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Combinatorial optimization problems in self-assembly

Len Adleman, Qi Cheng, Ashish Goel, Ming-Deh Huang, David Kempe, Pablo Moisset de Espanés, Paul Wilhelm Karl Rothemund
2002 Proceedings of the thiry-fourth annual ACM symposium on Theory of computing - STOC '02  
In this paper, we study two combinatorial optimization problems related to efficient self-assembly of shapes in the Tile Assembly Model of self-assembly proposed by Rothemund and Winfree [18] .  ...  Self-assembly is the ubiquitous process by which simple objects autonomously assemble into intricate complexes.  ...  Acknowledgements We would like to thank Matt Cook, Lila Kari, and Erik Winfree for useful discussions about self-assembly in general, and the topics studied in this paper in particular. REFERENCES  ... 
doi:10.1145/509909.509913 fatcat:xkto5kkhh5bidmtfknfzyvnqze

Combinatorial optimization problems in self-assembly

Len Adleman, Qi Cheng, Ashish Goel, Ming-Deh Huang, David Kempe, Pablo Moisset de Espanés, Paul Wilhelm Karl Rothemund
2002 Proceedings of the thiry-fourth annual ACM symposium on Theory of computing - STOC '02  
In this paper, we study two combinatorial optimization problems related to efficient self-assembly of shapes in the Tile Assembly Model of self-assembly proposed by Rothemund and Winfree [18] .  ...  Self-assembly is the ubiquitous process by which simple objects autonomously assemble into intricate complexes.  ...  Acknowledgements We would like to thank Matt Cook, Lila Kari, and Erik Winfree for useful discussions about self-assembly in general, and the topics studied in this paper in particular. REFERENCES  ... 
doi:10.1145/509907.509913 dblp:conf/stoc/AdlemanCGHKER02 fatcat:36e2isz7dnf5jl6v5gja3slbz4

Catalysts through self-assembly for combinatorial homogeneous catalysis

Bernhard Breit
2008 Pure and Applied Chemistry  
Thus, employing A-T analogous complementary hydrogen-bonding templates, self-assembly of monodentate to bidentate ligands in the coordination sphere of a transition-metal salt occurs to give defined self-assembly  ...  Inspired by the principle of DNA base-pairing, a new concept for the self-assembly of molecular catalysts is described herein.  ...  In conclusion, the self-assembly concept of monodentate to bidentate ligands has become a very promising approach to the combinatorial generation of novel ligand libraries.  ... 
doi:10.1351/pac200880050855 fatcat:ner2zs4jerhhtpcmzfxz2vklpa

Combinatorial 3D Shape Generation via Sequential Assembly [article]

Jungtaek Kim, Hyunsoo Chung, Jinhwi Lee, Minsu Cho, Jaesik Park
2020 arXiv   pre-print
Sequential assembly with geometric primitives has drawn attention in robotics and 3D vision since it yields a practical blueprint to construct a target shape.  ...  An evaluation function conveys global structure guidance for an assembly process and stability in terms of gravity and external forces simultaneously.  ...  In this work, we solve a sequential assembling problem with Bayesian optimization-based framework of combinatorial 3D Figure 1 : Generated assembling sequence that creates a car shape with 118 unit primitives  ... 
arXiv:2004.07414v2 fatcat:ulozcgeacjd2xj2xxqhdy5weoq

Guest Editorial: Special Issue on Combinatorial Optimization and Applications

Zaixin Lu, Donghyun Kim
2018 Algorithmica  
The aim of this special issue is devoted to the theme of combinatorial optimization and its application.  ...  The sixth paper is "Optimal self-assembly of finite shapes at temperature 1 in 3D", by Scott Summers et al.  ...  This paper is devoted to developing a Turing-universal way of guiding the self-assembly of a scaled-up, just-barely 3D version of an arbitrary input shape at temperature 1 with optimal tile complexity.  ... 
doi:10.1007/s00453-018-0430-9 fatcat:mcjumcuvgvduzirlwpztbx4uoy

Memcomputing for Accelerated Optimization [article]

John Aiken, Fabio L. Traversa
2020 arXiv   pre-print
In particular for this work, we discuss self-organizing gates, namely Self-Organizing Algebraic Gates (SOAGs), aimed to solve linear inequalities and therefore used to solve optimization problems in Integer  ...  When appropriately assembled to represent a given ILP problem, the corresponding self-organizing circuit converges to the equilibria that express the solutions to the problem at hand.  ...  combinatorial optimization problems such as maximum satisfiability (MAXSAT) [4] , [5] , quadratic unconstrained binary optimization (QUBO) and spinglass problems [7] , and training of deep networks  ... 
arXiv:2003.10644v1 fatcat:gaw4danghndmbl35qdajx7wwku

Ensembles of DNA letters for the design of unique DNA library using a modified version of multi-criteria VEDEPSO optimizer

Krishna Veni Selvan, Mohd Saufee Muhammad, Sharifah Masniah Wan Masra
2012 2012 IEEE Congress on Evolutionary Computation  
The DNA code words designing is a multi-criteria combinatorial optimization task.  ...  A novel multi-population optimizer, M-VEDEPSO, is employed to design sets of DNA strands.  ...  Thus, many research works had been proposed to solve this complex optimization problem. [33] [34] [35] [36] [37] .  ... 
doi:10.1109/cec.2012.6256500 dblp:conf/cec/SelvanMM12 fatcat:ipauy23ribhrlllrm2wpiyzsly

Combinatorial Optimization and Verification in Self-Assembly [chapter]

Robert Schweller
2016 Encyclopedia of Algorithms  
Problem Definition Tile Assembly Models Two of the most studied tile self-assembly models in the literature are the abstract Tile Assembly Model (aTAM) [7] and the Two-Handed Tile Assembly Model (2HAM)  ...  Both models constitute a mathematical model of self-assembly in which system components are four-sided Wang tiles with glue types assigned to each tile edge.  ...  Toward the goal of minimizing assembly time, the problem of selecting an optimal concentration distribution over the tiles of a given set is considered in the Tile Concentration Problem.  ... 
doi:10.1007/978-1-4939-2864-4_665 fatcat:wsitilfpjbb4thfpevveujjn4m

A Survey on Bio-Inspired Multi-Agent System for Versatile Manufacturing Assembly Line

Mohd Nor Akmal Khalid, Umi Kalsom Yusof, Ku Munirah Ku Aman
2016 ICIC Express Letters  
Consequently, balancing the resources in the assembly line is a complex combinatorial problem, which if not efficiently managed, may entail significant costs.  ...  Bio-inspired methods have been popularly adopted in assembly line where several real-world problems have been successfully solved.  ...  The authors wish to thank the Universiti Sains Malaysia (USM) for the support it has extended in the completion of the present research through the Fundamental Research Grant Scheme (203/PKOMP/6711463)  ... 
doi:10.24507/icicel.10.01.1 fatcat:uead5xiyvrgb7jkhhbzi6s3ly4

Algorithmic DNA Self-assembly [chapter]

Ming-Yang Kao
2006 Lecture Notes in Computer Science  
DNA self-assembly for constructing 3D boxes. In P. Eades and T.  ...  The enhanced double digest problem for DNA physical mapping. Journal of Combinatorial Optimization, 7(1):69-78, 2003. Kao, M. Sanghi, and R. Schweller. Randomized fast design of short DNA words.  ... 
doi:10.1007/11775096_2 fatcat:tlsmyn6uqnakfla2pih4oglonm

Rhodium-catalyzed asymmetric hydrogenation using self-assembled chiral bidentate ligands

James M. Takacs, Kittichai Chaiseeda, Shin A. Moteki, D. Sahadeva Reddy, Di Wu, Kusumlata Chandra
2006 Pure and Applied Chemistry  
The chirality-directed self-assembly of bifunctional subunits around a structural metal - typically, zinc(II) - is used to form a heteroleptic complex in which a second set of ligating groups are suitably  ...  We find that subtle changes in the structural backbone (i.e., ligand scaffold) of such chiral bidentate self-assembled ligands (SALs) can be used to manipulate the ligand topography and chiral environment  ...  We thank the NSF (CHE-0091975) and UNL CMRA for purchase of the diffractometer and the NSF (CHE-009 1975, MRI-0079750) and NIH (SIG-1-5 10-RR-06307) for purchases of the NMR spectrometers used in these  ... 
doi:10.1351/pac200678020501 fatcat:icuecxicrnh6theidbqaupkfcu

Optimizing Tile Concentrations to Minimize Errors and Time for DNA Tile Self-assembly Systems [chapter]

Ho-Lin Chen, Ming-Yang Kao
2011 Lecture Notes in Computer Science  
DNA tile self-assembly has emerged as a rich and promising primitive for nano-technology.  ...  This paper studies the problems of minimizing assembly time and error rate by changing the tile concentrations because changing the tile concentrations is easy to implement in actual lab experiments.  ...  DNA tiles which self-assemble according to simple rules have been developed in lab [31] and mathematically analyzed based on the combinatorial tile assembly model (aTAM) proposed by Rothemund and Winfree  ... 
doi:10.1007/978-3-642-18305-8_2 fatcat:x76grifp2zdqbnwqi5gdcorwv4

Optimizing Tile Concentrations to Minimize Errors and Time for DNA Tile Self-Assembly Systems [article]

Ho-Lin Chen, Ming-Yang Kao
2012 arXiv   pre-print
DNA tile self-assembly has emerged as a rich and promising primitive for nano-technology.  ...  This paper studies the problems of minimizing assembly time and error rate by changing the tile concentrations because changing the tile concentrations is easy to implement in actual lab experiments.  ...  DNA tiles which self-assemble according to simple rules have been developed in lab [31] and mathematically analyzed based on the combinatorial tile assembly model (aTAM) proposed by Rothemund and Winfree  ... 
arXiv:1210.5786v1 fatcat:xdldxzn5ezeobdbipjwhdewkai

Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability

Gang Wu, Ming-Yang Kao, Guohui Lin, Jia-Huai You
2008 Algorithms for Molecular Biology  
Algorithmic DNA self-assembly. In S.-W. Cheng and C. K.  ...  DNA self-assembly for constructing 3D boxes. In P. Eades and T.  ... 
doi:10.1186/1748-7188-3-1 pmid:18218120 pmcid:PMC2267719 fatcat:4aw4wvv4pvehviz7bwdrph7tai

Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results

Sorin Istrail, Fumei Lam
2009 Communications in Information and Systems  
We present a comprehensive survey of combinatorial algorithms and theorems about lattice protein folding models obtained in the almost 15 years since the publication in 1995 of the first protein folding  ...  walks and HP-folds, combinatorics and algorithmics of side-chain models, bi-sphere packing and the Kepler conjecture, and the protein side-chain self-assembly conjecture.  ...  Thanks go to Ron Unger who challenged the first author in 1994 with the beautiful HP-model problem, which in turn, led to his work on protein folding.  ... 
doi:10.4310/cis.2009.v9.n4.a2 fatcat:lcfdu3ff4bhkvj7tgdtv74dxny
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