Sensitivity Estimation and Inverse Problems in Spatial Stochastic Models of Chemical Kinetics

Sensitivity estimation and inverse problems in spatial stochastic models of chemical kinetics

[1]  John A. Nelder,et al.  A Simplex Method for Function Minimization , 1965, Comput. J..

[2]  M. Petric,et al.  SPORADIC CASES OF HAEMOLYTIC-URAEMIC SYNDROME ASSOCIATED WITH FAECAL CYTOTOXIN AND CYTOTOXIN-PRODUCING ESCHERICHIA COLI IN STOOLS , 1983, The Lancet.

[3]  W. Cray,et al.  Experimental infection of calves and adult cattle with Escherichia coli O157:H7 , 1995, Applied and environmental microbiology.

[4]  Muruhan Rathinam,et al.  Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks. , 2010, The Journal of chemical physics.

[5]  John V. Goodman Auditing magnetic-tape systems , 1964, Comput. J..

[6]  Andreas Hellander,et al.  URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries , 2012, BMC Systems Biology.

[7]  Andreas Hellander,et al.  Simulation of Stochastic Reaction-Diffusion Processes on Unstructured Meshes , 2008, SIAM J. Sci. Comput..

[8]  P. Holme,et al.  Predicting and controlling infectious disease epidemics using temporal networks , 2013, F1000prime reports.

[9]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[10]  P. Rousseeuw,et al.  Wiley Series in Probability and Mathematical Statistics , 2005 .

[11]  T. Besser,et al.  The control of VTEC in the animal reservoir. , 2001, International journal of food microbiology.

[12]  Alejandro Duran,et al.  Ompss: a Proposal for Programming Heterogeneous Multi-Core Architectures , 2011, Parallel Process. Lett..

[13]  W. O. Kermack,et al.  A contribution to the mathematical theory of epidemics , 1927 .

[14]  Martin Tillenius,et al.  SuperGlue: A Shared Memory Framework Using Data Versioning for Dependency-Aware Task-Based Parallelization , 2015, SIAM J. Sci. Comput..

[15]  Raúl Sánchez,et al.  Event-based parareal: A data-flow based implementation of parareal , 2012, J. Comput. Phys..

[16]  Luis F. Gordillo,et al.  Stochastic Epidemic Modeling , 2009 .

[17]  S. Ethier,et al.  Markov Processes: Characterization and Convergence , 2005 .

[18]  Konstantin Andreev,et al.  Balanced Graph Partitioning , 2004, SPAA '04.

[19]  A. Hill,et al.  The North American Animal Disease Spread Model: a simulation model to assist decision making in evaluating animal disease incursions. , 2007, Preventive veterinary medicine.

[20]  Dale D. Hancock,et al.  Comparison of Cultures from Rectoanal-Junction Mucosal Swabs and Feces for Detection of Escherichia coli O157 in Dairy Heifers , 2006, Applied and Environmental Microbiology.

[21]  Robert Hooke,et al.  `` Direct Search'' Solution of Numerical and Statistical Problems , 1961, JACM.

[22]  Mark D. F. Shirley,et al.  The impacts of network topology on disease spread , 2005 .

[23]  Michael A. Gibson,et al.  Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .

[24]  David R. Jefferson,et al.  Virtual time , 1985, ICPP.

[25]  Richard M. Fujimoto,et al.  Parallel and Distribution Simulation Systems , 1999 .

[26]  R. M. Fujimoto,et al.  Parallel discrete event simulation , 1989, WSC '89.

[27]  D. Applebaum Lévy Processes and Stochastic Calculus: Preface , 2009 .

[28]  Stefan Engblom,et al.  On the Stability of Stochastic Jump Kinetics , 2012, 1202.3892.

[29]  M. Petric,et al.  ESCHERICHIA COLI CYTOTOXIN, HAEMOLYTIC-URAEMIC SYNDROME, AND HAEMORRHAGIC COLITIS , 1983, The Lancet.

[30]  Jack J. Dongarra,et al.  A novel hybrid CPU–GPU generalized eigensolver for electronic structure calculations based on fine-grained memory aware tasks , 2014, Int. J. High Perform. Comput. Appl..

[31]  Cédric Augonnet,et al.  StarPU: a unified platform for task scheduling on heterogeneous multicore architectures , 2011, Concurr. Comput. Pract. Exp..

[32]  Christos G. Cassandras,et al.  Systems and Models , 2021, Introduction to Discrete Event Systems.

[33]  M. Keeling Models of foot-and-mouth disease , 2005, Proceedings of the Royal Society B: Biological Sciences.

[34]  M. Ehrenberg,et al.  Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Harry B. McGee,et al.  Hemorrhagic colitis associated with a rare Escherichia coli serotype , 1983 .

[36]  J. Kiefer,et al.  Sequential minimax search for a maximum , 1953 .

[37]  Qingyu Meng,et al.  Scalable large‐scale fluid–structure interaction solvers in the Uintah framework via hybrid task‐based parallelism algorithms , 2014, Concurr. Comput. Pract. Exp..

[38]  P. Glasserman,et al.  Some Guidelines and Guarantees for Common Random Numbers , 1992 .

[39]  Christopher D. Carothers,et al.  Efficient optimistic parallel simulations using reverse computation , 1999, Proceedings Thirteenth Workshop on Parallel and Distributed Simulation. PADS 99. (Cat. No.PR00155).

[40]  J. Elf,et al.  Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. , 2004, Systems biology.