scholarly journals User-Friendly Software for Simulating Non-Equilibrium Self-Assembly Using Reaction-Diffusion

2019 ◽  
Vol 116 (3) ◽  
pp. 196a
Author(s):  
Matthew J. Varga ◽  
Margaret E. Johnson
Keyword(s):  
Self Assembly ◽  
Reaction Diffusion ◽  
User Friendly ◽  
Non Equilibrium

scholarly journals NERDSS: a non-equilibrium simulator for multibody self-assembly at the cellular scale

2019 ◽  
Author(s):  
Matthew J. Varga ◽  
Spencer Loggia ◽  
Yiben Fu ◽  
Osman N Yogurtcu ◽  
Margaret E. Johnson
Keyword(s):  
Self Assembly ◽  
Reaction Diffusion ◽  
High Yield ◽  
Sufficient Detail ◽  
Significant Barrier ◽  
Active Processes ◽  
Component Assembly ◽  
Non Equilibrium

AbstractCurrently, a significant barrier to building predictive models of cell-based self-assembly processes is that molecular models cannot capture minutes-long cellular dynamics that couple distinct components with active processes, while reaction-diffusion models lack sufficient detail for capturing assembly structures. Here we introduce the Non-Equilibrium Reaction-Diffusion Self-assembly Simulator (NERDSS), which addresses this gap by integrating a structure-resolved reaction-diffusion algorithm with rule-based model construction. By representing proteins as rigid, multi-site molecules that adopt well-defined orientations upon binding, NERDSS simulates formation of large reversible structures with sites that can be acted on by reaction rules. We show how NERDSS allows for directly comparing and optimizing models of multi-component assembly against time-dependent experimental data. Applying NERDSS to assembly steps in clathrin-mediated endocytosis, we capture how the formation of clathrin caged structures can be driven by modulating the strength of clathrin-clathrin interactions, by adding cooperativity, or by localizing clathrin to the membrane. NERDSS further predicts how clathrin lattice disassembly can be driven by enzymes that irreversibly change lipid populations on the membrane. By modeling viral lattice assembly and recapitulating oscillations in protein expression levels for a circadian clock model, we illustrate the wide usability and adaptability of NERDSS. NERDSS simulates user-defined assembly models that were previously inaccessible to existing software tools, with broad applications to predicting self-assembly in vivo and designing high-yield assemblies in vitro.

scholarly journals Miniaturization of analytical systems

1998 ◽  
Vol 44 (9) ◽  
pp. 2008-2014 ◽  
Author(s):  
Larry J Kricka
Keyword(s):  
Self Assembly ◽  
New Technologies ◽  
Analytical Techniques ◽  
Sample Volume ◽  
Clinical Diagnostics ◽  
Key Issues ◽  
User Friendly ◽  
Near Future ◽  
Long Term Trend

Abstract Miniaturization has been a long-term trend in clinical diagnostics instrumentation. Now a range of new technologies, including micromachining and molecular self-assembly, are providing the means for further size reduction of analyzers to devices with micro- to nanometer dimensions and submicroliter volumes. Many analytical techniques (e.g., mass spectrometry and electrophoresis) have been successfully implemented on microchips made from silicon, glass, or plastic. The new impetus for miniaturization stems from the perceived benefits of faster, easier, less costly, and more convenient analyses and by the needs of the pharmaceutical industry for microscale, massively parallel drug discovery assays. Perfecting a user-friendly interface between a human and a microchip and determining the realistic lower limit for sample volume are key issues in the future implementation of these devices. Resolution of these issues will be important for the long-term success of microminiature analyzers; in the meantime, the scope, diversity, and rate of progress in the development of these devices promises products in the near future.

Self-assembling outside equilibrium: emergence of structures mediated by dissipation

2019 ◽  
Vol 21 (32) ◽  
pp. 17475-17493 ◽  
Author(s):  
A. Arango-Restrepo ◽  
D. Barragán ◽  
J. M. Rubi
Keyword(s):  
Self Assembly ◽  
Equilibrium Conditions ◽  
Self Assembling ◽  
Non Equilibrium

Self-assembly under non-equilibrium conditions may give rise to the formation of structures not available at equilibrium.

scholarly journals A non-equilibrium transient phase revealed by in situ GISAXS tracking of the solvent-assisted nanoparticle self-assembly

2014 ◽  
Vol 16 (8) ◽  
Author(s):  
Karol Vegso ◽  
Peter Siffalovic ◽  
Matej Jergel ◽  
Martin Weis ◽  
Eva Majkova ◽  
...  
Keyword(s):  
Self Assembly ◽  
Transient Phase ◽  
Non Equilibrium

Evolving Reaction-Diffusion Ecosystems with Self-Assembling Structures in Thin Films

1998 ◽  
Vol 4 (1) ◽  
pp. 25-40 ◽  
Author(s):  
Jens Breyer ◽  
Jörg Ackermann ◽  
John McCaskill
Keyword(s):  
Self Assembly ◽  
Flexible Structures ◽  
Reaction Diffusion ◽  
In Vitro Evolution ◽  
Spatially Resolved ◽  
Self Assembling ◽  
Artificial Dna ◽  
Additional Stabilization ◽  
Artificial Chemistries

Recently, new types of coupled isothermal polynucleotide amplification reactions for the investigation of in vitro evolution have been established that are based on the multi-enzyme 3SR reaction. Microstructured thin-film open bioreactors have been constructed in our laboratory to run these reactions spatially resolved in flow experiments. Artificial DNA/RNA chemistries close to the in vitro biochemistry of these systems have been developed, which we have studied in computer simulations in configurable hardware (NGEN). These artificial chemistries are described on the level of individual polynucleotide molecules, each with a defined sequence, and their complexes. The key feature of spatial pattern formation provides a weak stabilization of cooperative catalytic properties of the evolving molecules. Of great interest is the step to include extended self-assembly processes of flexible structures—allowing the additional stabilization of cooperation through semipermeable, flexible, self-organizing membrane boundaries. We show how programmable matter simulations of experimentally relevant molecular in vitro evolution can be extended to include the influence of self-assembling flexible membranes.

scholarly journals Free-standing supramolecular hydrogel objects by reaction-diffusion

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Matija Lovrak ◽  
Wouter E. J. Hendriksen ◽  
Chandan Maity ◽  
Serhii Mytnyk ◽  
Volkert van Steijn ◽  
...  
Keyword(s):  
Structure Formation ◽  
Self Assembly ◽  
Reaction Diffusion ◽  
Building Blocks ◽  
Assembly Process ◽  
Supramolecular Hydrogel ◽  
Free Standing ◽  
Spatial Control ◽  
Self Assembling ◽  
Vast Range

Abstract Self-assembly provides access to a variety of molecular materials, yet spatial control over structure formation remains difficult to achieve. Here we show how reaction–diffusion (RD) can be coupled to a molecular self-assembly process to generate macroscopic free-standing objects with control over shape, size, and functionality. In RD, two or more reactants diffuse from different positions to give rise to spatially defined structures on reaction. We demonstrate that RD can be used to locally control formation and self-assembly of hydrazone molecular gelators from their non-assembling precursors, leading to soft, free-standing hydrogel objects with sizes ranging from several hundred micrometres up to centimeters. Different chemical functionalities and gradients can easily be integrated in the hydrogel objects by using different reactants. Our methodology, together with the vast range of organic reactions and self-assembling building blocks, provides a general approach towards the programmed fabrication of soft microscale objects with controlled functionality and shape.

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