相关论文: Resolution exchange simulation with incremental co…
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical…
Scanning Electron Microscopy (SEM) is pivotal in revealing intricate micro- and nanoscale features across various research fields. However, obtaining high-resolution SEM images presents challenges, including prolonged scanning durations and…
We created an efficient algorithm suitable for graphics processing units (GPUs) to perform Monte Carlo simulations of a subset of reaction-diffusion models. The algorithm uses techniques that are specific to GPU programming, and combines…
We propose a scheme for the creation of robust entanglement between a movable mirror and atomic ensemble at the macroscopic level in coupled optomechanical system. In experimentally accessible parameter regimes, we show that critical…
Diffusion models have gained popularity for generating images from textual descriptions. Nonetheless, the substantial need for computational resources continues to present a noteworthy challenge, contributing to time-consuming processes.…
Resampling is a standard step in particle filters and more generally sequential Monte Carlo methods. We present an algorithm, called chopthin, for resampling weighted particles. In contrast to standard resampling methods the algorithm does…
We address the problem of image color quantization using a Maximum Entropy based approach. Focusing on pixel mapping we argue that adding thermal noise to the system yields better visual impressions than that obtained from a simple energy…
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences. RE simulations involve the concurrent execution of independent simulations which infrequently interact and exchange information. The…
A new algorithm for Monte Carlo calculation of the double exchange model is studied. The algorithm is commonly applicable to wide classes of strongly correlated electron systems which involve itinerant electrons coupled with…
Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…
We describe a general radiative equilibrium and temperature correction procedure for use in Monte Carlo radiation transfer codes with sources of temperature-independent opacity, such as astrophysical dust. The technique utilizes the fact…
Flow-based generative super-resolution (SR) models learn to produce a diverse set of feasible SR solutions, called the SR space. Diversity of SR solutions increases with the temperature ($\tau$) of latent variables, which introduces random…
Sampling Boltzmann probability distributions plays a key role in machine learning and optimization, motivating the design of hardware accelerators such as Ising machines. While the Ising model can in principle encode arbitrary optimization…
We present a novel scattering emulator utilizing the complex scaling method to enhance nuclear reaction analysis. This approach leverages a single set of reduced bases, allowing for efficient and simultaneous emulation across multiple…
A method for integrating the chemical equations associated with nuclear combustion at high temperature is presented and extensively checked. Following the idea of E. M\"uller, the feedback between nuclear rates and temperature was taken…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
Markov Chain Monte Carlo (MCMC) underlies both statistical physics and combinatorial optimization, but mixes slowly near critical points and in rough landscapes. Parallel Tempering (PT) improves mixing by swapping replicas across…
We present a study of the parallel tempering (replica exchange) Monte Carlo method, with special focus on the feedback-optimized parallel tempering algorithm, used for generating an optimal set of simulation temperatures. This method is…
To fully leverage the power of image simulation to corroborate and explain patterns and structures in atomic resolution microscopy (e.g., electron and scanning probe), an initial correspondence between the simulation and experimental image…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…