0README

|-- chandler-rate-theory
|   |-- chandler.mm
|   |-- chandler.mm.ps
|   |-- chand-summary.mm
|   |-- chand-summary.mm.ps
|   |-- chand-sum-short.mm
|   |-- chand-sum-short.mm.ps
|   |-- kapral.mm
|   `-- kapral.mm.ps



|-- chandler-rate-theory

|   |-- chandler.mm
|   |-- chandler.mm.ps
	Derivation with explanation of equations of Chandlers theory
	of reaction rates, as given in chapter by Chandler.
	24 pages
	outline form
	troff and PS files;
		NOTES ON CHAPTER 1
		BARRIER CROSSINGS: 
		CLASSICAL THEORY OF RARE BUT IMPORTANT EVENTS
		by David Chandler
		in "Classical and Quantum Dynamics in Condensed Phase 
		Simulations", B. J. Berne, G.  Ciccotti, and D. F. Coker, eds., 
		pp 583-616, World Scientific, Singapore, 1998.
			1. - INTRODUCTION (Excellent read!)
			2. - CYCLOHEXANE ISOMERIZATION
			3. - HIGH BARRIERS, RARE EVENTS
			4. - REACTION COORDINATE, q(t)
			5. - RATE CONSTANTS AND TIME CORRELATION FUNCTIONS
			6. - REACTIVE FLUX CORRELATION FUNCTION:
			7. - CHOOSING THE TRANSITION STATE
			8. - LINDEMANN-HINSHELWOOD AND KRAMERS REGIMES
			9. - CYCLOHEXANE REACTIVE FLUX
	9

|   |-- chand-summary.mm
|   |-- chand-summary.mm.ps
	Derivation and explanation of Chandler's theory of reaction rates.
	9 pages
	outline form
	troff and PS files;
		SUMMARY OF CHANDLER'S REACTIVE FLUX METHOD
		I. ONSAGER'S HYPOTHESIS RELATES MACROSCOPIC AND
		MICROSCOPIC DYNAMICS:
		II. MACROSCOPIC PROPERTIES; PHENOMENOLOGICAL
		DESCRIPTION OF A REACTING
			A. Prepare the system for study:
			B. Measure the rate of reaction (rate of relaxation)
			as the system returns to equilibrium
			C. Analyze the data, to obtain the rate law:
		III. MICROSCOPIC DESCRIPTION; DECAY OF FLUCTUATIONS IN AN
		EQUILIBRIUM SYSTEM:
			A. Background:
			B. Construct a function describing the isomerization
			state of the system, and a function describing a
			fluctuation of the isomerization state about
			the equilibrium state:
			C. Analyze the relaxation of the fluctuations:
			D. Identify $k sub macroscopic ~=~ k sub microscopic$:
			E. Definition of the reactive flux:
			F. Analysis of the reactive flux for the
			limit $t -> 0 sup +$:
			G. Analysis of the reactive flux for times
			$ t*$, $tau sub mol < t* << tau sub rxn = 1/k$:
	9
	
|   |-- chand-sum-short.mm
|   |-- chand-sum-short.mm.ps
	A short version of above 9-page summary.
    	3 pages
	outline form
	troff and PS files;
	7

|   |-- kapral.mm
|   |-- kapral.mm.ps
	Derivation with explanation of equations of Chandlers theory
	of reaction rates, based on the Mori-Zwanzig Generalized
	Langevin Equation.
	Kapral's analysis is rigorous and formal.
	The comments below explain Kapral's derivation and are keyed
	to the text of the Kapral chapter.
    	9 pages
	troff and PS files;
		CHEMICAL RATE LAWS AND RATE CONSTANTS
		by Raymond Kapral, Styliani Consta, and Liam McWhirter,
		in "Classical and Quantum Dynamics in Condensed Phase 
		Simulations", B. J. Berne, G.  Ciccotti, and D. F. Coker, eds., 
		pp 583-616, World Scientific, Singapore, 1998.
			2. - Derivation of chemical rate laws.
				2.1 Phenomenological description.
				Define a progress variable,
				2.3 Rate law derivation. 
				2.4 Structure of the rate kernel.
			3. - Classical systems.
			COMMENT: The importance of Chandler's
			reactive flux method:
	9


John Rupley
 rupley@u.arizona.edu -or- jar@rupley.com
 30 Calle Belleza, Tucson AZ 85716 - (520) 325-4533; fax - (520) 325-4991
 Dept. Biochemistry & Molecular Biophysics, Univ. Arizona, Tucson AZ 85721