Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity

Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and thermal denaturation, as well as proteolytic degradation. Despite its significance, specific mechanisms governing kinetic stability remain largely unknown, and few studies address the rational design of kinetic stability. Here, we describe a method for designing protein kinetic stability that uses protein long-range order, absolute contact order, and simulated free energy barriers of unfolding to quantitatively analyze and predict unfolding kinetics. We analyze two β-trefoil proteins: hisactophilin, a quasi-three-fold symmetric natural protein with moderate stability, and ThreeFoil, a designed three-fold symmetric protein with extremely high kinetic stability. The quantitative analysis identifies marked differences in long-range interactions across the protein hydrophobic cores that partially account for the differences in kinetic stability. Swapping the core interactions of ThreeFoil into hisactophilin increases kinetic stability with close agreement between predicted and experimentally measured unfolding rates. These results demonstrate the predictive power of readily applied measures of protein topology for altering kinetic stability and recommend core engineering as a tractable target for rationally designing kinetic stability that may be widely applicable.

Large-Area Uniaxially Oriented Sub-5 nm Line Patterns of Hybrid Liquid Crystals Constructed by Perylene Diimide and Oligo(Dimethylsiloxane)

Construction of sub-5 nm long-range ordered structures through self-assembly has received increasing attention. Herein, a series of ODMS-based thermotropic liquid crystals (LCs) containing perylene diimide (PDI) were designed and synthesized. These LCs can form ordered nanostructures with periodic sizes around 5 nm including smectic J (SmJ), oblique columnar (Col_ob ), and hexagonal columnar (Col_h ) phases with change in the volume fraction of ODMS, where the layer spacing of the SmJ phase is less than 5 nm. Thin films with parallel oriented nanolines with line width less than 5 nm can be obtained on PDMS-modified silicon substrates by spin-casting and simple thermal annealing processes. Moreover, owing to the strong π-π interaction between PDI cores, these nanolines are long-range ordered with uniaxial orientation in relatively large areas (1.5×1.5 μm² ) with over 300 continuous microdomains without pre-patterning. These nanostructures provide the possibility of preparing nanotemplates by oxygen plasma etching.

Adapting UFF4MOF for Heterometallic Rare-Earth Metal-Organic Frameworks

Heterometallic metal-organic frameworks based on rare-earth metals (RE-MOFs) have potential in a number of applications where energy transfer between nearby metal atoms is required. This observation implies that it is important to understand the level of local mixing that is achieved between metals of different types during synthesis of RE-MOFs. Density functional theory calculations can give quantitative information on the relative energy of different configurations of RE-MOFs, but these calculations cannot be applied to the full range of medium- and long-range orderings that are possible in heterometallic materials. This limitation can be overcome using force field (FF)-based calculations if appropriate FFs are available. We show that an existing generic FF for MOFs, UFF4MOF, does not accurately predict energies of mixing in heterometallic Nd/Yb MOFs and introduce a modified FF to address this shortcoming. The resulting FF is used to explore metal orderings in large simulation volumes for a Nd/Yb MOF, illustrating the complexities that can arise in the structure of heterometallic RE-MOFs.

Magnetic Properties of A2Ni2TeO6 (A = K, Li): Zigzag Order in the Honeycomb Layers of Ni2+ Ions Induced by First and Third Nearest-Neighbor Spin Exchanges

The static and dynamic magnetic properties and the specific heat of K₂Ni₂TeO₆ and Li₂Ni₂TeO₆ were examined and it was found that they undergo a long-range ordering at T_N = 22.8 and 24.4 K, respectively, but exhibit a strong short-range order. At high temperature, the magnetic susceptibilities of K₂Ni₂TeO₆ and Li₂Ni₂TeO₆ are described by a Curie-Weiss law, with Curie-Weiss temperatures Θ of approximately -13 and -20 K, respectively, leading to the effective magnetic moment of about 4.46 ± 0.01 μ_B per formula unit, as expected for Ni²⁺ (S = 1) ions. In the paramagnetic region, the ESR spectra of K₂Ni₂TeO₆ and Li₂Ni₂TeO₆ show a single Lorentzian-shaped line characterized by the isotropic effective g-factor, g = 2.19 ± 0.01. The energy-mapping analysis shows that the honeycomb layers of A₂Ni₂TeO₆ (A = K, Li) and Li₃Ni₂SbO₆ adopt a zigzag order, in which zigzag ferromagnetic chains are antiferromagnetically coupled, because the third nearest-neighbor spin exchanges are strongly antiferromagnetic while the first nearest-neighbor spin exchanges are strongly ferromagnetic, and that adjacent zigzag-ordered honeycomb layers prefer to be ferromagnetically coupled. The short-range order of the zigzag-ordered honeycomb lattices of K₂Ni₂TeO₆ and Li₂Ni₂TeO₆ is equivalent to that of an antiferromagnetic uniform chain, and is related to the short-range order of the ferromagnetic chains along the direction perpendicular to the chains.

Emerging Long-Range Order from a Freeform Disordered Metasurface

Recently, disordered metasurfaces have attracted considerable interest due to their potential applications in imaging, holography, and wavefront shaping. However, how to emerge long-range ordered phase distribution in disordered metasurfaces remains an outstanding problem. Here, a general framework is proposed to generate a spatially homogeneous in-plane phase distribution from a disordered metasurface, by engineering disorder parameters together with topology optimization. As a proof-of-concept demonstration, an all-dielectric disordered supercell metasurface with relatively homogeneous in-plane phase fluctuation is designed by disorder parameter engineering, manifesting as polarization conversion-dependent random scattering or unidirectional transmission. Then, a topology optimization approach is utilized to overcome the lattice coupling effect and to further improve the homogeneity of complex electric field fluctuation. In comparison with the initial supercell metasurface, both the phase fluctuation range and the relative efficiency of the topology-optimized freeform metasurface are significantly improved, leading to a long-range ordered electric field distribution. Moreover, three experimental realizations are performed, all of which agree well with the theoretical results. This methodology may inspire more exotic optical phenomena and find more promising applications in disordered metasurfaces and disordered optics.

Long-Range-Ordered Assembly of Micro-/Nanostructures at Superwetting Interfaces

On-chip integration of solution-processable materials imposes stringent and simultaneous requirements of controlled nucleation and growth, tunable geometry and dimensions, and long-range-ordered assembly, which is challenging in solution process far from thermodynamic equilibrium. Superwetting interfaces, underpinned by programmable surface chemistry and topography, are promising for steering transport, dewetting, and microfluid dynamics of liquids, thus opening a new paradigm for micro-/nanostructure assembly in solution process. Herein, assembly methods on the basis of superwetting interfaces are reviewed for constructing long-range-ordered micro-/nanostructures. Confined capillary liquids, including capillary bridges and capillary corner menisci realized by controlling local wettability and surface topography, are highlighted for simultaneously attained deterministic patterning and long-range order. The versatility and robustness of confined capillary liquids are discussed with assembly of single-crystalline micro-/nanostructures of organic semiconductors, metal-halide perovskites, and colloidal-nanoparticle superlattices, which lead to enhanced device performances and exotic functionalities. Finally, a perspective for promising directions in this realm is provided.

Small-Angle X-ray Scattering Analysis of Colloidal Crystals and Replica Materials Made from l-Arginine-Stabilized Silica Nanoparticles

Colloidal crystals made from sub-100 nm silica nanoparticles have provided a versatile platform for the template-assisted synthesis of three-dimensionally interconnected semiconducting, metallic, and magnetic replicas. However, the detailed structure of these materials has not yet been characterized. In this study, we investigated the structures of colloidal crystalline films and germanium replicas by scanning electron microscopy and small angle X-ray scattering. The structures of colloidal crystals made by evaporative assembly depends on the size of l-arginine-capped silica nanoparticles. Particles smaller than ∼31 nm diameter assemble into non-close-packed arrangements (bcc) whereas particles larger than 31 nm assemble into random close-packed structures with disordered hexagonal phase. Polycrystalline films of these materials retain their structures and long-range order upon infiltration at high temperature and pressure, and the structure is preserved in Ge replicas. The shear force during deposition and dispersity of silica nanoparticles contributes to the size-based variation in the structure and to the size of crystal domains in the colloidal crystal films.

Realization of Regular-Mixed Quasi-1D Borophene Chains with Long-Range Order

The polymorphism of borophene makes it a promising system to realize tunable physical or chemical properties. Various pure borophene phases consisting of quasi-1D boron chains with different widths have been commonly obtained in experimental studies. Here, it is shown that, due to a substrate mediation effect, artificial long-range ordered phases of borophene consisting of different combinations of boron chains seamlessly joined together can be achieved on Ag(100). Scanning tunneling microscopy measurements and theoretical calculations reveal that mixed-chain phases are more stable than the pure phase, and interact only weakly with the substrate. The mixed-chain phases with various proportions of different chains can be well separated based on the crystal direction of the substrate. The successful growth of mixed-chain phases is expected to deepen the impact of substrate tailored synthesis of borophene.

Combinatorial Selection Among Geometrical Isomers of Discrete Long-Carbon-Chain Naphthalenediimides Induces Local Order at the Liquid/Solid Interface

We report two families of naphthalenediimides (NDIs) symmetrically functionalized with discrete carbon chains comprising up to 55 carbon atoms (C_n-NDI-C_n, n = 39, 44, 50, and 55) and their self-assembly at the 1-phenyloctane/highly oriented pyrolytic graphite interface (1-PO/HOPG interface). The compounds differ by the presence or absence of two or three internal double bonds in the carbon chains (unsaturated and saturated C_n-NDI-C_n, respectively). Combinatorial distributions of geometrical isomers displaying either the E- or Z-configuration at each double bond are obtained for the unsaturated compounds. Analysis of the self-assembled monolayers of equally long unsaturated and saturated C_n-NDI-C_n by scanning tunneling microscopy (STM) reveal that all C_n-NDI-C_n tend to form lamellar systems featuring alternating areas of aromatic cores and carbon chains. Extended chain lengths are found to significantly increase disorder in the self-assembled monolayers due to misalignments and enhanced strength of interchain interactions. This phenomenon is antagonized by the local order-inducing effect of the internal double bonds: unsaturated C_n-NDI-C_n give qualitatively more ordered self-assembled monolayers compared to their saturated counterparts. The use of combinatorial distributions of unsaturated C_n-NDI-C_n geometrical isomers does not represent a limitation to achieve local order in the self-assembled monolayers. The self-assembly process operates a combinatorial search and selects the geometrical isomer(s) affording the most thermodynamically stable pattern, highlighting the adaptive character of the system. Finally, the antagonistic interplay between the extended carbon chain lengths and the presence of internal double bonds brings to the discovery of the lamellar "phase C" morphology for unsaturated C_n-NDI-C_n with n ≥ 50.

Directed Self-Assembly of Templatable Block Copolymers by Easily Accessible Magnetic Control

Magnetic control has been a prosperous and powerful contactless approach in arraying materials into high-order nanostructures. However, it is tremendously difficult to control organic polymers in this way on account of the weak magnetic response. The preparation of block copolymers (BCPs) with high magnetostatic energy is reported here, relying on an effective electrostatic coupling between paramagnetic ions and polymer side chains. As a result, the BCPs undergo a magnetically directed self-assembly to form microphase-segregated nanostructures with long-range order. It is emphasized that such a precisely controlled alignment of the BCPs is performed upon a single commercial magnet with low-intensity field (0.35 Tesla). This strategy is profoundly easy-to-handle in contrast to routine electromagnetic methods with high-intensity field (5-10 Tesla). More significantly, the paramagnetic metal component in the BCP samples can be smartly removed, providing a template effect with a preservation of the directed self-assembled nanofeatures for patterning follow-up functionalized species through the original binding site.

Exact Expressions of Spin-Spin Correlation Functions of the Two-Dimensional Rectangular Ising Model on a Finite Lattice

We employ the spinor analysis method to evaluate exact expressions of spin-spin correlation functions of the two-dimensional rectangular Ising model on a finite lattice, special process enables us to actually carry out the calculation process. We first present some exact expressions of correlation functions of the model with periodic-periodic boundary conditions on a finite lattice. The corresponding forms in the thermodynamic limit are presented, which show the short-range order. Then, we present the exact expression of the correlation function of the two farthest pair of spins in a column of the model with periodic-free boundary conditions on a finite lattice. Again, the corresponding form in the thermodynamic limit is discussed, from which the long-range order clearly emerges as the temperature decreases.

On the mechanism of long-range orientational order of fibroblasts

Long-range alignment ordering of fibroblasts have been observed in the vicinity of cancerous tumors and can be recapitulated with in vitro experiments. However, the mechanisms driving their ordering are not understood. Here, we show that local collision-driven nematic alignment interactions among fibroblasts are insufficient to explain observed long-range alignment. One possibility is that there exists another orientation field coevolving with the cells and reinforcing their alignment. We propose that this field reflects the mechanical cross-talk between the fibroblasts and the underlying fibrous material on which they move. We show that this long-range interaction can give rise to high nematic order and to the observed patterning of the cancer microenvironment.

Sub-10 nm features obtained from directed self-assembly of semicrystalline polycarbosilane-based block copolymer thin films

Highly-ordered arrays with sub-10 nm features are produced with topographical-directed self-assembly of low-molecular-weight poly(1,1-dimethyl silacyclobutane)-block-poly(methyl methacrylate). This system turns out to be of high interest for lithographic applications since the domain orientation is solely controlled through the polymer layer thickness, while the promotion of the microphase separation is obtained by a short thermal annealing process under mild conditions.

A modulation wave approach to the order hidden in disorder

The usefulness of a modulation wave approach to understanding and interpreting the highly structured continuous diffuse intensity distributions characteristic of the reciprocal spaces of the very large family of inherently flexible materials which exhibit ordered 'disorder' is pointed out. It is shown that both longer range order and truly short-range order are simultaneously encoded in highly structured diffuse intensity distributions. The long-range ordered crystal chemical rules giving rise to such diffuse distributions are highlighted, along with the existence and usefulness of systematic extinction conditions in these types of structured diffuse distributions.

Direct 3-D nanoparticle assemblies in thin films via topographically patterned surfaces

Simple yet versatile routes to generate macroscopically aligned 3-D NP arrays with tunable structures in supramolecular nanocomposite thin films are presented using faceted and lithographically patterned surfaces. These studies provide a powerful platform for the investigation of emerging structure-property relationships in functional nanocomposites, paving the way for the realization of next-generation devices.

Cell envelope and shape of Escherichia coli K12

Rod-shaped "ghosts" that are free of murein have been isolated from E. coli. The shape of these "ghosts" is maintained by a unit membrane soluble in sodium dodecyl sulfate. Ghosts consist of about 20-30% phospholipid (almost exclusively phosphatidylethanolamine) and 50-60% protein; a large fraction of the remaining material is lipopolysaccharide. Sodium dodecyl sulfate-gel electrophoresis reveals 4-5 different bands corresponding to molecular weights between 10,000 and 40,000. Treatment of ghosts with Pronase reduces this number to 3, and the rod shape still is not lost. Results of treatment of ghosts with a crude extract from Dictyostelium discoideum have supplied tentative evidence that at least one of these proteins is involved in the maintenance of rod shape. It does not appear too unlikely that these polypeptide chains are the final products of the genetic information specifying cellular shape.