Super Atomic Clusters: Design Rules and Potential for Building Blocks of Materials

2018 ◽  
Vol 118 (11) ◽  
pp. 5755-5870 ◽  
Author(s):  
Puru Jena ◽  
Qiang Sun
Keyword(s):  
Building Blocks ◽  
Atomic Clusters ◽  
Design Rules

scholarly journals Biocatalysis of d,l-Peptide Nanofibrillar Hydrogel

Molecules ◽  
2020 ◽  
Vol 25 (13) ◽  
pp. 2995 ◽  
Author(s):  
Tiziano Carlomagno ◽  
Maria C. Cringoli ◽  
Slavko Kralj ◽  
Marina Kurbasic ◽  
Paolo Fornasiero ◽  
...  
Keyword(s):  
Self Assembly ◽  
Solid Phase ◽  
Building Blocks ◽  
Cd Spectroscopy ◽  
Tem Analysis ◽  
Design Rules ◽  
Self Assembling ◽  
Transmission Electron ◽  
Oscillatory Rheometry ◽  
The Many

Self-assembling peptides are attracting wide interest as biodegradable building blocks to achieve functional nanomaterials that do not persist in the environment. Amongst the many applications, biocatalysis is gaining momentum, although a clear structure-to-activity relationship is still lacking. This work applied emerging design rules to the heterochiral octapeptide sequence His–Leu–DLeu–Ile–His–Leu–DLeu–Ile for self-assembly into nanofibrils that, at higher concentration, give rise to a supramolecular hydrogel for the mimicry of esterase-like activity. The peptide was synthesized by solid-phase and purified by HPLC, while its identity was confirmed by 1H-NMR and electrospray ionization (ESI)-MS. The hydrogel formed by this peptide was studied with oscillatory rheometry, and the supramolecular behavior of the peptide was investigated with transmission electron microscopy (TEM) analysis, circular dichroism (CD) spectroscopy, thioflavin T amyloid fluorescence assay, and attenuated total reflectance (ATR) Fourier-transform infrared (FT-IR) spectroscopy. The biocatalytic activity was studied by monitoring the hydrolysis of p-nitrophenyl acetate (pNPA) at neutral pH, and the reaction kinetics followed an apparent Michaelis–Menten model, for which a Lineweaver–Burk plot was produced to determine its enzymatic parameters for a comparison with the literature. Finally, LC–MS analysis was conducted on a series of experiments to evaluate the extent of, if any, undesired peptide acetylation at the N-terminus. In conclusion, we provide new insights that allow gaining a clearer picture of self-assembling peptide design rules for biocatalysis.

Morphology control and property design of boronate dynamic nanostructures

2019 ◽  
Vol 10 (19) ◽  
pp. 2436-2446 ◽  
Author(s):  
Fuli Zhao ◽  
Anjie Dong ◽  
Liandong Deng ◽  
Ruiwei Guo ◽  
Jianhua Zhang
Keyword(s):  
Morphology Control ◽  
Building Blocks ◽  
Design Rules

The morphogenesis of boronate dynamic nanostructures (BDNs) with different building blocks was systematically investigated to elucidate their design rules.

scholarly journals Exploring the rules of chimeric antigen receptor phenotypic output using combinatorial signaling motif libraries and machine learning

2022 ◽  
Author(s):  
Kyle G Daniels ◽  
Shangying Wang ◽  
Milos S Simic ◽  
Hersh K Bhargava ◽  
Sara Capponi ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Chimeric Antigen Receptor ◽  
Antigen Receptor ◽  
Building Blocks ◽  
Cell Fates ◽  
Design Rules ◽  
Binding Motifs ◽  
The Neural Network ◽  
Tumor Killing

Chimeric antigen receptor (CAR) costimulatory domains steer the phenotypic output of therapeutic T cells. In most cases these domains are derived from native immune receptors, composed of signaling motif combinations selected by evolution. To explore if non-natural combinations of signaling motifs could drive novel cell fates of interest, we constructed a library of CARs containing ~2,300 synthetic costimulatory domains, built from combinations of 13 peptide signaling motifs. The library produced CARs driving diverse fate outputs, which were sensitive motif combinations and configurations. Neural networks trained to decode the combinatorial grammar of CAR signaling motifs allowed extraction of key design rules. For example, the non-native combination of TRAF- and PLCg1-binding motifs was found to simultaneously enhance cytotoxicity and stemness, a clinically desirable phenotype associated with effective and durable tumor killing. The neural network accurately predicts that addition of PLCg1-binding motifs improves this phenotype when combined with TRAF-binding motifs, but not when combined with other immune signaling motifs (e.g. PI3K- or Grb2- binding motifs). This work shows how libraries built from the minimal building blocks of signaling, combined with machine learning, can efficiently guide engineering of receptors with desired phenotypes.

On the Geometry of Stiffness and Compliance Under Concatenation

2019 ◽  
Author(s):  
Charles J. Kim
Keyword(s):  
Building Block ◽  
Compliant Mechanisms ◽  
Building Blocks ◽  
Design Rules ◽  
Multiple Mechanism ◽  
Kinematic Behavior ◽  
Geometric Nature

Abstract Eigentwists and eigenwrenches capture the stationary stiffness behavior of compliant mechanisms and can be related to a mechanism’s primary kinematic behavior. The nature of concatenation of multiple mechanism building blocks is not well-understood. In this paper, we consider the mechanics of concatenation and develop design rules that capture the geometric nature of concatenation in terms of eigenwrenches and eigentwists. The rules are illustrated through mechanisms from the literature. The design rules have potential to provide intelligent guidance for systematic building block synthesis of compliant mechanisms.

Design Language for Airplane Geometries Using the Unified Modeling Language

2009 ◽  
Author(s):  
Daniel Bo¨hnke ◽  
Axel Reichwein ◽  
Stephan Rudolph
Keyword(s):  
Production System ◽  
Unified Modeling Language ◽  
Object Oriented ◽  
Building Blocks ◽  
Modeling Language ◽  
Design Rules ◽  
Unified Modeling ◽  
Design Language ◽  
Design Languages ◽  
Specific Rule

The design language allows the construction of a variety of airplan designs. The syntax of the design language relies on the standardized Unified Modeling Language (UML) and consists of an object-oriented vocabulary (i.e. points, lines, profiles, wings, etc.) comparable to building blocks, and design rules (i.e. building laws) which represent the building knowledge used. In the terminology of graph-based design languages, the building blocks are the information objects which represent the static aspects of the design because they represent indivisible design entities. They are represented as UML classes and instances and their interrelation forms an object-oriented class hierarchy. The design rules represent the dynamic aspects of the design and express the building knowledge as stepwise activities. Finally, a production system (i.e. a specific rule set) is able to create an airplane geometry and generates design variants through manual modifications of the production system.

On the Geometry of Stiffness and Compliance Under Concatenation

2020 ◽  
Vol 12 (2) ◽  
Author(s):  
Charles J. Kim
Keyword(s):  
Building Block ◽  
Design Problem ◽  
Compliant Mechanisms ◽  
Building Blocks ◽  
Design Rules ◽  
Multiple Mechanism ◽  
Kinematic Behavior ◽  
Geometric Nature

Abstract Eigentwists and eigenwrenches capture the stationary stiffness behavior of compliant mechanisms and can be related to a mechanism’s primary kinematic behavior. The nature of concatenation of multiple mechanism building blocks is not well understood. In this paper, we consider the mechanics of concatenation and develop design rules that capture the geometric nature of concatenation in terms of eigenwrenches and eigentwists. The rules are illustrated through mechanisms from the literature and an example design problem. The design rules have potential to provide intelligent guidance for systematic building block synthesis of compliant mechanisms.

DESIGNING CLUSTERS AS SUPERELEMENTS

1996 ◽  
Vol 03 (01) ◽  
pp. 993-999 ◽  
Author(s):  
P. JENA ◽  
S.N. KHANNA ◽  
B.K. RAO
Keyword(s):  
Building Blocks ◽  
Design Guidelines ◽  
Atomic Clusters ◽  
New Class ◽  
Cluster Interaction ◽  
State Of Matter ◽  
The Stability ◽  
Material Form ◽  
Atomic And Electronic Structure ◽  
New State Of Matter

Atomic clusters formed by agglomeration of atoms constitute a new state of matter with novel properties which depend uniquely on their size, shape, dimensionality, and composition. If clusters could be designed in such a way that they can retain their structure when assembled into a material form, it is possible to envision a new class of solids with clusters as building blocks. These cluster-assembled materials would exhibit rather uncommon properties, thus enlarging the frontiers of material science. Self-consistent calculations have been carried out to study the effect of composition and geometry on the stability and reactivity of clusters. An understanding of the role that atomic and electronic structure play on cluster-cluster interaction would enable us to design cluster materials. This paper deals with the design guidelines, as well as properties of cluster-assembled crystals. It is shown that clusters designed to mimic the properties of known atoms can be viewed as superelements and thus help extend the limits of the current periodic table.

Atomic clusters: Building blocks for a class of solids

1995 ◽  
Vol 51 (19) ◽  
pp. 13705-13716 ◽  
Author(s):  
S. N. Khanna ◽  
P. Jena
Keyword(s):  
Building Blocks ◽  
Atomic Clusters

scholarly journals An All-Optical Excitonic Switch Templated on a DNA Scaffold Operated in the Liquid and Solid Phases

2020 ◽  
Author(s):  
Donald L. Kellis
Keyword(s):  
Self Assembly ◽  
Light Harvesting ◽  
Dna Nanotechnology ◽  
Building Blocks ◽  
Optically Active ◽  
Electronic Circuits ◽  
Design Rules ◽  
All Optical ◽  
Solid Phases ◽  
Liquid And Solid Phases

The natural excitonic circuitry of photosynthetic organisms, including light harvesting antennas, provides a distinctive example of a highly attractive bio-inspired alternative to electronic circuits. Excitonics, which capitalizes on spatially arranged optically active molecules ability to capture and transfer light energy below the diffraction limit of light has garnered recognition as a potential disruptive replacement for electronic circuits. However, assembly of optically active molecules to construct even simple excitonic devices has been impeded by the limited maturity of suitable molecular scale assembly technologies. An example of nanophotonic circuitry, natural light harvesting antennas employ proteins as scaffolds to organize and self-assemble light-active molecules into excitonic networks capable of capturing and converting light to excitonic energy, and transferring that energy at ambient temperature. Protein self-assembly is extremely complex due to the over 20 amino acids building blocks used in the self-assembly process and the difficulty of predicting how proteins actually fold. An alternative method for organization and self-assembly may be found in the field DNA nanotechnology. DNA nanotechnology provides the most viable means to organize optically active molecules as there are only four nucleic acid building blocks and well-established simple design rules. Leveraging DNA nanotechnology will meet the requirements of precise proximity (selectivity) and appropriate number (specificity) needed to create larger arrays of multifunctional optically active molecules. Employing the design rules of DNA self-assembly, we have designed, engineered and operated an all-optical excitonic switch consisting of donor and acceptor chromophores and diarylethene photochromic modulating units assembled with nanometer scale precision. This work demonstrates the first integration of three diarylethene photochromic units into a single DNA oligonucleotide. Photoisomerization of diarylethenes has been shown to be one of the fastest photochemical reactions thereby affording potential switching speeds in the 10's of picoseconds. Adopting diarylethenes as optically reversible switching units provided the ability to operate the all-optical excitonic switch through nearly 200 cycles without overt cyclic fatigue and excellent ON/OFF stability in both the liquid and solid phases. Assessing the static and dynamic cycling behavior of the all-optical excitonic switch allowed for the development of a model to predict characteristic switching times (τ) of 17.0 and 23.3 seconds for the liquid and solid phases, respectively which align well with the experimental data thereby validating the model. While these times are much faster than that of other non-optically based DNA-templated excitonic switches (τ ~ 10's of minutes), the times noted here are limited by the steady-state optical instrumentation, (i.e., photon flux, detector integration time, and slit cycling speed), used to characterize the all-optical excitonic switches. Our model predicts switching times in the picosecond range could be achieved with the use of a high peak power ultrafast laser. First-order calculations estimate the all-optical excitonic switch has a footprint 37X smaller, a smaller volume by over 3 orders of magnitude and over an order of magnitude less energy per cycle than a state-of-the-art MOSFET. These findings, combined with no production of waste products and the potential ability to switch at speeds in the 10's of picoseconds, establishes a prospective pathway toward all-optical excitonic circuits.

Photochemical Evolution of Interstellar/Precometary Organic Material

1997 ◽  
Vol 161 ◽  
pp. 23-47 ◽  
Author(s):  
Louis J. Allamandola ◽  
Max P. Bernstein ◽  
Scott A. Sandford
Keyword(s):  
Origin Of Life ◽  
Building Blocks ◽  
Complex Species ◽  
Infrared Observations ◽  
Interstellar Ice ◽  
Polycyclic Aromatic ◽  
Ultraviolet Photolysis ◽  
The Origin Of Life ◽  
Simple Molecules ◽  
Complex Organic

AbstractInfrared observations, combined with realistic laboratory simulations, have revolutionized our understanding of interstellar ice and dust, the building blocks of comets. Since comets are thought to be a major source of the volatiles on the primative earth, their organic inventory is of central importance to questions concerning the origin of life. Ices in molecular clouds contain the very simple molecules H2O, CH3OH, CO, CO2, CH4, H2, and probably some NH3and H2CO, as well as more complex species including nitriles, ketones, and esters. The evidence for these, as well as carbonrich materials such as polycyclic aromatic hydrocarbons (PAHs), microdiamonds, and amorphous carbon is briefly reviewed. This is followed by a detailed summary of interstellar/precometary ice photochemical evolution based on laboratory studies of realistic polar ice analogs. Ultraviolet photolysis of these ices produces H2, H2CO, CO2, CO, CH4, HCO, and the moderately complex organic molecules: CH3CH2OH (ethanol), HC(= O)NH2(formamide), CH3C(= O)NH2(acetamide), R-CN (nitriles), and hexamethylenetetramine (HMT, C6H12N4), as well as more complex species including polyoxymethylene and related species (POMs), amides, and ketones. The ready formation of these organic species from simple starting mixtures, the ice chemistry that ensues when these ices are mildly warmed, plus the observation that the more complex refractory photoproducts show lipid-like behavior and readily self organize into droplets upon exposure to liquid water suggest that comets may have played an important role in the origin of life.

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