National Energy Research Scientific Computing Center 2004 Annual Report
Navigation
research news
applied mathematics
Crystallization in Silico
C. Yang, E. G. Ng, and P. A. Penczek, “Unified 3-D structure and projection orientation refinement using quasi-Newton algorithm,” J. Struct. Biol. 149, 53 (2005). BER, ASCR-MICS, NIH, LBNL
Single-particle electron cryomicroscopy (cryo-EM) offers a promising alternative
to x-ray crystallography for discovering the structures of proteins and
other macromolecules that cannot be crystallized without distorting their
structures. Cryo-EM creates 2D images of thousands of randomly oriented
“single particles” of the macromolecule. But constructing an
accurate 3D model from noisy images of 2D single particles has been difficult
as well as computationally infeasible for large molecules. Yang et al. found
a new way of formulating the problem mathematically — an algorithm
that simultaneously refines the 3D model while tightening the parameters
for the orientation of the individual 2D projections used to reconstruct
the model. The method is faster, more efficient, and more accurate than
any of its predecessors.
Simulating Supernova Flames
J. B. Bell, M. S. Day, C. A. Rendleman, S. E. Woosley, and M. Zingale, “Direct numerical simulations of Type Ia supernovae flames II: The Rayleigh-Taylor instability,” Astrophys. J. 608, 883 (2004). ASCR-MICS, HEP, SciDAC, NASA, NSF
Accelerating a thermonuclear flame to a large fraction of the speed of sound (possibly supersonic) is one of the main difficulties in modeling Type Ia supernova explosions, which likely begin as a nuclear runaway near the center of a carbon-oxygen white dwarf. The outward propagating flame is unstable, which accelerates it toward the speed of sound. Bell et al. investigated the unstable flame at the transition from the flamelet regime to the distributed-burning regime through detailed, fully resolved simulations. At the low end of the density range, the instability dominated the burning (Figure 2), whereas at the high end the burning suppressed the instability. In all cases, significant acceleration of the flame was observed.
Figure 2. Carbon mass fraction for a 384 cm wide, 6.67 x 106 g cm–3 C/O flame shown every 1.6 x 10–3 s until 8.12 x 10–2 s. The fuel appears red (carbon mass fraction = 0.5), and gravity points toward increasing y. At this low density, the instability dominates over the burning, and a large mixed region develops.
Chemical Shifts in Amino Acids
Y. Yoon, B. G. Pfrommer, S. G. Louie, and A. Canning, “NMR chemical shifts in amino acids: Effects of environments in the condensed phase,” Solid State Comm. 131, 15 (2004). ASCR-MICS, SciDAC, NSF
Nuclear magnetic resonance (NMR) chemical shifts can be useful as fingerprints for detailing the structure and chemical composition of biomolecules, especially proteins and amino acids. Yoon et al. used the parallel electronic structure code PARATEC to calculate NMR chemical shifts in crystalline phases of the amino acids glycine, alanine, and alanyl-alanine. They explored the effects of environment on the chemical shifts in selected glycine geometries. In the crystalline and dilute molecular limits, the calculated NMR chemical shifts were attributed to intermolecular hydrogen-bonds and to dipole electric field effects, respectively.