scholarly journals A generalized kinetic model for amine modification of proteins with application to phage display

BioTechniques ◽  
2009 ◽  
Vol 46 (3) ◽  
pp. 175-182 ◽  
Author(s):  
Xiaofang Jin ◽  
Jessica Rose Newton ◽  
Stephen Montgomery-Smith ◽  
George P. Smith
1991 ◽  
Vol 24 (7) ◽  
pp. 1641-1647 ◽  
Author(s):  
Y. Yong Tan ◽  
Gert O. R. Alberda van Ekenstein

2019 ◽  
Vol 20 (19) ◽  
pp. 4911 ◽  
Author(s):  
Xie ◽  
Guo ◽  
Chen

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.


2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Diya'uddeen Basheer Hasan ◽  
Abdul Aziz Abdul Raman ◽  
Wan Mohd Ashri Wan Daud

The mineralisation kinetics of petroleum refinery effluent (PRE) by Fenton oxidation were evaluated. Within the ambit of the experimental data generated, first-order kinetic model (FKM), generalised lumped kinetic model (GLKM), and generalized kinetic model (GKM) were tested. The obtained apparent kinetic rate constants for the initial oxidation step (k2′), their final oxidation step (k1′), and the direct conversion to endproducts step (k3′) were 10.12, 3.78, and 0.24 min−1for GKM; 0.98, 0.98, and nil min−1for GLKM; and nil, nil, and >0.005 min−1for FKM. The findings showed that GKM is superior in estimating the mineralization kinetics.


2013 ◽  
Vol 90 ◽  
pp. 200-212 ◽  
Author(s):  
G. Ipek Yucelen ◽  
Dun-Yen Kang ◽  
Ingeborg Schmidt-Krey ◽  
Haskell W. Beckham ◽  
Sankar Nair

2015 ◽  
Vol 7 (2) ◽  
pp. 245-266 ◽  
Author(s):  
Songze Chen ◽  
Kun Xu ◽  
Qingdong Cai

AbstractThe Ellipsoidal Statistical model (ES-model) and the Shakhov model (Smodel) were constructed to correct the Prandtl number of the original BGK model through the modification of stress and heat flux. With the introduction of a new parameter to combine the ES-model and S-model, a generalized kinetic model can be developed. This new model can give the correct Navier-Stokes equations in the continuum flow regime. Through the adjustment of the new parameter, it provides abundant dynamic effect beyond the ES-model and S-model. Changing the free parameter, the physical performance of the new model has been tested numerically. The unified gas kinetic scheme (UGKS) is employed for the study of the new model. In transition flow regime, many physical problems, i.e., the shock structure and micro-flows, have been studied using the generalized model. With a careful choice of the free parameter, good results can be achieved for most test cases. Due to the property of the Boltzmann collision integral, the new parameter in the generalized kinetic model cannot be fully determined. It depends on the specific problem. Generally speaking, the Smodel predicts more accurate numerical solutions in most test cases presented in this paper than the ES-model, while ES-model performs better in the cases where the flow is mostly driven by temperature gradient, such as a channel flow with large boundary temperature variation at high Knudsen number.


2021 ◽  
Author(s):  
Brandon Jolly ◽  
Chong Liu

Compartmentalization is an attractive approach to enhance catalytic activity by retaining reactive intermediates and mitigating deactivating pathways. Such a concept has been well explored in biochemical and more recently, organometallic catalysis to ensure high reaction turnovers with minimal side reactions. However, a scarcity of theoretical framework towards confined organometallic chemistry impedes a broader utility for the implementation of compartmentalization. Herein, we report a general kinetic model and offer design guidance for a compartmentalized organometallic catalytic cycle. In comparison to a non-compartmentalized catalysis, compartmentalization is quantitatively shown to prevent the unwanted intermediate deactivation, boost the corresponding reaction efficiency (𝛾), and subsequently increase catalytic turnover frequency (𝑇𝑂𝐹). The key parameter in the model is the volumetric diffusive conductance (𝐹 ) that describes catalysts’ diffusion propensity across a compartment’s boundary. Optimal values of 𝐹 for a specific organometallic chemistry are needed to achieve maximal values of 𝛾 and 𝑇𝑂𝐹. Our model suggests a tailored compartment design, including the use of nanomaterials, is needed to suit a specific organometallic catalysis. This work provides justification and design principles for further exploration into compartmentalizing organometallics to enhance catalytic performance.


2021 ◽  
Author(s):  
Di Wu

Ion channels conduct various ions across biological membranes to maintain the membrane potential, to transmit the electrical signals, and to elicit the subsequent cellular responses by the signaling ions. Ion channels differ in their capabilities to select and conduct ions, which can be studied by the patch-clamp recording method that compares the current traces responding to the test voltage elicited at different conditions. In these experiments, the current-voltage curves are usually fitted by a sigmoidal function containing the Boltzmann factor. This equation is quite successful in fitting the experimental data in many cases, but it also fails in several others. Regretfully, some useful information may be lost in these data, which otherwise can reveal the ion-permeation mechanisms. Here we present a generalized kinetic model that captures the essential features of the current-voltage relations and describes the simple mechanism of the ion permeation through different ion channels. We demonstrate that this model is capable to fit various types of the patch-clamp data and explain their ion-permeation mechanisms.


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