551 research outputs found
Studies Towards the Elucidation of the Function of the <i>Cassava Brown Streak Virus </i>HAM1h Protein
Photochemical Initiation of Polariton Propagation
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 effective masses and very high group velocities. While
in experiments polariton propagation is typically initiated with laser pulses,
tuned to be resonant either with the polaritonic branches that are delocalized
over many molecules, or with an uncoupled higher-energy electronic excited
state that is localized on a single molecule, practical implementations of
polariton-mediated exciton transport into devices would require operation under
low-intensity incoherent light conditions. Here, we propose to initiate
polaritonic exciton transport with a photo-acid, which upon absorption of a
photon in a spectral range not strongly reflected by the cavity mirrors,
undergoes ultra-fast excited-state proton transfer into a red-shifted
excited-state photo-product that can couple collectively with a large number of
suitable dye molecules to the modes of the cavity. By means of atomistic
molecular dynamics simulations we demonstrate that cascading energy from a
photo-excited donor into the strongly coupled acceptor-cavity states can indeed
induce long-range polariton-mediated exciton transport
Controlling the photoreactivity of the photoactive yellow protein chromophore by substituting at the p-coumaric acid group.
Tuning the Coherent Propagation of Organic Exciton-Polaritons through the Cavity Q-factor
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 lifetime is determined by the Q(uality)-factor of the optical
resonator, the polariton group velocity is not. Instead, the latter is solely
determined by the polariton dispersion. Yet, experiments suggest that the
Q-factor also controls the polariton propagation velocity. To understand this
observation, we performed molecular dynamics simulations of Rhodamine
chromophores strongly coupled to Fabry-P\'erot cavities with various Q-factors.
Our results suggest that propagation in the aforementioned experiments is
initially dominated by ballistic motion of upper polariton states at their
group velocities, which leads to a rapid expansion of the wavepacket. Cavity
decay in combination with non-adiabatic population transfer into dark states,
rapidly depletes these bright states, causing the wavepacket to contract.
However, because population transfer is reversible, propagation continues, but
as a diffusion process, at lower velocity. By controlling the lifetime of
bright states, the Q-factor determines the duration of the ballistic phase and
the diffusion coefficient in the diffusive regime. Thus, polariton propagation
in organic microcavities can be effectively tuned through the Q-factor.Comment: arXiv admin note: text overlap with arXiv:2209.0730
Accurate three states model for amino acids with two chemically coupled titrating sites in explicit solvent atomistic constant pH simulations and pK<sub>a</sub> calculations.
Correct protonation of titratable groups in biomolecules is crucial for their accurate description by molecular dynamics simulations. In the context of constant pH simulations, an additional protonation degree of freedom is introduced for each titratable site, allowing the protonation state to change dynamically with changing structure or electrostatics. Here, we extend previous approaches for an accurate description of chemically coupled titrating sites. A second reaction coordinate is used to switch between two tautomeric states of an amino acid with chemically coupled titratable sites, such as aspartate (Asp), glutamate (Glu), and histidine (His). To this aim, we test a scheme involving three protonation states. To facilitate charge neutrality as required for periodic boundary conditions and Particle Mesh Ewald (PME) electrostatics, titration of each respective amino acid is coupled to a “water” molecule that is charged in the opposite direction. Additionally, a force field modification for Amber99sb is introduced and tested for the description of carboxyl group protonation. Our three states model is tested by titration simulations of Asp, Glu, and His, yielding a good agreement, reproducing the correct geometry of the groups in their different protonation forms. We further show that the ion concentration change due to the neutralizing “water” molecules does not significantly affect the protonation free energies of the titratable groups, suggesting that the three states model provides a good description of biomolecular dynamics at constant pH
Fatty acid aggregates simulated using constant pH molecular dynamics with a coarse-grained model.
The 'hidden side' of spin labeled oligonucleotides: Molecular Dynamics study focusing on the EPR-silent components of base pairing Corresponding authors
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