Related papers: Transfer matrix algorithm for computing the exact …
We present a method to approximate partition functions of quantum systems using mixed-state quantum computation. For positive semi-definite Hamiltonians, our method has expected running-time that is almost linear in $(M/(\epsilon_{\rm…
We determine the scaling exponents of polymer translocation (PT) through a nanopore by extensive computer simulations of various microscopic models for chain lengths extending up to N=800 in some cases. We focus on the scaling of the…
An algorithm for computing an analytic function of a matrix $A$ is described. The algorithm is intended for the case where $A$ has some close eigenvalues, and clusters (subsets) of close eigenvalues are separated from each other. This…
The pivot algorithm is a Markov Chain Monte Carlo algorithm for simulating the self-avoiding walk. At each iteration a pivot which produces a global change in the walk is proposed. If the resulting walk is self-avoiding, the new walk is…
Obtaining reliable estimates of the statistical properties of complex macromolecules by computer simulation is a task that requires high computational effort as well as the development of highly efficient simulation algorithms. We present…
We study numerical integration of smooth functions defined over the $s$-dimensional unit cube. A recent work by Dick et al. (2019) has introduced so-called extrapolated polynomial lattice rules, which achieve the almost optimal rate of…
This paper presents a novel meta algorithm, Partition-Merge (PM), which takes existing centralized algorithms for graph computation and makes them distributed and faster. In a nutshell, PM divides the graph into small subgraphs using our…
We propose a divide-and-conquer algorithm to find recursively the Scattering matrix of general tight-binding structures. The Scattering matrix allows a direct calculation of transport properties in mesoscopic systems by using the Landauer…
For many hard computational problems, simple algorithms that run in time $2^n \cdot n^{O(1)}$ arise, say, from enumerating all subsets of a size-$n$ set. Finding (exponentially) faster algorithms is a natural goal that has driven much of…
We present a new exact algorithm for estimating all elements of the quark propagator. The advantage of the method is that the exact all-to-all propagator is reproduced in a large but finite number of inversions. The efficacy of the…
We propose a novel stochastic algorithm that randomly samples entire rows and columns of the matrix as a way to approximate an arbitrary matrix function using the power series expansion. This contrasts with existing Monte Carlo methods,…
We present an efficient algorithm for computing the exact exchange contributions in the Hartree-Fock and hybrid density functional theory models on the basis of the fast multipole method (FMM). Our algorithm is based on the observation that…
We study the efficiency of the incomplete enumeration algorithm for linear and branched polymers. There is a qualitative difference in the efficiency in these two cases. The average time to generate an independent sample of $n$ sites for…
The separability of clusters is one of the most desired properties in clustering. There is a wide range of settings in which different clusterings of the same data set appear. We are interested in applications where there is a need for an…
We describe the first nearly linear-time approximation algorithms for explicitly given mixed packing/covering linear programs, and for (non-metric) fractional facility location. We also describe the first parallel algorithms requiring only…
The current best practice for computing optimal transport (OT) is via entropy regularization and Sinkhorn iterations. This algorithm runs in quadratic time as it requires the full pairwise cost matrix, which is prohibitively expensive for…
Exact diagonalization is a well-established method for simulating small quantum systems. Its applicability is limited by the exponential growth of the so-called Hamiltonian matrix that needs to be diagonalized. Physical symmetries are…
Computation of the trace of a matrix function plays an important role in many scientific computing applications, including applications in machine learning, computational physics (e.g., lattice quantum chromodynamics), network analysis and…
We present exact calculations of the partition function for the q-state Potts model for general q, temperature and magnetic field on strips of the square lattices of width $L_{y}=2$ and arbitrary length $L_x = m $ with periodic longitudinal…
We develop off-lattice simulations of semiflexible polymer chains subjected to applied mechanical forces using Markov Chain Monte Carlo. Our approach models the polymer as a chain of fixed-length bonds, with configurations updated through…