scholarly journals Combining Kinetic and Constraint-Based Modelling to Better Understand Metabolism Dynamics

Processes ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1701
Author(s):  
Cecile Moulin ◽  
Laurent Tournier ◽  
Sabine Peres

To understand the phenotypic capabilities of organisms, it is useful to characterise cellular metabolism through the analysis of its pathways. Dynamic mathematical modelling of metabolic networks is of high interest as it provides the time evolution of the metabolic components. However, it also has limitations, such as the necessary mechanistic details and kinetic parameters are not always available. On the other hand, large metabolic networks exhibit a complex topological structure which can be studied rather efficiently in their stationary regime by constraint-based methods. These methods produce useful predictions on pathway operations. In this review, we present both modelling techniques and we show how they bring complementary views of metabolism. In particular, we show on a simple example how both approaches can be used in conjunction to shed some light on the dynamics of metabolic networks.

2018 ◽  
Vol 14 (1) ◽  
pp. 4-10
Author(s):  
Fang Jing ◽  
Shao-Wu Zhang ◽  
Shihua Zhang

Background:Biological network alignment has been widely studied in the context of protein-protein interaction (PPI) networks, metabolic networks and others in bioinformatics. The topological structure of networks and genomic sequence are generally used by existing methods for achieving this task.Objective and Method:Here we briefly survey the methods generally used for this task and introduce a variant with incorporation of functional annotations based on similarity in Gene Ontology (GO). Making full use of GO information is beneficial to provide insights into precise biological network alignment.Results and Conclusion:We analyze the effect of incorporation of GO information to network alignment. Finally, we make a brief summary and discuss future directions about this topic.


1991 ◽  
Vol 69 (7) ◽  
pp. 433-441 ◽  
Author(s):  
Jack Ferrier ◽  
Angela Kesthely ◽  
Eva Lagan ◽  
Conrad Richter

A model for cytosolic Ca2+ spikes is presented that incorporates continual influx of Ca2+, uptake into an intracellular compartment, and Ca2+-induced Ca2+ release from the compartment. Two versions are used. In one, release is controlled by explicit thresholds, while in the other, release is a continuous function of cytosolic and compartmental [Ca2+]. Some model predictions are as follows. Starting with low Ca2+ influx and no spikes: (1) induction of spiking when Ca2+ influx is increased. Starting with spikes: (2) increase in magnitude and decrease in frequency when influx is reduced; (3) inhibition of spiking if influx is greatly reduced; (4) decrease in the root-mean-square value when influx is increased; and (5) elimination of spiking if influx is greatly increased. Since there is good evidence that hyperpolarizing spikes reflect cytosolic Ca2+ spikes, we used electrophysiological measurements to test the model. Each model prediction was confirmed by experiments in which Ca2+ influx was manipulated. However, the original spike activity tended to return within 5–30 min, indicating a cellular resetting process.Key words: calcium, electrophysiology, mathematical modelling.


2019 ◽  
pp. 15-31
Author(s):  
Zuzanna Benincasa

For persons who wanted to invest their resources in international commerce, the necessity of a sea voyage significantly increased the risk connected to this venture. Thus the contracts, which took into account the risk related to navigation, constituted under Roman law a special category of contracts, as they modified standard contracts such as a loan or a partnership contract. In the contract of maritime loan the fact that the creditor assumed the risk of losing money in case the condition si salva navis pervenerit was not fulfilled and in exchange could claim high interest to compensate him for such risk transforms this contract into an instrument used for the joint gain of profits. The classical scheme, in which all partners were obliged to share both profits and losses was modified by a partnership contract, in which a partner whose contribution involved exclusively undertaking risky sea voyages was exempt from bearing losses. This pactum made it possible to treat pecuniary contributions and in-kind contributions as equivalent in value. This prevented a situation in which the partner whose sole contribution involved services, in spite of due performance of his obligations, would be liable to repay a part of the loss to the partner who brought capital, if the activity of the partnership resulted in the loss. A typical example, referred to by jurists, of a situation in which services performed by a partner justified discharging him from participating in the loss, was the case in which one of the socii financed the purchase of goods to be subsequently sold with profit in another port, while the other one carried out this venture risking his life during the sea voyage. Therefore, undoubtedly, services entailing a dangerous sea voyage constituted a good example of a partnership, in which the value of a contribution of opera was even greater than the value of the capital invested, and this justified releasing one of the partners from participation in the loss. Therefore, the risk related to navigation, and more specifically the willingness to assume it, starts to be considered as having a certain economic and market value. This value constitutes a special periculi pretium, that is to be taken into consideration in a contract relationship. The acknowledgement by Roman jurists that the willingness to assume the risk connected with certain types of business constituted an economic value, means that the importance of such factors as the partner’s efficiency, resourcefulness, or willingness to embark on a risky activity (in most cases crucial for a success of an enterprise) – was fully appreciated.


2021 ◽  
Author(s):  
Sevtap Tırınk ◽  
Alper Nuhoğlu ◽  
Sinan Kul

Abstract This study encompasses investigation of treatment of pistachio processing industry wastewaters in a batch reactor under aerobic conditions, calculation of kinetic parameters and comparison of different inhibition models. The mixed microorganism culture used in the study was adapted to pistachio processing industry wastewaters for nearly one month and then concentrations from 50-1000 mg L− 1 of pistachio processing industry wastewaters were added to the medium and treatment was investigated in batch experiments. The Andrews, Han-Levenspiel, Luong and Aiba biokinetic equations were chosen for the correlations between the concentration of pistachio processing industry wastewaters and specific growth rates, and the kinetic parameters in these biokinetic equations were calculated. The µmax, Ks and Ki parameters, included in the Aiba biokinetic equation providing best fit among the other equations, had values calculated as 0.25 h− 1, 19 mg L− 1, and 516 mg L− 1, respectively.


2017 ◽  
Vol 70 (4) ◽  
pp. 387-400 ◽  
Author(s):  
Mansoor H Alshehri ◽  
James M Hill

Summary Deoxyribonucleic acid (DNA) and carbon nanotubes (CNTs) constitute hybrid materials with the potential to provide new components with many applications in various technology areas, such as molecular electronics, field devices and medical applications. Using classical applied mathematical modelling, we investigate the suction force experienced by a double-stranded DNA (dsDNA) molecule which is assumed to be located on the axis near an open end of a semi-infinite single-walled CNT. We employ both the 6-12 Lennard-Jones potential and the continuum approximation, which assumes that a discrete atomic structure can be replaced by a surface with constant average atomic density. While most research in the area is dominated by molecular dynamics simulations, here we use elementary mechanical principles and classical applied mathematical modelling techniques to formulate explicit analytical criteria and ideal model behaviour. We observe that the suction behaviour depends on the radius of the CNT, and we predict that it is less likely for a dsDNA molecule to be accepted into the CNT when the value of the tube radius is ${<}12.9$ Å. The dsDNA molecule will be accepted into the CNT for radii lager than 13 Å, and we show that the optimal single-walled CNT necessary to fully enclose the DNA molecule has a radius of 13.56 Å, which approximately corresponds to the chiral vector numbers (20, 20). This means that the ideal single-walled CNT to be used to encapsulate a dsDNA is (20, 20) which has the required radius of 13.56 Å.


Author(s):  
Theodoros G Kostis

The radar equation is the fundamental mathematical model of the basic function of a radar system. Moreover, there are many versions of the radar equation, which correspond to particular radar operations, like low pulse repetition frequency (PRF), high PRF, or surveillance mode. In many cases, all these expressions of the radar equation exist in their combined forms, giving little information to the actual physics and signal geometry between the radar and the target involved in the process. In this case study, we divide the radar equation into its major steps and present a descriptive mathematical modelling of the radar and other related equations utilizing the free space loss and target gain concepts to simulate the effect of a white noise jammer on an adversary radar. We believe that this work will be particularly beneficial to instructors of radar courses and to radar simulation engineers because of its analytical block approach to the main equations related to the fields of radar and electronic warfare. Finally, this work falls under the field of predictive dynamics for radar systems using mathematical modelling techniques.


2020 ◽  
Author(s):  
Peter Krizan ◽  
Michal Kozubek ◽  
Jan Lastovicka

Abstract. Ozone is a very important trace gas in the stratosphere and thus we need to know its time evolution over the globe. The ground based measurements are rare, especially in the Southern Hemisphere. Satellite ozone data have broader coverage, but they are not available from everywhere. On the other hand, the reanalyse data have regular spatial and temporal structure, which is very good for trend analyses. But there are discontinuities in these data.These discontinuities may influence the result of trend studies. The aim of this paper is to detect the discontinuity occurrence (DO) in the following reanalyses: MERRA-2, ERA-5 and JRA-55 with the help of the Pettitt homogeneity test at all common layers above 500 hPa. The discontinuities are sorted according to their size to the significant and the insignificant ones; the former can affect the ozone trend studies. It was shown that DO for the significant discontinuities is the smallest in JRA-55. In the upper model layers, the discontinuity occurrence is the highest. The other area of high DO is the troposphere.


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