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We describe optimized parallel tempering simulations of the 46-residue B-fragment of protein A. Native-like configurations with a root-mean-square deviation of approximately 3A to the experimentally determined structure (Protein Data Bank…
Extremal optimization is a new general-purpose method for approximating solutions to hard optimization problems. We study the method in detail by way of the NP-hard graph partitioning problem. We discuss the scaling behavior of extremal…
Using molecular dynamics computer simulations we investigate how in silica the glass transition and the properties of the resulting glass depend on the cooling rate with which the sample is cooled. By coupling the system to a heat bath with…
Many big-data clusters store data in large partitions that support access at a coarse, partition-level granularity. As a result, approximate query processing via row-level sampling is inefficient, often requiring reads of many partitions.…
Cooling of particles to mK-temperatures is essential for a variety of experiments with trapped charged particles. However, many species of interest lack suitable electronic transitions for direct laser cooling. We study theoretically the…
We investigate the scheduling of $n$ jobs divided into $c$ classes on $m$ identical parallel machines. For every class there is a setup time which is required whenever a machine switches from the processing of one class to another class.…
We give a rigorous complexity analysis of the simulated annealing algorithm by Kalai and Vempala [Math of OR 31.2 (2006): 253-266] using the type of temperature update suggested by Abernethy and Hazan [arXiv 1507.02528v2, 2015]. The…
In this paper, we design efficient algorithms to approximately count the number of edges of a given $k$-hypergraph, and to sample an approximately uniform random edge. The hypergraph is not given explicitly, and can be accessed only through…
Recent research has developed several Monte Carlo methods for estimating the normalization constant (partition function) based on the idea of annealing. This means sampling successively from a path of distributions that interpolate between…
We present a new approach to study the thermodynamic properties of $d$-dimensional classical systems by reducing the problem to the computation of ground state properties of a $d$-dimensional quantum model. This classical-to-quantum mapping…
This paper deals with the stochastic Ising model with a temperature shrinking to zero as time goes to infinity. A generalization of the Glauber dynamics is considered, on the basis of the existence of simultaneous flips of some spins. Such…
In this paper, we demonstrate the efficiency of simulations via direct computation of the partition function under various macroscopic conditions, such as different temperatures or volumes. The method can compute partition functions by…
The problem of sampling edge-colorings of graphs with maximum degree $\Delta$ has received considerable attention and efficient algorithms are available when the number of colors is large enough with respect to $\Delta$. Vizing's theorem…
We prove a hardness of sampling result for the anti-ferromagnetic Ising model on random graphs of average degree $d$ for large constant $d$, proving that when the normalized inverse temperature satisfies $\beta>1$ (asymptotically…
Recent inapproximability results of Sly (2010), together with an approximation algorithm presented by Weitz (2006) establish a beautiful picture for the computational complexity of approximating the partition function of the hard-core…
We initiate the study of numerical linear algebra in the sliding window model, where only the most recent $W$ updates in a stream form the underlying data set. We first introduce a unified row-sampling based framework that gives randomized…
This paper considers the problem of cardinality estimation in data stream applications. We present a statistical analysis of probabilistic counting algorithms, focusing on two techniques that use pseudo-random variates to form…
Motivated by the study of matrix elimination orderings in combinatorial scientific computing, we utilize graph sketching and local sampling to give a data structure that provides access to approximate fill degrees of a matrix undergoing…
We study the spin n-point functions of the planar Ising model on a simply connected domain \Omega discretised by the square lattice \delta\mathbb{Z}^{2} under near-critical scaling limit. While the scaling limit on the full-plane \mathbb{C}…
The topic we address in this paper concerns the minimization of a Hamiltonian function for an Ising model through the application of simulated annealing algorithms based on (single-site) Glauber dynamics and stochastic cellular automata…