Optimal DNA Codes for Computing and Self-Assembly

2011 ◽  
pp. 1-14
Author(s):  
Max H. Garzon ◽  
Vinhthuy Phan ◽  
Andrew Neel
Keyword(s):  
Gibbs Energy ◽  
Self Assembly ◽  
Building Blocks ◽  
Exhaustive Search ◽  
High Quality ◽  
Quantitative Characterization ◽  
Dna Codes ◽  
Large Sets ◽  
Very High

DNA has been re-discovered and explored in the last decade as a “smart glue” for self-assembly from the “bottom-up” at nanoscales through mesoscales to micro- and macro-scales. These applications require an unprecedented degree of precision in placing atom-scale components. Finding large sets of probes to serve as anchors for such applications has been thus explored in the last few years through several methods. We describe results of a tour de force to conduct an exhaustive search to produce large codes that are (nearly) maximal sets while guaranteeing high quality, as measured by the minimum Gibbs energy between any pair of code words, and other criteria. We also present a quantitative characterization of the sets for sizes up to 20-mers and show how critical building blocks can be extracted to produce codes of very high quality for larger lengths by probabilistic combinations, for which an exhaustive search is out of reach.

scholarly journals Synthesis and characterization of poly(amino acid methacrylate)-stabilized diblock copolymer nano-objects

2015 ◽  
Vol 6 (10) ◽  
pp. 1805-1816 ◽  
Author(s):  
Vincent Ladmiral ◽  
Alexandre Charlot ◽  
Mona Semsarilar ◽  
Steven. P. Armes
Keyword(s):  
Amino Acid ◽  
Diblock Copolymer ◽  
Michael Addition ◽  
Self Assembly ◽  
Building Blocks ◽  
Synthesis And Characterization

Two amino acid methacrylates prepared via Michael addition are used as building blocks to prepare novel diblock copolymer nano-objects via polymerisation-induced self-assembly.

scholarly journals Epitaxial Growth of III-Nitride Layers on Aluminum Nitride Substrates

1999 ◽  
Vol 4 (S1) ◽  
pp. 411-416 ◽  
Author(s):  
L.J. Schowalter ◽  
Y. Shusterman ◽  
R. Wang ◽  
I. Bhat ◽  
G. Arunmozhi ◽  
...  
Keyword(s):  
Epitaxial Growth ◽  
Electrical Characterization ◽  
High Quality ◽  
Force Microscopy ◽  
Ion Channeling ◽  
Atomic Force ◽  
Image Position ◽  
Nitride Layers ◽  
Very High

High quality, epitaxial growth of AlN and AlxGa1−xN by OMVPE has been demonstrated on single-crystal AlN substrates. Here we report characterization of epitaxial layers on an a-face AlN substrate using Rutherford Backscattering/ion channeling, atomic force microscopy (AFM), x-ray rocking curves, and preliminary electrical characterization. Ion channeling along the [100] axis gives a channeling minimum yield of 1.5% indicating a very high quality epitaxial layer.

Epitaxial Growth of III-Nitride Layers on Aluminum Nitride Substrates

1998 ◽  
Vol 537 ◽  
Author(s):  
L.J. Schowalter ◽  
Y. Shusterman ◽  
R. Wang ◽  
I. Bhat ◽  
G. Arunmozhi ◽  
...  
Keyword(s):  
Epitaxial Growth ◽  
Electrical Characterization ◽  
High Quality ◽  
X Ray ◽  
Force Microscopy ◽  
Ion Channeling ◽  
Atomic Force ◽  
Nitride Layers ◽  
Very High

AbstractHigh quality, epitaxial growth of AlN and AlxGal-xN by OMVPE has been demonstrated on single-crystal AIN substrates. Here we report characterization of epitaxial layers on an a-face AlN substrate using Rutherford Backscattering/ion channeling, atomic force microscopy (AFM), x-ray rocking curves, and preliminary electrical characterization. Ion channeling along the [1010] axis gives a channeling minimum yield of 1.5% indicating a very high quality epitaxial layer.

scholarly journals Bioinformatics Analysis of Targeted Metabolomics—Uncovering Old and New Tales of Diabetic Mice under Medication

Endocrinology ◽  
2008 ◽  
Vol 149 (7) ◽  
pp. 3478-3489 ◽  
Author(s):  
Elisabeth Altmaier ◽  
Steven L. Ramsay ◽  
Armin Graber ◽  
Hans-Werner Mewes ◽  
Klaus M. Weinberger ◽  
...  
Keyword(s):  
Drug Testing ◽  
Diabetic Mice ◽  
Quantitative Characterization ◽  
Data Set ◽  
Systematic Analysis ◽  
Large Sets ◽  
Medical Disorders ◽  
Rosiglitazone Treatment ◽  
Target Effects

Metabolomics is a powerful tool for identifying both known and new disease-related perturbations in metabolic pathways. In preclinical drug testing, it has a high potential for early identification of drug off-target effects. Recent advances in high-precision high-throughput mass spectrometry have brought the metabolomic field to a point where quantitative, targeted, metabolomic measurements with ready-to-use kits allow for the automated in-house screening for hundreds of different metabolites in large sets of biological samples. Today, the field of metabolomics is, arguably, at a point where transcriptomics was about 5 yr ago. This being so, the field has a strong need for adapted bioinformatics tools and methods. In this paper we describe a systematic analysis of a targeted quantitative characterization of more than 800 metabolites in blood plasma samples from healthy and diabetic mice under rosiglitazone treatment. We show that known and new metabolic phenotypes of diabetes and medication can be recovered in a statistically objective manner. We find that concentrations of methylglutaryl carnitine are oppositely impacted by rosiglitazone treatment of both healthy and diabetic mice. Analyzing ratios between metabolite concentrations dramatically reduces the noise in the data set, allowing for the discovery of new potential biomarkers of diabetes, such as the N-hydroxyacyloylsphingosyl-phosphocholines SM(OH)28:0 and SM(OH)26:0. Using a hierarchical clustering technique on partial η2 values, we identify functionally related groups of metabolites, indicating a diabetes-related shift from lysophosphatidylcholine to phosphatidylcholine levels. The bioinformatics data analysis approach introduced here can be readily generalized to other drug testing scenarios and other medical disorders.

scholarly journals Bottom-up Chemoenzymatic Synthesis Towards Novel Fluorinated Cellulose-like Materials

2020 ◽  
Author(s):  
Peterson de Andrade ◽  
Juan Munoz ◽  
Giulia Pergolizzi ◽  
Valeria Gabrielli ◽  
Sergey Nepogodiev ◽  
...  
Keyword(s):  
Self Assembly ◽  
Soft Matter ◽  
Water Solubility ◽  
Hierarchical Structures ◽  
Building Blocks ◽  
Chemoenzymatic Synthesis ◽  
Cellulose Ii ◽  
Fluorinated Building Blocks ◽  
A Minor

Understanding the fine details of self-assembly of building blocks into complex hierarchical structures represents a major challenge en route to the design and preparation of soft matter materials with specific properties. Enzymatically-synthesised cellodextrins are known to have limited water solubility beyond DP9, a point at which they self-assemble into particles resembling the anti-parallel cellulose II crystalline packing. We have prepared and characterized a series of site-selectively fluorinated cellodextrins of different degrees of fluorination and substitution patterns by chemoenzymatic synthesis. The structural characterization of these materials at different length scales, combining advanced NMR and microscopy methods, showed that multiply 6-fluorinated cellodextrin chains assembled into particles presenting morphological and crystallinity features that are unprecedented for cellulose-like materials. In contrast, the introduction of a single fluorine atom per cellodextrin chain had a minor impact on materials structure. Our work emphasizes the strength of combining chemoenzymatic synthesis, fluorinated building blocks and advanced NMR and microscopy methods for the thorough characterization of hierarchical structures, leading to the controlled design of new biomaterials with specific properties.

Self-Assembly of Cyclic Dipeptides: Platforms for Functional Materials

2020 ◽  
Vol 27 (8) ◽  
pp. 688-697
Author(s):  
Yu Chen ◽  
Kai Tao ◽  
Wei Ji ◽  
Pandeeswar Makam ◽  
Sigal Rencus-Lazar ◽  
...  
Keyword(s):  
Self Assembly ◽  
Functional Materials ◽  
Building Blocks ◽  
Cyclic Dipeptide ◽  
Design Synthesis ◽  
Cyclic Dipeptides ◽  
The Past ◽  
Supramolecular Architectures ◽  
Structural Rigidity

Supramolecular self-assembled functional materials comprised of cyclic dipeptide building blocks have excellent prospects for biotechnology applications due to their exceptional structural rigidity, morphological flexibility, ease of preparation and modification. Although the pharmacological uses of many natural cyclic dipeptides have been studied in detail, relatively little is reported on the engineering of these supramolecular architectures for the fabrication of functional materials. In this review, we discuss the progress in the design, synthesis, and characterization of cyclic dipeptide supramolecular nanomaterials over the past few decades, highlighting applications in biotechnology and optoelectronics engineering.

scholarly journals Synthesis by self-assembly and structural characterization of a new co-crystal system {[Cu(NO3)2(H2O)2]L1(NO3)2} (L1 = 1,1′-dibenzyl-3,3′-butyl-diimidazolium-2,2′-diylidene) from copper nitrate and a carbene precursor

2008 ◽  
Vol 6 (4) ◽  
pp. 505-508 ◽  
Author(s):  
Jorge Doimeadios
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Structural Characterization ◽  
Self Assembly ◽  
Three Dimensional ◽  
Building Blocks ◽  
Copper Nitrate ◽  
Supramolecular Network ◽  
Crystal System

AbstractHerein, the first example of a co-crystal system formed by an imidazolium nitrate, a carbene precursor, and copper (II) nitrate, {[Cu(NO3)2(H2O)2]L1(NO3)2} (1) (L1 = 1,1′-dibenzyl-3,3′-butyl-diimidazolium-2,2′-diylidene) is reported. These two building blocks are connected in the solid state through hydrogen bonds to generate a three-dimensional supramolecular network.

scholarly journals Invention as a combinatorial process: evidence from US patents

2015 ◽  
Vol 12 (106) ◽  
pp. 20150272 ◽  
Author(s):  
Hyejin Youn ◽  
Deborah Strumsky ◽  
Luis M. A. Bettencourt ◽  
José Lobo
Keyword(s):  
New Technologies ◽  
Building Blocks ◽  
The United States ◽  
Quantitative Characterization ◽  
Inventive Activity ◽  
Reduced Rate ◽  
Patented Inventions ◽  
States Patent ◽  
Combinatorial Process

Invention has been commonly conceptualized as a search over a space of combinatorial possibilities. Despite the existence of a rich literature, spanning a variety of disciplines, elaborating on the recombinant nature of invention, we lack a formal and quantitative characterization of the combinatorial process underpinning inventive activity. Here, we use US patent records dating from 1790 to 2010 to formally characterize invention as a combinatorial process. To do this, we treat patented inventions as carriers of technologies and avail ourselves of the elaborate system of technology codes used by the United States Patent and Trademark Office to classify the technologies responsible for an invention's novelty. We find that the combinatorial inventive process exhibits an invariant rate of ‘exploitation’ (refinements of existing combinations of technologies) and ‘exploration’ (the development of new technological combinations). This combinatorial dynamic contrasts sharply with the creation of new technological capabilities—the building blocks to be combined—that has significantly slowed down. We also find that, notwithstanding the very reduced rate at which new technologies are introduced, the generation of novel technological combinations engenders a practically infinite space of technological configurations.

scholarly journals Bottom-up Chemoenzymatic Synthesis Towards Novel Fluorinated Cellulose-like Materials

2020 ◽  
Author(s):  
Peterson de Andrade ◽  
Juan Munoz ◽  
Giulia Pergolizzi ◽  
Valeria Gabrielli ◽  
Sergey Nepogodiev ◽  
...  
Keyword(s):  
Self Assembly ◽  
Soft Matter ◽  
Water Solubility ◽  
Hierarchical Structures ◽  
Building Blocks ◽  
Chemoenzymatic Synthesis ◽  
Cellulose Ii ◽  
Fluorinated Building Blocks ◽  
A Minor

Understanding the fine details of self-assembly of building blocks into complex hierarchical structures represents a major challenge en route to the design and preparation of soft matter materials with specific properties. Enzymatically-synthesised cellodextrins are known to have limited water solubility beyond DP9, a point at which they self-assemble into particles resembling the anti-parallel cellulose II crystalline packing. We have prepared and characterized a series of site-selectively fluorinated cellodextrins of different degrees of fluorination and substitution patterns by chemoenzymatic synthesis. The structural characterization of these materials at different length scales, combining advanced NMR and microscopy methods, showed that multiply 6-fluorinated cellodextrin chains assembled into particles presenting morphological and crystallinity features that are unprecedented for cellulose-like materials. In contrast, the introduction of a single fluorine atom per cellodextrin chain had a minor impact on materials structure. Our work emphasizes the strength of combining chemoenzymatic synthesis, fluorinated building blocks and advanced NMR and microscopy methods for the thorough characterization of hierarchical structures, leading to the controlled design of new biomaterials with specific properties.

scholarly journals Controlled Formation of Catalytic and Emissive Gold Nanoclusters with a Synthetic Self-Assembled Protein Toroid

2020 ◽  
Author(s):  
David Bouzada ◽  
Ester Polo ◽  
Elena López ◽  
Yolanda Pérez ◽  
Cristian Vidal ◽  
...  
Keyword(s):  
Chemical Synthesis ◽  
Self Assembly ◽  
Solid Phase ◽  
Recombinant Expression ◽  
Solid Phase Peptide Synthesis ◽  
Gold Nanoclusters ◽  
Building Blocks ◽  
Biophysical Characterization ◽  
Self Assembled

<div>Self-assembled proteins are privileged building blocks for the bottom-up organization of matter at the nanoscale. However, since most proteins are very large, they have to be produced by recombinant expression, which is less versatile and flexible than chemical synthesis. Here, we show that we can bridge the potential of proteins for nanofabrication with the simplicity and versatility of solid-phase peptide synthesis by relying on the self-assembly of the viral protein gp23.1, a small 50-residue protein that oligomerizes in solution to form a stable toroidal hexamer. We report the chemical synthesis and basic biophysical characterization of a gp23.1 mutant and show that its self-assembled hexamer templates the formation of highly monodisperse gold nanoclusters of about 1.3 nm inside its central cavity. The resulting nanoclusters show catalytic activity in cycloisomerization reactions as well as luminescence emission. This work demonstrates the versatility of this small self- assembled ring protein for a variety of nanotechnological applications.</div>

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