Engineering topics

Zhu, Pengfei

Publications and source records attributed to Zhu, Pengfei.

4 records

DOE OSTI2024

Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis

Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA’s enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Ultrafast formation of topological defects in a two-dimensional charge density wave

Topological defects play a central role in dynamical systems undergoing a non-adiabatic transition. In solids, topological defects as a result of femtosecond laser excitation have attracted increasing interest not only because they are key to understanding phase transitions but also because they can generate a variety of hidden orders that are not accessible in thermal equilibrium. Despite the common occurrence of these defects in a non-equilibrium system, the fundamental limit on how fast they can emerge in solids and the generic pathway for defect creation at such fast timescales have remained open questions. Here we apply ultrafast electron diffraction to study the reciprocal-space signatures of transient defects in a two-dimensional charge density wave, where simultaneous measurements of both defect and phonon dynamics yield a microscopic view of defect formation in the femtosecond regime. We find that one-dimensional domain walls are generated well within 1 ps following photoexcitation, during which the defect growth is not dictated by the amplitude of the order parameter but is mediated by a non-thermal population of longitudinal optical phonons. In conclusion, our work provides a framework for the ultrafast engineering of topological defects that are coupled to specific collective modes, which will prove useful for the dynamical control of non-equilibrium phases in correlated materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment

Bathyarchaeia, as one of the most abundant microorganisms on Earth, play vital roles in the global carbon cycle. However, our understanding of their origin, evolution, and ecological functions remains poorly constrained. Here, we present the largest dataset of Bathyarchaeia metagenome assembled genome to date and reclassify Bathyarchaeia into eight order-level units corresponding to the former subgroup system. Highly diversified and versatile carbon metabolisms were found among different orders, particularly atypical C1 metabolic pathways, indicating that Bathyarchaeia represent overlooked important methylotrophs. Molecular dating results indicate that Bathyarchaeia diverged at ~3.3 billion years, followed by three major diversifications at ~3.0, ~2.5, and ~1.8 to 1.7 billion years, likely driven by continental emergence, growth, and intensive submarine volcanism, respectively. The lignin-degrading Bathyarchaeia clade emerged at ~300 million years perhaps contributed to the sharply decreased carbon sequestration rate during the Late Carboniferous period. The evolutionary history of Bathyarchaeia potentially has been shaped by geological forces, which, in turn, affected Earth’s surface environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Light-induced dimension crossover dictated by excitonic correlations

In low-dimensional systems with strong electronic correlations, the application of an ultrashort laser pulse often yields novel phases that are otherwise inaccessible. The central challenge in understanding such phenomena is to determine how dimensionality and many-body correlations together govern the pathway of a non-adiabatic transition. To this end, we examine a layered compound, 1T-TiSe 2 , whose three-dimensional charge-density-wave (3D CDW) state also features exciton condensation due to strong electron-hole interactions. We find that photoexcitation suppresses the equilibrium 3D CDW while creating a nonequilibrium 2D CDW. Remarkably, the dimension reduction does not occur unless bound electron-hole pairs are broken. This relation suggests that excitonic correlations maintain the out-of-plane CDW coherence, settling a long-standing debate over their role in the CDW transition. Our findings demonstrate how optical manipulation of electronic interaction enables one to control the dimensionality of a broken-symmetry order, paving the way for realizing other emergent states in strongly correlated systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗