Spontaneous Oscillations of Collective Molecular Motors

We analyze a simple stochastic model to describe motor molecules which cooperate in large groups and present a physical mechanism which can lead to oscillatory motion if the motors are elastically coupled to their environment. Beyond a critical fuel concentration, the non-moving state of the system becomes unstable with respect to a mode with angular frequency omega. We present a perturbative description of the system near the instability and demonstrate that oscillation frequencies are determined by the typical timescales of the motors.Comment: 11 pages, Revtex, 4 pages Figure

SCOTCH and SODA: A Transformer Video Shadow Detection Framework

Shadows in videos are difficult to detect because of the large shadow deformation between frames. In this work, we argue that accounting for shadow deformation is essential when designing a video shadow detection method. To this end, we introduce the shadow deformation attention trajectory (SODA), a new type of video self-attention module, specially designed to handle the large shadow deformations in videos. Moreover, we present a new shadow contrastive learning mechanism (SCOTCH) which aims at guiding the network to learn a unified shadow representation from massive positive shadow pairs across different videos. We demonstrate empirically the effectiveness of our two contributions in an ablation study. Furthermore, we show that SCOTCH and SODA significantly outperforms existing techniques for video shadow detection. Code is available at the project page: https://lihaoliu-cambridge.github.io/scotch_and_soda/Comment: Accepted to CVPR 202

Increasing the uptake of HIV testing to reduce undiagnosed infection and prevent transmission among black African communities living in England: Barriers to HIV testing

Globally, the HIV epidemic continues to have an impact on the lives of millions of people. In 2008, there were an estimated 83,000 people living with HIV (both diagnosed and undiagnosed), equivalent to 1.3 per 1000 population in the UK. In that same year, 7,798 people were newly diagnosed with HIV. The global epidemic is reflected in the UK; around 38% (2,790) of these newly diagnosed infections were among black Africans who acquired their HIV through heterosexual contact. It is thought that most (87%) of these infections among black Africans in the UK were acquired abroad, mainly in sub-Saharan Africa (Health Protection Agency 2009). Late diagnosis of HIV is defined as diagnosis taking place after anti-retroviral treatment would normally have begun, or when the person has an illness which defines them as having AIDS. It is the most important factor associated with HIVrelated disease and death in the UK and is a particular problem among black Africans. In 2007, over 40% of new diagnoses among black Africans were classified as ‘late’. HIV testing can help reduce transmission of the virus. People who find out they have HIV may change their sexual behaviour as a result of the diagnosis. A negative HIV test provides an opportunity for preventive education and advice and may also lead to changes in behaviour. Increasing the frequency of testing may result in earlier detection of HIV following infection - when it is most virulent - providing greater opportunity to reduce transmissio

Active Membrane Fluctuations Studied by Micropipet Aspiration

We present a detailed analysis of the micropipet experiments recently reported in J-B. Manneville et al., Phys. Rev. Lett. 82, 4356--4359 (1999), including a derivation of the expected behaviour of the membrane tension as a function of the areal strain in the case of an active membrane, i.e., containing a nonequilibrium noise source. We give a general expression, which takes into account the effect of active centers both directly on the membrane, and on the embedding fluid dynamics, keeping track of the coupling between the density of active centers and the membrane curvature. The data of the micropipet experiments are well reproduced by the new expressions. In particular, we show that a natural choice of the parameters quantifying the strength of the active noise explains both the large amplitude of the observed effects and its remarkable insensitivity to the active-center density in the investigated range. [Submitted to Phys Rev E, 22 March 2001]Comment: 14 pages, 5 encapsulated Postscript figure

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

Energy Transduction of Isothermal Ratchets: Generic Aspects and Specific Examples Close to and Far from Equilibrium

We study the energetics of isothermal ratchets which are driven by a chemical reaction between two states and operate in contact with a single heat bath of constant temperature. We discuss generic aspects of energy transduction such as Onsager relations in the linear response regime as well as the efficiency and dissipation close to and far from equilibrium. In the linear response regime where the system operates reversibly the efficiency is in general nonzero. Studying the properties for specific examples of energy landscapes and transitions, we observe in the linear response regime that the efficiency can have a maximum as a function of temperature. Far from equilibrium in the fully irreversible regime, we find a maximum of the efficiency with values larger than in the linear regime for an optimal choice of the chemical driving force. We show that corresponding efficiencies can be of the order of 50%. A simple analytic argument allows us to estimate the efficiency in this irreversible regime for small external forces.Comment: 16 pages, 10 figure

Molecular motor that never steps backwards

We investigate the dynamics of a classical particle in a one-dimensional two-wave potential composed of two periodic potentials, that are time-independent and of the same amplitude and periodicity. One of the periodic potentials is externally driven and performs a translational motion with respect to the other. It is shown that if one of the potentials is of the ratchet type, translation of the potential in a given direction leads to motion of the particle in the same direction, whereas translation in the opposite direction leaves the particle localized at its original location. Moreover, even if the translation is random, but still has a finite velocity, an efficient directed transport of the particle occurs.Comment: 4 pages, 5 figures, Phys. Rev. Lett. (in print

Self-organized Beating and Swimming of Internally Driven Filaments

We study a simple two-dimensional model for motion of an elastic filament subject to internally generated stresses and show that wave-like propagating shapes which can propel the filament can be induced by a self-organized mechanism via a dynamic instability. The resulting patterns of motion do not depend on the microscopic mechanism of the instability but only of the filament rigidity and hydrodynamic friction. Our results suggest that simplified systems, consisting only of molecular motors and filaments could be able to show beating motion and self-propulsion.Comment: 8 pages, 2 figures, REVTe

Force Dependence of the Michaelis Constant in a Two-State Ratchet Model for Molecular Motors

We present a quantitative analysis of recent data on the kinetics of ATP hydrolysis, which has presented a puzzle regarding the load dependence of the Michaelis constant. Within the framework of coarse grained two-state ratchet models, our analysis not only explains the puzzling data, but provides a modified Michaelis law, which could be useful as a guide for future experiments.Comment: 4 pages, 3 eps figures, accepted for publication on Physical Review Letter

Renewal processes and fluctuation analysis of molecular motor stepping

We model the dynamics of a processive or rotary molecular motor using a renewal processes, in line with the work initiated by Svoboda, Mitra and Block. We apply a functional technique to compute different types of multiple-time correlation functions of the renewal process, which have applications to bead-assay experiments performed both with processive molecular motors, such as myosin V and kinesin, and rotary motors, such as F1-ATPase