Ion Translocation in Artificial Molecule-based Systems Induced by Light, Electrons, or Chemicals

2011 ◽  
Vol 64 (10) ◽  
pp. 1301 ◽  
Author(s):  
Robin Bofinger ◽  
Aurélien Ducrot ◽  
Laura Jonusauskaite ◽  
Nathan D. McClenaghan ◽  
Jean-Luc Pozzo ◽  
...  
Keyword(s):  
Chemical Reaction ◽  
Building Blocks ◽  
Redox Process ◽  
Biological Processes ◽  
Natural Systems ◽  
Short Overview ◽  
Ion Translocation ◽  
Synthetic Molecules ◽  
Artificial Molecule ◽  
Chemical Messengers

Synthetic molecules and nanodevices, like their more elaborate biological counterparts, have been shown to perform several sophisticated functions, using even fairly simple molecular architectures. One limitation to developing artificial molecular arrays and networks from these miniscule building blocks is the lack of a unifying strategy whereby they can communicate or interact together, which has been successfully developed in natural systems. Understanding and harnessing these efficient biological processes could prove key in the development of future integrated molecule-based nanodevices and networks. Herein, we give a short overview of some manifestations of intra- and intermolecular communication based on chemical messengers in artificial systems, in some ways analogous to natural systems, which are in turn controlled by light, a redox process or a chemical reaction or interaction. Some advantages, limitations, and challenges are highlighted.

Chemical reaction bonding of building blocks using red mud and orthophosphoric acid binder

1996 ◽  
Vol 15 (19) ◽  
pp. 1667-1668 ◽  
Author(s):  
J. L. Gumaste ◽  
B. C. Swain ◽  
B. C. Mohanty ◽  
J. S. Murty
Keyword(s):  
Chemical Reaction ◽  
Red Mud ◽  
Orthophosphoric Acid ◽  
Building Blocks ◽  
Reaction Bonding

Molecular assembly at surfaces: progress and challenges

2017 ◽  
Vol 204 ◽  
pp. 9-33 ◽  
Author(s):  
R. Raval
Keyword(s):  
Building Blocks ◽  
Covalent Bonding ◽  
Molecular Assembly ◽  
Theoretical Modelling ◽  
Top Down ◽  
Molecular Systems ◽  
Natural Systems ◽  
Surfaces And Interfaces ◽  
Macromolecular Systems ◽  
Determine System

Molecules provide versatile building blocks, with a vast palette of functionalities and an ability to assemble via supramolecular and covalent bonding to generate remarkably diverse macromolecular systems. This is abundantly displayed by natural systems that have evolved on Earth, which exploit both supramolecular and covalent protocols to create the machinery of life. Importantly, these molecular assemblies deliver functions that are reproducible, adaptable, finessed and responsive. There is now a real need to translate complex molecular systems to surfaces and interfaces in order to engineer 21st century nanotechnology. ‘Top-down’ and ‘bottom-up’ approaches, and utilisation of supramolecular and covalent assembly, are currently being used to create a range of molecular architectures and functionalities at surfaces. In parallel, advanced tools developed for interrogating surfaces and interfaces have been deployed to capture the complexities of molecular behaviour at interfaces from the nanoscale to the macroscale, while advances in theoretical modelling are delivering insights into the balance of interactions that determine system behaviour. A few examples are provided here that outline molecular behaviour at surfaces, and the level of complexity that is inherent in such systems.

scholarly journals Grip on complexity in chemical reaction networks

2017 ◽  
Vol 13 ◽  
pp. 1486-1497 ◽  
Author(s):  
Albert S Y Wong ◽  
Wilhelm T S Huck
Keyword(s):  
Complex Networks ◽  
Chemical Reaction ◽  
Biological Networks ◽  
Chemical Reaction Networks ◽  
Living Systems ◽  
Reaction Networks ◽  
Natural Systems ◽  
Systems Chemistry ◽  
Single Chemical ◽  
And Control

A new discipline of “systems chemistry” is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework. Living systems rely on complex networks of chemical reactions to control the concentration of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. To truly understand how living systems function, we need a complete understanding of how chemical reaction networks (CRNs) create function. We propose the development of a bottom-up approach to design and construct CRNs where we can follow the influence of single chemical entities on the properties of the network as a whole. Ultimately, this approach should allow us to not only understand such complex networks but also to guide and control their behavior.

scholarly journals The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

2020 ◽  
Author(s):  
Vasundra Touré ◽  
Steven Vercruysse ◽  
Marcio Luis Acencio ◽  
Ruth C Lovering ◽  
Sandra Orchard ◽  
...  
Keyword(s):  
Molecular Interaction ◽  
Regulatory Networks ◽  
Building Blocks ◽  
Supplementary Information ◽  
Biological Processes ◽  
Causal Interaction ◽  
End User ◽  
Minimum Information ◽  
Causal Statement ◽  
In Cells

Abstract Motivation A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a so-called ‘causal interaction’ takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g. gene regulation) need to be described with a careful appreciation of the underlying molecular reactions. A proper description of this information enables archiving, sharing and reuse by humans and for automated computational processing. Various representations of causal relationships between biological components are currently used in a variety of resources. Results Here, we propose a checklist that accommodates current representations, called the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while fostering uniformity and interoperability of the data across resources. Availability and implementation The checklist together with examples is accessible at https://github.com/MI2CAST/MI2CAST Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Single cell ecology

2019 ◽  
Vol 374 (1786) ◽  
pp. 20190076 ◽  
Author(s):  
Thomas A. Richards ◽  
Ramon Massana ◽  
Stefano Pagliara ◽  
Neil Hall
Keyword(s):  
Single Cell ◽  
Building Blocks ◽  
Biological Properties ◽  
Natural Environments ◽  
Biological Processes ◽  
Special Issue ◽  
New Approaches ◽  
New Methodologies ◽  
Biological Entities ◽  
The Way

Cells are the building blocks of life, from single-celled microbes through to multi-cellular organisms. To understand a multitude of biological processes we need to understand how cells behave, how they interact with each other and how they respond to their environment. The use of new methodologies is changing the way we study cells allowing us to study them on minute scales and in unprecedented detail. These same methods are allowing researchers to begin to sample the vast diversity of microbes that dominate natural environments. The aim of this special issue is to bring together research and perspectives on the application of new approaches to understand the biological properties of cells, including how they interact with other biological entities. This article is part of a discussion meeting issue ‘Single cell ecology’.

scholarly journals BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Pau Andrio ◽  
Adam Hospital ◽  
Javier Conejero ◽  
Luis Jordá ◽  
Marc Del Pino ◽  
...  
Keyword(s):  
Building Blocks ◽  
Biological Processes ◽  
Software Management ◽  
Software Library ◽  
Management Tools ◽  
Software Packages ◽  
Biomolecular Simulations ◽  
Software And Hardware ◽  
A Chain ◽  
Workflow Orchestration

Abstract In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.

Bubble Based Micro/Nano Fabrication Method

2007 ◽  
Author(s):  
Xiao-Dan Bai ◽  
Jing Liu
Keyword(s):  
Chemical Reaction ◽  
Large Scale ◽  
Large Diameter ◽  
Building Blocks ◽  
Membrane Thickness ◽  
Fabrication Method ◽  
Specific Chemical ◽  
Soap Bubbles ◽  
Nano Fabrication ◽  
Nano Structures

Micro/nano structures, especially those in one dimensional, such as nano wires, are commonly used building blocks for the bottom-up assembly of electronic, photonic or mechanical devices. However, their fabrications are generally limited to the expensive equipments and methods capable of only working in an extremely small space. A big challenge facing the current scientific society is to overcome this barrier and build up a bridge between the macroscopic manipulation/observation and the fabrication in small world. Here, we proposed a new conceptual fabrication method, which can easily be implemented to synthesize, etch and construct micro or nano structures through manipulating the large scale bubbles composed of specific chemical compounds. The core of the method lies in the chemical reaction occurring at the interfaces between two or more soap bubbles. A surprisingly unique virtue of the bubble is that it can have a rather large diameter however an extremely small membrane thickness, whose smallest size even reaches nano scale. Therefore, the chemical reaction and synthesis occurred in the common boundary of such contacting bubbles would lead to products with very small size. Most important of all, all these were achieved via a much easy and straightforward way. To better understand the physical picture of the new method, the principle and mechanism for the bubble based fabrication process were interpreted. Several fundamental equations for characterizing the bubbles were proposed and preliminarily discussed. As the first trial to demonstrate the new concept, several typical micro structures were successfully fabricated in our lab. Particularly, a micro wire which can be used as tiny temperature sensor was made and tested. Being flexible, easily controllable and observable, environmentally friend and extremely low in cost, the present method is expected to be a significant technical route for making micro/nano structures in the near future. It also indicated for the first time that blowing soap bubbles means not just funny but also opens a new world for micro/nano fabrication.

Processing Complex and Uniform Nanoparticles for Microelectronic and Photonic Applications

2001 ◽  
Vol 704 ◽  
Author(s):  
Nobuyuki Kambe
Keyword(s):  
Refractive Index ◽  
Chemical Reaction ◽  
Surface Engineering ◽  
Building Blocks ◽  
Size Distributions ◽  
Direct Deposition ◽  
Device Structures ◽  
Inorganic Nanocomposites ◽  
Planar Lightwave ◽  
Reaction Processes

AbstractTwo major challenges that exist in order to utilize nanoparticles as building blocks for microelectronic and photonic applications are presented. The first challenge is how to make uniform nanoparticles in industrial-scale. The second challenge is how to convert these nano-building blocks to application forms such as device structures or coatings. In this paper, materials and processing guidelines to provide the solutions for these challenges are described on the basis of (a) laser-driven chemical reaction processes to generate a versatile range of nanoparticles having extremely narrow size distributions, and (b) unique organic-inorganic nanocomposites using surface engineering over nanoparticles. As promising applications, direct deposition of nanoparticles and nanocomposites are discussed in conjunction with planar lightwave devices, photonic nanocomposites for the refractive index engineering, and planarization processes for electronic chips.

scholarly journals Beyond icosahedral symmetry in packings of proteins in spherical shells

2017 ◽  
Vol 114 (34) ◽  
pp. 9014-9019 ◽  
Author(s):  
Majid Mosayebi ◽  
Deborah K. Shoemark ◽  
Jordan M. Fletcher ◽  
Richard B. Sessions ◽  
Noah Linden ◽  
...  
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Multiple Scales ◽  
Building Blocks ◽  
Icosahedral Symmetry ◽  
Protein Cages ◽  
Natural Systems ◽  
Wide Range ◽  
Stable Arrangement ◽  
Symmetric Structures

The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral cage. In turn, this has inspired synthetic biologists to design de novo protein cages. We use simple models, on multiple scales, to investigate the self-assembly of a spherical cage, focusing on the regularity of the packing of protein-like objects on the surface. Using building blocks, which are able to pack with icosahedral symmetry, we examine how stable these highly symmetric structures are to perturbations that may arise from the interplay between flexibility of the interacting blocks and entropic effects. We find that, in the presence of those perturbations, icosahedral packing is not the most stable arrangement for a wide range of parameters; rather disordered structures are found to be the most stable. Our results suggest that (i) many designed, or even natural, protein cages may not be regular in the presence of those perturbations and (ii) optimizing those flexibilities can be a possible design strategy to obtain regular synthetic cages with full control over their surface properties.

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