Individual Building Blocks Research Articles

Carbonless DNA.

Carbonless DNA was designed by replacing all carbon atoms in the standard DNA building blocks with boron and nitrogen, ensuring isoelectronicity. Electronic structure quantum chemistry methods (DFT(ωB97XD)/aug-cc-pVDZ) were employed to study both the individual building blocks and the larger carbon-free DNA fragments. The reliability of the results was validated by comparing selected structures and binding energies using more accurate methods such as MP2, CCSD, and SAPT2+3(CCD)δMP2. Carbonless analogs of DNA components, including cytosine, thymine, guanine, adenine, and deoxyribose, were investigated, showing strong resemblance to the carbon-based versions in terms of spatial structure, polarity, and molecular interaction capabilities. Complementary base pairs of the carbonless analogs exhibited a similar number and length of hydrogen bonds as those found in their carbon-containing counterparts, with binding energies for A-T and G-C analogs remaining comparable. Carbonless DNA fragments containing two and six base pairs were studied, revealing double-helix structures analogous to natural DNA. Structural parameters such as fragment size, hydrogen bond lengths, and rise per base pair were consistent with those observed in unmodified DNA. Docking simulations with a 12 base pair fragment and netropsin as a ligand indicated a slight shift in binding preference for the carbonless DNA through the minor groove, with an approximate 25% increase in binding affinity compared to natural DNA.

Photonic circuit of arbitrary non-unitary systems

A design framework to implement non-unitary input–output operations to a practical unitary photonic integrated circuit is described. This is achieved by utilising the cosine-sine decomposition to recover the unitarity of the original operation. The recovered unitary operation is decomposed into fundamental unitary building blocks, forming a photonic integrated circuit network based on directional couplers and waveguide phase shifters. The individual building blocks are designed and optimised by three-dimensional full-wave simulations and scaled up using a circuit approach. The paper investigates the scalability and robustness of the design approach. Our study demonstrates that the proposed approach of performing unitary matrix completion can be applied to any arbitrary matrices. This design approach allows for implementation of non-unitary operations to perform various linear functions in neuromorphic photonics for computing, sensing, signal processing and communications.

The Impact of a Catalytic Site Mutation on the Shape and Mechanics of Tubulin Protofilaments

Alpha-beta heterodimers of tubulin proteins serve as the building blocks of microtubules, which are key biopolymers forming one of the principal systems of the cellular cytoskeleton. A detailed study of these building blocks, as well as their alterations caused by point mutations, contributes to a deeper understanding of physiological and pathological processes related to the cytoskeleton. This study presents an analysis of the impact of the E254N point mutation in the catalytic site of α-tubulin on the bending conformations of human recombinant tubulin tetramers using molecular dynamics methods. The models were constructed based on high-resolution cryo-electron microscopy data, allowing the reconstruction of three-dimensional structures of both wild-type and mutant tetramers. The simulations revealed that the primary difference between wild-type and mutant tubulin lies in the equilibrium bending direction of the protofilaments, while the bending amplitude, twisting, and associated stiffness remain largely unchanged. We propose that the observed differences in bending directions may be related to variations in protofilament tilts within microtubules, which aligns with previously published cryo-electron microscopy data. These findings provide valuable insights into the principles underlying the formation of the polymeric structure of microtubules based on the properties of their individual building blocks.

Improving operational decision-making through decision mining - utilizing method engineering for the creation of a decision mining method

ContextThis study addresses the challenge of enhancing the efficiency and agility of decision support software supporting both operational decision-making and software production teams developing decision support software. It centers on creating a method that assists in mining decisions, checking decisions on conformance, and improving decisions, which supports software production teams in developing decision support software. ObjectiveThe primary objective is to develop an explicit, clear, and structured approach for discovering, checking, and improving decisions using decision support software. The study aims to create a blueprint for software production teams to develop Decision Mining (DM) software, in line with recent advancements in the field. Additionally, it seeks to provide a consolidated, methodical overview of activities and deliverables in the DM research field. MethodThe research employs method engineering principles to construct a method for DM that leverages the existing body of knowledge by utilizing a Systematic Literature Review (SLR). The study focuses on developing individual building blocks and method fragments incorporated into seven DM scenarios. ResultsThe study led to the creation of a Decision Mining Method (DMM), which includes 138 method fragments grouped into eleven categories. These fragments were systematically merged to form a comprehensive DMM. The method encapsulates the complexity of DM and provides practical applicability in real-world scenarios, highlighted by the identification of seven distinct scenarios in DM phases. The study also conducted the first SLR in the DM field, providing a comprehensive overview of current practices and outcomes. ConclusionThe study helps in advancing the DM field by creating a structured approach and a comprehensive method for DM, aligning with recent developments in the field. It successfully aggregated the fragmented DM domain into a cohesive methodological overview, crucial for future research. The study also lays out a detailed agenda for future research, focusing on expanding and validating the DMM, incorporating cross-disciplinary insights, and addressing the challenges in machine learning within DM. The future research directions aim to refine and broaden the applicability of the DMM, ensuring its effectiveness in diverse practical contexts and contributing to a more holistic and comprehensive approach to decision mining.

Bond-centric modular design of protein assemblies.

We describe a modular bond-centric approach to protein nanomaterial design inspired by the rich diversity of chemical structures that can be generated from the small number of atomic valencies and bonding interactions. We design protein building blocks with regular coordination geometries and bonding interactions that enable the assembly of a wide variety of closed and opened nanomaterials using simple geometrical principles. Experimental characterization confirms successful formation of more than twenty multi-component polyhedral protein cages, 2D arrays, and 3D protein lattices, with a high (10-50 %) success rate and electron microscopy data closely matching the corresponding design models. Because of the modularity, individual building blocks can assemble with different partners to generate distinct regular assemblies, resulting in an economy of parts and enabling the construction of reconfigurable systems.

The Role of Alkyl Chains in the Thermoresponse of Supramolecular Network.

Supramolecular materials provide a pathway for achieving precise, highly ordered structures while exhibiting remarkable response to external stimuli, a characteristic not commonly found in covalently bonded materials. The design of self-assembled materials, where properties could be predicted/design from chemical nature of the individual building blocks, hinges upon ourability to relate macroscopic properties to individual building blocks - a feat which has thus far remained elusive. Here, a design approach is demonstrated to chemically engineer the thermal expansion coefficient of 2D supramolecular networks by over an order of magnitude (\boldmath 120 to \boldmath 1000 × 10-6K-1). This systematic study provides a clear pathway on how to carefully design the thermal expansion coefficient of a 2D molecular assembly. Specifically, a linear relation has been identified between the length of decorating alkyl chains and the thermal expansion coefficient. Counter-intuitively, the shorter the chains the larger is the thermal expansion coefficient. This precise control over thermo-mechanical properties marks a significant leap forward in the de-novo design of advanced 2D materials. The possibility to chemically engineer their thermo-mechanical properties holds promise for innovations in sensors, actuators, and responsive materials across diversefields.

The Antecedents of Utilitarian and Hedonic Motivations for Online Shopping Satisfaction

Empirical studies indicate that utilitarian and hedonic shopping motivations have a profound effect on customer satisfaction in a physical brick-and-mortar shopping environment. Studies have also started to surface which underscore the importance of these motivations in the realm of e-commerce. The study, therefore, seeks to determine the antecedents of utilitarian and hedonic motivations for online shopping satisfaction. A quantitative research method with a descriptive research design was implemented in this study. The data was collected through a survey method from a sample of 215 online shoppers in an emerging economy, South Africa. The study utilised previously validated scales. Multivariate regression analysis was performed to determine the factors that influence utilitarian and hedonic motivations for online shopping satisfaction. The results reveal that information availability, cost saving, wider selection, convenience, and efficiency are the antecedents of utilitarian dimensions that determine online shopping satisfaction, while status, adventure, social shopping, idea shopping, and gratification are considered the antecedents of hedonic motivations of online shopping that influence satisfaction. The results of the study offer insight into why consumers engage in online shopping by determining the factors that influence utilitarian and hedonic motivations. Accordingly, the study offers practical recommendations to e-retailers on how to best serve their customers by focusing on the individual building blocks of utilitarian and hedonic shopping motivations.

LiFe0.3Mn0.7PO4-on-MXene heterostructures as highly reversible cathode materials for Lithium-ion batteries

Two-dimensional (2D) heterostructure materials, incorporating the collective strengths and synergetic properties of individual building blocks, have attracted great interest as a novel paradigm in electrode materials science. The family of 2D transition metal carbides and nitrides (e.g., MXenes) has become an appealing platform for fabricating functional materials with strong application performance. Herein, a 2D LiFe0.3Mn0.7PO4 (LFMP)–on-MXene heterostructure composite is prepared through an electrostatic self-assembly procedure. The functional groups on the surface of MXenes possess highly electronegative properties that facilitate the incorporation of LFMPs into MXenes to construct heterostructure composites. The special heterostructure of nanosized-LiFe0.3Mn0.7PO4 and MXene provides rapid Li+ and electron transport in the cathodes. This LiFe0.3Mn0.7PO4-3.0 wt% MXene composite can exhibit an excellent rate capability of 98.3 mAh g−1 at 50C and a very stable cycling performance with a capacity retention of 94.3 % at 5C after 1000 cycles. Furthermore, NaFe0.3Mn0.7PO4-3.0 wt% MXene with stable cyclability can be obtained by an electrochemical conversion method with LiFe0.3Mn0.7PO4-3.0 wt% MXene. Ex-situ XRD suggests that LiFe0.3Mn0.7PO4-on-MXene achieves a highly reversible structural evolution with a solid solution phase transformation (LFMP→LixFe0.3Mn0.7PO4 (LxFMP), LxFMP→LFMP) and a two-phase reaction (LxFMP←→Fe0.3Mn0.7PO4 (FMP)). This work provides a new direction for the use of MXenes to fabricate 2D heterostructures for lithium-ion batteries.

(Keynote) Macroscopic Materials Synthesized from Nanoparticle Superlattices

One of the promises of nanotechnology in its early developmental stages was the ability to make designer materials with precise control over individual building block composition and organization in 3D space. In recent years, material synthesis methods have advanced to be able to create a multitude of nanoparticles of varying sizes, shapes, and compositions, providing a vast array of building blocks to use as materials fabrication components. Additionally, processing methods have been developed to arrange these nanoparticles into ordered arrays, to dry them into thin films, and even to sinter them into more complex bulk solids. However, the fundamental promise of being able to build a material with controlled hierarchical structure across all length scales (atomic crystal structure, molecular composition; nanoscale feature size, shape, and organization; microstructure; macroscopic form) has been challenging to realize. A materials synthesis and processing route that could create free-standing, macroscopic materials or arbitrary three-dimensional shapes with precisely controlled nanoparticle positions across the entirety of the material composition would therefore be a major advancement. Here, we demonstrate a nanoparticle-based building block called a “Nanocomposite Tecton (NCT)” that enables a self-assembly route to fabricating free-standing 3D solids of arbitrary macroscopic shapes that can utilize a multitude of different nanoparticle compositions, and also possess specifically programmed nanoscale particle arrangements and controlled microstructure. This talk will outline the key synthesis and processing steps that enable this method of making materials with programmed material structure across ~7 orders of magnitude in length scale, thereby realizing a long-standing goal of nanomaterials fabrication.

Design and engineering of 3D plasmonic superstructure based on Pickering emulsion templates for surface-enhanced Raman spectroscopy applications in chemical and biomedical sensing

The integration of Pickering emulsion as a versatile template facilitates the assembly of nanoscale and microscale NPs, leading to the formation of intricate 3D superstructures. These superstructures exhibit collective properties, including optical, electric, and catalytic functionalities, surpassing individual building block. This review comprehensively explores the design and engineering principles behind the creation of these multifaceted superstructures. The exploration begins with the fundamental aspects of surface chemistry governing nanoparticles, a crucial factor in directing their assembly behavior at the curved liquid–liquid emulsion interface. Emphasis is placed on understanding emulsion stability, a pivotal element guiding the formation of stable 3D architectures. The discussion extends to unraveling the underlying mechanisms promoting the formation of these 3D superstructures. The focus lies in elucidating the optical functionalities of these superstructures, particularly in the context of surface-enhanced Raman spectroscopy application. The surveyed literature showcases diverse Pickering emulsion-based strategies employed in the assembly of plasmonic nanoparticles into intricate superstructures, offering controlled architectures and unlocking unique potentials for chemical and biochemical sensing.

Experimental and Numerical Heat Transfer Assessment and Optimization of an IMSI Based Individual Building Block System of the Kingdom of Bahrain

The increase in energy consumption in Bahrain is a significant issue. Insulation blocks are crucial for reducing heat transfer from outside to inside buildings. However, there’s limited research on the thermal performance of Bahrain’s insulation building blocks. No research to date has been conducted in Bahrain to study the effect of plaster and insulation inserts on the R-value of the blocks. This study examines and optimizes the thermal resistance (R-value) of an ‘Integrated Masonry System International, Ltd. (IMSI)’ block, chosen due to its common use in Bahrain’s commercial and residential construction. The study involves experimental analysis using a hot box setup and numerical analysis through the finite element method (FEM), along with assessing the impact of insulation inserts in the block’s cavities. R-values are calculated and validated for accuracy. The R-value discrepancy between numerical and experimental findings is 2.411%, and between numerical and manufacturer’s data is 5.743%. It is also observed that a 25 mm external plaster, as required by Bahrain’s government (EWA), enhances the R-value by 79.34%. Furthermore, optimizing the IMSI block’s height increased the R-value by 10.67%.

Interfacial-Assembly-Induced In Situ Transformation from Aligned 1D Nanowires to Quasi-2D Nanofilms.

As the dimensionality of materials generally affects their characteristics, thin films composed of low-dimensional nanomaterials, such as nanowires (NWs) or nanoplates, are of great importance in modern engineering. Among various bottom-up film fabrication strategies, interfacial assembly of nanoscale building blocks holds great promise in constructing large-scale aligned thin films, leading to emergent or enhanced collective properties compared to individual building blocks. As for 1D nanostructures, the interfacial self-assembly causes the morphology orientation, effectively achieving anisotropic electrical, thermal, and optical conduction. However, issues such as defects between each nanoscale building block, crystal orientation, and homogeneity constrain the application of ordered films. The precise control of transdimensional synthesis and the formation mechanism from 1D to 2D are rarely reported. To meet this gap, we introduce an interfacial-assembly-induced interfacial synthesis strategy and successfully synthesize quasi-2D nanofilms via the oriented attachment of 1D NWs on the liquid interface. Theoretical sampling and simulation show that NWs on the liquid interface maintain their lowest interaction energy for the ordered crystal plane (110) orientation and then rearrange and attach to the quasi-2D nanofilm. This quasi-2D nanofilm shows enhanced electric conductivity and unique optical properties compared with its corresponding 1D geometry materials. Uncovering these growth pathways of the 1D-to-2D transition provides opportunities for future material design and synthesis at the interface.

Light-Induced Self-Assembled Polydiacetylene/Carbon Dot Functional "Honeycomb".

The design of functional supramolecular assemblies from individual molecular building blocks is a fundamental challenge in chemistry and material science. We report on the fabrication of "honeycomb" films by light-induced coassembly of diacetylene derivatives and carbon dots. Specifically, modulating noncovalent interactions between the carbon dots, macrocyclic diacetylene, and anthraquinone diacetylene facilitates formation of thin films exhibiting a long-range, uniform pore structure. We show that light irradiation at distinct wavelengths plays a key role in the assembly process and generation of unique macro-porous morphology, by both initiating interactions between the carbon dots and the anthraquinone moieties and giving rise to the topotactic polymerization of the polydiacetylene network. We further demonstrate utilization of the macro-porous film as a photocatalytic platform for water pollutant degradation and as potential supercapacitor electrodes, both applications taking advantage of the high surface area, hydrophobicity, and pore structure of the film.

Iron-carbohydrate complexes treating iron anaemia: Understanding the nano-structure and interactions with proteins through orthogonal characterisation

Intravenous (IV) iron-carbohydrate complexes are widely used nanoparticles (NPs) to treat iron deficiency anaemia, often associated with medical conditions such as chronic kidney disease, heart failure and various inflammatory conditions. Even though a plethora of physicochemical characterisation data and clinical studies are available for these products, evidence-based correlation between physicochemical properties of iron-carbohydrate complexes and clinical outcome has not fully been elucidated yet. Studies on other metal oxide NPs suggest that early interactions between NPs and blood upon IV injection are key to understanding how differences in physicochemical characteristics of iron-carbohydrate complexes cause variance in clinical outcomes. We therefore investigated the core-ligand structure of two clinically relevant iron-carbohydrate complexes, iron sucrose (IS) and ferric carboxymaltose (FCM), and their interactions with two structurally different human plasma proteins, human serum albumin (HSA) and fibrinogen, using a combination of cryo-scanning transmission electron microscopy (cryo-STEM), x-ray diffraction (XRD), small-angle x-ray scattering (SAXS) and small-angle neutron scattering (SANS). Using this orthogonal approach, we defined the nano-structure, individual building blocks and surface morphology for IS and FCM. Importantly, we revealed significant differences in the surface morphology of the iron-carbohydrate complexes. FCM shows a localised carbohydrate shell around its core, in contrast to IS, which is characterised by a diffuse and dynamic layer of carbohydrate ligand surrounding its core. We hypothesised that such differences in carbohydrate morphology determine the interaction between iron-carbohydrate complexes and proteins and therefore investigated the NPs in the presence of HSA and fibrinogen. Intriguingly, IS showed significant interaction with HSA and fibrinogen, forming NP-protein clusters, while FCM only showed significant interaction with fibrinogen. We postulate that these differences could influence bio-response of the two formulations and their clinical outcome. In conclusion, our study provides orthogonal characterisation of two clinically relevant iron-carbohydrate complexes and first hints at their interaction behaviour with proteins in the human bloodstream, setting a prerequisite towards complete understanding of the correlation between physicochemical properties and clinical outcome.

Chirality in topologically interlocked material systems

The present study focuses on the mechanical chirality in plate-type topologically interlocked material systems. Topologically interlocked material (TIM) systems are a class of dense architectured materials for which the mechanical response emerges from the elastic behavior of the building blocks and the contact-frictions interactions between the blocks. The resulting mechanical behavior is strongly non-linear due to the stability-instability characteristics of the internal load transfer pattern. Two tessellations are considered (square and hexagonal) and patches from each are used as templates. While individual building blocks are achiral, chirality emerges from the assembly pattern. The measure of microstructure circulation is introduced to identify the geometric chirality of TIM systems. TIM systems identified as geometrically chiral are demonstrated to possess mechanical chiral response with a force-torque coupling under transverse mechanical loading of the TIM plate. The chiral length is found to be constant during the elastic response, yet size-dependent. During nonlinear deformation, the chiral length scale increases significantly and again exhibits a strong size dependence. The principle of dissection is introduced to transform non-chiral TIM systems into chiral ones. In the linear deformation regime, the framework of chiral elasticity is shown to be applicable. In the non-linear deformation regime, chirality is found to strongly affect the mechanical behavior more significantly than in the linear regime. Experiments on selected TIM systems validate key findings of the main computational study with the finite element method.

Space-tiled colloidal crystals from DNA-forced shape-complementary polyhedra pairing.

Generating space-filling arrangements of most discrete polyhedra nanostructures of the same shape is not possible. However, if the appropriate individual building blocks are selected (e.g., cubes), or multiple shapes of the appropriate dimensions are matched (e.g., octahedra and tetrahedra) and their pairing interactions are subsequently forced, space-filled architectures may be possible. With flexible molecular ligands (polyethylene glycol-modified DNA), the shape of a polyhedral nanoparticle can be deliberately altered and used to realize geometries that favor space tessellation. In this work, 10 new colloidal crystals were synthesized from DNA-modified nanocrystal building blocks that differed in shapes and sizes, designed to form space-filling architectures with micron-scale dimensions. The insights and capabilities provided by this new strategy substantially expand the scope of colloidal crystals possible and provide an expanded tool kit for researchers interested in designing metamaterials.

Polyoxometalate Induced Assembly Into Surface Functionalized Multidimensional Heterostructures with Enhanced Catalytic Activity.

The self-assembly of inorganic nanocrystals offers an efficient way for the fabrication of functional materials. However, it is still challenging for the construction of multidimensional nanostructures with controllable shapes, compositions and functions. Here, a series of heterostructures in different dimensions by surface modification of polyoxometalate (POM) clusters is developed. Three kinds of POM clusters(phosphomolybdic acid (PMA), phosphotungstic acid (PTA) and silicotungstic acid (STA) and five kinds of metal oxides (TiO2, VOx, La2O3, In2O3 and Gd2O3) can be used as building blocks, and a class of 1D, 2D and 3D heterostructures can be achieved by the control of surface ligand coverage. Compared with individual building blocks and other cluster-based superstructures, TiO2-PMA superstructures exhibit enhanced catalytic activity toward thioether oxidations, which is attributed to the electron transfer between TiO2 and POM clusters.

Modelling of Modular Soft Robots: From a Single to Multiple Building Blocks

Despite the advances in soft robots, their modelling is still one of the research challenges due to the complexity and non-linearity of their soft nature. A novel design of reconfigurable soft robots was recently introduced to bring more maturity to the field of soft robots. Here, a modelling study of the building blocks and the assembled soft robot is developed for a deeper understanding of the system and for predicting their behaviours. The model is validated using several sets of individual and multiple building blocks and the results show good tracking between the model and the experiments with reasonable errors. Towards adopting the model in robotic applications, a grasping setup of 2 assembled soft fingers is demonstrated where the model is used to predict the grasping force and compared to feedback sensing. The force prediction reveals the adaptability of the model and its robustness.

A broad-spectrum antibacterial hydrogel based on the synergistic action of Fmoc-phenylalanine and Fmoc-lysine in a co-assembled state.

Multicomponent biomolecular self-assembly is fundamental for accomplishing complex functionalities of biosystems. Self-assembling peptides, amino acids, and their conjugates serve as a versatile platform for developing biomaterials. However, the co-assembly of multiple building blocks showing synergistic interplay between individual components and producing biomaterials with emergent functional attributes is much less explored. In this study, we have formulated minimalistic co-assembled hydrogels composed of Fmoc-phenylalanine and Fmoc-lysine. The co-assembled systems display broad-spectrum antimicrobial potency, a feature absent in individual building blocks. A comprehensive biophysical analysis demonstrates the physicochemical features of the hydrogels eliciting the antibacterial response. MD simulation further reveals a unique fibrillar architecture with Fmoc-phenylalanine forming the fibril core surrounded by positively charged Fmoc-lysine surface residues, thereby enhancing the interaction with negatively charged bacterial membranes, causing membrane disruption and cell death. Thus, this study provides molecular-level insight into the emergent properties of a multicomponent system, affording an excellent paradigm for developing novel biomaterials.

Directing and reconfiguring colloidal assembly by disclination networks in nematic liquid crystal as templates

Exotic structures with interesting physical and chemical properties can be achieved by self-organizing engineered building blocks. The central aim for self-assembly is to precisely control the position and orientation of individual building blocks. In this work, we use topological defects (disclinations) in nematic liquid crystals as templates to direct the self-assembly of colloidal particles into designable 3D structures. By photopatterning preprogrammed molecular orientations at two confining surfaces, we created pre-designable disclination networks and characterized their interactions with spherical colloidal particles. We find that colloidal particles are attracted to different disclinations depending on the orientation of the point defect (elastic dipole) around the colloids. We demonstrate that the positions, network structures, and orientation of the elastic dipoles of the colloidal chains can be pre-designed and reconfigured with remote illumination of polarized light.