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A class of analog computers built from large numbers of microscopic probabilistic machines is discussed. It is postulated that such computers are implemented in biological systems as ensembles of protein molecules. The formalism is based on…
Time domain simulations of electromagnetic problems are highly valuable in engineering applications, as they allow for the analysis of transient behavior and broadband responses. These simulations utilize time stepping schemes, where each…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
Economic model predictive control (EMPC) is a promising methodology for optimal operation of dynamical processes that has been shown to improve process economics considerably. However, EMPC performance relies heavily on the accuracy of the…
Numerical simulation of the complex plasma dynamics associated with high power, high frequency microwave breakdown at high pressures, leading to the formation of filamentary plasma structures such as self-organized plasma arrays, is a…
State-of-the-art models represent proteins and molecules in separate embedding manifolds, limiting the modeling of systemic biological processes. We introduce ReactEmbed, a lightweight, plug-and-play module that bridges this gap. ReactEmbed…
This work aims to extend the residual distribution (RD) framework to stiff relaxation problems. The RD is a class of schemes which is used to solve hyperbolic system of partial differential equations. Up to our knowledge, it was used only…
We present an implementation of Smoothed Particle Hydrodynamics (SPH) in an adaptive-mesh PPPM algorithm. The code evolves a mixture of purely gravitational particles and gas particles. The code retains the desirable properties of previous…
The conformational kinetics of enzymes can be reliably revealed when they are governed by Markovian dynamics. Hidden Markov Models (HMMs) are appropriate especially in the case of conformational states that are hardly distinguishable.…
The emergence of new nanoporous materials, based e.g. on 2D materials, offers new avenues for water filtration and energy. There is accordingly a need to investigate the molecular mechanisms at the root of the advanced performances of these…
The problem of successfully simulating ionic fluids at low temperature and low density states is well known in the simulation literature: using conventional methods, the system is not able to equilibrate rapidly due to the presence of…
Discrete-state stochastic models are a popular approach to describe the inherent stochasticity of gene expression in single cells. The analysis of such models is hindered by the fact that the underlying discrete state space is extremely…
In this paper, a new adaptive multi-batch experience replay scheme is proposed for proximal policy optimization (PPO) for continuous action control. On the contrary to original PPO, the proposed scheme uses the batch samples of past…
We present a new implementation of radiation hydrodynamics (RHD) in the adaptive mesh refinement (AMR) code RAMSES. The multi-group radiative transfer (RT) is performed on the AMR grid with a first-order Godunov method using the M1 closure…
In calculations of heavy-atom molecules with the shape-consistent Relativistic Effective Core Potential (RECP), only valence and some outer-core shells are treated explicitly, the shapes of spinors are smoothed in the atomic core regions…
Progress in Prognostics and Health Management (PHM) is hindered by the lack of standardized and reusable evaluation practices across tasks, datasets, and application domains. Reported results are often difficult to reproduce and compare, as…
Recently it has been found that stable and accurate molecular dynamics (MD) of B-DNA duplexes can be obtained in relatively inexpensive computational conditions with the bulk solvent represented implicitly, but the minor groove filled with…
Regular expression (regex) matching is fundamental in many applications, especially in web services. However, matching by backtracking -- preferred by most real-world implementations for its practical performance and backward compatibility…
Reservoir computing (RC) represents a class of state-space models (SSMs) characterized by a fixed state transition mechanism (the reservoir) and a flexible readout layer that maps from the state space. It is a paradigm of computational…
An algorithm for the simulation of the evolution of slightly entangled quantum states has been recently proposed as a tool to study time-dependent phenomena in one-dimensional quantum systems. Its key feature is a time-evolving…