arXiv subjects

Juan J. de Pablo

Publications and source records attributed to Juan J. de Pablo.

At least 19 recordsLinked to original sources

arXiv2026

VESPER: Online Learning of Free Energies with a Multi-Tempered Variational Objective

Computing molecular free-energy landscapes over collective variables (CVs) is central to understanding molecular mechanisms, but poses a difficult learning problem without training data available a priori. Samples of the marginal CV distribution must be generated by molecular dynamics (MD), whose trajectories can remain trapped in metastable states and rarely cross the free-energy barriers governing conformational changes or chemical reactions. We introduce VESPER, which couples the generation of these samples to neural-network-driven free-energy learning: MD supplies configurations for learning, while the evolving model biases the MD to accelerate exploration and generate further training data. VESPER minimizes a single variational objective that is convex in the free energy and can combine several tempering levels, each flattening the free-energy landscape to promote barrier crossing. Every level has the same physical free energy as its minimizer, allowing data from all levels to train one shared model without reweighting. Learning uses the difference in mean parameter gradients between biased MD configurations and auxiliary walkers that explore the flattened model in CV space. We prove conditional convergence of the coupled overdamped population dynamics without replica exchange under log-Sobolev and Polyak-Lojasiewicz assumptions. VESPER matches or improves on established enhanced-sampling methods on alanine dipeptide and yields self-consistent free-energy reconstructions from three to six CVs on alanine tetrapeptide. For methane dehydrogenation on Ni(511) with a machine-learned interatomic potential, it recovers two-CV Boltzmann marginals and a reactant-to-saddle free-energy difference along a three-CV path, both qualitatively consistent with the lower-dimensional reference. It also samples RMSD-defined folded and unfolded regions of chignolin while biasing seventeen CVs.

physics.chem-ph↗

arXiv2026

MIRRA: Fast, High-Fidelity Molecular Generation with Chemistry-Informed Discrete Flow Matching

Fast, high-fidelity molecular generation requires accurate chemical choices and efficient sampling. Chemical building blocks reduce graph size, but make each node a choice among tens of thousands of related identities. We introduce MIRRA (Molecular Identity Representation, Refresh and Assembly), a discrete flow-matching generator that learns from chemical knowledge and evaluates identity probabilities only when needed, while keeping every identity in its vocabulary available. Chemical features share information across related blocks, and learned identity corrections distinguish them in molecular context. By deciding which positions will refresh before computing their probabilities, the sampler avoids unused predictions while preserving each sampling transition. Against the strongest baselines in each task, MIRRA reduces chemical and graph distribution errors on ZINC250k by 29-31% and 53-60%, respectively, with generation up to 8.6 times faster. Property targeting yields an estimated 7.8-20.8 times more distinct novel hits per second. On a held-out polymer test set, MIRRA achieves 100% periodic validity with known chain topology, versus 57.0% for a polymer variational autoencoder. These results demonstrate fast, high-fidelity generation with the full chemical vocabulary available throughout sampling.

cs.LG↗

arXiv2026

NEMORA: Neural Equivariant Multipole Operators for Long-Range Atomistic Learning

Equivariant graph neural networks have emerged as foundational architectures for machine-learned interatomic potentials, approaching quantum-chemical accuracy at a fraction of the computational cost. These models describe local atomic environments accurately, but finite spatial cutoffs truncate long-range information flow, and stacking message-passing layers can lead to over-smoothing and over-squashing. Existing long-range extensions either prescribe a fixed analytical propagation kernel, restrict long-range communication to scalars or degree-preserving channels, are only approximately equivariant, or incur super-linear computational cost. Combining learnable long-range equivariant transport with multiscale many-body expressivity and efficient scaling for larger systems remains a central challenge. We introduce Neural Equivariant Multipole Operators (NEMORA), a neural equivariant extension of the Fast Multipole Method (FMM) for learning long-range tensorial representations. NEMORA generalizes the FMM's analytical multipole expansion and translation operators to learned equivariant counterparts on an adaptive spatial hierarchy. Its operators couple angular degrees and form many-body interactions across length scales, retaining the FMM's hierarchical organization and analytical radial factors as physical inductive biases while learning data-dependent long-range couplings. NEMORA evaluates in linear time and memory complexity, allowing it to treat larger systems than other long-range methods reaching hundreds of thousands of atoms, and it augments both symmetry-constrained and unconstrained short-range backbones. On non-local benchmarks, it reduces force and energy errors relative to the short-range backbones by over an order of magnitude and up to three orders of magnitude, respectively, which is better than or competitive with existing long-range extensions in accuracy.

cs.LG↗

arXiv2026

HiPoly: a hierarchical polymer-native AI framework for property prediction and generative design

Polymeric materials are central to modern technologies, with applications ranging from energy to health and transportation. Although AI has made significant advances in materials discovery, the hierarchical structure of polymers across multiple length scales makes them inherently difficult to represent in a unified and physically meaningful way. Here we introduce HiPoly, a polymer-native AI framework that processes complete polymer descriptions through a three-level hierarchical graph architecture built on the G2RINS representation. HiPoly encodes stochastic inter-monomer connectivity, composition, and molecular weight directly within its architecture, using physically motivated design principles that mirror the multi-scale nature of polymeric systems. The framework establishes an end-to-end AI-driven workflow from experimental formulation data to property prediction, generative molecular design, and physics-based validation through molecular simulations, all unified by a single polymer representation. We demonstrate state-of-the-art prediction accuracy for thermophysical properties of multi-component polymer systems, with ablation studies confirming that each hierarchical design choice contributes independently to model performance. As an example, the generative design pathway is applied here to the discovery of sustainable alternatives to persistent fluorinated polymers, where it is possible to identify and independently validate PFAS-free candidates with target surface-energy properties. This work demonstrates how polymer-native AI can accelerate discovery by linking representation, prediction, and design across complex polymer chemistries.

physics.chem-ph↗

arXiv2025

Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials

Silicon carbide (SiC) divacancies are attractive candidates for spin defect qubits possessing long coherence times and optical addressability. The high activation barriers associated with SiC defect formation and motion pose challenges for their study by first-principles molecular dynamics. In this work, we develop and deploy machine learning interatomic potentials (MLIPs) to accelerate defect dynamics simulations while retaining ab initio accuracy. We employ an active learning strategy comprising symmetry-adapted collective variable discovery and enhanced sampling to compile configurationally diverse training data, calculation of energies and forces using density functional theory (DFT), and training of an E(3)-equivariant MLIP based on the Allegro model. The trained MLIP reproduces DFT-level accuracy in defect transition activation free energy barriers, enables the efficient and stable simulation of multi-defect 216-atom supercells, and permits an analysis of the temperature dependence of defect thermodynamic stability and formation/annihilation kinetics to propose an optimal annealing temperature to maximally stabilize VV divacancies.

cond-mat.mtrl-sci↗

arXiv2025

Quorum sensing of light-activated colloids in nematic liquid crystals

Motile living organisms routinely probe their surroundings to adapt in ever-evolving environments. Although synthetic microswimmers offer surrogates for self-propelled living entities, they often lack the complex feedback mechanisms that enable organisms to adapt. In this work, we present an experimental platform in which light-activated colloids dispersed in a nematic liquid crystal can (i) switch from directed to active Brownian motion depending on the nematic anchoring and (ii) mechanically adjust their motility in response to crowding, effectively enforcing quorum-sensing interactions. Both features are caused by a distinctive self-propulsion mechanism as unveiled through experiments, simulations, and theory. We characterize the dynamics of a single colloid and demonstrate that its motion is captured by an active Brownian particle model if the nematic anchoring is homeotropic, and by directed self-propulsion along the nematic director if the anchoring is planar. Next, we investigate the many-body dynamics, showing that it undergoes a clustering phase separation through effective quorum-sensing interactions. Our work suggests how to create adaptive materials with life-like capabilities using readily accessible properties of liquid crystals and colloids without explicitly engineering any of the needed mechano-chemical feedbacks.

cond-mat.soft↗

arXiv2025

Autodifferentiable Geometric Restraints for Enhanced Sampling Simulations with Classical and Machine Learned Force Fields

The use of external restraints is ubiquitous in advanced molecular simulation techniques. In general, restraints serve to reduce the configurational space that is available for sampling, thereby reducing the computational demands associated with a given simulations. Examples include the use of positional restraints in docking simulations or positional restraints in studies of catalysis. Past work has sought to couple complex restraining potentials with enhanced sampling methods, including Metadynamics or Extended Adaptive Biasing Force approaches. Here, we introduce the use of more general geometric potentials coupled with enhanced sampling methods that incorporate neural networks or spectral decomposition to achieve more efficient sampling in the context of advanced materials design.

physics.comp-ph↗

arXiv2025

IEC-Independent Coupling Between Water Uptake and Ionic Conductivity in Anion-Conducting Polymer Films

Anion exchange membranes (AEMs) are promising candidates for replacing proton exchange membranes (PEMs) in electrochemical devices such as fuel cells, electrolyzers, batteries, and osmotic energy extraction systems. However, optimizing the AEM design requires a deeper understanding of the ionic conduction mechanism in the hydrated polymer matrix. This study investigates this mechanism by seeking to understand the relationship between ion exchange capacity (IEC), water absorption, and ionic conductivity in polynorbornene-based thin films. We combine experimental measurements with computational simulations using a newly developed minimal model of the polymer film. Our model is able to reproduce key experimental observations, including water sorption isotherms and ion conduction behavior as a function of relative humidity, and successfully captures the relationship between them. By comparing experimental data with computational results, we explain the commonly reported correlation between conductivity and hydration level and show how the correlation between these variables is affected by the charge density and temperature of the material. Our research advances our understanding of the physical mechanisms that govern the performance of the polyelectrolyte membrane, which is essential for the development of more efficient, stable, and environmentally friendly electrochemical systems.

cond-mat.soft↗

arXiv2025

Attention-Based Functional-Group Coarse-Graining: A Deep Learning Framework for Molecular Prediction and Design

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML training. In this study, we report a data-efficient, deep-learning framework for molecular discovery that integrates a coarse-grained functional-group representation with a self-attention mechanism to capture intricate chemical interactions. Our approach exploits group-contribution theory to create a graph-based intermediate representation of molecules, serving as a low-dimensional embedding that substantially reduces the data demands typically required for training. By leveraging the self-attention mechanism to learn subtle chemical context, our method consistently outperforms conventional methods in predicting multiple thermophysical properties. In a case study focused on adhesive polymer monomers, we train on a limited dataset comprising just 6,000 unlabeled and 600 labeled monomers. The resulting chemistry prediction model achieves over 92% accuracy in forecasting properties directly from SMILES strings, exceeding the performance of current state-of-the-art techniques. Furthermore, the latent molecular embedding is invertible, allowing the design pipeline to incorporate a decoder that can automatically generate new monomers from the learned chemical subspace. We illustrate this functionality by targeting high and low glass transition temperatures ($T_g$), successfully identifying novel candidates whose $T_g$ extends beyond the range observed in the training data. The ease with which our coarse-grained, attention-based framework navigates both chemical diversity and data scarcity offers a compelling route to accelerate and broaden the search for functional materials.

physics.chem-ph↗

arXiv2024

Light-Activated Motion, Geometry- and Confinement-Induced Optical Effects of 2D Platelets in a Nematic Liquid Crystal

Motile liquid crystal (LC) colloids show peculiar behavior due to the high sensitivity to external stimuli driven by the LC elastic and surface effects. However, few studies focus on harnessing the LC phase transitions to propel colloidal inclusions by the nematic-isotropic (NI) interface. We engineer a quasi-2D active system consisting of solid micron-sized light-absorbent platelets immersed in a thermotropic nematic LC. The platelets self-propel in the presence of light while self-inducing a localized NI phase transition. The sample's temperature, light intensity, and confinement determine three different regimes: a 2D large regime where the platelet-isotropic phase bubble is static and the NI interface remains stable; a compact motile-2D regime where the NI interface lies closer to the platelet's contour; and a motile-3D-confinement regime characterized by the emergence of multipolar configurations of the LC. We perform continuum-theory simulations that predict stationary platelet-LC states when confined in 3D. Our study in an intrinsically far-from-equilibrium landscape is crucial for designing simple synthetic systems that contribute to our understanding of harnessing liquid crystals' phase transitions to propel colloidal inclusions and trigger tunable topological reconfigurations leading to photonic responses.

cond-mat.soft↗

arXiv2024

The Importance of Learning without Constraints: Reevaluating Benchmarks for Invariant and Equivariant Features of Machine Learning Potentials in Generating Free Energy Landscapes

Machine-learned interatomic potentials (MILPs) are rapidly gaining interest for molecular modeling, as they provide a balance between quantum-mechanical level descriptions of atomic interactions and reasonable computational efficiency. However, questions remain regarding the stability of simulations using these potentials, as well as the extent to which the learned potential energy function can be extrapolated safely. Past studies have reported challenges encountered when MILPs are applied to classical benchmark systems. In this work, we show that some of these challenges are related to the characteristics of the training datasets, particularly the inclusion of rigid constraints. We demonstrate that long stability in simulations with MILPs can be achieved by generating unconstrained datasets using unbiased classical simulations if the fast modes are correctly sampled. Additionally, we emphasize that in order to achieve precise energy predictions, it is important to resort to enhanced sampling techniques for dataset generation, and we demonstrate that safe extrapolation of MILPs depends on judicious choices related to the system's underlying free energy landscape and the symmetry features embedded within the machine learning models.

physics.comp-ph↗

arXiv2024

Rheology of bidisperse non-Brownian suspensions

We study the rheology of bidisperse non-Brownian suspensions using particle-based simulation, mapping the viscosity as a function of the size ratio of the species, their relative abundance, and the overall solid content. The variation of the viscosity with applied stress exhibits shear thickening phenomenology irrespective of composition, though the stress-dependent limiting solids fraction governing the viscosity and its divergence point are non-monotonic in the mixing ratio. Contact force data demonstrate an asymmetric exchange in dominant stress contribution from large-large to small-small particle contacts as the mixing ratio of the species evolves. Combining a prior model for shear thickening with one for composition-dependent jamming, we obtain a full description of the rheology of bidisperse non-Brownian suspensions capable of predicting effects such as the viscosity reduction observed upon adding small particle fines to a suspension of large particles.

cond-mat.soft↗

arXiv2024

Light-responsive active particles in a thermotropic liquid crystal

The development of synthetic microswimmers has advanced our understanding of the fundamental self-propelled mechanisms of living systems. However, there are scarce studies at the microscale within highly structured anisotropic media, such as bacteria or cellular receptors that swim in concentrated solutions of filamentous proteins or lipids with viscoelastic properties. Synthetic liquid crystals (LCs) have the potential to serve as biomimetic surrogates to study the structure and dynamics of living systems. Nevertheless, studies on thermotropic LCs have mainly focused on electro and magneto-phoretic effects, with a few others on diffusiophoresis or light-driven distortions of the LC nematic director. To the best of our knowledge, here we report self-thermophoretic experiments on thermotropic LCs for the first time. Our system consists of 2D confined Janus particles in 5CB with homeotropic anchoring on the particle and LC cell surfaces. The Janus particles include a conductive titanium coating that, upon exposure to an LED source, is heated and induces a local steady nematic-isotropic phase transition, leading to the self-propulsion of the particles orthogonally to the LC director. The trajectories of the Janus particles were tracked at different intensities of the applied light. A model is developed to describe the mean-squared displacement of a Janus particle suspended in a nematic LC. The model assumes that the Janus particle feels the LC as a continuum with the anisotropic viscosity of the bulk nematic phase. Moreover, the viscoelasticity of the LC is also considered. The model describes the experimental data well, and the fitting parameter related to the magnitude of the swimming force increases with the intensity of the applied light. Moreover, our approach represents an important step for developing a platform for highly structured anisotropic active materials.

cond-mat.soft↗

arXiv2024

Numerical Study of Cleavable Bond-Modified Polyethylene for Circular Polymer Design

There is considerable interest in designing new polymeric materials with built-in mechanisms for recycling. In this work, we present a systematic exploration of several polyethylene-based polymers that contain strategically incorporated cleavable bonds that are susceptible to chemical degradation. We consider ten distinct telechelic functionalities across varying chain lengths: ester, aromatic ester, anhydride, carbonate, urethane, siloxane, oxalate, acetal, urea, and amide linkages. Our study is focused on the effects of cleavable bonds on density, diffusion, enthalpy, and melting temperatures. We also examine the crystallization process. These are key properties for polymer processing and, by comparing them to those of linear polyethylene, we establish a platform that will help guide future synthetic efforts towards the design of sustainable plastics with performance comparable to that of traditional, high-performance polyolefin-based materials.

cond-mat.soft↗

arXiv2024

Thermodynamic and Transport Properties of Binary Mixtures of Polyethylene and Higher n-Alkanes from Physics-Informed and Machine-Learned Models

The thermodynamics and transport properties of polymeric materials are essential for the design of reactors and for the development of polymer deconstruction processes. Existing property prediction tools such as correlations based on entropy scaling, kinetic gas theory, and free-volume model are inadequate for polymers. In this paper, we introduce a data-driven model for polyolefins based on data from molecular dynamics simulations that can accurately predict the transport properties of polyethylenes and their binary mixtures with higher n-alkanes across a range of temperatures, pressures, concentrations, and oligomer molecular weights.

cond-mat.soft↗

arXiv2024

Synthetic active liquid crystals powered by acoustic waves

Active nematics are materials composed of mobile, elongated particles that can transform energy from the environment into a mechanical motion. Current experimental realizations of the active nematics are of biological origin and include cell layers, suspensions of elongated bacteria in liquid crystal, and combinations of bio-filaments with molecular motors. Here, we report the realization of a fully synthetic active nematic system comprised of a lyotropic chromonic liquid crystal energized by ultrasonic waves. This artificial active liquid crystal is free from biological degradation and variability, exhibits stable material properties, and enables precise and rapid activity control over a significantly extended range. We demonstrate that the energy of the acoustic field is converted into microscopic extensile stresses disrupting long-range nematic order and giving rise to an undulation instability, development of active turbulence, and proliferation of topological defects. We reveal the emergence of unconventional free-standing persistent vortices in the nematic director field at high activity levels. The results provide a foundation for the design of externally energized active nematic fluids with stable material properties and tunable topological defects dynamics crucial for the realization of reconfigurable microfluidic systems.

cond-mat.soft↗

arXiv2023

Prediction of Diblock Copolymer Morphology via Machine Learning

A machine learning approach is presented to accelerate the computation of block polymer morphology evolution for large domains over long timescales. The strategy exploits the separation of characteristic times between coarse-grained particle evolution on the monomer scale and slow morphological evolution over mesoscopic scales. In contrast to empirical continuum models, the proposed approach learns stochastically driven defect annihilation processes directly from particle-based simulations. A UNet architecture that respects different boundary conditions is adopted, thereby allowing periodic and fixed substrate boundary conditions of arbitrary shape. Physical concepts are also introduced via the loss function and symmetries are incorporated via data augmentation. The model is validated using three different use cases. Explainable artificial intelligence methods are applied to visualize the morphology evolution over time. This approach enables the generation of large system sizes and long trajectories to investigate defect densities and their evolution under different types of confinement. As an application, we demonstrate the importance of accessing late-stage morphologies for understanding particle diffusion inside a single block. This work has implications for directed self-assembly and materials design in micro-electronics, battery materials, and membranes.

physics.chem-ph↗

arXiv2023

LCPOM: Precise Reconstruction of Polarized Optical Microscopy Images of Liquid Crystals

When viewed with a cross-polarized optical microscope (POM), liquid crystals display interference colors and complex patterns that depend on the material's microscopic orientation. That orientation can be manipulated by application of external fields, which provides the basis for applications in optical display and sensing technologies. The color patterns themselves have a high information content. Traditionally, however, calculations of the optical appearance of liquid crystals have been performed by assuming that a single-wavelength light source is employed, and reported in a monochromatic scale. In this work, the original Jones matrix method is extended to calculate the colored images that arise when a liquid crystal is exposed to a multi-wavelength source. By accounting for the material properties, the visible light spectrum and the CIE color matching functions, we demonstrate that the proposed approach produces colored POM images that are in quantitative agreement with experimental data. Results are presented for a variety of systems, including radial, bipolar, and cholesteric droplets, where results of simulations are compared to experimental microscopy images. The effects of droplet size, topological defect structure, and droplet orientation are examined systematically. The technique introduced here generates images that can be directly compared to experiments, thereby facilitating machine learning efforts aimed at interpreting LC microscopy images, and paving the way for the inverse design of materials capable of producing specific internal microstructures in response to external stimuli.

cond-mat.soft↗