arXiv subjects

Artur F. Izmaylov

Publications and source records attributed to Artur F. Izmaylov.

86 records · Page 5Linked to original sources

arXiv2016

Nuclear dynamics investigation of the initial electron transfer in the cyclobutane pyrimidine dimer lesion repair process by photolyases

Photolyases are proteins capable of harvesting the sunlight to repair DNA damages caused by UV light. In this work we focus on the first step in the repair process of the cyclobutane pyrimidine dimer photoproduct (CPD) lesion, which is an electron transfer (ET) from a flavine cofactor to CPD, and study the role of various nuclear degrees of freedom (DOF) in this step. The ET step has been experimentally studied using transient spectroscopy and the corresponding data provide excellent basis for testing the quality of quantum dynamical models. Based on previous theoretical studies of electronic structure and conformations of the protein active site, we present a procedure to build a diabatic Hamiltonian for simulating the ET reaction in a molecular complex mimicking the enzyme's active site. We generate a reduced nuclear dimensional model that provides a first non-empirical quantum dynamical description of the structural features influencing the ET rate. By varying the nuclear DOF parametrization in the model to assess the role of different nuclear motions, we demonstrate that the low frequency flavin butterfly bending mode slows ET by reducing Franck-Condon overlaps between donor and acceptor states and also induces decoherence.

physics.chem-ph↗

arXiv2015

Fast numerical evaluation of time-derivative nonadiabatic couplings for mixed quantum-classical methods

We have developed a numerical differentiation scheme which eliminates evaluation of overlap determinants in calculating the time-derivative non-adiabatic couplings (TDNACs). Evaluation of these determinants was the bottleneck in previous implementations of mixed quantum-classical methods using numerical differentiation of electronic wave functions in the Slater-determinant representation. The central idea of our approach is, first, to reduce the analytic time derivatives of Slater determinants to time derivatives of molecular orbitals, and then to apply a finite-difference formula. Benchmark calculations prove the efficiency of the proposed scheme showing impressive several-order-of-magnitude speedups of the TDNAC calculation step for midsize molecules.

physics.chem-ph↗

arXiv2015

Problem-free time-dependent variational principle for open quantum systems

Methods of quantum nuclear wave-function dynamics have become very efficient in simulating large isolated systems using the time-dependent variational principle (TDVP). However, a straightforward extension of the TDVP to the density matrix framework gives rise to methods that do not conserve the energy in the isolated system limit and the total system population for open systems where only energy exchange with the environment is allowed. These problems arise when the system density is in a mixed state and is simulated using an incomplete basis. Thus, the basis set incompleteness, which is inevitable in practical calculations, creates artificial channels for energy and population dissipation. To overcome this unphysical behavior, we have introduced a constrained Lagrangian formulation of TDVP applied to the non-stochastic open system Schrodinger equation (NOSSE) [L. Joubert-Doriol, I. G. Ryabinkin, and A. F. Izmaylov, J. Chem. Phys. 141, 234112 (2014)]. While our formulation can be applied to any variational ansatz for the system density matrix, derivation of working equations and numerical assessment are done within the variational multiconfiguration Gaussian approach for a two-dimensional linear vibronic coupling model system interacting with a harmonic bath.

physics.chem-ph↗

arXiv2015

Why do mixed quantum-classical methods describe short-time dynamics through conical intersections so well? Analysis of geometric phase effects

Adequate simulation of non-adiabatic dynamics through conical intersection requires account for a non-trivial geometric phase (GP) emerging in electronic and nuclear wave-functions in the adiabatic representation. Popular mixed quantum-classical (MQC) methods, surface hopping and Ehrenfest, do not carry a nuclear wave-function to be able to incorporate the GP into nuclear dynamics. Surprisingly, the MQC methods reproduce ultra-fast interstate crossing dynamics generated with the exact quantum propagation so well as if they contained information about the GP. Using two-dimensional linear vibronic coupling models we unravel how the MQC methods can effectively mimic the most significant dynamical GP effects: 1) compensation for repulsive diagonal second order non-adiabatic couplings and 2) transfer enhancement for a fully cylindrically symmetric component of a nuclear distribution.

physics.chem-ph↗

arXiv2014

An efficient implementation of the localized operator partitioning method for electronic energy transfer

The localized operator partitioning method [Y. Khan and P. Brumer, J. Chem. Phys. 137, 194112 (2012)] rigorously defines the electronic energy on any subsystem within a molecule and gives a precise meaning to the subsystem ground and excited electronic energies, which is crucial for investigating electronic energy transfer from first principles. However, an efficient implementation of this approach has been hindered by complicated one- and two-electron integrals arising in its formulation. Using a resolution of the identity in the definition of partitioning we reformulate the method in a computationally efficient manner that involves standard one- and two-electron integrals. We apply the developed algorithm to the 9-((1-naphthyl)-methyl)-anthracene (A1N) molecule by partitioning A1N into anthracenyl and CH2-naphthyl groups as subsystems, and examine their electronic energies and populations for several excited states using Configuration Interaction Singles method. The implemented approach shows a wide variety of different behaviors amongst the excited electronic states.

physics.chem-ph↗

arXiv2014

Non-stochastic matrix Schrödinger equation for open systems

We propose an extension of the Schrödinger equation for a quantum system interacting with environment. This equation describes dynamics of auxiliary wave-functions $\mathbf{m}$, from which the system density matrix can be reconstructed as $\hatρ = \mathbf{m} \mathbf{m}^\dagger$. We formulate a compatibility condition, which ensures that the reconstructed density satisfies a given quantum master equation for the system density. The resulting non-stochastic evolution equation preserves positive-definiteness of the system density and is applicable to both Markovian and non-Markovian system-bath treatments. Our formalism also resolves a long-standing problem of energy non-conservation in the time-dependent variational principle applied to mixed states of closed systems.

physics.chem-ph↗

arXiv2014

A perturbative formalism for electronic transitions through conical intersections in a fully quadratic vibronic model

We consider a fully quadratic vibronic model Hamiltonian for studying photoinduced electronic transitions through conical intersections. Using a second order perturbative approximation for diabatic couplings we derive an analytical expression for the time evolution of electronic populations at a given temperature. This formalism extends upon a previously developed perturbative technique for a linear vibronic coupling Hamiltonian. The advantage of the quadratic model Hamiltonian is that it allows one to use separate quadratic representations for potential energy surfaces of different electronic states and a more flexible representation of interstate couplings. We explore features introduced by the quadratic Hamiltonian in a series of 2D models, and then apply our formalism to the 2,6-bis(methylene) adamantyl cation, and its dimethyl derivative. The Hamiltonian parameters for the molecular systems have been obtained from electronic structure calculations followed by a diabatization procedure. The evolution of electronic populations in the molecular systems using the perturbative formalism shows a good agreement with that from variational quantum dynamics.

physics.chem-ph↗

arXiv2014

When do we need to account for the geometric phase in excited state dynamics ?

We investigate the role of the geometric phase (GP) in an internal conversion process when the system changes its electronic state by passing through a conical intersection (CI). Local analysis of a two-dimensional linear vibronic coupling (LVC) model Hamiltonian near the CI shows that the role of the GP is twofold. First, it compensates for a repulsion created by the so-called diagonal Born-Oppenheimer correction (DBOC). Second, the GP enhances the non-adiabatic transition probability for a wave-packet part that experiences a central collision with the CI. To assess the significance of both GP contributions we propose two indicators that can be computed from parameters of electronic surfaces and initial conditions. To generalize our analysis to N-dimensional systems we introduce a reduction of a general N-dimensional LVC model to an effective 2D LVC model using a mode transformation that preserves short-time dynamics of the original N-dimensional model. Using examples of the bis(methylene) adamantyl and butatriene cations, and the pyrazine molecule we have demonstrated that their effective 2D models reproduce the short-time dynamics of the corresponding full dimensional models, and the introduced indicators are very reliable in assessing GP effects.

physics.chem-ph↗

arXiv2014

Local operator partitioning of electronic energy for electronic energy transfer: An efficient algorithm

An efficient computational algorithm to implement a local operator approach to partitioning electronic energy in general molecular systems is presented. This approach, which rigorously defines the electronic energy on any subsystem within a molecule, gives a precise meaning to the subsystem ground and excited electronic energies, which is crucial for investigating electronic energy transfer from first principles. We apply the technique to the $9-$(($1-$naphthyl)$-$methyl)-anthracene (A1N) molecule by partitioning A1N into anthracenyl and CH$_2-$naphthyl groups as subsystems, and examine their electronic energies and populations for several excited states using Configuration Interaction Singles method. The implemented approach shows a wide variety of different behaviors amongst these excited electronic states.

physics.chem-ph↗

arXiv2013

Analysis of geometric phase effects in the quantum-classical Liouville formalism

We analyze two approaches to the quantum-classical Liouville (QCL) formalism that differ in the order of two operations: Wigner transformation and projection onto adiabatic electronic states. The analysis is carried out on a two-dimensional linear vibronic model where geometric phase (GP) effects arising from a conical intersection profoundly affect nuclear dynamics. We find that the Wigner-then-Adiabatic (WA) QCL approach captures GP effects, whereas the Adiabatic-then-Wigner (AW) QCL approach does not. Moreover, the Wigner transform in AW-QCL leads to an ill-defined Fourier transform of double-valued functions. The double-valued character of these functions stems from the nontrivial GP of adiabatic electronic states in the presence of a conical intersection. In contrast, WA-QCL avoids this issue by starting with the Wigner transform of single-valued quantities of the full problem. Since the WA-QCL approach uses solely the adiabatic potentials and non-adiabatic derivative couplings as an input, our results indicate that WA-QCL can capture GP effects in general two-state crossing problems using first-principles electronic structure calculations without prior diabatization or introduction of explicit phase factors.

quant-ph↗

arXiv2013

Geometric phase effects in low-energy dynamics near conical intersections: A study of the multidimensional linear vibronic coupling model

In molecular systems containing conical intersections (CIs), a nontrivial geometric phase (GP) appears in the nuclear and electronic wave-functions in the adiabatic representation. We study GP effects in nuclear dynamics of an N-dimensional linear vibronic coupling (LVC) model. The main impact of GP on low-energy nuclear dynamics is reduction of population transfer between the local minima of the LVC lower energy surface. For the LVC model, we proposed an isometric coordinate transformation that confines non-adiabatic effects within a two-dimensional subsystem interacting with an N-2 dimensional environment. Since environmental modes do not couple electronic states, all GP effects originate from nuclear dynamics within the subsystem. We explored when the GP affects nuclear dynamics of the isolated subsystem, and how the subsystem-environment interaction can interfere with GP effects. Comparing quantum dynamics with and without GP allowed us to devise simple rules to determine significance of the GP for nuclear dynamics in this model.

quant-ph↗

arXiv2013

Geometric phase effects in dynamics near conical intersections: Symmetry breaking and spatial localization

We show that finite systems with conical intersections can exhibit spontaneous symmetry breaking which manifests itself in spatial localization of eigenstates. This localization has a geometric phase origin and is robust against variation of model parameters. The transition between localized and delocalized eigenstate regimes resembles a continuous phase transition. The localization slows down the low-energy quantum nuclear dynamics at zero and low temperatures.

quant-ph↗

arXiv2008

Analytical infrared intensities for periodic systems with local basis sets

We report a method for the efficient evaluation of analytic infrared (IR) intensities within generalized Kohn-Sham density functional theory using Gaussian orbitals and periodic boundary conditions. A discretized form of the Berry phase is used to evaluate a periodic dipole moment and its derivatives with respect to in-phase nuclear coordinate displacements. Benchmark calculations are presented for one-dimensional chains of water molecules and poly(paraphenylenevinylene).

cond-mat.mtrl-sci↗

arXiv2006

On universality and non-universality for a quantum dot in the Kondo regime

The time-dependent non-crossing approximation is employed for the single-electron transistor to calculate the transient response of the conductance for a variety of temperatures and biases. We consider the case when the dot-lead tunneling constant is suddenly changed such that the Kondo effect is present in the final state. In the fast non-universal timescale, which was previously identified, we see rapid oscillations. The frequency of these oscillations is equal to the dot level and their amplitude is modulated by the initial and final tunneling constants. To study the slow universal timescale, we develop a new numerical scheme. We compute the conductance for two systems which have different Kondo temperatures down to a fraction of $T_{K}$ in infinitesimal bias with this scheme. We conclude that universality is preserved as a function of $T/ T_{K}$. We also investigate the decay rate of recently identified SKP oscillations down to zero temperature and compare it with the previous analytical results obtained with the perturbative renormalization group.

cond-mat.str-el↗