Impact of Two Water-Miscible Ionic Liquids on the Temperature-Dependent Self-Assembly of the (EO) 6 –(PO) 34 –(EO) 6 Block Copolymer
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Results for “block structure”
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Disentangling Pauli Blocking of Atomic Decay from Cooperative Radiation and Atomic Motion in a 2D Fermi Gas
The observation of Pauli blocking of atomic spontaneous decay via direct measurements of the atomic population requires the use of long-lived atomic gases where quantum statistics, atom recoil, and cooperative radiative processes are all relevant. In this work, we develop a theoretical framework capable of simultaneously accounting for all these effects in the many-body quantum degenerate regime. We apply it to atoms in a single 2D pancake or arrays of pancakes featuring an effective Λ level structure (one excited and two degenerate ground states). We identify a parameter window in which a factor of 2 extension in the atomic lifetime clearly attributable to Pauli blocking should be experimentally observable in deeply degenerate gases with ~10 3 atoms. We experimentally observe a suppressed excited-state decay rate, fully consistent with the theory prediction of an enhanced excited-state lifetime, on the 1 S 0 – 3 P 1 transition in 87 Sr atoms.
74 ATOMIC AND MOLECULAR PHYSICS↗
Crystal structures of Salmonella enterica FraB deglycase reveal a conformational heterodimer with remarkable structural plasticity at the active site
Abstract Thefralocus ofSalmonella entericaencodes five genes for metabolism of fructose‐asparagine, an Amadori product formed by condensation of asparagine with glucose. In the last step of this pathway, the FraB deglycase cleaves 6‐phospho‐fructose‐aspartate into glucose‐6‐phosphate and aspartate. In homology models, FraB forms a homodimer with two equivalent active sites located at the dimer interface. E214 and H230, two invariant residues essential for catalysis, project into each active site cleft from opposing subunits of the dimer. Here, we have determined six crystal structures of FraB, three of a variant containing an N‐terminal His 6 tag and two mutations needed for crystallization (hereafter referred to as WT′), two with additional mutations to active site residues (E214A and P232A), and one of a variant with C‐terminal residues 313–325 deleted. Surprisingly, in the WT′ FraB structure, the two catalytic residues, E214 (general base) and H230 (general acid), are positioned ~22 Å apart. In the E214A and C‐terminus‐truncated FraB variants, however, a conformational change in the E214‐residing helix brings E214 and H230* to ~7 Å (* indicates residue from the second protomer that creates the inter‐subunit catalytic center). The loop bearing H230 also exhibits significant variation, ranging from being completely disordered to adopting open or closed states, with the nearby P232* residue being eithercisortrans. The C‐terminal residues 313–325 form a flexible “C‐tail” that can be fully disordered, bind in the active site to block access of substrate, or angle across the active site to wrap across the other subunit of the dimer and potentially close over substrate. Collectively, these structures reveal that FraB is a conformational heterodimer with two chemically identical subunits that are constrained to adopt different structures as they come together for catalysis. This plasticity likely involves correlated opening and closure of the two active sites for their respective binding and release of substrates and ligands.
Biochemistry & Molecular Biology↗
Realizing mechanical frustration at the nanoscale using DNA origami
Structural designs inspired by physical and biological systems have been previously utilized to develop mechanical metamaterials with enhanced properties based on clever geometric arrangement of constituent building blocks. Here, we use the DNA origami method to realize a nanoscale metastructure exhibiting mechanical frustration, a counterpart of the well-known phenomenon of magnetic frustration. By selectively actuating reconfigurable struts, it adopts either frustrated or non-frustrated states, each characterized by distinct free energy profiles. While the non-frustrated state distributes the strain homogeneously, the frustrated mode concentrates it at a specific location. Molecular dynamics simulations reconcile the contrasting behaviors and provide insights into underlying mechanics. We explore the design space further by tailoring responses through structural modifications. Our work combines programmable DNA self-assembly with mechanical design principles to overcome engineering limitations encountered at the macroscale to design dynamic, deformable nanostructures with potential applications in elastic energy storage, nanomechanical computation, and allosteric mechanisms in DNA-based nanomachinery.
DNA nanostructures↗
Electron Spin Polarization and Rectification Driven by Chiral Perylene Diimide-Based Nanodonuts
The chirality-induced spin selectivity (CISS) effect allows thin-film layers of chiral conjugated molecules to function as spin filters at ambient temperature. Through solvent-modulated dropcasting of chiral l- and d-perylene diimide (PDI) monomeric building blocks, two types of aggregate morphologies, nanofibers and nanodonuts, may be realized. Spin-diode behavior is evidenced in the nanodonut structures. Stacked PDI units, which form the conjugated core of these nanostructures, dominate the nanodonut–Au electrode contact; in contrast, the AFM tip contacts largely the high-resistance solubilizing alkyl chains of the chiral monomers that form these nanodonuts. Current–voltage responses of the nanodonuts, measured by magnetic conductive AFM (mC-AFM), demonstrate substantial spin polarizations as well as spin current rectification ratios (>10) that exceed the magnitudes of those determined to date for other chiral nanoscale systems. Furthermore, these results underscore the potential for chiral nanostructures, featuring asymmetric molecular junctions, to enable CISS-based nanoscale spin current rectifiers.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Dynamical Ion Correlations in Polymer and Membrane Electrolytes: Recent Advances and Open Questions
Ion transport in polymer and membrane electrolytes is often described using uncorrelated models like the Nernst–Einstein (NE) approximation, which link conductivity, transference number, and salt diffusivity to individual ion mobilities. However, growing evidence shows that dynamical ion correlations─arising from ion pairing, polymer-mediated coupling, confinement, and electrostatic interactions─can substantially alter macroscopic transport properties. The Onsager transport formalism offers a rigorous framework to quantify these effects via cross-correlated ionic displacements. This Perspective highlights how such correlations manifest across dry and hydrated systems, including salt-doped polymers, block copolymers, hydrogels, and ion-exchange membranes. Here, we examine key physical origins, the influence of salt chemistry and polymer structure, and open questions in measuring and controlling correlated motion. Embracing correlation-aware design enables new pathways to optimize conductivity, transference number, and selectivity─shifting the focus from individual ion mobility to engineered collective dynamics for next-generation electrolytes in energy storage and separations.
Charge transport↗
Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography
Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.
59 BASIC BIOLOGICAL SCIENCES↗
X-ray structure of a human cardiac muscle troponin C/troponin I chimera in two crystal forms
The X-ray crystal structure of a human cardiac muscle troponin C/troponin I chimera has been determined in two different crystal forms and shows a conformation of the complex that differs from that previously observed by NMR. The chimera consists of the N-terminal domain of troponin C (cTnC; residues 1–80) fused to the switch region of troponin I (cTnI; residues 138–162). In both crystal forms, the cTnI residues form a six-turn α-helix that lays across the hydrophobic groove of an adjacent cTnC molecule in the crystal structure. In contrast to previous models, the cTnI helix runs in a parallel direction relative to the cTnC groove and completely blocks the calcium desensitizer binding site of the cTnC–cTnI interface.
59 BASIC BIOLOGICAL SCIENCES↗
Beyond Generalized Eigenvalues
Two analysis techniques, the generalized eigenvalue method (GEM) or Prony's method (PM), are commonly used to analyze statistical estimates of correlation functions produced in lattice quantum field theory calculations. GEM takes full advantage of the matrix structure of correlation functions but only considers individual pairs of time separations when much more data exists. PM can be applied to many time separations and many individual matrix elements simultaneously but does not fully exploit the matrix structure of the correlation function. We combine both these methods into a single framework based on matrix polynomials which we call block Prony method (BPM).
Fleming, George T.↗
High-Resolution Imaging of Unstained Polymer Materials
Electron microscopy has played an important role in polymer characterization. Traditionally, electron diffraction is used to study crystalline polymers while transmission electron microscopy is used to study microphase separation in stained block copolymers and other multiphase systems. We describe developments that eliminate the barrier between these two approaches - it is now possible to image polymer crystals with atomic resolution. The focus of this Review is on high-resolution imaging (30 Å and smaller) of unstained polymers. Recent advances in hardware allow for capturing numerous (as many as 105) low-dose images from an unperturbed specimen; beam damage is a significant barrier to high-resolution electron microscopy of polymers. Machine-learning-based software is then used to sort and average the images to retrieve pristine structural information from a collection of noisy images. Acknowledging the heterogeneity in polymer samples prior to averaging is essential. Molecular conformations in a wide range of amphiphilic block copolymers, polymerized ionic liquids, and conjugated polymers can be gleaned from two-dimensional projections (2D), three-dimensional (3D) tomograms, and four-dimensional (4D) scanning transmission electron microscopy (STEM) data sets where 2D diffraction patterns are taken as a function of position. Some methods such as phase contrast STEM have been used to image closely related materials such as metal-organic frameworks but not polymers. With improvements in hardware and software, such methods may soon be applied to polymers. Our goal is to provide a comprehensive understanding of the strategies toward the high-resolution imaging of radiation sensitive polymer materials at different length scales.
36 MATERIALS SCIENCE↗
Cocrystals combining order and correlated disorder via colloidal crystal engineering with DNA
Colloidal cocrystallization enables the formation of multicomponent materials with unique physicochemical properties, yet the role of nanoparticle (NP) shape and specific ligand interactions to cocrystallize anisotropic and isotropic NPs, with order and correlated disorder, remains underexplored. Here, geometry-inspired strategies along with programmable DNA interactions are combined to achieve structural control of colloidal cocrystal assemblies. Coassembling polyhedral and spherical NPs with complementary DNA yields two classes of cocrystals: one where both components order, and another where polyhedral NPs form a periodic lattice, while spherical NPs remain disordered but spatially correlated with polyhedral edges and corners. The size ratio of the building blocks can be used to control the ordering of spherical NPs—smaller octahedral-to-sphere size ratios favor fully ordered cocrystals. Molecular dynamics simulations further elucidate the role of NP shapes and dimensions in the structural outcome of the cocrystal. This work provides a framework for deliberately targeting and accessing crystals with exotic multicomponent structures.
Li, Yuanwei [Northwestern Univ., Evanston, IL (Uni↗
Observing neutron alignment at high angular momenta in heavy deformed actinides
An outstanding puzzle in the structure of very heavy nuclei lies in the rotation response of deformed transuranic isotopes. While the rotation alignment of pairs of 𝑖 13/2 protons is ubiquitous and well understood, observing the analogous alignment of the 𝑗 15/2 neutrons has been elusive. In this work we present a new quantitative analysis approach: from their moments of inertia as a function of frequency, we compare the alignments of rotational bands with both “low” and high-𝑗 intrinsic structures in the 𝑁 = 151 isotones of Pu, Cm, Cf, and No, thereby distinguishing between the alignments of neutron versus proton pairs through “blocking” effects. In this way, the alignment of 𝑗 15/2 neutrons can be clearly identified for the first time. The protons and neutrons begin aligning at a very similar frequency. The contribution of 𝑗 15/2 neutrons to the total alignment is found to grow with increasing 𝑍 compared to 𝑖 13/2 protons. To explain these observations, it is necessary to adopt a self-consistent set of single-particle energies corresponding to the nuclear shape that minimizes the mass. The shape description needs to include high-order deformations up to at least 𝛽 6 .
A ≥ 220↗
Decision-tree structures utilizing a phase-transition material
The rich internal physics due to competing electronic phases present in phase-transition materials such as VO2 offer the potential for compact building block design for emerging non-von Neumann computing technologies. Here, based on the relaxation dynamics of an insulator-metal phase transition, we demonstrate experimentally a decision-tree classifier embedded within a single volatile resistive switching device. The tree is constructed by the combination of the voltage pulse and relaxation time and can adapt to different tasks. We use machine learning to analyze the relaxation process, enabling a predictive voltage-relaxation time phase diagram for the electrical resistance state. Classification of the etiology of the chronic cough is presented as a proof-of-principle use case. Further, our approach can be generalized to broader classes of solid-state and solid-liquid interfacial systems that demonstrate a variety of phase relaxations.
36 MATERIALS SCIENCE↗
Effect of Polymer Removal on the Morphology and Phase of the Nanoparticles in All-Inorganic Heterostructures Synthesized via Two-Step Polymer Infiltration
Polymer templates play an essential role in the robust infiltration-based synthesis of functional multicomponent heterostructures with controlled structure, porosity, and composition. Such heterostructures are be used as hybrid organic–inorganic composites or as all-inorganic systems once the polymer templates are removed. Using iron oxide/alumina heterostructures formed by two-step infiltration of polystyrene-block-polyvinyl pyridine block copolymer with iron and aluminum precursors from the solution and vapor-phases, respectively, we show that the phase and morphology of iron oxide nanoparticles dramatically depend on the approach used to remove the polymer. We demonstrate that thermal and plasma oxidative treatments result in iron oxide nanoparticles with either solid or hollow morphologies, respectively, that lead to different magnetic properties of the resulting materials. Our study extends the boundaries of structure manipulations in multicomponent heterostructures synthesized using polymer infiltration synthesis, and hence their properties.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition
Optimal phage propagation depends on the regulation of the lysis of the infected host cell. In T4 phage infection, lysis occurs when the holin protein (T) forms lesions in the host membrane. However, the lethal function of T can be blocked by an antiholin (RI) during lysis inhibition (LIN). LIN sets if the infected cell undergoes superinfection, then the lysis is delayed until host/phage ratio becomes more favorable for the release of progeny. It has been thought that a signal derived from the superinfection is required to activate RI. Here we report structures that suggest a radically different model in which RI binds to T irrespective of superinfection, causing it to accumulate in a membrane as heterotetrameric 2RI–2T complex. Moreover, we show the complex binds non-specifically to DNA, suggesting that the gDNA from the superinfecting phage serves as the LIN signal and that stabilization of the complex by DNA binding is what defines LIN. Finally, we show that soluble domain of free RI crystallizes in a domain-swapped homotetramer, which likely works as a sink for RI molecules released from the RI–T complex to ensure efficient lysis. These results constitute the first structural basis and a new model not only for the historic LIN phenomenon but also for the temporal regulation of phage lysis in general.
59 BASIC BIOLOGICAL SCIENCES↗
Skeletides: A Modular, Simplified Physical Model of Protein Secondary Structure
Three-dimensional (3D) models are essential for visualization and conceptual understanding of complex architectures such as protein structure. Although there is a plethora of software platforms that allow digital depictions of protein structure at an atomic level in silico, physical models are needed to convey an intuitive understanding of biomolecular architecture. However, it is a challenge to represent all the relevant features of proteins in a single physical model due to their sheer structural complexity. Here, we describe a modular protein model that focuses only on representation of the secondary structure—the underlying structural skeleton. The simplified model consists of amino acid units, which can be linked together to reproduce the two most fundamental structural features of protein secondary structure: the relative positions of the amino acid alpha carbon atoms, and the intra-main chain hydrogen bonding pattern. We use 3D printing and magnets to create a set of three modular amino acid building blocks, which when linked together into a chain, can faithfully represent alpha helices, beta sheets, and turns. These simple to make models can be used to quickly assemble the alpha carbon trace of an entire protein domain, which conveys a tactile experience of the complexity of protein skeletal architecture. These models highlight the modularity of protein structure: where a single structural unit, the amino acid, can be linked together to form a larger, regular secondary structure. These models also have a propensity to spontaneously organize into alpha helices and beta sheets, as demonstrated by their ability to autonomously assemble when placed in a circulating water tank. These models provide a missing educational tool to expand knowledge of protein structure, foster deeper insight into protein folding, and inspire greater interest in biomacromolecular architecture.
36 MATERIALS SCIENCE↗
The development of Nanosota-1 as anti-SARS-CoV-2 nanobody drug candidates
Combating the COVID-19 pandemic requires potent and low-cost therapeutics. We identified a series of single-domain antibodies (i.e., nanobody), Nanosota-1, from a camelid nanobody phage display library. Structural data showed that Nanosota-1 bound to the oft-hidden receptor-binding domain (RBD) of SARS-CoV-2 spike protein, blocking viral receptor angiotensin-converting enzyme 2 (ACE2). The lead drug candidate possessing an Fc tag (Nanosota-1C-Fc) bound to SARS-CoV-2 RBD ~3000 times more tightly than ACE2 did and inhibited SARS-CoV-2 pseudovirus ~160 times more efficiently than ACE2 did. Administered at a single dose, Nanosota-1C-Fc demonstrated preventive and therapeutic efficacy against live SARS-CoV-2 infection in both hamster and mouse models. Unlike conventional antibodies, Nanosota-1C-Fc was produced at high yields in bacteria and had exceptional thermostability. Pharmacokinetic analysis of Nanosota-1C-Fc documented an excellent in vivo stability and a high tissue bioavailability. As effective and inexpensive drug candidates, Nanosota-1 may contribute to the battle against COVID-19.
60 APPLIED LIFE SCIENCES↗
Influence of Terminal Carboxyl Groups on the Structure and Reactivity of Functionalized m-Carboranethiolate Self-Assembled Monolayers
The structure and function of self-assembled monolayers (SAMs) at the nanoscale are determined by the steric and electronic effects of their building blocks. Carboranethiol molecules form pristine monolayers that provide tunable two-dimensional systems to probe lateral and interfacial interactions. Additional ω-functionality, such as carboxyl groups, can be introduced to change the properties of the exposed surfaces. Here, two geometrically similar isomeric m-carborane analogues of m-mercaptobenzoic acid, 1-COOH-7-SH-1,7-C 2 B 10 H 10 and racem-1-COOH-9-SH-1,7-C 2 B 10 H 10 , are characterized and their SAMs on Au{111} are examined. The latter isomer belongs to the rare group of chiral cage molecules and becomes, to our knowledge, the first example assembled on Au{111}. Although different in symmetry, molecules of both isomers assemble into similar hexagonal surface patterns. The nearest-neighbor spacing of 8.4 ± 0.4 Å is larger than that of non-carboxylated isomers, consistent with the increased steric demands of the carboxyl groups. Computational modeling reproduced this spacing and suggests a tilt relative to the surface normal. However, tilt domains are not observed experimentally, suggesting the presence of strong lateral interactions. Analyses of the influence of the functional groups through the pseudo-aromatic m-carborane skeleton showed that the thiol group attached to either carbon or boron atoms increases the carboxyl group acidity in solution. In contrast, the acidity of the exposed carboxyl group in the SAMs decreases upon surface attachment; computational analyses suggest that the driving force of this shift is the dielectric of the environment in the monolayer as a result of confined intermolecular interactions, proximity to the Au surface, and partial desolvation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗