Structural anisotropy stabilises asymmetric beating in instability-driven filaments

Southern bean mosaic virus (SBMV) is a spherical plant virus. It possesses an intrinsic (structural) anisotropy due to the orientation of valence bonds of the amino acid and/or nucleic acid residues. According to the light scattering theory of Rayleigh and Gans for optically anisotropic spheres, the degree of linear polarization of the scattered light depends on the intrinsic anisotropy, the relative refractive index of the sphere to the solvent, the scattering angle, and the inclination angle of linearly polarized incident light to the scattering plane. By using the theoretical expression of the degree of linear polarization, the intrinsic anisotropy parameter of southern bean mosaic virus in the compact spherical state was calculated with the appropriate experimental values. This novel method should be useful in elucidating the internal structure of spherical viruses and other spherical complexes of macromolecules. © 1993 John Wiley & Sons, Inc.

Intrinsic optical anisotropy of southern bean mosaic virus

We simulated the freely falling motion of an inhomogeneous flexible filament immersed in an incompressible viscous fluid under the action of gravity by the immersed boundary method. Our simulations show that the falling motion of an inhomogeneous filament is stable with respect to disturbances of small magnitude irrespective of the mass and bending modulus distributions. However, sufficiently large disturbances may bring the filament motion into a significantly different state: the filament deforms, rotates, and drifts towards one of the side boundaries while falling in the flowing fluid under the action of gravity. In addition our results indicate unstable filament motion depends more strongly on the bending modulus than the mass density. Our simulations also show the existence of two similar states for a homogeneous filament. The motions of inhomogeneous and homogeneous filaments are compared, and both quantitative and qualitative differences in the unstable motions are found. This is a starting point to understand the role of inhomogeneous filament properties in deciding its motion.

The motion of two-filament artificial swimmers is modeled by assuming interfilament coupling via hydrodynamic viscous drag. The filaments are assumed to be in parallel and attached to a rigid spherical head. The boundary actuation is assumed to occur at the head-filament joint through an external oscillatory magnetic field and the filament motion is taken to be confined to the flexural plane. The hydrodynamic coupling modifies the viscous drag on one filament due to motion of the other. Assuming in-phase, small amplitude, low frequency actuation the swimmer performance metrics (propulsive thrust, propulsion speed and energy efficiency) are calculated using Lauga's formulation for the swimmer kinematics coupled with filament dynamics. The results are compared with the performance of a single-filament and an uncoupled two-filament swimmer. The hydrodynamic coupling is found to enhance the performance measures in a parametric window. Also, it is found that there occurs an optimum combination of head size and swimmer length that can maximize the microswimmer performance. The findings are in agreement with the experimental observations on multi-filament artificial microswimming.

BackgroundRecent research into ciliary structure and function provides important insights into inherited diseases termed ciliopathies and other cilia-related disorders. This wealth of knowledge needs to be translated into a computational representation to be fully exploitable by the research community. To this end, members of the Gene Ontology (GO) and SYSCILIA Consortia have worked together to improve representation of ciliary substructures and processes in GO.MethodsMembers of the SYSCILIA and Gene Ontology Consortia suggested additions and changes to GO, to reflect new knowledge in the field. The project initially aimed to improve coverage of ciliary parts, and was then broadened to cilia-related biological processes. Discussions were documented in a public tracker. We engaged the broader cilia community via direct consultation and by referring to the literature. Ontology updates were implemented via ontology editing tools.ResultsSo far, we have created or modified 127 GO terms representing parts and processes related to eukaryotic cilia/flagella or prokaryotic flagella. A growing number of biological pathways are known to involve cilia, and we continue to incorporate this knowledge in GO. The resulting expansion in GO allows more precise representation of experimentally derived knowledge, and SYSCILIA and GO biocurators have created 199 annotations to 50 human ciliary proteins. The revised ontology was also used to curate mouse proteins in a collaborative project. The revised GO and annotations, used in comparative ‘before and after’ analyses of representative ciliary datasets, improve enrichment results significantly.ConclusionsOur work has resulted in a broader and deeper coverage of ciliary composition and function. These improvements in ontology and protein annotation will benefit all users of GO enrichment analysis tools, as well as the ciliary research community, in areas ranging from microscopy image annotation to interpretation of high-throughput studies. We welcome feedback to further enhance the representation of cilia biology in GO.

Very recent experimental work has demonstrated the existence of Kelvin waves along quantized vortex filaments in superfluid helium. The possible configurations and motions of such filaments is of great physical interest, and Svistunov previously obtained a Hamiltonian formulation for the dynamics of quantum vortex filaments in the low-temperature limit under the assumption that the vortex filament is essentially aligned along one axis, resulting in a two-dimensional (2D) problem. It is standard to approximate the dynamics of thin filaments by employing the local induction approximation (LIA), and we show that by putting the two-dimensional LIA into correspondence with the first equation in the integrable Wadati-Konno-Ichikawa-Schimizu (WKIS) hierarchy, we immediately obtain solutions to the two-dimensional LIA, such as helix, planar, and self-similar solutions. These solutions are obtained in a rather direct manner from the WKIS equation and then mapped into the 2D-LIA framework. Furthermore, the approach can be coupled to existing inverse scattering transform results from the literature in order to obtain solitary wave solutions including the analog of the Hasimoto one-soliton for the 2D-LIA. One large benefit of the approach is that the correspondence between the 2D-LIA and the WKIS allows us to systematically obtain vortex filament solutions directly in the Cartesian coordinate frame without the need to solve back from curvature and torsion. Implications of the results for the physics of experimentally studied solitary waves, Kelvin waves, and postvortex reconnection events are mentioned.

The Flagella Beat of Chlamydomonas Has Distinctly Regulated Static and Dynamic Components, which Accord with Curvature Controlled Dynein Activity

We elaborate on a generalization of the 2D wormlike chain (WLC) model that accounts for the presence of long-range correlations (LRC) in the intrinsic curvature distribution of eukaryotic DNA. This model predicts some decrease of the DNA persistence length resulting from some large-scale intrinsic curvature induced by sequence-dependent persistent random distribution of local bending sites. When assisting exact analytical calculations by numerical DNA simulations, we show that the conjugated contributions of i) the thermal curvature fluctuations characterized by the "dynamic" persistence length ℓ(p)(d) = 2A, where A is the elastic bending modulus, and ii) the intrinsic LRC curvature disorder of amplitude σ(o) and Hurst exponent H > 1/2, characterized by a "static" persistence length ℓ(p)(H) = A(1/2H)σ(o)(-1/H) Γ(1/2H + 1), can be described by a continuum of generalized WLC (GWLC) models parametrized by the LRC exponent H. We use perturbation analysis to investigate the two limiting cases of weak static disorder (w(H) << 1 and weak dynamical fluctuations (1/w (H) << 1), where w(H) = l(p)(d)/l(p)(H) is a dimensionless parameter. From a quantitative point of view, our study demonstrates that even for a small value of the LRC (H approximately equal 0.6-0.8) static disorder amplitude σ(o) ~ 10(-2), as previously reported for genomic DNA, the decrease of the persistence length from the WLC prediction l(p)(d) can be very significant, up to twofold. The implications of these results on the first steps of compaction of DNA in eukaryotic cells are discussed.

The influence of cholesterol on phospholipid membrane curvature and bending elasticity

Violet phosphorus (VP), a layered allotrope of elemental phosphorus, possesses a unique monoclinic structure and intrinsic anisotropy, making it a promising candidate for future electronic and optoelectronic devices. In this study, we report the synthesis of high-quality VP via chemical vapor transport and the fabrication of few-layer VP-based field-effect transistors (FETs) using pre-defined electrodes. The devices demonstrate typical n-type behavior with strong gate modulation, stable transport characteristics, and a high on/off current ratio of $\sim 10^{4}-10^{5}$. The electrical performance is stable across multiple gate voltage sweeps, although a notable hysteresis is observed, attributable to interface traps and residual carriers. Our results establish VP as a viable wide-bandgap N-type semiconductors with potential application in high-performance memristors.

Micrometre-sized, densely packed natural cilia that perform non-reciprocal 3D motions with dynamically tunable collective patterns are crucial for biological processes such as microscale locomotion1, nutrient acquisition2, cell trafficking3–5 and embryonic and neurological development6–8. However, replicating these motions in artificial systems remains challenging given the limits of scalable, locally controllable soft-bodied actuation at the micrometre scale. Overcoming this challenge would enhance our understanding of ciliary dynamics, clarify their biological importance and enable new microscale devices and bioinspired technologies. Here we show a previously unrecognized fast electrical response of micrometre-scale hydrogels, induced by voltages down to 1.5 V without hydrolysis, with bending motions driven by ion migration across a nanometre-scale hydrogel network 3D-printed by two-photon polymerization, occurring within milliseconds. On the basis of these findings, we print gel microcilia arrays composed of a soft acrylic acid-co-acrylamide (AAc-co-AAm) hydrogel (modulus of approximately 1,000 Pa) that respond to electrical stimuli within milliseconds. Each microcilium measures 2–10 µm in diameter and 18–90 µm in height, achieving 3D rotational bending motion at up to 40 Hz, mirroring the geometry and dynamics of natural cilia. These gel microcilia maintain functionality after 330,000 continuous actuation cycles with less than 30% performance degradation. The gel microcilia arrays can be integrated on flexible polyimide substrates and fabricated at large scale using conventional lithography techniques. They also offer individual dynamic control by means of microelectrode arrays and enable fluid manipulation and particle transport at the micrometre scale.

We present the mechanical model of an array of elastic filaments and simulate the response with different mechanical couplings. This class of systems is inspired by robust and elegant solutions for locomotion mechanics that have emerged in several small-scale biological entities in the form of beating protrusions, such as cellular cilia and eukaryotic flagella. The collective dynamics of cilia arrays reveals important features such as array alignments, two-phase asymmetric beating of individual filaments, and the emergence of metachronal coordination, which make them suitable for bio-inspired terrestrial and aquatic locomotion. The model presented here is the basis for further developments towards the design of terrestrial and aquatic locomotion systems for general purpose robotic devices.

Ion Channel Regulation by Lipid Bilayers: Theory & Simulation of Deformed Membranes around Gramicidin A

Cell membrane remodelling during key processes such as endocytosis, exocytosis, pore formation, and cell division involves large changes in the curvature, which are governed by bending, Gaussian and tilt moduli. While bending rigidity has been extensively studied, it has been a major challenge to experimentally measure Gaussian and tilt moduli due to fundamental limitations imposed by the Gauss-Bonnet theorem on closed membranes and the nanometric size of the constituents. We address these issues by studying a fluid monolayer model membrane consisting of aligned, micron-length rod-like particles, known as colloidal membranes. Their continuum deformation follows the Helfrich curvature energy, while their micron-scale thickness allows easy observation of tilt deformation modes at optically resolvable length-scales. We use high-speed interference reflectance microscopy to measure complete 3D surface profiles of fluctuating membranes with nanometer precision, which offers significant advantages over conventional fluctuation spectroscopy that measures membrane cross-section dynamics. We detect both tilt and bending modes and extract the corresponding moduli from the thermal fluctuation spectrum. We also demonstrate that these moduli can be tuned by varying the self-assembly conditions and particle geometry. The open membrane edges exhibited enhanced long-wavelength fluctuations with a negative Gaussian curvature, enabling experimental determination of the elusive Gaussian modulus.

Modulation of Membrane Rigidity by Sar1, a Vesicle Trafficking Protein