publications

2024

1. Quantum embedding study of strain- and electric-field-induced Stark effects on the NV- center in diamond

   Gabriel I. López-Morales, Joanna M. Zajac, Johannes Flick, Carlos A. Meriles, and Cyrus E. Dreyer

   Phys. Rev. B, Dec 2024

   DOI
2. Cavity Born–Oppenheimer approximation for molecules and materials via electric field response

   John Bonini, Iman Ahmadabadi, and Johannes Flick

   The Journal of Chemical Physics, Oct 2024

   Abs DOI

   We present an ab initio method for computing vibro-polariton and phonon-polariton spectra of molecules and solids coupled to the photon modes of optical cavities. We demonstrate that if interactions of cavity photon modes with both nuclear and electronic degrees of freedom are treated on the level of the cavity Born–Oppenheimer approximation, spectra can be expressed in terms of the matter response to electric fields and nuclear displacements, which are readily available in standard density functional perturbation theory implementations. In this framework, results over a range of cavity parameters can be obtained without the need for additional electronic structure calculations, enabling efficient calculations on a wide range of parameters. Furthermore, this approach enables results to be more readily interpreted in terms of the more familiar cavity-independent molecular electric field response properties, such as polarizability and Born effective charges, which enter into the vibro-polariton calculation. Using corresponding electric field response properties of bulk insulating systems, we are also able to obtain the Γ point phonon-polariton spectra of two dimensional (2D) insulators. Results for a selection of cavity-coupled molecular and 2D crystal systems are presented to demonstrate the method.

3. Emergent Optical Resonances in Atomically Phase-Patterned Semiconducting Monolayers of WS2

   John M. Woods, Saroj B. Chand, Enrique Mejia, Ashok Adhikari, Takashi Taniguchi, Kenji Watanabe, Johannes Flick, and Gabriele Grosso

   ACS Photonics, Oct 2024

   DOI
4. Photoinduced Charge Injection from Shallow Point Defects in Diamond into Water

   Kang Xu, Daniela Pagliero, Gabriel I. López-Morales, Johannes Flick, Abraham Wolcott, and Carlos A. Meriles

   ACS Applied Materials & Interfaces, Oct 2024

   PMID: 38976775

   DOI
5. Probing Correlation of Optical Emission and Defect Sites in Hexagonal Boron Nitride by High-Resolution STEM-EELS

   Sakal Singla, Pragya Joshi, Gabriel I. López-Morales, Suman Sarkar, Suman Sarkar, Johannes Flick, and Biswanath Chakraborty

   Nano Letters, Oct 2024

   PMID: 38888554

   DOI
6. Semiempirical ab initio modeling of bound states of deep defects in semiconductor quantum technologies

   YunHeng Chen, Lachlan Oberg, Johannes Flick, Artur Lozovoi, Carlos A. Meriles, and Marcus W. Doherty

   Phys. Rev. B, May 2024

   DOI
7. Photo-Induced Charge State Dynamics of the Neutral and Negatively Charged Silicon Vacancy Centers in Room-Temperature Diamond

   G. Garcia-Arellano, G. I. López-Morales, N. B. Manson, J. Flick, A. A. Wood, and C. A. Meriles

   Advanced Science, May 2024

   Abs DOI

   Abstract The silicon vacancy (SiV) center in diamond is drawing much attention due to its optical and spin properties, attractive for quantum information processing and sensing. Comparatively little is known, however, about the dynamics governing SiV charge state interconversion mainly due to challenges associated with generating, stabilizing, and characterizing all possible charge states, particularly at room temperature. Here, multi-color confocal microscopy and density functional theory are used to examine photo-induced SiV recombination — from neutral, to single-, to double-negatively charged — over a broad spectral window in chemical-vapor-deposition (CVD) diamond under ambient conditions. For the SiV0 to SiV- transition, a linear growth of the photo-recombination rate with laser power at all observed wavelengths is found, a hallmark of single photon dynamics. Laser excitation of SiV‒, on the other hand, yields only fractional recombination into SiV2‒, a finding that is interpreted in terms of a photo-activated electron tunneling process from proximal nitrogen atoms.

8. Simulating Polaritonic Ground States on Noisy Quantum Devices

   Mohammad Hassan, Fabijan Pavošević, Derek S. Wang, and Johannes Flick

   The Journal of Physical Chemistry Letters, May 2024

   PMID: 38287217

   DOI
9. Ab Initio Calculations of Quantum Light–Matter Interactions in General Electromagnetic Environments

   Mark Kamper Svendsen, Kristian Sommer Thygesen, Angel Rubio, and Johannes Flick

   Journal of Chemical Theory and Computation, May 2024

   PMID: 38189259

   DOI

2023

1. Detection and Modeling of Hole Capture by Single Point Defects under Variable Electric Fields

   Artur Lozovoi, YunHeng Chen, Gyorgy Vizkelethy, Edward Bielejec, Johannes Flick, Marcus W. Doherty, and Carlos A. Meriles

   Nano Letters, May 2023

   PMID: 37141536

   DOI

2022

1. Chemical reactivity under collective vibrational strong coupling

   Derek S. Wang, Johannes Flick, and Susanne F. Yelin

   The Journal of Chemical Physics, Dec 2022

   Abs DOI

   Recent experiments of chemical reactions in optical cavities have shown great promise to alter and steer chemical reactions, but still remain poorly understood theoretically. In particular, the origin of resonant effects between the cavity and certain vibrational modes in the collective limit is still subject to active research. In this paper, we study the unimolecular dissociation reactions of many molecules, collectively interacting with an infrared cavity mode, through their vibrational dipole moment. We find that the reaction rate can slow down by increasing the number of aligned molecules, if the cavity mode is resonant with a vibrational mode of the molecules. We also discover a simple scaling relation that scales with the collective Rabi splitting, to estimate the onset of reaction rate modification by collective vibrational strong coupling and numerically demonstrate these effects for up to 104 molecules.

2. Shining light on the microscopic resonant mechanism responsible for cavity-mediated chemical reactivity

   Christian Schäfer, Johannes Flick, Enrico Ronca, Prineha Narang, and Angel Rubio

   Nature Communications, Dec 2022

   DOI
3. Simple Exchange-Correlation Energy Functionals for Strongly Coupled Light-Matter Systems Based on the Fluctuation-Dissipation Theorem

   Johannes Flick

   Phys. Rev. Lett., Sep 2022

   DOI
4. Frequency-Dependent Sternheimer Linear-Response Formalism for Strongly Coupled Light–Matter Systems

   Davis M. Welakuh, Johannes Flick, Michael Ruggenthaler, Heiko Appel, and Angel Rubio

   Journal of Chemical Theory and Computation, Sep 2022

   PMID: 35675628

   DOI
5. Error rate reduction of single-qubit gates via noise-aware decomposition into native gates

   Thomas J. Maldonado, Johannes Flick, Stefan Krastanov, and Alexey Galda

   Scientific Reports, Apr 2022

   DOI
6. Cavity-Modified Unimolecular Dissociation Reactions via Intramolecular Vibrational Energy Redistribution

   Derek S. Wang, Tomáš Neuman, Susanne F. Yelin, and Johannes Flick

   The Journal of Physical Chemistry Letters, Apr 2022

   PMID: 35389664

   DOI
7. Ab Initio Linear-Response Approach to Vibro-Polaritons in the Cavity Born–Oppenheimer Approximation

   John Bonini, and Johannes Flick

   Journal of Chemical Theory and Computation, Apr 2022

   PMID: 35404591

   DOI
8. Cavity-Modulated Proton Transfer Reactions

   Fabijan Pavošević, Sharon Hammes-Schiffer, Angel Rubio, and Johannes Flick

   Journal of the American Chemical Society, Apr 2022

   PMID: 35271261

   DOI
9. Ab-initio investigation of Er3+ defects in tungsten disulfide

   Gabriel I. López-Morales, Alexander Hampel, Gustavo E. López, Vinod M. Menon, Johannes Flick, and Carlos A. Meriles

   Computational Materials Science, Apr 2022

   Abs DOI

   We use density functional theory (DFT) to explore the physical properties of an ErW point defect in monolayer WS2. Our calculations indicate that electrons localize at the dangling bonds associated with a tungsten vacancy (VW) and at the Er3+ ion site, even in the presence of a net negative charge in the supercell. The system features a set of intra-gap defect states, some of which are reminiscent of those present in isolated Er3+ ions. In both instances, the level of hybridization is low, i.e., orbitals show either strong Er or W character. Through the calculation of the absorption spectrum as a function of wavelength, we identify a broad set of transitions, including one possibly consistent with the Er3+ 4I15/2→4I13/2 observed in other hosts. Combined with the low native concentration of spin-active nuclei as well as the two-dimensional nature of the host, these properties reveal Er:WS2 as a potential platform for realizing spin qubits that can be subsequently integrated with other nanoscale optoelectronic devices.

2021

1. Polaritonic Unitary Coupled Cluster for Quantum Computations

   Fabijan Pavošević, and Johannes Flick

   The Journal of Physical Chemistry Letters, Apr 2021

   PMID: 34520211

   DOI
2. Investigation of photon emitters in Ce-implanted hexagonal boron nitride

   Gabriel I. López-Morales, Mingxing Li, Alexander Hampel, Sitakanta Satapathy, Nicholas V. Proscia, Harishankar Jayakumar, Artur Lozovoi, Daniela Pagliero, Gustavo E. Lopez, Vinod M. Menon, Johannes Flick, and Carlos A. Meriles

   Opt. Mater. Express, Oct 2021

   Abs DOI

   Color centers in hexagonal boron nitride (hBN) are presently attracting broad interest as a novel platform for nanoscale sensing and quantum information processing. Unfortunately, their atomic structures remain largely elusive and only a small percentage of the emitters studied thus far have the properties required to serve as optically addressable spin qubits. Here, we use confocal fluorescence microscopy at variable temperatures to study a new class of point defects produced via cerium ion implantation in thin hBN flakes. We find that, to a significant fraction, emitters show bright room-temperature emission, and good optical stability suggesting the formation of Ce-based point defects. Using density functional theory (DFT) we calculate the emission properties of candidate emitters, and single out the CeVB center—formed by an interlayer Ce atom adjacent to a boron vacancy—as one possible microscopic model. Our results suggest an intriguing route to defect engineering that simultaneously exploits the singular properties of rare-earth ions and the versatility of two-dimensional material hosts.

3. Optical activation and detection of charge transport between individual colour centres in diamond

   Artur Lozovoi, Harishankar Jayakumar, Damon Daw, Gyorgy Vizkelethy, Edward Bielejec, Marcus W. Doherty, Johannes Flick, and Carlos A. Meriles

   Nature Electronics, Oct 2021

   DOI
4. Defect Polaritons from First Principles

   Derek S. Wang, Susanne F. Yelin, and Johannes Flick

   ACS Nano, Oct 2021

   PMID: 34459200

   DOI
5. Machine learning band gaps from the electron density

   Javier Robledo Moreno, Johannes Flick, and Antoine Georges

   Phys. Rev. Mater., Aug 2021

   DOI
6. Cavity control of nonlinear phononics

   Dominik M. Juraschek, Tomá\ifmmode \checks\else š\fi Neuman, Johannes Flick, and Prineha Narang

   Phys. Rev. Res., Aug 2021

   DOI
7. Light–matter interaction of a molecule in a dissipative cavity from first principles

   Derek S. Wang, Tomáš Neuman, Johannes Flick, and Prineha Narang

   The Journal of Chemical Physics, Mar 2021

   Abs DOI

   Cavity-mediated light–matter coupling can dramatically alter opto-electronic and physico-chemical properties of a molecule. Ab initio theoretical predictions of these systems need to combine non-perturbative, many-body electronic structure theory-based methods with cavity quantum electrodynamics and theories of open-quantum systems. Here, we generalize quantum-electrodynamical density functional theory to account for dissipative dynamics of the cavity and describe coupled cavity–single molecule interactions in the weak-to-strong-coupling regimes. Specifically, to establish this generalized technique, we study excited-state dynamics and spectral responses of benzene and toluene under weak-to-strong light–matter coupling. By tuning the coupling, we achieve cavity-mediated energy transfer between electronically excited states. This generalized ab initio quantum-electrodynamical density functional theory treatment can be naturally extended to describe cavity-mediated interactions in arbitrary electromagnetic environments, accessing correlated light–matter observables and thereby closing the gap between electronic structure theory, quantum optics, and nanophotonics.

8. Hybridized Defects in Solid-State Materials as Artificial Molecules

   Derek S. Wang, Christopher J. Ciccarino, Johannes Flick, and Prineha Narang

   ACS Nano, Mar 2021

   PMID: 33600145

   DOI
9. Quantum Information and Algorithms for Correlated Quantum Matter

   Kade Head-Marsden, Johannes Flick, Christopher J. Ciccarino, and Prineha Narang

   Chemical Reviews, Mar 2021

   PMID: 33326218

   DOI

2020

1. Group-III quantum defects in diamond are stable spin-1 color centers

   Isaac Harris, Christopher J. Ciccarino, Johannes Flick, Dirk R. Englund, and Prineha Narang

   Phys. Rev. B, Nov 2020

   DOI
2. Ab initio polaritonic potential-energy surfaces for excited-state nanophotonics and polaritonic chemistry

   Johannes Flick, and Prineha Narang

   The Journal of Chemical Physics, Sep 2020

   Abs DOI

   Advances in nanophotonics, quantum optics, and low-dimensional materials have enabled precise control of light–matter interactions down to the nanoscale. Combining concepts from each of these fields, there is now an opportunity to create and manipulate photonic matter via strong coupling of molecules to the electromagnetic field. Toward this goal, here we demonstrate a first principles framework to calculate polaritonic excited-state potential-energy surfaces, transition dipole moments, and transition densities for strongly coupled light–matter systems. In particular, we demonstrate the applicability of our methodology by calculating the polaritonic excited-state manifold of a formaldehyde molecule strongly coupled to an optical cavity. This proof-of-concept calculation shows how strong coupling can be exploited to alter photochemical reaction pathways by influencing avoided crossings with tuning of the cavity frequency and coupling strength. Therefore, by introducing an ab initio method to calculate excited-state potential-energy surfaces, our work opens a new avenue for the field of polaritonic chemistry.

3. Strong spin–orbit quenching via the product Jahn–Teller effect in neutral group IV qubits in diamond

   Christopher J. Ciccarino, Johannes Flick, Isaac B. Harris, Matthew E. Trusheim, Dirk R. Englund, and Prineha Narang

   npj Quantum Materials, Oct 2020

   DOI
4. Bioinspiration in light harvesting and catalysis

   Andrew H. Proppe, Yuguang C. Li, Alán Aspuru-Guzik, Curtis P. Berlinguette, Christopher J. Chang, Richard Cogdell, Abigail G. Doyle, Johannes Flick, Nathaniel M. Gabor, Rienk Grondelle, Sharon Hammes-Schiffer, Shaffiq A. Jaffer, Shana O. Kelley, Mario Leclerc, Karl Leo, Thomas E. Mallouk, Prineha Narang, Gabriela S. Schlau-Cohen, Gregory D. Scholes, Aleksandra Vojvodic, Vivian Wing-Wah Yam, Jenny Y. Yang, and Edward H. Sargent

   Nature Reviews Materials, Aug 2020

   DOI
5. Low-Temperature Electron–Phonon Interaction of Quantum Emitters in Hexagonal Boron Nitride

   Gabriele Grosso, Hyowon Moon, Christopher J. Ciccarino, Johannes Flick, Noah Mendelson, Lukas Mennel, Milos Toth, Igor Aharonovich, Prineha Narang, and Dirk R. Englund

   ACS Photonics, Aug 2020

   DOI
6. Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems

   Nicolas Tancogne-Dejean, Micael J. T. Oliveira, Xavier Andrade, Heiko Appel, Carlos H. Borca, Guillaume Le Breton, Florian Buchholz, Alberto Castro, Stefano Corni, Alfredo A. Correa, Umberto De Giovannini, Alain Delgado, Florian G. Eich, Johannes Flick, Gabriel Gil, Adrián Gomez, Nicole Helbig, Hannes Hübener, René Jestädt, Joaquim Jornet-Somoza, Ask H. Larsen, Irina V. Lebedeva, Martin Lüders, Miguel A. L. Marques, Sebastian T. Ohlmann, Silvio Pipolo, Markus Rampp, Carlo A. Rozzi, David A. Strubbe, Shunsuke A. Sato, Christian Schäfer, Iris Theophilou, Alicia Welden, and Angel Rubio

   The Journal of Chemical Physics, Mar 2020

   Abs DOI

   Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light–matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).

2019

1. Light–Matter Response in Nonrelativistic Quantum Electrodynamics

   Johannes Flick, Davis M. Welakuh, Michael Ruggenthaler, Heiko Appel, and Angel Rubio

   ACS Photonics, Mar 2019

   PMID: 31788500

   DOI
2. Quantum Materials with Atomic Precision: Artificial Atoms in Solids: Ab Initio Design, Control, and Integration of Single Photon Emitters in Artificial Quantum Materials

   Prineha Narang, Christopher J. Ciccarino, Johannes Flick, and Dirk Englund

   Advanced Functional Materials, Mar 2019

   Abs DOI

   Abstract This Progress Report explores advances and opportunities in the atomic-scale design, fabrication, and imaging of quantum materials toward creating artificial atoms in solids with tailored optoelectronic and quantum properties. The authors outline an “ab initio” approach to quantitatively linking first-principles calculations and atomic imaging with atomic patterning, setting the stage for new designer quantum nanomaterials.

3. Variational Theory of Nonrelativistic Quantum Electrodynamics

   Nicholas Rivera, Johannes Flick, and Prineha Narang

   Phys. Rev. Lett., May 2019

   DOI
4. Lead-related quantum emitters in diamond

   Matthew E. Trusheim, Noel H. Wan, Kevin C. Chen, Christopher J. Ciccarino, Johannes Flick, Ravishankar Sundararaman, Girish Malladi, Eric Bersin, Michael Walsh, Benjamin Lienhard, Hassaram Bakhru, Prineha Narang, and Dirk Englund

   Phys. Rev. B, Feb 2019

   DOI

2018

1. Cavity-Correlated Electron-Nuclear Dynamics from First Principles

   Johannes Flick, and Prineha Narang

   Phys. Rev. Lett., Sep 2018

   DOI
2. Strong light-matter coupling in quantum chemistry and quantum photonics

   Johannes Flick, Nicholas Rivera, and Prineha Narang

   Nanophotonics, Sep 2018

   DOI
3. Ab Initio Optimized Effective Potentials for Real Molecules in Optical Cavities: Photon Contributions to the Molecular Ground State

   Johannes Flick, Christian Schäfer, Michael Ruggenthaler, Heiko Appel, and Angel Rubio

   ACS Photonics, Sep 2018

   PMID: 29594185

   DOI
4. From a quantum-electrodynamical light–matter description to novel spectroscopies

   Michael Ruggenthaler, Nicolas Tancogne-Dejean, Johannes Flick, Heiko Appel, and Angel Rubio

   Nature Reviews Chemistry, Mar 2018

   DOI

2017

1. Exact functionals for correlated electron–photon systems

   Tanja Dimitrov, Johannes Flick, Michael Ruggenthaler, and Angel Rubio

   New Journal of Physics, Nov 2017

   Abs DOI

   For certain correlated electron–photon systems we construct the exact density-to-potential maps, which are the basic ingredients of a density-functional reformulation of coupled matter-photon problems. We do so for numerically exactly solvable models consisting of up to four fermionic sites coupled to a single photon mode. We show that the recently introduced concept of the intra-system steepening (Dimitrov et al 2016 New J. Phys. 18 083004) can be generalized to coupled fermion-boson systems and that the intra-system steepening indicates strong exchange-correlation effects due to the coupling between electrons and photons. The reliability of the mean-field approximation to the electron–photon interaction is investigated and its failure in the strong coupling regime analyzed. We highlight how the intra-system steepening of the exact density-to-potential maps becomes apparent also in observables such as the photon number or the polarizability of the electronic subsystem. We finally show that a change in functional variables can make these observables behave more smoothly and exemplify that the density-to-potential maps can give us physical insights into the behavior of coupled electron–photon systems by identifying a very large polarizability due to ultra-strong electron–photon coupling.

2. Cavity Born–Oppenheimer Approximation for Correlated Electron–Nuclear-Photon Systems

   Johannes Flick, Heiko Appel, Michael Ruggenthaler, and Angel Rubio

   Journal of Chemical Theory and Computation, Nov 2017

   PMID: 28277664

   DOI
3. Atoms and molecules in cavities, from weak to strong coupling in quantum-electrodynamics (QED) chemistry

   Johannes Flick, Michael Ruggenthaler, Heiko Appel, and Angel Rubio

   Proceedings of the National Academy of Sciences, Nov 2017

   Abs DOI

   Traditionally, quantum chemistry investigates molecular systems assuming that the photon field, which leads to the interaction of charged particles, is well approximated by the Coulomb interaction. On the other hand, quantum optics describe the photon field in detail while approximating the matter systems via few levels. Recent experiments at the interface between these two areas of research have uncovered situations where both the molecular system and the photon field have to be treated in detail. In this work, we show how theoretical approaches have to be adapted to treat such coupled matter–photon problems and which effects can be anticipated. Our quantum electrodynamics density-functional formalism provides the theoretical framework to open a field of research able to deal with emergent properties of matter. In this work, we provide an overview of how well-established concepts in the fields of quantum chemistry and material sciences have to be adapted when the quantum nature of light becomes important in correlated matter–photon problems. We analyze model systems in optical cavities, where the matter–photon interaction is considered from the weak- to the strong-coupling limit and for individual photon modes as well as for the multimode case. We identify fundamental changes in Born–Oppenheimer surfaces, spectroscopic quantities, conical intersections, and efficiency for quantum control. We conclude by applying our recently developed quantum-electrodynamical density-functional theory to spontaneous emission and show how a straightforward approximation accurately describes the correlated electron–photon dynamics. This work paves the way to describe matter–photon interactions from first principles and addresses the emergence of new states of matter in chemistry and material science.

2015

1. Kohn–Sham approach to quantum electrodynamical density-functional theory: Exact time-dependent effective potentials in real space

   Johannes Flick, Michael Ruggenthaler, Heiko Appel, and Angel Rubio

   Proceedings of the National Academy of Sciences, Nov 2015

   Abs DOI

   Density-functional theory (DFT) is a well-established method to study many-electron systems. Over the past decades advanced algorithms have been designed that allow even large systems to be solved computationally very efficiently. Only recently, DFT has been generalized to correctly incorporate the quantum nature of light, which becomes important, e.g., in cavity quantum electrodynamics (QED). In general, the accuracy in density-functional theory depends crucially on the capability to construct good approximations that reflect the features of the exact effective potential for the Kohn–Sham system. In this work, we introduce a fixed-point scheme to construct these exact effective potentials for a cavity QED system and demonstrate their features for the ground-state and time-dependent situations. The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe electron–photon interactions in terms of effective Kohn–Sham potentials. In this work, we numerically construct the exact electron–photon Kohn–Sham potentials for a prototype system that consists of a trapped electron coupled to a quantized electromagnetic mode in an optical high-Q cavity. Although the effective current that acts on the photons is known explicitly, the exact effective potential that describes the forces exerted by the photons on the electrons is obtained from a fixed-point inversion scheme. This procedure allows us to uncover important beyond-mean-field features of the effective potential that mark the breakdown of classical light–matter interactions. We observe peak and step structures in the effective potentials, which can be attributed solely to the quantum nature of light; i.e., they are real-space signatures of the photons. Our findings show how the ubiquitous dipole interaction with a classical electromagnetic field has to be modified in real space to take the quantum nature of the electromagnetic field fully into account.

2. Optimized Effective Potential for Quantum Electrodynamical Time-Dependent Density Functional Theory

   Camilla Pellegrini, Johannes Flick, Ilya V. Tokatly, Heiko Appel, and Angel Rubio

   Phys. Rev. Lett., Aug 2015

   DOI

2014

1. Quantum-electrodynamical density-functional theory: Bridging quantum optics and electronic-structure theory

   Michael Ruggenthaler, Johannes Flick, Camilla Pellegrini, Heiko Appel, Ilya V. Tokatly, and Angel Rubio

   Phys. Rev. A, Jul 2014

   DOI
2. Nonadiabatic and Time-Resolved Photoelectron Spectroscopy for Molecular Systems

   Johannes Flick, Heiko Appel, and Angel Rubio

   Journal of Chemical Theory and Computation, Jul 2014

   PMID: 26580375

   DOI

2012

1. Modeling loop backbone flexibility in receptor-ligand docking simulations

   Johannes Flick, Frank Tristram, and Wolfgang Wenzel

   Journal of Computational Chemistry, Jul 2012

   Abs DOI

   Abstract The relevance of receptor conformational change during ligand binding is well documented for many pharmaceutically relevant receptors, but is still not fully accounted for in in silico docking methods. While there has been significant progress in treatment of receptor side chain flexibility sampling of backbone flexibility remains challenging because the conformational space expands dramatically and the scoring function must balance protein–protein and protein–ligand contributions. Here, we investigate an efficient multistage backbone reconstruction algorithm for large loop regions in the receptor and demonstrate that treatment of backbone receptor flexibility significantly improves binding mode prediction starting from apo structures and in cross docking simulations. For three different kinase receptors in which large flexible loops reconstruct upon ligand binding, we demonstrate that treatment of backbone flexibility results in accurate models of the complexes in simulations starting from the apo structure. At the example of the DFG-motif in the p38 kinase, we also show how loop reconstruction can be used to model allosteric binding. Our approach thus paves the way to treat the complex process of receptor reconstruction upon ligand binding in docking simulations and may help to design new ligands with high specificity by exploitation of allosteric mechanisms. © 2012 Wiley Periodicals, Inc.