Juan de Pablo

• University of Chicago

Reflection and refraction are ubiquitous phenomena with extensive applications, yet minimizing energy loss and information distortion during these processes remains a significant challenge. This study examines the behavior of structurally stable solitons, known as directrons, in nematic liquid crystals interacting with an interface where the direct...

The physical organization of DNA within the nucleus is fundamental to a wide range of biological processes. The experimental investigation of the structure of genomic DNA remains challenging due to its large size and hierarchical arrangement. These challenges present considerable opportunities for combined experimental and modeling approaches. Phys...

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 positio...

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. T...

Active nematic materials combine orientational order with activity at the microscopic level. Current experimental realizations of active nematics include vibrating elongated particles, cell layers, suspensions of elongated bacteria, and a mixture of bio‐filaments with molecular motors. The majority of active nematics are of biological origin. The r...

Blue phases (BPs), formed through the self‐assembly of chiral liquid crystal molecules into 3D nanolattices with cubic symmetries, exhibit dynamic photonic bandgaps in the visible spectrum, offering transformative opportunities for advanced optical circuits, sensing and communication technologies. However, their thermal stability is restricted to a...

Molecular simulations of biological and physical phenomena generally involve sampling complicated, rough energy landscapes characterized by multiple local minima. In this work, we introduce a new family of methods for advanced sampling that draw inspiration from functional representations used in machine learning and approximation theory. As shown...

A borrowing hydrogen approach to produce bio‐based surfactants is described. The process utilizes ubiquitous amino acids and common alcohols without protecting group manipulations. Surfactants are synthesized in a single step using a commercially available ruthenium‐based catalyst in a waste‐free manner with nearly ideal atom economy. The versatili...

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 inte...

Water is a critical component in polyelectrolyte anion exchange membranes (AEMs). It plays a central role in ion transport in electrochemical systems. Gaining a better understanding of molecular transport and conductivity in AEMs has been challenged by the lack of a general methodology capable of capturing and connecting water dynamics, water struc...

IFNλ4 has posed a conundrum in human immunology since its discovery in 2013, with its expression linked to complications with viral clearance. While genetic and cellular studies revealed the detrimental effects of IFNλ4 expression, extensive structural and functional characterization has been limited by the inability to express and purify the prote...

Machine learning interatomic potentials (MLIPs) 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...

We theoretically investigate how the intranuclear environment influences the charge of a nucleosome core particle (NCP)—the fundamental unit of chromatin consisting of DNA wrapped around a core of histone proteins. The molecular-based theory explicitly considers the size, shape, conformation, charge, and chemical state of all molecular species—ther...

We theoretically investigate how the intranuclear environment influences the charge of a nucleosome core particle (NCP) - the fundamental unit of chromatin consisting of DNA wrapped around a core of histone proteins. The molecular-based theory explicitly considers the size, shape, conformations, charges, and chemical states of all molecular species...

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 th...

We investigate the steady state of an ellipsoidal active nematic shell using experiments and numerical simulations. We create the shells by coating microsized ellipsoidal droplets with a protein-based active cytoskeletal gel, thus obtaining ellipsoidal core-shell structures. This system provides the appropriate conditions of confinement and geometr...

Water auto-ionization is critical in a wide range of chemical, biological, physical, and industrial processes. In this work, we describe a series of hitherto unknown collective molecular processes leading to auto-ionization. Specifically, by combining machine-learned interatomic potentials and spectral adaptive biasing force techniques, we determin...

Polymer electrolytes are of interest for applications in energy storage. Molecular simulations of ion transport in polymer electrolytes have been widely used to study the conductivity in these materials. Such simulations have generally relied on classical force fields. A peculiar feature of such force fields has been that in the particular case of...

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 mi...

Within the realm of soft matter, particularly liquid crystals, the ability to leverage material properties to create switchable diffraction gratings holds significant importance in disciplines such as optics and information science. However, designing switchable patterns and compiling information based on output images remain challenging. Here, we...

Within the realm of soft matter, particularly liquid crystals, the ability to leverage material properties to create switchable diffraction gratings holds significant importance in disciplines such as optics and information science. However, designing switchable patterns and compiling information based on output images remain challenging. Here, we...

Solid-state electrolytes, particularly polymer/ceramic composite electrolytes, are emerging as promising candidates for lithium-ion batteries due to their high ionic conductivity and mechanical flexibility. The interfaces that arise between the inorganic and organic materials in these composites play a crucial role in ion transport mechanisms. Whil...

Multidimensional solitons are prevalent in numerous research fields. In orientationally ordered soft matter system, three-dimensional director solitons exemplify the localized distortion of molecular orientation. However, their precise manipulation remains challenging due to unpredictable and uncontrolled generation. Here, we utilize preimposed pro...

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...

Nonequilibrium states in soft condensed matter require a systematic approach to characterize and model materials, enhancing predictability and applications. Among the tools, X-ray photon correlation spectroscopy (XPCS) provides exceptional temporal and spatial resolution to extract dynamic insight into the properties of the material. However, exist...

Redox-active polymers serving as the active materials in solid-state electrodes offer a promising path toward realizing all-organic batteries. While both cathodic and anodic redox-active polymers are needed, the diversity of the available anodic materials is limited. Here, we predict solid-state structural, ionic, and electronic properties of anodi...

Auxetic materials have a negative Poisson’s ratio and are of significant interest in applications that include impact mitigation, membrane separations and biomedical engineering. While there are numerous examples of structured materials that exhibit auxetic behavior, the examples of engineered auxetic structures is largely limited to periodic latti...

Solitons in nematic liquid crystals facilitate the rapid transport and sensing in microfluidic systems. Little is known about the elementary conditions needed to create solitons in nematic materials. In this study, we apply a combination of theory, computational simulations, and experiments to examine the formation and propagation of solitary waves...

Redox-active polymers serving as the active materials in solid-state electrodes offer a promising path towards realizing all-organic batteries. While both cathodic and an- odic redox-active polymers are needed, the diversity of the available anodic materials is limited. Here, we predict solid-state structural, ionic, and electronic properties of an...

This study explores how conformational asymmetry influences the bulk phase behavior of linear-brush block copolymers. We synthesized 60 diblock copolymers composed of poly(trifluoroethyl methacrylate) as the linear block and poly[oligo(ethylene glycol) methyl ether methacrylate] as the brush block, varying the molecular weight, composition, and sid...

Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of the relevant underlying free energy landscapes. In this sense, software that can be seamlessly adapted to a br...

Dense suspensions are a prototype of fluid that can dynamically enhance their viscosity to resist strong forcing. Recent work established that the key to a large viscosity increase—often in excess of an order of magnitude—is the ability to switch from lubricated, frictionless particle interactions at low stress to a network of frictional contacts a...

A strategy to efficiently synthesize thermally reprogrammable but mechanically stable liquid crystalline elastomers (LCEs) is reported by investigating the catalytic effects of para-substituted phenols on dynamic aza-Michael reactions. The synthesis of aza-Michael LCEs was optimized based on a study of catalyzed small-molecule aza-Michael reactions...

Rheology of bidisperse non-Brownian suspensions using numerical simulations. A constitutive model that combines stress-dependent rheology with bidisperse jamming is proposed.

The BigSMILES notation, a concise tool for polymer ensemble representation, is augmented here by introducing an enhanced version called generative BigSMILES. G-BigSMILES is designed for generative workflows, and is complemented by tailored software tools for ease of use. This extension integrates additional data, including reactivity ratios (or con...

Solitons in liquid crystals have generated considerable interest. Several hypotheses of varying complexity have been advanced to explain how they arise, but consensus has not emerged yet about the underlying forces responsible for their formation or their structure. In this work, we present a minimal model for solitons in achiral nematic liquid cry...

From flocks of birds to biomolecular assemblies, systems in which many individual components independently consume energy to perform mechanical work exhibit a wide array of striking behaviors. Methods to quantify the dynamics of these so-called active systems generally aim to extract important length or time scales from experimental fields. Because...

Dynamic liquid crystal elastomers (LCEs) are a class of polymer networks characterized by the inclusion of both liquid crystalline monomers and dynamic covalent bonds. The unique properties realized through the combination of these moieties has produced a plethora of stimuli‐responsive materials to address a range of emerging technologies. While pr...

Emerging solid polymer electrolyte (SPE) designs for efficient Li-ion (Li⁺) conduction have relied on polarity and mobility contrast to improve conductivity. To further develop this concept, we employ simulations to examine Li⁺ solvation and transport in poly(oligo ethylene methacrylate) (POEM) and its copolymers with poly(glycerol carbonate methac...

Recently, a high-throughput screen of 1900 clinically used drugs identified masitinib, an orally bioavailable tyrosine kinase inhibitor, as a potential treatment for COVID-19. Masitinib acts as a broad-spectrum inhibitor for human coronaviruses, including SARS-CoV-2 and several of its variants. In this work, we rely on atomistic molecular dynamics...

Electrostatic interactions in polymeric systems are responsible for a wide range of liquid–liquid phase transitions that are of importance for biology and materials science. Such transitions are referred to as complex coacervation, and recent studies have sought to understand the underlying physics and chemistry. Most theoretical and simulation eff...

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 empir...

Polyelectrolyte complexation plays an important role in materials science and biology. The internal structure of the resultant polyelectrolyte complex (PEC) phase dictates properties such as physical state, response to external stimuli, and dynamics. Small-angle scattering experiments with X-rays and neutrons have revealed structural similarities b...

Blue phase (BP) liquid crystals are chiral fluids wherein millions of molecules self-assemble into cubic lattices that are on the order of hundred nanometers. As the unit cell sizes of BPs are comparable to the wavelength of light, they exhibit selective Bragg reflections in the visible. The exploitation of the photonic properties of BPs for techno...

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 p...

Chiral liquid crystals (ChLCs) exhibit an inherent twist that originates at the molecular scale and can extend over multiple length scales when unconstrained. Under confinement, the twist is thwarted, leading to formation of defects in the molecular order that offer distinct optical responses and opportunities for colloidal driven assembly. Past st...

A combined machine learning-physics-based approach is explored for molecular and materials engineering. Specifically, collective variables, akin to those used in enhanced sampled simulations, are constructed using a machine learning model trained on data gathered from a single system. Through the constructed collective variables, it becomes possibl...

Scanning transmission electron microscopy tomography with ChromEM staining (ChromSTEM), has allowed for the three-dimensional study of genome organization. By leveraging convolutional neural networks and molecular dynamics simulations, we have developed a denoising autoencoder (DAE) capable of postprocessing experimental ChromSTEM images to provide...

Electrostatic interactions in polymeric systems are responsible for a wide range of liquid-liquid phase transitions that are of importance for biology and materials science. Such transitions are referred to as complex coacervation, and recent studies have sought to understand the underlying physics and chemistry. Most theoretical and simulation eff...

The properties of soft electronic materials depend on the coupling of electronic and conformational degrees of freedom over a wide range of spatiotemporal scales. The description of such properties requires multiscale approaches capable of, at the same time, accessing electronic properties and sampling the conformational space of soft materials. Th...

The optical properties of liquid crystals serve as the basis for display, diagnostic, and sensing technologies. Such properties are generally controlled by relying on electric fields. In this work, we investigate the effects of microfluidic flows and acoustic fields on the molecular orientation and the corresponding optical response of nematic liqu...

Stretchable light-emitting materials are the key components for realizing skin-like displays and optical biostimulation. All the stretchable emitters reported to date, to the best of our knowledge, have been based on electroluminescent polymers that only harness singlet excitons, limiting their theoretical quantum yield to 25%. Here we present a de...

From flocks of birds to biomolecular assemblies, systems in which many individual components independently consume energy to perform mechanical work exhibit a wide array of striking behaviors. Methods to quantify the dynamics of these so called active systems generally aim to extract important length or time scales from experimental fields. Because...

Cells are fundamental building blocks of living organisms displaying an array of shapes, morphologies, and textures that encode specific functions and physical behaviors. Elucidating the rules of this code remains a challenge. In this work, we create biomimetic structural building blocks by coating ellipsoidal droplets of a smectic liquid crystal w...

Suspensions of polymeric nano- and microparticles are fascinating stress-responsive material systems that, depending on their composition, can display a diverse range of flow properties under shear, such as drastic thinning, thickening, and even jamming (reversible solidification driven by shear). However, investigations to date have almost exclusi...

The Community Resource for Innovation in Polymer Technology (CRIPT) data model is designed to address the high complexity in defining a polymer structure and the intricacies involved with characterizing material properties.

We develop a scaling theory for the structure and dynamics of "hybrid" complex coacervates formed from linear polyelectrolytes (PEs) and oppositely charged spherical colloids, such as globular proteins, solid nanoparticles, or spherical micelles of ionic surfactants. At low concentrations, in stoichiometric solutions, PEs adsorb at the colloids to...

Molecular dynamics simulations are a core element of research in physics, chemistry and biology. A key aspect for extending the capability of simulation tools is providing access to advanced sampling methods and techniques that permit calculation of the relevant, underlying free energy landscapes. In this sense, software tools that can be seamlessl...

Dense suspensions are a prototype of fluid that can dynamically enhance its viscosity to resist strong forcing. Recent work established that the key to a large viscosity increase, often in excess of an order of magnitude, is the ability to switch from lubricated, frictionless particle interactions at low stress to a network of frictional contacts a...

From chemical reactivity to mechanical strength, crystal texture plays a central role in determining the key properties of solids. In organic electronics, texture determines the charge carrier mobility of the...

The growing interest in integrating liquid crystals (LCs) into flexible and miniaturized technologies brings about the need to understand the interplay between spatially curved geometry, surface anchoring, and the order associated with these materials. Here, we integrate experimental methods and computational simulations to explore the competition...

The ability to impart multiple covarying properties into a single material represents a grand challenge in manufacturing. In the design of block copolymers (BCPs) for directed self-assembly and nanolithography, materials often balance orthogonal properties to meet constraints related to processing, structure and defectivity. Although iterative synt...

Recent advances in nano-rheology require that new methods and models be developed to describe the equilibrium and non-equilibrium properties of entangled polymeric materials and their interfaces at a molecular level of detail. In this work we present a Slip-Spring (SLSP) model capable of describing the dynamics of entangled polymers at interfaces,...

Solitons in nematic liquid crystals offer intriguing opportunities for transport and sensing in microfluidic systems. Little is known about the elementary conditions that are needed to create solitons in nematic materials. In this work, theory, simulations and experiments are used to study the generation and propagation of solitary waves (or "solit...

Autonomous experimental systems offer a compelling glimpse into a future where closed-loop, iterative cycles—performed by machines and guided by artificial intelligence (AI) and machine learning (ML)—play a foundational role in materials research and development. This perspective draws attention to the roles of networks and interfaces—of and betwee...

Solitons in liquid crystals have generated considerable interest. Several hypotheses of varying complexity have been advanced to explain how they emerge, and a consensus has not emerged yet about the underlying forces responsible for their formation or their structure. In this work, we present a minimal model for soliton structures in achiral nemat...

Role of Water Molecules in Enabling Site Hopping and Vehicular Transport Mechanisms in Polynorbornene-based Anion Exchange Membrane Zhongyang Wang, ⸹ Ge Sun ， ⸹ Mrinmay Mandal, ‡ , Paul A. Kohl, ‡, Juan de Pablo, ⸹ Shrayesh N. Patel, ⸹ and Paul F. Nealey ⸹ ‡ School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta,...

A multiscale simulation method is used to calculate the rheological properties of entangled Nylon 6 melts, including the stress relaxation modulus, storage and loss moduli, and the melt viscosity. The three-level multiscale approach includes all-atom, coarse-grained and slip-spring models, each operating at different levels of resolution and encomp...

Many crystallization processes, including biomineralization and ice-freezing, occur in small and curved volumes, where surface curvature can strain the crystal, leading to unusual configurations and defect formation. The role of curvature on crystallization, however, remains poorly understood. Here, we study the crystallization of blue phase (BP) l...