Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states

E Brunk, U Rothlisberger - Chemical reviews, 2015 - ACS Publications
The quantum nature of electrons and nuclei is manifested in countless biological events
including the rearrangements of electrons in biochemical reactions, electron and proton …

Coherence in Chemistry: Foundations and Frontiers

JD Schultz, JL Yuly, EA Arsenault, K Parker… - Chemical …, 2024 - ACS Publications
Coherence refers to correlations in waves. Because matter has a wave-particle nature, it is
unsurprising that coherence has deep connections with the most contemporary issues in …

Decoherence-induced surface hopping

HM Jaeger, S Fischer, OV Prezhdo - The Journal of chemical physics, 2012 - pubs.aip.org
A simple surface hopping method for nonadiabatic molecular dynamics is developed. The
method derives from a stochastic modeling of the time-dependent Schrödinger and master …

Intramolecular vibrations in excitation energy transfer: Insights from real-time path integral calculations

S Kundu, N Makri - Annual Review of Physical Chemistry, 2022 - annualreviews.org
Excitation energy transfer (EET) is fundamental to many processes in chemical and
biological systems and carries significant implications for the design of materials suitable for …

Non-Markovian entanglement dynamics in the presence of system-bath coherence

AG Dijkstra, Y Tanimura - Physical review letters, 2010 - APS
A complete treatment of the entanglement of two-level systems, which evolves through the
contact with a thermal bath, must include the fact that the system and the bath are not fully …

[HTML][HTML] Ab initio quantum direct dynamics simulations of ultrafast photochemistry with Multiconfigurational Ehrenfest approach

DV Makhov, C Symonds, S Fernandez-Alberti… - Chemical Physics, 2017 - Elsevier
Abstract The Multiconfigurational Ehrenfest (MCE) method is a quantum dynamics technique
which allows treatment of a large number of quantum nuclear degrees of freedom. This …

PathSum: A C++ and Fortran suite of fully quantum mechanical real-time path integral methods for (multi-) system+ bath dynamics

S Kundu, N Makri - The Journal of Chemical Physics, 2023 - pubs.aip.org
This paper reports the release of PATHSUM, a new software suite of state-of-the-art path
integral methods for studying the dynamics of single or extended systems coupled to …

Synthetic control of exciton dynamics in bioinspired cofacial porphyrin dimers

PP Roy, S Kundu, J Valdiviezo, G Bullard… - Journal of the …, 2022 - ACS Publications
Understanding how the complex interplay among excitonic interactions, vibronic couplings,
and reorganization energy determines coherence-enabled transport mechanisms is a grand …

Simulation of open quantum dynamics with bootstrap-based long short-term memory recurrent neural network

K Lin, J Peng, FL Gu, Z Lan - The Journal of Physical Chemistry …, 2021 - ACS Publications
The recurrent neural network with the long short-term memory cell (LSTM-NN) is employed
to simulate the long-time dynamics of open quantum systems. The bootstrap method is …

Quantum mechanics of dissipative systems

YJ Yan, RX Xu - Annu. Rev. Phys. Chem., 2005 - annualreviews.org
▪ Abstract Quantum dissipation involves both energy relaxation and decoherence, leading
toward quantum thermal equilibrium. There are several theoretical prescriptions of quantum …