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Chemical Reactions01:19

Chemical Reactions

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A chemical reaction is a process by which the bonds in the atoms of substances are rearranged to generate new substances. Matter cannot be created or destroyed in a chemical reaction—the same type and number of atoms that make up the reactants are still present in the products. Merely, the rearrangement of chemical bonds produces new compounds.
Chemical Reactions Rearrange Atoms into New Substances
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A balanced chemical equation provides the information of chemical formulas of the reactants and products involved in the chemical change. A reaction’s stoichiometry helps predict how much of the reactant is needed to produce the desired amount of product, or in some cases, how much product will be formed from a specific amount of the reactant.
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Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Cells often couple the energy-releasing reaction with the energy-requiring one to carry out important cell functions. 
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All chemical reactions begin with a reactant, the general term for one or more substances entering the reaction. Sodium and chloride ions, for example, are the reactants in the production of table salt. One or more substances produced by a chemical reaction are called the product. Chemical reactions follow the law of conservation of mass, which means that matter cannot be created nor destroyed in a chemical reaction. The components of the reactants—the number of atoms and the...
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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks
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Programming and simulating chemical reaction networks on a surface.

Samuel Clamons1, Lulu Qian1,2, Erik Winfree1,2,3

  • 1Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA.

Journal of the Royal Society, Interface
|May 27, 2020
PubMed
Summary
This summary is machine-generated.

Surface chemical reaction networks (CRNs) offer a new model for molecular programming by utilizing spatial organization. This study demonstrates their ability to perform computations, create patterns, and exhibit swarm behaviors.

Keywords:
molecular programmingnanotechnologysurface chemistry

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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology
  • Chemical Engineering

Background:

  • Well-mixed chemical reaction networks (CRNs) are foundational for programmable molecular systems.
  • Spatial organization is increasingly recognized as crucial for CRN functionality.
  • Previous models did not fully leverage spatial interactions.

Purpose of the Study:

  • To explore the surface CRN model for chemical computing.
  • To demonstrate the computational and pattern-forming capabilities of surface CRNs.
  • To introduce novel synchronization techniques and analyze design trade-offs.

Main Methods:

  • Emulation of deterministic cellular automata (asynchronous and synchronous).
  • Implementation of continuously active Boolean logic circuits.
  • Development of three new techniques for local synchronization.
  • Demonstration of pattern formation and swarm behaviors.

Main Results:

  • Surface CRNs can emulate cellular automata and Boolean logic.
  • Novel synchronization methods offer varying spatial and chemical complexity trade-offs.
  • Complex spatial patterns and swarm behaviors can be generated from simple rules.
  • A Python simulator with a web interface is provided for surface CRN design.

Conclusions:

  • Surface CRNs provide a powerful platform for spatially organized molecular computation.
  • The model allows for precise control over molecular placement and interactions.
  • The developed simulator facilitates further research and design in surface CRNs.