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There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…

Biomolecules · Quantitative Biology 2023-05-24 Malin Luking , David van der Spoel , Johan Elf , Gareth A. Tribello

Vibrational dynamics in conventional molecules usually takes place on a timescale of picoseconds or shorter. A striking exception are ultralong-range Rydberg molecules, for which dynamics is dramatically slowed down as a consequence of the…

We consider the certification of temporal quantum correlations using the pseudo-density matrix (PDM), an extension of the density matrix to the time domain, where negative eigenvalues are key indicators of temporal correlations.…

Quantum Physics · Physics 2025-04-25 Hongfeng Liu , Zhenhuan Liu , Shu Chen , Xinfang Nie , Xiangjing Liu , Dawei Lu

Precision spectroscopy of atoms and molecules allows one to search for and to put stringent limits on the variation of fundamental constants. These experiments are typically interpreted in terms of variations of the fine structure constant…

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…

Chemical Physics · Physics 2014-08-08 Wei Feng , Luting Xu , Xin-Qi Li , Weihai Fang , YiJing Yan

Exposing a molecule to intense light pulses may bring this molecule to a nonstationary quantum state, thus launching correlated dynamics of electronic and nuclear subsystems. Although much had been achieved in the understanding of…

Chemical Physics · Physics 2024-04-11 Nikolay V. Golubev , Jiří Vaníček

The rotating-wave approximation to light-matter interactions is widely used in the quantum electrodynamics Hamiltonian; however, its validity has long been a matter of debate. In this article, we explore the impact of the rotating-wave…

Quantum Physics · Physics 2024-03-04 Yi-Ting Chuang , Liang-Yan Hsu

In this manuscript, we undertake an examination of a classical plasma deployed on two finite co-planar surfaces: a circular region $\Omega_{in}$ into an annular region $\Omega_{out}$ with a gap in between. It is studied both from the point…

Statistical Mechanics · Physics 2024-07-02 Robert Salazar , Cristian Cobos , Diego Jaramillo , Camilo Bayona

Recording molecular movies on ultrafast timescales has been a longstanding goal for unravelling detailed information about molecular dynamics. We present the direct experimental recording of very-high-resolution and -fidelity molecular…

We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non uniform density profile. Results match quite well as long as the lengthscale of density…

We introduce a theoretical framework for resource-efficient characterization and control of non-Markovian open quantum systems, which naturally allows for the integration of given, experimentally motivated, control capabilities and…

We describe a framework for interactive molecular dynamics in a multiuser virtual reality environment, combining rigorous cloud-mounted physical atomistic simulation with commodity virtual reality hardware, which we have made accessible to…

Quantum material systems upon applying ultrashort laser pulses provide a rich platform to access excited material phases and their transformations that are not entirely like their equilibrium counterparts. The addressability and potential…

Strongly Correlated Electrons · Physics 2021-08-19 Xiaoyi Sun , Shuaishuai Sun , Chong-Yu Ruan

In the past two decades, the density matrix renormalization group (DMRG) has emerged as an innovative new method in quantum chemistry relying on a theoretical framework very different from that of traditional electronic structure…

Computational Physics · Physics 2020-02-18 Alberto Baiardi , Markus Reiher

Quantum Molecular Dynamics (QMD) calculations of central collisions between heavy nuclei are used to study fragment production and the creation of collective flow. It is shown that the final phase space distributions are compatible with the…

Quantum mechanics/molecular mechanics (QM/MM) is a standard computational tool for describing chemical reactivity in systems with many degrees of freedom, including polymers, enzymes, and reacting molecules in complex solvents. However,…

Chemical Physics · Physics 2020-07-22 Alexander V. Mironenko , Gregory A. Voth

Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…

Distributed, Parallel, and Cluster Computing · Computer Science 2014-03-03 Jana Pazúriková

Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…

Computational Physics · Physics 2022-06-22 Ludwig Winkler , Klaus-Robert Müller , Huziel E. Sauceda

We investigate ultrafast vibronic dynamics triggered by intense femtosecond infrared pulses in small molecules. Our study is based on numerical simulations performed with 2D model molecules, and analyzed in the perspective of the renown…

This paper introduces a novel approach to probabilistic deep learning, kernel density matrices, which provide a simpler yet effective mechanism for representing joint probability distributions of both continuous and discrete random…

Machine Learning · Computer Science 2024-05-01 Fabio A. González , Raúl Ramos-Pollán , Joseph A. Gallego-Mejia
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