Volume 81, issue 8, 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

Authors
- Yang Cao
- Petzold Linda
- Effrosyni Seitaridou
- Content type: Editorial
- Published: 01 July 2019
- Pages: 2819 - 2821
Generalizing Gillespie’s Direct Method to Enable Network-Free Simulations

Authors (first, second and last of 6)
- Ryan Suderman
- Eshan D. Mitra
- William S. Hlavacek
- Content type: Special Issue: Gillespie and His Algorithms
- Published: 28 March 2018
- Pages: 2822 - 2848
Stochastic Dynamics of Eukaryotic Flagellar Growth

Authors
- Muruhan Rathinam
- Yuriy Sverchkov
- Content type: Special Issue: Gillespie and his Algorithms
- Published: 11 April 2018
- Pages: 2849 - 2872
The Linear Noise Approximation for Spatially Dependent Biochemical Networks

Authors
- Per Lötstedt
- Content type: Special Issue: Gillespie and His Algorithms
- Open Access
- Published: 11 April 2018
- Pages: 2873 - 2901
Low Variance Couplings for Stochastic Models of Intracellular Processes with Time-Dependent Rate Functions

Authors
- David F. Anderson
- Chaojie Yuan
- Content type: Special Issue: Gillespie and his Algorithms
- Published: 18 April 2018
- Pages: 2902 - 2930
Quasi-Monte Carlo Methods Applied to Tau-Leaping in Stochastic Biological Systems

Authors
- Casper H. L. Beentjes
- Ruth E. Baker
- Content type: Special Issue: Gillespie and his Algorithms
- Open Access
- Published: 25 May 2018
- Pages: 2931 - 2959
Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches

Authors
- Stephen Smith
- Ramon Grima
- Content type: Special Issue: Gillespie and his Algorithms
- Open Access
- Published: 21 May 2018
- Pages: 2960 - 3009
Stochastic Simulation of Pattern Formation in Growing Tissue: A Multilevel Approach

Authors
- Stefan Engblom
- Content type: Special Issue: Gillespie and His Algorithms
- Open Access
- Published: 20 June 2018
- Pages: 3010 - 3023
Accuracy Analysis of Hybrid Stochastic Simulation Algorithm on Linear Chain Reaction Systems

Authors
- Minghan Chen
- Shuo Wang
- Yang Cao
- Content type: Special Issue: Gillespie and His Algorithms
- Published: 10 July 2018
- Pages: 3024 - 3052
A Critical Comparison of Rejection-Based Algorithms for Simulation of Large Biochemical Reaction Networks

Authors
- Vo Hong Thanh
- Content type: Special Issue: Gillespie and His Algorithms
- Published: 06 July 2018
- Pages: 3053 - 3073
S-Leaping: An Adaptive, Accelerated Stochastic Simulation Algorithm, Bridging \(\tau \)-Leaping and R-Leaping

Authors (first, second and last of 5)
- Jana Lipková
- Georgios Arampatzis
- Petros Koumoutsakos
- Content type: Special Issue: Gillespie and His Algorithms
- Published: 10 July 2018
- Pages: 3074 - 3096
Data-Driven Method for Efficient Characterization of Rare Event Probabilities in Biochemical Systems

Authors
- Min K. Roh
- Content type: Special Issue: Gillespie and His Algorithms
- Open Access
- Published: 17 September 2018
- Pages: 3097 - 3120
Sensitivity Analysis for Multiscale Stochastic Reaction Networks Using Hybrid Approximations

Authors
- Ankit Gupta
- Mustafa Khammash
- Content type: Special Issue: Gillespie and His Algorithms
- Published: 09 October 2018
- Pages: 3121 - 3158
Exact Variance-Reduced Simulation of Lattice Continuous-Time Markov Chains with Applications in Reaction Networks

Authors
- P. A. Maginnis
- M. West
- G. E. Dullerud
- Content type: Special Issue: Gillespie and His Algorithms
- Published: 13 February 2019
- Pages: 3159 - 3184
Multiscale Stochastic Reaction–Diffusion Algorithms Combining Markov Chain Models with Stochastic Partial Differential Equations

Authors
- Hye-Won Kang
- Radek Erban
- Content type: Special Issue: Gillespie and His Algorithms
- Open Access
- Published: 04 June 2019
- Pages: 3185 - 3213
Introduction

Authors (first, second and last of 5)
- Mark Alber
- Christophe Godin
- Eric Mjolsness
- Content type: Editorial
- Published: 22 July 2019
- Pages: 3214 - 3218
Are Homeostatic States Stable? Dynamical Stability in Morphoelasticity

Authors
- Alexander Erlich
- Derek E. Moulton
- Alain Goriely
- Content type: Special Issue: Multiscale Modeling of Tissue Growth and Shape
- Open Access
- Published: 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

Authors (first, second and last of 7)
- Mikahl Banwarth-Kuhn
- Ali Nematbakhsh
- Mark Alber
- Content type: Special Issue: Multi-scale Modeling of Tissue Growth and Shape
- Published: 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

Authors
- J. Jiang
- K. Garikipati
- S. Rudraraju
- Content type: Special Issue: Multiscale Modeling of Tissue Growth and Shape
- Published: 18 February 2019
- Pages: 3282 - 3300
Interplay Between the Persistent Random Walk and the Contact Inhibition of Locomotion Leads to Collective Cell Behaviors

Authors (first, second and last of 4)
- Abdel-Rahman Hassan
- Thomas Biel
- Taeyoon Kim
- Content type: Special Issue: Multi-scale Modeling of Tissue Growth and Shape
- Published: 20 February 2019
- Pages: 3301 - 3321
Adapting a Plant Tissue Model to Animal Development: Introducing Cell Sliding into VirtualLeaf

Authors
- Henri B. Wolff
- Lance A. Davidson
- Roeland M. H. Merks
- Content type: Special Issue: Multiscale Modeling of Tissue Growth and Shape
- Open Access
- Published: 29 March 2019
- Pages: 3322 - 3341
Strain- or Stress-Sensing in Mechanochemical Patterning by the Phytohormone Auxin

Authors
- Jean-Daniel Julien
- Alain Pumir
- Arezki Boudaoud
- Content type: Special Issue: Multiscale Modeling of Tissue Growth and Shape
- Published: 22 March 2019
- Pages: 3342 - 3361
Simulating Turgor-Induced Stress Patterns in Multilayered Plant Tissues

Authors (first, second and last of 4)
- Olivier Ali
- Hadrien Oliveri
- Christophe Godin
- Content type: Special Issue: Multiscale Modeling of Tissue Growth and Shape
- Published: 11 June 2019
- Pages: 3362 - 3384
Prospects for Declarative Mathematical Modeling of Complex Biological Systems

Authors
- Eric Mjolsness
- Content type: Special Issue: Multiscale Modeling of Tissue Growth and Shape
- Open Access
- Published: 07 June 2019
- Pages: 3385 - 3420

Volume 81, issue 8, August 2019

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

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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