Gerrit Groenhof
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View article: Incorporating QM/MM molecular dynamics into the few-mode quantization approach for light-matter interactions in nanophotonic structures
Incorporating QM/MM molecular dynamics into the few-mode quantization approach for light-matter interactions in nanophotonic structures Open
In the context of light-matter interactions between organic chromophores and confined photons of (plasmonic) nano-resonators, we introduce a general framework that couples ab initio QM/MM molecular dynamics with few-mode field quantization…
View article: Perspective on Many-Body Methods for Molecular Polaritonic Systems
Perspective on Many-Body Methods for Molecular Polaritonic Systems Open
Recent advances in strong light-matter interactions have revealed a wealth of new physical phenomena in molecules embedded in optical cavities, including modified chemical reactivity, altered excitation spectra, and novel quantum correlati…
View article: Quantum dynamics simulation of exciton-polariton transport
Quantum dynamics simulation of exciton-polariton transport Open
View article: Disentangling Enhanced Diffusion and Ballistic Motion of Excitons Coupled to Bloch Surface Waves with Molecular Dynamics Simulations
Disentangling Enhanced Diffusion and Ballistic Motion of Excitons Coupled to Bloch Surface Waves with Molecular Dynamics Simulations Open
Placing an organic material on top of a Bragg mirror can significantly enhance the exciton transport. Such enhancement has been attributed to strong coupling between the evanescent Bloch surface waves (BSW) on the mirror and the excitons i…
View article: Crystal optics select weak response of ultrafast crystallography of the Photoactive Yellow Protein
Crystal optics select weak response of ultrafast crystallography of the Photoactive Yellow Protein Open
Ultrafast crystallography of light-induced processes can directly capture structural differences driven by short-pulse laser illumination. With short pump-probe observation time and short laser pulse durations, the electronic and nuclear d…
View article: Chirality Effects in Peptide‐Based Dynamic Combinatorial Chemistry
Chirality Effects in Peptide‐Based Dynamic Combinatorial Chemistry Open
Naturally occurring peptides are almost exclusively composed of L‐amino acids, and the incorporation of D‐amino acids can profoundly alter their ability to fold and self‐assemble. Here we explore the effects of chirality on the formation o…
View article: Discovery of a Noncompetitive Open-Flap Selective Inhibitor of Plasmepsin II with Antiplasmodial Activity
Discovery of a Noncompetitive Open-Flap Selective Inhibitor of Plasmepsin II with Antiplasmodial Activity Open
Here, we predicted that Plasmepsin II (PlmII) can explore open-flap conformations not sampled for human aspartic proteases: Cathepsin D, Renin, and Pepsin were used in molecular dynamics simulations. We combined 24 independent (50 ns) MD r…
View article: Disentangling enhanced diffusion and ballistic motion of excitons coupled to Bloch surface waves with molecular dynamics simulations
Disentangling enhanced diffusion and ballistic motion of excitons coupled to Bloch surface waves with molecular dynamics simulations Open
Placing an organic material on top of a Bragg mirror can significantly enhance exciton transport. Such enhancement has been attributed to strong coupling between the evanescent Bloch surface waves (BSW) on the mirror, and the excitons in t…
View article: Quantum dynamics simulation of exciton-polariton transport
Quantum dynamics simulation of exciton-polariton transport Open
Strong coupling between excitons and confined modes of light presents a promising pathway to tunable and enhanced energy transport in organic materials. By forming hybrid light-matter quasiparticles, exciton-polaritons, electronic excitati…
View article: Thermal disorder prevents the suppression of ultra-fast photochemistry in the strong light-matter coupling regime
Thermal disorder prevents the suppression of ultra-fast photochemistry in the strong light-matter coupling regime Open
Strong coupling between molecules and confined light modes of optical cavities to form polaritons can alter photochemistry, but the origin of this effect remains largely unknown. While theoretical models suggest a suppression of photochemi…
View article: Ultra-fast photochemistry in the strong light-matter coupling regime
Ultra-fast photochemistry in the strong light-matter coupling regime Open
Strong coupling between molecules and confined light modes of optical cavities to form polaritons can alter photochemistry, but the origin of this effect remains largely unknown. While theoretical models suggest a suppression of photochemi…
View article: Alternant Hydrocarbon Diradicals as Optically Addressable Molecular Qubits
Alternant Hydrocarbon Diradicals as Optically Addressable Molecular Qubits Open
High-spin molecules allow for bottom-up qubit design and are promising platforms for magnetic sensing and quantum information science. Optical addressability of molecular electron spins has also been proposed in first-row transition-metal …
View article: Do all paths lead to Rome? How reliable is umbrella sampling along a single path?
Do all paths lead to Rome? How reliable is umbrella sampling along a single path? Open
Molecular dynamics (MD) simulations are widely applied to estimate absolute binding free energies of protein-ligand and protein-protein complexes. A routinely used method for binding free energy calculations with MD is umbrella sampling (U…
View article: Polariton-assisted long-distance energy transfer between excitons in two-dimensional semiconductors
Polariton-assisted long-distance energy transfer between excitons in two-dimensional semiconductors Open
| openaire: EC/H2020/872049/EU//IPN-Bio | openaire: EC/H2020/834742/EU//ATOP
View article: Non-Hermitian molecular dynamics simulations of exciton–polaritons in lossy cavities
Non-Hermitian molecular dynamics simulations of exciton–polaritons in lossy cavities Open
The observation that materials can change their properties when placed inside or near an optical resonator has sparked a fervid interest in understanding the effects of strong light–matter coupling on molecular dynamics, and several approa…
View article: Photochemical initiation of polariton-mediated exciton propagation
Photochemical initiation of polariton-mediated exciton propagation Open
Placing a material inside an optical cavity can enhance transport of excitation energy by hybridizing excitons with confined light modes into polaritons, which have a dispersion that provides these light–matter quasi-particles with low eff…
View article: phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS
phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS Open
Constant pH molecular dynamics (MD) is a powerful technique that allows the protonation state of residues to change dynamically, thereby enabling the study of pH dependence in a manner that has not been possible before. Recently, a constan…
View article: Do all roads lead to Rome? Convergence issues in umbrella sampling simulations
Do all roads lead to Rome? Convergence issues in umbrella sampling simulations Open
Molecular dynamics (MD) simulations are widely applied to estimate absolute binding free energies of protein-ligand and protein-protein complexes. A routinely used method for binding free energy calculations with MD is umbrella sampling (U…
View article: Non-Hermitian molecular dynamics simulations of exciton-polaritons in lossy cavities
Non-Hermitian molecular dynamics simulations of exciton-polaritons in lossy cavities Open
The observation that materials can change their properties when placed inside or near an optical resonator, has sparked a fervid interest in understanding the effects of strong light-matter coupling on molecular dynamics, and several appro…
View article: Multi-scale molecular dynamics simulations of enhanced energy transfer in organic molecules under strong coupling
Multi-scale molecular dynamics simulations of enhanced energy transfer in organic molecules under strong coupling Open
View article: Photochemical Initiation of Polariton Propagation
Photochemical Initiation of Polariton Propagation Open
Placing a material inside an optical cavity can enhance transport of excitation energy by hybridizing excitons with confined light modes into polaritons, which have a dispersion that provides these light-matter quasi-particles with low eff…
View article: Tuning the Coherent Propagation of Organic Exciton‐Polaritons through the Cavity Q‐factor
Tuning the Coherent Propagation of Organic Exciton‐Polaritons through the Cavity Q‐factor Open
Transport of excitons in organic materials can be enhanced through polariton formation when the interaction strength between these excitons and the confined light modes of an optical resonator exceeds their decay rates. While the polariton…
View article: Ultra-fast photochemistry in the strong light-matter coupling regime
Ultra-fast photochemistry in the strong light-matter coupling regime Open
Strong coupling between molecules and confined light modes of optical cavities to form polaritons can alter photochemistry, but the origin of this effect remains largely unknown. While theoretical models suggest a suppression of photochemi…
View article: gmXtal: Cooking Crystals with GROMACS
gmXtal: Cooking Crystals with GROMACS Open
Molecular dynamics (MD) simulations are routinely performed of biomolecules in solution, because this is their native environment. However, the structures used in such simulations are often obtained with X-ray crystallography, which provid…
View article: Ultra-fast photochemistry in the strong light-matter coupling regime
Ultra-fast photochemistry in the strong light-matter coupling regime Open
Strong coupling between molecules and confined light modes of optical cavities to form polaritons can alter photochemistry, but the origin of this effect remains largely unknown. While theoretical models suggest a suppression of photochemi…
View article: phbuilder: a tool for efficiently setting up constant pH molecular dynamics simulations in GROMACS
phbuilder: a tool for efficiently setting up constant pH molecular dynamics simulations in GROMACS Open
Constant pH molecular dynamics (MD) is a powerful technique that allows the protonation state of residues to change dynamically, thereby enabling the study of pH-dependence in a manner not possible before. Recently, a constant pH implement…
View article: Optical control of ultrafast structural dynamics in a fluorescent protein
Optical control of ultrafast structural dynamics in a fluorescent protein Open
View article: Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism
Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism Open
Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and directio…
View article: gmXtal: Cooking crystals with GROMACS
gmXtal: Cooking crystals with GROMACS Open
Molecular dynamics (MD) simulations are routinely performed of biomolecules in solution, because this is their native environment. However, the structures used in such simulations are often obtained with x-ray crystallography, which provid…
View article: Tuning the Coherent Propagation of Organic Exciton-Polaritons through the Cavity Q-factor
Tuning the Coherent Propagation of Organic Exciton-Polaritons through the Cavity Q-factor Open
Transport of excitons in organic materials can be enhanced through polariton formation when the interaction strength between these excitons and the confined light modes of an optical resonator exceeds their decay rates. While the polariton…