Volume 81, Issue 8

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August 2019

Special Issue: Gillespie and his Algorithms and Special Issue: Multiscale Modelling of Tissue Growth and Shape

Issue Editors:

Yang Cao,
Petzold Linda,
Effrosyni Seitaridou,
Mark Alber,
Christophe Godin,
Philip Maini,
Roeland Merks,
Eric Mjolsness

24 articles in this issue

Stochastic Simulation of Biochemical Systems: In Memory of Dan T. Gillespie’s contributions
Yang Cao
Petzold Linda
Effrosyni Seitaridou
Editorial 01 July 2019 Pages: 2819 - 2821
Generalizing Gillespie’s Direct Method to Enable Network-Free Simulations
Ryan Suderman
Eshan D. Mitra
William S. Hlavacek
Special Issue: Gillespie and His Algorithms 28 March 2018 Pages: 2822 - 2848
Stochastic Dynamics of Eukaryotic Flagellar Growth
Muruhan Rathinam
Yuriy Sverchkov
Special Issue: Gillespie and his Algorithms 11 April 2018 Pages: 2849 - 2872
The Linear Noise Approximation for Spatially Dependent Biochemical Networks
Per Lötstedt
Special Issue: Gillespie and His Algorithms Open access 11 April 2018 Pages: 2873 - 2901
Low Variance Couplings for Stochastic Models of Intracellular Processes with Time-Dependent Rate Functions
David F. Anderson
Chaojie Yuan
Special Issue: Gillespie and his Algorithms 18 April 2018 Pages: 2902 - 2930
Quasi-Monte Carlo Methods Applied to Tau-Leaping in Stochastic Biological Systems
Casper H. L. Beentjes
Ruth E. Baker
Special Issue: Gillespie and his Algorithms Open access 25 May 2018 Pages: 2931 - 2959
Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches
Stephen Smith
Ramon Grima
Special Issue: Gillespie and his Algorithms Open access 21 May 2018 Pages: 2960 - 3009
Stochastic Simulation of Pattern Formation in Growing Tissue: A Multilevel Approach
Stefan Engblom
Special Issue: Gillespie and His Algorithms Open access 20 June 2018 Pages: 3010 - 3023
Accuracy Analysis of Hybrid Stochastic Simulation Algorithm on Linear Chain Reaction Systems
Minghan Chen
Shuo Wang
Yang Cao
Special Issue: Gillespie and His Algorithms 10 July 2018 Pages: 3024 - 3052
A Critical Comparison of Rejection-Based Algorithms for Simulation of Large Biochemical Reaction Networks
Vo Hong Thanh
Special Issue: Gillespie and His Algorithms 06 July 2018 Pages: 3053 - 3073
S-Leaping: An Adaptive, Accelerated Stochastic Simulation Algorithm, Bridging \(\tau \)-Leaping and R-Leaping
Jana Lipková
Georgios Arampatzis
Petros Koumoutsakos
Special Issue: Gillespie and His Algorithms 10 July 2018 Pages: 3074 - 3096
Data-Driven Method for Efficient Characterization of Rare Event Probabilities in Biochemical Systems
Min K. Roh
Special Issue: Gillespie and His Algorithms Open access 17 September 2018 Pages: 3097 - 3120
Sensitivity Analysis for Multiscale Stochastic Reaction Networks Using Hybrid Approximations
Ankit Gupta
Mustafa Khammash
Special Issue: Gillespie and His Algorithms 09 October 2018 Pages: 3121 - 3158
Exact Variance-Reduced Simulation of Lattice Continuous-Time Markov Chains with Applications in Reaction Networks
P. A. Maginnis
M. West
G. E. Dullerud
Special Issue: Gillespie and His Algorithms 13 February 2019 Pages: 3159 - 3184
Multiscale Stochastic Reaction–Diffusion Algorithms Combining Markov Chain Models with Stochastic Partial Differential Equations
Hye-Won Kang
Radek Erban
Special Issue: Gillespie and His Algorithms Open access 04 June 2019 Pages: 3185 - 3213
Introduction
Mark Alber
Christophe Godin
Eric Mjolsness
Editorial 22 July 2019 Pages: 3214 - 3218
Are Homeostatic States Stable? Dynamical Stability in Morphoelasticity
Alexander Erlich
Derek E. Moulton
Alain Goriely
Special Issue: Multiscale Modeling of Tissue Growth and Shape Open access 21 September 2018 Pages: 3219 - 3244
Cell-Based Model of the Generation and Maintenance of the Shape and Structure of the Multilayered Shoot Apical Meristem of Arabidopsis thaliana
Mikahl Banwarth-Kuhn
Ali Nematbakhsh
Mark Alber
Special Issue: Multi-scale Modeling of Tissue Growth and Shape 14 December 2018 Pages: 3245 - 3281
A Diffuse Interface Framework for Modeling the Evolution of Multi-cell Aggregates as a Soft Packing Problem Driven by the Growth and Division of Cells
J. Jiang
K. Garikipati
S. Rudraraju
Special Issue: Multiscale Modeling of Tissue Growth and Shape 18 February 2019 Pages: 3282 - 3300
Interplay Between the Persistent Random Walk and the Contact Inhibition of Locomotion Leads to Collective Cell Behaviors
Abdel-Rahman Hassan
Thomas Biel
Taeyoon Kim
Special Issue: Multi-scale Modeling of Tissue Growth and Shape 20 February 2019 Pages: 3301 - 3321
Adapting a Plant Tissue Model to Animal Development: Introducing Cell Sliding into VirtualLeaf
Henri B. Wolff
Lance A. Davidson
Roeland M. H. Merks
Special Issue: Multiscale Modeling of Tissue Growth and Shape Open access 29 March 2019 Pages: 3322 - 3341
Strain- or Stress-Sensing in Mechanochemical Patterning by the Phytohormone Auxin
Jean-Daniel Julien
Alain Pumir
Arezki Boudaoud
Special Issue: Multiscale Modeling of Tissue Growth and Shape 22 March 2019 Pages: 3342 - 3361
Simulating Turgor-Induced Stress Patterns in Multilayered Plant Tissues
Olivier Ali
Hadrien Oliveri
Christophe Godin
Special Issue: Multiscale Modeling of Tissue Growth and Shape 11 June 2019 Pages: 3362 - 3384
Prospects for Declarative Mathematical Modeling of Complex Biological Systems
Eric Mjolsness
Special Issue: Multiscale Modeling of Tissue Growth and Shape Open access 07 June 2019 Pages: 3385 - 3420

Volume 81, Issue 8

Stochastic Simulation of Biochemical Systems: In Memory of Dan T. Gillespie’s contributions

Generalizing Gillespie’s Direct Method to Enable Network-Free Simulations

Stochastic Dynamics of Eukaryotic Flagellar Growth

The Linear Noise Approximation for Spatially Dependent Biochemical Networks

Low Variance Couplings for Stochastic Models of Intracellular Processes with Time-Dependent Rate Functions

Quasi-Monte Carlo Methods Applied to Tau-Leaping in Stochastic Biological Systems

Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches

Stochastic Simulation of Pattern Formation in Growing Tissue: A Multilevel Approach

Accuracy Analysis of Hybrid Stochastic Simulation Algorithm on Linear Chain Reaction Systems

A Critical Comparison of Rejection-Based Algorithms for Simulation of Large Biochemical Reaction Networks

S-Leaping: An Adaptive, Accelerated Stochastic Simulation Algorithm, Bridging \(\tau \)-Leaping and R-Leaping

Data-Driven Method for Efficient Characterization of Rare Event Probabilities in Biochemical Systems

Sensitivity Analysis for Multiscale Stochastic Reaction Networks Using Hybrid Approximations

Exact Variance-Reduced Simulation of Lattice Continuous-Time Markov Chains with Applications in Reaction Networks

Multiscale Stochastic Reaction–Diffusion Algorithms Combining Markov Chain Models with Stochastic Partial Differential Equations

Introduction

Are Homeostatic States Stable? Dynamical Stability in Morphoelasticity

Cell-Based Model of the Generation and Maintenance of the Shape and Structure of the Multilayered Shoot Apical Meristem of Arabidopsis thaliana

A Diffuse Interface Framework for Modeling the Evolution of Multi-cell Aggregates as a Soft Packing Problem Driven by the Growth and Division of Cells

Interplay Between the Persistent Random Walk and the Contact Inhibition of Locomotion Leads to Collective Cell Behaviors

Adapting a Plant Tissue Model to Animal Development: Introducing Cell Sliding into VirtualLeaf

Strain- or Stress-Sensing in Mechanochemical Patterning by the Phytohormone Auxin

Simulating Turgor-Induced Stress Patterns in Multilayered Plant Tissues

Prospects for Declarative Mathematical Modeling of Complex Biological Systems

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