Classical force field parameters for the heme prosthetic group of cytochrome c

Accurate force fields are essential for describing biological systems in a molecular dynamics simulation. To analyze the docking of the small redox protein cytochrome c (cyt c) requires simulation parameters for the heme in both the reduced and oxidized states. This work presents parameters for the partial charges and geometries for the heme in both redox states with ligands appropriate to cyt c. The parameters are based on both protein X-ray structures and ab initio density functional theory (DFT) geometry optimizations at the B3LYP/6-31G* level. The simulations with the new parameter set reproduce the geometries of the X-ray structures and the interaction energies between water and heme prosthetic group obtained from B3LYP/6-31G* calculations. The parameter set developed here will provide new insights into docking processes of heme containing redox proteins.     

Non-Newtonian behavior in simple fluids

Using nonequilibrium molecular dynamics simulations, we study the non-Newtonian rheology of a microscopic sample of simple fluid. The calculations were performed using a configurational thermostat which unlike previous nonequilibrium molecular dynamics or nonequilibrium Brownian dynamics methods does not exert any additional constraint on the flow profile. Our findings are in agreement with experimental results on concentrated "hard sphere"-like colloidal suspensions. We observe: (i) a shear thickening regime under steady shear; (ii) a strain thickening regime under oscillatory shear at low frequencies; and (iii) shear-induced ordering under oscillatory shear at higher frequencies. These results significantly differ from previous simulation results which showed systematically a strong ordering for all frequencies. They also indicate that shear thickening can occur even in the absence of a solvent.     

Efficient synthesis of tris(4-imidazolyl)methanol derivatives

Biomimetic tris(4-imidazolyl)carbinol derivatives are prepared from imidazole in a short, high-yielding sequence via sulfonamide 1, which is converted to the 2-silylated carbinol 2 by one-pot, sequential 2-functionalization and then 4(5)-functionalization. Alcohol 2 can be transformed either to the parent carbinol 3 or to a desilylated sulfonamide derivative 4. The tripodal alcohol 3 is a convenient precursor to ethers by solvolysis and to metal complexes, as illustrated by the preparation of a bis-tripod complex with iron(III).     

Rationality, regularity, and -cofiniteness

We demonstrate that, for vertex operator algebras of CFT type, -cofiniteness and rationality is equivalent to regularity. For -cofinite vertex operator algebras, we show that irreducible weak modules are ordinary modules and -cofinite, is -cofinite, and the fusion rules are finite.

     

Self-healing femtosecond light filaments

A recent experiment [Appl. Phys. Lett. 83, 213 (2003)] indicated that filaments created in femtosecond high-power pulses propagating in air are surprisingly robust when interacting with microscopic water droplets. We present numerical modeling of the dynamics of the filament-droplet interaction. Our simulation results provide further insight into the interplay between the filament's core and the wide transverse pedestal of the pulse. It is shown that the robustness of the filament comes from the transverse low-intensity pedestal that controls the formation of the central hot spot. Implications for penetration of wide, high-power beams through obscurants are discussed.     

Estimating good discrete partitions from observed data: symbolic false nearest neighbors

A symbolic analysis of observed time series requires a discrete partition of a continuous state space containing the dynamics. A particular kind of partition, called "generating," preserves all deterministic dynamical information in the symbolic representation, but such partitions are not obvious beyond one dimension. Existing methods to find them require significant knowledge of the dynamical evolution operator. We introduce a statistic and algorithm to refine empirical partitions for symbolic state reconstruction. This method optimizes an essential property of a generating partition, avoiding topological degeneracies, by minimizing the number of "symbolic false nearest neighbors." It requires only the observed time series and is sensible even in the presence of noise when no truly generating partition is possible.     

Characterization and optimization of magnetron sputtered Sc/Si multilayers for extreme ultraviolet optics

Scandium/silicon multilayers have been deposited by magnetron sputtering and characterized by several techniques. Experimental peak reflectances of 0.22 and 0.37 have been measured respectively at wavelengths of 40 nm and 46 nm, for 10° incidence angle. The corresponding theoretical values for a perfect Sc/Si structure are respectively 0.38 and 0.57. In order to explain these differences between calculated and measured reflectivity, thin film and multilayer characterizations have been done. Effects of multilayer imperfections on the reflectivity have been estimated independently by means of simulation. Based on these results, a new design of Sc/Si multilayer is proposed with top layer thickness optimization. With this design, the experimental peak reflectance reaches 0.46 at a wavelength of 46 nm. PACS 78.67.Pt; 78.66.-W; 81.15.Cd     

Air-broadening coefficients of the HO2 radical in the 2ν1 band measured using cw-CRDS

In this paper we present measurements of the air-broadening coefficients of HO₂ at room temperature in the 2ν₁ band around 1.5 microns. The HO₂ radicals were created by flash photolysis of SOCl₂ in a flow of O₂/CH₃OH mixtures. To observe air-broadening, N₂ (79%) and O₂ (21%) were added using calibrated flow controllers and a total pressure controller. The total pressure was monitored in parallel using a capacitive pressure gauge. Air-broadening coefficients at 296 K were determined for 34 absorption lines between 6631 and 6671 cm⁻¹. The air-broadening coefficients of HO₂ show a rotational dependence (decreasing from about 0.14 cm⁻¹/atm for N″ = 3 to about 0.09 cm⁻¹/atm for N″ = 10). No evidence for collisional narrowing was observed.