scholarly journals Constraining kinetics of metastable olivine in the Marianas slab from seismic observations and dynamic models

2012 ◽  
Vol 526-529 ◽  
pp. 48-55 ◽  
Author(s):  
Javier Quinteros ◽  
Stephan V. Sobolev
2021 ◽  
Vol 118 (49) ◽  
pp. e2111477118
Author(s):  
Ruian Ke ◽  
Carolin Zitzmann ◽  
David D. Ho ◽  
Ruy M. Ribeiro ◽  
Alan S. Perelson

The within-host viral kinetics of SARS-CoV-2 infection and how they relate to a person’s infectiousness are not well understood. This limits our ability to quantify the impact of interventions on viral transmission. Here, we develop viral dynamic models of SARS-CoV-2 infection and fit them to data to estimate key within-host parameters such as the infected cell half-life and the within-host reproductive number. We then develop a model linking viral load (VL) to infectiousness and show a person’s infectiousness increases sublinearly with VL and that the logarithm of the VL in the upper respiratory tract is a better surrogate of infectiousness than the VL itself. Using data on VL and the predicted infectiousness, we further incorporated data on antigen and RT-PCR tests and compared their usefulness in detecting infection and preventing transmission. We found that RT-PCR tests perform better than antigen tests assuming equal testing frequency; however, more frequent antigen testing may perform equally well with RT-PCR tests at a lower cost but with many more false-negative tests. Overall, our models provide a quantitative framework for inferring the impact of therapeutics and vaccines that lower VL on the infectiousness of individuals and for evaluating rapid testing strategies.


2012 ◽  
Vol 2012 ◽  
pp. 1-34 ◽  
Author(s):  
Vilda Purutçuoğlu ◽  
Ernst Wit

The MAPK/ERK pathway is a major signal transduction system which regulates many fundamental cellular processes including the growth control and the cell death. As a result of these roles, it has a crucial importance in cancer as well as normal developmental processes. Therefore, it has been intensively studied resulting in a wealth of knowledge about its activation. It is also well documented that the activation kinetics of the pathway is crucial to determine the nature of the biological response. However, while individual biochemical steps are well characterized, it is still difficult to predict or even understand how the activation kinetics works. The aim of this paper is to estimate the stochastic rate constants of the MAPK/ERK network dynamics. Accordingly, taking a Bayesian approach, we combined underlying qualitative biological knowledge in several competing dynamic models via sets of quasireactions and estimated the stochastic rate constants of these reactions. Comparing the resulting estimates via the BIC and DIC criteria, we chose a biological model which includes EGFR degradation—Raf-MEK-ERK cascade without the involvement of RKIPs.


Author(s):  
Ruian Ke ◽  
Carolin Zitzmann ◽  
Ruy M. Ribeiro ◽  
Alan S. Perelson

SARS-CoV-2 is a human pathogen that causes infection in both the upper respiratory tract (URT) and the lower respiratory tract (LRT). The viral kinetics of SARS-CoV-2 infection and how they relate to infectiousness and disease progression are not well understood. Here, we develop data-driven viral dynamic models of SARS-CoV-2 infection in both the URT and LRT. We fit the models to viral load data from patients with likely infection dates known, we estimated that infected individuals with a longer incubation period had lower rates of viral growth, took longer to reach peak viremia in the URT, and had higher chances of presymptomatic transmission. We then developed a model linking viral load to infectiousness. We found that to explain the substantial fraction of transmissions occurring presymptomatically, the infectiousness of a person should depend on a saturating function of the viral load, making the logarithm of the URT viral load a better surrogate of infectiousness than the viral load itself. Comparing the roles of target-cell limitation, the innate immune response, proliferation of target cells and spatial infection in the LRT, we found that spatial dissemination in the lungs is likely to be an important process in sustaining the prolonged high viral loads. Overall, our models provide a quantitative framework for predicting how SARS-CoV-2 within-host dynamics determine infectiousness and represent a step towards quantifying how viral load dynamics and the immune responses determine disease severity.


2022 ◽  
Vol 18 (1) ◽  
pp. e1009610
Author(s):  
Arno Strouwen ◽  
Bart M. Nicolaï ◽  
Peter Goos

Dynamic models based on non-linear differential equations are increasingly being used in many biological applications. Highly informative dynamic experiments are valuable for the identification of these dynamic models. The storage of fresh fruit and vegetables is one such application where dynamic experimentation is gaining momentum. In this paper, we construct optimal O2 and CO2 gas input profiles to estimate the respiration and fermentation kinetics of pear fruit. The optimal input profiles, however, depend on the true values of the respiration and fermentation parameters. Locally optimal design of input profiles, which uses a single initial guess for the parameters, is the traditional method to deal with this issue. This method, however, is very sensitive to the initial values selected for the model parameters. Therefore, we present a robust experimental design approach that can handle uncertainty on the model parameters.


2020 ◽  
Author(s):  
Cory Simon

<div>The classic Susceptible-Infectious-Recovered (SIR) mathematical model of the dynamics of infectious disease transmission resembles a dynamic model of a batch reactor carrying out an autocatalytic reaction with catalyst deactivation. This analogy between disease transmission and chemical reactions allows chemists and chemical engineers to peer into dynamic models of infectious disease transmission used to forecast epidemics and assess mitigation strategies. Moreover, analysis of SIR model dynamics gives insights into the kinetics of autocatalytic reactions.</div>


2021 ◽  
Author(s):  
Ruian Ke ◽  
Carolin Zitzmann ◽  
David D Ho ◽  
Ruy Ribeiro ◽  
Alan S Perelson

The within-host viral kinetics of SARS-CoV-2 infection and how they relate to a person's infectiousness are not well understood. This limits our ability to quantify the impact of interventions on viral transmission. Here, we develop data-driven viral dynamic models of SARS-CoV-2 infection and estimate key within-host parameters such as the infected cell half-life and the within-host reproductive number. We then develop a model linking viral load (VL) to infectiousness, showing that infectiousness increases sub-linearly with VL. We show that the logarithm of the VL in the upper respiratory tract (URT) is a better surrogate of infectiousness than the VL itself. Using data on VL and the predicted infectiousness, we further incorporated data on antigen and reverse transcription polymerase chain reaction (RT-PCR) tests and compared their usefulness in detecting infection and preventing transmission. We found that RT-PCR tests perform better than antigen tests assuming equal testing frequency; however, more frequent antigen testing may perform equally well with RT-PCR tests at a lower cost, but with many more false-negative tests. Overall, our models provide a quantitative framework for inferring the impact of therapeutics and vaccines that lower VL on the infectiousness of individuals and for evaluating rapid testing strategies.


2006 ◽  
Vol 80 (15) ◽  
pp. 7590-7599 ◽  
Author(s):  
Prasith Baccam ◽  
Catherine Beauchemin ◽  
Catherine A. Macken ◽  
Frederick G. Hayden ◽  
Alan S. Perelson

ABSTRACT Currently, little is known about the viral kinetics of influenza A during infection within an individual. We utilize a series of mathematical models of increasing complexity, which incorporate target cell limitation and the innate interferon response, to examine influenza A virus kinetics in the upper respiratory tracts of experimentally infected adults. The models were fit to data from an experimental H1N1 influenza A/Hong Kong/123/77 infection and suggest that it is important to include the eclipse phase of the viral life cycle in viral dynamic models. Doing so, we estimate that after a delay of ∼6 h, infected cells begin producing influenza virus and continue to do so for ∼5 h. The average lifetime of infected cells is ∼11 h, and the half-life of free infectious virus is ∼3 h. We calculated the basic reproductive number, R 0, which indicated that a single infected cell could produce ∼22 new productive infections. This suggests that antiviral treatments have a large hurdle to overcome in moderating symptoms and limiting infectiousness and that treatment has to be initiated as early as possible. For about 50% of patients, the curve of viral titer versus time has two peaks. This bimodal behavior can be explained by incorporating the antiviral effects of interferon into the model. Our model also compared well to an additional data set on viral titer after experimental infection and treatment with the neuraminidase inhibitor zanamivir, which suggests that such models may prove useful in estimating the efficacies of different antiviral therapies for influenza A infection.


1988 ◽  
Vol 41 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Mohamed Samir Hefzy ◽  
Edward S. Grood

This paper is a review of static and dynamic models of the human knee joint. Both phenomenological and anatomically based models are discussed. The phenomenological models can be classified into two groups: first, models which consider the human knee to be a simple hinge joint and, second, rheological models. The simple hinge models have generally been used in larger models developed to predict human body dynamics during gait activities. The rheological models, which describe the knee as an equivalent viscoelastic hinge, have been used to describe the response of the knee joint during dynamic loading conditions. Anatomically based models have been used to predict the kinematics and kinetics of the knee and its structural components. The majority of kinetic models have treated static and quasistatic equilibrium conditions, and only a few have addressed nonequilibrium dynamic loading. In reviewing the static and quasistatic models, we have divided them into four groups. First, models developed to determine the forces in the muscles and the ligaments at the knee joint during various activities, second, models developed to determine the forces in the ligaments as a function of joint position, third, models used to determine the contact stresses between the femur and the tibia, and, fourth, more comprehensive models developed to study the stiffness and load–displacement characteristics of the knee joint which include both ligamentous structures and the geometric constraints of the knee. In our survey, we found few models of the patello-femoral joint. A more complete model of the human knee joint describing the interactions between the tibia, femur, patella, and fibula still needs to be developed. On the other hand, the geometric and mechanical properties of a single real knee, required to validate any model are not presently available.


Author(s):  
J. F. DeNatale ◽  
D. G. Howitt

The electron irradiation of silicate glasses containing metal cations produces various types of phase separation and decomposition which includes oxygen bubble formation at intermediate temperatures figure I. The kinetics of bubble formation are too rapid to be accounted for by oxygen diffusion but the behavior is consistent with a cation diffusion mechanism if the amount of oxygen in the bubble is not significantly different from that in the same volume of silicate glass. The formation of oxygen bubbles is often accompanied by precipitation of crystalline phases and/or amorphous phase decomposition in the regions between the bubbles and the detection of differences in oxygen concentration between the bubble and matrix by electron energy loss spectroscopy cannot be discerned (figure 2) even when the bubble occupies the majority of the foil depth.The oxygen bubbles are stable, even in the thin foils, months after irradiation and if van der Waals behavior of the interior gas is assumed an oxygen pressure of about 4000 atmospheres must be sustained for a 100 bubble if the surface tension with the glass matrix is to balance against it at intermediate temperatures.


Author(s):  
R. J. Lauf

Fuel particles for the High-Temperature Gas-Cooled Reactor (HTGR) contain a layer of pyrolytic silicon carbide to act as a miniature pressure vessel and primary fission product barrier. Optimization of the SiC with respect to fuel performance involves four areas of study: (a) characterization of as-deposited SiC coatings; (b) thermodynamics and kinetics of chemical reactions between SiC and fission products; (c) irradiation behavior of SiC in the absence of fission products; and (d) combined effects of irradiation and fission products. This paper reports the behavior of SiC deposited on inert microspheres and irradiated to fast neutron fluences typical of HTGR fuel at end-of-life.


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