Cellular automata machines: a new environment for modeling
Cellular automata machines: a new environment for modeling
Models of massive parallelism: analysis of cellular automata and neural networks
Models of massive parallelism: analysis of cellular automata and neural networks
Molecular Modeling and Simulation: An Interdisciplinary Guide
Molecular Modeling and Simulation: An Interdisciplinary Guide
Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
Biomolecular Computation in Virtual Test Tubes
DNA 7 Revised Papers from the 7th International Workshop on DNA-Based Computers: DNA Computing
Special Issue on Biomolecular Machines and Artificial Evolution
Genetic Programming and Evolvable Machines
Computation by Self-assembly of DNA Graphs
Genetic Programming and Evolvable Machines
Virtual Test Tubes: A New Methodology for Computing
SPIRE '00 Proceedings of the Seventh International Symposium on String Processing Information Retrieval (SPIRE'00)
DNA-like genomes for evolution in silico
GECCO'03 Proceedings of the 2003 international conference on Genetic and evolutionary computation: PartI
Search and validation of short genome-wide biomarkers for bacterial biological phylogenies
DNA'10 Proceedings of the 16th international conference on DNA computing and molecular programming
DNA chips for species identification and biological phylogenies
Natural Computing: an international journal
In search of optimal codes for DNA computing
DNA'06 Proceedings of the 12th international conference on DNA Computing
Theory and applications of DNA codeword design
TPNC'12 Proceedings of the First international conference on Theory and Practice of Natural Computing
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By their structure and operation, biomolecules have resolved fundamental problems as a distributed computational system that we are just beginning to unveil. One advantageous approach to gain a good understanding of the processes and algorithms involved is simulation on conventional computers. Simulations allow better understanding of the capabilities of molecules because they can occur at the level of reliability, efficiency, and programmability that are standard in conventional computation and are desirable for experiments in vitro. Here, we describe in some detail the architecture of a general-purpose simulation environment in silico, EdnaCo, establish its soundness and reliability, and benchmark its performance. The system can be described as an emulation of the events in a real test tube. We describe the major pieces of its architecture, namely, a distributed memory (file) system, a kinetic engine, and input/output mechanisms. Finally, the ability of this environment in preserving major features of the wet counterpart in vitro is evaluated via an implementation on a cluster of PCs. The results of several simulations are summarized that establish the soundness, utility, applicability, and cost efficiency of the software to facilitate experimentation in vitro.