Dataset Information

The intimate relationship between structural relaxation and the energy landscape of monatomic liquid metals.

ABSTRACT: The characteristic property of a liquid, discriminating it from a solid, is its fluidity, which can be expressed by a velocity field. The reaction of the velocity field on forces is enshrined in the transport parameter viscosity. In contrast, a solid reacts to forces elastically through a displacement field, the particles are trapped in their potential minimum. The flow in a liquid needs enough thermal energy to overcome the changing potential barriers, which is supported through a continuous rearrangement of surrounding particles. Cooling a liquid will decrease the fluidity of a particle and the mobility of the neighbouring particles, resulting in an increase of the viscosity until the system comes to an arrest. This process with a concomitant slowing down of collective particle rearrangements might already start deep inside the liquid state. The idea of the potential energy landscape provides an attractive picture for these dramatic changes. However, despite the appealing idea there is a scarcity of quantitative assessments, in particular, when it comes to experimental studies. Here we present results on a monatomic liquid metal through a combination of ab initio molecular dynamics, neutron spectroscopy and inelastic x-ray scattering. We investigated the collective dynamics of liquid aluminium to reveal the changes in dynamics when the high temperature liquid is cooled towards solidification. The results demonstrate the main signatures of the energy landscape picture, a reduction in the internal atomic structural energy, a transition to a stretched relaxation process and a deviation from the high-temperature Arrhenius behavior of the relaxation time. All changes occur in the same temperature range at about [Formula: see text], which can be regarded as the temperature when the liquid aluminium enters the landscape influenced phase and enters a more viscous liquid state towards solidification. The similarity in dynamics with other monatomic liquid metals suggests a universal dynamic crossover above the melting point.

SUBMITTER: Demmel F

PROVIDER: S-EPMC8175717 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundStructural excursions of a protein at equilibrium are key to biomolecular recognition and function modulation. Protein modeling research is driven by the need to aid wet laboratories in characterizing equilibrium protein dynamics. In principle, structural excursions of a protein can be directly observed via simulation of its dynamics, but the disparate temporal scales involved in such excursions make this approach computationally impractical. On the other hand, an informative representation of the structure space available to a protein at equilibrium can be obtained efficiently via stochastic optimization, but this approach does not directly yield information on equilibrium dynamics.MethodsWe present here a novel methodology that first builds a multi-dimensional map of the energy landscape that underlies the structure space of a given protein and then queries the computed map for energetically-feasible excursions between structures of interest. An evolutionary algorithm builds such maps with a practical computational budget. Graphical techniques analyze a computed multi-dimensional map and expose interesting features of an energy landscape, such as basins and barriers. A path searching algorithm then queries a nearest-neighbor graph representation of a computed map for energetically-feasible basin-to-basin excursions.ResultsEvaluation is conducted on intrinsically-dynamic proteins of importance in human biology and disease. Visual statistical analysis of the maps of energy landscapes computed by the proposed methodology reveals features already captured in the wet laboratory, as well as new features indicative of interesting, unknown thermodynamically-stable and semi-stable regions of the equilibrium structure space. Comparison of maps and structural excursions computed by the proposed methodology on sequence variants of a protein sheds light on the role of equilibrium structure and dynamics in the sequence-function relationship.ConclusionsApplications show that the proposed methodology is effective at locating basins in complex energy landscapes and computing basin-basin excursions of a protein with a practical computational budget. While the actual temporal scales spanned by a structural excursion cannot be directly obtained due to the foregoing of simulation of dynamics, hypotheses can be formulated regarding the impact of sequence mutations on protein function. These hypotheses are valuable in instigating further research in wet laboratories.

Dataset Information

The intimate relationship between structural relaxation and the energy landscape of monatomic liquid metals.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets