Gregory E. Scott

Performance of binary-encounter-Bethe (BEB) theory for electron-impact ionization cross sections of molecules containing heavy elements (Z > 10)

Gregory E. Scott et al. — Fri, 28 Oct 2011 08:40:04 PDT

The binary-encounter-Bethe (BEB) theory developed by Kim and coworkers has been successful for computing electron-impact ionization cross sections of many molecules. However, some recent publications have stated that BEB theory performs poorly for molecules that contain heavier elements such as chlorine and sulfur. We have found that the BEB calculations in those publications were performed incorrectly. When performed correctly, BEB predictions are as good for heavy-element molecules as for light-element molecules. We recommended recently that an alternative, less-confusing procedure be used for molecules that contain heavier elements. The alternative procedure, based upon effective core potentials (ECPs), does not require explicit kinetic energy corrections. For peak cross sections of a group of 18 molecules, the root-mean-square difference between BEB predictions and experimental values is 13%. Results are presented for CCl₃CN, C₂Cl₆, C₂HCl₅, C₂Cl₄, both isomers of C₂H₂Cl₄, CCl₄, TiCl₄, CBr₄, CHBr₃, CH₂Br₂, GaCl, CS₂, H₂S, CH₃I, Al(CH₃)₃, Ga(CH₃)₃, and hexamethyldisiloxane. Incorrect BEB calculations have been reported in the literature for several of these molecules.

Solving the Low Dimensional Smoluchowski Equation with a Singular Value Basis Set

Gregory E. Scott et al. — Fri, 28 Oct 2011 08:40:01 PDT

Reaction kinetics on free energy surfaces with small activation barriers can be computed directly with the Smoluchowski equation. The procedure is computationally expensive even in a few dimensions. We present a propagation method that considerably reduces computational time for a particular class of problems: when the free energy surface suddenly switches by a small amount, and the probability distribution relaxes to a new equilibrium value. This case describes relaxation experiments. To achieve efficient solution, we expand the density matrix in a basis set obtained by singular value decomposition of equilibrium density matrices. Grid size during propagation is reduced from (100–1000)^N to (2–4)^N in N dimensions. Although the scaling with N is not improved, the smaller basis set nonetheless yields a significant speed up for low-dimensional calculations. To demonstrate the practicality of our method, we couple Smoluchowsi dynamics with a genetic algorithm to search for free energy surfaces compatible with the multiprobe thermodynamics and temperature jump experiment reported for the protein α₃D.

A natural missing link between activated and downhill protein folding scenarios

Feng Liu et al. — Fri, 28 Oct 2011 08:39:59 PDT

We propose protein PTB1:4W as a good candidate for engineering into a downhill folder. PTB1:4W has a probe-dependent thermal unfolding curve and sub-millisecond T-jump relaxation kinetics on more than one time scale. Its refolding rate in denaturant is a non-linear function of denaturant concentration (curved chevron plot). Yet at high denaturant concentration its unfolding is probe-independent, and the folding kinetics can be fitted to a single exponential decay. The domain appears to fold via a mechanism between downhill folding and activated folding over several small barriers, and when denaturant is added, one of these barriers greatly increases and simplifies the observed folding to apparent two-state kinetics. We predict the simplest free energy function consistent with the thermai denaturation and kinetics experiments by using the singular value Smoluchowski dynamics (SVSD) model. PTB1:4W is a natural 'missing link' between downhill and activated folding. We suggest mutations that could move the protein into the downhill folding limit.

Better biomolecule thermodynamics from kinetics

Kiran Girdhar et al. — Fri, 28 Oct 2011 08:39:57 PDT

Protein stability is measured by denaturation: When solvent conditions are changed (e.g., temperature, denaturant concentration, or pH) the protein population switches between thermodynamic states. The resulting denaturation curves have baselines. If the baselines are steep, nonlinear, or incomplete, it becomes difficult to characterize protein denaturation. Baselines arise because the chromophore probing denaturation is sensitive to solvent conditions, or because the thermodynamic states evolve structurally when solvent conditions are changed, or because the barriers are very low (downhill folding). Kinetics can largely eliminate such baselines: Relaxation of chromophores, or within thermodynamic states, is much faster than the transition over activation barriers separating states. This separation of time scales disentangles population switching between states (desired signal) from chromophore or population relaxation within states (baselines).We derive simple formulas to extract unfolding thermodynamics from kinetics. The formulas are tested with model data and with a difficult experimental test case: the apparent two-state folder PI3K SH3 domain. Its melting temperature T_m can be extracted reliably by our “thermodynamics from kinetics approach,” even when conventional fitting is unreliable.

Direct Imaging of Two-State Dynamics on the Amorphous Silicon Surface

S. Ashtekar et al. — Fri, 28 Oct 2011 08:39:54 PDT

Amorphous silicon is an important material, amidst a debate whether or not it is a glass. We produce amorphous Si surfaces by ion bombardment and vapor growth, and image discrete Si clusters which hop by two-state dynamics at 295 K. Independent of surface preparation, these clusters have an average diameter of ~5 atoms. Given prior results for metallic glasses, we suggest that this cluster size is a universal feature. The hopping activation free energy of 0.93 ± 0.15 eV is rather small, in agreement with a previously untested surface glass model. Hydrogenation quenches the two-state dynamics, apparently by increasing surface crystallinity.