Related papers: On excited state reaction path in reversibly switc…
Protein translocation in cells has been modelled by \emph{Brownian ratchets}. In such models, the protein diffuses through a nanopore. On one side of the pore, ratcheting molecules bind to the protein and hinder it to diffuse out of the…
Theories unifying gravity with other interactions suggest spatial and temporal variation of fundamental "constants" in the Universe. A change in the fine structure constant, alpha, could be detected via shifts in the frequencies of atomic…
Photosynthesis relies on efficient energy relaxation within the excited-state manifold of pigment-protein complexes. Since the protein scaffold is rather flexible, the resulting energetic and structural disorder gives rise to a complex…
Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level…
Alignment of molecules through electric fields minimizes the averaging over orientations, e. g., in single particle imaging experiments. The response of molecules to external ac electric fields is governed by their polarizability tensor,…
Next-generation communication networks require > Tbit/s single-channel data transfer and processing with sub-picosecond switches and routers at network nodes. Materials enabling ultrafast all-optical switching have high potential to solve…
We simulate the nonequilibrium steady state \textit{cis-trans} photoisomerization of retinal chromophore in rhodopsin based on a two-state-two-mode model coupled to a thermal environment. By analyzing the systematic trends within an…
Molecular hydrogen transitions in the sub-damped Lyman alpha absorber at redshift z = 2.69, toward the background quasar SDSS J123714.60+064759.5, were analyzed in order to search for a possible variation of the proton-to-electron mass…
We investigate theoretically the spectrum of resonance fluorescence of a harmonically trapped atom, whose internal transitions are $\Lambda$--shaped and driven at two-photon resonance by a pair of lasers, which cool the center--of--mass…
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…
The primary steps of photosynthesis rely on the generation, transport, and trapping of excitons in pigment-protein complexes (PPCs). Generically, PPCs possess highly structured vibrational spectra, combining many discrete intra-pigment…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
There is now a certain consensus that Transcription Factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D-diffusion in…
Point spread function (PSF) engineering of the emitter can code higher spatial frequency information of an image to break diffraction limit but suffer from the complexed optical systems. Here we present a robust strategy to simultaneously…
The increasing interest in photoactivated proteins as natural replacement of standard inorganic materials in photocells drives to the compared analysis of bacteriorhodopsin and proteorhodopsin, two widely diffused proteins belonging to the…
The kinetic energy of an atom recoiling due to absorption of a photon was measured as a frequency using an interferometric technique called ``contrast interferometry''. Optical standing wave pulses were used as atom-optical elements to…
We construct two strong-field path integral methods with full Coulomb distortion, in which the quantum pathways are mimicked by interfering electron orbits: the rate-based CQSFA (R-CQSFA) and the hybrid forward-boundary CQSFA (H-CQSFA). The…
In natural and artificial light-harvesting complexes (LHC) the resonant energy transfer (RET) between chromophores enables an efficient and directional transport of solar energy between collection and reaction centers. The detailed…
The engineering of the optical response of materials is a paradigm that demands microscopic-level accuracy and reliable predictive theoretical tools. Here we compare and contrast the dispersive permittivity tensor, using both a low-energy…
We investigate the folding mechanism of the WW domain Fip35 using a realistic atomistic force field by applying the Dominant Reaction Pathways (DRP) approach. We find evidence for the existence of two folding pathways, which differ by the…