Pracownicy

Streszczenie:
We theoretically investigate electron-electron interaction effects on the single-particle Green's function of doped monolayer MoS2, employing a massless Dirac continuum model within the random phase approximation and incorporating long-range Coulomb interactions via a modified Keldysh potential. Our calculations provide quantitative predictions for the many-body spectral function, the renormalized quasiparticle energy dispersion, and the renormalized velocity at both zero and finite temperatures, taking into account carrier density, electric field intensity, and spin polarization. We identify experimentally detectable many-body signatures that are substantially enhanced with decreasing carrier density, electric field, and spin polarization, alongside intriguing instabilities in the excitation spectrum at small wave vectors where interactions completely destroy the noninteracting linear dispersion. The velocity renormalization exhibits a leading-order temperature correction that is linear and positive, with a universal, density-independent slope in the high-density limit. We further predict an enhanced effective velocity at low temperatures and a nonmonotonic temperature dependence at higher temperatures (e.g.

Streszczenie:
Time-averaged restraints from nuclear magnetic resonance (NMR) measurements have been implemented in the UNRES coarse-grained model of polypeptide chains in order to develop a tool for data-assisted modeling of the conformational ensembles of multistate proteins, intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs), many of which are essential in cell biology. A numerically stable variant of molecular dynamics with time-averaged restraints has been introduced, in which the total energy is conserved in sections of a trajectory in microcanonical runs, the bath temperature is maintained in canonical runs, and the time-average-restraint-force components are scaled up with the length of the memory window so that the restraints affect the simulated structures. The new approach restores the conformational ensembles used to generate ensemble-averaged distances, as demonstrated with synthetic restraints. The approach results in a better fitting of the ensemble-averaged interproton distances to those determined experimentally for multistate proteins and proteins with intrinsically disordered regions, which puts it at an advantage over all-atom approaches with regard to the determination of the conformational ensembles of proteins with diffuse structures, owing to a faster and more robust conformational search.

Streszczenie:
The influence of distance restraints from chemical cross-link mass spectroscopy (XL-MS) on the quality of protein structures modeled with the coarse-grained UNRES force field was assessed by using a protocol based on multiplexed replica exchange molecular dynamics, in which both simulated and experimental cross-link restraints were employed, for 23 small proteins. Six cross-links with upper distance boundaries from 4 Å to 12 Å (azido benzoic acid succinimide (ABAS), triazidotriazine (TATA), succinimidyldiazirine (SDA), disuccinimidyl adipate (DSA), disuccinimidyl glutarate (DSG), and disuccinimidyl suberate (BS3)) and two types of restraining potentials ((i) simple flat-bottom Lorentz-like potentials dependent on side chain distance (all cross-links) and (ii) distance- and orientation-dependent potentials determined based on molecular dynamics simulations of model systems (DSA, DSG, BS3, and SDA)) were considered. The Lorentz-like potentials with properly set parameters were found to produce a greater number of higher-quality models compared to unrestrained simulations than the MD-based potentials, because the latter can force too long distances between side chains. Therefore, the flat-bottom Lorentz-like potentials are recommended to represent cross-link restraints. It was also found that significant improvement of model quality upon the introduction of cross-link restraints is obtained when the sum of differences of indices of cross-linked residues exceeds 150.