Kathleen J. Stebe

This repository contains the MATLAB simulation code accompanying the paper: "Native propulsion architecture enables bundle-preserving run-reverse-turn motility in the human pathobiont Selenomonas sputigena" by Zhi Ren*, Albane Théry*, Yee-Wai Cheung, Nigel Steager, Zixuan Wen, Michelle Crispin, Julia Radzio, Edward Steager, Li Shen, Yi-Wei Chang, Paulo E. Arratia, Kathleen J Stebe and Hyun Koo. The code simulates the swimming of a flagellated bacterium by coupling an elastic flagellum model (Kirchhoff rod theory) with a rigid cell body and low-Reynolds-number hydrodynamics (regularised Stokeslets and rotlets). It was used to investigate how cell body shape, flagellum implantation site, and motor torque together determine the run-reverse-turn motility characteristic of S. sputigena.

This repository contains the MATLAB simulation code accompanying the paper: "Native propulsion architecture enables bundle-preserving run-reverse-turn motility in the human pathobiont Selenomonas sputigena" by Zhi Ren*, Albane Théry*, Yee-Wai Cheung, Nigel Steager, Zixuan Wen, Michelle Crispin, Julia Radzio, Edward Steager, Li Shen, Yi-Wei Chang, Paulo E. Arratia, Kathleen J Stebe and Hyun Koo. The code simulates the swimming of a flagellated bacterium by coupling an elastic flagellum model (Kirchhoff rod theory) with a rigid cell body and low-Reynolds-number hydrodynamics (regularised Stokeslets and rotlets). It was used to investigate how cell body shape, flagellum implantation site, and motor torque together determine the run-reverse-turn motility characteristic of S. sputigena.

Zn-air batteries (ZABs) are promising energy storage systems, but their performance is often limited by sluggish oxygen reduction reaction (ORR) kinetics and electrolyte flooding at the air cathode. Here, we introduce a tri-continuous carbon-based electrocatalyst (TRICE) derived from bijels-templated carbonization to address these challenges. The resulting nanoporous framework provides interconnected channels for air and electrolyte, enhancing three-phase boundary formation and mass transport. To investigate the role of wettability, two TRICE samples, specifically unmodified and hydrophobic TRICE were evaluated. The hydrophobic TRICE electrodes exhibited strong resistance to electrolyte flooding and maintained stable electrochemical operation during repeated cycling. Despite being fully metal-free, their power densities remained competitive with those of noble-metal and metal-oxide air cathodes. These results demonstrate that wettability tuning in TRICE structures effectively improves flooding tolerance and air cathode stability, offering a promising pathway for durable ZABs.

Nematic liquid crystals can dramatically reconfigure under dynamic forcing, providing exciting opportunities in active matter. Here, we study a hybrid disk colloid rotated by an external field which generates a dynamic companion topological defect. The disk moves faster when the defect sweeps across the disk's face. We identify the defect as a non-singular twist wall, characterize the twist energy landscape, and identify the sweeping motion as a topological instability. As the defect sweeps, it reverses the handedness of twist and lowers the free energy in the fluid in the gap above the disk. Landau-de Gennes modeling shows that the sweeping wall behaves as a propagating director texture: the director field is nearly stationary in the wall frame, while nematogens rotate locally as the wall passes. The nematogens' rotation generates a viscous stress on the surface of the disk that hastens its propulsion. Thus, the defect acts as a flagellum that powers colloid swimming, providing an example of a dissipative topological structure whose dynamics can be harnessed to perform useful work.

Nematic liquid crystals can dramatically reconfigure under dynamic forcing, providing exciting opportunities in active matter. Here, we study a hybrid disk colloid rotated by an external field which generates a dynamic companion topological defect. The disk moves faster when the defect sweeps across the disk's face. We identify the defect as a non-singular twist wall, characterize the twist energy landscape, and identify the sweeping motion as a topological instability. As the defect sweeps, it reverses the handedness of twist and lowers the free energy in the fluid in the gap above the disk. Landau-de Gennes modeling shows that the sweeping wall behaves as a propagating director texture: the director field is nearly stationary in the wall frame, while nematogens rotate locally as the wall passes. The nematogens' rotation generates a viscous stress on the surface of the disk that hastens its propulsion. Thus, the defect acts as a flagellum that powers colloid swimming, providing an example of a dissipative topological structure whose dynamics can be harnessed to perform useful work.

Abstract Herein the components of the nanoscale structure of a bicontinuous interfacially jammed emulsion gel (bijel) were modeled using coarse‐graining (Dissipative Particle Dynamics, DPD). The details of the computational approach are described and validated. The behavior of a macromolecule was then investigated in both continuous phases of the bijel, with emphasis on the computational protocol for obtaining physically sound and verified properties at the macroscale. Sensitivity analysis was performed and a regression model was developed that predicts the macromolecule structure given the DPD model parameters. The case study of messenger ribonucleic acid biopolymer in the system followed, allowing the investigation of its interactions with each of the bijel solvents and comparisons to experiments and theory. Finally, the diffusivity of the mRNA in each phase was computed, providing insights for designing reaction‐separation bijel systems.

Rare earth elements (REEs) are essential for clean energy technologies, yet their separation remains difficult due to their similar ionic radii and oxidation states. Conventional liquid–liquid extraction is energy-intensive and environmentally harmful, which motivates the development of more sustainable alternatives. Silica nanoparticles (SiO 2 NPs), widely used as supports in solid-phase extraction, offer high surface area and tunable surface chemistry. However, the direct use of unmodified SiO 2 NPs as selective REE adsorbents has been largely overlooked. In this study, we investigate the interactions between REEs and unmodified SiO 2 NPs over a range of pH conditions to uncover the underlying mechanisms governing REE adsorption and desorption and explore their use to selectively separate REEs. We identify three distinct pH-dependent interaction regimes: the negligible interaction (near the SiO 2 NPs isoelectric point), electrostatic, and hydrolysis-mediated regimes. In the negligible interaction regime, near the SiO 2 NPs’ isoelectric point, electrostatic interactions are absent, and the REE cations are stable in the bulk phase, resulting in minimal REE uptake. In the electrostatic interaction regime, at intermediate pH, negatively charged SiO 2 NPs interact electrostatically with REE cations, resulting in the REE capture. Finally, in the hydrolysis-mediated regime, at high pH, neutral REE hydroxides deposit on the surfaces of the SiO 2 NP, which serve as nuclei for hydroxide deposition. These interaction modes are reversible, enabling REE capture and release from the SiO 2 NP via pH swing. Within the electrostatic regime, SiO 2 NPs exhibit clear size-dependent selectivity, favoring the adsorption of smaller, more charge-dense REEs over larger REEs. This selectivity persists under competitive conditions in both binary and ternary mixtures. Selectivity is also observed in REE desorption: lowering the pH selectively releases smaller REEs while retaining larger REEs. This work provides fundamental insight into REE–SiO 2 NP interactions and demonstrates a ligand-free, pH-responsive strategy for selective REE capture and separation using silica-based materials.

Zn-air batteries (ZABs) are promising energy storage systems, but their performance is often limited by sluggish oxygen reduction reaction (ORR) kinetics and electrolyte flooding at the air cathode. Here, we introduce a tri-continuous carbon-based electrocatalyst (TRICE) derived from bijels-templated carbonization to address these challenges. The resulting nanoporous framework provides interconnected channels for air and electrolyte, enhancing three-phase boundary formation and mass transport. To investigate the role of wettability, two TRICE samples, specifically unmodified and hydrophobic TRICE were evaluated. The hydrophobic TRICE electrodes exhibited strong resistance to electrolyte flooding and maintained stable electrochemical operation during repeated cycling. Despite being fully metal-free, their power densities remained competitive with those of noble-metal and metal-oxide air cathodes. These results demonstrate that wettability tuning in TRICE structures effectively improves flooding tolerance and air cathode stability, offering a promising pathway for durable ZABs.

Bicontinuous emulsion gels are mixtures with interpenetrating arrangements of two immiscible liquids stabilized with particles. The structures of such gels are readily made into simple macroscale geometries, like sheets and fibers; however, achieving more complex macroscopic structures while maintaining control over microscopic features and morphological bicontinuity remains a challenge. In this study, the ability to fabricate complex 3D structures of bicontinuous emulsion gels using direct ink writing (DIW) is demonstrated. The emulsion precursors are formulated with a mixture of hydrophilic and hydrophobic fumed silica particles; these precursors exhibit shear-thinning and yield stress behavior necessary for DIW. The thixotropic nature of the precursor further promotes the formation of bicontinuous emulsion gels through vaporization-induced phase separation and stabilization through both interfacial jamming and bulk stabilization mechanisms. This fabrication technique enables the creation of functional bicontinuous structures with complex architectures, paving the way for application in biomedical implants, catalytic reactors, and beyond.

Abstract Kinases are enzymes that catalyze phosphorylation and play crucial roles in a myriad of cellular regulatory processes and hemostasis. Patient-specific genetic mutations that aberrantly activate kinases can profoundly influence cancer progression and alter drug efficacy. Predicting the impact of such missense mutations across the human kinome on protein function and cellular signaling is therefore a critical step toward personalized targeted therapy. Here, we present Kinome-AI, an integrative machine learning framework that classifies kinase missense mutations as activating or non-activating. Kinome-AI is trained on a rich multi-modal feature set, including residue-level biochemical changes, sequence embeddings from a protein language model, and structural descriptors of kinase–ATP–substrate complexes derived from molecular modeling. Notably, detailed structural features were available for only 21% of mutants; we leverage these as privileged information during training to impute missing structural data for the remaining ∼79. This strategy boosts performance without requiring structural inputs for new (unseen) mutations. The resulting classifier achieves an area under the receiver operating characteristic curve (AUROC) of 0.85 and a balanced accuracy (BACC) of 0.76 across 1,003 mutations spanning 110 different kinases —substantially outperforming existing bioinformatics and general-purpose variant effect predictors. This work provides a robust approach to quantify sequence–structure– function relationships of cancer-driving kinase mutations, paving the way for improved personalized cancer treatment. Significance Statement In cancer patients, numerous mutations in diverse protein kinases lead to marked differences in disease progression and drug response. Identifying which kinase mutations are activating in individual patients is therefore critical for precision oncology. Drawing inspiration from teacher– student (privileged information) learning, we developed a deep learning framework that integrates structural features from molecular simulations with sequence embeddings from protein language models. This approach enables accurate binary classification of the activation status of kinase mutations. Our study demonstrates how data-driven algorithms can leverage accumulated sequence and structural knowledge of known mutations to predict the effects of novel variants a priori . The model, termed Kinome-AI, shows significant promise for incorporation into personalized cancer therapy decision pipelines.

High Resolution Image Download MS PowerPoint Slide Selective and eco-friendly separation and purification methods for rare earth elements (REEs) are necessary to meet the increasing demand for these valuable metals, which are extensively used in modern electronics and clean energy technologies. Mining feedstocks consist of REE mixtures as stable trivalent cations (Ln 3+ ) that are difficult to separate due to their identical charge and similar size. Lanthanide-binding tags (LBTs), peptide chelates that coordinate Ln 3+ in binding pockets, show promise as selective, high-affinity extractants. We demonstrate that the LBT variant LBTLLA 5–, designed for high selectivity for Tb 3+, is an effective extractant, forming complexes with REEs in solution that subsequently organize into self-assembling structures rich in Ln 3+ . These structures condense into aggregates that can be separated, enabling an efficient, all-aqueous, eco-friendly separation process. The self-assembled structures are studied using dynamic light scattering, ζ-potential measurements, transmission electron microscopy, anomalous small-angle X-ray scattering, inductively coupled plasma optical emission spectroscopy, and ultraviolet–visible absorption spectroscopy, which confirm LBTLLA 5– peptide-REE ion binding and the further assembly of micron-scale structures rich in REEs. Molecular dynamics simulations reveal the interactions promoting aggregation as well as the integrity of the binding pocket upon self-assembly. We find that LBTLLA 5–:Ln 3+ complexes recruit excess cations within the macrostructures, and we demonstrate that aggregation and selective separation can be controlled by manipulating the metal-peptide ratio in solution. Furthermore, we demonstrate separation from equimolar mixtures of REE pairs Tb 3+ -Lu 3+ and Tb 3+ -La 3+, supporting the application of LBT peptides as a platform for the selective separation of REEs.

mRNA, a versatile vaccine and therapeutic platform of growing global importance, is notoriously unstable in aqueous environments due to various chemical degradation pathways, significantly limiting its potential. mRNA is particularly susceptible to hydrolytic degradation, often catalyzed by ubiquitous ribonucleases (RNases). Current stabilization methods rely heavily on cold-chain logistics, which are expensive and challenging to maintain, particularly in resource-limited settings. To address these challenges, ionic liquids and deep eutectic solvents have been explored as non-aqueous solvents for RNA extraction and preservation. However, most previously studied media contain toxic heavy metals or form ternary aqueous two-phase systems that do not protect against RNases. Moreover, model RNAs used in prior studies are simple and not representative of mRNAs. Here, we report the use of a simple, metal-free, hydrophobic deep eutectic solvent (hDES) composed of methyltrioctylammonium chloride and 1-decanol to extract and preserve mRNA at room temperature. Under optimized conditions, we achieve near 100% extraction efficiency into the protective hDES phase that effectively preserves mRNA integrity as assessed by capillary gel electrophoresis and an in vitro assay. We also demonstrate that this hDES system can extract complex mRNA strands of clinically relevant lengths and modifications. Importantly, the hDES phase also shields mRNA from RNase A exposure and suppresses hydrolytic degradation, enabling long-term preservation of mRNAs at room temperature for at least 227 days. Due to its ability to partition, preserve, and release mRNA, hDES composed of fatty alcohols and quaternary ammonium salts could be tailored for use as shelf-stable, non-aqueous precursors to RNA-based therapeutics such as cationic emulsions and lipid nanoparticles. This work potentially informs new strategies for the development of stable mRNA formulations, essential for next-generation vaccines and therapeutics.

mRNA, a versatile vaccine and therapeutic platform of growing global importance, is notoriously unstable in aqueous environments due to various chemical degradation pathways, significantly limiting its potential. mRNA is particularly susceptible to hydrolytic degradation, often catalyzed by ubiquitous ribonucleases (RNases). Current stabilization methods rely heavily on cold-chain logistics, which are expensive and challenging to maintain, particularly in resource-limited settings. To address these challenges, ionic liquids and deep eutectic solvents have been explored as non-aqueous solvents for RNA extraction and preservation. However, most previously studied media contain toxic heavy metals or form ternary aqueous two-phase systems that do not protect against RNases. Moreover, model RNAs used in prior studies are simple and not representative of mRNAs. Here, we report the use of a simple, metal-free, hydrophobic deep eutectic solvent (hDES) composed of methyltrioctylammonium chloride and 1-decanol to extract and preserve mRNA at room temperature. Under optimized conditions, we achieve near 100% extraction efficiency into the protective hDES phase that effectively preserves mRNA integrity as assessed by capillary gel electrophoresis and an in vitro assay. We also demonstrate that this hDES system can extract complex mRNA strands of clinically relevant lengths and modifications. Importantly, the hDES phase also shields mRNA from RNase A exposure and suppresses hydrolytic degradation, enabling long-term preservation of mRNAs at room temperature for at least 227 days. Due to its ability to partition, preserve, and release mRNA, hDES composed of fatty alcohols and quaternary ammonium salts could be tailored for use as shelf-stable, non-aqueous precursors to RNA-based therapeutics such as cationic emulsions and lipid nanoparticles. This work potentially informs new strategies for the development of stable mRNA formulations, essential for next-generation vaccines and therapeutics.

Abstract Lanthanide‐binding tag (LBT) peptides selectively complex lanthanide cations (Ln 3+ ) in their binding pockets and are promising for lanthanide separation. However, designing LBTs that selectively target specific Ln 3+ cations remains a challenge due to limited molecular‐level understanding and control of interactions within the lanthanide‐binding pocket. In this study, we reveal that the N5 asparagine residue acts as a gatekeeper in the binding pocket, resulting in a 100‐fold selectivity for smaller Lu 3+ over larger La 3+ cations. Nuclear magnetic resonance spectroscopy and molecular dynamics simulations show that the N5 residue weakly binds to the larger La 3+ cation, permitting H 2 O molecules inside the pocket. For the smaller Lu 3+ cations, the N5 residue forms an inter‐arm hydrogen bond with the E14 glutamic acid residue, locking the Lu 3+ cation in the pocket and preventing H 2 O infiltration. Mutating the N5 asparagine to a D5 aspartic acid prevents such a hydrogen bond, eliminating the gatekeeping mechanism and precipitously reducing selectivity. The resulting binding affinity to Ln 3+ cations is non‐monotonic but generally increases with cation size. These results suggest a molecular design paradigm: the reduced affinity for larger lanthanides is due to open pocket conformations, while the selectivity of smaller Ln 3+ cations over larger ones is due to the gatekeeping hydrogen bond.

High Resolution Image Download MS PowerPoint Slide A metal-oxide-decorated mesoporous silica (MOMS) chemiresistor platform enables the selective detection of disease-specific volatile organic compounds (VOCs) in exhaled breath. Functionalization of these mesoporous structures with metals and metal oxides facilitates the detection of a wide range of VOCs. To create a sensing architecture with a bicontinuous morphology that optimizes molecular diffusion and electron transport pathways, we employ physically confined polymerization-induced phase separation (PC-PIPS) to fabricate template-directed mesoporous structures with controlled film thicknesses ranging from 1 to 5 μm. Incorporation of metal oxides (SnO 2, ZnO) and noble metals (Pt, Au) forms p–n heterojunctions, enhancing sensitivity and selectivity through modulation of electron depletion layers. The MOMS chemiresistors demonstrate distinct response patterns toward key biomarkers, including hydrogen sulfide (periodontal disease), toluene (gingivitis), formaldehyde (oral carcinoma), and acetone (diabetes mellitus). Response magnitudes range from 1.75–5.66 at 10 ppm to 5.56–12.13 at 100 ppm of H 2 S, with unique electronic signatures, enabling identification of complex gas mixtures. This scalable and versatile fabrication approach establishes MOMS chemiresistors as a promising platform for noninvasive, early-stage disease detection via breath analysis.

Correction for ‘Interfacial rheology of lanthanide binding peptide surfactants at the air–water interface’ by Stephen A. Crane et al. , Soft Matter , 2024, 20 , 9161–9173, https://doi.org/10.1039/D4SM00493K.

Multistable Elastic Pixels (MEPs) are liquid crystal-based unit cells designed to enable nonvolatile reconfiguration of scattering inclusions. We experimentally demonstrate MEPs and build metasurfaces composed of MEP arrays to achieve tunable diffraction of visible wavelengths.

Rare earth elements (REEs) are critical materials to modern technologies. They are obtained by selective separation from mining feedstocks consisting of mixtures of their trivalent cation. We are developing an all-aqueous, bioinspired, interfacial separation using peptides as amphiphilic molecular extractants. Lanthanide binding tags (LBTs) are amphiphilic peptide sequences based on the EF-hand metal binding loops of calcium-binding proteins which complex selectively REEs. We study LBTs optimized for coordination to Tb 3+ using luminescence spectroscopy, surface tensiometry, X-ray reflectivity, and X-ray fluorescence near total reflection, and find that these LBTs capture Tb 3+ in bulk and adsorb the complex to the interface. Molecular dynamics show that the binding pocket remains intact upon adsorption. We find that, if the net negative charge on the peptide results in a negatively charged complex, excess cations are recruited to the interface by nonselective Coulombic interactions that compromise selective REE capture. If, however, the net negative charge on the peptide is −3, resulting in a neutral complex, a 1:1 surface ratio of cation to peptide is achieved. Surface adsorption of the neutral peptide complexes from an equimolar mixture of Tb 3+ and La 3+ demonstrates a switchable platform dictated by bulk and interfacial effects. The adsorption layer becomes enriched in the favored Tb 3+ when the bulk peptide is saturated, but selective to La 3+ for undersaturation due to a higher surface activity of the La 3+ complex.

Fluorescent unnatural amino acids give biochemists, biophysicists, and bioengineers new ways to probe the properties of proteins and peptides. Here, the synthesis of acridon-2-ylalanine (Acd) is optimized for large-scale production to enable ribosomal incorporation through genetic code expansion (GCE), and fluorenylmethoxycarbonyl (Fmoc)-protected Acd is prepared for solid-phase peptide synthesis (SPPS). We demonstrate the utility of Acd in several applications: first, Acd quenching by Tyr is used in the design of fluorescent protease sensors made by SPPS. Second, we demonstrate Acd incorporation into a lanthanide-binding peptide that is generated either by GCE or by SPPS and demonstrate the utility of Acd for sensitizing the emission of Eu 3+ . Finally, Acd is inserted into the intrinsically disordered protein, α-synuclein, using GCE and used to study ion binding and aggregation.

HYPOTHESIS Lanthanide Binding Tag (LBT) peptides that coordinate selectively with lanthanide ions can be used to replace the energy intensive processes used for the separation of rare earth elements (REEs). These surface-active biomolecules, once selectively complexed with the trivalent REE cations, can adsorb to air/aqueous interfaces of bubbles for foam-based REEs recovery. Glutaraldehyde, an organic compound that is a homobifunctional crosslinker for proteins and peptides, can be used to enhance the adsorption and interfacial stabilization of lanthanide-bound peptides films. EXPERIMENTS The stability of the interfacial cross-linked films was tested by measuring their dilational and shear surface rheological properties. Surface activity of the adsorbed species was analyzed using pendant drop tensiometry, while surface density and molecular arrangement were determined using x-ray reflectivity and x-ray fluorescence near total reflection. FINDINGS Glutaraldehyde cross-linked REE-peptide complexes enhance the adsorption of lanthanides to air-water interfaces, resulting in thicker interfacial structures. Subsequently, these thicker layers enhance the dilational and shear interfacial rheological properties. The interfacial film stabilization and REEs extraction promoted by the cross-linker presented in this work provides an approach to integrate glutaraldehyde as a substitute of common foam stabilizers such as polymers, surfactants, and particles to optimize the recovery of REEs when using biomolecules as extractants.

Abstract Bi‐continuous jammed emulsion (bijel) membrane reactors, integrating simultaneous reaction and separation, offer a promising avenue for enhancing membrane reactor processes. In this study, we present a comprehensive macroscopic‐scale physicochemical model for tubular bijel membrane reactors and a numerical solution strategy for solving the governing partial differential equations. The model captures the co‐continuous network of two immiscible phases stabilized by nanoparticles at the liquid–liquid interface. We present the derivation of model equations and an efficient numerical solution strategy. The model is validated with experimental results from a conventional enzymatic biphasic membrane reactor for oleuropein hydrolysis, already reported in the literature. Simulation results indicate accurate prediction of reactor behavior, highlighting the potential superiority of bijel membrane reactors over current technologies. This research contributes a valuable tool for scale‐up, design, and optimization of bijel membrane reactors, filling a critical gap in this emerging field.

Abstract Microneedle (MN) technology offers a powerful approach for transdermal delivery enabling painless injection and facilitating self‐administration without the need for professional assistance. However, the weak mechanical strength of MNs can lead to inefficient drug delivery and serious skin irritation if the MNs fracture during administration and leave fragments under the skin. Thus, the MNs need to be mechanically robust to avoid fracture during penetration through the skin while maintaining efficient drug delivery. Herein, the polymer‐based MNs with layer‐by‐layer (LbL) films of silica (SiO 2 ) nanoparticles (NPs) and a polycation (poly(diallyldimethylammonium chloride) (PDADMAC)) followed by hydrothermal calcination are reinforced. The mechanical strength of the MNs is significantly improved after LbL assembly and shows lower threshold pressure to penetrate skins. Moreover, their drug loading and releasing properties are significantly enhanced due to an increase in the surface area and interfacial interaction. These SiO 2 nanoparticle‐containing LbL thin films have great potential for the surface modification of 3D microstructured devices such as MNs, as evidenced by their enhanced mechanical strength and drug coating efficiency that result in a promising MN drug delivery model.

We are developing an all-aqueous, bio-inspired approach using peptides as surfactants that selectively bind rare earth element (REE) cations and adsorb at the air/water interface to enable green capture and separation. REEs are essential components in modern electronic devices and clean energy technologies which must be separated from feedstocks of aqueous mixtures. Their selective capture is particularly challenging owing to their similarity in size and charge. Lanthanide binding tags (LBTs) are amphiphilic peptide sequences based on the binding loop in the evolutionarily conserved EF-hand metal binding motif. We study LBTs optimized for coordination to Tb^{3+} using a suite of experimental methods including luminescence spectroscopy, surface tensiometry, x-ray reflectivity and x-ray fluorescence near total reflection, and find that these LBTs capture Tb^{3+} in bulk and adsorb at the interface. Molecular dynamics show that the binding pocket remains intact upon adsorption. We find that, if the net negative charge on the peptide results in a negatively charged complex, excess cations are recruited to the interface by non-selective Coulombic interactions that compromise selective REE capture. If, however, the net negative charge on the binding loop is -3, resulting in a neutral complex, a 1:1 surface ratio of cation to peptide is achieved. We demonstrate selective interfacial extraction from an equimolar mixture of Tb^{3+} and La^{3+}, validating an LBT-mediated interfacial separation of REEs.

We are developing an all-aqueous, bio-inspired approach using peptides as surfactants that selectively bind rare earth element (REE) cations and adsorb at the air/water interface to enable green capture and separation. REEs are essential components in modern electronic devices and clean energy technologies which must be separated from feedstocks of aqueous mixtures. Their selective capture is particularly challenging owing to their similarity in size and charge. Lanthanide binding tags (LBTs) are amphiphilic peptide sequences based on the binding loop in the evolutionarily conserved EF-hand metal binding motif. We study LBTs optimized for coordination to Tb$^{3+}$ using a suite of experimental methods including luminescence spectroscopy, surface tensiometry, x-ray reflectivity and x-ray fluorescence near total reflection, and find that these LBTs capture Tb$^{3+}$ in bulk and adsorb at the interface. Molecular dynamics show that the binding pocket remains intact upon adsorption. We find that, if the net negative charge on the peptide results in a negatively charged complex, excess cations are recruited to the interface by non-selective Coulombic interactions that compromise selective REE capture. If, however, the net negative charge on the binding loop is -3, resulting in a neutral complex, a 1:1 surface ratio of cation to peptide is achieved. We demonstrate selective interfacial extraction from an equimolar mixture of Tb$^{3+}$ and La$^{3+}$, validating an LBT-mediated interfacial separation of REEs.

Peptide surfactants (PEPS) are studied to capture and retain rare earth elements (REEs) at air-water interfaces to enable REE separations. Peptide sequences, designed to selectively bind REEs, depend crucially on the position of ligands within their binding loop domain. These ligands form a coordination sphere that wraps and retains the cation. We study variants of lanthanide binding tags (LBTs) designed to complex strongly with Tb$^{3+}$. The peptide LBT$^{5-}$ (with net charge -5) is known to bind Tb$^{3+}$ and adsorb with more REE cations than peptide molecules, suggesting that undesired non-specific Coulombic interactions occur. Rheological characterization of interfaces of LBT$^{5-}$ and Tb$^{3+}$ solutions reveal the formation of an interfacial gel. To probe whether this gelation reflects chelation among intact adsorbed LBT$^{5-}$:Tb$^{3+}$ complexes or destruction of the binding loop, we study a variant, LBT$^{3-}$, designed to form net neutral LBT$^{3-}$:Tb$^{3+}$ complexes. Solutions of LBT$^{3-}$ and Tb$^{3+}$ form purely viscous layers in the presence of excess Tb$^{3+}$, indicating that each peptide binds a single REE in an intact coordination sphere. We introduce the variant RR-LBT$^{3-}$ with net charge -3 and anionic ligands outside of the coordination sphere. We find that such exposed ligands promote interfacial gelation. Thus, a nuanced requirement for interfacial selectivity of PEPS is proposed: that anionic ligands outside of the coordination sphere must be avoided to prevent the non-selective recruitment of REE cations. This view is supported by simulation, including interfacial molecular dynamics simulations, and interfacial metadynamics simulations of the free energy landscape of the binding loop conformational space.

Understanding the dynamics of polymers in confined environments is pivotal for diverse applications ranging from polymer upcycling to bioseparations. In this study, we develop an entropic barrier model using self-consistent field theory that considers the effect of attractive surface interactions, solvation, and confinement on polymer kinetics. In this model, we consider the translocation of a polymer from one cavity into a second cavity through a single-segment-width nanopore. We find that, for a polymer in a good solvent (i.e., excluded volume, u0 > 0), there is a nonmonotonic dependence of mean translocation time (τ) on surface interaction strength, ɛ. At low ɛ, excluded volume interactions lead to an energetic penalty and longer translocation times. As ɛ increases, the surface interactions counteract the energetic penalty imposed by excluded volume and the polymer translocates faster through the nanopore. However, as ɛ continues to increase, an adsorption transition occurs, which leads to significantly slower kinetics due to the penalty of desorption from the first cavity. The ɛ at which this adsorption transition occurs is a function of the excluded volume, with higher u0 leading to an adsorption transition at higher ɛ. Finally, we consider the effect of translocation across different size cavities. We find that the kinetics for translocation into a smaller cavity speeds up while translocation to a larger cavity slows down with increasing ɛ due to higher surface contact under stronger confinement.

The behavior of fluid interfaces far from equilibrium plays central roles in nature and in industry. Active swimmers trapped at interfaces can alter transport at fluid boundaries with far reaching implications. Swimmers can become trapped at interfaces in diverse configurations and swim persistently in these surface adhered states. The self-propelled motion of bacteria makes them ideal model swimmers to understand such effects. We have recently characterized the swimming of interfacially-trapped Pseudomonas aeruginosa PA01 moving in pusher mode. The swimmers adsorb at the interface with pinned contact lines, which fix the angle of the cell body at the interface and constrain their motion. Thus, most interfacially-trapped bacteria swim along circular paths. Fluid interfaces form incompressible two-dimensional layers, altering leading order interfacial flows generated by the swimmers from those in bulk. In our previous work, we have visualized the interfacial flow around a pusher bacterium and described the flow field using two dipolar hydrodynamic modes; one stresslet mode whose symmetries differ from those in bulk, and another bulk mode unique to incompressible fluid interfaces. Based on this understanding, swimmers-induced tracer displacements and swimmer-swimmer pair interactions are explored using analysis and experiment. The settings in which multiple interfacial swimmers with circular motion can significantly enhance interfacial transport of tracers or promotemixing of other swimmers on the interface are identified through simulations and compared to experiment. This study identifies important factors of general interest regarding swimmers on or near fluid boundaries, and in the design of biomimetic swimmers to enhance transport at interfaces

PA01 moving in pusher mode. The swimmers adsorb at the interface with pinned contact lines, which fix the angle of the cell body at the interface and constrain their motion. Thus, swimmers become trapped at interfaces in diverse configurations and swim persistently in these surface adhered states. We observe that most interfacially trapped bacteria swim along circular paths. Fluid interfaces also typically form incompressible two-dimensional layers. These effects influence the flow generated by the swimmers. In our previous work, we have visualized the interfacial flow around a pusher bacterium and described the flow field using two dipolar hydrodynamic modes; one stresslet mode whose symmetries differ from those in bulk, and another bulk mode unique to incompressible fluid interfaces. Based on this understanding, swimmer-induced tracer displacements and swimmer-swimmer pair interactions are explored using analysis and experiment. The settings in which multiple interfacial swimmers with circular motion can significantly enhance interfacial transport of tracers or promote mixing of other swimmers on the interface are identified through simulations and compared to experiment. This study shows the importance of biomixing by swimmers at fluid interfaces and identifies important factors in the design of biomimetic active colloids to enhance interfacial transport.

with net charge -3 and anionic ligands outside of the coordination sphere. We find that such exposed ligands promote interfacial gelation. Thus, a nuanced requirement for interfacial selectivity of PEPS is proposed: that anionic ligands outside of the coordination sphere must be avoided to prevent the non-selective recruitment of REE cations. This view is supported by simulation, including interfacial molecular dynamics simulations, and interfacial metadynamics simulations of the free energy landscape of the binding loop conformational space.

Motile bacteria play essential roles in biology that rely on their dynamic behaviours, including their ability to navigate, interact and self-organize. However, bacteria dynamics on fluid interfaces are not well understood. Swimmers adsorbed on fluid interfaces remain highly motile, and fluid interfaces are highly non-ideal domains that alter swimming behaviour. To understand these effects, we study flow fields generated by Pseudomonas aeruginosa PA01 in the pusher mode. Analysis of correlated displacements of tracers and bacteria reveals dipolar flow fields with unexpected asymmetries that differ significantly from their counterparts in bulk fluids. We decompose the flow field into fundamental hydrodynamic modes for swimmers in incompressible fluid interfaces. We find an expected force-doublet mode corresponding to propulsion and drag at the interface plane, and a second dipolar mode, associated with forces exerted by the flagellum on the cell body in the aqueous phase that are countered by Marangoni stresses in the interface. The balance of these modes depends on the bacteria's trapped interfacial configurations. Understanding these flows is broadly important in nature and in the design of biomimetic swimmers.

Passive daytime radiative cooling (PDRC) relies on simultaneous reflection of sunlight and radiation toward cold outer space. Current designs of PDRC coatings have demonstrated potential as eco-friendly alternatives to traditional electrical air conditioning (AC). While many features of PDRC have been individually optimized in different studies, for practical impact, it is essential for a system to demonstrate excellence in all essential aspects, like the materials that nature has created. We propose a bioinspired PDRC structure templated by bicontinuous interfacially jammed emulsion gels (bijels) that possesses excellent cooling, thinness, tunability, scalability, and mechanical robustness. The unique bicontinuous disordered structure captures key features of Cyphochilus beetle scales, enabling a thin (130 μm) bijel PDRC coating to achieve high solar reflectance (≳0.97) and high longwave-infrared (LWIR) emissivity (≳0.93), resulting in a subambient temperature drop of ∼5.6 °C under direct sunlight. We further demonstrate switchable cooling inspired by the exoskeleton of the Hercules beetle and mechanical robustness in analogy to spongy bone structures.

This perspective article urges the academic community to adopt a coordinated approach uniting dental medicine and engineering to support research, training, and entrepreneurship to address the unmet needs and spur oral health care innovations. We describe a new interschool institute that brings together dentists, scientists and engineers, resources, and a training program dedicated for affordable oral health care innovations, which may serve as a template for dental medicine-engineering integration.

Computer-aided molecular design and protein engineering emerge as promising and active subjects in bioengineering and biotechnological applications. On one hand, due to the advancing computing power in the past decade, modeling toolkits and force fields have been put to use for accurate multiscale modeling of biomolecules including lipid, protein, carbohydrate, and nucleic acids. On the other hand, machine learning emerges as a revolutionary data analysis tool that promises to leverage physicochemical properties and structural information obtained from modeling in order to build quantitative protein structure-function relationships. We review recent computational works that utilize state-of-the-art computational methods to engineer peptides and proteins for various emerging biomedical, antimicrobial, and antifreeze applications. We also discuss challenges and possible future directions toward developing a roadmap for efficient biomolecular design and engineering.

a two-step solvent removal process. The resulting bijels are characterized quantitatively to verify the uniformity and sub-micrometer scale of the domains. Moreover, these bijels have structures that resemble the microstructure of the scale of the white beetle Cyphochilus. We find that such bijel films with relatively small thicknesses (<150 μm) exhibit strong solar reflectance as well as high brightness and whiteness in the visible range. Considering their scalability in manufacturing, we believe that VIPS-STRIPS bijels have great potential in large-scale applications including passive cooling, solar cells, and light emitting diodes (LEDs).