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Electronic coarse-graining (ECG) methods predict quantum-mechanical electronic properties directly from coarse-grained (CG) molecular configurations, enabling electronic predictions at mesoscale length scales. Here, we present a diagnostic assessment of the feasibility of chemically transferable ECG models across a broad polymer-relevant chemical space using all-atom, united-atom, and Martini-scale representations. While high-resolution ECG models achieve near-quantitative accuracy, we show that chemically transferable ECG at the Martini resolution fails because the CG force field does not sample the same configurational distribution of local molecular structure as that underlying the DFT-parameterized ECG model. We demonstrate that our proposed Element-Count-Label (ECL) representation, which augments Martini beads with explicit stoichiometric data, significantly improves chemical generalization across diverse polymer chemistries. However, we find that even with improved chemical resolution, the model cannot recover electronic property distributions that are absent from the configurational space sampled by the CG force field. These results demonstrate that chemically transferable ECG requires future Martini-like force fields to explicitly preserve quantum chemistry–compatible local molecular structure in addition to thermodynamic and structural fidelity.
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.
Microbial metabolism is a complex, emergent system driven by the coordinated interplay of intricate and dynamic molecular processes. To elucidate cellular behavior and enable biotechnological applications, quantitative models that address the inherent complexity of metabolism have been developed from a resource allocation perspective. Here, we synthesize recent advances in coarse-grained resource allocation frameworks and their applications in understanding microbial physiology and guiding gene circuit design. Here, these frameworks reveal global regulatory constraints and predict cellular adaptation to nutrient and environmental changes. In addition, they enable the quantification of metabolic costs, the dissection of circuit–host interactions, and the development of strategies for burden mitigation. Collectively, these modeling frameworks provide a powerful platform for uncovering quantitative principles of microbial growth and engineering robust synthetic biological systems.
Abstract In order to accurately simulate the fouling process of proteins onto polyzwitterion brushes, models that accurately capture the hydration properties and chain conformations of such brushes must first be established. We developed a Martini coarse-grained (CG) model for amine oxide polyzwitterion (PNOMA) brushes, a promising class of antifouling materials, in polarizable water and ions by fitting to all-atom bond and angle distributions, monomer hydration free energy, monomer–monomer distance potential of mean force (PMF), and monomer–salt radial distribution functions (RDFs). Martini 2.2P was selected for compatibility with the established polarizable water and ion models. For comparison with PNOMA, we also constructed models for conventional sulfobetaine (PSBMA) and phosphorylcholine (PMPC) polyzwitterions and the polycation PMETAC using established nonbonded bead types from the literature and refitting bond and angle potentials. We simulated each polymer brush chemistry for varying grafting density and chain length, validating brush height scaling relations against experimental data. The CG models captured the relative hydration strengths among different polyzwitterion chemistries, and brush heights extrapolated to higher molecular weights are in agreement with experimental ellipsometry data. We find that chain swelling of the superhydrophilic PNOMA brushes lies between that of the traditional polyzwitterions PSBMA/PMPC and the polycation PMETAC. For PNOMA brushes in NaCl solution, simulated brush height decreases with salt concentration due to the selectively strong interactions between amine oxide and sodium ions.
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.
The morphological and electronic properties of conjugated polyelectrolytes (CPEs) are highly sensitive to their ionic environment and remain poorly understood. To elucidate structure–property relationships in CPEs, we investigate the role of salt concentration on CPE morphology and hole conductivity using a quantum mechanically informed coarse-grained (CG) model coupled with semiclassical rate theory. Under good solvent conditions, high salt concentration induces torsional disorder along the conjugated backbone, decreasing hole delocalization. In contrast, under poor solvent conditions, high salt concentration promotes CPE aggregation, leading to thicker fibers and increased hole mobilities. Collectively, this work characterizes the competing interactions governing CPE assembly and hole transport as a function of salt concentration, highlighting ion engineering as a powerful strategy for tailoring the properties of mixed-conducting polymers.
Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems are coarse-grained into low-dimensional models, the entropic loss of information leads to emergent physics which are dissipative, history-dependent, and stochastic. To machine learn coarse-grained dynamics from time-series observations of particle trajectories, we propose a framework using the metriplectic bracket formalism that preserves these properties by construction; most notably, the framework guarantees discrete notions of the first and second laws of thermodynamics, conservation of momentum, and a discrete fluctuation-dissipation balance crucial for capturing non-equilibrium statistics. We introduce the mathematical framework abstractly before specializing to a particle discretization. As labels are generally unavailable for entropic state variables, we introduce a novel self-supervised learning strategy to identify emergent structural variables. We validate the method on benchmark systems and demonstrate its utility on two challenging examples: (1) coarse-graining star polymers at challenging levels of coarse-graining while preserving non-equilibrium statistics, and (2) learning models from high-speed video of colloidal suspensions that capture coupling between local rearrangement events and emergent stochastic dynamics. We provide open-source implementations in both PyTorch and LAMMPS, enabling large-scale inference and extensibility to diverse particle-based systems.
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
Surfactants found in consumer products can compromise eye corneal membrane integrity upon accidental exposure. Traditional in vitro and in vivo approaches to evaluate membrane–surfactant interaction pose experimental limitations such as species variability, reproducibility, and most often do not provide the overall picture. These limitations motivate the use of in silico models to study phenomena like cellular disruption assays caused by surfactants at the molecular scale. In this work, coarse-grained molecular dynamics simulations have been employed to investigate how nonionic alcohol ethoxylate (AE) and anionic surfactant alcohol ethoxy sulfate (AES) interact with lipid bilayer liposomes that mimic corneal epithelial cell membranes. The spherical liposome is composed of 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-di(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-di(9Z-octadecenoyl)-sn-glycero-3-phospho-l-serine (DOPS), and cholesterol, resembling the composition of the corneal epithelial cells’ membrane bilayer. The simulation consisted of varying degrees of representative surfactant compositions and two initial types of surfactant configurations within or outside the liposome. Our results reveal that both surfactants induce outer leaflet bulging, agreeing with membrane solubilization models. The more highly ethoxylated surfactant, AE, caused more consistent inner leaflet disruption than AES, resulting in significantly more water permeation and membrane thinning. In addition, both surfactants increase the lateral diffusion of lipids within the membrane layers, with higher ethoxylated AE showing a stronger effect than AES. This study demonstrates how surfactant structure and localization influence bilayer membrane integrity, offering mechanistic insights into the irritation potential, thus guiding the rational design of effective surfactant-based formulations.
We propose a new statistical ensemble of toric bases for elliptic Calabi-Yaus used in F-theory models, by focusing on only the convex hull of the base, i.e., the base polytope. This physically motivated coarse-graining greatly simplifies the combinatorial complexity of the part of the 4d F-theory landscape with toric bases. We develop a Monte Carlo approach that randomly samples the base polytopes within fixed boxes, with proper statistical weights. We first apply the algorithm to the set of 2d base polytopes, generating an enlarged set of toric 2d bases that include certain types of codimension-two (4,6) points, and we validate our approach against exact numbers. We then explore the set of 3d base polytopes which fit in a set of “maximal” 3d boxes, and estimate the total number of inequivalent 3d base polytopes to be 10 85 –10 90 . We provide statistical data such as the distribution of non-Higgsable gauge groups on these bases. Amusingly, a similar method can also be applied to generate reflexive polytopes in various dimensions. In both the reflexive and base polytope cases, the number of relevant polytopes obeys a Gaussian distribution as a function of the number of vertices, which can be understood in terms of other results on random polytopes in the math literature.
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.
Accurate prediction of the rheological behavior of biomass is essential for the design and operation of hoppers, feeders, and storage systems in biorefineries. This study examines whether the classical, coarse-grained discrete element method (DEM) formulation can simultaneously reproduce the compressibility and flowability of milled herbaceous biomass, using Miscanthus × giganteus as a representative material. The model represents particles as rigid spheres interacting through Hertz-Mindlin elastic-frictional contacts augmented with an area-dependent cohesion term. Laboratory cyclic compression and wedge-shaped hopper discharge experiments were used as calibration benchmarks. Although the model can independently reproduce each behavior by appropriately tuning particle Young's modulus E and cohesion energy density k, an extensive parametric investigation comprising more than 600 simulations reveals that the optimal parameter regions for compression and hopper flow are distinct and non-overlapping in (E, k) space. Surrogate surface analysis further shows that the corresponding objective-function valleys exhibit similar trends but are approximately parallel and spatially offset, precluding a unified calibration within the explored domain. Sensitivity analysis indicates that compressibility is governed predominantly by stiffness and cohesion, whereas the slope of the mass flow rate-opening relation in hopper discharge is primarily controlled by tangential friction. Extensions incorporating particle size distribution and clumped-sphere representations do not eliminate the incompatibility. These results systematically reveal, for the first time, the structural limitation of simplified DEM formulations in representing biomass rheological behavior, underscoring the necessity for models incorporating additional physical mechanisms, such as particle deformability or enhanced interlocking, to achieve unified predictive capability for biomass handling behavior.
In this work, we evaluate the biomolecular dynamics behaviors when conventionally iterating between all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations over multiple cycles. We implemented the workflow to iterate between AA and CG in OpenMM, namely the iterative multiscale MD (iMMD) simulation workflow. In particular, we aim to identify practical applications for iterating between AA and CG simulations in a conventional manner without any constraints or model modifications. We evaluate the iMMD workflow on four representative systems, spanning folding of two soluble proteins and protein-protein as well as protein-lipid interactions of two membrane proteins. We observe that iteration between AA and CG representations could help the soluble proteins exit undesirable metastable states to fold, resulting from random protein structural distortions due to cycling. Consequently, the most reliable use of iterative AA and CG simulations appears to be to accelerating complex lipid mixing for membrane-bound protein systems rather than sampling protein conformational space. Our work explores the practical usages and limitations for iterative AA and CG simulations using readily available AA and CG force fields. The evaluated iMMD workflow in OpenMM is made available at https://github.com/lanl/iMMD.
Existing models of thermoset deconstruction facilitated by incorporating cleavable comonomers rely on a mean-field reverse gel point paradigm, which predicts network dissolution once cleavable bonds reach a critical stoichiometric threshold, but does not account for where those bonds reside within the network architecture. Using reactive coarse-grained molecular dynamics simulations coupled with graph-theoretic analysis, we extend this stoichiometric picture to show that deconstructability is governed by the curing-imprinted network topology rather than stoichiometry alone. This topological organization is hierarchical: at the local scale, the elastic effectiveness of cross-link junctions determines which cross-links constitute the load-bearing scaffold; at the mesoscale, the cross-linking rate kinetically templates that scaffold into topologically modular communities─densely cross-linked clusters connected by sparse bridging strands that sustain network connectivity. Using betweenness centrality to identify nodes that disproportionately lie on intercommunity shortest paths, we demonstrate that effective deconstruction of the network into macromolecular fragments requires cleavable comonomers to intercept these high-centrality bridging strands. We further find that under uniform, disassortative comonomer incorporation, this topological requirement provides a mechanistic basis for extending the reverse gel point to incorporate network topology. We also show that modularity imposes a fundamental limit on fragment uniformity that persists even when the centrality requirement is met. Finally, we demonstrate that chain stiffness provides a nearly independent lever to suppress mechanically redundant cross-links and raise the glass transition temperature without significantly altering the deconstruction outcome. Together, these findings reframe the thermoset design space around network topology and provide actionable guidelines for engineering thermoset copolymers with predictable deconstructability and targeted thermomechanical performance.
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.
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.