Excited-State Charge Transfer Coupling from Quasiparticle Energy Density Functional Theory.

The recently developed Quasiparticle Energy (QE) scheme, based on a DFT calculation with one more (or less) electron, offers a good description of excitation energies, even with charge transfer characters. In this work, QE is further extended to calculate electron transfer (ET) couplings involving two excited states. We tested it with a donor-acceptor complex, consisting of a furan and a 1,1-dicyanoethylene (DCNE), in which two low lying charge transfer and local excitation states are involved.

Two inhibitory neuronal classes govern acquisition and recall of spinal sensorimotor adaptation.

Spinal circuits are central to movement adaptation, yet the mechanisms within the spinal cord responsible for acquiring and retaining behavior upon experience remain unclear. Using a simple conditioning paradigm, we found that dorsal inhibitory neurons are indispensable for adapting protective limb-withdrawal behavior by regulating the transmission of a specific set of somatosensory information to enhance the saliency of conditioning cues associated with limb position. By contrast, maintaining previously acquired motor adaptation required the ventral inhibitory Renshaw cells.

Reformulation of thermally assisted-occupation density functional theory in the Kohn-Sham framework.

We reformulate the thermally assisted-occupation density functional theory (TAO-DFT) into the Kohn-Sham single-determinant framework and construct two new post-self-consistent field (post-SCF) static correlation correction schemes, named rTAO and rTAO-1. In contrast to the original TAO-DFT with the density in an ensemble form, in which each orbital density is weighted with a fractional occupation number, the ground-state density is given by a single-determinant wavefunction, a regular Kohn-Sham (KS) density, and total ground state energy is expressed in the normal KS form with a static correlation energy formulated in terms of the KS orbitals. In post-SCF calculations with rTAO functionals, an efficient energy scanning to quantitatively determine θ is also proposed.

Evaluation of Immuno-Rolling Circle Amplification for Multiplex Detection and Profiling of Antigen-Specific Antibody Isotypes.

Antibody characterization is essential for understanding the immune system and development of diagnostics and therapeutics. Current technologies are mainly focusing on the detection of antigen-specific immunoglobulin G (IgG) using bulk singleplex measurements, which lack information on other isotypes and specificity of individual antibodies. Digital immunoassays based on nucleic acid amplification have demonstrated superior performance by allowing the detection of single molecules in a multiplex and sensitive manner.

Time-Domain Line-Shape Analysis from 2D Spectroscopy to Precisely Determine Hamiltonian Parameters for a Photosynthetic Complex.

Optical signals come from coherences between quantum states, with spectral line widths determined by the coherences' dephasing dynamics. Using a 2D electronic spectrometer, we observe weak coherence- and rephasing-time-domain signals persisting to 1 ps in the Fenna-Matthews-Olson complex at 77 K. These are coherences between the ground and excited states prepared after the complex interacts once or three times with light, rather than zero-quantum coherences that are more frequently investigated following two interactions.

Excitation energies from thermally assisted-occupation density functional theory: Theory and computational implementation.

The time-dependent density functional theory (TDDFT) has been broadly used to investigate the excited-state properties of various molecular systems. However, the current TDDFT heavily relies on outcomes from the corresponding ground-state DFT calculations, which may be prone to errors due to the lack of proper treatment in the non-dynamical correlation effects. Recently, thermally assisted-occupation DFT (TAO-DFT) [J.

Orientational Dynamics of Transition Dipoles and Exciton Relaxation in LH2 from Ultrafast Two-Dimensional Anisotropy.

Light-harvesting complexes in photosynthetic organisms display fast and efficient energy transfer dynamics, which depend critically on the electronic structure of the coupled chromophores within the complexes and their interactions with their environment. We present ultrafast anisotropy dynamics, resolved in both time and frequency, of the transmembrane light-harvesting complex LH2 from Rhodobacter sphaeroides in its native membrane environment using polarization-controlled two-dimensional electronic spectroscopy. Time-dependent anisotropy obtained from both experiment and modified Redfield simulation reveals an orientational preference for excited state absorption and an ultrafast equilibration within the B850 band in LH2.

Elucidation of near-resonance vibronic coherence lifetimes by nonadiabatic electronic-vibrational state character mixing.

Recent work suggests that the long-lived coherences observed in both natural and artificial light-harvesting systems (such as the Fenna-Matthews-Olson complex) could be attributed to the mixing of the pigments' electronic and vibrational degrees of freedom. To investigate the underlying mechanism of these long coherence lifetimes, a sophisticated description of interactions between the molecular aggregates and the nonequilibrium fluctuations in the surrounding environment is necessary. This is done by implementing the hierarchical equations of motion approach on model homodimers, a method used in the intermediate coupling regime for many molecular aggregates wherein the nonequilibrium environment phonons play nontrivial roles in exciton dynamics.

Simulated two-dimensional electronic spectroscopy of the eight-bacteriochlorophyll FMO complex.

The Fenna-Matthews-Olson (FMO) protein-pigment complex acts as a molecular wire conducting energy between the outer antenna system and the reaction center; it is an important photosynthetic system to study the transfer of excitonic energy. Recent crystallographic studies report the existence of an additional (eighth) bacteriochlorophyll a (BChl a) in some of the FMO monomers. To understand the functionality of this eighth BChl, we simulated the two-dimensional electronic spectra of both the 7-site (apo form) and the 8-site (holo form) variant of the FMO complex from green sulfur bacteria, Prosthecochloris aestuarii.

Population and coherence dynamics in light harvesting complex II (LH2).

The electronic excitation population and coherence dynamics in the chromophores of the photosynthetic light harvesting complex 2 (LH2) B850 ring from purple bacteria (Rhodopseudomonas acidophila) have been studied theoretically at both physiological and cryogenic temperatures. Similar to the well-studied Fenna-Matthews-Olson (FMO) protein, oscillations of the excitation population and coherence in the site basis are observed in LH2 by using a scaled hierarchical equation of motion approach. However, this oscillation time (300 fs) is much shorter compared to the FMO protein (650 fs) at cryogenic temperature.

Inhibition of histone deacetylase activity is a novel function of the antifolate drug methotrexate.

Methotrexate (MTX) is a dihydrofolate reductase (DHFR) inhibitor widely used for treating human cancers, and overexpression of histone deacetylase (HDAC) is usually found in tumors. HDAC inhibitors (HDACi) can reactivate tumor suppressor genes and serve as potential anti-cancer drugs. In this study, we found that MTX shared structural similarity with some HDACi and molecular modeling showed that MTX indeed docks into the active site of HDLP, a bacterial homologue of HDAC.

Statins increase p21 through inhibition of histone deacetylase activity and release of promoter-associated HDAC1/2.

Statins are 3-hydroxy-3-methylglutaryl-CoA reductase inhibitors broadly used for the control of hypercholesterolemia. Recently, they are reported to have beneficial effects on certain cancers. In this study, we show that statins inhibited the histone deacetylase (HDAC) activity and increased the accumulation of acetylated histone-H3 and the expression of p21(WAF/CIP) in human cancer cells.