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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.

In reticular chemistry, molecular building blocks are designed to create crystalline open frameworks. A key principle of reticular chemistry is that the most symmetrical networks are the likely outcomes of reactions, particularly when highly symmetrical building blocks are involved. The strategy of synthesizing low-dimensional networks aims to reduce explicitly the symmetry of the molecular building blocks. Here we report the spontaneous formation of hydrogen-bonded fibrous structures from trigonal prismatic building blocks, which were designed to form three-dimensional crystalline networks on account of their highly symmetrical structures. Utilizing different microscopic and spectroscopic techniques, we identify the structures at the early stages of the assembly process in order to and understand the growth mechanism. The symmetrical molecular building blocks are incorporated preferentially in the longitudinal direction, giving rise to anisotropic hydrogen-bonded porous organic nanotubes. Entropy-driven anisotropic growth provides micrometer-scale unidirectional nanotubes with high porosity. By combining experimental evidence and theoretical modeling, we have obtained a deep understanding of the nucleation and growth processes. Our findings offer fundamental insight into the molecular design of tubular structures. The nanotubes evolve further in the transverse directions to provide extended higher-order fibrous structures [nano- and microfibers], ultimately leading to large-scale interconnected hydrogen-bonded fiber-like structures with twists and turns. Our work provides fundamental understanding and paves the way for innovative molecular designs in low-dimensional networks.

Peptide amphiphiles (PAs) self-assemble into cylindrical nanofibers with applications in protein purification, tissue engineering, and regenerative medicine. For these applications, functionalized PAs are often co-assembled with oppositely charged filler PAs. Finding the conditions at which these fibers are homogeneously mixed or segregated is crucial for the required application. We co-assemble negative C 12 VVEE fillers and positive C 12 VVKK-OEG 4 -Z33 ligands, which are important for antibody purifications. Our results show that the ligands tend to cluster and locally segregate in the fiber surfaces. The Z33s are overall neutral and form large aggregates in bulk solution due to short range attractions. However, full segregation of the C 12 VVKK-OEG 4 -Z33 is not observed in the cylindrical surface due to the electrostatic penalty of forming large domains of similarly charged molecules. This is commensurate with previous theoretical predictions, showing that the competition between short-range attractive interactions and long-range electrostatic repulsions leads to pattern formation in cylindrical surfaces. This work offers valuable insight into the design of functionalized nanofibers for various biomedical and chemical applications.

Elicitation of effective antitumor immunity following cancer vaccination requires the selective activation of distinct effector cell populations and pathways. Here we report a therapeutic approach for generating potent T cell responses using a modular vaccination platform technology capable of inducing directed immune activation, termed the Protein-like Polymer (PLP). PLPs demonstrate increased proteolytic resistance, high uptake by antigen-presenting cells (APCs), and enhanced payload-specific T cell responses. Key design parameters, namely payload linkage chemistry, degree of polymerization, and side chain composition, were varied to optimize vaccine formulations. Linking antigens to the polymer backbone using an intracellularly cleaved disulfide bond copolymerized with a diluent amount of oligo(ethylene glycol) (OEG) resulted in the highest payload-specific potentiation of antigen immunogenicity, enhancing dendritic cell (DC) activation and antigen-specific T cell responses. Vaccination with PLPs carrying either gp100, E7, or adpgk peptides significantly increased the survival of mice inoculated with B16F10, TC-1, or MC38 tumors, respectively, without the need for adjuvants. B16F10-bearing mice immunized with gp100-carrying PLPs showed increased antitumor CD8 + T cell immunity, suppressed tumor growth, and treatment synergy when paired with two distinct stimulator of interferon gene (STING) agonists. In a human papillomavirus-associated TC-1 model, combination therapy with PLP and 2'3'-cGAMP resulted in 40% of mice completely eliminating implanted tumors while also displaying curative protection from rechallenge, consistent with conferment of lasting immunological memory. Finally, PLPs can be stored long-term in a lyophilized state and are highly tunable, underscoring the unique properties of the platform for use as generalizable cancer vaccines.

Recent findings suggest that shell protein distribution and the morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. We explore how the morphology and component patterning are coupled through the competition of mean and gaussian bending energies in multicomponent elastic shells that form three-component irregular polyhedra. We observe two softer components with lower bending rigidities allocated on the edges and vertices while the harder component occupies the faces. When subjected to a nonzero interfacial line tension, the two softer components further separate and pattern into subdomains that are mediated by the gaussian curvature. We find that this degree of fractionation is maximized when there is a weaker line tension and when the ratio of bending rigidities between the two softer domains ≈2. Our results reveal a patterning mechanism in multicomponent shells that can capture the observed morphologies of bacterial microcompartments, and moreover, can be realized in synthetic vesicles.

Successful and selective inhibition of the cytosolic protein-protein interaction (PPI) between nuclear factor erythroid 2-related factor 2 (Nrf2) and Kelch-like ECH-associating protein 1 (Keap1) can enhance the antioxidant response, with the potential for a therapeutic effect in a range of settings including in neurodegenerative disease (ND). Small molecule inhibitors have been developed, yet many have off-target effects, or are otherwise limited by poor cellular permeability. Peptide-based strategies have also been attempted to enhance specificity, yet face challenges due to susceptibility to degradation and lack of cellular penetration. Herein, these barriers are overcome utilizing a polymer-based proteomimetics. The protein-like polymer (PLP) consists of a synthetic, lipophilic polymer backbone displaying water soluble Keap1-binding peptides on each monomer unit forming a brush polymer architecture. The PLPs are capable of engaging Keap1 and displacing the cellular protective transcription factor Nrf2, which then translocates to the nucleus, activating the antioxidant response element (ARE). PLPs exhibit increased Keap1 binding affinity by several orders of magnitude compared to free peptides, maintain serum stability, are cell-penetrant, and selectively activate the ARE pathway in cells, including in primary cortical neuronal cultures. Keap1/Nrf2-inhibitory PLPs have the potential to impact the treatment of disease states associated with dysregulation of oxidative stress, such as NDs., (© 2024 The Authors. Advanced Materials published by Wiley‐VCH GmbH.)

Dielectric interfaces are crucial to the behavior of charged membranes, from graphene to synthetic and biological lipid bilayers. Understanding electrolyte behavior near these interfaces remains a challenge, especially in the case of rough dielectric surfaces. A lack of analytical solutions consigns this problem to numerical treatments. We report an analytic method for determining electrostatic potentials near curved dielectric membranes in a two-dimensional periodic "slab" geometry using a periodic summation of Green's functions. This method is amenable to simulating arbitrary groups of charges near surfaces with two-dimensional deformations. We concentrate on one-dimensional undulations. We show that increasing membrane undulation increases the asymmetry of interfacial charge distributions due to preferential ionic repulsion from troughs. In the limit of thick membranes, we recover results mimicking those for electrolytes near a single interface. Our work demonstrates that rough surfaces generate charge patterns in electrolytes of charged molecules or mixed-valence ions., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The interaction between passive and active/driven particles has introduced a new way to control colloidal suspension properties from particle aggregation to crystallization. Here, we focus on the hydrodynamic interaction between a single rotational driven particle and a suspension of passive particles near the floor. Using experiments and Stokesian dynamics simulations that account for near-field lubrication, we demonstrate that the flow induced by the driven particle can induce long-ranged rearrangement in a passive suspension. We observe an accumulation of passive particles in front of the driven particle and a depletion of passive particles behind the driven particle. This restructuring generates a pattern that can span a range more than 10 times the driven particles radius. We further show that size scale of the pattern is only a function of the particles height above the floor.

Electrostatic forces in solutions are highly relevant to a variety of fields, ranging from electrochemical energy storage to biology. However, their manifestation in concentrated electrolytes is not fully understood, as exemplified by counterintuitive observations of colloidal stability and long-ranged repulsions in molten salts. Highly charged biomolecules, such as DNA, respond sensitively to ions in dilute solutions. Here, we use non-base-pairing DNA-coated nanoparticles (DNA-NP) to analyze electrostatic interactions in concentrated salt solutions. Despite their negative charge, these conjugates form colloidal crystals in solutions of sufficient divalent cation concentration. We utilize small-angle X-ray scattering (SAXS) to study such DNA-NP assemblies across the full accessible concentration ranges of aqueous CaCl 2 , MgCl 2 , and SrCl 2 solutions. SAXS shows that the crystallinity and phases of the assembled structures vary with cation type. For all tested salts, the aggregates contract with added ions at low salinities and then begin expanding above a cation-dependent threshold salt concentration. Wide-angle X-ray scattering (WAXS) reveals enhanced positional correlations between ions in the solution at high salt concentrations. Complementary molecular dynamics simulations show that these ion-ion interactions reduce the favorability of dense ion configurations within the DNA brushes below that of the bulk solution. Measurements in solutions with lowered permittivity demonstrate a simultaneous increase in ion coupling and decrease in the concentration at which aggregate expansion begins, thus confirming the connection between these phenomena. Our work demonstrates that interactions between charged objects continue to evolve considerably into the high-concentration regime, where classical theories project electrostatics to be of negligible consequence., Competing Interests: Competing interests statement:The authors F.J.-Á. and M.O.d.l.C. participated in a Faraday Discussion meeting on iontronics in June 2023, at Edinburgh, UK, which the reviewer S.P. and her group also attended. F.J.-Á. presented an article [Felipe Jiménez-Ángeles, Ali Ehlen, and Monica Olvera de la Cruz, Faraday Discuss. 246, 576–591 (2023)], and a member of the group of S.P. also presented an article in this meeting [Y. K. Catherine Fung and Susan Perkin, Faraday Discuss. 246, 370–386 (2023)]. The questions and answers on the presentations during all the different session in the meting are also published in Faraday Discuss. 2023, Vol. 246, under manuscripts with titles such as “Ionotronic coupling: general discussion” and “Iontronics under confinement: general discussion”, where F.J.-Á. participated on pages 592–617 and 157–178 and M.O.d.l.C. on pages 592–617, 466–486, and 322–355. These manuscripts are only reports on the discussions among the participants concerning articles presented during the meeting; For example, F.J.-Á. answered a short question by S.P. (in addition to 5 more questions by others) published on Vol. 246, pages 592–617, and M.O.d.l.C. asked a question to Christian Holm in the same session. Both F.J.-Á. and M.O.d.l.C. declare no conflict of interest with S.P.

Colloidal crystals have applications in water treatments, including water purification and desalination technologies. It is, therefore, important to understand the interactions between colloids as a function of electrolyte concentration. We study the assembly of DNA-grafted gold nanoparticles immersed in concentrated electrolyte solutions. Increasing the concentration of divalent Ca 2+ ions leads to the condensation of nanoparticles into face-centered-cubic (FCC) crystals at low electrolyte concentrations. As the electrolyte concentration increases, the system undergoes a phase change to body-centered-cubic (BCC) crystals. This phase change occurs as the interparticle distance decreases. Molecular dynamics analysis suggests that the interparticle interactions change from strongly repulsive to short-range attractive as the divalent-electrolyte concentration increases. A thermodynamic analysis suggests that increasing the salt concentration leads to significant dehydration of the nanoparticle environment. We conjecture that the intercolloid attractive interactions and dehydrated states favour the BCC structure. Our results gain insight into salting out of colloids such as proteins as the concentration of salt increases in the solution.

Charged colloidal particles propel themselves through asymmetric fluxes of chemically generated ions on their surface. We show that asymmetry in the surface charge distribution provides an additional mode of self-propulsion at the nanoscale for chemically active particles that produce ionic species. Particles of sizes smaller than or comparable to the Debye length achieve directed self-propulsion through surface charge asymmetry even when ionic flux is uniform over its surface. Janus nanoparticles endowed with both surface charge and ionic flux asymmetries result in enhanced propulsion speeds of the order of μm/s or higher. Our work suggests an alternative avenue for specifying surface properties that optimize self-propulsion in ionic media.

Layered materials that perform mixed electron and ion transport are promising for energy harvesting, water desalination, and bioinspired functionalities. These functionalities depend on the interaction between ionic and electronic charges on the surface of materials. Here we investigate ion transport by an external electric field in an electrolyte solution confined in slit-like channels formed by two surfaces separated by distances that fit only a few water layers. We study different electrolyte solutions containing monovalent, divalent, and trivalent cations, and we consider walls made of non-polarizable surfaces and conductors. We show that considering the surface polarization of the confining surfaces can result in a significant increase in ionic conduction. The ionic conductivity is increased because the conductors' screening of electrostatic interactions enhances ionic correlations, leading to faster collective transport within the slit. While important, the change in water's dielectric constant in confinement is not enough to explain the enhancement of ion transport in polarizable slit-like channels.

Soft swimming microrobots have attracted considerable attention due to their potential applications in diverse fields ranging from biomedicines to environmental remediation. The locomotion control is of importance to the research of micromachines and microrobots. Inspired by the motility strategies of living microorganisms, such as flagella, cilia, and euglenoids, we focus on propulsion mechanisms with a design of Janus magnetoelastic crystalline membrane microswimmers actuated by time-varying magnetic fields. Such a Janus swimmer consists of a ferromagnetic cap completed by a magnetoelastic membrane body, where superparamagnetic particles are uniformly distributed on the surface. Under the influence of external magnetic fields, the swimmer undergoes complex shape transitions due to the interplay between the magnetic dipole-dipole interactions, the elasticity of the magnetoelastic membranes, and also the hydrodynamics of surrounding fluids. We show that those shape changes are nonreciprocal, which can generate locomotion such that the propulsion speed can be optimized by tailoring the membrane elastic properties. Besides, we also demonstrate that the Janus swimmer can be magnetically guided in a spiral trajectory. With such adequate control of locomotion in both speed and direction via non-invasive magnetic fields, this study provides another promising candidate design for the future development of microswimmers.

An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Overall, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.

We investigate the usage of polyelectrolyte complex materials for water remediation purposes, specifically their ability to remove nanoplastics from water, on which there is currently little to no prior research. We demonstrate that oppositely charged random copolymers are effective at quantitatively removing nanoplastic contamination from aqueous solution. The mechanisms underlying this remediation ability are explored through computational simulations, with corroborating quartz crystal microbalance adsorption experiments. We find that hydrophobic nanostructures and interactions likely play an important role.

Nanoparticles with highly asymmetric sizes and charges that self-assemble into crystals via electrostatics may exhibit behaviors reminiscent of those of metals or superionic materials. Here, we use coarse-grained molecular simulations with underdamped Langevin dynamics to explore how a binary charged colloidal crystal reacts to an external electric field. As the field strength increases, we find transitions from insulator (ionic state), to superionic (conductive state), to laning, to complete melting (liquid state). In the superionic state, the resistivity decreases with increasing temperature, which is contrary to metals, yet the increment decreases as the electric field becomes stronger. Additionally, we verify that the dissipation of the system and the fluctuation of charge currents obey recently developed thermodynamic uncertainty relation. Our results describe charge transport mechanisms in colloidal superionic conductors.

We study size- and charge-asymmetric oppositely charged colloids driven by an external electric field. The large particles are connected by harmonic springs, forming a hexagonal-lattice network, while the small particles are free of bonds and exhibit fluidlike motion. We show that this model exhibits a cluster formation pattern when the external driving force exceeds a critical value. The clustering is accompanied with stable wave packets in vibrational motions of the large particles.

The dynamic motion produced by precessing magnetic fields can drive matter into far-from-equilibrium states. We predict 1D periodic ordering in systems of precessing rods when magnetic interactions between rods remain insignificant. The precession angle of the rods is completely determined by the field's precession angle and the ratio of the field's precession frequency and the characteristic response frequency of the rods. We develop a molecular dynamics model that explicitly calculates magnetic interactions between particles, and we also simulate rods in the limit of a strong and fast precessing magnetic field where inter-rod magnetic interactions are negligible, using a purely steric model. Our simulations show how steric interactions drive the rods from a positionally disordered phase (nematic) to a layered (smectic) phase. As the rod precession angle increases, the nematic-smectic transition density significantly decreases. The minimization of unfavorable steric interactions also induces phase separation in binary mixtures of rods of different lengths. This effect is general to any force that produces precession in elongated particles. This work will advance the understanding and control of out-of-equilibrium soft matter systems.

Understanding electrostatic interactions among dielectric bodies in the atmosphere and aerosols is central to controlling their aggregation. Polarization effects, which are frequently ignored, are crucial to determine interactions when geometrical anisotropies are present due to surface-induced charge segregation. Here, we adopt a direct integral formulation that accounts for the problem of charged dielectric bodies immersed in a continuum media to explore particle aggregation via geometrical tuning. We show that by breaking the structural symmetry and modifying the close-contact surface between particles of equal charge, it is possible to obtain attractive regimes at short and long distances. We evaluate the electrostatic forces and energy of a set of dimers and trimers composed of spheres, oblates, and prolates in a vacuum, where no counter-ions are present, to construct a phase diagram with the conditions required to form stable aggregates as a function of the geometrical anisotropy. We found that it is possible to direct the aggregation (or dispersion) of two and three positive dielectric particles by adjusting their geometry and controlling the contact surface among them. Our results give insight into a way to control the aggregation of dielectric systems and offer a prospect for directing the assembly of complex particle structures.

Size-asymmetric binary charged colloidal solutions can assemble into ionic colloidal crystals. These are often stabilized by ionic-type bonding, where the components with smaller size and charge sit at fixed points within the lattice of large particles. Here, we study the transition termed ionic to metallic bonding transition, by which the lattice of the smaller component melts while the crystal of the large particles is preserved, as in metallic bonding. We simulate a charged colloidal crystal in equilibrium with a solution containing small colloidal particles and counterions using the Coulomb interaction between the finite-size components. We find ionic to metallic first-order transitions by increasing either the temperature or the concentration of the small particles in the solution. The transition is accompanied by a lattice expansion and increased absorption of small particles into the crystal. We compute the free energies of the ionic and metallic states using the Madelung constant and Wigner-Seitz cell approaches, respectively, combined with the quasi-harmonic lattice model. The calculation reproduces the simulated transition and reveals that the enthalpic gain is more pronounced than the entropic gain in the transition from ionic to metallic bonding when material is exchanged with the solution.

How molecular chirality manifests at the nano- to macroscale has been a scientific puzzle since Louis Pasteur discovered biochirality. Chiral molecules assemble into meso-shapes such as twisted and helical ribbons, helicoidal scrolls (cochleates), or möbius strips (closed twisted ribbons). Here we analyze self-assembly for a series of amphiphiles, C n -K, consisting of an ionizable amino acid [lysine (K)] coupled to alkyl tails with n = 12, 14, or 16 carbons. This simple system allows us to probe the effects of electrostatic and van der Waals interactions in chiral assemblies. Small/wide-angle X-ray scattering (SAXS/WAXS) reveals that at low pH, where the headgroups are ionized (+1), C 16 -K forms high aspect ratio, planar crystalline bilayers. Molecular dynamics (MD) simulations reveal that tilted tails of the bilayer leaflets are interdigitated. SAXS shows that, with increasing salt concentration, C 16 -K molecules assemble into cochleates, whereas at elevated pH (reduced degree of ionization), helices are observed for all C n -K assemblies. The shape selection between helices and scrolls is explained by a membrane energetics model. The nano- to meso-scale structure of the chiral assemblies can be continuously controlled by solution ionic conditions. Overall, our study represents a step toward an electrostatics-based approach for shape selection and nanoscale structure control in chiral assemblies., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

Engineering subcellular organization in microbes shows great promise in addressing bottlenecks in metabolic engineering efforts; however, rules guiding selection of an organization strategy or platform are lacking. Here, we study compartment morphology as a factor in mediating encapsulated pathway performance. Using the 1,2-propanediol utilization microcompartment (Pdu MCP) system from Salmonella enterica serovar Typhimurium LT2, we find that we can shift the morphology of this protein nanoreactor from polyhedral to tubular by removing vertex protein PduN. Analysis of the metabolic function between these Pdu microtubes (MTs) shows that they provide a diffusional barrier capable of shielding the cytosol from a toxic pathway intermediate, similar to native MCPs. However, kinetic modeling suggests that the different surface area to volume ratios of MCP and MT structures alters encapsulated pathway performance. Finally, we report a microscopy-based assay that permits rapid assessment of Pdu MT formation to enable future engineering efforts on these structures., (© 2022. The Author(s).)

SignificanceThe use of biological enzyme catalysts could have huge ramifications for chemical industries. However, these enzymes are often inactive in nonbiological conditions, such as high temperatures, present in industrial settings. Here, we show that the enzyme PETase (polyethylene terephthalate [PET]), with potential application in plastic recycling, is stabilized at elevated temperature through complexation with random copolymers. We demonstrate this through simulations and experiments on different types of substrates. Our simulations also provide strategies for designing more enzymatically active complexes by altering polymer composition and enzyme charge distribution.

Colloidal nanocrystals of metals, semiconductors, and other functional materials can self-assemble into long-range ordered crystalline and quasicrystalline phases, but insulating organic surface ligands prevent the development of collective electronic states in ordered nanocrystal assemblies. We reversibly self-assembled colloidal nanocrystals of gold, platinum, nickel, lead sulfide, and lead selenide with conductive inorganic ligands into supercrystals exhibiting optical and electronic properties consistent with strong electronic coupling between the constituent nanocrystals. The phase behavior of charge-stabilized nanocrystals can be rationalized and navigated with phase diagrams computed for particles interacting through short-range attractive potentials. By finely tuning interparticle interactions, the assembly was directed either through one-step nucleation or nonclassical two-step nucleation pathways. In the latter case, the nucleation was preceded by the formation of two metastable colloidal fluids.

Peptide amphiphiles are a class of molecules that can self-assemble into a variety of supramolecular structures, including high-aspect-ratio nanofibers. It is challenging to model and predict the charges in these supramolecular nanofibers because the ionization state of the peptides are not fixed but liable to change due to the acid-base equilibrium that is coupled to the structural organization of the peptide amphiphile molecules. Here, we have developed a theoretical model to describe and predict the amount of charge found on self-assembled peptide amphiphiles as a function of pH and ion concentration. In particular, we computed the amount of charge of peptide amphiphiles nanofibers with the sequence C 16 - V 2 A 2 E 2 . In our theoretical formulation, we consider charge regulation of the carboxylic acid groups, which involves the acid-base chemical equilibrium of the glutamic acid residues and the possibility of ion condensation. The charge regulation is coupled with the local dielectric environment by allowing for a varying dielectric constant that also includes a position-dependent electrostatic solvation energy for the charged species. We find that the charges on the glutamic acid residues of the peptide amphiphile nanofiber are much lower than the same functional group in aqueous solution. There is a strong coupling between the charging via the acid-base equilibrium and the local dielectric environment. Our model predicts a much lower degree of deprotonation for a position-dependent relative dielectric constant compared to a constant dielectric background. Furthermore, the shape and size of the electrostatic potential as well as the counterion distribution are quantitatively and qualitatively different. These results indicate that an accurate model of peptide amphiphile self-assembly must take into account charge regulation of acidic groups through acid-base equilibria and ion condensation, as well as coupling to the local dielectric environment., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Nap, Qiao, Palmer, Stupp, Olvera de la Cruz and Szleifer.)

The concept of origami has influenced the development of responsive materials that can mimic complex functions performed by living organisms. An ultimate goal is to discover and design soft materials that can be remotely actuated into diverse structures. To achieve this goal, we design and synthesize here a light-responsive spiropyran hydrogel system that can display dynamic shape changes upon irradiation with local light. We use a continuum polymer model to analyze the behavior of the constructed photoactive hydrogel, which is in good agreement with the experimental results. We explore different buckling modalities and patterns in a different range of parameters. The synthesis and fabrication of these materials demonstrate that the theoretical model can be used to drive the development of responsive photoactive systems.

The use of surfactants to attract dissolved ions to water surfaces and interfaces is an essential step in both solvent-based and solvent-free separation processes. We have studied the interactions of lanthanide ions in the aqueous subphase with monolayers of dihexadecyl phosphate at air-water interfaces. With heavier lanthanides (atomic number Z ≥ 65) in the subphase, the floating layer can be compressed to an area/molecule of about half the molecular cross section, indicating bilayer formation. X-ray fluorescence and reflectivity data support this conclusion. In the presence of lighter lanthanides ( Z < 65), only monolayers are observed. Subphase-concentration-dependent studies using Er 3+ (heavier) and Nd 3+ (lighter) lanthanides show a stepwise progression, with ions attaching to the monolayer only when the solution concentration is >3 × 10 -7 M. Above ∼10 -5 M, bilayers form but only in the presence of the heavier lanthanide. Grazing incidence X-ray diffraction shows evidence of lateral ion-ion correlations in the bilayer structure but not in monolayers. Explicit solvent all-atom molecular dynamics simulations confirm the elevated ion-ion correlation in the bilayer system. This bilayer structure isolates heavier lanthanides but not lighter lanthanides from an aqueous solution and is therefore a potential mechanism for the selective separation of heavier lanthanides.

Mesoscopic clusters composed of oppositely charged particles are ubiquitous in synthetic and biological soft materials. The effective interaction between these clusters is influenced by their polarizability, that is, the ability of their constituent charges to re-arrange in response to an external electrical field. Here, using coarse-grained simulations, we show that the polarizability of electrically neutral ionic clusters decreases as the number of constituent charges increases and/or their Coulombic interaction strength increases for various ion valencies, ion densities, and degrees of cluster boundary hardness. For clusters of random ionomers and their counterions, their polarizability is shown to depend on the number of polymer chains. The variation of the cluster polarizability with the cluster size indicates that throughout the assembly, the induced-dipole interactions between the clusters may be reduced substantially as they acquire more charges while maintaining zero net charge. Under certain conditions, the induced-dipole interactions may become repulsive, as inferred from our simulations with a polarizable solvent. As a result, the dipole-induced related interactions can serve as a counterbalancing force that contributes to the self-limiting aggregation of charge-containing assemblies.

Protein enzymes have shown great potential in numerous technological applications. However, the design of supporting materials is needed to preserve protein functionality outside their native environment. Direct enzyme-polymer self-assembly offers a promising alternative to immobilize proteins in an aqueous solution, achieving higher control of their stability and enzymatic activity in industrial applications. Herein, we propose a modeling-based design to engineering hydrogels of cytochrome P450 and of PETase with styrene/2-vinylpyridine (2VP) random copolymers. By tuning the copolymer fraction of polar groups and of charged groups via quaternization of 2VP for coassembly with cytochrome P450 and via sulfonation of styrene for coassembly with PETase, we provide quantitative guidelines to select either a protein-polymer hydrogel structure or a single-protein encapsulation. The results highlight that, regardless of the protein surface domains, the presence of polar interactions and hydration effects promote the formation of a more elongated enzyme-polymer complex, suggesting a membrane-like coassembly. On the other hand, the effectiveness of a single-protein encapsulation is reached by decreasing the fraction of polar groups and by increasing the charge fraction up to 15%. Our computational analysis demonstrates that the enzyme-polymer assemblies are first promoted by the hydrophobic interactions which lead the protein nonpolar residues to achieve the maximum coverage and to play the role of the most robust contact points. The mechanisms of coassembly are unveiled in the light of both protein and polymer physical-chemistry, providing bioconjugate phase diagrams for the optimal material design.

Ion-containing polymers often are good glass formers, and the glass transition temperature is an important parameter to consider for practical applications, which prescribes the working temperature range for different mechanical and dynamic properties. In this work, we present a systematic molecular dynamics simulation study on the coupling of ionic correlations with the glass transition, based on a generic coarse-grained model of ionic polymers. The variation of the glass transition temperature is examined concerning the influence of the electrostatic interaction strength, charge fraction, and charge sequence. The interplay with the film thickness effect is also discussed. Our results reveal a few typical features about the glass transition process that are in qualitative agreement with previous studies, further highlighting the effects of counterion entropy at weak ionic correlations and physical crosslinking of ionic aggregates at strong ionic correlations. Detailed parametric dependencies are displayed, which demonstrate that introducing strong ionic correlations promotes vitrification while adopting a precise charge sequence and applying strong confinement with weak surface affinity reduce the glass transition temperature. Overall, our investigation provides an improved picture towards a comprehensive understanding of the glass transition in ion-containing polymeric systems from a molecular simulation perspective.

Self-organized shells are fundamental in biological compartmentalization. They protect genomic material or enclose enzymes to aid the metabolic process. Studies of crystalline shells have shown the importance of the mechanical properties of building units in the shell morphology. However, the mechanism underlying the morphology of multicomponent assemblies is still poorly understood. Here, we analyze multicomponent closed shells that have different mechanical properties. By minimizing elastic energy, we show that heterogeneous bending rigidities regulate the surface pattern into circular, spikes, and ridge shapes. Interestingly, our continuum elasticity model recovers the patterns that have been proposed in bacterial microcompartments (BMCs), which are self-organized protein shells that aid the breakdown of complex molecules and allow bacteria to survive in hostile environments. In addition, our work elucidates the principles of pattern formation that can be used to design and engineer multicomponent microcompartments with a specific surface distribution of the components.

In solid-liquid, or liquid-liquid, interfaces with dielectric contrast, charged particles interact with the induced polarization charge of the interface. These interactions contribute to an effective self-energy of the bulk ions and mediate ion-ion interactions. For flat interfaces, the self-energy and the mediated interactions are neatly constructed by the image charge method. For other geometries, explicit results are scarce and the problem must be treated via approximations or direct computation. The case of interfaces with roughness is of great practical importance. This article provides analytical results, valid to first-order in perturbation theory, for the self-energy of particles near rough substrates. Explicit formulas are provided for the case of a sinusoidal deformation of a flat surface. Generic deformations can be treated by superposition. In addition to results for the self-energy, the surface polarization charge is presented as a quadrature. The interaction between an ion and the deformed surface is modified by the change in relative distance as well as by the local curvature of the surface. Solid walls, with a lower dielectric constant than the liquid, repel all ions. We show that the repulsion is reduced by local convexity and enhanced by concavity; dimples are more repulsive than pimples.

Janus particles with different patch sizes, confined to two dimensions, generate a series of patterns of interest to the field of nanoscience. Here we observe reverse melting, where for some densities the system melts under cooling. For a broad range of hydrophobic patch sizes (60^{∘}<θ&#95;{0}<90^{∘}), a reentrant transition from solid to liquid and then to an ordered phase emerges as temperature (T) decreases due to the formation of rhombus chains at low T. This reentrant phase has pseudo long-range orientational order but short-range translational order, similar to a hexatic phase. Our work provides guidelines to study the melting and assembly of Janus particles in two dimensions, as well as mechanisms to generate phases with specific symmetry.

Nature harnesses the disorder of intrinsically disordered proteins to organize enzymes and biopolymers into membraneless organelles. The heterogeneous nature of synthetic random copolymers with charged, polar, and hydrophobic groups has been exploited to mimic intrinsically disordered proteins, forming complexes with enzymatically active proteins and delivering them into nonbiological environments. Here, the properties of polyelectrolyte complexes composed of two random copolymer polyelectrolytes are studied experimentally and via simulation with the aim of exploiting such complexes for segregating organic molecules from water. The anionic polyelectrolyte contains hydrophilic and hydrophobic side chains and forms self-assembled hydrophobic domains. The cationic polymer is a high-molecular-weight copolymer of hydrophilic and charged side groups and acts as a flocculant. We find that the polyelectrolyte complexes obtained with this anionic and cationic random copolymer system are capable of absorbing small cationic, anionic, and hydrophobic organic molecules, including perfluorooctanoic acid, a compound of great environmental and toxicologic concern. Importantly, these macroscopic complexes can be easily removed from water, thereby providing a simple approach for organic contaminant removal in aqueous media. MARTINI and coarse-grained molecular dynamics simulations explore how the microscale heterogeneity of these random copolymer complexes relates to their segregation functionality., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)

Bacterial microcompartments compartmentalize the enzymes that aid chemical and energy production in many bacterial species. They are postulated to help bacteria survive in hostile environments. Metabolic engineers are interested in repurposing these organelles for non-native functions. Here, we use computational, theoretical, and experimental approaches to determine mechanisms that effectively control microcompartment self-assembly. We find, via multiscale modeling and mutagenesis studies, the interactions responsible for the binding of hexamer-forming proteins in a model system, the propanediol utilization bacterial microcompartments from Salmonella enterica serovar Typhimurium LT2. We determine how the changes in the microcompartment hexamer protein preferred angles and interaction strengths can modify the assembled morphologies. We demonstrate that such altered strengths and angles are achieved via amino acid mutations. A thermodynamic model provides guidelines to design microcompartments of various morphologies. These findings yield insight in controlled protein assembly and provide principles for assembling microcompartments for biochemical or energy applications as nanoreactors., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)

Ion-containing polymers have numerous potential applications as energy storage and conversion devices, water purification membranes, and gas separation membranes, to name a few. Given the low dielectric constant of the media, ions and charges on polymers in a molten state interact strongly producing large effects on chain statistics, thermodynamics, and diffusion properties. Here, we discuss recent research accomplishments on the effects of ionic correlation and dielectric heterogeneity on the phase behavior of ion-containing polymers. Progress made in studying ion transport properties in these material systems is also highlighted. Charged block copolymers (BCPs), among all kinds of ion-containing polymers, have a particular advantage owing to their robust mechanical support and ion conducting paths provided by the segregation of the neutral and charged blocks. Coulombic interactions among the charges play a critical role in determining the phase segregation in charged BCPs and the domain size of charge-rich regions. We show that strongly charged BCPs display ordered phases as a result of electrostatic interactions alone. In addition, bulky charge-containing side groups attached to the charged block lead to the formation of morphologies that provide continuous channels and better dissociation for ion conduction purposes. Finally, a few avenues for designing ion-containing polymers for energy applications are discussed.

Patterns and morphology develop in living systems such as embryos in response to chemical signals. To understand and exploit the interplay of chemical reactions with mechanical transformations, chemomechanical polymer systems have been synthesized by attaching chemicals into hydrogels. In this work, we design autonomous responsive elastic shells that undergo morphological changes induced by chemical reactions. We couple the local mechanical response of the gel with the chemical processes on the shell. This causes swelling and deswelling of the gel, generating diverse morphological changes, including periodic oscillations. We further introduce a mechanical instability and observe buckling-unbuckling dynamics with a response time delay. Moreover, we investigate the mechanical feedback on the chemical reaction and demonstrate the dynamic patterns triggered by an initial deformation. We show the chemical characteristics that account for the shell morphology and discuss the future designs for autonomous responsive materials., Competing Interests: The authors declare no competing interest.

The transport of polyelectrolytes confined by oppositely charged surfaces and driven by a constant electric field is of interest in studies of DNA separation according to size. Using molecular dynamics simulations that include the surface polarization effect, we find that the mobilities of the polyelectrolytes and their counterions change non-monotonically with the confinement surface charge density. For an optimum value of the confinement charge density, efficient separation of polyelectrolytes can be achieved over a wide range of polyelectrolyte charge due to the differential friction imparted by oppositely charged confinement on the polyelectrolyte chains. Furthermore, by altering the placement of the charged confinement counterions, enhanced polyelectrolyte separation can be achieved by utilizing the surface polarization effect due to dielectric mismatch between the media inside and outside the confinement.

The encapsulation of enzymes within porous materials has shown great promise, not only in protecting the enzymes from denaturation under nonbiological environments, but also, in some cases, in facilitating their enzymatic reaction rates at favorable reaction conditions. While a number of hypotheses have been developed to explain this phenomenon, the detailed structural changes of the enzymes upon encapsulation within the porous material, which are closely related to their activity, remain largely elusive. Herein, the structural change of cytochrome c (Cyt c) upon encapsulation within a hierarchical metal-organic framework, NU-1000, is investigated through a combination of experimental and computational methods, such as electron paramagnetic resonance, solid-state ultraviolet-visible spectroscopy, and all-atom explicit solvent molecular dynamics simulations. The enhanced catalytic performance of Cyt c after being encapsulated within NU-1000 is supported by the physical and in silico observations of a change around the heme ferric active center.

The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.

Natural biomolecules such as peptides and DNA can dynamically self-organize into diverse hierarchical structures. Mimicry of this homopolymer self-assembly using synthetic systems has remained limited but would be advantageous for the design of adaptive bio/nanomaterials. Here, we report both experiments and simulations on the dynamic network self-assembly and subsequent collapse of the synthetic homopolymer poly(propylene sulfone). The assembly is directed by dynamic noncovalent sulfone-sulfone bonds that are susceptible to solvent polarity. The hydration history, specified by the stepwise increase in water ratio within lower polarity water-miscible solvents like dimethylsulfoxide, controls the homopolymer assembly into crystalline frameworks or uniform nanostructured hydrogels of spherical, vesicular, or cylindrical morphologies. These electrostatic hydrogels have a high affinity for a wide range of organic solutes, achieving >95% encapsulation efficiency for hydrophilic small molecules and biologics. This system validates sulfone-sulfone bonding for dynamic self-assembly, presenting a robust platform for controllable gelation, nanofabrication, and molecular encapsulation.

The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein plays a crucial role in binding the human cell receptor ACE2 that is required for viral entry. Many studies have been conducted to target the structures of RBD-ACE2 binding and to design RBD-targeting vaccines and drugs. Nevertheless, mutations distal from the SARS-CoV-2 RBD also impact its transmissibility and antibody can target non-RBD regions, suggesting the incomplete role of the RBD region in the spike protein-ACE2 binding. Here, in order to elucidate distant binding mechanisms, we analyze complexes of ACE2 with the wild-type spike protein and with key mutants via large-scale all-atom explicit solvent molecular dynamics simulations. We find that though distributed approximately 10 nm away from the RBD, the SARS-CoV-2 polybasic cleavage sites enhance, via electrostatic interactions and hydration, the RBD-ACE2 binding affinity. A negatively charged tetrapeptide (GluGluLeuGlu) is then designed to neutralize the positively charged arginine on the polybasic cleavage sites. We find that the tetrapeptide GluGluLeuGlu binds to one of the three polybasic cleavage sites of the SARS-CoV-2 spike protein lessening by 34% the RBD-ACE2 binding strength. This significant binding energy reduction demonstrates the feasibility to neutralize RBD-ACE2 binding by targeting this specific polybasic cleavage site. Our work enhances understanding of the binding mechanism of SARS-CoV-2 to ACE2, which may aid the design of therapeutics for COVID-19 infection.

Understanding nanoscale interactions at the interface between two media with different dielectric constants is crucial for controlling many environmental and biological processes, and for improving the efficiency of energy storage devices. In this contributed paper, we show that polarization effects due to such dielectric mismatch remarkably influence the double-layer structure of a polyelectrolyte solution confined between two charged surfaces. Surprisingly, the electrostatic potential across the adsorbed polyelectrolyte double layer at the confining surface is found to decrease with increasing surface charge density, indicative of a negative differential capacitance. Furthermore, in the presence of polarization effects, the electrostatic energy stored in the double-layer structure is enhanced with an increase in the charge amplification, which is the absorption of ions on a like-charged surface. We also find that all of the important double-layer properties, such as charge amplification, energy storage, and differential capacitance, strongly depend on the polyelectrolyte backbone flexibility and the solvent quality. These interesting behaviors are attributed to the interplay between the conformational entropy of the confined polyelectrolytes, the Coulombic interaction between the charged species, and the repulsion from the surfaces with lower dielectric constant., Competing Interests: The authors declare no competing interest.