Modeling and Simulation of Biological Self-Assembly Structures from Nanoscale Entities

2007 ◽  
Vol 7 (12) ◽  
pp. 4248-4253 ◽  
Author(s):  
Ramana M. Pidaparti ◽  
David Primeaux ◽  
Brandon Saunders
Keyword(s):  
Modeling And Simulation ◽  
Thermodynamic Equilibrium ◽  
Self Assembly ◽  
Biological Systems ◽  
The Self ◽  
Eukaryotic Cells ◽  
Assembly Process ◽  
Equilibrium Conditions ◽  
Preliminary Results ◽  
Computational Methodology

Many natural and biological systems are formed by the process of molecular self-assembly. Molecular self-assembly is defined as the spontaneous organization of molecules under thermodynamic equilibrium conditions into structurally well defined and rather stable arrangements. In this paper, we developed a novel computational methodology to investigate the self-assembly process of simple 1-D structures representing protein monomers into long filaments, rings, pyramids, bundles, etc. Based on the preliminary results obtained, the methodology was extended to mimic the microtubule self-assembly, which occurs in all eukaryotic cells.

scholarly journals Self-Assembled Nanomaterials Based on Complementary Sn(IV) and Zn(II)-Porphyrins, and Their Photocatalytic Degradation for Rhodamine B Dye

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3598
Author(s):  
Nirmal K. Shee ◽  
Hee-Joon Kim
Keyword(s):  
Aqueous Solution ◽  
Visible Light Irradiation ◽  
Rhodamine B ◽  
Self Assembly ◽  
The Self ◽  
Assembly Process ◽  
Absorption Bands ◽  
Ligand Coordination ◽  
Rhodamine B Dye ◽  
Metal Ligand

A series of porphyrin triads (1–6), based on the reaction of trans-dihydroxo-[5,15-bis(3-pyridyl)-10,20-bis(phenyl)porphyrinato]tin(IV) (SnP) with six different phenoxy Zn(II)-porphyrins (ZnLn), was synthesized. The cooperative metal–ligand coordination of 3-pyridyl nitrogens in the SnP with the phenoxy Zn(II)-porphyrins, followed by the self-assembly process, leads to the formation of nanostructures. The red-shifts and remarkable broadening of the absorption bands in the UV–vis spectra for the triads in CHCl3 indicate that nanoaggregates may be produced in the self-assembly process of these triads. The emission intensities of the triads were also significantly reduced due to the aggregation. Microscopic analyses of the nanostructures of the triads reveal differences due to the different substituents on the axial Zn(II)-porphyrin moieties. All these nanomaterials exhibited efficient photocatalytic performances in the degradation of rhodamine B (RhB) dye under visible light irradiation, and the degradation efficiencies of RhB in aqueous solution were observed to be 72~95% within 4 h. In addition, the efficiency of the catalyst was not impaired, showing excellent recyclability even after being applied for the degradation of RhB in up to five cycles.

scholarly journals Metal Oxide-Related Dendritic Structures: Self-Assembly and Applications for Sensor, Catalysis, Energy Conversion and Beyond

Nanomaterials ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1686
Author(s):  
Ruohong Sui ◽  
Paul A. Charpentier ◽  
Robert A. Marriott
Keyword(s):  
Metal Oxide ◽  
Energy Conversion ◽  
Self Assembly ◽  
Hierarchical Structures ◽  
The Self ◽  
Assembly Process ◽  
Electronic Noses ◽  
Dendritic Nanostructures ◽  
Energy Conversion And Storage ◽  
The Aesthetic

In the past two decades, we have learned a great deal about self-assembly of dendritic metal oxide structures, partially inspired by the nanostructures mimicking the aesthetic hierarchical structures of ferns and corals. The self-assembly process involves either anisotropic polycondensation or molecular recognition mechanisms. The major driving force for research in this field is due to the wide variety of applications in addition to the unique structures and properties of these dendritic nanostructures. Our purpose of this minireview is twofold: (1) to showcase what we have learned so far about how the self-assembly process occurs; and (2) to encourage people to use this type of material for drug delivery, renewable energy conversion and storage, biomaterials, and electronic noses.

Thioderivatives of Resorcin[4]arene and Pyrogallol[4]arene: Are Thiols Tolerated in the Self-Assembly Process?

2021 ◽  
Author(s):  
Suren J. Nemat ◽  
Konrad Tiefenbacher
Keyword(s):  
Self Assembly ◽  
The Self ◽  
Assembly Process

Controllable Synthesis of Cobalt Porphyrin Nanocrystals through Micelle Confinement Self-Assembly

MRS Advances ◽  
2020 ◽  
Vol 5 (42) ◽  
pp. 2147-2155
Author(s):  
Sudi Chen ◽  
Xitong Ren ◽  
Shufang Tian ◽  
Jiajie Sun ◽  
Feng Bai
Keyword(s):  
Self Assembly ◽  
Water Oxidation ◽  
Separation Efficiency ◽  
Noncovalent Interactions ◽  
Building Blocks ◽  
The Self ◽  
Hexagonal Prism ◽  
Assembly Process ◽  
Surfactant Micelles ◽  
Cobalt Porphyrin

AbstractThe self-assembly of optically active building blocks into functional nanocrystals as high-activity photocatalysts is a key in the field of photocatalysis. Cobalt porphyrin with abundant catalytic properties is extensively studied in photocatalytic water oxidation and CO2 reduction. Here, we present the fabrication of cobalt porphyrin nanocrystals through a surfactant-assisted interfacial self-assembly process using Co-tetra(4-pyridyl) porphyrin as building block. The self-assembly process relies on the combined noncovalent interactions such as π-π stacking and axial Co-N coordination between individual porphyrin molecules within surfactant micelles. Tuning different reaction conditions (temperature, the ratio of co-solvent DMF) and types of surfactant, various nanocrystals with well-defined 1D to 3D morphologies such as nanowires, nanorods and nano hexagonal prism were obtained. Due to the ordered accumulation of molecules, the nanocrystals exhibit the properties of the enhanced capability of visible light capture and can conduce to improve the transport and separation efficiency of the photogenerated carriers, which is important for photocatalysis. Further studies of photocatalytic CO2 reduction are being performed to address the relationship between the size and shape of the nanocrystals with the photocatalytic activity.

ChemInform Abstract: The Importance of the Self-Assembly Process to Control Mechanical Properties of Low Molecular Weight Hydrogels

ChemInform ◽  
2013 ◽  
Vol 44 (36) ◽  
pp. no-no
Author(s):  
Jaclyn Raeburn ◽  
Andre Zamith Cardoso ◽  
Dave J. Adams
Keyword(s):  
Mechanical Properties ◽  
Molecular Weight ◽  
Self Assembly ◽  
The Self ◽  
Low Molecular Weight ◽  
Assembly Process

scholarly journals Modification of a Single Atom Affects the Physical Properties of Double Fluorinated Fmoc-Phe Derivatives

2021 ◽  
Vol 22 (17) ◽  
pp. 9634
Author(s):  
Moran Aviv ◽  
Dana Cohen-Gerassi ◽  
Asuka A. Orr ◽  
Rajkumar Misra ◽  
Zohar A. Arnon ◽  
...  
Keyword(s):  
Amino Acid ◽  
Physical Properties ◽  
Self Assembly ◽  
Deep Understanding ◽  
Building Blocks ◽  
The Self ◽  
Single Atom ◽  
Supramolecular Organization ◽  
Assembly Process ◽  
Wide Range

Supramolecular hydrogels formed by the self-assembly of amino-acid based gelators are receiving increasing attention from the fields of biomedicine and material science. Self-assembled systems exhibit well-ordered functional architectures and unique physicochemical properties. However, the control over the kinetics and mechanical properties of the end-products remains puzzling. A minimal alteration of the chemical environment could cause a significant impact. In this context, we report the effects of modifying the position of a single atom on the properties and kinetics of the self-assembly process. A combination of experimental and computational methods, used to investigate double-fluorinated Fmoc-Phe derivatives, Fmoc-3,4F-Phe and Fmoc-3,5F-Phe, reveals the unique effects of modifying the position of a single fluorine on the self-assembly process, and the physical properties of the product. The presence of significant physical and morphological differences between the two derivatives was verified by molecular-dynamics simulations. Analysis of the spontaneous phase-transition of both building blocks, as well as crystal X-ray diffraction to determine the molecular structure of Fmoc-3,4F-Phe, are in good agreement with known changes in the Phe fluorination pattern and highlight the effect of a single atom position on the self-assembly process. These findings prove that fluorination is an effective strategy to influence supramolecular organization on the nanoscale. Moreover, we believe that a deep understanding of the self-assembly process may provide fundamental insights that will facilitate the development of optimal amino-acid-based low-molecular-weight hydrogelators for a wide range of applications.

Construction of homochiral alkaline–lanthanide heteronuclear helicates with Na+-selective bonding in the self-assembly process

2019 ◽  
Vol 48 (39) ◽  
pp. 14595-14599 ◽  
Author(s):  
Ge Li ◽  
Li Wang ◽  
Qingxin Han ◽  
Weisheng Liu
Keyword(s):  
Metal Ions ◽  
Self Assembly ◽  
The Self ◽  
Assembly Process

A supramolecular approach to distinguish Na+ from other biologically important metal ions.

scholarly journals Quantitative Analysis of the Self-Assembly Process of Hexagonal PtII Macrocyclic Complexes: Effect of the Solvent and the Components

2017 ◽  
Vol 24 (4) ◽  
pp. 754-754
Author(s):  
Ayako Baba ◽  
Tatsuo Kojima ◽  
Shuichi Hiraoka
Keyword(s):  
Quantitative Analysis ◽  
Self Assembly ◽  
Macrocyclic Complexes ◽  
The Self ◽  
Assembly Process

A reaction model on the self-assembly process of octahedron-shaped coordination capsules

2017 ◽  
Vol 19 (31) ◽  
pp. 20338-20342 ◽  
Author(s):  
Yoshihiro Matsumura ◽  
Shuichi Hiraoka ◽  
Hirofumi Sato
Keyword(s):  
Master Equation ◽  
Time Evolution ◽  
Self Assembly ◽  
Reaction Model ◽  
The Self ◽  
Assembly Process

Master equation was utilized to track the time evolution in a self-assembly process.

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