Instabilities and waves in thin films of living fluids

We formulate the thin-film hydrodynamics of a suspension of polar self-driven particles and show that it is prone to several instabilities through the interplay of activity, polarity and the existence of a free surface. Our approach extends, to self-propelling systems, the work of Ben Amar and Cummings [Phys Fluids 13 (2001) 1160] on thin-film nematics. Based on our estimates the instabilities should be seen in bacterial suspensions and the lamellipodium, and are potentially relevant to the morphology of biofilms. We suggest several experimental tests of our theory.Comment: 4 pages, pdflatex, accepted for publication in Phys Rev Let

Self-organized Pattern Formation in Motor-Microtubule Mixtures

We propose and study a hydrodynamic model for pattern formation in mixtures of molecular motors and microtubules. The steady state patterns we obtain in different regimes of parameter space include arrangements of vortices and asters separately as well as aster-vortex mixtures and fully disordered states. Such stable steady states are observed in experiments in vitro. The sequence of patterns obtained in the experiments can be associated with smooth trajectories in a non-equilibrium phase diagram for our model.Comment: 11 pages Latex file, 2 figures include

Two-Component Fluid Membranes Near Repulsive Walls: Linearized Hydrodynamics of Equilibrium and Non-equilibrium States

We study the linearized hydrodynamics of a two-component fluid membrane near a repulsive wall, via a model which incorporates curvature- concentration coupling as well as hydrodynamic interactions. This model is a simplified version of a recently proposed one [J.-B. Manneville et al. Phys. Rev. E, 64, 021908 (2001)] for non-equilibrium force-centres embedded in fluid membranes, such as light-activated bacteriorhodopsin pumps incorporated in phospholipid (EPC) bilayers. The pump/membrane system is modeled as an impermeable, two-component bilayer fluid membrane in the presence of an ambient solvent, in which one component, representing active pumps, is described in terms of force dipoles displaced with respect to the bilayer midpoint. We first discuss the case in which such pumps are rendered inactive, computing the mode structure in the bulk as well as the modification of hydrodynamic properties by the presence of a nearby wall. We then discuss the fluctuations and mode structure in steady state of active two-component membranes near a repulsive wall. We find that proximity to the wall smoothens membrane height fluctuations in the stable regime, resulting in a logarithmic scaling of the roughness even for initially tensionless membranes. This explicitly non-equilibrium result, a consequence of the incorporation of curvature-concentration coupling in our treatment, also indicates that earlier scaling arguments which obtained an increase in the roughness of active membranes near repulsive walls may need to be reevaluated.Comment: 39 page Latex file, 3 encapsulated Postscript figure

Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer

Somatic mutations within non-coding regions and even exons may have unidentified regulatory consequences that are often overlooked in analysis workflows. Here we present RegTools ( www.regtools.org ), a computationally efficient, free, and open-source software package designed to integrate somatic variants from genomic data with splice junctions from bulk or single cell transcriptomic data to identify variants that may cause aberrant splicing. We apply RegTools to over 9000 tumor samples with both tumor DNA and RNA sequence data. RegTools discovers 235,778 events where a splice-associated variant significantly increases the splicing of a particular junction, across 158,200 unique variants and 131,212 unique junctions. To characterize these somatic variants and their associated splice isoforms, we annotate them with the Variant Effect Predictor, SpliceAI, and Genotype-Tissue Expression junction counts and compare our results to other tools that integrate genomic and transcriptomic data. While many events are corroborated by the aforementioned tools, the flexibility of RegTools also allows us to identify splice-associated variants in known cancer drivers, such as TP53, CDKN2A, and B2M, and other genes

Quantum Hall Skyrmion Lattices at g≈0g \approx 0

We investigate the classical ground state configurations of a collection of skyrmions in the limit of vanishing L\'ande $g$ factor. We show that in this limit, the skyrmions which are large and overlapping, behave qualitatively differently from small skyrmions. We investigate the system in various regimes of spin stiffness. We find that in all regimes, at $g=0$, the ground state configuration is a rectangular skyrmion lattice with N\'eel orientational ordering. The charge distribution has a higher symmetry of a face-centered rectangular lattice and the $z$-component of the spin polarization is zero. We also present general argument for the vanishing of spin polarization at $g=0$ at finite temperature and in the presence of disorder and discuss some experimental consequences of our results.Comment: Latex file, 15 figures, To appear in Physical Review