We discuss the consequences of the quantum uncertainty on the spectrum of the electron emitted by the beta-processes of a tritium atom bound to a graphene sheet. We analyze quantitatively the issue ...recently raised by Cheipesh, Cheianov, and Boyarsky Phys. Rev. D 104, 116004 (2021), and discuss the relevant timescales and the degrees of freedom that can contribute to the intrinsic spread in the electron energy. We perform careful calculations of the potential between tritium and graphene with different coverages and geometries. With this at hand, we propose possible avenues to mitigate the effect of the quantum uncertainty.
We report the spontaneous formation of a GaP fullerene cage in ab initio molecular dynamics simulations starting from a bulk fragment. A systematic study of the geometric and electronic properties of ...neutral and ionized GaP clusters suggests the stability of heterofullerenes formed by a compound with zinc blende bulk structure. We find that GaP fullerenes up to 28 atoms have high symmetry, closed electronic shells, large highest occupied molecular orbital-lowest unoccupied molecular orbital energy gaps, and do not dissociate when ionized. We compare our results for GaP with those obtained by other groups for the corresponding BN clusters.
We analyze the encounter of a peptide substrate with the native HIV-1 protease, the mechanism of substrate incorporation in the binding cleft, and the dissociation of products after substrate ...hydrolysis. To account for the substrate, we extend a coarse-grained model force field, which we previously developed to study the flap opening dynamics of HIV-1 protease on a microsecond timescale. Molecular and Langevin dynamics simulations show that the flaps need to open for the peptide to bind and that the protease interaction with the substrate influences the flap opening frequency and interval. On the other hand, release of the products does not require flap opening because they can slide out from the binding cleft to the sides of the enzyme. Our data show that in the protease-substrate complex the highest fluctuations correspond to the 17- and 39-turns and the substrate motion is anticorrelated with the 39-turn. Moreover, the active site residues and the flap tips move in phase with the peptide. We suggest some mechanistic principles for how the flexibility of the protein may be involved in ligand binding and release.
The internal motions of proteins may serve as a “gate” in some systems, which controls ligand-protein association. This study applies Brownian dynamics simulations in a coarse-grained model to study ...the gated association rate constants of HIV-1 proteases and drugs. The computed gated association rate constants of three protease mutants, G48V/V82A/I84V/L90M, G48V, and L90M with three drugs, amprenavir, indinavir, and saquinavir, yield good agreements with experiments. The work shows that the flap dynamics leads to “slow gating”. The simulations suggest that the flap flexibility and the opening frequency of the wild-type, the G48V and L90M mutants are similar, but the flaps of the variant G48V/V82A/I84V/L90M open less frequently, resulting in a lower gated rate constant. The developed methodology is fast and provides an efficient way to predict the gated association rate constants for various protease mutants and ligands.
We derive a simple expression for the vacancy formation energy in a quantal crystal near to melting in terms of its Lindemann parameter and of the density response of the liquid near to freezing. ...Numerical illustrations are given for vacancies in 4He and 3He crystals.
The coherent dynamics of vibronic wave packets in the green fluorescent protein is reported. At room temperature the nonstationary dynamics following impulsive photoexcitation displays an oscillating ...optical transmissivity pattern with components at 67 fs (497 cm(-1)) and 59 fs (593 cm(-1)). Our results are complemented by ab initio calculations of the vibrational spectrum of the chromophore. This analysis shows the interplay between the dynamics of the aminoacidic structure and the electronic excitation in the primary optical events of green fluorescent proteins.
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