scholarly journals EVOLVING INDUCTIVE GENERALIZATION VIA GENETIC SELF-ASSEMBLY

2006 ◽  
Vol 09 (01n02) ◽  
pp. 1-29 ◽  
Author(s):  
RUDOLF M. FÜCHSLIN ◽  
THOMAS MAEKE ◽  
UWE TANGEN ◽  
JOHN S. McCASKILL
Keyword(s):  
Complex Systems ◽  
Infinite Number ◽  
Self Assembly ◽  
Evolutionary Design ◽  
Full Generality ◽  
Inductive Generalization ◽  
Self Assembling ◽  
Genetic Encoding ◽  
Evolutionary Role

We propose that genetic encoding of self-assembling components greatly enhances the evolution of complex systems and provides an efficient platform for inductive generalization, i.e. the inductive derivation of a solution to a problem with a potentially infinite number of instances from a limited set of test examples. We exemplify this in simulations by evolving scalable circuitry for several problems. One of them, digital multiplication, has been intensively studied in recent years, where hitherto the evolutionary design of only specific small multipliers was achieved. The fact that this and other problems can be solved in full generality employing self-assembly sheds light on the evolutionary role of self-assembly in biology and is of relevance for the design of complex systems in nano- and bionanotechnology.

Directive Effect of Chain Length in Modulating Peptide Nano-assemblies

2020 ◽  
Vol 27 (9) ◽  
pp. 923-929
Author(s):  
Gaurav Pandey ◽  
Prem Prakash Das ◽  
Vibin Ramakrishnan
Keyword(s):  
Electron Microscopy ◽  
Amino Acids ◽  
Light Scattering ◽  
Chain Length ◽  
Self Assembly ◽  
The Self ◽  
Ionic Charge ◽  
Self Assembling ◽  
Biophysical Techniques

Background: RADA-4 (Ac-RADARADARADARADA-NH2) is the most extensively studied and marketed self-assembling peptide, forming hydrogel, used to create defined threedimensional microenvironments for cell culture applications. Objectives: In this work, we use various biophysical techniques to investigate the length dependency of RADA aggregation and assembly. Methods: We synthesized a series of RADA-N peptides, N ranging from 1 to 4, resulting in four peptides having 4, 8, 12, and 16 amino acids in their sequence. Through a combination of various biophysical methods including thioflavin T fluorescence assay, static right angle light scattering assay, Dynamic Light Scattering (DLS), electron microscopy, CD, and IR spectroscopy, we have examined the role of chain-length on the self-assembly of RADA peptide. Results: Our observations show that the aggregation of ionic, charge-complementary RADA motifcontaining peptides is length-dependent, with N less than 3 are not forming spontaneous selfassemblies. Conclusion: The six biophysical experiments discussed in this paper validate the significance of chain-length on the epitaxial growth of RADA peptide self-assembly.

Sticky ends in a self-assembling ABA triblock copolymer: the role of ureas in stimuli-responsive hydrogels

2019 ◽  
Vol 4 (1) ◽  
pp. 91-102 ◽  
Author(s):  
Ryan T. Shafranek ◽  
Joel D. Leger ◽  
Song Zhang ◽  
Munira Khalil ◽  
Xiaodan Gu ◽  
...  
Keyword(s):  
Self Assembly ◽  
Viscoelastic Properties ◽  
Triblock Copolymer ◽  
Thermal Response ◽  
Stimuli Responsive ◽  
Self Assembling ◽  
Polymeric Hydrogels ◽  
Aba Triblock Copolymer ◽  
Responsive Hydrogels

Directed self-assembly in polymeric hydrogels allows tunability of thermal response and viscoelastic properties.

scholarly journals Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Chun Yin Jerry Lau ◽  
Federico Fontana ◽  
Laurens D. B. Mandemaker ◽  
Dennie Wezendonk ◽  
Benjamin Vermeer ◽  
...  
Keyword(s):  
Thermodynamic Stability ◽  
Self Assembly ◽  
Biomedical Applications ◽  
Supramolecular Assemblies ◽  
Mechanistic Studies ◽  
Molecular Changes ◽  
Self Assembling ◽  
Charged Residues ◽  
Β Sheet

AbstractSelf-assembling peptides are an exemplary class of supramolecular biomaterials of broad biomedical utility. Mechanistic studies on the peptide self-assembly demonstrated the importance of the oligomeric intermediates towards the properties of the supramolecular biomaterials being formed. In this study, we demonstrate how the overall yield of the supramolecular assemblies are moderated through subtle molecular changes in the peptide monomers. This strategy is exemplified with a set of surfactant-like peptides (SLPs) with different β-sheet propensities and charged residues flanking the aggregation domains. By integrating different techniques, we show that these molecular changes can alter both the nucleation propensity of the oligomeric intermediates and the thermodynamic stability of the fibril structures. We demonstrate that the amount of assembled nanofibers are critically defined by the oligomeric nucleation propensities. Our findings offer guidance on designing self-assembling peptides for different biomedical applications, as well as insights into the role of protein gatekeeper sequences in preventing amyloidosis.

All-or-none switching of photon upconversion in self-assembled organogel systems

2017 ◽  
Vol 196 ◽  
pp. 305-316 ◽  
Author(s):  
Pengfei Duan ◽  
Deepak Asthana ◽  
Takuya Nakashima ◽  
Tsuyoshi Kawai ◽  
Nobuhiro Yanai ◽  
...  
Keyword(s):  
Self Assembly ◽  
Room Temperature ◽  
Stimuli Responsive ◽  
Molecular Systems ◽  
Controlled Assembly ◽  
Outstanding Problem ◽  
Self Assembling ◽  
New Strategy ◽  
Donor Acceptor

Aggregation-induced photon upconversion (iPUC) based on a triplet–triplet annihilation (TTA) process is successfully developed via controlled self-assembly of donor–acceptor pairs in organogel nanoassemblies. Although segregation of donor from acceptor assemblies has been an outstanding problem in TTA-based UC and iPUC, we resolved this issue by modifying both the triplet donor and aggregation induced emission (AIE)-type acceptor with glutamate-based self-assembling moieties. These donors and acceptors co-assemble to form organogels without segregation. Interestingly, these donor–acceptor binary gels show upconversion at room temperature but the upconversion phenomena were lost upon dissolution of the gels on heating. The observed changes in TTA-UC emission were thermally reversible, reflecting the controlled assembly/disassembly of the binary molecular systems. The observed on/off ratio of UC emission was much higher than that of the aggregation-induced fluorescence of the acceptor, which highlights the important role of iPUC, i.e., multi-exciton TTA for photoluminescence switching. This work bridges iPUC and supramolecular chemistry and provides a new strategy for designing stimuli-responsive upconversion systems.

Labeling of Nanofiber-Forming Peptides by Site-Directed Bioconjugation: Effect of Spacer Length on Self-Assembly

2019 ◽  
Vol 16 (2) ◽  
pp. 319-325
Author(s):  
Alessandra Scelsi ◽  
Brigida Bochicchio ◽  
Antonietta Pepe
Keyword(s):  
Self Assembly ◽  
Organic Molecules ◽  
Periodate Oxidation ◽  
Photonic Devices ◽  
Serine Residue ◽  
Spacer Length ◽  
Small Organic Molecules ◽  
Self Assembling ◽  
Versatile Tool

Background: The conjugation of small organic molecules to self-assembling peptides is a versatile tool to decorate nanostructures with original functionalities. Labeling with chromophores or fluorophores, for example, creates optically active fibers with potential interest in photonic devices. Aim and Objective: In this work, we present a rapid and effective labeling procedure for a self-assembling peptide able to form nanofibers. Rapid periodate oxidation of the N-terminal serine residue of the peptide and subsequent conjugation with dansyl moiety generated fluorophore-decorated peptides. Results: Three dansyl-conjugated self-assembling peptides with variable spacer-length were synthesized and characterized and the role of the size of the linker between fluorophore and peptide in self-assembling was investigated. Our results show that a short linker can alter the self-assembly in nanofibers of the peptide. Conclusions: Herein we report on an alternative strategy for creating functionalized nanofibrils, able to expand the toolkit of chemoselective bioconjugation strategies to be used in site-specific decoration of self-assembling peptides.

The crucial role of self-assembly in nonlinear optical properties of polymeric composites based on crown-substituted ruthenium phthalocyaninate

2015 ◽  
Vol 3 (26) ◽  
pp. 6692-6700 ◽  
Author(s):  
Yulia G. Gorbunova ◽  
Antonina D. Grishina ◽  
Alexander G. Martynov ◽  
Tatiyana V. Krivenko ◽  
Alexandra A. Isakova ◽  
...  
Keyword(s):  
Thin Film ◽  
Optical Properties ◽  
Single Crystal ◽  
Self Assembly ◽  
Crucial Role ◽  
Nonlinear Optical ◽  
Polymeric Composites ◽  
Self Assembling ◽  
Optical Behavior

Single-crystal, thin film and polymeric composites of [(15C5)4Pc]Ru(pyz) with polyvinylcarbazole were studied and crucial role of self-assembling in their nonlinear optical behavior was revealed.

Self-assembly of peptide amphiphiles for drug delivery: the role of peptide primary and secondary structures

2017 ◽  
Vol 5 (12) ◽  
pp. 2369-2380 ◽  
Author(s):  
Zhenhua Song ◽  
Xing Chen ◽  
Xinru You ◽  
Keqing Huang ◽  
Arvind Dhinakar ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Self Assembly ◽  
Secondary Structures ◽  
Peptide Amphiphiles ◽  
Alkyl Chains ◽  
Self Assembling

Peptide amphiphiles (PAs), functionalized with alkyl chains, are capable of self-assembling into various nanostructures.

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
Author(s):  
Hueyling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
New Approach ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-RXDX Conjugate β-Sheets

2020 ◽  
Author(s):  
Ryan Weber ◽  
Martin McCullagh
Keyword(s):  
Biological Imaging ◽  
Ph Sensing ◽  
Hydrophobic Residue ◽  
Ideal Candidate ◽  
Self Assembling ◽  
Sensing Applications ◽  
Β Sheets ◽  
The Stability ◽  
Dynamics Simulations

<p>pH-switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X=Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)<sub>4</sub> systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X=Ala are found to be unstable and both pHs while conjugates with X=Val, Leu, Ile and Phe are found to form stable β-sheets at least at neutral pH. The (RFDF)<sub>4</sub>-coumarin conjugate is found to have the largest relative entropy value of 0.884 +/- 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)<sub>4</sub> containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.</p>

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