scholarly journals Direct immunoassays and their performance – theoretical modelling of the effects of antibody orientation and associated kinetics

2018 ◽  
Vol 10 (10) ◽  
pp. 598-604 ◽  
Author(s):  
Dana Mackey ◽  
Eilís Kelly ◽  
Robert Nooney ◽  
Richard O'Kennedy

Mathematical and computational modelling are used to quantify immunoassay signals for various immobilized antibody orientations, antigen sizes and kinetic parameters, in order to determine optimal surface coverage.

2021 ◽  
Author(s):  
Shuvodeep De

The manufacturing of interconnects and the packaging of integrated circuits are achieved with electrodeposition of copper or other metals. In order to increase the rate of deposition, especially for the large features in packaging, forced convection is provided with certain agitation mechanisms. Although this reduces deposition time, it leads to non-uniform mass transport within each feature and between different features. Special organic additives are used in the solution during the process in order to tune the nucleation and growth of metal, as well as to modify the deposition rate and improve the uniformity. A mathematical model to describe the behavior of organic additives in conjugation with fluid flow and features of various geometry and dimensions is very much desired to facilitate chemistry and process development. In order to achieve this, the physiochemical kinetics of additive and their influence on the Cu deposition rate need to be described precisely. This presentation focuses on a method to extract the kinetic parameters describing the combined effect of multiple additives during copper deposition using rotating disk electrode (RDE). The one-dimensional steady state convection-diffusion equation for each of the chemical species including copper is solved by a semi-analytical method for a range of potentials. The boundary conditions of these differential equations are coupled on the surface of the RDE through the surface coverage of the absorbed species. The steady state of surface coverage of the species represents a dynamic equilibrium of three key processes i.e., adsorption, desorption, and consumption (incorporation). When equilibrium is achieved, the net rate of adsorption and desorption becomes equal to the rate of consumption. At each value of potential, the surface coverage of the additives is solved. At first, the solution is obtained with only one species known as suppressor and it was found that in a specific range of voltage and kinetic parameter multiple solutions of the surface coverage exist at same applied potential. This mathematically explains the S-shaped negative differential resistance (NDR) feature in experimental Cyclic Voltammogram (CV) curves. Figure 1 shows three such experimental S-shaped curves for different concentration of suppressors. The NDR region obtained in the theoretical CV curve is sensitive to the kinetic parameters of the additives. It is possible to match the theoretical and the experimental CV curves by optimizing the kinetic parameters. Determination of the kinetic parameters by particle swarm optimization using experimental data for multiple additive concentration will be discussed in detail in this talk.


2019 ◽  
Vol 72 (8) ◽  
pp. 574 ◽  
Author(s):  
Nevena Todorova ◽  
Irene Yarovsky

Molecular level insight into the interplay between protein sequence, structure, and conformational dynamics is crucial for the comprehensive understanding of protein folding, misfolding, and aggregation phenomena that are pertinent to the formation of amyloid fibrils implicated in several degenerative diseases. Computational modelling provides insight into protein behaviour at spatial and temporal resolution still largely outside the reach of experiments. Herein we present an account of our theoretical modelling research conducted in collaboration with several experimental groups where we explored the effects of local environment on the structure and aggregation propensity of several types of amyloidogenic peptides and proteins, including apolipoprotein C-II, insulin, amylin, and amyloid-β using a variety of computational approaches.


2004 ◽  
Vol 1 (2) ◽  
pp. 107-114 ◽  
Author(s):  
Semahat S. Demir

Five decades of histological, electrophysiological, pharmacological and biochemical investigations exist, but relatively little is known regarding the ionic mechanisms underlying the action potential variations in the ventricle associated with healthy and disease conditions. The computational modelling in murine ventricular myocytes can complement our knowledge of the experimental data and provide us with more quantitative descriptions in understanding different conditions related to normal and disease conditions. This paper initially reviews the theoretical modelling for cardiac ventricular action potentials of various species and the related experimental work. It then focuses on the progress of computational modelling of cardiac ventricular cells for normal, diabetic and spontaneously hypertensive rats. Also presented is the recent modelling efforts of the action potential in mouse ventricular cells. The computational insights gained into the ionic mechanisms in rodents will enhance our understanding of the heart and provide us with new knowledge for future studies to treat cardiac diseases in children and adults.


2019 ◽  
Vol 1 (2) ◽  
pp. 30-37
Author(s):  
Diah Riski Gusti

Surface coverage and corrosion rate of taro tuber methanol extract on mild steel in dilute 0.5 M sulfuric acid solution were studied through weight loss method, FT-IR spectroscopy and SEM.The result obtained in 0.5 M sulfuric acid solution for 72 hours with optimal surface coveragewas 0.86. The corrosion ratewas found to be decreased and surface coveragewas increased with the increasing concentration of taro tuber methanol extract which was added. The results showed that taro tuber methanol extract was a good corrosion inhibitor.


2020 ◽  
Author(s):  
Jonathan R. Bowles ◽  
Caroline Hoppe ◽  
Hilary L. Ashe ◽  
Magnus Rattray

AbstractMotivationThe MS2-McP (MS2 coat protein) live imaging system allows for visualisation of transcription dynamics through the introduction of hairpin stem-loop sequences into a gene. A fluorescent signal at the site of nascent transcription in the nucleus quantifies mRNA production. computational modelling can be used to infer the promoter states along with the kinetic parameters governing transcription, such as promoter switching frequency and polymerase loading rate. However, modelling of the fluorescent trace presents a challenge due its persistence; the observed fluorescence at a given time point depends on both current and previous promoter states. A memory-adjusted Hidden Markov Model (mHMM) was recently introduced to allow inference of promoter activity from MS2-McP data. However, the computational time for inference scales exponentially with gene length and the mHMM is therefore not currently practical for application to many eukaryotic genes.ResultsWe present a scalable implementation of the mHMM for fast inference of promoter activity and transcriptional kinetic parameters. This new method can model genes of arbitrary length through the use of a time-adaptive truncated compound state space. The truncated state space provides a good approximation to the full state space by retaining the most likely set of states at each time during the forward pass of the algorithm. Testing on MS2-MCP fluorescent data collected from early Drosophila melanogaster embryos indicates that the method provides accurate inference of kinetic parameters within a computationally feasible timeframe. The inferred promoter traces generated by the model can also be used to infer single-cell transcriptional parameters.AvailabilityPython implementation available at https://github.com/ManchesterBioinference/burstInfer, along with code to reproduce the examples presented here.


2018 ◽  
Vol 20 (39) ◽  
pp. 25314-25323 ◽  
Author(s):  
Juan D. Gonzalez ◽  
Kambiz Shojaee ◽  
Brian S. Haynes ◽  
Alejandro Montoya

This study reveals the kinetic parameters of NO, N2and N2O formation on Pt(111) as a function of surface coverage.


1994 ◽  
Vol 144 ◽  
pp. 1-9
Author(s):  
A. H. Gabriel

The development of the physics of the solar atmosphere during the last 50 years has been greatly influenced by the increasing capability of observations made from space. Access to images and spectra of the hotter plasma in the UV, XUV and X-ray regions provided a major advance over the few coronal forbidden lines seen in the visible and enabled the cooler chromospheric and photospheric plasma to be seen in its proper perspective, as part of a total system. In this way space observations have stimulated new and important advances, not only in space but also in ground-based observations and theoretical modelling, so that today we find a well-balanced harmony between the three techniques.


Sign in / Sign up

Export Citation Format

Share Document