scholarly journals Force Dependence of Velocity and Run Length of Kinesin-1, Kinesin-2 and Kinesin-5 Family Molecular Motors

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 287 ◽  
Author(s):  
Si-Kao Guo ◽  
Wei-Chi Wang ◽  
Peng-Ye Wang ◽  
Ping Xie
Keyword(s):  
Experimental Data ◽  
Atpase Activity ◽  
Rate Constants ◽  
Molecular Motors ◽  
Quantitative Agreement ◽  
Run Length ◽  
Movement Dynamics ◽  
Proposed Model ◽  
Movement Mechanism ◽  
The Difference

Kinesin-1, kinesin-2 and kinesin-5 are three families of a superfamily of motor proteins; which can walk processively on microtubule filaments by hydrolyzing ATP. It was experimentally shown that while the three kinesin dimers show similar feature on the force dependence of velocity, they show rather different features on the force dependence of run length. However, why the three families of kinesins show these rather different features is unclear. Here, we computationally studied the movement dynamics of the three dimers based on our proposed model. The simulated results reproduce well the available experimental data on the force dependence of velocity and run length. Moreover, the simulated results on the velocity and run length for the three dimers with altered neck linker lengths are also in quantitative agreement with the available experimental data. The studies indicate that the three families of kinesins show much similar movement mechanism and the rather different features on the force dependence of run length arise mainly from the difference in rate constants of the ATPase activity and neck linker docking. Additionally, the asymmetric (limping) movement dynamics of the three families of homodimers with and without altered neck linker lengths are studied, providing predicted results.

scholarly journals Run length distribution of dimerized kinesin-3 molecular motors: comparison with dimeric kinesin-1

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Si-Kao Guo ◽  
Xiao-Xuan Shi ◽  
Peng-Ye Wang ◽  
Ping Xie
Keyword(s):  
Molecular Motors ◽  
Average Run Length ◽  
Length Distribution ◽  
Dissociation Rate ◽  
Run Length ◽  
Proposed Model ◽  
Run Length Distribution ◽  
Run Lengths ◽  
Kinesin Superfamily ◽  
Single Exponential

AbstractKinesin-3 and kinesin-1 molecular motors are two families of the kinesin superfamily. It has been experimentally revealed that in monomeric state kinesin-3 is inactive in motility and cargo-mediated dimerization results in superprocessive motion, with an average run length being more than 10-fold longer than that of kinesin-1. In contrast to kinesin-1 showing normally single-exponential distribution of run lengths, dimerized kinesin-3 shows puzzlingly Gaussian distribution of run lengths. Here, based on our proposed model, we studied computationally the dynamics of kinesin-3 and compared with that of kinesin-1, explaining quantitatively the available experimental data and revealing the origin of superprocessivity and Gaussian run length distribution of kinesin-3. Moreover, predicted results are provided on ATP-concentration dependence of run length distribution and force dependence of mean run length and dissociation rate of kinesin-3.

scholarly journals A Generalized Kinetic Model for Coupling between Stepping and ATP Hydrolysis of Kinesin Molecular Motors

2019 ◽  
Vol 20 (19) ◽  
pp. 4911 ◽  
Author(s):  
Xie ◽  
Guo ◽  
Chen
Keyword(s):  
Kinetic Model ◽  
Atpase Activity ◽  
Single Molecule ◽  
Rate Constants ◽  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Power Production ◽  
Wild Type ◽  
Chemomechanical Coupling ◽  
Generalized Kinetic Model

A general kinetic model is presented for the chemomechanical coupling of dimeric kinesin molecular motors with and without extension of their neck linkers (NLs). A peculiar feature of the model is that the rate constants of ATPase activity of a kinesin head are independent of the strain on its NL, implying that the heads of the wild-type kinesin dimer and the mutant with extension of its NLs have the same force-independent rate constants of the ATPase activity. Based on the model, an analytical theory is presented on the force dependence of the dynamics of kinesin dimers with and without extension of their NLs at saturating ATP. With only a few adjustable parameters, diverse available single molecule data on the dynamics of various kinesin dimers, such as wild-type kinesin-1, kinesin-1 with mutated residues in the NLs, kinesin-1 with extension of the NLs and wild-type kinesin-2, under varying force and ATP concentration, can be reproduced very well. Additionally, we compare the power production among different kinesin dimers, showing that the mutation in the NLs reduces the power production and the extension of the NLs further reduces the power production.

scholarly journals Quantum Tunneling and Reaction Rates in Selenoxides and Sulfoxides Elimination

2020 ◽  
Author(s):  
Caio M. Porto ◽  
Nelson H. Morgon
Keyword(s):  
Organic Chemistry ◽  
Experimental Data ◽  
Barrier Height ◽  
Rate Constants ◽  
Quantum Tunneling ◽  
Reaction Rates ◽  
Striking Difference ◽  
Variational Theory ◽  
The Difference ◽  
Good Agreement

Selenoxides and sulfoxides elimination reactions are important, not only to Organic Chemistry synthesis, but also to other areas, as Biochemistry. These reactions were studied, using direct dynamics calculations, at the canonical variational theory (CVT) and small curvature tunneling (SCT) level. The calculated rate constants for the selenoxide reaction were in good agreement with experimental data, 8.83 × 10-5 s -1 and 3.20 × 10-5 s -1 , respectively. The rate constants for the sulfoxide reaction are very small at 37°C, namely 2.43 × 10-9 , and there is also a significant tunneling correction, which shows quantum tunneling effects occur in both reactions, although with very different magnitudes. One of the most striking difference comes from the barrier height, which is almost 2000 cm-1 bigger for the sulfoxide elimination, and helps to explain the difference in reaction rates.

A non-tight chemomechanical coupling model for force-dependence of movement dynamics of molecular motors

2018 ◽  
Vol 20 (7) ◽  
pp. 4752-4759 ◽  
Author(s):  
Ping Xie ◽  
Hong Chen
Keyword(s):  
Experimental Data ◽  
Single Molecule ◽  
Molecular Motors ◽  
General Model ◽  
Coupling Model ◽  
Myosin V ◽  
Chemomechanical Coupling ◽  
Movement Dynamics

We present a simple yet general model that can quantitatively reproduce diverse single-molecule experimental data on dimeric kinesin and myosin-V.

Dual Release Model to Evaluate Dissolution Profiles from Swellable Drug Polyelectrolyte Matrices

2020 ◽  
Vol 17 (6) ◽  
pp. 511-522 ◽  
Author(s):  
Alicia Graciela Cid ◽  
María Verónica Ramírez-Rigo ◽  
María Celeste Palena ◽  
Elio Emilio Gonzo ◽  
Alvaro Federico Jimenez-Kairuz ◽  
...  
Keyword(s):  
Experimental Data ◽  
Drug Release ◽  
Inflection Point ◽  
Release Profile ◽  
Experimental Point ◽  
Extended Model ◽  
Release Process ◽  
Proposed Model ◽  
Dual Release ◽  
Release Model

Background: Mathematical modeling in modified drug release is an important tool that allows predicting the release rate of drugs in their surrounding environment and elucidates the transport mechanisms involved in the process. Objective: The aim of this work was to develop a mathematical model that allows evaluating the release profile of drugs from polymeric carriers in which the swelling phenomenon is present. Methods: Swellable matrices based on ionic complexes of alginic acid or carboxymethylcellulose with ciprofloxacin were prepared and the effect of adding the polymer sodium salt on the swelling process and the drug release was evaluated. Experimental data from the ciprofloxacin release profiles were mathematically adjusted, considering the mechanisms involved in each stage of the release process. Results: A proposed model, named “Dual Release” model, was able to properly fit the experimental data of matrices presenting the swelling phenomenon, characterized by an inflection point in their release profile. This entails applying the extended model of Korsmeyer-Peppas to estimate the percentage of drug released from the first experimental point up to the inflection point and then a model called Lumped until the final time, allowing to adequately represent the complete range of the drug release profile. Different parameters of pharmaceutical relevance were calculated using the proposed model to compare the profiles of the studied matrices. Conclusion: The “Dual Release” model proposed in this article can be used to predict the behavior of complex systems in which different mechanisms are involved in the release process.

Simple explicit model of liquid mean flow in region above axial impeller

1985 ◽  
Vol 50 (11) ◽  
pp. 2396-2410
Author(s):  
Miloslav Hošťálek ◽  
Ivan Fořt
Keyword(s):  
Vortex Flow ◽  
Flow Model ◽  
Quantitative Agreement ◽  
Mean Flow ◽  
Flat Bottom ◽  
Proposed Model ◽  
Minimum Number ◽  
The Mean ◽  
Model Equations ◽  
Radial Circulation

The study describes a method of modelling axial-radial circulation in a tank with an axial impeller and radial baffles. The proposed model is based on the analytical solution of the equation for vortex transport in the mean flow of turbulent liquid. The obtained vortex flow model is tested by the results of experiments carried out in a tank of diameter 1 m and with the bottom in the shape of truncated cone as well as by the data published for the vessel of diameter 0.29 m with flat bottom. Though the model equations are expressed in a simple form, good qualitative and even quantitative agreement of the model with reality is stated. Apart from its simplicity, the model has other advantages: minimum number of experimental data necessary for the completion of boundary conditions and integral nature of these data.

scholarly journals Epistemic values of quantity and variety of evidence in biological mechanism research

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Yin Chung Au
Keyword(s):  
Experimental Data ◽  
Causal Inference ◽  
Case Studies ◽  
Biological Mechanism ◽  
Data Generation ◽  
Extended Version ◽  
Epistemic Values ◽  
Difference Making ◽  
Mechanism Research ◽  
The Difference

AbstractThis paper proposes an extended version of the interventionist account for causal inference in the practical context of biological mechanism research. This paper studies the details of biological mechanism researchers’ practices of assessing the evidential legitimacy of experimental data, arguing why quantity and variety are two important criteria for this assessment. Because of the nature of biological mechanism research, the epistemic values of these two criteria result from the independence both between the causation of data generation and the causation in question and between different interventions, not techniques. The former independence ensures that the interventions in the causation in question are not affected by the causation that is responsible for data generation. The latter independence ensures the reliability of the final mechanisms not only in the empirical but also the formal aspects. This paper first explores how the researchers use quantity to check the effectiveness of interventions, where they at the same time determine the validity of the difference-making revealed by the results of interventions. Then, this paper draws a distinction between experimental interventions and experimental techniques, so that the reliability of mechanisms, as supported by the variety of evidence, can be safely ensured in the probabilistic sense. The latter process is where the researchers establish evidence of the mechanisms connecting the events of interest. By using case studies, this paper proposes to use ‘intervention’ as the fruitful connecting point of literature between evidence and mechanisms.

A New Dynamic Wettability-Alteration Model for Oil-Wet Cores During Surfactant-Solution Imbibition

SPE Journal ◽  
2013 ◽  
Vol 18 (05) ◽  
pp. 818-828 ◽  
Author(s):  
M. Hosein Kalaei ◽  
Don W. Green ◽  
G. Paul Willhite
Keyword(s):  
Experimental Data ◽  
Oil Recovery ◽  
History Matching ◽  
Mechanistic Model ◽  
Surfactant Solution ◽  
Experimental Tests ◽  
Quantitative Agreement ◽  
Wettability Alteration ◽  
Porous Rock ◽  
Surfactant Solutions

Summary Wettability modification of solid rocks with surfactants is an important process and has the potential to recover oil from reservoirs. When wettability is altered by use of surfactant solutions, capillary pressure, relative permeabilities, and residual oil saturations change wherever the porous rock is contacted by the surfactant. In this study, a mechanistic model is described in which wettability alteration is simulated by a new empirical correlation of the contact angle with surfactant concentration developed from experimental data. This model was tested against results from experimental tests in which oil was displaced from oil-wet cores by imbibition of surfactant solutions. Quantitative agreement between the simulation results of oil displacement and experimental data from the literature was obtained. Simulation of the imbibition of surfactant solution in laboratory-scale cores with the new model demonstrated that wettability alteration is a dynamic process, which plays a significant role in history matching and prediction of oil recovery from oil-wet porous media. In these simulations, the gravity force was the primary cause of the surfactant-solution invasion of the core that changed the rock wettability toward a less oil-wet state.

Wear of a Tool in Double-Disk Lapping of Silicon Wafers

2010 ◽  
Author(s):  
Adam Barylski ◽  
Mariusz Deja
Keyword(s):  
Experimental Data ◽  
Integrated Circuits ◽  
Tool Wear ◽  
Silicon Wafers ◽  
Silicon Ingot ◽  
Proposed Model ◽  
Tool Wear Prediction ◽  
Simulation Results ◽  
High Degree ◽  
Kinematical Parameters

Silicon wafers are the most widely used substrates for fabricating integrated circuits. A sequence of processes is needed to turn a silicon ingot into silicon wafers. One of the processes is flattening by lapping or by grinding to achieve a high degree of flatness and parallelism of the wafer [1, 2, 3]. Lapping can effectively remove or reduce the waviness induced by preceding operations [2, 4]. The main aim of this paper is to compare the simulation results with lapping experimental data obtained from the Polish producer of silicon wafers, the company Cemat Silicon from Warsaw (www.cematsil.com). Proposed model is going to be implemented by this company for the tool wear prediction. Proposed model can be applied for lapping or grinding with single or double-disc lapping kinematics [5, 6, 7]. Geometrical and kinematical relations with the simulations are presented in the work. Generated results for given workpiece diameter and for different kinematical parameters are studied using models programmed in the Matlab environment.

Effect of Interaction Modeling in AFM-Based Nanomanipulation

2008 ◽  
Author(s):  
Fakhreddine Landolsi ◽  
Fathi H. Ghorbel ◽  
James B. Dabney
Keyword(s):  
Experimental Data ◽  
Numerical Simulations ◽  
Interaction Model ◽  
Collision Process ◽  
Visual Sensing ◽  
Proposed Model ◽  
Interaction Modeling

AFM-based nanomanipulation is very challenging because of the complex mechanics in tip-sample interactions and the limitations in AFM visual sensing capabilities. In the present paper, we investigate the modeling of AFM-based nanomanipulation emphasizing the effects of the relevant interactions at the nanoscale. The major contribution of the present work is the use of a combined DMT-JKR interaction model in order to describe the complete collision process between the AFM tip and the sample. The coupling between the interactions and the friction at the nanoscale is emphasized. The efficacy of the proposed model to reproduce experimental data is demonstrated via numerical simulations.

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