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

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 $5P_{3/2}\to nD_{5/2}$ transitions with $20<n<48$ 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

Steric constraints in model proteins

A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable. Furthermore, several of the encodable structures are highly designable and are the non-degenerate ground state of several sequences. Even though the native state conformations are typically compact, not all compact conformations are encodable. The incorporation of the hydrophobic and polar nature of amino acids further enhances the attractive features of the model.Comment: RevTex, 5 pages, 3 postscript figure