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At least 55 records · Page 3

Interfacial Inversion of Stealth Surfactants

Amphiphilic macromolecular surfactants segregate to liquid–liquid interfaces, thereby reducing the interfacial tension and free energy. Here, we investigated “stealth surfactants” in the form of core–shell bottlebrush polymers comprised of pH-responsive diblock copolymer side chains forming a hydrophilic core and a hydrophobic shell, enabling solubility in oil. At liquid–liquid interfaces, these polymers undergo a structural “inversion”, with hydrophilic blocks segregating into the aqueous phase and hydrophobic blocks residing in the oil phase. The reconfiguration kinetics and surfactant properties are influenced by multiple factors, including the molecular weights of the backbone and side chain components, the hydrophilic-to-hydrophobic balance of the side chains, and the pH of the aqueous phase. An observed nonmonotonic dependence of interfacial tension with time is attributed to a progressive structural inversion, where the projected area of the macromolecule onto the interface decreases. To validate this inversion hypothesis, interfacial properties were characterized by sum-frequency generation vibrational spectroscopy, which revealed configurational changes of the core–shell bottlebrush polymers at the fluid interface and revealed a pH-dependent interfacial coverage. Coarse-grained molecular dynamics simulations supported these experimental findings, showing that the pH-responsive core and hydrophobic shell assume a time-averaged configuration with orientations parallel and perpendicular to the plane of the interface, respectively. These findings open routes to design multistimuli-responsive polymeric surfactants and compatibilizers, expanding their potential applications in advanced interfacial systems.

Stealth surfactants

Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria

In Gram-negative bacteria, the enzymatic modification of Lipid A with aminoarabinose (L-Ara4N) leads to resistance against polymyxin antibiotics and cationic antimicrobial peptides. ArnC, an integral membrane glycosyltransferase, attaches a formylated form of aminoarabinose to the lipid undecaprenyl phosphate, enabling its association with the bacterial inner membrane. Here, we present cryo-electron microscopy structures of ArnC from S. enterica in apo and nucleotide-bound conformations. These structures reveal a conformational transition that takes place upon binding of the partial donor substrate. Using coarse-grained and atomistic simulations, we provide insights into substrate coordination before and during catalysis, and we propose a catalytic mechanism that may operate on all similar metal-dependent polyprenyl phosphate glycosyltransferases. The reported structures provide a new target for drug design aiming to combat polymyxin resistance.

Ashraf, Khuram U. [Rutgers University, Newark, NJ

Investigating PVC polymer–plasticizer interactions with atomistic MD simulations and potential of mean force calculations

For this work, atomistic molecular dynamics (MD) simulations coupled with potential of mean force (PMF) calculations were employed to investigate the interactions between PVC polymer chains containing 6–20 repeating units and various plasticizers, with the goal of identifying potential replacements for the toxic plasticizer di(2-ethylhexyl)phthalate (DEHP) used in blood bags. The selected plasticizers belong to various chemical families, such as orthophthalates, citrates, adipates, and the terephthalate DEHT. Both the polymer and the plasticizers lack ionizable groups, and their interactions are primarily governed by van der Waals and electrostatic forces. A model correlating PMF profiles with interaction forces was developed and validated across polyvinyl chloride (PVC) polymers of different lengths and all investigated plasticizers. This model provides insight into how structural variations in plasticizers influence their respective PMF values. The study ranks the investigated plasticizers based on binding affinity, identifying TOTM (tris(2-ethylhexyl) trimellitate, TEHTM), BTHC (butyryl trihexyl citrate, Citroflex B-6), ATHC (acetyl trihexyl citrate, Citroflex A-6, CA-6), and DEHT (bis(2-ethylhexyl)terephthalate, DOTP/DEHTP) as promising alternatives for further investigation. This comprehensive study encompasses PVC polymers of four different lengths and 14 plasticizers, with all data averaged over 30 independent simulations. The approach provides a deeper understanding of molecular interactions, enabling the tailoring of polymer–plasticizer systems for diverse applications, including extractables and leachables, with relevance spanning materials science to biomedical engineering, and also serves as a basis for developing coarse-grained simulation protocols. Overall, this study provides valuable insights for designing safer and more efficient plasticizer substitutes and is well supported by other studies.

Shet, Sai Athmeeya G. [Sri Sathya Sai Institute of

Assembly of small silica nanoparticles using lipid-tethered DNA ‘bonds’

Single-stranded DNA molecules modified with cholesterol functional groups are physically tethered to silica nanoparticles (diameter 25 nm) that are encapsulated in a lipid bilayer. Such tethering increases the azimuthal mobility of the DNA molecules across the nanoparticle surface and enables nonspecific bonding, eliminating the need for specialized surface chemistries (such as silane or thiol ligands). To induce assembly, double-stranded DNA ‘bridge’ molecules are then added with complementary nucleotides to the DNA ‘anchor’ molecules that are physically tethered to the lipids on the surface of the particles. Assembly is observed to occur at room temperature and without the need for temperature annealing. Using automated liquid handling tools, assemblies are created in high throughput and rapidly characterized using SAXS. It is determined that the relative concentration of DNA-to-silica and the ionic strength of the solution are important parameters that affect the resulting assembly. Analysis of SAXS data is performed using coarse-grained particle dynamics simulations. The results support the spontaneous formation of semi-crystalline particle assemblies by particle condensation, where the interparticle distance is tuned by the sequence of the DNA ‘bridge’ used to link the particles. Crystallinity analysis performed on the resulting simulations, optimized to match SAXS observations, suggest that particle clusters display increased crystallinity in the center of the clusters, but their maximum size remains relatively small (sub-micron) before settling occurs, which limits the extent of crystallization.

Chiang, Huat Thart [Univ. of Washington, Seattle,

Molecular dynamics based study on the effects of cation size on the local structure and diffusion in polymerized ionic liquids

We have used coarse-grained molecular dynamics simulations to understand the effect of cation size on ion diffusion in polymerized ionic liquids at temperatures well above the glass transition temperature of the polymers. We investigated dependencies of the diffusion constant on the cation radius and static dielectric constant and interpreted these results in terms of underlying structural changes, and decoupling phenomenon. We have found non-monotonic effects of the cation radius on the diffusion constant, with a maximum at an intermediate radius resulting from two different size dependent effects. Changes in the radial distribution functions characterizing spatial distribution of cations with respect to anions result in a monotonic increase in the coordination number. This yields an increase in the effective interaction energy as a function of cation radius, which can explain the decrease in the diffusion constant. This increase is counteracted at small cation radii by a corresponding increase in decoupling of cation and anion dynamics. In addition, the diffusion constant is found to increase on increasing the static dielectric constant for all radii of the cations. These results highlight the significant role of decoupling in designing polymerized ionic liquids with an enhanced diffusion constant of cations.

Gillespie, Colin [ORNL] (ORCID:0000000320287080)

Data-based filtered dissipation rate modelling for multi-modal turbulent combustion: evaluating a priori model generalizability

Manifold-based models offer a computationally efficient alternative to directly transporting the thermochemical state in computational simulations of turbulent reacting flows, projecting the high-dimensional thermochemical state-space onto a low-dimensional manifold. Recent efforts have yielded a manifold-based model applicable to multi-modal combustion, enabling reconstruction of the thermochemical state from solutions to two-dimensional manifold equations in mixture fraction and generalized progress variable that are parameterised by three scalar dissipation rates. In coarse-grained simulations such as Large Eddy Simulation (LES), closure of the multi-modal manifold equations and subfilter variances/covariance requires closure of three filtered scalar dissipation rates. Here, the present work adopts a data-based approach, providing closure for the three filtered scalar dissipation rates via deep neural networks (DNNs). High-fidelity datasets corresponding to an autoigniting n-dodecane jet flame and a bluff body swirl-stabilized confined lifted spray flame of two aviation fuels (Jet-A and C1) with different ignition propensities are leveraged to generate training data that spans a diverse range of thermodynamic conditions and combustion modes, including low- and high-temperature ignition regimes in addition to premixed and nonpremixed behaviour. A final DNN model is trained to enforce inherent physical constraints by learning nonlinear functional transformations of the three filtered scalar dissipation rates. The generalizability of this constrained DNN model is demonstrated a priori via conditional statistics evaluated on the lifted spray flame with C1–a configuration that had not been included in the training data. Excellent DNN agreement with conditional DNS statistics is observed, and integrated gradients are computed to identify the most sensitive input variables. The similarity of the marginal PDFs of the most informative input variables and outputs across configurations are quantified via the Wasserstein metric, demonstrating that data-based models may successfully generalize to unseen parametric conditions so long as the most informative input variables share similar distributions across training and testing datasets.

Data-based modelling

High-throughput small-angle X-ray scattering reveals effective structure factor transitions linked to high-concentration antibody viscosity

High-concentration monoclonal antibody (mAb) formulations are often constrained by elevated viscosity, largely driven by protein–protein interactions, which complicates manufacturing and limits subcutaneous delivery. Early viscosity risk assessment is essential during discovery, yet traditional measurements require large sample volumes, and lack high-throughput capability. Here, we develop a high-throughput small-angle X-ray scattering (SAXS) protocol to detect mAb self-association at dilute concentrations, enabling early predictive insights into high-concentration viscosity. Synchrotron SAXS measurements were conducted for 21 mAbs formulated in a histidine buffer at pH 6.0. An initial subset of 10 mAbs analyzed across 1–150 mg/mL revealed that effective structure factor transitions in the low-q region, indicative of interparticle interactions, consistently emerged below 25 mg/mL. Subsequently, 11 additional mAbs were analyzed at 1–25 mg/mL using automated liquid handling and flow cells to enable high-throughput screening. High-viscosity mAbs exhibited detectable low-q upturns at concentrations ≤10 mg/mL, whereas low-viscosity mAbs showed downturns. A classification criterion based on effective structure factor transitions accurately classified all high- and low-viscosity mAbs at 150 mg/mL, offering a scalable, sample-efficient alternative to conventional methods. These results extend recent findings on the concentration-dependent sensitivity of SAXS to short-range attractions, demonstrating that they can emerge at lower concentrations than previously reported. This study presents the most comprehensive and diverse SAXS dataset for mAbs reported to date within a single formulation, providing a valuable resource for developing and validating coarse-grained models that can more accurately capture intermolecular interactions governing high-concentration solution behavior, thereby enabling rational antibody engineering and improved developability.

36 MATERIALS SCIENCE

Analog and symbolic computation through the Koopman framework

We develop a Koopman operator framework for studying the computational structure of dynamical systems. Specifically, we show that the resolvent of the Koopman operator provides a natural abstraction of halting, yielding a ‘Koopman halting problem’ that is recursively enumerable in general. For symbolic systems, such as those defined on Cantor space, this operator formulation captures reachability between clopen sets, while for equicontinuous systems we prove that the Koopman halting problem is decidable. Our framework demonstrates that absorbing (halting) states in coarse-grained finite automata correspond to Koopman eigenfunctions with eigenvalue one, while cycles in the transition graph impose spectral constraints associated with periodic dynamics. These results provide a unifying perspective on computation in symbolic and analog systems, showing how computational universality is reflected in operator spectra, invariant subspaces, and algebraic structures. Beyond symbolic dynamics, this operator-theoretic lens opens pathways to analyze the computational properties of a broader class of dynamical systems, including polynomial and analog models, and suggests that computational hardness may admit dynamical signatures in terms of Koopman spectral structure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

Closed-Loop Control of Active Nematic Flows

Stabilizing and shaping autonomous flows of active fluids is a fundamental challenge and a prerequisite for applications. We embed a light-responsive microtubule-based nematic in a proportional-integral control loop that adjusts the applied light intensity in response to real-time measurements of the spatially averaged flow speed. The self-regulating hardware-software-wetware system maintains a target flow speed against external or internal perturbations, including protein aging and aggregation, sample-to-sample variability, and temperature variation. Varying the controller’s gains reveals antagonistic roles between feedback and intrinsic processes, leading to nontrivial dynamics observed in fluctuation spectra. In particular, oscillations emerge from the interplay between the controller, motor binding kinetics, and active hydrodynamic relaxation. Accounting for the underlying binding timescale, our coarse-grained model and nematohydrodynamics simulations corroborate these observations. This work provides insight into the coupled dynamics of controlled active matter, laying the foundation for spatiotemporal patterning of active stress to generate and stabilize new dynamical configurations.

Active nematics

From Spin to Pseudospin Symmetry: The Origin of Magic Numbers in Nuclear Structure

Magic numbers lie at the heart of nuclear structure, reflecting enhanced stability in nuclei with closed shells. While the emergence of magic numbers beyond 20 is commonly attributed to strong spin-orbit coupling, the microscopic origin of the spin-orbit potential remains elusive, owing to its dependence on the resolution scale and renormalization scheme of nuclear forces. Here, we investigate the evolution of nuclear shell structure with varying momentum resolution in nuclear interactions derived from chiral effective field theory, using the similarity renormalization group to link different scales. We uncover a novel transition from spin symmetry to pseudospin symmetry as the resolution scale decreases, during which magic numbers emerge naturally. A similar pattern is found in calculations using relativistic one-boson-exchange potentials, underscoring the robustness of the phenomenon. This establishes a direct connection between realistic nuclear forces with a high resolution scale and effective nuclear forces at coarse-grained scales, offering a first-principles explanation for the origin of magic numbers and pseudospin symmetry in nuclear shell structure and new insights into the structure of exotic nuclei far from stability

Energy levels

Structured interactions drive abrupt transitions in the spatial organization of microbial communities

Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Some of these mechanisms are species specific and enable cells to modulate their movement based on the ecological identity of neighboring species. Here, we introduce a model in which bacteria interact via local signals that either enhance or suppress the motility of neighboring cells depending on species type. Through large-scale simulations and a coarse-grained stochastic model, we demonstrate the emergence of a sharp transition driven by nucleation processes: increasing the density of motility-suppressing interactions drives the system from a fully mixed, motile phase to a state characterized by large, stationary bacterial clusters. Remarkably, in systems with a large number of interacting species, this transition can be triggered solely by altering the structure of the motility-regulation interaction matrix while maintaining species and interaction densities constant. In particular, we find that heterogeneous and modular interactions promote the transition more readily than homogeneous random ones. These findings add a dimension to the theory of motility-induced phase separation and contribute to the ongoing effort to understand microbial interactions, suggesting that structured, nonrandom ones may be key to reproducing commonly observed spatial patterns in microbial communities.

bacterial communities

Seamlessly joining length scales: From atomistic thermal graphs to anisotropic continuum conductivity

Thermal transport in complex solids is governed by local structure, defects, and anisotropy, yet most continuum models still rely on oversimplified and homogenized conductivities. Here, we bridge atomistic and continuum descriptions by building finite element (FE) models directly from the site-projected thermal conductivity (SPTC), an atomic-level decomposition of the Green–Kubo thermal conductivity. We introduce a toolkit, the “Simulator Collection for Atomic-to-Continuum Scales (SCACS)”, which uses a graph neural network to predict SPTC on large atomic structures, coarse-grains these fields into anisotropic conductivity tensors, and embeds them into the heat-flow FE equation with a customized, anisotropy-aware adaptive mesh refinement scheme. Applied to silicon nanostructures, the resulting FE models act as representative volume elements, reproduce bulk conductivities, and capture interfacial and defect-driven anisotropy while maintaining thermodynamic consistency. Additionally, SCACS predicts experimental conductance trends and fields. This work demonstrates a general route for transferring atomistic transport information into device-scale thermal simulations with physics-based approximations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND

Complex orders and chirality in the classical Kitaev-Γ model

It is well recognized that the low-energy physics of many Kitaev materials is governed by two dominant energy scales, the Ising-type Kitaev coupling 𝐾 and the symmetric off-diagonal Γ coupling. An understanding of the interplay between these two scales is therefore the natural starting point toward a quantitative description that includes subdominant perturbations that are inevitably present in real materials. This study focuses on the classical 𝐾−Γ model on the honeycomb lattice, with a specific emphasis on the region 𝐾< 0 and Γ > 0 , which is the most relevant for the available materials and which remains enigmatic in both quantum and classical limits, despite much effort. We employ large-scale Monte Carlo simulations on specially designed finite-size clusters and unravel the presence of a complex multisublattice magnetic order in a wide region of the phase diagram, whose structure is characterized in detail. We show that this order can be quantified in terms of a coarse-grained scalar-chirality order, featuring a counterrotating modulation on the two spin sublattices. Here, we also provide a comparison to previous studies and discuss the impact of quantum fluctuations on the phase diagram.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND

iMMD

Iterative Multiscale Molecular Dynamics in OpenMM: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Molecular Dynamics Simulations

Do, Hung Nguyen [Los Alamos National Laboratory]

Why Seeding Works When Nucleation Barriers Vanish

This paper explains why seeds can speed up crystallization even when the formation of new crystal nuclei is not the slow step. In zeolite synthesis, local crystalline order can form relatively early, but the material may still appear poorly crystalline by X-ray diffraction because many small crystallites are misoriented and lack long-range coherence. Using coarse-grained molecular simulations, the study showed that seeds help solve this coherence problem. Rather than primarily lowering a nucleation barrier, seeds impose a common orientation on nearby growing crystallites, allowing them to merge into larger, better aligned domains. This accelerates the development of X-ray-detectable crystallinity even if the total amount of locally ordered material has not changed much. The work changes how induction times in zeolite synthesis should be interpreted: the delay before X-ray crystallinity appears can reflect the time needed to build long-range structural coherence, not simply the time needed to form crystalline material. This provides a new explanation for why seeding is effective in growth-limited crystallization and offers design principles for controlling crystallization rate and crystal quality.

36 MATERIALS SCIENCE

Evidence for carbon dioxide removal via enhanced rock weathering with steel slag, though not basalt, in a midwestern U.S. field trial

Enhanced weathering is an emergent pathway for permanent atmospheric carbon dioxide removal (CDR). However, despite a dramatic increase in academic and commercial research, there remain relatively few published examples of field evidence demonstrating the effectiveness of enhanced weathering. Here, we present results from a three-year field trial that evaluated steel slag and crushed basalt applied as amendments in a conventional agricultural system in the Midwestern United States. Steel slag applied to initially acidic soil increased porewater pH and alkalinity and increased soil pH and Ca-saturation. Together, changes in porewater chemistry and soil properties provide strong evidence for steel slag weathering and CDR. However, steel slag applied to soils with a neutral initial pH did not generate significant changes in soil or porewater chemistry. In addition, coarse-grained crushed basalt did not generate significant change in any of the soils. Strong acid effects were apparent in all 3 years of monitoring soil porewater chemistry. Overall, our results demonstrate clear evidence of CDR from applying steel slag amendments to acidic cropland soils while also highlighting the difficulty of greenhouse gas reduction accounting from enhanced weathering and the variable outcomes that can occur depending on feedstock and soil type.

Geosciences

High-Order Methods in NASA’s Next Generation of Computational Fluid Dynamics Tools

The missions of the National Aeronautics and Space Administration (NASA) routinely produce unique requirements and challenges for development and application of Computational Fluid Dynamics (CFD) methods. NASA presently embodies four distinct Mission Directorates: Aeronautics Research, Exploration Systems, Science, and Space Operations. These missions generate requirements for systems that operate in a wide variety of environments. They range from the high-speed flight of aerodynamically optimized vehicles operating in the earth’s atmosphere to spacecraft designed for missions that don’t favor aerodynamic optimization, some operating in the atmosphere of planets and planetary moons such as Mars and Venus or Saturn’s moon Titan. Systems supporting these vehicles, such as rocket and jet propulsion, reaction control systems, fluid and thermal transfer systems, etc. can also generate their own unique set of flow phenomena that challenge today’s CFD methodology. Through the NASA Engineering and Safety Center (NESC), NASA annually conducts state-of-the-discipline assessments in fifteen distinct engineering disciplines. These assessments are performed by the NASA Technical Fellows that lead Technical Discipline Teams (TDT) of recognized experts in these fifteen areas. In the Aerosciences discipline, three topics have been identified as the top challenges for the discipline: aero-plume interaction prediction, unsteady separated flows, and aerothermodynamic prediction. These challenge areas are defined by the Agency’s high-risk projects and problems on which the NESC is requested to perform independent testing, analysis, and assessments. When viewed as a whole, these tests, analyses, and assessments provide a clear view of the recurring technical challenges facing Agency engineers and researchers and can be used to guide future research and technology development. The present state-of-the-art in the application of CFD at NASA is the use of Reynolds-Averaged Navier- Stokes (RANS) solvers, primarily executed in a steady-state mode of operation. In isolated cases, Unsteady RANS (URANS) solvers have been employed when steady RANS solutions produce poorly converging or oscillating results or in cases, such as aeroelastic analysis, which require unsteady aerodynamic simulation. For most traditional external and internal aerodynamic flows, structured overset grids or unstructured grids are employed to minimize geometric modeling and grid generation times. Grid adaptation, primarily as a series of coarse-grain intermediate processing steps is also seeing use on particularly complex flow problems and configurations. In the case of aerothermodynamic flows, engineers have been forced to continue to employ structured grid techniques as the present unstructured grid methodology has proven inadequate in the prediction of surface heating. In the area of aero-plume interaction modeling, two-gas, frozen chemistry simulation is generally the state-of-the- art, with some production solvers capable of predicting flows with only a single gas component. Prediction of flows falling into the afore-mentioned top Aerosciences technical challenges have severely stressed the present state-of-the-art in CFD prediction and for some problems, such as unsteady separated flows and aero-plume interaction cases, engineers have begun employing Large Eddy Simulation (LES) and Hybrid RANS/LES techniques. In some isolated aero-propulsion interaction cases, chemically reacting flow simulations have been applied. These methods are highly evolutionary and engineers have little experience in their application, so they cannot be heavily relied upon in today’s application environment. Therefore, this leads one to muse over which numerical technologies will be included in the CFD tools that will be employed 30 years in the future. This presentation will describe specific technical problems that have stressed NASA’s traditional CFD methods to their breaking point and will link these issues to the Agency’s top Aerosciences technical challenges. The discussion will then shift to the characteristics of future CFD solvers that will be required to attack these challenges and how these characteristics differ from the present state-of-the- art. High-order methods certainly appear to have a place in the development of future CFD tools and some of the physical characteristics of our most challenging problems suggest that high-order methods are the only way to effectively solve them. But there are some relatively severe implementation issues that face these methods, particularly in the area of general applicability and robust operation as an engineering tool. Desired characteristics of next-generation CFD solvers will be discussed and the author’s view of which emerging numerical technologies might be employed to address these attributes will also be presented

David M Schuster

Thermomechanical Modeling of Woven Materials With Particle-Based, Explicit-Fiber Simulations

Fiber-based materials are extensively used to protect spacecraft during entry. Insulative fibers, often in a fiber network or woven, provide rigidity, strength, and control of material anisotropy and density. Woven thermal protection materials, such as ADEPT (Adaptable, Deployable Entry and Placement Technology), 3D-MAT (3-Dimensional Multifunctional Ablative Thermal Protection), and 3MDCP (3D Woven Mid-Density Carbon Phenolic), enable missions with stronger and denser materials for entry profiles with high shear and heat flux. Vulnerabilities to woven thermal protection materials include manufacturing-induced material property variation, and impact from micrometeoroids. Simulating woven materials under these conditions require models that can resolve hierarchal structures, thermomechanical behavior, and failure. To address this, we simulate weave thermal conduction and mechanical deformation. We simulate the full weave with a coarse-grained yarn model is presented. The model combines a validated, high-resolution single 3MDCP yarn model and phenolic resin model. Instead of modeling every fiber, each yarn ply with order 10, instead of order 1000, fibers. The discrete element bonded particle model (DEM-BPM) of fibers captures the thermal and mechanical behavior within and between fibers. We study the proportion of heat transfer and stress via the contact network, fiber bonds, and overall weave geometry.

bonded particle