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DOE OSTI2026

Curvilinear Magnonic Crystal Based on 3D Hierarchical Nanotemplates

Curvilinear magnetic nanostructures enable control of magnetization dynamics through geometry-induced anisotropy and chiral interactions, as well as magnetic field modulation. In this work, we report a curvilinear magnonic crystal based on large-area square arrays of truncated nanospikes fabricated by conformal coating of 3D hierarchical templates with permalloy thin films. Brillouin light scattering spectroscopy reveals an anisotropic band structure with multiple dispersive and folded Bloch-type dispersive spin-wave modes as well as nondispersive modes exhibiting direction-dependent frequency shifts and intensity asymmetries along lattice principal axes. Finite element micromagnetic simulations indicate that curvature-induced variations of the demagnetizing field govern the magnonic response, enabling the identification of modes propagating in nanochannels and others localized on nanospike apexes or along the ridges connecting adjacent nanospikes. The combination of geometric curvature and optical probing asymmetry produces directional dependence of magnonic bands, establishing 3D hierarchical templates as a versatile platform for curvature-engineered magnonics.

3D hierarchical templates↗

DOE OSTI2025

A compact catenane with tuneable mechanical chirality

Catenanes are formed by the mechanical interlocking of two or more rings. Enantiomers of a catenane can exist even if the rings themselves are achiral. Here we demonstrate that two achiral rings, each featuring a polarized cavity and two mirror planes, in addition to a two-fold axis of symmetry, can form a catenane with mechanical chirality. The catenane has been designed using an isostructural desymmetrization strategy, enabling the catenane to adopt a compact co-conformation similar to that of its achiral isostructural counterpart. Mechanical chirality in the catenane occurs when its two rings become interlocked in the compact co-conformation, leading to the loss of the two planes of symmetry present in its individual rings. The resulting enantiomers, which both have two-fold axes of symmetry, exist as a racemic modification in the solid state. Dynamic 1 H NMR spectroscopy carried out in acetonitrile-d 3 reveals a barrier of 16.4 kcal mol −1 to racemization between the two enantiomeric catenanes, the equilibrium of which can be influenced by the addition of chiral disulfonate anions, which support induced chirality and exhibit optical activity. One of the salts crystallizes to give only one diastereoisomer in the solid state. Furthermore, this research highlights the potential of using the isostructural desymmetrization strategy to create and study mechanical chirality along with its properties.

Interlocked molecules↗

DOE OSTI2025

Cosmological quasiparticles and the cosmological collider

The interplay between cosmology and strongly coupled dynamics can yield transient spectral features that vanish at late times, but which may leave behind phenomenological signatures in the spectrum of primordial fluctuations. Of particular interest are strongly coupled extensions of the standard model featuring approximate conformal invariance. In flat space, the spectral density for a scalar operator in a conformal field theory is characterized by a continuum with scaling law governed by the dimension of the operator, and is otherwise featureless. Anti–de Sitter/conformal field theory arguments suggest that for large 𝑁, in an inflationary background with Hubble rate 𝐻, this continuum is gapped. We demonstrate that there can be additional peak structures that become sharp and particlelike at phenomenologically interesting regions in parameter space, and we estimate their contribution to cosmological observables. We find phenomena that are potentially observable in future experiments that are unique to these models, including displaced oscillatory features in the squeezed limit of the bispectrum. These particles can be either fundamental, and localized to a UV brane, or composite at the Hubble scale, 𝐻, and bound to a horizon in the bulk of the 5D geometry. We comment on how stabilization of conformal symmetry breaking vacua can be correlated with these spectral features and their phenomenology.

conformal field theory↗

DOE OSTI2025

Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering

Abstract Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.6 Å. The collapse is monophasic and is complete in <600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, showing that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.

Biochemistry & Molecular Biology↗

DOE OSTI2025

Quantum complexity in gravity, quantum field theory, and quantum information science

Quantum complexity quantifies the difficulty of preparing a state or implementing a unitary transformation with limited resources. Applications range from quantum computation to condensed matter physics and quantum gravity. Here, we seek to bridge the approaches of these fields, which define and study complexity using different frameworks and tools. We describe several definitions of complexity, along with their key properties. In quantum information theory, we focus on complexity growth in random quantum circuits. In quantum many-body systems and quantum field theory (QFT), we discuss a geometric definition of complexity in terms of geodesics on the unitary group. In dynamical systems, we explore a definition of complexity in terms of state or operator spreading, as well as concepts from tensor-networks. We also outline applications to simple quantum systems, quantum many-body models, and QFTs including conformal field theories (CFTs). Finally, we explain the proposed relationship between complexity and gravitational observables within the holographic anti-de Sitter (AdS)/CFT correspondence.

Baiguera, Stefano [Istituto Nazionale di Fisica Nu↗

DOE OSTI2025

Quantum Adiabatic Optimization with Rydberg Arrays: Localization Phenomena and Encoding Strategies

Quantum adiabatic optimization seeks to solve combinatorial problems using quantum dynamics, requiring the Hamiltonian of the system to align with the problem of interest. However, these Hamiltonians are often incompatible with the native constraints of quantum hardware, necessitating encoding strategies to map the original problem into a hardware-conformant form. While the classical overhead associated with such mappings is easily quantifiable and typically polynomial in problem size, it is much harder to quantify their overhead on the quantum algorithm, e.g., the transformation of the adiabatic timescale. In this work, we address this challenge on the concrete example of the encoding scheme proposed in [Nguyen , PRX Quantum , 010316 (2023)], which is designed to map optimization problems on arbitrarily connected graphs into Rydberg atom arrays. We consider the fundamental building blocks underlying this encoding scheme and determine the scaling of the minimum gap with system size along adiabatic protocols. Even when the original problem is trivially solvable, we find that the encoded problem can exhibit an exponentially closing minimum gap. We show that this originates from a quantum coherent effect, which gives rise to an unfavorable localization of the ground-state wave function. On the QuEra Aquila neutral atom machine, we observe such localization and its effect on the success probability of finding the correct solution to the encoded optimization problem. Finally, we propose quantum-aware modifications of the encoding scheme that avoid this quantum bottleneck and lead to an exponential improvement in the adiabatic performance. This highlights the crucial importance of accounting for quantum effects when designing strategies to encode classical problems onto quantum platforms. Published by the American Physical Society 2025

Bombieri, Lisa (ORCID:0009000950422897)↗

DOE OSTI2025

Molecular Insights Into the Ionic Assembly of Poly-Galacturonic Acid Oligomers - Impact of Charge, Ionic Radius, and Polymer Functionalization

Pectin, a major class of matrix polysaccharides present in plant cell walls (PCW), contains widespread anionic saccharides that cross-link in the presence of cations. It modulates important functions such as cell-cell adhesion and determines the PCW's biomechanical properties. It is known that mono-, di-, and tri-valent cations facilitate cross-linking; however, significant knowledge gaps remain in understanding the structure and mechanism of pectin cross-linking. In this study, replica-exchange molecular dynamics (REMD) simulations were employed to elucidate the role of ionic charge, ionic radii, and functional groups on the cross-linking of homogalacturonan (HG), the most abundant pectin molecule. Our enhanced sampling approach in fully solvated environments suggests more effective cross-linking with higher-valent and smaller ions, and that the "zipper" conformation is more favorable than the prevalent "egg-box" conformation. These findings advance our fundamental understanding of pectin matrix structure in PCWs and provide a solid foundation to probe structure-property relationships in pectic polysaccharides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Understanding Viscoelasticity of an Entangled Silicone Copolymer via Coarse-Grained Molecular Dynamics Simulations

Entangled dynamics is important for understanding rheological properties of long-chain polymers. For entangled homopolymers, the classic tube-reptation model and its refinements have been successfully applied to quantify properties like diffusion coefficient and zero-rate viscosity. However, the application of such models to copolymers has been limited despite scientific and industrial importance. Here, we study the entangled melt dynamics of poly(dimethyl-co-diphenyl)siloxane random copolymer for a range of mean-composition-ratio ϕ of the diphenyl component via long-term molecular dynamics simulation with a recently developed coarse-grained model. We found that the segmental relaxation is heterogeneous at the monomeric level because of compositional fluctuations. However, at the chain-entanglement level and higher length scales, the viscoelastic response is homogeneous with compositional dependence only through the overall diphenyl fraction ϕ. The relaxation modulus of the entangled copolymer melt conforms to the Likhtman–McLeish model, and the viscosity predicted using our current coarse-grained parameters is in good quantitative agreement with experimental data.

Copolymers↗

DOE OSTI2026

Small-molecule modulation of β-arrestins

β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily. Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein–receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin–receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.

Kahsai, Alem W. [Duke University, Durham, NC (Unit↗

DOE OSTI2024

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Primordial black holes and magnetic fields in conformal neutrino mass models

Sufficiently strong and long-lasting first-order phase transitions can produce primordial black holes (PBHs) that contribute substantially to the dark matter abundance of the Universe, and can produce large-scale primordial magnetic fields. Here, we study these mechanisms in a generic class of conformal U(1)' models that also explain active neutrino oscillation data via the type-I seesaw mechanism. We find that phase transitions that occur at seesaw scales between 10 4 GeV and 10 11 GeV produce gravitational wave signals (from the dynamics of the phase transition and from the decay of cosmic string loops) at LISA/ET that can be correlated with microlensing signals of PBHs at the Roman Space Telescope, while scales near 10 11 GeV can be correlated with Hawking evaporation signals at future gamma-ray telescopes. LISA can probe the entire range of PBH masses between 1 × 10 -16 M ⊙ and 8 × 10 -11 M ⊙ if PBHs fully account for the dark matter abundance. For Z' masses between 40 TeV and 10 4 TeV, and 10 TeV right-handed neutrinos, helical magnetic fields can be produced with magnitudes ≳ 0.5 pG and coherence lengths ≳ 0.008 Mpc, above current blazar lower bounds.

cosmological phase transitions↗

DOE OSTI2024

Designed 2D protein crystals as dynamic molecular gatekeepers for a solid-state device

The sensitivity and responsiveness of living cells to environmental changes are enabled by dynamic protein structures, inspiring efforts to construct artificial supramolecular protein assemblies. However, despite their sophisticated structures, designed protein assemblies have yet to be incorporated into macroscale devices for real-life applications. We report a 2D crystalline protein assembly of C98/E57/E66 L-rhamnulose-1-phosphate aldolase ( CEE RhuA) that selectively blocks or passes molecular species when exposed to a chemical trigger. CEE RhuA crystals are engineered via cobalt(II) coordination bonds to undergo a coherent conformational change from a closed state (pore dimensions <1 nm) to an ajar state (pore dimensions ~4 nm) when exposed to an HCN(g) trigger. When layered onto a mesoporous silicon (pSi) photonic crystal optical sensor configured to detect HCN (g) , the 2D CEE RhuA crystal layer effectively blocks interferents that would otherwise result in a false positive signal. The 2D CEE RhuA crystal layer opens in selective response to low-ppm levels of HCN (g) , allowing analyte penetration into the pSi sensor layer for detection. These findings illustrate that designed protein assemblies can function as dynamic components of solid-state devices in non-aqueous environments.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Link statistics of dislocation network during strain hardening

Dislocations are line defects in crystals that multiply and self-organize into a complex network during strain hardening. The length of dislocation links, connecting neighboring nodes within this network, contains crucial information about the evolving dislocation microstructure. By analyzing data from Discrete Dislocation Dynamics (DDD) simulations in face-centered cubic (fcc) Cu, we characterize the statistical distribution of link lengths of dislocation networks during strain hardening on individual slip systems. Here, our analysis reveals that link lengths on active slip systems follow a double-exponential distribution, while those on inactive slip systems conform to a single-exponential distribution. The distinctive long tail observed in the double-exponential distribution is attributed to the stress-induced bowing out of long links on active slip systems, a feature that disappears upon removal of the applied stress. We further demonstrate that both observed link length distributions can be explained by extending a one-dimensional Poisson process to include different growth functions. Specifically, the double-exponential distribution emerges when the growth rate for links exceeding a critical length becomes super-linear, which aligns with the physical phenomenon of long links bowing out under stress. This work advances our understanding of dislocation microstructure evolution during strain hardening and elucidates the underlying physical mechanisms governing its formation.

Crystal plasticity↗

DOE OSTI2024

On the holographic dual of a topological symmetry operator

We study the holographic dual of a topological symmetry operator in the context of the AdS/CFT correspondence. Symmetry operators arise from topological field theories localized on a subspace of the boundary conformal field theory spacetime. We use bottom up considerations to construct the topological sector associated with their bulk counterparts. In particular, by exploiting the structure of entanglement wedge reconstruction we argue that the bulk counterpart has a nontopological world volume action, i.e., it describes a dynamical object. As a consequence, we find that there are no global 𝑝-form symmetries for 𝑝 ≥ 0 in asymptotically anti–de Sitter spacetimes, which includes the case of noninvertible symmetries. Provided one has a suitable notion of subregion-subregion duality, our argument for the absence of bulk global symmetries applies to more general spacetimes. These considerations also motivate us to consider for general QFTs (holographic or not) the notion of lower-form symmetries, namely, (−𝑚)-form symmetries for 𝑚 ≥ 2.

quantum gravity↗

DOE OSTI2026

Charge And Dynamic Current On Tubular Antennas For Various Drive Conditions

The mixed boundary value problem of a tubular conductor is solved using an approximate representation of its Fourier coefficients. A two term solution is derived, which represents the solution over an extremely broad range of aspect ratios. This representation is used to find the electrostatic solution and capacitance of a charged tube as well as the solution of a tube in a uniform field and its dipole moment. This second case is directly useful as a model for a monopole electric field probe. This approximation is a special case of a representation using a combination of Chebyshev and Legendre polynomials. Combining the charged tube and tube in a uniform field allows the solution of voltage driven tubular antennas. Comparisons are made with numerical solutions using piecewise sinusoidal representations of the current. The results are also generalized to the dynamic case and up to and beyond the first resonance. Simple corrections for finite gap and delta gap drives to magnetic frill drives are examined using infinite tube integral transform representations. Corrections between magnetic frill drives and coaxial drives are also given. Approximate drive corrections using conformal mapping and an effective radius are also discussed. Finally, this efficient current representation is applied to the magnetic problem involving simple tubular solenoids.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Entanglement asymmetry and symmetry defects in boundary conformal field theory

A state in a quantum system with a given global symmetry, G, can be sensitive to the presence of boundaries, which may either preserve or break this symmetry. In this work, we investigate how conformal invariant boundary conditions influence the G-symmetry breaking through the lens of the entanglement asymmetry, a quantifier of the “distance” between a symmetry-broken state and its symmetrized counterpart. By leveraging 2D boundary conformal field theory (BCFT), we investigate the symmetry breaking for both finite and compact Lie groups. Beyond the leading order term, we also compute the subleading corrections in the subsystem size, highlighting their dependence on the symmetry group G and the BCFT operator content. We further explore the entanglement asymmetry following a global quantum quench, where a symmetry-broken state evolves under a symmetry-restoring Hamiltonian. In this dynamical setting, we compute the entanglement asymmetry by extending the method of images to a BCFT with non-local objects such as invertible symmetry defects.

Field Theories in Lower Dimensions↗

DOE OSTI2025

Discovery of an autoinhibited conformation in mesotrypsin reveals a strategy for selective serine protease inhibition

Selective inhibition of the more than 100 S1 family serine proteases is a long-standing challenge due to their active site similarity. Mesotrypsin, implicated in cancer progression, exemplifies these difficulties; no current inhibitors achieve selectivity over other human trypsins. We found an unexpected autoinhibited conformation of mesotrypsin via x-ray crystallography, revealing a cryptic pocket adjacent to the active site. Using high-throughput virtual screening targeting this cryptic pocket, we identified a conformationally selective small-molecule inhibitor that stabilizes the inactive state of mesotrypsin. This inhibitor demonstrates selectivity for mesotrypsin over other trypsins. Our findings challenge the accepted view of digestive trypsins as constitutively active enzymes lacking potential for allosteric regulation. Furthermore, analyses of other structures suggest that dynamic sampling of closed states with analogous allosteric cryptic pockets appears widespread among S1 serine proteases. These observations point to a potentially generalizable strategy to achieve selective inhibition, offering broad implications for drug development targeting serine proteases in cancer and other diseases.

Coban, Matt↗

DOE OSTI2024

Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

Residing in the 5' untranslated region of the mRNA, the 2'-deoxyguanosine (2'-dG) riboswitch mRNA element adopts an alternative structure upon binding of the 2'-dG molecule, which terminates transcription. RNA conformations are generally strongly affected by positively charged metal ions (especially Mg 2+ ). We have quantitatively explored the combined effect of ligand (2'-dG) and Mg 2+ binding on the energy landscape of the aptamer domain of the 2'-dG riboswitch with both explicit solvent all-atom molecular dynamics simulations (99 μsec aggregate sampling for the study) and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments. We show that both ligand and Mg 2+ are required for the stabilization of the aptamer domain; however, the two factors act with different modalities. The addition of Mg 2+ remodels the energy landscape and reduces its frustration by the formation of additional contacts. In contrast, the binding of 2'-dG eliminates the metastable states by nucleating a compact core for the aptamer domain. Mg 2+ ions and ligand binding are required to stabilize the least stable helix, P1 (which needs to unfold to activate the transcription platform), and the riboswitch core formed by the backbone of the P2 and P3 helices. Mg 2+ and ligand also facilitate a more compact structure in the three-way junction region.

59 BASIC BIOLOGICAL SCIENCES↗