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Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
Stochastic dynamical systems are fundamental in state estimation, system identification and control. System models are often provided in continuous time, while a major part of the applied theory is developed for discrete-time systems.…
The paper deals with the developing of the methodological backgrounds for the modeling and simulation of complex dynamical objects. Such backgrounds allow us to perform coordinate transformation and formulate the algorithm of its usage for…
Accurate simulation of dynamical processes in molecules and reactions is among the most challenging problems in quantum chemistry. Quantum computers promise efficient chemical simulation, but the existing quantum algorithms require many…
The modeling of complicated time-evolving physical dynamics from partial observations is a long-standing challenge. Particularly, observations can be sparsely distributed in a seemingly random or unstructured manner, making it difficult to…
Practical challenges in simulating quantum systems on classical computers have been widely recognized in the quantum physics and quantum chemistry communities over the past century. Although many approximation methods have been introduced,…
We extend the phase field crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
Quantum simulation is a foundational application for quantum computers, projected to offer insights into complex quantum systems beyond the reach of classical computation. However, with the exception of Trotter-based methods, which suffer…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
In cosmology numerical simulations of structure formation are now of central importance, as they are the sole instrument for providing detailed predictions of current cosmological models for a whole class of important constraining…
Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical…
Simulating key static and dynamic properties of matter -- from creation in the Big Bang to evolution into sub-atomic and astrophysical environments -- arising from the underlying fundamental quantum fields of the Standard Model and their…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
Molecular optimization is a fundamental goal in the chemical sciences and is of central interest to drug and material design. In recent years, significant progress has been made in solving challenging problems across various aspects of…
A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…