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Flexible Versus Rigid Tile Assembly [chapter]

Nataša Jonoska, Gregory L. McColm
2006 Lecture Notes in Computer Science  
This paper considers both models of rigid and flexible tiles. A model representing complexes assembled out of rigid tiles based on tile displacements is presented.  ...  DNA molecules have been assembled in rigid DX and TX molecules, arrayed in assemblies similar to Wang tiles, and, as flexible branched junction molecules with flexible arms have been used in assemblies  ...  In this note, we use flexible tile assembly to simulate rigid tile assembly, and in order to do this, we devise a mathematical formalization of rigid tile assemblages.  ... 
doi:10.1007/11839132_12 fatcat:4d4lhjpaajds3mja7gk4olycau

DNA Nanostructures as Models for Evaluating the Role of Enthalpy and Entropy in Polyvalent Binding

Jeanette Nangreave, Hao Yan, Yan Liu
2011 Journal of the American Chemical Society  
were designed to serve as models to study the binding behavior of polyvalent molecules and gain insight into how small changes to the ligand/receptor scaffolds, intended to vary their conformational flexibility  ...  (A) Rigid DX tile added to preassembled flexible, J/J dimer. (B) Rigid DX tile added to preassembled semirigid J/DX tile. (C) Flexible J tile added to preassembled rigid, DX/DX dimer.  ...  A-D in Figure 2 illustrates the J and DX monomer tiles used for the assembly of dimers that can be described as flexible (J/J homo-dimer), semi-rigid (DX/J hetero-dimer) and rigid (DX/DX homo-dimer).  ... 
doi:10.1021/ja1103298 pmid:21381740 pmcid:PMC3085351 fatcat:b3kzqvgpyjcotihtzayls5fi5q

Self-assembly of 3-D Structures Using 2-D Folding Tiles [chapter]

Jérôme Durand-Lose, Jacob Hendricks, Matthew J. Patitz, Ian Perkins, Michael Sharp
2018 Lecture Notes in Computer Science  
In this paper, we present a new mathematical model of self-assembly, based on the abstract Tile Assembly Model (aTAM), called the Flexible Tile Assembly Model (FTAM).  ...  In the FTAM, the individual components are 2-dimensional square tiles as in the aTAM, but in the FTAM, bonds between the edges of tiles can be flexible, allowing bonds to flex and entire structures to  ...  of rigid configurations which a flexible assembly (formed during a first stage of assembly) can be locked into, based on the number of new tile types added during a second stage of assembly.  ... 
doi:10.1007/978-3-030-00030-1_7 fatcat:bpahyus2zzaqjlaet5iwgaoit4

Self-Assembly of 3-D Structures Using 2-D Folding Tiles [article]

Jerome Durand-Lose and Jacob Hendricks and Matthew J. Patitz and Ian Perkins and Michael Sharp
2018 arXiv   pre-print
In this paper, we present a new mathematical model of self-assembly, based on the abstract Tile Assembly Model (aTAM), called the Flexible Tile Assembly Model (FTAM).  ...  In the FTAM, the individual components are 2-dimensional square tiles as in the aTAM, but in the FTAM, bonds between the edges of tiles can be flexible, allowing bonds to flex and entire structures to  ...  of rigid configurations which a flexible assembly (formed during a first stage of assembly) can be locked into, based on the number of new tile types added during a second stage of assembly.  ... 
arXiv:1807.04818v2 fatcat:scsau4olw5frbhwovfrsunx744

Kinetics of DNA Tile Dimerization

Shuoxing Jiang, Hao Yan, Yan Liu
2014 ACS Nano  
Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility.  ...  The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential  ...  Supporting Information Available: Data analysis, DNA sequences and design details, gel characterization of the individual DNA tiles and dimers, thermodynamic measurements, and additional kinetic measurements  ... 
doi:10.1021/nn500721n pmid:24794259 pmcid:PMC4072410 fatcat:zoxywaumanew5iwr6vk5moux2u

The architectonics of programmable RNA and DNA nanostructures

Luc Jaeger, Arkadiusz Chworos
2006 Current Opinion in Structural Biology  
The past several years have witnessed the emergence of a new world of nucleic-acid-based architectures with highly predictable and programmable self-assembly properties.  ...  A subtle balance of flexibility and stress is required for building good self-assembling tiles [31] , but stable rigid 38 structure motifs are not an absolute requirement.  ...  Tensegrity involves rigid struts (helices) that push outward and flexible tendons (junctions) that pull inward, creating stable rigid structures.  ... 
doi:10.1016/j.sbi.2006.07.001 pmid:16843653 fatcat:ago3wburbbhg7o2rvi5ffhdq34

Complex tiling patterns in liquid crystals

C. Tschierske, C. Nurnberger, H. Ebert, B. Glettner, M. Prehm, F. Liu, X.- B. Zeng, G. Ungar
2011 Interface Focus  
in the complexity of soft self-assembly.  ...  Relations to biological self-assembly are discussed shortly.  ...  Hence, the proper combination of rigid and flexible molecular units in a specific topology seems to be a successful approach to functionality by self-assembly.  ... 
doi:10.1098/rsfs.2011.0087 pmid:24098852 pmcid:PMC3438576 fatcat:q6l46jg4pfebpieny242tvnvti

Self-assembly and tunable mechanics of reconfigurable colloidal crystals

Kevin L. Kohlstedt, Sharon C. Glotzer
2013 Physical Review E  
We show that this degenerate crystal differs from, and assembles more easily than, its counterpart known for rigid dimers.  ...  We find that even a small amount of reconfigurability in an assembly of otherwise rigid building blocks can greatly affect mechanical properties.  ...  MECHANICAL BEHAVIOR We investigate the mechanical differences between the assembled crystals of rigid versus reconfigurable building blocks under shear deformation.  ... 
doi:10.1103/physreve.87.032305 fatcat:2oy3fxl5ova3rlzf7shvaeamcy

Rapid and High-Throughput Evaluation of Diverse Configurations of Engineered Lysins Using the VersaTile Technique

Lisa Duyvejonck, Hans Gerstmans, Michiel Stock, Dennis Grimon, Rob Lavigne, Yves Briers
2021 Antibiotics  
Therefore, rigid linkers might improve the activity more than flexible linkers.  ...  However, in this study, we did not observe a significant overrepresentation of the rigid linkers compared to the flexible linkers.  ... 
doi:10.3390/antibiotics10030293 pmid:33799561 fatcat:sv5d6phixve3fflc4u4kg6t4xy

Truncated tetrahedral quantum dots self-assemble into quasicrystalline superlattices

Ahmad R. Kirmani
2019 MRS bulletin  
The decagons form quasicrystalline superlattices by making their edges flexible, utilizing our flexible polygon tiling rule," Chen says.  ...  The demonstration of QCSLs from single-component building blocks enabled by the discovery of the "flexible polygon tiling rule" has opened a new realm in the field of quasicrystalline structures and will  ... 
doi:10.1557/mrs.2019.61 fatcat:jfxk4azbhfckhgc4mfjiwnj4om

Flexible Dermal Armor in Nature

Wen Yang, Irene H. Chen, Joanna Mckittrick, Marc A. Meyers
2012 JOM: The Member Journal of TMS  
This combination significantly increases the strength and flexibility in comparison with a simple monolithic mineral composite or rigid dermal armor.  ...  The dermal armor in these animals is flexible and has a hierarchical structure with collagen fibers joining mineralized units (scales, tiles, or plates).  ...  Thus, the individual scales are more rigid and are not as flexible as the arapaima scales, which is a prerequisite for slashing and puncturing.  ... 
doi:10.1007/s11837-012-0301-9 fatcat:i3cmjdjx2jevhd5dh7m2iokmce

Engineering Circular Gliding of Actin Filaments Along Myosin-Patterned DNA Nanotube Rings To Study Long-Term Actin–Myosin Behaviors

Rizal F. Hariadi, Abhinav J. Appukutty, Sivaraj Sivaramakrishnan
2016 ACS Nano  
) versus 0.36 ± 0.01 for the flexible linker (N = 15 movies and 200 analyzed transitions; Figure 5e, right; p<0.001).  ...  and DNA nanotube rings from single-stranded tiles (SSTs) (a) DNA SSTs self-assemble into one-dimensional nuclei with precise circumferences.  ... 
doi:10.1021/acsnano.6b01294 pmid:27571140 pmcid:PMC5450935 fatcat:ea3ebjpwrzfvpbcjv2qx7ocgva

Characterizing the bending and flexibility induced by bulges in DNA duplexes

John S. Schreck, Thomas E. Ouldridge, Flavio Romano, Ard A. Louis, Jonathan P. K. Doye
2015 Journal of Chemical Physics  
tune the self-assembly product as well as the detailed geometry of the resulting nanostructures.  ...  The unstacking probability, however, is highest for loops of intermediate lengths, when the rigidity of single-stranded DNA is significant and the loop resists compression.  ...  the self-assembly of the Z tiles into 1D nanostructures.  ... 
doi:10.1063/1.4917199 pmid:25933790 fatcat:m5tr5cp72vbrxab52fkvptnggu

An Origami-Inspired Reconfigurable Suction Gripper for Picking Objects With Variable Shape and Size

Zhenishbek Zhakypov, Florian Heremans, Aude Billard, Jamie Paik
2018 IEEE Robotics and Automation Letters  
Gripper adaptability to handle objects of different shape and size brings high flexibility to manipulation.  ...  Constructed from rigid and soft components and driven by compact shape memory alloy actuators, the gripper can effectively self-fold into three shape modes to pick large and small flat, narrow cylindrical  ...  (b) The number of tiles versus the number of actuators and achievable number of modes plot.  ... 
doi:10.1109/lra.2018.2847403 dblp:journals/ral/ZhakypovHBP18 fatcat:i5hzbfkconbttg3dzg6ainufoe

Self-assembly of crystalline nanotubes from monodisperse amphiphilic diblock copolypeptoid tiles

Jing Sun, Xi Jiang, Reidar Lund, Kenneth H. Downing, Nitash P. Balsara, Ronald N. Zuckermann
2016 Proceedings of the National Academy of Sciences of the United States of America  
More broadly, this work suggests that flexible, low-molecular-weight sequence-defined polymers can serve as molecular tile units that can assemble into precision supramolecular architectures. peptoid polymers  ...  assemble into hollow, crystalline nanotubes in water.  ...  Typically, molecular tiles are relatively rigid units that either self-assemble in two dimensions on a surface (29) , or in solution (30, 31) .  ... 
doi:10.1073/pnas.1517169113 pmid:27035944 pmcid:PMC4839393 fatcat:o4whdvwgrvhzlo2iyidkaz4kgu
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