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DOE OSTI2022

Scattering Amplitudes and QFT Insight (Final Scientific Report)

The calculation of scattering amplitudes provides an invariant window into the physical dynamic content of relativistic quantum field theory. Yet with traditional methods, for empirically relevant theories, these calculations scale with a factorial complexity in external particles and precision. If we aspire to collapse the theoretical uncertainty obscuring new physics hidden at all scales from the microscopic probed at high energy colliders to the largest effective field theory in the universe governing the evolution of large scale structure, this complexity challenge necessitates new ideas and methods in calculation. Novel approaches like the color-kinematics duality and the associated double-copy construction have drastically simplified the situation, relating both gauge and gravity theory predictions to a much smaller kernel of invariant kinematic data. This project supporting research by the PI's Amplitudes and Insights group at Northwestern University looked to push insight deep into both the IR and the UV by establishing how novel structures must constrain the predictions of counterterms in both gauge and gravity theories, setting the groundwork to exploring the high energy behavior of particular gravity theories via constituent gauge-theory calculations, and confronting fundamental challenges at the interface between QFT amplitudes analysis and next generation gravitational wave science as well as well as inflationary and large scale structure cosmology.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Holographic measurement in CFT thermofield doubles

We extend the results of arXiv:2209.12903 by studying local projective measurements performed on subregions of two copies of a CFT 2 in the thermofield double state and investigating their consequences on the bulk double-sided black hole holographic dual. We focus on CFTs defined on an infinite line and consider measurements of both finite and semi-infinite subregions. In the former case, the connectivity of the bulk spacetime is preserved after the measurement. In the latter case, the measurement of two semi-infinite intervals in one CFT or of one semi-infinite interval in each CFT can destroy the Einstein-Rosen bridge and disconnect the bulk dual spacetime. In particular, we find that a transition between a connected and disconnected phase occurs depending on the relative size of the measured and unmeasured subregions and on the specific Cardy state the measured subregions are projected on. We identify this phase transition as an entangled/disentangled phase transition of the dual CFT system by computing the post-measurement holographic entanglement entropy between the two CFTs. We also find that bulk information encoded in one CFT in the absence of measurement can sometimes be reconstructed from the other CFT when a measurement is performed, or can be erased by the measurement. Finally, we show that a purely CFT calculation of the Renyi entropy using the replica trick yields results compatible with those obtained in our bulk analysis.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

In vitro recombination method

The present invention relates, e.g., to in vitro method, using isolated protein reagents, for joining two double stranded (ds) DNA molecules of interest, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule share a region of sequence identity, comprising contacting the two DNA molecules in a reaction mixture with (a) a non-processive 5′ exonuclease; (b) a single stranded DNA binding protein (SSB) which accelerates nucleic acid annealing; (c) a non strand-displacing DNA polymerase; and (d) a ligase, under conditions effective to join the two DNA molecules to form an intact double stranded DNA molecule, in which a single copy of the region of sequence identity is retained. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

In vitro recombination method

Young, Lei↗

DOE OSTI2022

A model of persistent breaking of continuous symmetry

We consider a UV-complete field-theoretic model in general dimensions, including d=2+1, which consists of two copies of the long-range vector models, with O(m) and O(N-m) global symmetry groups, perturbed by double-trace operators. Using conformal perturbation theory we find weakly-coupled IR fixed points for N\geq 6 N ≥ 6 that reveal a spontaneous breaking of global symmetry. Namely, at finite temperature the lower rank group is broken, with the pattern persisting at all temperatures due to scale-invariance. We provide evidence that the models in question are unitary and invariant under full conformal symmetry. Furthermore, we show that this model exhibits a continuous family of weakly interacting field theories at finite N.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Kaposi's sarcoma herpesvirus exploits the DNA damage response to circularize its genome

Abstract To establish lifelong, latent infection, herpesviruses circularize their linear, double-stranded, DNA genomes through an unknown mechanism. Kaposi's sarcoma (KS) herpesvirus (KSHV), a gamma herpesvirus, is tightly linked with KS, primary effusion lymphoma, and multicentric Castleman's disease. KSHV persists in latently infected cells as a multi-copy, extrachromosomal episome. Here, we show the KSHV genome rapidly circularizes following infection, and viral protein expression is unnecessary for this process. The DNA damage response (DDR) kinases, ATM and DNA-PKcs, each exert roles, and absence of both severely compromises circularization and latency. These deficiencies were rescued by expression of ATM and DNA-PKcs, but not catalytically inactive mutants. In contrast, γH2AX did not function in KSHV circularization. The linear viral genomic ends resemble a DNA double strand break, and non-homologous DNA end joining (NHEJ) and homologous recombination (HR) reporters indicate both NHEJ and HR contribute to KSHV circularization. Last, we show, similar to KSHV, ATM and DNA-PKcs have roles in circularization of the alpha herpesvirus, herpes simplex virus-1 (HSV-1), while γH2AX does not. Therefore, the DDR mediates KSHV and HSV-1 circularization. This strategy may serve as a general herpesvirus mechanism to initiate latency, and its disruption may provide new opportunities for prevention of herpesvirus disease.

Li, Shijun↗

DOE OSTI2023

Targeted mutagenesis with sequence–specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects

Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome–editing platforms employ sequence–specific nucleases (SSNs) to generate DNA double–stranded breaks at their target gene. Such DNA breaks are typically repaired via the error–prone nonhomologous end–joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end–use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN–mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Rescuing a black hole in the large- q coupled SYK model

In this paper, we develop a general effective theory for two copies of the Sachdev-Ye-Kitaev (SYK) model with a time-dependent bilinear coupling. For a quantum quench problem with an initial state of the thermofield double state, we show how the evolution of the system is described by a complex reparametrization field with a classical Hamiltonian. We study correlation functions in this system and compare the large-q theory with the bulk low energy effective theory. In particular, we study the special case of a “rescued black hole”, which describes how a time-evolved thermofield double state can evolve to the ground state of a coupled SYK model by a carefully tuned time-dependent coupling. In the low energy region, there is a holographic dual interpretation, which is a geometry that crosses over from an eternal black hole to a global AdS2 vacuum. This family of geometries allow us to access the bulk region that would be the black hole interior without the rescue process. By comparing the large-q and low energy theory, we find that even in the low energy region the deviation from the low energy theory cannot be neglected if the rescue process starts late. This provides evidence that the low energy effective theory of the bulk fails near the inner horizon of the black hole. We note the possibility of a connection to a two-dimensional analog of the higher-dimensional black hole singularity.

2D Gravity↗

DOE OSTI2021

Entanglement and confinement in coupled quantum systems

We study some general properties of coupled quantum systems. We consider simple interactions between two copies of identical Hamiltonians such as the SYK model, Pauli spin chains with random magnetic field and harmonic oscillators. Such couplings make the ground states close to the thermofield double states of the uncoupled Hamiltonians. For the coupled SYK model, we push the numerical computation further towards the thermodynamic limit so that an extrapolation in the size of the system is possible. We find good agreement between the extrapolated numerical result and the analytic result in the large-q limit. We also consider the coupled gauged matrix model and vector model, and argue that the deconfinement is associated with the loss of the entanglement, similarly to the previous observation for the coupled SYK model. The understanding of the microscopic mechanism of the confinement/deconfinement transition enables us to estimate the quantum entanglement precisely, and backs up the dual gravity interpretation which relates the deconfinement to the disappearance of the wormhole. Our results demonstrate the importance of the entanglement between the color degrees of freedom in the emergence of the bulk geometry from quantum field theory via holography.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

A symmetry algebra in double-scaled SYK

The double-scaled limit of the Sachdev-Ye-Kitaev (SYK) model takes the number of fermions and their interaction number to infinity in a coordinated way. In this limit, two entangled copies of the SYK model have a bulk description of sorts known as the “chord Hilbert space”. We analyze a symmetry algebra acting on this Hilbert space, generated by the two Hamiltonians together with a two-sided operator known as the chord number. This algebra is a deformation of the JT gravitational algebra, and it contains a subalgebra that is a deformation of the \mathfrak{sl}_2 𝔰 𝔩 2 near-horizon symmetries. The subalgebra has finite-dimensional unitary representations corresponding to matter moving around in a discrete Einstein-Rosen bridge. In a semiclassical limit the discreteness disappears and the subalgebra simplifies to \mathfrak{sl}_2 𝔰 𝔩 2 , but with a non-standard action on the boundary time coordinate. One can make the action of \mathfrak{sl}_2 𝔰 𝔩 2 algebra more standard at the cost of extending the boundary circle to include some “fake” portions. Such fake portions also accommodate certain subtle states that survive the semi-classical limit, despite oscillating on the scale of discreteness. We discuss applications of this algebra, including sub-maximal chaos, the traversable wormhole protocol, and a two-sided OPE.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Novel genetic tools improve Penicillium expansum patulin synthase production in Aspergillus niger

Since the first CRISPR (clustered regularly interspaced short palindromic repeats)‐Cas (CRISPR‐associated) system was developed for creating double‐stranded DNA breaks, it has been adapted and improved for different biotechnological applications. In this issue of The FEBS Journal , Arentshorst et al . developed a novel approach to enhance transgene expression of a specific protein, patulin synthase (PatE) from Penicillium expansum , in the important industrial filamentous fungus Aspergillus niger . Their technique involved the disruption of selected genes with counter‐effects on targeted protein production and simultaneous integration of glucoamylase landing sites into the disrupted gene locus such as protease regulator ( prtT ) in an ATP‐dependent DNA helicase II subunit 1 ( kusA or ku70 ) ‐ deletion strain. Multiple copies of the PatE transgene expression cassette were introduced by CRISPR‐Cas9‐mediated insertion. The purified PatE was further used for structural and functional studies, and the technique laid the foundation for elevating the overall production of various proteins or chemicals in those industrially important fungi.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Geospatial Data from the Alpine Treeline Warming Experiment (ATWE) on Niwot Ridge, Colorado, USA

This is a collection of all GPS- and computer-generated geospatial data specific to the Alpine Treeline Warming Experiment (ATWE), located on Niwot Ridge, Colorado, USA. The experiment ran between 2008 and 2016, and consisted of three sites spread across an elevation gradient. Geospatial data for all three experimental sites and cone/seed collection locations are included in this package. –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––Geospatial files include cone collection, experimental site, seed trap, and other GPS location/terrain data. File types include ESRI shapefiles, ESRI grid files or Arc/Info binary grids, TIFFs (.tif), and keyhole markup language (.kml) files. Trimble-imported data include plain text files (.txt), Trimble COR (CorelDRAW) files, and Trimble SSF (Standard Storage Format) files. Microsoft Excel (.xlsx) and comma-separated values (.csv) files corresponding to the attribute tables of many files within this package are also included. A complete list of files can be found in this document in the “Data File Organization” section in the included Data User's Guide. Maps are also included in this data package for reference and use. These maps are separated into two categories, 2021 maps and legacy maps, which were made in 2010. Each 2021 map has one copy in portable network graphics (.png) format, and the other in .pdf format. All legacy maps are in .pdf format. .png image files can be opened with any compatible programs, such as Preview (Mac OS) and Photos (Windows). All GIS files were imported into geopackages (.gpkg) using QGIS, and double-checked for compatibility and data/attribute integrity using ESRI ArcGIS Pro. Note that files packaged within geopackages will open in ArcGIS Pro with “main.” preceding each file name, and an extra column named “geom” defining geometry type in the attribute table. The contents of each geospatial file remain intact, unless otherwise stated in “niwot_geospatial_data_list_07012021.pdf/.xlsx”. This list of files can be found as an .xlsx and a .pdf in this archive.As an open-source file format, files within gpkgs (TIFF, shapefiles, ESRI grid or “Arc/Info Binary”) can be read using both QGIS and ArcGIS Pro, and any other geospatial softwares. Text and .csv files can be read using TextEdit/Notepad/any simple text-editing software; .csv’s can also be opened using Microsoft Excel and R. .kml files can be opened using Google Maps or Google Earth, and Trimble files are most compatible with Trimble’s GPS Pathfinder Office software. .xlsx files can be opened using Microsoft Excel. PDFs can be opened using Adobe Acrobat Reader, and any other compatible programs. A selection of original shapefiles within this archive were generated using ArcMap with associated FGDC-standardized metadata (xml file format). We are including these original files because they contain metadata only accessible using ESRI programs at this time, and so that the relationship between shapefiles and xml files is maintained. Individual xml files can be opened (without a GIS-specific program) using TextEdit or Notepad. Since ESRI’s compatibility with FGDC metadata has changed since the generation of these files, many shapefiles will require upgrading to be compatible with ESRI’s latest versions of geospatial software. These details are also noted in the “niwot_geospatial_data_list_07012021” file.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Data for Discovery, Characterization, and Application of Chromosomal Integration Sites for Stable Heterologous Gene Expression in Rhodotorula toruloides

Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides . We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. We validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides . These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides .

Conversion↗

DOE OSTI2025

Discovery, characterization, and application of chromosomal integration sites for stable heterologous gene expression in Rhodotorula toruloides

Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides. We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. Here, we validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides. These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Dark matter in a mirror solution to the strong C P problem

We study thermal production of dark matter (DM) in a realization of the minimal models of Bonnefoy [], where parity is used to solve the strong C P problem by transforming the entire Standard Model (SM) into a mirror copy. Although the mirror electron e ′ is a good DM candidate, its viability is mired by the presence of the mirror up quark u ′ , whose abundance is intimately related to the e ′ abundance and must be suppressed. This can be achieved through a sequential freeze-in mechanism, where mirror photons are first produced from SM gluons, and then the mirror photons produce e ′ . After computing the details of this double freeze-in, we discuss the allowed parameter space of the model, which lies at the threshold of experimental observations. We find that this origin of e ′ DM requires a low reheating temperature after inflation and is consistent with the baryon asymmetry arising from leptogenesis, providing mirror neutrinos have a significant degeneracy. Finally, we show that this e ′ DM is not compatible with Higgs parity, the simplest scheme with exact parity, unless SM parameters deviate significantly from their central values or the minimal model is extended. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Pseudorandomness from Subset States

We show it is possible to obtain quantum pseudorandomness and pseudoentanglement from random subset states -- i.e. quantum states which are equal superpositions over (pseudo)random subsets of strings. This answers an open question of Aaronson et al. [arXiv:2211.00747], who devised a similar construction augmented by pseudorandom phases. Our result follows from a direct calculation of the trace distance between t copies of random subset states and the Haar measure, via the representation theory of the symmetric group. We show that the trace distance is negligibly small, as long as the subsets are of an appropriate size which is neither too big nor too small. In particular, we analyze the action of basis permutations on the symmetric subspace, and show that the largest component is described by the Johnson scheme: the double-cosets of the symmetric group S N by the subgroup S t x S N-t . The Gelfand pair property of this setting implies that the matrix eigenbasis coincides with the symmetric group irreducible blocks, with the largest eigenblock asymptotically approaching the Haar average. An immediate corollary of our result is that quantum pseudorandom and pseudoentangled state ensembles do not require relative phases.

Computational Complexity (cs.CC)↗

DOE OSTI2020

Encoding the complete electric field of an ultraviolet ultrashort laser pulse in a near-infrared nonlinear-optical signal

We introduce a variation on the cross-correlation frequency-resolved optical gating (XFROG) technique that uses a near-infrared (NIR) nonlinear-optical signal to characterize pulses in the ultraviolet (UV). Using a transient-grating XFROG beam geometry, we create a grating using two copies of the unknown UV pulse and diffract a NIR reference pulse from it. We show that, by varying the delay between the UV pulses creating the grating, the UV pulse intensity-and-phase information can be encoded into a NIR signal. We also implemented a modified generalized-projections phase-retrieval algorithm for retrieving the UV pulses from these spectrograms. We performed proof-of-principle measurements of chirped pulses and double pulses, all at 400 nm. This approach should be extendable deeper into the UV and potentially even into the extreme UV or x-ray range.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Fitness Landscape-Guided Engineering of Locally Supercharged Virus-like Particles with Enhanced Cell Uptake Properties

Protein-based nanoparticles are useful models for the study of self-assembly and attractive candidates for drug delivery. Virus-like particles (VLPs) are especially promising platforms for expanding the repertoire of therapeutics that can be delivered effectively as they can deliver many copies of a molecule per particle for each delivery event. However, their use is often limited due to poor uptake of VLPs into mammalian cells. In this study, we use the fitness landscape of the bacteriophage MS2 VLP as a guide to engineer capsid variants with positively charged surface residues to enhance their uptake into mammalian cells. By combining mutations with positive fitness scores that were likely to produce assembled capsids, we identified two key double mutants with internalization efficiencies as much as 67-fold higher than that of wtMS2. Internalization of these variants with positively charged surface residues depends on interactions with cell surface sulfated proteoglycans, and yet, they are biophysically similar to wtMS2 with low cytotoxicity and an overall negative charge. Additionally, the best-performing engineered MS2 capsids can deliver a potent anticancer small-molecule therapeutic with efficacy levels similar to antibody-drug conjugates. Through this work, we were able to establish fitness landscape-based engineering as a successful method for designing VLPs with improved cell penetration. These findings suggest that VLPs with positive surface charge could be useful in improving the delivery of small-molecule- and nucleic acid-based therapeutics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗