Article

Implementation of a discrete event simulator for biological self-assembly systems

Authors:

Russell SchwartzAuthors Info & Claims

WSC '05: Proceedings of the 37th conference on Winter simulation

Pages 2223 - 2231

Published: 04 December 2005 Publication History

Abstract

We have implemented a simulation tool for the study of computationally challenging biological self-assembly systems, particularly viral protein shells. The simulator implements a generic model of self-assembly based on simple local binding interactions to specify the behavior of complex self-assembly reactions. Recently developed discrete event methods allow for fast quantitative simulation of these systems. The new simulator uses the Java language to implement the model in a portable, interactive graphical tool. The Java libraries can also be used directly to build customized simulations. This paper discusses the simulator model, the theoretical basis for its efficient operation, and implementation issues in its design. It also discusses empirical validation of the simulator package and presents sample applications.

References

[1]

Berger, B., P. W. Shor, L. Tucker-Kellog, and J. King. 1994. Local rule-based theory of virus shell assembly. Proceedings of the National Academy of Sciences USA 91(16): 7732--7736.

[2]

Bruinsma, R. F., W. M. Gelbart, D. Reguera, J. Rudnick, and R. Zandi. Viral self-assembly as a thermodynamic process. Physical Review Letters 90(24):24801--24804.

[3]

Caspar, D. L. D., and Klug, A. 1962. Physical principles in the construction of regular viruses. Cold Spring Harbor Symposium on Quantitative Biology 27: 1--24.

[4]

Caspar, D. L. D. 1980. Movement and self-control in protein assemblies: quasi-equivalence revisited. Biophysical Journal 32 (1): 103--138.

[5]

Endres, D. and A. Zlotnick. 2002. Model-based analysis of assembly kinetics for virus capsids or other spherical polymers. Biophysical Journal 83: 1217--1230.

[6]

Gillespie, D. T. 1976. A general method for numerically simulating the stochastic time evolution of couples chemical reactions. Journal of Computational Physics 22: 403--434.

[7]

Jamalyaria, F., R. Rohlfs, and R. Schwartz. 2005. Queue-based method for efficient simulation of biological self-assembly systems. Journal of Computational Physics 204: 100--120.

Digital Library

[8]

Prevelige, P. E., Thomas, D. and King, J. 1993. Nucleation and growth phases in the polymerization of coat and scaffolding subunits into icosahedral procapsid shells. Biophysical Journal 64: 824--835.

[9]

Reddy, V. S., H. A. Giesing, R. T. Morton, A. Kumar, C. B. Post, C. L. Brooks, 3rd, and J. E. Johnson. 1998. Energetic of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses. Biophysical Journal 74: 546--558.

[10]

Schwartz, R. The local rules dynamics model for self-assembly simulation. Computer science Ph.D. thesis, Massachusetts Institute of Technology, 2000. (also published as MIT Laboratory for Computer Science Technical report MIT-LCS-TR-800)

Digital Library

[11]

Schwartz, R., P. W. Shor, P. E. Prevelige, and B. Berger. 1998. Local rules simulation of the kinetics of virus capsid self-assembly. Biophysical Journal 75(6): 2626--2636.

[12]

Schwartz, R., R. L. Garcea, and B. Berger. 2000. Local rules theory applied to polyomavirus polymorphic capsid assemblies. Virology 268: 461--470.

[13]

Turner, T. E., Schnell, S., Burrage, K. 2004. Stochastic approaches for modelling in vivo reactions. Computational Biology and Chemistry 28(3): 165--78.

Digital Library

[14]

Twarock, R. 2004. A tiling approach to virus capsid assembly explaining a structural puzzle in virology. Journal of Theoretical Biology 226(4): 477--482.

[15]

Whitesides, G. M. 1995. Self-assembling materials. Scientific American. September: 146--149.

[16]

Whitesides, G. M. 2002. Self-assembly at all scales. Science 295: 2418--2421.

[17]

Zlotnick, A. 1994. To build a virus capsid: an equilibrium model of the self-assembly of polyhedral protein complexes. Journal of Molecular Biology 241(1): 59--67.

[18]

Zlotnick, A., J. M. Johnson, P. W. Wingfield, S. J. Stahl, and D. Endres. 1999. A theoretical model successfully identifies features of hepatitis B virus capsid assembly. Biochemistry 38: 14644--14652.

Cited By

Ellabaan MBosman PYu TEkárt A(2007)Activation energy-based simulation for self-assembly of multi-shape tilesProceedings of the 9th annual conference companion on Genetic and evolutionary computation10.1145/1274000.1274011(2462-2467)Online publication date: 7-Jul-2007
https://dl.acm.org/doi/10.1145/1274000.1274011

Implementation of a discrete event simulator for biological self-assembly systems
1. Applied computing
  1. Life and medical sciences

Recommendations

Investigation of virus capsid self-assembly kinetics using discrete-event stochastic simulation
Inside discrete-event simulation software: how it works and why it matters
WSC '10: Proceedings of the Winter Simulation Conference

This paper provides simulation practitioners and consumers with a grounding in how discrete-event simulation software works. Topics include discrete-event systems; entities, resources, control elements and operations; simulation runs; entity states; ...
Inside discrete-event simulation software: how it works and why it matters
WSC '13: Proceedings of the 2013 Winter Simulation Conference: Simulation: Making Decisions in a Complex World

This paper provides simulation practitioners and consumers with a grounding in how discrete-event simulation software works. Topics include discrete-event systems; entities, resources, control elements and operations; simulation runs; entity states; ...

Comments

Information & Contributors

Information

Published In

cover image ACM Conferences

WSC '05: Proceedings of the 37th conference on Winter simulation

December 2005

2769 pages

ISBN:0780395190

Sponsors

SIGSIM: ACM Special Interest Group on Simulation and Modeling

Publisher

Winter Simulation Conference

Publication History

Published: 04 December 2005

Check for updates

Qualifiers

Article

Acceptance Rates

WSC '05 Paper Acceptance Rate 209 of 316 submissions, 66%;

Overall Acceptance Rate 3,413 of 5,075 submissions, 67%

Contributors

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

1
Total Citations
View Citations
203
Total Downloads

Downloads (Last 12 months)0
Downloads (Last 6 weeks)0

Reflects downloads up to 02 Mar 2025

Other Metrics

View Author Metrics

Citations

Cited By

Ellabaan MBosman PYu TEkárt A(2007)Activation energy-based simulation for self-assembly of multi-shape tilesProceedings of the 9th annual conference companion on Genetic and evolutionary computation10.1145/1274000.1274011(2462-2467)Online publication date: 7-Jul-2007
https://dl.acm.org/doi/10.1145/1274000.1274011

View Options

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Full Access

Get this Publication

View options

PDF

View or Download as a PDF file.

eReader

View online with eReader.

Figures

Tables

Media

View Table of Conten