Michael W. Deem

A biased Monte Carlo scheme for zeolite structure solution

We describe a new, biased Monte Carlo scheme to determine the crystal structures of zeolites from powder diffraction data. We test the method on all publicly known zeolite materials, with success in all cases. We show that the method of parallel tempering is a powerful supplement to the biased Monte Carlo.

A hierarchical approach to protein molecular evolution

Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with Monte Carlo simulations. These simulations demonstrate that nonhomologous juxtaposition of encoded structure is the rate-limiting step in the production of new tertiary protein folds. Nonhomologous swapping of low-energy secondary structures increased the binding constant of a simulated protein by approximately 10(7) relative to base substitution alone. Applications of our approach include the generation of new protein folds and modeling the molecular evolution of disease.

Strict detailed balance is unnecessary in Monte Carlo simulation

Detailed balance is an overly strict condition to ensure a valid Monte Carlo simulation. We show that, under fairly general assumptions, a Monte Carlo simulation need satisfy only the weaker balance condition. Not only does our proof show that sequential updating schemes are correct, but also it establishes the correctness of a whole class of new methods that simply leave the Boltzmann distribution invariant.

Efficient Monte Carlo methods for cyclic peptides

We present a new, biased Monte Carlo scheme for simulating complex, cyclic peptides. Backbone atoms are equilibrated with a biased rebridging scheme, and side-chain atoms are equilibrated with a look-ahead configurational bias Monte Carlo. Parallel tempering is shown to be an important ingredient in the construction of an efficient approach.

Future directions in solid state chemistry: report of the NSF-sponsored workshop

Abstract A long-established area of scientific excellence in Europe, solid state chemistry has emerged in the US in the past two decades as a field experiencing rapid growth and development. At its core, it is an interdisciplinary melding of chemistry, physics, engineering, and materials science, as it focuses on the design, synthesis and structural characterization of new chemical compounds and characterization of their physical properties. As a consequence of this inherently interdisciplinary character, the solid state chemistry community is highly open to the influx of new ideas and directions. The inclusionary character of the field’s culture has been a significant factor in its continuing growth and vitality. This report presents an elaboration of discussions held during an NSF-sponsored workshop on Future Directions in Solid State Chemistry , held on the UC Davis Campus in October 2001. That workshop was the second of a series of workshops planned in this topical area. The first, held at NSF headquarters in Arlington, Virginia, in January of 1998, was designed to address the core of the field, describing how it has developed in the US and worldwide in the past decade, and how the members of the community saw the central thrusts of research and education in solid state chemistry proceeding in the next several years. A report was published on that workshop (J.M. Honig, chair, “Proceedings of the Workshop on the Present Status and Future Developments of Solid State Chemistry and Materials”, Arlington, VA, January 15–16, 1998) describing the state of the field and recommendations for future development of the core discipline. In the spirit of continuing to expand the scope of the solid state chemistry community into new areas of scientific inquiry, the workshop elaborated in this document was designed to address the interfaces between our field and fields where we thought there would be significant opportunity for the development of new scientific advancements through increased interaction. The 7 topic areas, described in detail in this report, ranged from those with established ties to solid state chemistry such as Earth and planetary sciences, and energy storage and conversion, to those such as condensed matter physics, where the connections are in their infancy, to biology, where the opportunities for connections are largely unexplored. Exciting ties to materials chemistry were explored in discussions on molecular materials and nanoscale science, and a session on the importance of improving the ties between solid state chemists and experts in characterization at national experimental facilities was included. The full report elaborates these ideas extensively.

DISORDER-INDUCED ANOMALOUS KINETICS IN THE A + A 0 REACTION

We address the two-dimensional bimolecular annihilation reaction

Effect of static disorder and reactant segregation on the A+B[over →]0 reaction

A + A to emptyset

Numerical observation of disorder-induced anomalous kinetics in the A+A→∅ reaction

in the presence of random impurities. Impurities with sufficiently long-ranged interaction energies are known to lead to anomalous diffusion,

Strategies for high throughput, templated zeolite synthesis

sim t^{1-delta}

Reaction, Lévy flights, and quenched disorder.

, in the absence of reaction. Applying renormalization group theory to a field theoretic description of this reaction, we find that this disorder also leads to anomalous kinetics in the long time limit: