scholarly journals A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

2014 ◽  
Vol 141 (21) ◽  
pp. 214108 ◽  
Author(s):  
Michael W. Chevalier ◽  
Hana El-Samad
Keyword(s):  
Master Equation ◽  
Time Dependent ◽  
Biochemical Systems ◽  
Rate Functions ◽  
Moment Approach

scholarly journals Novel domain expansion methods to improve the computational efficiency of the Chemical Master Equation solution for large biological networks

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Rahul Kosarwal ◽  
Don Kulasiri ◽  
Sandhya Samarasinghe
Keyword(s):  
Master Equation ◽  
State Space ◽  
Performance Management ◽  
Numerical Solutions ◽  
De Novo ◽  
Exact Analytical Solution ◽  
Chemical Master Equation ◽  
The State ◽  
Biochemical System ◽  
Biochemical Systems

Abstract Background 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. Most importantly, the exponential growth of the size of the state-space, with respect to the number of different species in the system makes this a challenging assignment. When the biochemical system has a large number of variables, the CME solution becomes intractable. We introduce the intelligent state projection (ISP) method to use in the stochastic analysis of these systems. For any biochemical reaction network, it is important to capture more than one moment: this allows one to describe the system’s dynamic behaviour. ISP is based on a state-space search and the data structure standards of artificial intelligence (AI). It can be used to explore and update the states of a biochemical system. To support the expansion in ISP, we also develop a Bayesian likelihood node projection (BLNP) function to predict the likelihood of the states. Results To demonstrate the acceptability and effectiveness of our method, we apply the ISP method to several biological models discussed in prior literature. The results of our computational experiments reveal that the ISP method is effective both in terms of the speed and accuracy of the expansion, and the accuracy of the solution. This method also provides a better understanding of the state-space of the system in terms of blueprint patterns. Conclusions The ISP is the de-novo method which addresses both accuracy and performance problems for CME solutions. It systematically expands the projection space based on predefined inputs. This ensures accuracy in the approximation and an exact analytical solution for the time of interest. The ISP was more effective both in predicting the behavior of the state-space of the system and in performance management, which is a vital step towards modeling large biochemical systems.

scholarly journals Stepwise introduction of model complexity in a generalized master equation approach to time-dependent transport

2012 ◽  
Vol 61 (2-3) ◽  
pp. 305-316 ◽  
Author(s):  
V. Gudmundsson ◽  
O. Jonasson ◽  
Th. Arnold ◽  
C-S. Tang ◽  
H.-S. Goan ◽  
...  
Keyword(s):  
Master Equation ◽  
Time Dependent ◽  
Model Complexity ◽  
Equation Approach ◽  
Master Equation Approach ◽  
Dependent Transport ◽  
Generalized Master Equation

scholarly journals Equivalence between Redfield- and master-equation approaches for a time-dependent quantum system and coherence control

2011 ◽  
Vol 83 (6) ◽  
Author(s):  
D. O. Soares-Pinto ◽  
M. H. Y. Moussa ◽  
J. Maziero ◽  
E. R. deAzevedo ◽  
T. J. Bonagamba ◽  
...  
Keyword(s):  
Master Equation ◽  
Quantum System ◽  
Time Dependent

scholarly journals Time-dependent Markovian quantum master equation

2018 ◽  
Vol 98 (5) ◽  
Author(s):  
Roie Dann ◽  
Amikam Levy ◽  
Ronnie Kosloff
Keyword(s):  
Master Equation ◽  
Time Dependent ◽  
Quantum Master Equation

scholarly journals Time-dependent magnetotransport in semiconductor nanostructures via the generalized master equation

2011 ◽  
Vol 182 (1) ◽  
pp. 46-48
Author(s):  
Vidar Gudmundsson ◽  
Chi-Shung Tang ◽  
Cosmin Mihai Gainar ◽  
Valeriu Moldoveanu ◽  
Andrei Manolescu
Keyword(s):  
Master Equation ◽  
Semiconductor Nanostructures ◽  
Time Dependent ◽  
Generalized Master Equation
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