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We present an algorithm for the optimization and thermal equilibration of spin glasses - or more generally, cost functions of the Ising form $H=\sum_{\langle i j\rangle} J_{ij} s_i s_j + \sum_i h_i s_i$, defined on graphs with arbitrary…
We describe a generalized scheme for the probability-changing cluster (PCC) algorithm, based on the study of the finite-size scaling property of the correlation ratio, the ratio of the correlation functions with different distances. We…
We have proposed a cluster heat bath method in Monte Carlo simulations of Ising models in which one of the possible spin configurations of a cluster is selected in accordance with its Boltzmann weight. We have argued that the method…
Magnetron sputtering is an essential technique in combinatorial materials science, enabling the efficient synthesis of thin-film materials libraries with continuous compositional gradients. For exploring multidimensional search spaces,…
We present a novel and open-source implementation of the worm algorithm, which is an algorithm to simulate Bose-Hubbard and sign-positive spin models using a path integral representation of the partition function. The code can deal with…
We introduce a new update scheme to systematically improve the efficiency of parallel tempering simulations. We show that by adapting the number of sweeps between replica exchanges to the canonical autocorrelation time, the average…
Using a cluster-flipping Monte Carlo algorithm combined with a generalization of the histogram reweighting scheme of Ferrenberg and Swendsen, we have studied the equilibrium properties of the thermal random-field Ising model on a cubic…
Variational Monte Carlo studies employing projected entangled-pair states (PEPS) have recently shown that they can provide answers on long-standing questions such as the nature of the phases in the two-dimensional $J_1 - J_2$ model. The…
Calibration of individual based models (IBMs), successful in modeling complex ecological dynamical systems, is often performed only ad-hoc. Bayesian inference can be used for both parameter estimation and uncertainty quantification, but its…
Monte Carlo simulations are useful tools for modeling quantum systems, but in some cases they suffer from a sign problem, leading to an exponential slow down in their convergence to a value. While solving the sign problem is generically…
We present a detailed description of the idea and procedure for the newly proposed Monte Carlo algorithm of tuning the critical point automatically, which is called the probability-changing cluster (PCC) algorithm [Y. Tomita and Y. Okabe,…
The method for calculation of the correlation functions of the Ising-type systems with short-range interaction and with arbitrary value of spin is developed within cluster approximation. For the Ising model (spin $S^z=\pm1$) the expressions…
ConIII (pronounced CON-ee) is an open-source Python project providing a simple interface to solving the pairwise and higher order Ising model and a base for extension to other maximum entropy models. We describe the maximum entropy problem…
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.…
The high-performance scalable parallel algorithm for rigorous calculation of partition function of lattice systems with finite number Ising spins was developed. The parallel calculations run by C++ code with using of Message Passing…
We report single-cluster Monte Carlo simulations of the Ising model on three-dimensional Poissonian random lattices with up to 128,000 approx. 503 sites which are linked together according to the Voronoi/Delaunay prescription. For each…
The two-component cold atom systems with anisotropic hopping amplitudes can be phenomenologically described by a two-dimensional Ising-XY coupled model with spatial anisotropy. At low temperatures, theoretical predictions [Phys. Rev. A 72,…
We introduce an exact algorithm for the computation of spin correlation functions for the two dimensional +/-J Ising spin glass in the ground state. Unlike with the transfer matrix method, there is no particular restriction on the shape of…
A sampling method for spin systems is presented. The spin lattice is written as the union of a nested sequence of sublattices, all but the last with conditionally independent spins, which are sampled in succession using their marginals. The…
Realizing compact and scalable Ising machines that are compatible with CMOS-process technology is crucial to the effectiveness and practicality of using such hardware platforms for accelerating computationally intractable problems. Besides…