Kinetic modeling is the tool of choice when developing new positron emission tomography (PET) tracers for quantitative functional analysis. Several approaches are widely used to facilitate this process. While all these approaches are inherently different, they are still subject to uncertainty arising from various stages of the modeling process. In this paper we propose a novel approach for deri...

Mathematical modeling and simulation of biochemical reaction networks facilitates our understanding of metabolic and signaling processes. For closed, well-mixed reaction systems, it is straightforward to derive kinetic equations that govern the concentrations of the reactants and products. The usual way of deriving kinetic equations involves application of the principle of conservation of mass ...

We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA-DNA, DNA-RNA, and RNA-RNA base pairing associated wi...

A kinetic model for methyl formate oxidation is generated using our open-source Reaction Mechanism Generator (RMG) software, supplemented with high level quantum calculations and transition state theory (TST). New rate coefficients are calculated for the decomposition pathways of methyl formate, methoxy-formyl (CH3OC ·O), and formyloxy-methyl (C H2OCHO), and hydrogen abstractions from methyl fo...

Most PET kinetic modeling approaches have at their basis a compartmental model that has first-order, constant coefficients. The present article outlines the one-, two-, and three-compartment models used to measure cerebral blood flow, cerebral glucose metabolism, and receptor binding, respectively. The number of compartments of each model is based on specific knowledge of the physiological and/...

Qualitative reasoning is an effective method for intelligent tutoring systems. It can provides causal explanation of behavior that cannot be achieved by numerical simulation. The causal explanation is obtained based on a set of differential equations. If a student doesn’t understand the explanation, we should explain the reason why the equations hold. Qualitative reasoning cannot answer this qu...

SUMMARY Structural kinetic modeling (SKM) enables the analysis of dynamical properties of metabolic networks solely based on topological information and experimental data. Current SKM-based experiments are hampered by the time-intensive process of assigning model parameters and choosing appropriate sampling intervals for Monte-Carlo experiments. We introduce a toolbox for the automatic and effi...

environment contamination by heavy metals is a major issue threatening human health. adsorption is one of the biological processes for removing toxic metals from wastewater. the aim of this study was to determine the rate of lead biosorption from industrial wastewater by spirulina platensis. this laboratory scale experimental study was performed during april 2014 to october 2014 in environmenta...

A prior analysis of turbidimetric data3 in terms of the specific physical and kinetic laws that describe this model led to the conclusion that the rate constants were identical. Such behavior is characteristic of a stochastic (Poisson) process, and if true, may imply the existence of a rate-limiting step common to both “sphering” (formally the A -‘ B reaction) and to the extension of long, fili...