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Zdenek Futera

Publications and source records attributed to Zdenek Futera.

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CP2K: An electronic structure and molecular dynamics software package - Dynamics, Transport, and Spectroscopic Response

One of the distinguishing aspects of CP2K is its seamless integration of diverse structural and transition-state optimization techniques with advanced sampling approaches including Monte Carlo, molecular dynamics, and metadynamics, enabling the efficient exploration of complex potential- and free-energy landscapes, including rare events. These capabilities are combined with a broad hierarchy of energy and force evaluation methods, ranging from classical and machine-learned interaction potentials and mixed quantum-classical multiscale and semiempirical schemes, to highly accurate quantum-mechanical electronic-structure approaches. At the heart of the latter lies the Gaussian and plane-wave framework, along with its augmented all-electron generalization, which have been described in detail in our previous code review [T. D. Kühne et al., J. Chem. Phys. 152, 194103 (2020)]. Building on this foundation, the present work revisits the methods within CP2K that turn electronic structure into dynamics, transport, and spectroscopic response. Particular emphasis is placed on the coupling between static response calculations and nuclear motion: spectra may be evaluated at optimized structures, averaged over thermally sampled configurations, obtained from time-correlation functions along ab-initio or path integral molecular trajectories, or followed in real time together with electronic and nuclear dynamics. The same modular structure also enables equilibrium and biased transport simulations, from Kubo-type linear response to open-boundary approaches under external potentials, highlighting CP2K's unique capability to unify quantum chemistry with quantum and statistical mechanics within a versatile, holistic simulation environment.

physics.chem-ph

Off-resonant coherent electron transport over three nanometers in multi-heme protein bioelectronic junctions

Multi-heme cytochromes (MHC) are fascinating proteins used by bacterial organisms to shuttle electrons within and between their cells. When placed in a solid state electronic junction, they support temperature-independent currents over several nanometers that are three orders of magnitude higher compared to other redox proteins of comparable size. To gain microscopic insight into their astonishingly high conductivities, we present herein the first current-voltage calculations of its kind, for a MHC sandwiched between two Au(111) electrodes, complemented by photo-emission spectroscopy experiments. We find that conduction proceeds via off-resonant coherent tunneling mediated by a large number of protein valence-band orbitals that are strongly delocalized over heme and protein residues, effectively "gating" the current between the two electrodes. This picture is profoundly different from the dominant electron hopping mechanism supported by the same protein in aqueous solution. Our results imply that current output in MHC junctions could be even further increased in the resonant regime, e.g. by application of a gate voltage, making these proteins extremely interesting for next-generation bionanoelectronic devices.

physics.bio-ph