Related papers: Particle-based simulation of non-elementary bimole…
The simulation of chemical reactions is an anticipated application of quantum computers. Using a Diels-Alder reaction as a test case, in this study we explore the potential applications of quantum algorithms and hardware in investigating…
An accurate treatment of the structures and dynamics that lead to enhanced chemical reactivity in enzymes requires explicit treatment of both electronic and nuclear quantum effects. The former can be captured in ab initio molecular dynamics…
Semiclassical approximations for quantum dynamic simulations in complex chemical systems range from rigorously accurate methods that are computationally expensive to methods that exhibit near-classical scaling with system size but are…
Mixed-quantum-classical molecular dynamics simulation implies an effective measurement on the electronic states owing to continuously tracking the atomic forces.Based on this insight, we propose a quantum trajectory mean-field approach for…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
Simulations of chemical dynamics are a powerful means for understanding chemistry. However, classical computers struggle to simulate many chemical processes, especially non-adiabatic ones, where the Born-Oppenheimer approximation breaks…
In this dissertation, a fully object-oriented, fully relativistic, multi-dimensional Particle-In-Cell code was developed and applied to answer key questions in plasma-based accelerator research. The simulations increase the understanding of…
This work introduces a unified emulation framework for studying continuum physics in finite quantum systems. Using a reduced basis method, we construct powerful emulators for the inhomogeneous Schr\"{o}dinger equation that operate in a…
The nonlinear space-charge effects play an important role in high intensity/high brightness accelerators. These effects can be self-consistently studied using multi-particle simulations. In this lecture, we will discuss the particle-in-cell…
Reaction-diffusion processes play an important role in a variety of physical, chemical, and biological systems. Conventionally, the kinetics of these processes are described by the law of mass action. However, there are various cases where…
Particle acceleration in collisionless plasma systems is a central question in astroplasma and astroparticle physics. The structure of the acceleration regions, electron-ion energy equilibration, preacceleration of particles at shocks to…
We present the first quantum-centric simulations of noncovalent interactions using a supramolecular approach. We simulate the potential energy surfaces (PES) of the water and methane dimers, featuring hydrophilic and hydrophobic…
We demonstrate that networks of locally connected processing units with a primitive learning capability exhibit behavior that is usually only attributed to quantum systems. We describe networks that simulate single-photon beam-splitter and…
In our recent work [H. Zhang, F.X. Trias, A. Oliva, D. Yang, Y. Tan, Y. Sheng. PIBM: Particulate immersed boundary method for fluid-particle interaction problems. Powder Technology. 272(2015), 1-13.], a particulate immersed boundary method…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
Studying chemical reactions, particularly in the gas phase, relies heavily on computing scattering matrix elements. These elements are essential for characterizing molecular reactions and accurately determining reaction probabilities.…
In this paper, we focus on the data-driven discovery of a general second-order particle-based model that contains many state-of-the-art models for modeling the aggregation and collective behavior of interacting agents of similar size and…
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent…
The analysis of data from multiple experiments, such as observations of several individuals, is commonly approached using mixed-effects models, which account for variation between individuals through hierarchical representations. This makes…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…