(Abstract of my talk at JNU School of Life Sciences, yesterday 12 May 2008, 3.30 p.m.)
Currently, molecular dynamics uses ordinary differential equations. I explain why functional differential equations are better suited to biology, how they arise naturally in classical physics, and how they relate to quantum mechanics. I also examine the feasibility of changing existing computer programs for molecular dynamics, such as AMBER, CHARMM, NAMD2, etc., to incorporate functional differential equations.
Background reading:
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Time: Towards a Consistent Theory, Kluwer Academic, Dordrecht, 1994.
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“On Time: 5b. Electromagnetic Time.” Physics Education, 9 (1992) 251-265.
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“On Time:6b. Quantum-Mechanical Time.” Physics Education 10 (1993) 143-161.
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“The Electrodynamic 2-Body Problem and the Origin of Quantum Mechanics” Found. Phys. 34 (2004) 937-62. arxiv.org:0511235
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“Time Travel and the Reality of Spontaneity” Found. Phys. 36 (2006) 1099-1113. arxiv.org: 0804.0830
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(with Suvrat Raju) “Radiative Damping and Functional Differential Equations”. arxiv.org: 0802:3390.
- A New Mathematical Model for Molecular Dynamics 1: Molecular Basis of Memory. arxiv.org: 0803:4367
For a non-technical account see the relevant chapters of
- The Eleven Pictures of Time, Sage, 2003.