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Measuring the growth of Alfvén wave parametric decay instability using counter-propagating waves: Theory and simulations

The parametric decay instability (PDI) of Alfvén waves—where a pump Alfvén wave decays into a backward-propagating child Alfvén wave and a forward ion acoustic wave—is a fundamental nonlinear wave-wave interaction and holds significant implications for space and laboratory plasmas. However, to date there has been no direct experimental measurement of PDI. Here, we propose a novel and experimentally viable scheme to quantify the growth of Alfvén wave PDI on a linear device using a large pump Alfvén wave and a small counter-propagating seed Alfvén wave, with the seed-wave frequency tuned to match the backward Alfvén wave generated by standard PDI. Using hybrid simulations, we show that energy transfer from the pump to the seed reduces the latter's spatial damping. By comparing seed-wave amplitudes with and without the pump wave, this damping reduction can be used as a direct and reliable proxy for PDI growth. The method is validated in our simulations across a range of plasma and wave parameters and agrees well with theoretical predictions. Notably, the scheme exhibits no threshold for PDI excitation and is, in principle, readily implementable under current laboratory conditions. Finally, this scheme is a critical step toward solving the challenge of experimentally accessing Alfvén wave PDI and provides an elegant method that may be used to validate fundamental theories of parametric instabilities in controlled laboratory settings.

heliosphere

A dual-species Rydberg array

Large-scale Rydberg atom arrays are used for highly coherent analogue quantum simulations and for digital quantum computations. However, advanced quantum protocols, such as quantum error correction, require midcircuit qubit operations, including the replenishment, reset and read-out of a subset of qubits. A compelling strategy for unlocking these capabilities is a dual-species architecture in which a second atomic species is controlled independently and entangled with the first through Rydberg interactions. Here, we realize a dual-species Rydberg array consisting of rubidium and caesium atoms and explore regimes of interactions and dynamics not accessible in single-species architectures. We achieve enhanced interspecies interactions by electrically tuning the Rydberg states close to a Förster resonance. In this regime, we demonstrate an interspecies Rydberg blockade and implement a quantum state transfer from one species to another. We then generate a Bell state between Rb and Cs hyperfine qubits through an interspecies controlled-phase gate. Finally, we combine interspecies entanglement with a native midcircuit read-out to achieve quantum non-demolition measurements.

atomic and molecular interactions with photons

Prospects for Antiferromagnetic Spintronic Devices

This article examines recent advances in the field of antiferromagnetic spintronics from the perspective of potential device realization and applications. We discuss advances in the electrical control of antiferromagnetic order by current-induced spin–orbit torques, particularly in antiferromagnetic thin films interfaced with heavy metals. We also review possible scenarios for using voltage-controlled magnetic anisotropy as a more efficient mechanism to control antiferromagnetic order in thin films with perpendicular magnetic anisotropy. Next, we discuss the problem of electrical detection (i.e., readout) of antiferromagnetic order and highlight recent experimental advances in realizing anomalous Hall and tunneling magnetoresistance effects in thin films and tunnel junctions, respectively, which are based on noncollinear antiferromagnets. Understanding the domain structure and dynamics of antiferromagnetic materials is essential for engineering their properties for applications. For this reason, we then provide an overview of imaging techniques as well as micromagnetic simulation approaches for antiferromagnets. Finally, we present a perspective on potential applications of antiferromagnets for magnetic memory devices, terahertz sources, and detectors.

36 MATERIALS SCIENCE

Towards Spatial Control of Reaction Selectivity on Photocatalysts using Area Selective Atomic Layer Deposition on Model Dual Site Electrocatalyst Platform

Photocatalytic water splitting is a promising route to low-cost H2; however, this approach is currently limited by solar-to-hydrogen (STH) conversion efficiencies in the sub-10% range. Z-scheme water splitting, in which H2 and O2 evolving particles are operated in separate compartments and electronically coupled by a soluble redox mediator, offers improvements in STH efficiency but introduces high rates of undesired side and back reactions. Nanoscopic oxide coatings (e.g., CrOx, and SiOx) have previously been used to selectively block undesired reactants from reaching active sites; however, a coating encapsulating the entire photocatalyst particle limits activity as the particle can no longer facilitate both half reactions. In contrast to photodeposition, which may produce non-uniform overlayers due to the difficulty of controlling local electrochemical reactivity on the surface, area-selective atomic layer deposition (AS-ALD) can be used to deposit conformal ultrathin oxide coatings while preserving access to non-growth areas of a substrate surface. To develop this technique for Z-scheme photocatalysts, we performed AS-ALD of TiO2 on a dual site planar electrocatalyst based on interdigitated arrays of Pt and Au. Self-assembled monolayers of 1-octadecanethiol (ODT) were used to block growth on the Au array, resulting in a patterned surface in which only the Pt sites were encapsulated with TiO2. These electrocatalysts demonstrated localized reaction selectivity for hydrogen evolution reaction (HER) over the TiO2/Pt sites, while the uncoated Au sites retained activity towards Fe(II)/Fe(III) redox (FeRR). Under independent potential control, these microelectrodes showed that selectively deposited TiO2 coatings can suppress the rate of back reactions on neighboring active sites by an order of magnitude compared to uncoated control samples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Deciphering Reaction Mechanisms of Molecular Proton Reduction Catalysts with Cyclic Voltammetry: Kinetic vs Thermodynamic Control

The kinetics and thermodynamics of elementary reaction steps involved in the catalytic reduction of protons to hydrogen define the reaction landscape for catalysis. The mechanisms can differ in the order of the elementary proton transfer, electron transfer, and bond-forming steps and can be further differentiated by the sites at which protons and electrons localize. Access to fully elucidated mechanistic, kinetic, and thermochemical details of molecular catalysts is crucial to facilitate the development of new catalysts that operate with optimal efficiency, selectivity, and durability. The mechanism by which a catalyst operates, as well as the kinetics and thermodynamics associated with the individual steps, can often be accessed through electroanalytical studies. Here, this Account details the application of cyclic voltammetry to interrogate reaction mechanisms and quantify the kinetics and thermodynamics of elementary reaction steps for a series of molecular catalysts that mediate electrochemical proton reduction. I distinguish the limiting scenarios wherein a catalyst operates under kinetic control vs thermodynamic control, with a focus on detecting how cyclic voltammetry features shift with proton source strength and concentration, as well as scan rate. For systems that operate under kinetic control, catalytic currents are observed at, or slightly positive toward, the formal potential for the redox process that triggers catalysis. Under thermodynamic control, catalytic responses shift as a function of the proton source pKa and effective pH of the solution. After drawing this distinction, we introduce the appropriate voltammetry experiments and accompanying analytical expressions for extracting key metrics from the data. To illustrate analytical strategies to quantify elementary reaction steps of catalysts operating under kinetic control, I describe our studies of proton reduction catalysts Co(dmgBF 2 ) 2 (CH 3 CN) 2 (dmgBF 2 = difluoroboryl-dimethylglyoxime) and [Ni(P 2 Ph N 2 Ph ) 2 ] 2+ (P 2 Ph N 2 Ph = 1,5-phenyl-3,7-phenyl-1,5-diaza-3,7-diphosphacyclooctane). Here, peak shift analysis, foot-of-the-wave analysis, and plateau current analysis are applied to data sets wherein voltammetric response are recorded as a function of catalyst concentration, proton source concentration, proton source strength, and scan rate to quantify rate constants for elementary proton transfer and bond-forming steps in a catalytic cycle. Further, the case study of [Ni(P 2 Ph N 2 Ph ) 2 ] 2+ illustrates how complementary spectroscopic methods can bolster the mechanistic assignment. Collectively, these two studies showcase how detailed mechanistic studies inform on rate-limiting elementary steps in catalysis and other key processes underpinning catalysis. Second, I present analytical strategies to interrogate catalysts operating under thermodynamic control, centered on the case study of [Ni II (P 2 Ph N 2 Bn ) 2 ] 2+ (P 2 Ph N 2 Bn = 1,5-dibenzyl-3,7-diphenyl-1,5-diaza-3,7-diphosphacyclooctane). Here, the application of nonaqueous Pourbaix theory to extract thermodynamic information is introduced, and the construction of a coupled Pourbaix diagram is detailed. This study identifies ligand-based protonation as the key process that places catalysis under thermodynamic control and influences the reaction mechanism. Together, the work detailed in this Account showcases the utility of electroanalytical methods to disentangle complex reaction mechanisms and extract key thermochemical and kinetic parameters for elementary steps of catalysis. Through detailed presentation of the key analytical expressions that underpin these analyses, this Account seeks to facilitate the adoption of cyclic voltammetry by the community to fully extract kinetic, thermochemical, and mechanistic information on electrochemical small-molecule activation.

catalysts

Benchmarking the performance of a high-Q cavity qudit using random unitaries

High-coherence cavity resonators are excellent resources for encoding quantum information in higher-dimensional Hilbert spaces, moving beyond traditional qubit-based platforms. A natural strategy is to use the Fock basis to encode information in qudits. One can perform quantum operations on the cavity mode qudit by coupling the system to a non-linear ancillary transmon qubit. However, the performance of the cavity-transmon device is limited by the noisy transmons. It is, therefore, important to develop practical benchmarking tools for these qudit systems in an algorithm-agnostic manner. We gauge the performance of these qudit platforms using sampling tests such as the heavy output generation test as well as the linear cross-entropy benchmark, by way of simulations of such a system subject to realistic dominant noise channels. We use selective number-dependent arbitrary phase and unconditional displacement gates as our universal gateset. Our results show that contemporary transmons comfortably enable controlling a few tens of Fock levels of a cavity mode. This framework allows benchmarking even higher dimensional qudits as those become accessible with improved transmons.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND

Living-off-the-land Techniques Unlikely to Supplant Energy Sector-Focused OT-Specific Malware

Despite increased reports of energy sector-focused threat actors using living-off-the-land (LOTL) techniques, it is unlikely LOTL techniques will wholly supplant malware in energy sector operational technology (OT)-focused cyber operations. Threat actors leverage LOTL techniques to access energy sector networks, abstracting process information and maintaining persistence. Although threat actors using LOTL techniques have successfully interrupted energy sector industrial control environments, designed features of OT-specific malware likely increase the cyber-physical impact of an attack and delay recovery of critical functions and services. Malicious actors will very likely continue to use LOTL techniques for stealth, while designing malware to bolster final impacts on cyber-physical systems in energy sector OT environments.

99 GENERAL AND MISCELLANEOUS

Adsorption Hysteresis Under Control: Tuning Host–Guest Interactions via a Genetic Algorithm

Mesoporous adsorbent materials offer a large volumetric capacity; however, cyclic adsorption/desorption processes in these systems often suffer from hysteresis and may require a significant pressure swing to access this capacity. To mitigate hysteresis, a proposed strategy is to include nucleation sites on the walls of the mesoporous material to facilitate droplet and bubble formation, lowering the free energy barriers to the respective phase transitions. It is unclear, however, what combination of adsorbate− adsorbent interactions and spatial patterning would be beneficial for a given application, considering that improvements to some sorption properties may come at the expense of other attributes. To understand these interconnected observables, we examine two model systems, planar-slit and cylindrical pores with tunable interaction sites, using GPU-accelerated transition matrix Monte Carlo simulations. The simulations provide a free energy map of the pressure−adsorption space in a matter of minutes, which we use to track adsorption isotherm characteristics as a function of adsorbent properties. We then leverage the rapid acquisition of simulation data to construct a genetic algorithm to iteratively modify interaction sites of the slit-pore wall to minimize the hysteresis of this system without sacrificing uptake. We find that the adsorption branch of the isotherm is easily modulated via the average host−guest interaction strength, but desorption is only adjustable if there is a suitable bubble nucleation site. Within the context of a slit-pore system, we identify relative interaction strengths and patch sizes required to gain control over both branches of the hysteresis loop.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Phosphoserine Charge State Drives Ion Condensation and Spatial Polyamine Presentation in Multirepeat Silaffin

Diatom silaffins direct silica biomineralization through heavily post-translationally modified repeat domains, yet how these modifications reshape the multirepeat conformational ensemble remains unknown. We report all-atom MD simulations of a 195-residue construct spanning repeats R1–R7 of Sil1p from Cylindrotheca fusiformis, carrying the full complement of native PTMs: phosphoserine (pSer), long-chain polyamines (LCPA), dimethyllysine (MLY), and trimethylhydroxylysine phosphate (TPL). We simulated three variants (Native, P1/singly deprotonated phosphate, and P2/doubly deprotonated phosphate) at two NaCl concentrations in triplicate for 500 ns each. All systems disorder from the AlphaFold 3 starting structure. Phosphate charge state, not ionic strength, is the dominant control of ensemble compaction and ion organization. Doubly deprotonated phosphate organizes an extensive Na + condensation shell (∼100 ions, 20% of box Na + ) and a heterogeneous bridging network that integrates both pSer and TPL phosphate groups. The resulting ensemble is compact with LCPA side chains exhibiting above-median solvent accessibility in 84% of simulation frames in P2 at 300 mM. This is higher than any other condition we simulated and indicates that polyamine groups are preferentially surface-presented in the most compact, ion-organized state. A charge-neutralization control confirms that this compact state is a structured intermediate maintained by the bridging network, not a simple collapsed globule. Here, this repeat-scale spatial organization is not captured by single-repeat peptide studies. Understanding the dynamics, mechanism, and spatial organization of PTM-rich silaffin at the repeat scale is a step closer to hierarchical biomimetic materials beyond simple silica morphologies.

Amines

Modulating Hole Transfer from CdSe Quantum Dots by Manipulating the Surface Ligand Density

The structure and density of surface capping ligands in cadmium chalcogenide quantum dots (QDs) are important considerations for controlling the efficiency of charge separation via the transfer of electrons or holes to molecular acceptors. Here we show how the manipulation of the surface ligand density of oleic acid-capped cadmium selenide (CdSe) QDs impacts the efficiency of hole transfer (HT) to polyoxovanadate alkoxides. Meerwein’s salt is used as a ligand-stripping agent, providing opportunities to quantitatively manipulate the ligand density at the surface of the nanocrystal, as evidenced by 1 H NMR spectroscopy. Time-resolved photoluminescence and transient absorption spectroscopies reveal that the extent of HT is quantitatively related to increased surface accessibility. Collectively, these results show that the reduction of surface ligand density can be used to tune the extent of interactions of molecular acceptors with QDs, providing a route to control charge-transfer processes relevant to improving the efficiency of QDs as photosensitizers.

77 NANOSCIENCE AND NANOTECHNOLOGY

Evaluating the role of green infrastructure features in post-disaster recovery – Case Study of Beaumont, Texas after tropical storm imelda

While green infrastructure (GI) can provide multiple environmental benefits, its role in post-disaster economic and social recovery remains relatively underexplored. This article investigates whether different characteristics of GI, such as size, shape, connectivity, and amenities, affect the resilience of local businesses following Tropical Storm Imelda in Beaumont, Texas. The study utilizes SafeGraph mobility data to analyze foot traffic patterns to local businesses before, during, and after the disaster. FRAGSTATS indices measure GI characteristics (e.g., area, shape index, fractal dimension, proximity) while park features such as sports facilities, playgrounds, water features, and accessibility are cataloged through manual observation. Ordinary Least Squares regression models assess the relationship between park characteristics and post-recovery business performance, controlling for demographic variables including income, race, and poverty levels. Results indicate that certain GI attributes significantly enhance business recovery. Points of interest within walking distance (0.5 miles) of parks demonstrated better post-recovery status compared to those beyond this range. Specifically, parks with larger areas (p < 0.01) and more complex shapes measured by fractal dimension index (p < 0.01) had the strongest positive impact on surrounding businesses' recovery. Interestingly, playgrounds showed a negative correlation with recovery (p < 0.05), likely due to flood damage rendering them unusable during the immediate recovery period. Social vulnerability factors, including higher poverty rates and minority populations, negatively affected recovery outcomes despite park proximity.

Economic resilience

Identification and control of the exhaust using gas perturbations in the DIII-D tokamak

This paper presents perturbative experiments that enable the validation and development of control-oriented models for exhaust control. We identify the response of the divertor plasma and scrape-off layer in the DIII-D tokamak to deuterium and nitrogen multi-sine perturbations, in favorable and unfavorable field directions for H-mode access. We obtained good signal-to-noise ratios in the 1–10 Hz frequency range by measuring Balmer-alpha, Lyman-alpha, and N 4+ line emission, radiated power, and neutral pressure. We find a similar phase response across gas species and magnetic field directions, while the gain response is nonlinear. With these experiments, we identify a control-oriented model to design a divertor radiated power controller to track specified reference waveforms in conjunction with resonant magnetic perturbations. Although the physics basis for compatibility between detachment and resonant magnetic perturbation edge-localized mode suppression remains to be demonstrated, the present results provide a robust controller that represents a promising step toward future joint control strategies.

detachment control

Foliar element determination from field survey in association with the National Ecological Observatory Network Airborne Observation Platform survey, East River, Colorado 2018

The purpose of this dataset is to support research aimed at understanding the coupling between hydrologic and biogeochemical processes at watershed scale, particularly the relationship between aboveground vegetation characteristics and subsurface soil properties. These data are intended to inform and calibrate models of catchment-scale biogeochemical fluxes, including rock-derived nutrient cycling, and they were procured to address the following questions: (1) What is the distribution of vegetation characteristics across the study catchments? (2) Are foliar concentrations of rock-derived nutrients related to underlying lithology and soil availability, or are these signals masked by biotic nutrient cycling and retention processes?This data package contains foliar elemental data collected during the 2018 National Ecological Observatory Networks (NEON) Airborne Observation Platform (AOP) imaging spectroscopy and lidar surveys in Gunnison County, Colorado. Folair samples were collected across the East River, Washington Gulch, Slate River, and Coal Creek watersheds and contain a mixture of vegetation including meadow, shrub, and tree foliar samples. The samples were processed using aqua regia digestion and analyzed for elemental determination on inductively coupled plasma optical emission spectrometry (ICP-OES).The data package includes: (1) raw foliar elemental data files in CSV and PDF formats, (2) quality control certificates in PDF format, and (3) an aggregated CSV file containing all elemental measurements compiled across samples. No specialized software is required to access or use these files.

2018 National Ecological Observatory Network Campa

Advanced Laboratory and Field Arrays (ALFA)/Lab Collaboration Project (LCP) for Marine Energy (Final Scientific/Technical Report)

The objective of the Advanced Laboratory and Field Arrays (ALFA) project was to reduce the Levelized Cost of Energy (LCOE) of Marine and Hydrokinetic (MHK) energy by leveraging research, development, and testing capabilities at Oregon State University, University of Washington, and the University of Alaska, Fairbanks. ALFA is a project within the Pacific Marine Energy Center (PMEC; formerly NNMREC), a multi-institution entity with a diverse funding base that focuses on research and development for marine renewables. The ALFA project aimed to accelerate the development of next-generation arrays of wave energy conversion (WEC) and tidal energy conversion (TEC) devices through a suite of field-focused R&D activities spanning a broad range of strategic opportunity areas identified in the Funding Opportunity Announcement: • Device and/or array operation and maintenance (O&M) logistics development; • High-fidelity resource characterization and/or modeling technique development and validation; • Array-specific component technology development (e.g. moorings and foundations, transmission, and other offshore grid components); • Array performance testing and evaluation; and • Novel cost-effective environmental monitoring techniques and instrumentation testing and evaluation. The objective of the Lab Collaboration Project (LCP) was to accelerate the development of next-generation marine energy conversion systems. The LCP aimed to achieve these project objectives in collaboration with the national laboratories by: • Developing concept generation and assessment tools; • Improving access to existing testing resources; • Validating collision risk models between fish and turbines; and • Advancing analysis and simulation capabilities for wave-WEC interactions and PTO analysis in nonlinear ocean waves. The ALFA portion of the project was comprised of six overarching technical tasks: • Task 1: Debris Modeling, Detection and Mitigation; • Task 2: Autonomous Monitoring & Intervention; • Task 3: Resource Characterization for Extreme Conditions; • Task 4: Robust Models for Design of Offshore Anchoring and Mooring Systems; • Task 5: Performance Enhancement for Marine Energy Converter (MEC) Arrays; and • Task 6: Evaluating Sampling Techniques for MHK Biological Monitoring. The LCP was divided into four overarching technical tasks: • Task 7: Project Management and Reporting • Task 8: Novel Design and Assessment Methodologies for Wave Energy Converter Design (Wave- SPARC) • Task 9: Testing Access for Commercial Marine Renewable Energy Technology Developers • Task 10: Quantifying Collision Risk for Fish and Turbines • Task 11: Nonlinear Ocean Waves and PTO Control Strategy Each ALFA/LCP task listed above functioned as a separate and discreet project. A final Technical Report was written for each individual task and these reports were uploaded to OSTI, after receiving DOE approval. The following document is a compilation of each of these final, approved reports arranged as individual chapters.

13 HYDRO ENERGY

Detector Response and Battery Reliability

The Sandia National Laboratories (SNL) Material Control and Accountability (MC&A) measurements team performs confirmation measurements of Special Nuclear Material (SNM) at different locations around Sandia. The measurement team has access to two High purity Germanium (HPGe) detectors, the AEGIS (Model: AEGIS-BEGE5030), and the ORTEC (Model: trans-SPEC-DX-100). These two can operate purely on battery power, but the response of the detectors while on battery power is not well documented. To enhance our knowledge with these detectors the team wants to investigate the detectors response to changes in battery range, wall charging, and mid operation battery swaps (Hot Swaps).

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND

Machine Learning–Guided Boolean Matrix Inference for Real-Time O-RAN Conflict Detection

Open Radio Access Networks (O-RAN) are emerging, software-driven cellular architectures that promote flexibility by enabling components from different vendors to interoperate. Multiple control applications called xApps can independently adjust network parameters in near real time, often without awareness of each other's actions. This creates a system highly prone to unintended conflicts and performance degradation due to the inherent complexity of such openness. To model such systems and ultimately prevent or mitigate xApp conflicts, it is essential to understand the dynamic relationships between xApps (A), the control parameters they adjust (P), and the resulting KPI responses (K). While the mappings from A to P and from K to A can often be derived from xApp specifications, the relationship from P to K is typically hidden within the system’s dynamics and must be inferred from observed data. We propose a novel data-driven Boolean inference framework that uncovers the hidden P?K dependencies using machine learning and interpretable rule induction. Continuous parameters and KPIs are first binarized using decision tree classifiers, and a binary influence matrix L is then inferred by solving Boolean matrix equations over time. This compact representation improves interpretability and enables real-time tracking of dynamically evolving parameter-KPI dependencies. We demonstrate the effectiveness of our method in a realistic mobile handover scenario, where it accurately recovers the underlying logic and enables proactive conflict detection.

42 - ENGINEERING

Bridging the Gap Between Modern UX Design and Particle Accelerator Control Room Interfaces

Accelerator control systems often represent relatively complex and safety-sensitive human-machine interfaces within process control industries. These systems are technically robust and reflect the cumulative integration of solutions built and adapted across decades. One of the regular, unfortunate casualties of provisional accelerator control system updates is their human-system interfaces (HSIs) which often lag behind modern usability and design standards. An additional challenge is that although there is a multitude of established human factors (HF), and user experience (UX) principles for everyday digital applications, there are very few (if any) established principles for complex and safety-critical applications for an accelerator. This paper argues for the importance of established HF and UX principles (herein referred to as human-centered design principles) into the development of accelerator HSIs, emphasizing the need for clarity, consistency, responsiveness, and cognitive accessibility. Drawing from HF/UX best practices and human-centered design, this paper discusses how these approaches can enhance operator performance, reduce human error, and improve accelerator personnel collaboration. Case studies from Accelerator Control Operations Research Network (ACORN) at Fermilab are explored to demonstrate how interfaces built with human-centered design principles can scale with system complexity while remaining intuitive and efficient for diverse user roles including operators, machine experts, and engineers. By bridging the gap between traditional control system design and modern human-centered design methods, this paper provides a roadmap for evolving accelerator HSIs into more usable, maintainable, and effective tools.

Hill, Rachael [Idaho Natl. Lab.]

Disruption of histone acetylation homeostasis reveals multilayered chromatin regulation for transcriptional resiliency

Background Epigenetic modifications, nucleosome occupancy, and three-dimensional chromatin architecture collectively create a multi-layered, highly interactive regulatory system for controlling genomic functionality. Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states. Therapies focused on epigenetic modulation can alter gene expression to correct dysfunction, though the perpetuation of these states and the relationships among chromatin regulatory layers is not well understood. Results Here, we investigated global and local chromatin structural and functional responses after acute histone deacetylase inhibitor treatment (suberoylanilide hydroxamic acid) in lung cancer cells across time. Treatment substantially increased global histone acetylation resulting in a pervasive but not distinctive signature. The spread of acetylation did not significantly impact global chromatin accessibility, and nucleosome remodeling largely occurred at finer scales in functionally relevant genomic regions. Indeed, both H 3 K 4 trimethylation, a mark of active transcription, and gene expression changes were altered in a controlled locus-specific manner, suggesting aberrant acetylation indirectly leads to balanced and bidirectional gene expression profiles from tighter regulation of other chromatin features. HDACi treatment induced (13%) genomic rearrangement in chromatin compartmentalization and moderate weakening of topologically associating domains. Conclusions Continuous wavelet analysis of these features demonstrates that scale-dependent, locus-specific factors influence the relationship between chromatin architecture and functional output, suggesting that regulation of transcription and nucleosome remodeling is not entirely (nor linearly) dependent upon large scale compartment exchange. Structural and functional responses are most pronounced early after treatment with partial persistence of differential local chromatin features and expression later in time; this highlights the plasticity of chromatin regulation, which may have implications for the efficacy of epigenetic treatments. These results demonstrate the effectiveness of multi-layered regulation of transcription: in resilient systems, disruption of one chromatin feature does not distort the regulation of other features in supporting a transcriptional program that allows for survival.

59 BASIC BIOLOGICAL SCIENCES