Related papers: On excited state reaction path in reversibly switc…
Transferable excited-state dynamics offer a route to efficient screening of photophysical behavior across molecular systems, but conventional nonadiabatic simulations remain prohibitively expensive. Here we introduce X-MACE, a transferable…
In recent years, pi-conjugated polymers are attracting considerable interest in view of their light-dependent torsional reorganization around the pi-conjugated backbone, which determines peculiar light-emitting properties. Motivated by the…
The coherent dynamics of vibronic wave packets in the green fluorescent protein is reported. At room temperature the non-stationary dynamics following impulsive photoexcitation displays an oscillating optical transmissivity pattern with…
The green fluorescent protein (GFP) chromophore is an asymmetric monomethine dye system. In the resonance color theory of dyes, a strong optical excitation arises from interactions of two valence-bond structures with a third, higher…
The photoisomerization reaction of the retinal chromophore in rhodopsin was computationally studied using a two-state two-mode model coupled to thermal baths. Reaction quantum yields at the steady state (10 ps and beyond) were found to be…
The functional properties of photoactive proteins are governed by the interplay between bright and dark excited states. While the bright states are well-studied, the dark states, which are fundamental to photostability and light harvesting,…
Optically-addressable spin qubits form the foundation of a new generation of emerging nanoscale sensors. The engineering of these sensors has mainly focused on solid-state systems such as the nitrogen-vacancy (NV) center in diamond.…
Photochemical reactions on semiconductors are anisotropic, since they occur with different rates on surfaces of different orientation. Understanding the origin of this anisotropy is crucial to engineering more efficient photocatalysts. In…
Nine quasar absorption spectra at 21-cm and UV rest-wavelengths are used to estimate possible variations in x=alpha^2 g_p mu, (alpha is the fine structure constant, g_p the proton g-factor and mu=me/mp the electron-to-proton mass ratio). We…
Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the…
We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy…
We consider reversible breaking of adhesion bonds or folding of proteins under the influence of a constant external force. We discuss the stochastic properties of the unbinding/rebinding events and analyze their mean number and their…
Temporally and spatially resolved measurements of protein transport inside cells provide important clues to the functional architecture and dynamics of biological systems. Fluorescence Recovery After Photobleaching (FRAP) technique has been…
In this paper we consider mathematical modeling of the dynamics of self-organized patterning of spatially confined human embryonic stem cells (hESCs) treated with BMP4 (gastruloids) described in recent experimental works. In the first part…
Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
In this study, we explore the electron transition mechanism and optical properties of the popular red fluorescent protein mCherry. By examining the charge transfer spectrum and combining it with the mCherry hole-electron distribution, we…
Fluorescence microscopy is rapidly turning into nanoscopy. Among the various nanoscopy methods, the STED/RESOLFT super-resolution family has recently been expanded to image even large fields of view within a few seconds. This advance relies…
An Ising--like model of proteins is used to investigate the mechanical unfolding of the Green Fluorescent Protein along different directions. When the protein is pulled from its ends, we recover the major and minor unfolding pathways…
QSO absorption spectra provide an extremely useful probe of possible cosmological variation in various physical constants. Comparison of H I 21cm absorption with corresponding molecular (rotational) absorption spectra allows us to constrain…