Related papers: An efficient Cellular Potts Model algorithm that f…
We propose a Multi-Cell Monte Carlo algorithm, or (MC)^2, for predicting stable phases in chemically complex crystalline systems. Free atomic transfer among cells is achieved via the application of the lever rule, where an assigned molar…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
Simulated tempering is popular method of allowing MCMC algorithms to move between modes of a multimodal target density {\pi}. One problem with simulated tempering for multimodal targets is that the weights of the various modes change for…
In this work, we develop a stochastic matrix product state (stoMPS) approach that combines the MPS technique and Monte Carlo samplings and can be applied to simulate quantum lattice models down to low temperature. In particular, we exploit…
We propose an efficient method for Monte Carlo simulation of quantum lattice models. Unlike most other quantum Monte Carlo methods, a single run of the proposed method yields the free energy and the entropy with high precision for the whole…
The Markov entropy decomposition (MED) is a recently-proposed, cluster-based simulation method for finite temperature quantum systems with arbitrary geometry. In this paper, we detail numerical algorithms for performing the required steps…
We describe CPMC-Lab, a Matlab program for the constrained-path and phaseless auxiliary-field Monte Carlo methods. These methods have allowed applications ranging from the study of strongly correlated models, such as the Hubbard model, to…
We employ the Partially Saturated Cells Method (PSM) to model the interaction between the fluid flow and solid moving objects as an extension to the conventional lattice Boltzmann method. We introduce an efficient and accurate method for…
Previous partial permutation synchronization (PPS) algorithms, which are commonly used for multi-object matching, often involve computation-intensive and memory-demanding matrix operations. These operations become intractable for large…
The numerical treatment of fluid-particle systems is a very challenging problem because of the complex coupling phenomena occurring between the two phases. Although accurate mathematical modelling is available to address this kind of…
In this article we create a new algorithm for the perfect simulation of the infinite Potts model at a sufficiently small or at a sufficiently high temperature, in particular under the transition phase temperature. We study the model for…
We propose and use a novel, hybrid Monte Carlo algorithm that combines configurational bias particle swaps with parallel tempering. We use this new method to simulate a standard model of a glass forming binary mixture above and below the…
The invaded cluster algorithm, a new method for simulating phase transitions, is described in detail. Theoretical, albeit nonrigorous, justification of the method is presented and the algorithm is applied to Potts models in two and three…
Perfectly-Matched Layers (PML) are widely used in Particle-In-Cell simulations, in order to absorb electromagnetic waves that propagate out of the simulation domain. However, when charged particles cross the interface between the simulation…
We present a new Monte Carlo muon propagation algorithm MUM (MUons+Medium) which possesses some advantages over analogous algorithms presently in use. The most important features of algorithm are described. Results on the test for accuracy…
Random batch algorithms are constructed for quantum Monte Carlo simulations. The main objective is to alleviate the computational cost associated with the calculations of two-body interactions, including the pairwise interactions in the…
Uncertainty quantification (UQ) in Large Language Models (LLMs) is essential for their safe and reliable deployment, particularly in critical applications where incorrect outputs can have serious consequences. Current UQ methods typically…
Memory-bound algorithms show complex performance and energy consumption behavior on multicore processors. We choose the lattice-Boltzmann method (LBM) on an Intel Sandy Bridge cluster as a prototype scenario to investigate if and how…
We present a sub-matrix update algorithm for the continuous-time auxiliary field method that allows the simulation of large lattice and impurity problems. The algorithm takes optimal advantage of modern CPU architectures by consistently…
In this paper, we address the modeling issues of cell movement and division with a special focus on the phenomenon of volume exclusion in a lattice-based, exact stochastic simulation framework. We propose a new exact method, called Reduced…