* update kinetic_formalism

git-svn-id: svn+ssh://hemlock.ucr.edu/srv/svn/misc/trunk/origins_of_life@613 25fa0111-c432-4dab-af88-9f31a2f6ac42

diff --git a/kinetic_formalism.Rnw b/kinetic_formalism.Rnw
index 2b19b6a01884fc9b80bcd64e505c81f1a6d5acf6..4c9222005d0b3bf0e1a5dec7e070e988191186cf 100644 (file)
--- a/kinetic_formalism.Rnw
+++ b/kinetic_formalism.Rnw
@@ -271,7 +271,7 @@ relatively matched curvatures in our environment.
 % 1.5 to 0.75 3 to 0.33
 <<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
 grid <- expand.grid(x=seq(0,max(c(sd(abs(log(c(1,3)))),
-                      sd(abs(log(c(1,0.33)))),sd(abs(log(c(0.33,3)))))),length.out=20),
+y                      sd(abs(log(c(1,0.33)))),sd(abs(log(c(0.33,3)))))),length.out=20),
                     y=seq(0,max(c(mean(log(c(1,3)),
                       mean(log(c(1,0.33))),
                       mean(log(c(0.33,3)))))),length.out=20))
@@ -330,6 +330,30 @@ bonds, for example) or decrease (by increasing the time taken to fully
 insert the acyl chain, for example) the rate of insertion or to what
 degree, so we do not take it into account in this formalism.
 
+\fixme{Incorporate McLean84 here}
+From McLean84LIB: Although it is difficult to measure cmc values for
+the sparingly soluble lipids used in this study, estimates for
+lysopalmitoylphosphatidylcholine( 7 X l0-6 M; Haberland \& Reynolds,
+1975), cholesterol (12.1 X 10-8 M, extrapolated to infinite dilution;
+Haberland \& Reynolds, 1973), and dipalmitoylphosphatidylcholine (4.6
+X l0-10 M; Smith \& Tanford, 1972) are available. A value of 1.1 X
+10-8 M for DMPC was estimated from the linear relationship between ln
+cmc and the number of carbons in the PC acyl chain by using data for n
+= 7, 8, 10, and 16 [summarized in Tanford (1980)].
+
+From Nichols85: The magnitude of the dissociation rate constant
+decreases by a factor of approximately 3.2 per carbon increase in acyl
+chain length (see Table II here) {take into account for the formula;
+  rz 8/17/2010}.
+
+From Nichols85: The magnitude of the partition coefficient increases
+with acyl chain length [Keq(M-C6-NBD-PC) = (9.8±2.1) X 106 M-1 and Keq
+(P-C6-NBD-PC) = (9.4±1.3) x 107 M-1. {take into account for the
+  formula; rz 8/17/2010}.
+
+From Nichols85: The association rate constant is independent of acyl
+chain length. {take into account for the formula; rz 8/17/2010}.
+
 
 <<fig=TRUE,echo=FALSE,results=hide,width=7,height=5>>=
 curve(2^x,from=0,to=sd(c(12,24)),
@@ -672,7 +696,7 @@ assume that they have the same $k_f$. For CHOL, Estronca07 found a
 value for $k_f$ of $5.1\cdot 10^7 \frac{1}{\mathrm{M}\cdot
   \mathrm{s}}$. For PE, Abreu04 found a value for $k_f$ of $2.3\cdot
 10^6$. \fixme{I'm missing the notes on these last two papers, so this
-  isn't correct yet.}
+ isn't correct yet.}
 
 \subsubsection{$k_b$ for lipid types}
 
@@ -682,17 +706,101 @@ calculated from the experiments of Nichols82 where the ratio of $k_b$
 of different types was measured to that of PC.
 See~\fref{tab:kinetic_parameters_lipid_types}.
 
-assigned accordingly. kb(PS) was assumed to be the same as kb(PG) given
-by Nichols82 (also ratio from kb(PC)).
-kb(SM) is taken from kb(PC) of Wimley90 (radioactive), and then a ratio of
-kb(PC)/kb(SM) taken from Bai97: = 34/2.2 = 15.45; 2.0 x 10-4 x 15.45 = 3.1 x
-10-3 s -1.
-kb(CHOL) taken from Jones90 (radioactive; POPC LUV; 37°).
+assigned accordingly. kb(PS) was assumed to be the same as kb(PG)
+given by Nichols82 (also ratio from kb(PC)). kb(SM) is taken from
+kb(PC) of Wimley90 (radioactive), and then a ratio of kb(PC)/kb(SM)
+taken from Bai97: = 34/2.2 = 15.45; 2.0 x 10-4 x 15.45 = 3.1 x 10-3 s
+-1. kb(CHOL) taken from Jones90 (radioactive; POPC LUV; 37°).
+
+PC 0.89
+PE 0.45 <- from Nichols82
+PG=PS 
+
+
 
 
 \subsubsection{Area for lipid types}
 
 
+From Sampaio05: Besides this work and our own earlier report on the
+association of NBD-DMPE with lipid bilayers (Abreu et al., 2004), we
+are aware of only one other report in the literature (Nichols, 1985)
+in which all the kinetic constants of lipid-derived amphiphile
+association with lipid bilayer membranes were experimentally measured.
+{indeed; everything is k- !!!; rz}
+
+From McLean84LIB: Although it is difficult to measure cmc values for
+the sparingly soluble lipids used in this study, estimates for
+lysopalmitoylphosphatidylcholine( 7 X l0-6 M; Haberland \& Reynolds,
+1975), cholesterol (12.1 X 10-8 M, extrapolated to infinite dilution;
+Haberland \& Reynolds, 1973), and dipalmitoylphosphatidylcholine (4.6
+X l0-10 M; Smith \& Tanford, 1972) are available. A value of 1.1 X
+10-8 M for DMPC was estimated from the linear relationship between ln
+cmc and the number of carbons in the PC acyl chain by using data for n
+= 7, 8, 10, and 16 [summarized in Tanford (1980)].
+
+From Toyota08: Recently, several research groups have reported
+self-reproducing systems of giant vesicles that undergo a series of
+sequential transformations: autonomous growth, self-division, and
+chemical reactions to produce membrane constituents within the giant
+vesicles.44-47
+
+Vesicle sizes of 25 nm for SUV and 150 nm for LUV were mentioned by
+Thomas02.
+
+From Lund-Katz88: Charged and neutral small unilamellar vesicles
+composed of either saturated PC, unsaturated PC, or SM had similar
+size distributions with diameters of 23 \& 2 nm.
+
+From Sampaio05LIB: The exchange of lipids and lipid derivatives
+between lipid bilayer vesicles has been studied for at least the last
+30 years. Most of this work has examined the exchange of amphiphilic
+molecules between a donor and an acceptor population. The measured
+efflux rates were shown in almost all cases, not surprisingly, to be
+first order processes. In all of this work, the insertion rate has
+been assumed to be much faster than the efflux rate. Having measured
+both the insertion and desorption rate constants for amphiphile
+association with membranes, our results show that this assumption is
+valid. In several cases reported in the literature, the insertion rate
+constant was assumed, although never demonstrated, to be a
+diffusion-controlled process.
+
+(for methods? From McLean84LIB: The activation free energies and free
+energies of transfer from self-micelles to water increase by 2.2 and
+2.1 kJ mol-' per methylene group, respectively. {see if we can use it
+  to justify arranging our changed in activating energy around 1
+  kcal/mol; rz}).
+
+Jones90 give diameter of LUV as 100 nm, and of SUV as 20 nm; that
+would give the number of molecules per outer leaflet of a vesicle as
+1500.
+
+Form Simard08: Parallel studies with SUV and LUV revealed that
+although membrane curvature does have a small effect on the absolute
+rates of FA transfer between vesicles, the ΔG of membrane desorption
+is unchanged, suggesting that the physical chemical properties which
+govern FA desorption are dependent on the dissociating molecule rather
+than on membrane curvature. However, disagreements on this fundamental
+issue continue (57, 61, 63, 64)
+
+(methods regarding the curvature effect: Kleinfeld93 showed that the
+transfer parameters of long-chain FFA between the lipid vesicles
+depend on vesicle curvature and composition. Transfer of stearic acid
+is much slower from LUV as compared to SUV).
+
+From McLean84: In a well-defined experimental system consisting of
+unilamellar lipid vesicles, in the absence of protein, the
+rate-limiting step for the overall exchange process is desorption
+(McLean \& Phillips, 1981). {thus I can take exchange data for the
+  estimation of k- rz; 8/11/08}.
+
+\subsubsection{Complex Formation 1}
+
+From Thomas88a: SM decreases the rate of cholesterol transfer, while
+phosphatidylethanolamine (PE) and phosphatidylserine (PS) have no
+effect at physiologically significant levels.
+
+
 \section{Simulation Methodology}
 
 \subsection{Overall Architecture}