Chrisantha Fernando

 

 

Chapter in Progress.

 

Code for Stochastic Model of Template Replication.

 

Bibliography.

Bishop, M. Roth, J. Frisch, H.L. Monte Carlo Models of Self-Replicating Macromolecules. 2 (1977) The Journal of Physical Chemistry 81 (25), 2500-2508 Download pdf.

Cantor, C.R. & Schimmel, P.R. Statistical mechanics and kinetics of nucleic acid interactions. (1980).In: Biophysical Chemistry , ed. W.H Freeman, San Fransisco. 1183-1264 iPhoto.

Elf, J. and Ehrenberg, M. Spontaneous seperation of bi-stable biochemical systems into spatial domains of opposite phases. Supplementary Methods Download paper. Download methods.

Frisch, H.L. Bishop, M. Roth, J. Monte Carlo Stidues of Self-Replicating Macromolecules. 1 (1977) The Journal of Chemical Physics 67(3) 1082-1084 Download pdf.

Gibson, M.A. and Bruck, J. Efficient Exact Stochastic Simulation of Chemical Systems with many Species and Many Channels. (2000). J. Phys. Chem. A 104, 1876-1889. Download pdf.

Gillespie, D.T. Exact Stochastic Simulation of Coupled Chemical Reactions. (1977) The Journal of Physical Chemistry 81(25) 2340-2361 Download pdf.

Kanavarioti, A. Baird, E. Hurley, B. Carruthers, J. Gangopadhyay, S. Unique catalysis and Regioselectivity Observed in the Poly(C)-Directed RNA Dimer Formation from 2-MeImpG: Kinetic Analysis as a Function of Monomer and Polymer Concentration. (1999) Journal of Organic Chemistry 64, 8223-8333 Download pdf.

Luque, B. An Introduction to Physical Theory of Molecular Evolution. (2003) CEJP 3. 516-555. Download pdf.

Murugan, R. Revised theory on DNA renaturation kinetics and its experimental verification. (2002) Biochemical and Biophysical Research Communications 293, 870-873 Download pdf.

Murugan, R. A Stochastic Model on DNA renaturation kinetics (2003) Biophysical Chemistry 104, 535-541 Download pdf.

Murugen, R. A theory on the origin of cooperativity in DNA renaturation kinetics. (2003) Biophysical chemistry 106, 173-178 Download pdf.

Nowick, J.S. Feng, Q. Tjivlkus, T. Ballester, P. Rebek Jr, J. Kinetic Studies and Modeling of Self-Replicating System. (1991) J. Am. Chem. Soc 113, 8831-8839. Download pdf.

Rau, D and Klotz, L. A Unified Theory of Nucleation-Rate-Limited DNA Renaturation Kinetics (1978) Biophysical Chemistry 8, 41-51 Download pdf.

Reynaldo, L.P. Vologodskii, A.V. Neri, B.P. Lyamichev, V.I. The Kinetics of Oligonucleotide Replacements. (2000) J. Mol. Biol, 297, 511-520 Download pdf.

Rohatgi, R. Bartel, D.P. Szostak, J.W. Kinetic and Mechanistic Analysis of Nonenzymatic, Template-Directed Oligoribonucleotide Ligation. (1996) J. Am Chem. Soc, 118, 3332-3339. Download pdf.

Santalucia, JR. J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. (1998) PNAS 95 , 1460-1465. Download pdf.

Schoneborn, H. Bulle, J, Von Kiedrowski, G. Kinetic Monitoring of Self-Replicating Systems through Measurement of Fluorescence Resonance Energy Transfer. (2001) ChemBioChem 12. 922-927. Download pdf.

Turner, D.H. Conformational Changes, Chapter 8 in Nucleic Acids: Structures, Properties and Functions , ed.   V.A. Bloomfield, D.M. Crothers and I. Tinoco, Jr., University Science Press, (2000).

Wattis, J.A.D. and Coveney, P.V. The Origin of the RNA World: a Kinetic Model. (1999) J. Phys. Chem. B 103, 4231-4250 Download pdf. other pdf.

Talks.

A talk about the stochastic model of non-enzymatic template replication, given to G. Von Kiedrowski's Department at the Rohr University in Bochum on 14th June 2005. Download ppt.

Papers

Fernando, C. Elf, J. Szathmary, E. Non-Enzymatic Elongation of Nucleic Acids by Staggered Associations at Low Temperature.  (in preperation). Download draft.

 

Illustration: http://www.gustavianum.uu.se/english.shtml If you are in Uppsala a trip to this museam is a must.