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We apply the "weighted ensemble" (WE) simulation strategy, previously employed in the context of molecular dynamics simulations, to a series of systems-biology models that range in complexity from one-dimensional to a system with 354…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here we reveal their potential as quantum…
Understanding complex chemical systems -- such as biomolecules, catalysts, and novel materials -- is a central goal of quantum simulations. Near-term strategies hinge on the use of variational quantum eigensolver (VQE) algorithms combined…
This paper presents a novel density estimation method for anomaly detection using density matrices (a powerful mathematical formalism from quantum mechanics) and Fourier features. The method can be seen as an efficient approximation of…
By considering momentum transfer in the Fermi constraint procedure, the stability of the initial nuclei and fragments produced in heavy-ion collisions can be further improved in the quantum molecular dynamics simulations. The case of the…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
Attochemistry aims to exploit the properties of coherent electronic wavepackets excited via attosecond pulses, to control the formation of photoproducts. Such molecular processes can in principle be simulated with various nonadiabatic…
Network traffic classification using self-supervised pre-training models based on Masked Autoencoders (MAE) has demonstrated a huge potential. However, existing methods are confined to isolated byte-level reconstruction of individual flows,…
The Axion Resonant InterAction Detection Experiment (ARIADNE) is a collaborative effort to search for the QCD axion using techniques based on nuclear magnetic resonance. In the experiment, axions or axion-like particles would mediate…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support…
We introduce KiNetX, a fully automated meta-algorithm for the kinetic analysis of complex chemical reaction networks derived from semi-accurate but efficient electronic structure calculations. It is designed to (i) accelerate the automated…
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…
Temporal analysis of products (TAP) reactors enable experiments that probe numerous kinetic processes within a single set of experimental data through variations in pulse intensity, delay, or temperature. Selecting additional TAP…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
An accelerated polynomial expansion scheme to construct the density matrix in quantum mechanical molecular dynamics simulations is proposed. The scheme is based on recursive density matrix expansions, e.g. [Phys. Rev. B. 66 (2002), p.…
Fueled by advances in hardware and algorithm design, large-scale automated explorations of chemical reaction space have become possible. Here, we present our approach to an open-source, extensible framework for explorations of chemical…
We introduce a novel enhanced sampling approach named OPES flooding for calculating the kinetics of rare events from atomistic molecular dynamics simulation. This method is derived from the On-the-fly-Probability-Enhanced-Sampling (OPES)…
Kernel density estimation on a finite interval poses an outstanding challenge because of the well-recognized bias at the boundaries of the interval. Motivated by an application in cancer research, we consider a boundary constraint linking…