R-Scripts

A browser can access this directory, R-Scripts, for navigation and listing (click on the link in this sentence or the Section header). Directory browsing is the only way to view the files in this directory or its subdirectories.

 

R is a system for computation and graphics. It is an implementation of the S language. As GNU S it is the free software successor to S and SPLUS, over which it arguably is a significant improvement. R builds under Mac OS X; binaries are available as disk images.

 

The R-Scripts subdirectories have S-language code that runs under R. Each subdirectory addresses a particular biophysical computation: molecular dynamics (atom fluctuation and driven protein motions); statistical physics (helix coil transition and percolation); fitting of data (hemoglobin oxygenation, linear and nonlinear enzyme-kinetics models, and batch calorimetry).

 

The file 0README in each subdirectory, although often long, explains the methods used and the contents of the subdirectory. It should be read first. References to the literature are conspicuously absent from 0README.

Click on a paragraph-heading link below to access that subdirectory for navigation and listing.

Click on a 0README link to display that directory's file in the browser.

R-Scripts/atom-fluctuations -- Analysis of the fluctuation of the dihedral angle χ-2 (chi-2) of tyrosine 35, from a molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI). The ring is modeled as a tethered Brownian oscillator. The time correlation function for ring libration is fit with two variable parameters: a spring constant and a relaxation time. For more see atom-fluctuations/0README.

R-Scripts/batch-calorimeter -- Analysis of the thermopile voltage from a batch calorimetric experiment: at time zero, the calorimeter cell contents are mixed, quickly generating a temperature difference and thus heat flow through the thermopiles and an associated voltage signal; the system slowly relaxes to thermal equilibrium and the baseline voltage. The data are fit by a two-exponential model. For more see batch-calorimeter/0README.

R-Scripts/driven-protein-motions -- In a molecular dynamics simulation, a sinusoidal force was applied at chi-2 of tyrosine 35 of BPTI. A maximum amplitude and phase (the lag in the response) are extracted by fit of the data and by Fourier transformation. For more see driven-protein-motions/0README.

R-Scripts/enzyme-kinetics-MM -- R has a built-in function, SSmicmen, that implements the Michaelis-Menten model. For more see enzyme-kinetics-MM/0README.

R-Scripts/enzyme-kinetics-nonlinear -- The steady-state mechanism for lactate dehydrogenase (LDH) is compulsory order with binary and ternary complexes and reactant and product abortive complexes. The applicable six-parameter non-linear rate equation is fit to data for the LDH reaction. The fit is displyed, and the quality of the fit examined, in analyses carried out under R. For more see enzyme-kinetics-nonlinear/0README.

R-Scripts/hemoglobin-oxygenation -- Analyis of Tyuma et al (1973) data for oxygen saturation of stripped adult human hemoglobin: fits to the Monod-Wyman-Changeux and Adair models (3 and 4 parameters, respectively), with uniform and "Hill equation" weighting. For more see hemoglobin-oxygenation/0README.

R-Scripts/percolation -- Percolation theory in more than one dimension is mathematically difficult but simple to demonstrate. Two instances are considered here. (1) Forest fires: there is a critical tree density at which the fire spreads to all regions of the forest; the time of the burn (time until the fire dies out) is a maximum at the critical density. (2) filling a square lattice randomly: this is presented as a tutorial exercise for a class. For more see percolation/0README.

R-Scripts/tutorial-examples -- Information and tutorials on R and the S language are found at the R project site, the UCLA R Portal, and elsewhere. The file venables.s in this directory is a set of tutorial commands extracted from splusnotes.s, by Venables and Smith (1992). For more see tutorial-examples/0README.

R-Scripts/zimm_bragg-helix_coil -- Zimm & Bragg (1959) were among several who applied the one-dimensional Ising model to the helix-coil transition. The theory gives the fraction coil state (fraction unfolded) and various other properties that characterize the transition as a function of three parameters: chain length, n; the coil-helix equilibrium constant, s; and the difficulty of initiation,σ (sigma). R functions in this directory evaluate the several properties for ranges of values of the three variable parameters. The results are plotted, generally as the propery over the n-s plane for fixed σ. The displays of the calculations are less sparse than those of the 1959 paper, which necessarily in that era were done by "hand" (with calculating machines). For more see zimm_bragg-helix_coil/0README.