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- J S McCaskill
- Biopolymers
- 1990

A novel application of dynamic programming to the folding problem for RNA enables one to calculate the full equilibrium partition function for secondary structure and the probabilities of various substructures. In particular, both the partition function and the probabilities of all base pairs are computed by a recursive scheme of polynomial order N3 in the… (More)

- Mark A. Bedau, John S. McCaskill, +6 authors Thomas S. Ray
- Artificial Life
- 2000

This article lists fourteen open problems in artificial life, each of which is a grand challenge requiring a major advance on a fundamental issue for its solution. Each problem is briefly explained, and, where deemed helpful, some promising paths to its solution are indicated.

- J S McCaskill
- Bio Systems
- 2001

The programmability and the integration of biochemical processing protocols are addressed for DNA computing using photochemical and microsystem techniques. A magnetically switchable selective transfer module (STM) is presented which implements the basic sequence-specific DNA filtering operation under constant flow. Secondly, a single steady flow system of… (More)

- J S Mccaskill, R M Füchslin, S Altmeyer
- Biological chemistry
- 2001

A fully stochastic chemical modelling technique is derived which describes the influence of spatial separation and discrete population size on the evolutionary stability of coupled amplification in biopolymers. The model is analytically tractable for an infinite-dimensional space (simplex geometry), which also provides insight into evolution in normal… (More)

- J Yin, J S McCaskill
- Biophysical journal
- 1992

An understanding of the viral replication process commonly referred to as "plaque growth" is developed in the context of a reaction-diffusion model. The interactions among three components: the virus, the healthy host, and the infected host are represented using rates of viral adsorption and desorption to the cell surface, replication and release by host… (More)

- S Bonhoeffer, J S McCaskill, P F Stadler, P Schuster
- European biophysics journal : EBJ
- 1993

Statistical properties of RNA folding landscapes obtained by the partition function algorithm (McCaskill 1990) are investigated in detail. The pair correlation of free energies as a function of the Hamming distance is used as a measure for the ruggedness of the landscape. The calculation of the partition function contains information about the entire… (More)

- R M Füchslin, J S McCaskill
- Proceedings of the National Academy of Sciences…
- 2001

Genetic encoding provides a generic construction scheme for biomolecular functions. This paper addresses the key problem of coevolution and exploitation of the multiple components necessary to implement a replicable genetic encoding scheme. Extending earlier results on multicomponent replication, the necessity of spatial structure for the evolutionary… (More)

- S. Bonhoeffer, J. S. McCaskill, P. F. Stadler, P. Schuster
- European Biophysics Journal
- 2004

Statistical properties of RNA folding landscapes obtained by the partition function algorithm (McCaskill 1990) are investigated in detail. The pair correlation of free energies as a function of the Hamming distance is used as a measure for the ruggedness of the landscape. The calculation of the partition function contains information about the entire… (More)

- B Wlotzka, J S McCaskill
- Chemistry & biology
- 1997

BACKGROUND
A novel approach to the study of in vitro evolution is provided by the investigation of continuous, functionally coupled, amplifying systems. To date, in vitro evolution experiments have focused on issues of mutation and selection. Our work contributes to the new field of in vitro molecular ecology studies in which detailed information about the… (More)

- Jens Breyer, Jörg Ackermann, John S. McCaskill
- Artificial Life
- 1998

Recently, new types of coupled isothermal polynucleotide amplification reactions for the investigation of in vitro evolution have been established that are based on the multi-enzyme 3SR reaction. Microstructured thin-film open bioreactors have been constructed in our laboratory to run these reactions spatially resolved in flow experiments. Artificial… (More)