Hydrodynamic phase-locking of swimming microorganisms

Some microorganisms, such as spermatozoa, synchronize their flagella when swimming in close proximity. Using a simplified model (two infinite, parallel, two-dimensional waving sheets), we show that phase-locking arises from hydrodynamics forces alone, and has its origin in the front-back asymmetry of the geometry of their flagellar waveform. The time-evolution of the phase difference between co-swimming cells depends only on the nature of this geometrical asymmetry, and microorganisms can phase-lock into conformations which minimize or maximize energy dissipation

Brownian motion near a partial-slip boundary: A local probe of the no-slip condition

Motivated by experimental evidence of violations of the no-slip boundary condition for liquid flow in micron-scale geometries, we propose a simple, complementary experimental technique that has certain advantages over previous studies. Instead of relying on externally-induced flow or probe motion, we suggest that colloidal diffusivity near solid surfaces contains signatures of the degree of fluid slip exhibited on those surfaces. To investigate, we calculate the image system for point forces (Stokeslets) oriented perpendicular and parallel to a surface with a finite slip length, analogous to Blake's solution for a Stokeslet near a no-slip wall. Notably, the image system for the point source and perpendicular Stokeslet contain the same singularities as Blake's solution; however, each is distributed along a line with a magnitude that decays exponentially over the slip length. The image system for the parallel Stokeslet involves a larger set of fundamental singularities, whose magnitude does not decay exponentially from the surface. Using these image systems, we determine the wall-induced correction to the diffusivity of a small spherical particle located `far' from the wall. We also calculate the coupled diffusivities between multiple particles near a partially-slipping wall. Because, in general, the diffusivity depends on `local' wall conditions, patterned surfaces would allow differential measurements to be obtained within a single experimental cell, eliminating potential cell-to-cell variability encountered in previous experiments. In addition to motivating the proposed experiments, our solutions for point forces and sources near a partial-slip wall will be useful for boundary integral calculations in slip systems.Comment: 34 pages, 5 figure

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

Biomedical Ontologies are intended to integrate diverse biomedical data to enable intelligent data-mining and facilitate translation of basic research into useful clinical knowledge. We present the first version of RNAO, an ontology for integrating RNA 3D structural, biochemical and sequence data. While each 3D data file depicts the structure of a specific molecule, such data have broader significance as representatives of classes of homologous molecules, which, while differing in sequence, generally share core structural features of functional importance. Thus, 3D structure data gain value by being linked to homologous sequences in genomic data and databases of sequence alignments. Likewise genomic data can increase in value by annotation of shared structural features, especially when these can be linked to specific functions. The RNAO is being developed in line with the developing standards of the Open Biomedical Ontologies (OBO) Consortium

Active particles in periodic lattices

Both natural and artificial small-scale swimmers may often self-propel in environments subject to complex geometrical constraints. While most past theoretical work on low-Reynolds number locomotion addressed idealised geometrical situations, not much is known on the motion of swimmers in heterogeneous environments. As a first theoretical model, we investigate numerically the behaviour of a single spherical micro-swimmer located in an infinite, periodic body-centred cubic lattice consisting of rigid inert spheres of the same size as the swimmer. Running a large number of simulations we uncover the phase diagram of possible trajectories as a function of the strength of the swimming actuation and the packing density of the lattice. We then use hydrodynamic theory to rationalise our computational results and show in particular how the far-field nature of the swimmer (pusher vs. puller) governs even the behaviour at high volume fractions

Hydrodynamic Coupling of Two Brownian Spheres to a Planar Surface

We describe direct imaging measurements of the collective and relative diffusion of two colloidal spheres near a flat plate. The bounding surface modifies the spheres' dynamics, even at separations of tens of radii. This behavior is captured by a stokeslet analysis of fluid flow driven by the spheres' and wall's no-slip boundary conditions. In particular, this analysis reveals surprising asymmetry in the normal modes for pair diffusion near a flat surface.Comment: 4 pages, 4 figure

Multimodality local consolidative treatment versus conventional care of advanced lung cancer after first-line systemic anti-cancer treatment: study protocol for the RAMON multicentre randomised controlled trial with an internal pilot

Introduction Lung cancer is the most common cause of cancer death worldwide and most patients present with extensive disease. One-year survival is improving but remains low (37%) despite novel systemic anti-cancer treatments forming the current standard of care. Although new therapies improve survival, most patients have residual disease after treatment, and little is known on how best to manage it. Therefore, residual disease management varies across the UK, with some patients receiving only maintenance systemic anti-cancer treatment while others receive local consolidative treatment (LCT), alongside maintenance systemic anti-cancer treatment. LCT can be a combination of surgery, radiotherapy and/or ablation to remove all remaining cancer within the lung and throughout the body. This is intensive, expensive and impacts quality of life, but we do not know if it results in better survival, nor the extent of impact on quality of life and what the cost might be for healthcare providers. The RAMON study (RAdical Management Of Advanced Non-small cell lung cancer) will evaluate the acceptability, effectiveness and cost-effectiveness of LCT versus no LCT after first-line systemic treatment for advanced lung cancer. Methods and analysis RAMON is a pragmatic open multicentre, parallel group, superiority randomised controlled trial. We aim to recruit 244 patients aged 18 years and over with advanced non-small-cell lung cancer from 40 UK NHS hospitals. Participants will be randomised in a 1:1 ratio to receive LCT alongside maintenance treatment, or maintenance treatment alone. LCT will be tailored to each patient’s specific disease sites. Participants will be followed up for a minimum of 2 years. The primary outcome is overall survival from randomisation. Ethics and dissemination The West of Scotland Research Ethics Committee (22/WS/0121) gave ethical approval in August 2022 and the Health Research Authority in September 2022. Participants will provide written informed consent before participating in the study. Findings will be presented at international meetings, in peer-reviewed publications, through patient organisations and notifications to patients. Trial registration number ISRCTN11613852

The long-time dynamics of two hydrodynamically-coupled swimming cells

Swimming micro-organisms such as bacteria or spermatozoa are typically found in dense suspensions, and exhibit collective modes of locomotion qualitatively different from that displayed by isolated cells. In the dilute limit where fluid-mediated interactions can be treated rigorously, the long-time hydrodynamics of a collection of cells result from interactions with many other cells, and as such typically eludes an analytical approach. Here we consider the only case where such problem can be treated rigorously analytically, namely when the cells have spatially confined trajectories, such as the spermatozoa of some marine invertebrates. We consider two spherical cells swimming, when isolated, with arbitrary circular trajectories, and derive the long-time kinematics of their relative locomotion. We show that in the dilute limit where the cells are much further away than their size, and the size of their circular motion, a separation of time scale occurs between a fast (intrinsic) swimming time, and a slow time where hydrodynamic interactions lead to change in the relative position and orientation of the swimmers. We perform a multiple-scale analysis and derive the effective dynamical system - of dimension two - describing the long-time behavior of the pair of cells. We show that the system displays one type of equilibrium, and two types of rotational equilibrium, all of which are found to be unstable. A detailed mathematical analysis of the dynamical systems further allows us to show that only two cell-cell behaviors are possible in the limit of $t\to\infty$, either the cells are attracted to each other (possibly monotonically), or they are repelled (possibly monotonically as well), which we confirm with numerical computations