Molecular Mechanism of Processive Stepping of Kinesin Motors

Kinesin-1 is a motor protein that can step processively on microtubule by hydrolyzing ATP molecules, playing an essential role in intracellular transports. To better understand the mechanochemical coupling of the motor stepping cycle, numerous structural, biochemical, single molecule, theoretical modeling and numerical simulation studies have been undertaken for the kinesin-1 motor. Recently, a novel ultraresolution optical trapping method was employed to study the mechanics of the kinesin-1 motor and new results were supplemented to its stepping dynamics. In this commentary, the new single molecule results are explained well theoretically with one of the models presented in the literature for the mechanochemical coupling of the kinesin-1 motor. With the model, various prior experimental results for dynamics of different families of N-terminal kinesin motors have also been explained quantitatively.

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S09A5 Single-molecule experiments of F1-ATPase correlating with the crystal structures and molecular simulation(Mechanism of F_1-ATPase Molecular Motor-A Cross Talk among Single Molecule, Structural Biology, and Molecular Simulation Studies-)

Seibutsu Butsuri ◽

10.2142/biophys.47.s13_4 ◽

2007 ◽

Vol 47 (supplement) ◽

pp. S13

Author(s):

Hiroyuki Noji

Keyword(s):

Crystal Structures ◽

Molecular Simulation ◽

Structural Biology ◽

Single Molecule ◽

Cross Talk ◽

Molecular Motor ◽

Simulation Studies ◽

F1 Atpase

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A Heterogeneous Graph Enhanced LSTM Network for Hog Price Prediction Using Online Discussion

Agriculture ◽

10.3390/agriculture11040359 ◽

2021 ◽

Vol 11 (4) ◽

pp. 359

Author(s):

Kai Ye ◽

Yangheran Piao ◽

Kun Zhao ◽

Xiaohui Cui

Keyword(s):

Decision Making ◽

Essential Role ◽

Online Discussion ◽

Professional Community ◽

Experimental Results ◽

Agricultural Products ◽

Price Prediction ◽

Price Data ◽

Rich Information ◽

Lstm Network

Forecasting the prices of hogs has always been a popular field of research. Such information has played an essential role in decision-making for farmers, consumers, corporations, and governments. It is hard to predict hog prices because too many factors can influence them. Some of the factors are easy to quantify, but some are not. Capturing the characteristics behind the price data is also tricky considering their non-linear and non-stationary nature. To address these difficulties, we propose Heterogeneous Graph-enhanced LSTM (HGLTSM), which is a method that predicts weekly hog price. In this paper, we first extract the historical prices of necessary agricultural products in recent years. Then, we utilize discussions from the online professional community to build heterogeneous graphs. These graphs have rich information of both discussions and the engaged users. Finally, we construct HGLSTM to make the prediction. The experimental results demonstrate that forum discussions are beneficial to hog price prediction. Moreover, our method exhibits a better performance than existing methods.

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Numerical simulation studies of Cs3Bi2I9 perovskite solar device with optimal selection of electron and hole transport layers

Optik ◽

10.1016/j.ijleo.2021.166417 ◽

2021 ◽

Vol 231 ◽

pp. 166417 ◽

Cited By ~ 1

Author(s):

Md Tohidul Islam ◽

Md Rafsun Jani ◽

Kazi Md Shorowordi ◽

Zameer Hoque ◽

Ali Mucteba Gokcek ◽

...

Keyword(s):

Numerical Simulation ◽

Hole Transport ◽

Optimal Selection ◽

Simulation Studies ◽

Hole Transport Layers ◽

Selection Of

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Advances in the study of the mechanochemical coupling of kinesin

International Journal of Modern Physics B ◽

10.1142/s0217979218400015 ◽

2018 ◽

Vol 32 (18) ◽

pp. 1840001 ◽

Cited By ~ 1

Author(s):

Ming Li ◽

Zhong-Can Ou-Yang ◽

Yao-Gen Shu

Keyword(s):

Molecular Dynamics ◽

Single Molecule ◽

Intracellular Transport ◽

Coordination Mechanism ◽

Personal Perspective ◽

Long Distance ◽

Future Studies ◽

Mechanochemical Coupling ◽

Dynamics Simulations ◽

Made In

Kinesin is a two-headed linear motor for intracellular transport. It can walk a long distance in a hand-over-hand manner along the track before detaching (i.e., high processivity), and it consumes one ATP molecule for each step (i.e., tight mechanochemical coupling). The mechanisms of the coordination of its two heads and the mechanochemical coupling are the central issues of numerous researches. A few advances have been made in recent decades, thanks to the development of single-molecule technologies and molecular dynamics simulations. In this paper, we review some progress of the studies on the kinematics, energetics, coordination mechanism, mechanochemical mechanism of kinesin. We also present a personal perspective on the future studies of kinesin.

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Simulation of a Free Standing Riser Model and Validation With Experimental Results

Volume 6A: Pipeline and Riser Technology ◽

10.1115/omae2014-23309 ◽

2014 ◽

Author(s):

Marcio Yamamoto ◽

Sotaro Masanobu ◽

Satoru Takano ◽

Shigeo Kanada ◽

Tomo Fujiwara ◽

...

Keyword(s):

Numerical Simulation ◽

Numerical Analysis ◽

Previous Experiment ◽

Numerical Results ◽

Experimental Results ◽

Previous Article ◽

Scale Model ◽

Analysis Software ◽

Free Standing ◽

Reduced Scale

In this article, we present the numerical analysis of a Free Standing Riser. The numerical simulation was carried out using a commercial riser analysis software suit. The numerical model’s dimensions were the same of a 1/70 reduced scale model deployed in a previous experiment. The numerical results were compared with experimental results presented in a previous article [1]. Discussion about the model and limitations of the numerical analysis is included.

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Numerical simulation studies of the turbulent airflow through a shrouded airborne aerosol sampling probe and estimation of the minimum sampler transmission efficiency

Journal of Aerosol Science ◽

10.1016/s0021-8502(98)80009-8 ◽

1998 ◽

Vol 29 (9) ◽

pp. 1145-1156 ◽

Cited By ~ 2

Author(s):

Stuart A. Cain ◽

Michael Ram

Keyword(s):

Numerical Simulation ◽

Transmission Efficiency ◽

Aerosol Sampling ◽

Simulation Studies ◽

Sampling Probe ◽

Turbulent Airflow

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Combining Optical Trapping and Single-Molecule Fluorescence Spectroscopy: Enhanced Photobleaching of Fluorophores

The Journal of Physical Chemistry B ◽

10.1021/jp049805+ ◽

2004 ◽

Vol 108 (20) ◽

pp. 6479-6484 ◽

Cited By ~ 68

Author(s):

Meindert A. van Dijk ◽

Lukas C. Kapitein ◽

Joost van Mameren ◽

Christoph F. Schmidt ◽

Erwin J. G. Peterman

Keyword(s):

Fluorescence Spectroscopy ◽

Single Molecule ◽

Optical Trapping ◽

Single Molecule Fluorescence ◽

Single Molecule Fluorescence Spectroscopy

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Single–motor mechanics and models of the myosin motor

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2000.0585 ◽

2000 ◽

Vol 355 (1396) ◽

pp. 441-447 ◽

Cited By ~ 37

Author(s):

T. Yanagida ◽

S. Esaki ◽

A. Hikikoshi Iwane ◽

Y. Inoue ◽

A. Ishijima ◽

...

Keyword(s):

Single Molecule ◽

Atp Hydrolysis ◽

Accurate Determination ◽

Step Size ◽

Single Molecule Level ◽

Detection Techniques ◽

Myosin Motor ◽

Mechanochemical Coupling ◽

Chemical Events

Recent progress in single–molecule detection techniques is remarkable. These techniques have allowed the accurate determination of myosin–head–induced displacements and how mechanical cycles are coupled to ATP hydrolysis, by measuring individual mechanical events and chemical events of actomyosin directly at the single–molecule level. Here we review our recent work in which we have made detailed measurements of myosin step size and mechanochemical coupling, and propose a model of the myosin motor.

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NUMERICAL SIMULATION OF DAM BREAK BY ADAPTIVE STENCIL DIFFUSE INTERFACE METHOD

Modern Physics Letters B ◽

10.1142/s0217984909018230 ◽

2009 ◽

Vol 23 (03) ◽

pp. 293-296 ◽

Cited By ~ 1

Author(s):

L. DING ◽

C. SHU ◽

N. ZHAO

Keyword(s):

Numerical Simulation ◽

Adaptive Algorithm ◽

Leading Edge ◽

Dam Break ◽

Experimental Results ◽

Diffuse Interface ◽

Fine Scale ◽

Experiment Data ◽

Interface Behavior

This paper presents the application of an adaptive stencil diffuse interface method to the simulation of dam break problem. The adaptive stencil diffuse interface method is the combination of the diffuse interface method and a stencil adaptive algorithm, where the diffuse interface method is used as the solver, and the adaptive stencil refinement scheme is applied to improve the resolution around the interface so that the fine-scale interface behavior can be captured. In this paper, we use this method to simulate the dam break problem, study the dam height and leading edge position, and compare our results with the experiment data available in the literature. It is shown that the results using the adaptive stencil diffuse interface method agree very well with the experimental results.

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