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Quantum computation is an attractive front for many problems that are intractable for computers today. One such problem is nonadiabatic quantum molecular dynamics, where quantized internal states coupling to parameterized modes result in a…
We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…
The modeling and simulation of coupled neuromusculoskeletal-exoskeletal systems play a crucial role in human biomechanical analysis, as well as in the design and control of exoskeletons. However, conventional dynamic simulation frameworks…
We provide a pedagogical approach to the problem of avoided crossings between electronic molecular curves and to diabatic and adiabatic transitions when the nuclei of a diatomic molecule move according to classical mechanics. For simplicity…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Quantum simulation has begun to penetrate the field of quantum chemistry in hopes of efficiently calculating ground state energies and approximating real-time evolution. With modern research highlighting nonadiabatic dynamics, tunably…
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…
An extension of the CCS-method [Chem. Phys. 2004, 304, p. 103-120] for simulating non-adiabatic dynamics with quantum effects of the nuclei is put forward. The time-dependent Schr\"{o}dinger equation for the motion of the nuclei is solved…
Describing dynamic medical systems using machine learning is a challenging topic with a wide range of applications. In this work, the possibility of modeling the blood glucose level of diabetic patients purely on the basis of measured data…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
This review article discusses advances in the use of time-resolved photoelectron spectroscopy for the study of non-adiabatic processes in molecules. A theoretical treatment of the experiments is presented together with a number of…
Trajectory-based mixed quantum-classical approaches to coupled electron-nuclear dynamics suffer from well-studied problems such as the lack of (or incorrect account for) decoherence in the trajectory surface hopping method and the inability…
We implement a rare-event sampling scheme for quantifying the rate of thermally-activated nonadiabatic transitions in the condensed phase. Our QM/MM methodology uses the recently developed INAQS package to interface between an elementary…
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of…
Choosing an appropriate representation of the molecular Hamiltonian is one of the challenges faced by simulations of the nonadiabatic quantum dynamics around a conical intersection. The adiabatic, exact quasidiabatic, and strictly diabatic…
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach…
Nonadiabatic quantum interferences emerge whenever nuclear wavefunctions in different electronic states meet and interact in a nonadiabatic region. In this work, we analyze how nonadiabatic quantum interferences translate in the context of…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…
The interfaces between metal electrodes and liquid electrolytes are prototypical in electrochemistry. That is why it is crucial to have a molecular and dynamical understating of such interfaces for both electrical properties and chemical…