Modelling of quantum information processing with Ehrenfest guided tra jectories: a case study

We apply a numerical method based on multi-configurational Ehrenfest tra jectories, and demonstrate converged results for the Choi fidelity of an entangling quantum gate between two two-level systems interacting through a set of bosonic modes. We consider both spin-boson and rotating wave Hamiltonians, for various numbers of mediating modes (from 1 to 100), and extend our treatment to include finite temperatures. Our results apply to two-level impurities interacting with the same band of a photonic crystal, or to two distant ions interacting with the same set of motional degrees of freedom.Comment: 12 pages, figures aplent

The effect of sampling techniques used in the multiconfigurational Ehrenfest method

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks

Simulation of protein pulling dynamics on second time scale with boxed molecular dynamics

We demonstrate how recently developed Boxed Molecular Dynamics (BXD) and kinetics [D. V. Shalashilin et al., J. Chem. Phys. 137, 165102 (2012)] can provide a kinetic description of protein pulling experiments, allowing for a connection to be made between experiment and the atomistic protein structure. BXD theory applied to atomic force microscopy unfolding is similar in spirit to the kinetic two-state model [A. Noy and R. W. Friddle, Methods 60, 142 (2013)] but with some differences. First, BXD uses a large number of boxes, and therefore, it is not a two-state model. Second, BXD rate coefficients are obtained from atomistic molecular dynamics simulations. BXD can describe the dependence of the pulling force on pulling speed. Similar to Shalashilin et al. [J. Chem. Phys. 137, 165102 (2012)], we show that BXD is able to model the experiment at a very long time scale up to seconds, which is way out of reach for standard molecular dynamics

Simulation of ultrafast photodynamics of pyrrole with a multiconfigurational Ehrenfest method

We report the first results of ab initio multiconfigurational Ehrenfest simulations of pyrrole photodynamics. We note that, in addition to the two intersections of 11A2 and 11B1 states with the ground state 11A1, which are known to be responsible for N–H bond fission, another intersection between the 12A2 and 12B1 states of the resulting molecular radical becomes important after the departure of the H atom. This intersection, which is effectively between the two lowest electronic states of the pyrrolyl radical, may play a significant role in explaining the branching ratio between the two states observed experimentally. The exchange of population between the two states of pyrrolyl occurs on a longer scale than that of N–H bond fission

An ab initio multiple cloning approach for the simulation of photoinduced dynamics in conjugated molecules

We present a new implementation of the Ab Initio Multiple Cloning (AIMC) method, which is applied for non-adiabatic excited-state molecular dynamics simulations of photoinduced processes in conjugated molecules. Within our framework, the multidimensional wave-function is decomposed into a superposition of a number of Gaussian coherent states guided by Ehrenfest trajectories that are suited to clone and swap their electronic amplitudes throughout the simulation. New generalized cloning criteria are defined and tested. Because of sharp changes of the electronic states, which are common for conjugated polymers, the electronic parts of the Gaussian coherent states are represented in the Time Dependent Diabatic Basis (TDDB). The input to these simulations in terms of the excited-state energies, gradients and non-adiabatic couplings, is calculated on-the-fly using the Collective Electron Oscillator (CEO) approach. As a test case, we consider the photoinduced unidirectional electronic and vibrational energy transfer between two- and three-ring linear poly(phenylene ethynylene) units linked by meta-substitution. The effects of the cloning procedure on electronic and vibrational coherence, relaxation and unidirectional energy transfer between dendritic branches are discussed

Fully Atomistic Simulations of Protein Unfolding in Low Speed Atomic Force Microscope and Force Clamp Experiments with the Help of Boxed Molecular Dynamics

The results of Boxed Dynamics (BXD) fully atomistic simulations of protein unfolding by Atomic Force Microscope (AFM), in both force clamp (FC) and velocity clamp (VC) modes are reported. In AFM experiments the unfolding occurs on time scale which is too long for standard atomistic Molecular Dynamics (MD) simulations, which are usually performed with the addition of forces which exceed those of experiment by many orders of magnitude. BXD can reach the time scale of slow unfolding and sample the very high free energy unfolding pathway, reproducing the experimental dependence of pulling force against extension and extension against time. Calculations show the presence of the pulling force ‘humps’ previously observed in the Velocity Clamp (VC) AFM experiments and allow the identification of intermediate protein conformations responsible for them. Fully atomistic BXD simulations can estimate the rate of unfolding in the Force Clamp (FC) experiments up to the time scale of seconds

Photoinduced non-adiabatic energy transfer pathways in dendrimer building blocks

The efficiency of the intramolecular energy transfer in light harvesting dendrimers is determined by their well-defined architecture with high degree of order. After photoexcitation, through-space and through-bond energy transfer mechanisms can take place, involving vectorial exciton migration among different chromophores within dendrimer highly branched structures. Their inherent intramolecular energy gradient depends on how the multiple chromophoric units have been assembled, subject to their inter-connects, spatial distances, and orientations. Herein, we compare the photoinduced nonadiabatic molecular dynamics simulations performed on a set of different combinations of a chain of linked dendrimer building blocks composed of two-, three-, and four-ring linear polyphenylene chromophoric units. The calculations are performed with the recently developed ab initio multiple cloning-time dependent diabatic basis implementation of the Multiconfigurational Ehrenfest (MCE) approach. Despite differences in short time relaxation pathways and different initial exciton localization, at longer time scales, electronic relaxation rates and exciton final redistributions are very similar for all combinations. Unlike the systems composed of two building blocks, considered previously, for the larger 3 block systems here we observe that bifurcation of the wave function accounted by cloning is important. In all the systems considered in this work, at the time scale of few hundreds of femtoseconds, cloning enhances the electronic energy relaxation by ∼13% compared to that of the MCE method without cloning. Thus, accurate description of quantum effects is essential for understanding of the energy exchange in dendrimers both at short and long time scales

Ultrafast X-ray Scattering from Molecules

We present a theoretical framework for the analysis of ultrafast X-ray scattering experiments using nonadiabatic quantum molecular dynamics simulations of photochemical dynamics. A detailed simulation of a pump-probe experiment in ethylene is used to examine the sensitivity of the scattering signal to simulation parameters. The results are robust with respect to the number of wavepackets included in the total expansion of the molecular wave function. Overall, the calculated scattering signals correlate closely with the dynamics of the molecule

A two-layer approach to the coupled coherent states method

In this paper a two-layer scheme is outlined for the coupled coherent states (CCS) method, dubbed two-layer CCS (2L-CCS). The theoretical framework is motivated by that of the multiconfigurational Ehrenfest (MCE) method, where different dynamical descriptions are used for different subsystems of a quantum mechanical system. This leads to a flexible representation of the wavefunction, making the method particularly suited to the study of composite systems. It was tested on a 20-dimensional asymmetric system-bath tunnelling problem, with results compared to a benchmark calculation, as well as existing CCS, MP/SOFT and CI expansion methods. The two-layer method was found to lead to improved short and long term propagation over standard CCS, alongside improved numerical efficiency and parallel scalability. These promising results provide impetus for future development of the method for on-the-fly direct dynamics calculations