相关论文: Structural Change of Myosin Motor Domain and Nucle…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of…
In this work, we apply phase field simulations to examine the coarsening behavior of morphologically complex two-phase microstructures in which the phases have highly dissimilar mobilities, a condition approaching that found in experimental…
Mechanically induced folding of passive cross-linkers is a fundamental biological phenomenon. A typical example is a conformational change in myosin II responsible for the power-stroke in skeletal muscles. In this paper we present an…
Recent experiments have shown how nematically-ordered tactoid shaped actin droplets can be reorganized and divided by the action of myosin molecular motors. In this paper, we consider how similar morphological changes can potentially be…
Myosin II plays a pivotal role in muscle contraction by generating force through the cooperative action of multiple motors on actin filaments. In this study, we integrate the nonlinear elasticity of the neck linker in individual myosin II…
Myosin II is the muscle molecular motor that works in two bipolar arrays in each thick filament of the striated (skeletal and cardiac) muscle, converting the chemical energy into steady force and shortening by cyclic ATP--driven…
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…
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and…
The aging dynamics of a colloidal glass has been studied by multiangle Dynamic Light Scattering, Neutron Spin Echo, X-ray Photon Correlation Spectroscopy and Molecular Dynamics simulations. The two relaxation processes, microscopic (fast)…
The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…
Myosin-V is a highly processive dimeric protein that walks with 36nm steps along actin tracks, powered by coordinated ATP hydrolysis reactions in the two myosin heads. No previous theoretical models of the myosin-V walk reproduce all the…
Muon spin relaxation is a powerful technique for probing static and dynamic local magnetic fields. The strong collision model, based on a Gaussian-Markovian process, is commonly used to account for dynamical effects. Yet, it remains limited…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
This Chapter is devoted to unravel the relaxation processes taking place after photoexcitation of isolated DNA/RNA nucleobases in gas phase from a time-dependent perspective. To this aim, several methods are at hand, ranging from full…
We study the dynamics of membrane vesicle motor transport into dendritic spines, which are bulbous intracellular compartments in neurons that play a key role in transmitting signals between neurons. We consider the stochastic analog of the…
Cortical actin networks are highly dynamic and play critical roles in shaping the mechanical properties of cells. The actin cytoskeleton undergoes significant reorganization over the course of the cell cycle, when cortical actin transitions…
Based on the Stochastic Inclined Rods Model (SIRM) proposed by H. Matsuura and M. Nakano, we study the microscopic motion of actin myosin system including the motion of the G-actin. Our model is composed of an inclined spring (rod), a…
Cellular migration is crucial for biological processes including embryonic development, immune response, and wound healing. The myosin-clutch model is a framework that describes how cells control migration through the interactions between…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…