a disordered model for the RNA secondary structure and
we find that it undergoes a phase transition, with a breaking of the replica
symmetry in the low temperature region (like in spin glasses). Our results are
based on the exact evaluation of the partition function.Comment: 4 pages, 3 figure
Effect of photoions on the line shapes of the F\"orster resonance and microwave transitions in cold rubidium Rydberg atoms
Experiments on the spectroscopy of the F\"orster resonance Rb(37P)+Rb(37P) ->
Rb(37S)+Rb(38S) and microwave transitions nP -> n'S, n'D between Rydberg states
of cold Rb atoms in a magneto-optical trap have been performed. Under ordinary
conditions, all spectra exhibited a 2-3 MHz line width independently of the
interaction time of atoms with each other or with microwave radiation, although
the ultimate resonance width should be defined by the inverse interaction time.
Analysis of the experimental conditions has shown that the main source of the
line broadening was the inhomogeneous electric field of cold photoions appeared
at the excitation of initial Rydberg nP states by broadband pulsed laser
radiation. Using an additional pulse of the electric field, which rapidly
removed the photoions after the laser pulse, lead to a substantial narrowing of
the microwave and F\"orster resonances. An analysis of various sources of the
line broadening in cold Rydberg atoms has been conducted.Comment: 10 pages, 6 figure
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