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A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…
A reduced-complexity variant of equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) method is formulated in terms of state-averaged excited state pair natural orbitals (PNO) designed to describe manifolds of excited states.…
Modeling of dynamic processes in nuclear reactors is carried out, mainly, on the basis of the multigroup diffusion approximation for the neutron flux. The basic model includes a multidimensional set of coupled parabolic equations and…
Accurate exploration of protein conformational ensembles is essential for uncovering function but remains hard because molecular-dynamics (MD) simulations suffer from high computational costs and energy-barrier trapping. This paper presents…
Performing a stable, long duration simulation of driven MHD turbulence with a high thermal Mach number and a strong initial magnetic field is a challenge to high-order Godunov ideal MHD schemes because of the difficulty in guaranteeing…
Numerous aqueous systems host elements in multiple redox states, with wide ranging implications such as their influence on the formation/dissolution of minerals, water toxicity, and nutrient cycling. To uncover governing mechanisms and…
Computational Fluid Dynamics (CFD) simulations are often constrained by the memory-bound nature of sparse matrix-vector operations, which eventually limits performance on modern high-performance computing (HPC) systems. This work introduces…
Intrinsically disordered proteins (IDPs) play a significant role in intracellular phenomena and are known to exist in an ensemble of inter-converting conformations in solution. Accurately modeling the conformations of IDPs in solution poses…
We treat the accurate simulation of the calcination reaction in particles, where the particles are large and, thus, the inner-particle processes must be resolved. Because these processes need to be described with coupled partial…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…
Experiment Directed Simulations (EDS) is a method within a class of techniques seeking to improve molecular simulations by minimally biasing the system Hamiltonian to reproduce certain experimental observables. In a previous application of…
The Shallow Recurrent Decoder networks are a novel paradigm recently introduced for state estimation, combining sparse observations with high-dimensional model data. This architecture features important advantages compared to standard…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
Extended dynamic mode decomposition (EDMD) is a popular data-driven method to predict the action of the Koopman operator, i.e., the evolution of an observable function along the flow of a dynamical system. In this paper, we leverage a…
While diffusion models can learn complex distributions, sampling requires a computationally expensive iterative process. Existing distillation methods enable efficient sampling, but have notable limitations, such as performance degradation…
We propose a demonstration-efficient strategy to compress a computationally expensive Model Predictive Controller (MPC) into a more computationally efficient representation based on a deep neural network and Imitation Learning (IL). By…
The development of small- and no-ELM regimes for ITER is a high priority topic due to the risks associated to type-I ELMs. By considering non-linear extended MHD simulations of the ASDEX Upgrade tokamak with the JOREK code, we probe a…
Stable oxygen sites on a PdO film over a Pd(100) thin structures with a (sqrt{5} times sqrt{5}) R27^circ surface-unit cell are determined using the first-principles electronic structure calculations with the generalized gradient…
Motivation: Modeling biological signaling networks using ordinary differential equations (ODEs) has proven to be a powerful technique for generating insight into cellular dynamics, but it typically requires estimating rate parameters based…