Motion of rotatory molecular motor and chemical reaction rate

真核生物鞭毛中动态模式的反应扩散基础

The reaction-diffusion basis of animated patterns in eukaryotic flagella

本研究提出极简几何非线性反应扩散系统，从第一性原理推导其作为真核生物鞭毛搏动模式的基础，成功解释公牛精子与莱茵衣藻的鞭毛搏动，揭示高内耗下自主行波的游动机制。

Active rotational dynamics of a self-diffusiophoretic colloidal motor

The dynamics of a spherical chemically-powered synthetic colloidal motor that operates by a self-diffusiophoretic mechanism and has a catalytic domain of arbitrary shape is studied using both continuum theory and particle-based simulations. The motor executes active rotational motion when self-generated concentration gradients and interactions between the chemical species and colloidal motor surface break spherical symmetry. Local variations of chemical reaction rates on the motor catalytic surface with catalytic domain sizes and shapes provide such broken symmetry conditions. A continuum theo…

Nonequilibrium energetics of a single F1-ATPase molecule

Molecular motors drive mechanical motions utilizing the free energy liberated from chemical reactions such as ATP hydrolysis. Although it is essential to know the efficiency of this free energy transduction, it has been a challenge due to the system's microscopic scale. Here, we evaluate the single-molecule energetics of a rotary molecular motor, F1-ATPase, by applying a recently derived nonequilibrium equality together with an electrorotation method. We show that the sum of the heat flow through the probe's rotational degree of freedom and the work against external load is almost equal to the…

Propulsion, deformation, and confinement response of hollow nanocellulose millimotors

Micromotor and nanomotor particles are typically made using dense solid particles that can sediment or be trapped in confined flow environments. Creation of much larger motors should be possible if a very low-density system is used with sufficient strength to carry liquid and still experience propulsive motion. Light, dense millimotors should also be able to deform more than dense solid ones in constrictions. Millimotors are created from permeable capsules of bacterial cellulose that are coated with catalase-containing metal-organic frameworks, enabling reactive propulsion in aqueous hydrogen …

Stochastic dynamics of small ensembles of non-processive molecular motors: the parallel cluster model

Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumption…

Coupling of Active Motion and Advection Shapes Intracellular Cargo Transport

Intracellular cargo transport can arise from passive diffusion, active motor-driven transport along cytoskeletal filament networks, and passive advection by fluid flows entrained by such motor/cargo motion. Active and advective transport are thus intrinsically coupled as related, yet different representations of the same underlying network structure. A reaction-advection-diffusion system is used here to show that this coupling affects the transport and localization of a passive tracer in a confined geometry. For sufficiently low diffusion, cargo localization to a target zone is optimized eithe…

Quantifying fluctuations in reversible enzymatic cycles and clocks

Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but also allows fluctuation measurements which may reveal the structure and dynamics of the underlying biochemical network. Here, we study non-equilibrium reaction cycles, such as the mechanochemical cycle of molecular motors, the phosphorylation cycle of circadian clock proteins, or the transition state cycle of enzymes. Fluctuations in such cycles may be measured using either of two classical definitions of the randomness parameter, which we show to be equivalent in general mic…

Interacting RNA polymerase motors on DNA track: effects of traffic congestion and intrinsic noise on RNA synthesis

RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input to move along the track formed by a DNA. In many circumstances, which are described in this paper, a large number of RNAPs move simultaneously along the same track; we refer to such collective movements of the RNAPs as RNAP traffic. Here we develop a theoretical model for RNAP traffic by incorporating the steric interactions between RNAPs as well as the mec…

小型生命形式中的代谢尺度

Metabolic scaling in small life forms

本文提出基于酶催化反应—位移动力学的细胞代谢尺度模型，解释小细胞非线性缩放并预测原核到真核的转变体积。

Distribution of active forces in the cell cortex

In this work, we study in detail the distribution of stochastic forces generated by the molecular motors activity, in the actin cortex of pre-muscular cells. By combining active and passive rheology experiments, performed on the same micro-bead bound to the actin network through membrane adhesive receptors, we measure the auto-correlation function Cff(t) of the average force pulling on the bead. Like for any out-of-equilibrium system, the force distribution differs from the thermodynamical equilibrium one, especially at long time scale t>1sec where the bead motion becomes partially directed. T…