Gas-phase formation of silicon carbides, oxides, and sulphides from atomic silicon ions

A systematic experimental study of the kinetics and mechanisms of the chemical reactions in the gas phase between ground-state Si(+)2p and a variety of astrophysical molecules. The aim of this study is to identify the reactions which trigger the formation of chemical bonds between silicon and carbon, oxygen and sulphur, and the chemical pathways which lead to further molecular growth. Such knowledge is valuable in the identification of new extraterrestrial silicon-bearing molecules and for an assessment of the gas-phase transition from atomic silicon to silicon carbide and silicate grain particles in carbon-rich and oxygen-rich astrophysical environments

Conformation gating as a mechanism for enzyme specificity

Acetylcholinesterase, with an active site located at the bottom of a narrow and deep gorge, provides a striking example of enzymes with buried active sites. Recent molecular dynamics simulations showed that reorientation of five aromatic rings leads to rapid opening and closing of the gate to the active site. In the present study the molecular dynamics trajectory is used to quantitatively analyze the effect of the gate on the substrate binding rate constant. For a 2.4-Å probe modeling acetylcholine, the gate is open only 2.4% of the time, but the quantitative analysis reveals that the substrate binding rate is slowed by merely a factor of 2. We rationalize this result by noting that the substrate, by virtue of Brownian motion, will make repeated attempts to enter the gate each time it is near the gate. If the gate is rapidly switching between the open and closed states, one of these attempts will coincide with an open state, and then the substrate succeeds in entering the gate. However, there is a limit on the extent to which rapid gating dynamics can compensate for the small equilibrium probability of the open state. Thus the gate is effective in reducing the binding rate for a ligand 0.4 Å bulkier by three orders of magnitude. This relationship suggests a mechanism for achieving enzyme specificity without sacrificing efficiency

I/O limitations in parallel molecular dynamics

Abstract We discuss data production rates and their impact on the performance of scientific applications using parallel computers. On one hand, too high rates of data production can be overwhelming, exceeding logistical capacities for transfer, storage and analysis. On the other hand, the rate limiting step in a computationally–based study should be the human–guided analysis, not the calculation. We present performance data for a biomolecular simulation of the enzyme, acetylcholinesterase, which uses the parallel molecular dynamics program EulerGROMOS. The actual production rates are compared against a typical time frame for results analysis where we show that the rate limiting step is the simulation, and that to overcome this will require improved output rates.