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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Graphene oxide gluing layer enabling macroscale tribology applications of pristine graphene

In recent studies of two-dimensional (2D) nanomaterial-based solid lubricants, the importance of durability has been emerging for real engineering-scale applications. To achieve this, a transfer layer formation is essential to prevent the wear of the mechanical systems. However, it has been challenging for pristine graphene (PG) to induce a material transfer due to chemical inertness. In this study, we suggest an easy-to-process strategy to promote the huge material transfer of the PG onto the counterpart contacting material. We utilized graphene oxide (GO) as a gluing layer between the PG film and the counterpart contact surface to realize the superior tribological performance. The high interaction energy of the GO from its functional groups makes a contribution to the material transfer of PG, which is unveiled by a systematic analysis of the counterpart contact surface and the wear track. The huge solid transfer layer not only makes a wear-resistant contact interface between the transfer layer and the underlying film by densification and oxidation, but also reduces surface interaction energies, finally resulting in a significant improvement in durability.

graphene oxide (GO)↗
DOE OSTI2025

Improvement and Verification of Online Cross Section Generation Capability of Griffin for TRISO-fueled Reactors

Griffin, a MOOSE-based reactor multiphysics code jointly developed by Idaho National Laboratory and Argonne National Laboratory under the DOE Office of Nuclear Energy’s NEAMS program, has pursued the development of an online multigroup cross section generation capability for a few years to enable high-fidelity, problem-dependent neutronics analyses of advanced thermal reactors. Recent advancements in Griffin’s online multigroup cross section generation capability have significantly improved the accuracy, robustness, and efficiency of self-shielding calculations for both prismatic and pebble-bed TRISO-fueled reactor applications. Key developments include a unified fuel self-shielding method applicable to both TRISO and annular compact/spherical shell fuel zone geometries; an advanced Dancoff Category-based Equivalence Theory using a bell function for non-fuel resonance treatment, achieving more than an order-of-magnitude speedup compared to the Tone method; an on-the-fly multigroup equivalence approach to mitigate group condensation errors; and a streaming correction method for pebble-bed homogenization. A proof-of-concept demonstration of on-the-fly group condensation with consistent P0 transport correction was also achieved. The method reproduced direct fine-group solutions with excellent accuracy (eigenvalue errors within 10 pcm and pin-power differences within 0.5%), but due to performance limitations of the current fixed-source solver, improvements to solver efficiency will be addressed in future work. Verification tests were performed on graphite-moderated TRISO-fueled two-dimensional core benchmark problems representing gas-cooled microreactors, heat pipe-cooled microreactors, gas-cooled pebble-bed reactors, and fluoride salt-cooled high-temperature reactors. Across all cases, Griffin showed excellent agreement with Serpent2 continuous energy Monte Carlo solutions: eigenvalue errors within 200 pcm, pin-power root-mean-square errors within 2%, and control rod and drum worth errors less than 2%. It should be noted that, for the benchmark problem, cross section generation contributed less than 3% of the total simulation times. These results demonstrate that Griffin’s online cross section generation capability delivers accurate and efficient reactor physics solutions across a wide spectrum of TRISO-fueled advanced reactor designs. With further improvements to the fine-group fixed-source solver and planned extensions to depletion, transients, and coupled neutron–gamma transport, Griffin will be well-positioned to become a powerful and comprehensive tool for advanced reactor analysis.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Multidimensional Coherent Spectroscopy of van der Waals materials and heterostructures (Final Technical Report)

This project advanced multidimensional coherent spectroscopy (MDCS) and related spectroscopic-imaging methods as quantitative probes of many-body optical excitations in two-dimensional (2D) van der Waals (vdW) semiconductors and their heterostructures. Monolayer transition-metal dichalcogenides (TMDs) such as MoSe 2 and WSe 2 provide a uniquely strong platform for excitonic physics due to reduced dielectric screening, which enhances Coulomb interactions and makes higher-order correlated states (e.g., biexcitons and exciton–trion correlations) more prominent than in conventional bulk semiconductors. At the same time, the same sensitivity that enables strong interactions also increases susceptibility to spatial inhomogeneity—e.g., strain gradients, wrinkles, nanoscale disorder potentials, and charge puddling—which can broaden resonances, obscure interaction signatures, and complicate device-to-device reproducibility. The work reported here addressed this dual opportunity and challenge by: (i) developing and deploying coherent multidimensional methods (including double-quantum MDCS) capable of isolating interaction signals with reduced background, (ii) integrating electrostatic control to tune carrier populations and interaction strengths in situ, and (iii) introducing complementary spatially resolved photoluminescence (PL) techniques—hyperspectral PL imaging and polarization-/field-dependent PL lineshape analysis—to directly quantify disorder, strain, and localization that govern the coherent response.

36 MATERIALS SCIENCE↗
DOE OSTI2026

An Integrated Modeling Framework for Sediment Dynamics During Urban Flooding: Application to Hurricane Harvey in Houston

Floodwater can mobilize and redistribute large volumes of sediment from upland to downstream urban areas, threatening infrastructure, water quality, and ecosystem health. However, existing modeling approaches often fail to capture sediment dynamics in urban floodplains due to the lack of integration between upland hydrological processes and riverine sediment transport. This study presents the first integrated modeling framework that couples the Energy Exascale Earth System Model (E3SM) land component, which simulates runoff and hillslope erosion, with TELEMAC-GAIA, a two-dimensional hydrodynamic and sediment transport model. This framework enables the fully distributed, process-based simulation of high-resolution (as fine as 30 m) sediment dynamics from hillslopes to floodplains. Applied to a highly urbanized watershed in Houston during Hurricane Harvey, this framework reproduced observed water levels at 16 USGS gauges (median R 2 = 0.83 and KGE = 0.78), key sediment dynamics such as sediment transport and deposition processes, and reproduced spatial deposition patterns consistent with LiDAR-derived data. Based on the simulation, we estimate 8.0 million m 3 of event-scale sediment deposition, including 5.7 million m 3 trapped in the flood-control reservoirs and 2.3 million m 3 deposited along major channels and floodplains. Using a representative unit removal cost, this corresponds to an estimated dredging cost of $581 million for total deposition. These results provide a first-order, physically based quantification of Harvey-scale sediment impacts. This study provides a valuable tool for the holistic analysis of sediment dynamics triggered by extreme urban flooding, supporting flood-resilience planning. More broadly, it highlights the importance of integrating physically based hydrological processes for urban flooding and sediment research.

Hurricane Harvey↗
DOE OSTI2026

The Modulated Crystal Structure of K 2 V 3 O 8

Weak lattice distortions can tune exchange pathways and magnetic interactions in square-lattice quantum magnets. K 2 V 3 O 8 is a mixed valence (V 4+ /V 5+ ) fresnoite oxide that exhibits strong spin–lattice coupling at low temperature. Here, we combine single-crystal neutron diffraction (90 K) and laboratory X-ray diffraction (50 K) to solve the low-temperature structure as an orthorhombic (3 + 1)D incommensurately modulated phase in superspace group Cmm2(β,0,1/2)0s0 [No. 196]. What initially appeared as two independent modulation vectors, q 1 = 0.3132(6)[$110$] + 1/2c* and q 2 = 0.3132(6)[$1\bar{10}$] + 1/2c*, are more naturally described as a single one-dimensional modulation wave q = 0.626(1)a* + 1/2c* in a C-centered orthorhombic lattice, related to the parent tetragonal cell by the transformation a + b, −a + b, c. Refinement with a 4-fold rotational twin inherited from the P4bm parent structure solves oxygen-dominated framework distortions and K + displacements. A de Wolff section (t = 0.40) enables a symmetry-mode decomposition, identifying three dominant mm2 (C 2v ) modes: GM3 for framework tilt, A5 for interlayer shear, and Z5 for c-axis breathing. The mode-resolved structure provides a unified, symmetry-based explanation for reported low-temperature Raman and IR anomalies and clarifies the structural origin of the spin–lattice coupling in the S = 1/2 two-dimensional quantum spin compound.

K2V3O8↗
DOE OSTI2025

Structure and mechanical properties of grain boundaries in molybdenum disulfide (MoS 2 )

Molybdenum disulfide (MoS 2 ) is a two-dimensional material widely used as a lubricant in many applications involving mechanical loading under a wide range of operating temperatures. Since many synthesis and processing techniques yield MoS 2 in its polycrystalline form, establishing grain boundary (GB) structure–property relations is key to designing MoS 2 microstructures with tailored properties. Here, we employ classical, reactive atomistic simulations to investigate the structure and mechanical behavior of a wide range of GBs in MoS 2 as a function of temperature. Using a bicrystal MoS 2 geometry, we characterize the atomic structure and calculate the energy of several low-angle GBs. Then, we simulate the tensile deformation behavior of MoS 2 bicrystals at several temperatures. Our results reveal that at temperatures above 100 K, the deformation of MoS 2 bicrystals is characterized by the nucleation of shear bands from GBs that grow, with subsequent loading, into the MoS 2 crystals. At low temperatures, the tensile deformation is characterized by the nucleation and propagation of deformation fronts, resulting in altered bond angles and bond lengths. Quantitative analysis reveals a decrease in the ultimate tensile stress and ultimate failure strain of MoS 2 bicrystals with the increase in temperature. Furthermore, our simulations of the mechanical behavior of metastable GBs reveal that the strength and ductility decrease with the increase in energy of these boundary structures. In broad terms, our work provides future avenues to employ GB engineering as a strategy to tailor the properties of MoS 2 microstructures.

Moore, Robert D. [Lehigh Univ., Bethlehem, PA (Uni↗
DOE OSTI2026

Strain-Modified Raman Responses in Monolayer MoS 2 Nanobubbles Resolved at 5 nm

The formation of nanoscale bubbles is an unavoidable consequence during the transfer of two-dimensional materials onto target substrates, driven by van der Waals interactions at the interface. While often viewed as imperfections, these nanoscale bubbles have garnered considerable scientific interest due to the substantial in-plane strain gradients they induce, which in turn give rise to a variety of intriguing optoelectronic effects, particularly in semiconducting transition metal dichalcogenides. Determining and analyzing the strain distribution within nanobubbles at the nanoscale is crucial for advancing our understanding of these underlying strain-induced effects. Here, we present a high-resolution scanning tunneling microscopy-based tip-enhanced Raman spectroscopic investigation of localized nanoscale strain distribution within the nanobubbles formed between monolayer MoS 2 and Au interface. By employing cryogenic temperature (78 K), we successfully differentiate the nanoscale Raman signatures between nanobubble edge and pristine MoS 2 . We verify a maximum tensile strain of ∽1.15–1.34% at the nanobubble edge, which gradually diminishes toward the center, yielding a cross-sectional strain profile consistent with a doughnut-shaped distribution. Furthermore, we report to achieve ∽5 nm spatial resolution in probing such edge-localized strain within the nanobubble. In addition, comparative average strain analysis of such MoS 2 nanobubbles is conducted via geometric mechanistic analysis such as membrane and nonlinear plate theories, providing key insight into the geometric nature near the bubble edge. Our work provide fundamental information about strain-induced nanoscale chemical understanding of 2D materials on the nanometer scale, paving the way for practical applications of nanobubbles in strain-engineered optoelectronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Raman Digital Twin of Monolayer Janus Transition Metal Dichalcogenides

Monolayer transition metal dichalcogenides (TMDs) are a key class of two-dimensional (2D) materials with broad technological potential. Their Janus counterparts exhibit unique properties due to broken out-of-plane symmetry and further enrich the functionalities of TMDs. However, experimental synthesis and identification of Janus TMDs remain challenging. It is thus highly desirable to have a rapid, simple, and in situ characterization technique to monitor, in real time, the conversion process from the parent to Janus structure. Raman spectroscopy stands out for such a task as it is a powerful, nondestructive, and very commonly used tool to characterize 2D materials both in situ and ex situ. To realize the full potential of Raman spectroscopy on rapid characterization of Janus TMDs, we present a computational “Raman digital twin” library for various monolayer Janus TMDs in both 2H and Td phases. We focus on group-6 TMDs: MoS 2 , WS 2 , MoSe 2 , WSe 2 , MoTe 2 , WTe 2 and their Janus variants: MoSSe, MoSTe, MoSeTe, WSSe, WSTe, and WSeTe. Using first-principles density functional theory (DFT), we calculate their vibrational properties and predict distinct Raman fingerprints. These phonon and Raman signatures reflect each material’s structural symmetry and atomic composition, enabling clear identification via Raman spectroscopy. Our theoretical work supports experimental efforts by providing benchmarks for material identification, structural analysis, and quality control. In conclusion, the computational library expedites the discovery and development of Janus 2D materials, facilitating tighter integration between theoretical predictions and experimental validation.

Chalcogenides↗
DOE OSTI2026

AnisONet: A deep neural operator-based anisotropic permeability upscaler from pore to Darcy scale

Directional permeability variations, which govern directional fluid flow in porous media with anisotropy, are important to accurately predict flow behavior, reactive transport, and fluid–solid interactions for various processes such as enhanced geothermal systems, energy storage devices, and biological systems. However, the intricate architecture of porous media makes it difficult to predict directional permeabilities. In this work, we present a novel machine learning (ML) framework, AnisONet, built upon an integration of a convolutional neural network, Swin transformer, and the deep operator network architecture, designed to predict anisotropic permeability and upscale predictions to larger spatial domains. First, AnisONet was evaluated with three classes of two-dimensional (2D) porous media, including synthetic circular and elliptical grains and natural sandstone grains from micro-computed tomography images. A lattice Boltzmann model (LBM) was used to calculate directional permeabilities at every 10° angle, producing 19 data points per image of porous media. AnisONet is then trained to predict permeability as a function of rotation angle. AnisONet showed strong predictive capability of directional permeability. Second, we tested our model for five upscaling cases with a large image size in the finite-element method (FEM) for 2D Darcy flow with various permeability tensor construction methods. Overall, upscaled permeability tensors in FEM simulations produce a reasonably good match with LBM results, highlighting the importance of selecting appropriate tensor formation strategies for accurate permeability upscaling. AnisONet, as a directional permeability estimator, could be further developed for more complex geometries, with the potential to develop a foundational ML model for various applications in porous media.

42 ENGINEERING↗
DOE OSTI2026

Living on the edge: a non-perturbative resolution to the negativity of bulk entropies

Lin, Maldacena, Rozenberg, and Shan (LMRS) presented a new information paradox in black hole physics by noticing that the entanglement and Rényi entropies in a two-sided black hole can become negative when the geometry contains a very large number of matter excitations behind the black hole horizon. While originally this puzzle was presented in the context of BPS two-sided black holes in two-dimensional supergravity, the negativity in fact persists for more general two-sided black holes in the presence of a large number of matter excitations. Since the entanglement and Rényi entropies in ordinary quantum systems cannot be negative, resolving this puzzle is a necessary step towards understanding the quantum mechanical description of black holes. In this paper, we explain how to address the entanglement negativity puzzle, both in the original setting discussed by LMRS and in more general non-supersymmetric settings, by summing over all non-perturbative contributions to the gravitational path integral. We then interpret this result from the point of view of a dual matrix integral, which we use to extend our analysis beyond the regime of validity of the genus re-summation performed in the gravitational path integral. In this regime, positivity is rescued by new saddles of the matrix integral, a one-eigenvalue instanton and a two-eigenvalue instanton. Finally, we formulate a similar puzzle and its resolution using random tensor network techniques.

2D Gravity↗
DOE OSTI2025

Hardware acceleration for HPS algorithms in two and three dimensions

We provide a flexible, open-source framework for hardware acceleration, namely massively-parallel execution on general-purpose graphics processing units (GPUs), applied to the hierarchical Poincaré–Steklov (HPS) family of algorithms for building fast direct solvers for linear elliptic partial differential equations. To take full advantage of the power of hardware acceleration, we propose two variants of HPS algorithms to improve performance on two- and three-dimensional problems. In the two-dimensional setting, we introduce a novel recomputation strategy that minimizes costly data transfers to and from the GPU; in three dimensions, we modify and extend the adaptive discretization technique of Geldermans and Gillman [1] to greatly reduce peak memory usage. We provide an open-source implementation of these methods written in JAX, a high-level accelerated linear algebra package, which allows for the first integration of a high-order fast direct solver with automatic differentiation tools. We conclude with extensive numerical examples showing our methods are fast and accurate on two- and three-dimensional problems.

Fast direct solvers↗
DOE OSTI2025

A machine-learning approach to measure 3D sample properties from 2D Transmission Electron Microscopy images

Transmission Electron Microscopy (TEM) is a powerful tool for the characterization of materials at the nanoscale; however, its inherent two-dimensional (2D) nature poses significant challenges to accurately measure three-dimensional (3D) properties. We introduce a supervised machine-learning model that predicts 3D structural information, such as sample thickness and curvature, from a series of conventional 2D TEM images. The model, a U-Net convolutional neural network, is trained on a large synthetic dataset generated from dynamical diffraction simulations that model TEM’s complex, nonlinear image formation, accounting for sample thickness and curvature. This physically realistic framework enables exploration of a broad parameter space impractical to sample experimentally. We demonstrate that the trained model has accurate predictions for experimental single-crystal silicon samples, achieving performance comparable to established measurement techniques. This work highlights the critical role of robust, simulation-based training in overcoming the limitations of real-world imaging artifacts and inconsistent sample geometries. By integrating machine learning with numerical simulations, we offer an efficient and scalable framework for quantitative TEM analysis, paving the way for more sophisticated 3D characterization of complex materials.

Dynamical diffraction↗
DOE OSTI2026

Ion Transport in Charged Membranes: Linking Electric-Field-Driven Mechanisms to Pore Size via Perturbation Analysis

Ion-exchange membranes are a critical component in electrochemical systems. Nevertheless, the understanding and modeling of ion transport within these porous structures have been limited by particular complexity reductions, either ignoring the dimensionality of their porous network architecture or imposing geometric assumptions (i.e., overlapping double layers). Before addressing this morphology-transport gap, a framework that relates the driving forces of transport to the geometry of a single pore is required. In this work, our modeling domain consists of a two-dimensional single pore with charged walls, connecting two identical electrolyte reservoirs. Using the Poisson-Nernst-Planck equations and regular perturbation theory, we decouple the electric fields and analyze the driving forces of ion transport, specifically electromigration and induced electroosmosis within the pore. These processes are described as analytical functions of the interaction aspect ratio, ?, defined as the ratio of the pore radius to the Debye length. Using this parameter, our study (i) describes the interplay between electromigrative and electroosmotic mechanisms that set ionic conductivity, (ii) identifies a dimensionless group of intrinsic electrolyte properties that indicates the predominant driving force, and (iii) provides a qualitative, confinement-dependent perspective on selectivity in ion-conducting membranes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

The 0E2 benchmarks for PWR UO 2 decay heat: an analysis from the NEA WPNCS

This paper presents the work performed in the subgroup 16 of the Working Party for Nuclear Criticality Safety (WPNCS) of the OECD Nuclear Energy Agency. The main goal was to define two decay heat benchmarks for Spent Nuclear Fuel (one pincell and one assembly), perform calculations and compare and analyze the results in light of existing calorimetric measurements. The selected case is the PWR UO2 assembly 0E2, irradiated at the Ringhals-3 reactor and measured at the Clab facility in Sweden. In total, 21 institutes worldwide participated to the exercise, leading to 55 calculated results (named C). It was found that the measured decay heat values (E) can be satisfactorily reproduced with two-dimensional assembly calculations, leading to an average C/E value of 0.99, with an uncertainty (or one standard deviation) of ±0.01.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Investigation of radiated-power for low aspect ratio fusion plasmas

Investigating radiated power in fusion plasmas is of utmost importance to understand the effect of undesired impurities, such as metals, in present devices, or also desired impurities, such as noble gasses, to purposefully radiate a large fraction of power in future devices. These studies are especially important for high Z impurities which will play a crucial role in future generation fusion pilot plants. In this work, we have developed a power radiation analysis module, which is used to investigate 2D distributions of impurity densities and radiated power asymmetries caused due to both plasma rotation and the cooling rate dependence on temperature profile for the cases of experimental NSTX plasmas and designed scenarios for the spherical tokamak advanced reactor (STAR), both being low aspect ratio tokamaks. Two different atomic databases have been tested during this work to study their impact on the radiated power distribution, especially for high Z impurities. Also in PRAM, self-consistent calculations of two-dimensional electron, main ion, and impurity ion densities are carried out using one-dimensional input density, temperature, and rotation profiles. In the case of NSTX, discharges with high rotation of ∼ 170 km s, measured with charge exchange recombination spectroscopy, have been investigated. Rotation-induced charge separation, leading to an electrostatic potential, is calculated iteratively to a self-consistent solution while testing high Z impurities to observe any 2D asymmetry in the core radiated power due to centrifugal forces. The STAR design, being much larger (R = 4 m), is projected to have a much lower rotation, and is shown to have low rotation-induced asymmetries, on the order of ten percent or less, between the low field and high field sides. However, another effect not due to rotation but to the dependence of impurity cooling rates on temperature can lead to radiation peaking off-axis, near the plasma edge. This effect is noticeable for argon in NSTX, for example, but can also be enhanced for certain impurities at much higher temperatures projected for STAR (T e0 ~ 32 keV), for example for undesired tungsten or possibly desired xenon.

NSTX↗
DOE OSTI2026

Josephson dynamics in two-dimensional ring-shaped condensates

We investigate Josephson transport in a fully closed, two-dimensional superfluid circuit formed by a ring-shaped 87 Rb Bose-Einstein condensate that contains two optical barriers acting as movable weak links. Translating these barriers at controlled speeds imposes a steady bias current, enabling direct mapping of the current-chemical-potential (𝐼−Δ⁢𝜇) characteristics. For narrow junctions (𝑤 ≈ 1µ⁢m), the circuit exhibits a pronounced dc branch that terminates at a critical current 𝐼 𝑐 = 9⁢(1) × 10 3 s −1 ; above this threshold, the system switches to an ac, resistive regime. Classical-field simulations that include the moving barriers quantitatively reproduce both the nonlinear 𝐼−Δ⁢𝜇 curve and the measured 𝐼 𝑐 , validating the underlying microscopic picture. Analysis of the ensuing phase dynamics shows that dissipation is mediated by the nucleation and traversal of vortex-antivortex pairs through the junctions, while the bulk condensate remains globally phase locked—direct evidence of the ring's topological constraint enforcing quantized circulation. These results establish a cold-atom analog of a superconducting quantum interference device in which Josephson dynamics can be resolved at the single-vortex level, providing a versatile platform for atomtronic circuit elements, nonreciprocal Josephson devices, and on-chip Sagnac interferometers for multiaxis rotation sensing.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Langevin and Fokker-Planck analyses for diffusion-mediated passing of circular and discorectangular species in two-dimensional channels

The propensity for pairs of diffusing species to pass each other within narrow channels or pores is of basic interest as a first-passage-type problem. It is also of relevance for solution-phase transport in nanoporous materials, and in particular for catalytic conversion reactions where high yield requires that product species can efficiently pass reactant species to exit the pores. Here, we analyze a two-dimensional model with nonoverlapping circular and discorectangular species confined to a rectangular channel, and where passing is mediated by Brownian dynamics in an implicit solvent. For narrower channels where passing is still possible, the discorectangle must align with the channel to pass the circular species. Behavior of the passing propensity, 𝑃, can be assessed by strongly damped Langevin simulations, or within an equivalent Fokker-Planck equation (FPE) formalism. The latter corresponds to a diffusion problem in a “higher-dimensional channel” with a constriction. We assess the variation of the passing propensity, 𝑃, for a broad range of channel width including its scaling just above the threshold where passing is sterically blocked. Analysis of 𝑃 versus the rotational diffusion coefficient 𝐷 𝑟 of the discorectangle reveals a significant decrease in 𝑃 for lower 𝐷 𝑟 for moderate channel width. This prompts a direct analysis of the regime where 𝐷 𝑟 → 0 , for which the FPE can be reduced to a three-dimensional diffusion problem, precise analysis of which is facilitated by adaptive-mesh finite element methods. The dependence of 𝑃 on the aspect ratio of the discorectangle is also assessed.

Rahman, Md Khaledur [Ames Laboratory (AMES), Ames,↗
DOE OSTI2026

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗