Phonon-assisted electron-proton transfer in [FeFe] hydrogenases: Topological role of clusters.

[FeFe] hydrogenases are enzymes that have acquired a unique capacity to synthesize or consume molecular hydrogen (H2). This function relies on a complex catalytic mechanism involving the active site and two distinct electron and proton transfer networks working in concert. By an analysis based on terahertz vibrations of [FeFe] hydrogenase structure, we are able to predict and identify the existence of rate-promoting vibrations at the catalytic site and the coupling with functional residues involved in reported electron and proton transfer networks. Our findings suggest that the positioning of the cluster is influenced by the response of the scaffold to thermal fluctuations, which in turn drives the formation of networks for electron transfer through phonon-assisted mechanisms. Thus, we address the problem of linking the molecular structure to the catalytic function through picosecond dynamics, while raising the functional gain brought by the cofactors or clusters, using the concept of fold-encoded localized vibrations.

Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins.

Proteins are among the most complex molecular structures, which have evolved to develop broad functions, such as energy conversion and transport, information storage and processing, communication, and regulation of chemical reactions. However, the mechanisms by which these dynamical entities coordinate themselves to perform biological tasks remain hotly debated. Here, a physical theory is presented to explain how functional dynamical behavior possibly emerge in complex/macro molecules, thanks to the effect that we term bilocalization of thermal vibrations. More specifically, our approach allows us to understand how structural irregularities lead to a partitioning of the energy of the vibrations into two distinct sets of molecular domains, corresponding to slow and fast motions. This shape-encoded spectral allocation, associated to the genetic sequence, provides a close access to a wide reservoir of dynamical patterns, and eventually allows the emergence of biological functions by natural selection. To illustrate our approach, the SPIKE protein structure of SARS-COV2 is considered.

The physical origin of rate promoting vibrations in enzymes revealed by structural rigidity.

Enzymes are the most efficient catalysts known to date. However, decades of research have failed to fully explain the catalytic power of enzymes, and most of the current attempts to uncloak the details of atomic motions at active sites remain incomplete. Here, a straightforward manner for understanding the interplay between the complex or irregular enzyme topology and dynamical effects at catalytic sites is introduced, by revealing how fast localized vibrations form spontaneously in the stiffest parts of the scaffold. While shedding light on a physical mechanism that allowed the selection of the picosecond (ps) timescale to increase the catalytic proficiency, this approach exposes the functional importance of localized motions as a by-product of the stability-function tradeoff in enzyme evolution. From this framework of analysis-directly accessible from available diffraction data-experimental strategies for engineering the catalytic rate in enzymatic proteins are proposed.

Universality of fold-encoded localized vibrations in enzymes.

Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. In this work, we use a powerful mathematical approach to show that rate-promoting vibrations in the picosecond range, specifically encoded in the 3D protein structure, are localized vibrations optimally coupled to the chemical reaction coordinates at the active site. Remarkably, our theory also exposes an hithertho unknown deep connection between the unique localization fingerprint and a distinct partition of the 3D fold into independent, foldspanning subdomains that govern long-range communication. The universality of these features is demonstrated on a pool of more than 900 enzyme structures, comprising a total of more than 10,000 experimentally annotated catalytic sites. Our theory provides a unified microscopic rationale for the subtle structure-dynamics-function link in proteins.

Nanoscale Brownian heating by interacting magnetic dipolar particles.

Clusters of magnetic nanoparticles have received considerable interest in various research fields. Their capacity to generate heat under an alternating magnetic field has recently opened the way to applications such as cancer therapy by hyperthermia. This work is an attempt to investigate the collective effects of interacting dipoles embedded in magnetic nano-particles (MNP) to predict their thermal dissipation with a liquid. We first present a general approach, based on the tracking of the microscopic dipole fluctuations, to access to the dissipation spectra of any spatial distribution of MNPs. Without any other assumption that the linear response regime, it is shown that increasing the particle concentration (dipolar interactions) dramatically diminishes and blueshifts the dissipation processes. This effect originates in a predominance of the coupling energy over the Brownian torques, which create a long-range ordering that saturates the response of the system to an external field. Consequently, the particle density is of fundamental importance to the control of the absorption of electromagnetic energy and its subsequent dissipation in the form of heat.

Classical to quantum transition of heat transfer between two silica clusters.

Heat transfer between two silica clusters is investigated by using the nonequilibrium Green's function method. In the gap range between 4 Å and 3 times the cluster size, the thermal conductance decreases as predicted by the surface charge-charge interaction. Above 5 times the cluster size, the volume dipole-dipole interaction predominates. Finally, when the distance becomes smaller than 4 Å, a quantum interaction where the electrons of both clusters are shared takes place. This quantum interaction leads to the dramatic increase of the thermal coupling between neighbor clusters due to strong interactions. This study finally provides a description of the transition between radiation and heat conduction in gaps smaller than a few nanometers.

Quantized thermal conductance of nanowires at room temperature due to Zenneck surface-phonon polaritons.

Based on the Landauer formalism, we demonstrate that the thermal conductance due to the propagation of Zenneck surface-phonon polaritons along a polar nanowire is independent of the material characteristics and is given by π2kB2T/3h. The giant propagation length of these energy carriers establishes that this quantization holds not only for a temperature much smaller than 1 K, as is the case for electrons and phonons, but also for temperatures comparable to room temperature, which can significantly facilitate its observation and application in the thermal management of nanoscale electronics and photonics.

Quantum thermal bath for molecular dynamics simulation.

Molecular dynamics (MD) is a numerical simulation technique based on classical mechanics. It has been taken for granted that its use is limited to a large temperature regime where classical statistics is valid. To overcome this limitation, the authors introduce in a universal way a quantum thermal bath that accounts for quantum statistics while using standard MD. The efficiency of the new technique is illustrated by reproducing several experimental data at low temperatures in a regime where quantum statistical effects cannot be neglected.