The incomplete beta function law for parallel tempering sampling of classical canonical systems

We show that the acceptance probability for swaps in the parallel tempering Monte Carlo method for classical canonical systems is given by a universal function that depends on the average statistical fluctuations of the potential and on the ratio of the temperatures. The law, called the incomplete beta function law, is valid in the limit that the two temperatures involved in swaps are close to one another. An empirical version of the law, which involves the heat capacity of the system, is developed and tested on a Lennard-Jones cluster. We argue that the best initial guess for the distribution of intermediate temperatures for parallel tempering is a geometric progression and we also propose a technique for the computation of optimal temperature schedules. Finally, we demonstrate that the swap efficiency of the parallel tempering method for condensed-phase systems decreases naturally to zero at least as fast as the inverse square root of the dimensionality of the physical system.Comment: 11 pages, 4 figures; minor changes; to appear in J. Chem. Phy

Combinatorial Formulas for Macdonald and Hall-Littlewood Polynomials of Types A and C. Extended Abstract

A breakthrough in the theory of (type A) Macdonald polynomials is due to Haglund, Haiman and Loehr, who exhibited a combinatorial formula for these polynomials in terms of fillings of Young diagrams. Recently, Ram and Yip gave a formula for the Macdonald polynomials of arbitrary type in terms of the corresponding affine Weyl group. In this paper, we show that a Haglund-Haiman-Loehr type formula follows naturally from the more general Ram-Yip formula, via compression. Then we extend this approach to the Hall-Littlewood polynomials of type C, which are specializations of the corresponding Macdonald polynomials at q=0. We note that no analog of the Haglund-Haiman-Loehr formula exists beyond type A, so our work is a first step towards finding such a formula

Optimal prediction of folding rates and transition state placement from native state geometry

A variety of experimental and theoretical studies have established that the folding process of monomeric proteins is strongly influenced by the topology of the native state. In particular, folding times have been shown to correlate well with the contact order, a measure of contact locality. Our investigation focuses on identifying additional topologic properties that correlate with experimentally measurable quantities, such as folding rates and transition state placement, for both two- and three-state folders. The validation against data from forty experiments shows that a particular topologic property which measures the interdepedence of contacts, termed cliquishness or clustering coefficient, can account with significant accuracy both for the transition state placement and especially for folding rates, the linear correlation coefficient being $r=0.71$. This result can be further improved to $r=0.74$, by optimally combining the distinct topologic information captured by cliquishness and contact order.Comment: Revtex, 15 pages, 8 figure