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Reliable quantum chemical methods for the description of molecules with dense-lying frontier orbitals are needed in the context of many chemical compounds and reactions. Here, we review developments that led to our newcomputational toolbo x…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
The dynamics of many open quantum systems are described by stochastic master equations. In the discrete-time case, we recall the structure of the derived quantum filter governing the evolution of the density operator conditioned to the…
In ordinary, non-relativistic, quantum physics, time enters only as a parameter and not as an observable: a state of a physical system is specified at a given time and then evolved according to the prescribed dynamics. While the state can,…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
This paper aims at presenting a few models of quantum dynamics whose description involves the analysis of random unitary matrices for which dynamical localization has been proven to hold. Some models come from physical approximations…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Experimenting with metastability in recording devices leads us to wonder about an interface between equations of motion and the stillness of experimental records. Here we delineate an interface between wave functions as language to describe…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Ultracold atomic systems offer a unique tool for understanding behavior of matter in the quantum degenerate regime, promising studies of a vast range of phenomena covering many disciplines from condensed matter to quantum information and…
Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large,…
In this manuscript we present a theoretical framework and its numerical implementation to simulate the out-of-equilibrium electron dynamics induced by the interaction of ultrashort laser pulses in condensed-matter systems. Our approach is…
We propose a quantum tomography (QT) approach to retrieve the temporally evolving reduced density matrix in elecotronic state basis, where the populations and coherence between ground state and excited state are reconstructed from the…
Quantum technology has been rapidly growing due to its potential revolutionary applications. In particular, superconducting qubits provide a strong light-matter interaction as required for quantum computation and in principle can be scaled…
The density matrix in the Lindblad form is used to describe the behavior of the Free-Electron Laser (FEL) operating in a quantum regime. The detrimental effects of the spontaneous emission on coherent FEL operation are taken into account.…
Computational molecular modeling and visualization has seen significant progress in recent years with sev- eral molecular modeling and visualization software systems in use today. Nevertheless the molecular biology community lacks…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…