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Biochemical reaction networks
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Biological processes such as metabolism, signaling, and macromolecular synthesis can be modeled as large networks of biochemical reactions. Large and comprehensive networks, like integrated networks that represent metabolism and macromolecular synthesis, are inherently multiscale because reaction rates can vary over many orders of magnitude.
6p
viwyoming2711
16-12-2020
17
0
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Stochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex biochemical networks. Typically, such mathematical models involve networks of coupled jump stochastic processes with a large number of parameters that need to be suitably calibrated against experimental data.
19p
viwyoming2711
16-12-2020
11
2
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Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized.
13p
vikentucky2711
26-11-2020
12
1
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Numerical solutions of the chemical master equation (CME) are important for understanding the stochasticity of biochemical systems. However, solving CMEs is a formidable task. This task is complicated due to the nonlinear nature of the reactions and the size of the networks which result in different realizations.
42p
vikentucky2711
24-11-2020
8
1
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Abnormalities in glycan biosynthesis have been conclusively related to various diseases, whereas the complexity of the glycosylation process has impeded the quantitative analysis of biochemical experimental data for the identification of glycoforms contributing to disease.
8p
vioklahoma2711
19-11-2020
15
1
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Metabolic pathway diagrams are a classical way of visualizing a linked cascade of biochemical reactions. However, to understand some biochemical situations, viewing a single pathway is insufficient, whereas viewing the entire metabolic network results in information overload.
10p
vioklahoma2711
19-11-2020
4
0
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We introduce the basic concepts and develop a theory for nonequilibrium steady-state biochemical systems applicable to analyzing large-scale complex isothermal reaction networks. In terms of the stoichiometric matrix, we dem-onstrate both Kirchhoff’s flux lawR‘J‘ ¼0 over a bio-chemical species, and potential law R‘l‘ ¼0overa reaction loop. They reflect mass and energy conservation, respectively.
7p
tumor12
20-04-2013
44
2
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Modelling of biochemical systems usually focuses on certain pathways, while the concentrations of so-called external metabolites are considered fixed. This approximation ignores feedback loops mediated by the environ-ment, that is, via external metabolites and reactions. To achieve a more realistic, dynamic description that is still numerically efficient, we propose a new methodology: the basic idea is to describe the environment by a lin-ear effective model of adjustable dimensionality.
10p
fptmusic
11-04-2013
30
1
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Our laboratory is interested in the biochemical and biophysical basis of cell structure. The structure of a cell is determined primarily by its cytoskeleton, which serves as a scaffold to sup-port the plasma membrane, and as a network of tracks along which motor proteins transport sub cellular structures. Our research is therefore focused on the mechanics of the cytoskele-ton, with a particular emphasis on microtubules and microtu-bule-based motors.
17p
fptmusic
11-04-2013
51
2
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In view of the increasing number of reported concentration oscillations in living cells, methods are needed that can identify the causes of these oscillations. These causes always derive from the influences that concentrations have on reaction rates. The influences reach over many molecular reaction steps and are defined by the detailed molecular topology of the network. So-called autoinfluence paths, which quantify the influence of one molecular species upon itself through a particular path through the network, can have positive or negative values....
11p
awards
05-04-2013
44
4
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Kinetic modelling of complex metabolic networks – a central goal of com-putational systems biology – is currently hampered by the lack of reliable rate equations for the majority of the underlying biochemical reactions and membrane transporters.
15p
vinaphone15
27-02-2013
42
1
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A global research community of scientists is teasing out the biochemical mechanisms that regulate normal cellular physiology in a variety of organisms. Much of current research aims to understand the network of molecular reactions that regulate cellular homeostasis, and to learn what allows cells to sense stress and activate appropriate biochemical responses.
210p
ktct_1669
09-05-2012
129
16
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