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Thermodynamic role of main reaction pathway and multi-body information flow in membrane transport [article]

Satoshi Yoshida, Yasushi Okada, Eiro Muneyuki, Sosuke Ito
2022 arXiv   pre-print
composed of two subsystems to the 16-state model composed of four subsystems representing the membrane transport.  ...  We also derive an upper bound on the free energy transport by the multi-body information flow representing the two-body or four-body correlations in the 16-state model by exploiting the cycle decomposition  ...  Enoki and M. Kuroda for inspiring discussion. We also thank T. Yoshii, J. Asada, T.  ... 
arXiv:2112.04024v2 fatcat:fckylhb7vjahplfptvoyhrri7e

Studies on biomechanics of skeletal muscle based on the working mechanism of myosin motors: An overview

YueHong Yin, Zhao Guo, Xing Chen, YuanJie Fan
2012 Chinese Science Bulletin  
We discussed the solution for experimental verification and induced a novel idea to study the biomechanics of skeletal muscle based on the microscopic working mechanism of molecular motor, which is the  ...  This paper reviewed the current researches on biomechanics of skeletal muscle, and concluded two strategies (top-down and bottom-up methods) for the biomechanical research of skeletal muscle.  ...  [58] presented a mechanical model for steady muscle contraction based on the conformational changes of a single motor, and studied the force-velocity relation of contraction, taking the actin filament  ... 
doi:10.1007/s11434-012-5438-y fatcat:6yfi6hfdnjdxdfneakqcdco6di

Oscillation-based methods for fixation and manipulation of nano-objects

Valentin L. Popov, Robbin Wetter
2015 2015 International Conference on Manipulation, Manufacturing and Measurement on the Nanoscale (3M-NANO)  
From this unifying standpoint, a series of actuation principles are discussed as dragging, ratchets, micro walking, friction-inertia actuators, oscillation tweezers, flagella motors for propulsion in liquids  ...  The underlying principles are scale-invariant and principally can be scaled down up to the molecular scale.  ...  Let us now take the force away and instead introduce an asymmetry of the substrate. We get a ratchet which was already discussed above Fig. 4b .  ... 
doi:10.1109/3m-nano.2015.7425469 fatcat:dsq66ekznndy7h7vygj5pxfpae

Natural selection can favor ratchet robustness over mutational robustness [article]

Yinghong Lan, Aaron Trout, Daniel M Weinreich, C Scott Wylie
2017 bioRxiv   pre-print
We designate these properties as ratchet robustness, which fundamentally reflects a negative feedback between mutation rate and the tendency to accumulate more mutations.  ...  Thus, mutational robustness also results in higher risk of long-term extinction by Muller's ratchet. Here, we explore the tension between short- and long- term response to deleterious mutations.  ...  The fitness landscape provides a unifying framework for exploring both mutational robustness 92 and ratchet robustness.  ... 
doi:10.1101/121087 fatcat:dqcucyxfy5egxg3gap2cikpakm

Identifying functional thermodynamics in autonomous Maxwellian ratchets

Alexander B Boyd, Dibyendu Mandal, James P Crutchfield
2016 New Journal of Physics  
that relies on the Kolmogorov-Sinai entropy for dynamical processes and not on changes purely in system configurational entropy, as previously employed.  ...  We introduce a family of Maxwellian Demons for which correlations among information bearing degrees of freedom can be calculated exactly and in compact analytical form.  ...  A unified approach to these perspectives was attempted in Refs. [40] [41] [42] .  ... 
doi:10.1088/1367-2630/18/2/023049 fatcat:lzusfqxu5bbmlnsgp7lvjcbe3u

On the calibration of the Chaboche hardening model and a modified hardening rule for uniaxial ratcheting prediction

Mohamad Rezaiee-Pajand, Sina Sinaie
2009 International Journal of Solids and Structures  
Finally, as an improvement to the decomposed model, a modification is made to one of the backstress components.  ...  A systematic mathematical approach is developed in the context of uniaxial cyclic ratcheting for the parameter determination of the decomposed Chaboche hardening rule.  ...  The C-H4T model is composed of three AF components and takes advantage of one modified AF component.  ... 
doi:10.1016/j.ijsolstr.2009.04.002 fatcat:pdqtqtkrh5hsbjwfscicp6jqam

Unidirectional Brownian motion observed in anin silicosingle molecule experiment of an actomyosin motor

Mitsunori Takano, Tomoki P. Terada, Masaki Sasai
2010 Proceedings of the National Academy of Sciences of the United States of America  
This unidirectionality was found to arise from the combination of a nonequilibrium condition realized by coupling to the ATP hydrolysis and a ratchet-like energy landscape inherent in the actin-myosin  ...  When we placed myosin on an actin filament and allowed myosin to move along the filament, we found that myosin exhibits a unidirectional Brownian motion along the filament.  ...  We thank Shin'ichi Ishiwata and Kazuhiko Kinosita Jr. for critically reading the manuscript. This work was partially supported by  ... 
doi:10.1073/pnas.0911830107 pmid:20385833 pmcid:PMC2867847 fatcat:bcwmippgk5cj5ol7ezsgwwdw3m

Stepwise translocation of nucleic acid motors

Sua Myong, Taekjip Ha
2010 Current Opinion in Structural Biology  
Combined with previous structural studies, NS3 is likely taking a single nucleotide step of translocation coupled to one ATP binding event and this mode may be conserved in multitude of helicases.  ...  Spontaneous dynamics displayed by ribosome ratcheting and SSB (single stranded DNA binding protein) diffusing on DNA were rectified by interacting cofactors and proteins, EF-G and RecA respectively.  ...  The 30S and 50S subunits are represented on the ribosome structure. C. The ribosome undergoes a spontaneous ratcheting motion in the absence of EF-G. A.  ... 
doi:10.1016/j.sbi.2009.12.008 pmid:20061135 pmcid:PMC2845851 fatcat:ab5hmh5p5nhudbn2kftm6ckrrq

Self-organization versus Watchmaker: Molecular motors and protein translocation

Alexei Kurakin
2006 Biosystems (Amsterdam. Print)  
It is counter-176 intuitive and takes an effort of mind to grasp.  ...  Importantly, the 302 Brownian ratchet provides a unifying principle of recti-303 fication of directional movement from the thermal chaos 304 at microscale (Hanggi and Bartussek, 1996).  ... 
doi:10.1016/j.biosystems.2005.09.007 pmid:16384632 fatcat:iadl7beltrhfrciwqkefrybmry

Brownian ratchets and Parrondo's games

Gregory P. Harmer, Derek Abbott, Peter G. Taylor, Juan M. R. Parrondo
2001 Chaos  
One possible interpretation pictures game A as a source of "noise" that is rectified by game B to produce overall positive drift-as in a Brownian ratchet.  ...  Game B is played with two biased coins and has state-dependent rules based on the player's current capital.  ...  The corresponding ''thermodynamic law'' for the discrete-time ratchet is somewhat different: here we can say that the gain in capital created by randomly mixing games A and B is less than a game composed  ... 
doi:10.1063/1.1395623 pmid:12779509 fatcat:r5kryvjgz5eptkhbkvjnfqlbjy

Characterization and modeling of the ratcheting behavior of the ferritic–martensitic steel P91

Kuo Zhang, Jarir Aktaa
2016 Journal of Nuclear Materials  
The ratcheting behavior of 9% Cr-1% Mo ferritic-martensitic (FM) steel P91 is investigated by uniaxial cyclic loading tests at room temperature and 550 °C.  ...  Accumulation rates of strains (ratcheting rates) under multiple loading conditions are recorded to build a database for P91 for further application in Generation IV fission reactors.  ...  A unified visco-plastic deformation model taking into account the complex nonsaturating cyclic softening of Reduced Activation Ferritic Martensitic (RAFM) steels is further modified to adapt the ratcheting  ... 
doi:10.1016/j.jnucmat.2015.10.050 fatcat:lkchigwe2vcavka6h7cbcojchm

Creep Fatigue Life Assessment of a Pipe Intersection with Dissimilar Material Joint by Linear Matching Method

Daniele Barbera, Hao Feng Chen, Ying Hua Liu
2016 Applied Mechanics and Materials  
The impact of the material mismatch, transitional thermal load, and creep dwell on the failure mechanism and location within the intersection is investigated.  ...  All the results demonstrate the capability of the method, and how a direct method is able to support engineers in the assessment and design of high temperature component in a complex loading scenario.  ...  Daniele Barbera, Haofeng Chen and Yinghua Liu  ... 
doi:10.4028/www.scientific.net/amm.853.366 fatcat:ugu3uixx75fxvdn2rrxqpg5o3q

Creep-fatigue behaviour of aluminum alloy-based metal matrix composite

Daniele Barbera, Haofeng Chen, Yinghua Liu
2016 International Journal of Pressure Vessels and Piping  
A detailed study of the creep ratchetting mechanism is also performed with the concentration on the impact of temperature and different loading conditions.  ...  The effects of reversed plasticity on stress relaxation and creep deformation of MMC are investigated, and the behaviours of cyclically enhanced creep and elastic followup are presented.  ...  Daniele Barbera, Haofeng Chen and Yinghua Liu  ... 
doi:10.1016/j.ijpvp.2016.02.004 fatcat:ichtzuo225bpnktvjim5tjok3a

Device/prototype production of synthetization of scaffolds the base of fibroin and Aloe barbadensis

Mayra Campista Corteletti, Pablo Prata de Almeida, Gerlane de Souza Pereira da Costa, Thalia Henke
2020 Journal of Biotechnology and Biodiversity  
Consisting of an experimental study, with materials selection and related equipment, projection and construction of a prototype aiming at processing on larger scale and the best cost-benefit ratio, making  ...  This research established itself as principle the building of a device/prototype specific for synthesis of scaffolds composed of gel Aloe barbadensis Miller and fibroin extracted from cocoons of Bombyx  ...  , pulleys, ratchets, PVC pipes, aluminum rails and shafts, screens, colorless plastic boxes, light board, valves, plywood for the development of the structural base, distributing and unifying the selected  ... 
doi:10.20873/jbb.uft.cemaf.v8n1.corteletti fatcat:mdxulzqwxjce5gyre32rpwlygu

A Small Post-Translocation Energy Bias Aids Nucleotide Selection in T7 RNA Polymerase Transcription

Jin Yu, George Oster
2012 Biophysical Journal  
Based on structural information and experimental data from single-molecule force measurements, we show that a small component of facilitated translocation or power stroke coexists with the Brownian-ratchet-driven  ...  motions, and plays a crucial role in nucleotide selection at pre-insertion.  ...  in a unified way.  ... 
doi:10.1016/j.bpj.2011.12.028 pmid:22325276 pmcid:PMC3274829 fatcat:52jqlb4gc5hdvdpgt3hot6fwmy
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