Fast kinetic simulator for relativistic matter.

Relativistic kinetic theory is ubiquitous to several fields of modern physics, finding application at large scales in systems in astrophysical contexts, all of the way down to subnuclear scales and into the realm of quark-gluon plasmas. This motivates the quest for powerful and efficient computational methods that are able to accurately study fluid dynamics in the relativistic regime as well as the transition to beyond hydrodynamics-in principle all of the way down to ballistic regimes. We present a family of relativistic lattice kinetic schemes for the efficient simulation of relativistic flows in both strongly (fluid) and weakly (rarefied gas) interacting regimes. The method can deal with both massless and massive particles, thereby encompassing ultra- and mildly relativistic regimes alike. The computational performance of the method for the simulation of relativistic flows across the aforementioned regimes is discussed in detail, along with prospects of future applications.

Asymmetric dynamic coupling promotes alternative evolutionary pathways in an enzyme dimer.

The importance of dynamic factors in enzyme evolution is gaining recognition. Here we study how the evolution of a new enzymatic activity exploits conformational tinkering and demonstrate that conversion of a dimeric phosphotriesterase to an arylesterase in Pseudomonas diminuta is accompanied by structural divergence between the two subunits. Deviations in loop conformations increase with promiscuity, leading to functionally distinct states, while they decrease during specialisation for the new function. We show that opposite loop movements in the two subunits are due to a dynamic coupling with the dimer interface, the importance of which is also corroborated by the co-evolution of the loop and interface residues. These results illuminate how protein dynamics promotes conformational heterogeneity in a dimeric enzyme, leading to alternative evolutionary pathways for the emergence of a new function.

Patterns of Dynamics Comprise a Conserved Evolutionary Trait.

The importance of protein dynamics in function may suggest an evolutionary selection on large-scale protein motions. Here we systematically studied the dynamic characteristics in 2221 protein domains (58477 sequences) of the Pfam database. We defined the patterns of dynamics (PODs) based on the estimated NMR order parameters and the predicted degree of disorder, and found a significant correlation between them in families of both structured and disordered protein domains. We demonstrate that conservation of dynamic patterns frequently exceeds conservation of sequence and is comparable to the patterns of hydropathy and nonspecific interaction potential. Similarity of dynamic patterns is weakly correlated to structure similarity and to the degree of disorder. We illustrate that POD alignments could be applied to sequentially divergent or intrinsically disordered regions. We propose that patterns of dynamics comprise a conserved evolutionary trait, which could be used to infer evolutionary relationships as an alternative to sequence and structure.