No abstract

No abstract

The field of model order reduction (MOR) is growing in importance due to its ability to extract the key insights from complex simulations while discarding computationally burdensome and superfluous information. We provide an overview of MOR methods for the creation of fast & accurate emulators of memory- and compute-intensive nuclear systems, focusing on eigen-emulators and variational emulators. As an example, we describe how "eigenvector continuation'' is a special case of a much more general and well-studied MOR formalism for parameterized systems. We continue with an introduction to the Ritz and Galerkin projection methods that underpin many such emulators, while pointing to the relevant MOR theory and its successful applications along the way. We believe that this will open the door to broader applications in nuclear physics and facilitate communication with practitioners in other fields.

The BUQEYE collaboration (Bayesian Uncertainty Quantification: Errors in Your effective field theory) presents a pedagogical introduction to projection-based, reduced-order emulators for applications in low-energy nuclear physics. The term emulator refers here to a fast surrogate model capable of reliably approximating high-fidelity models. As the general tools employed by these emulators are not yet well-known in the nuclear physics community, we discuss variational and Galerkin projection methods, emphasize the benefits of offline-online decompositions, and explore how these concepts lead to emulators for bound and scattering systems that enable fast and accurate calculations using many different model parameter sets. We also point to future extensions and applications of these emulators for nuclear physics, guided by the mature field of model (order) reduction. All examples discussed here and more are available as interactive, open-source Python code so that practitioners can readily adapt projection-based emulators for their own work.

ABSTRACTThe replisome functions in a dynamic environment that is at the intersection of parental and nascent chromatin. Parental nucleosomes are disrupted in front of the replication fork. The daughter duplexes are packaged with an equal amount of parental and newly synthesized histones in the wake of the replication fork through the action of the replication-coupled chromatin assembly pathway. Histone acetyltransferase 1 (Hat1) is responsible for the cytosolic diacetylation of newly synthesized histone H4 on lysines 5 and 12 that accompanies replication-coupled chromatin assembly. Analysis of the role of Hat1 in replication-coupled chromatin assembly demonstrates that Hat1 also physically associates with chromatin near sites of DNA replication. The association of Hat1 with newly replicated DNA is transient but can be stabilized by replication fork stalling. The association of Hat1 with nascent chromatin may be functionally relevant as loss of Hat1 results in a decrease in replication fork progression and an increase in replication fork stalling. In addition, in the absence of Hat1, stalled replication forks are unstable and newly synthesized DNA becomes susceptible to Mre11-dependent degradation. These results suggest that Hat1 links replication fork function to the proper processing and assembly of newly synthesized histones.