Related papers: Roadmap for Molecular Benchmarks in Nonadiabatic D…
Nonadiabaticity, i.e., the effect of mixing electronic states by nuclear motion, is a central phenomenon in molecular science. The strongest nonadiabatic effects arise due to the presence of conical intersections of electronic energy…
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…
We examine time-resolved X-ray diffraction from molecules in the gas phase which undergo nonadiabatic avoided-crossing dynamics involving strongly coupled electrons and nuclei. Several contributions to the signal are identified,…
Here we outline and test an extension of the energy grained master equation (EGME) for treating nonadiabatic (NA) hopping between different potential energy surfaces, which enables us to model the competition between stepwise collisional…
We lay the foundation for a benchmarking methodology for assessing current and future quantum computers. We pose and begin addressing fundamental questions about how to fairly compare computational devices at vastly different stages of…
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental…
Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular. The main obstacle seems to be the difficulty of parallelizing…
The interaction between electronic and vibrational degrees of freedom is an important mechanism in nonequilibrium charge transport through molecular nanojunctions. While adiabatic polaron-type coupling has been studied in great detail, new…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
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…
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…
Machine learning-based modeling of physical systems has experienced increased interest in recent years. Despite some impressive progress, there is still a lack of benchmarks for Scientific ML that are easy to use but still challenging and…
Scaling analysis exploiting timescale separation has been one of the most important techniques in the quantitative analysis of nonlinear dynamical systems in mathematical and theoretical biology. In the case of enzyme catalyzed reactions,…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
This work identifies geometric effects on dynamics due to nonadiabatic couplings in Born Oppenheimer systems and provides a systematic method for deriving corrections to mixed quantum-classical methods. Specifically, an exact path integral…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
The main obstacles to the realization of high-fidelity quantum gates are the control errors arising from inaccurate manipulation of a quantum system and the decoherence caused by the interaction between the quantum system and its…
Benchmarking is generally accepted as an important element in demonstrating the correctness of computer simulations. In the modern sense, a benchmark is a computer simulation result that has evidence of correctness, is accompanied by…