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We propose a mathematical model of DNA self-assembly using 2D tiles to form 3D nanostructures. This is the first work to combine studies in self-assembly and nanotechnology in 3D, just as Rothemund and Winfree did in the 2D case. Our model…

Computational Complexity · Computer Science 2007-05-23 Ming-Yang Kao , Vijay Ramachandran

In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…

Soft Condensed Matter · Physics 2024-12-10 Lara Koehler , Pierre Ronceray , Martin Lenz

Traditionally, computation within self-assembly models is hard to conceal because the self-assembly process generates a crystalline assembly whose computational history is inherently part of the structure itself. With no way to remove…

Emerging Technologies · Computer Science 2020-08-18 Angel A. Cantu , Austin Luchsinger , Robert Schweller , Tim Wylie

Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…

Soft Condensed Matter · Physics 2021-09-21 Alberto Scacchi , Sousa Javan Nikkhah , Maria Sammalkorpi , Tapio Ala-Nissila

Biological and robotic systems often operate in confined environments where material must be gathered without centralized control. Inspired by the effective collection strategies of aquatic worms (Lumbriculus variegatus and Tubifex…

Soft Condensed Matter · Physics 2025-05-09 R. Sinaasappel , K. R. Prathyusha , H. Tuazon , E. Mirzahossein , P. Illien , S. Bhamla , A. Deblais

Many proposals have already been made for realizing programmable matter, ranging from shape-changing molecules, DNA tiles, and synthetic cells to reconfigurable modular robotics. Envisioning systems of nano-sensors devices, we are…

Emerging Technologies · Computer Science 2015-04-09 Zahra Derakhshandeh , Robert Gmyr , Andrea W. Richa , Christian Scheideler , Thim Strothmann

Shape formation is one of the most thoroughly studied problems in programmable matter and swarm robotics. However, in many models, the class of shapes that can be formed is highly restricted due to the particles' limited memory. In the…

Data Structures and Algorithms · Computer Science 2025-11-18 Jonas Friemel , David Liedtke , Christian Scheffer

Equilibrium self-assembly and conventional materials processing techniques fall far short of mimicking dynamic self-actuating processes that are commonplace throughout biology. To bridge the gap between living and synthetic matter, we study…

Autonomous deployment and shape reconfiguration of structures is a crucial field of research in space exploration with emerging applications in the automotive, building and biomedical industries. Challenges in achieving autonomy include:…

Applied Physics · Physics 2017-11-02 Tian Chen , Kristina Shea

Self-supervised representation learning techniques utilize large datasets without semantic annotations to learn meaningful, universal features that can be conveniently transferred to solve a wide variety of downstream supervised tasks. In…

Computer Vision and Pattern Recognition · Computer Science 2022-07-19 Swetava Ganguli , C. V. Krishnakumar Iyer , Vipul Pandey

An autonomous system is presented to solve the problem of in space assembly, which can be used to further the NASA goal of deep space exploration. Of particular interest is the assembly of large truss structures, which requires precise and…

Robotics · Computer Science 2018-11-14 David Balaban , John Cooper , Erik Komendera

Several cellular automata (CA) models have been developed to simulate self-organization of multiple levels of structures. However, they do not obey microscopic reversibility and conservation laws. In this paper, we describe the construction…

Cellular Automata and Lattice Gases · Physics 2015-05-13 Takayuki Nozawa , Toshiyuki Kondo

Iterative cycles of theoretical prediction and experimental validation are the cornerstone of the modern scientific method. However, the proverbial "closing of the loop" in experiment-theory cycles in practice are usually ad hoc, often…

Amphiphilic molecules spontaneously form self-assembled structures of various shapes depending on their molecular structures, the temperature, and other physical conditions. The functionalities of these structures are dictated by their…

Soft Condensed Matter · Physics 2024-04-18 Takeo Sudo , Satoki Ishiai , Yuuki Ishiwatari , Takahiro Yokoyama , Kenji Yasuoka , Noriyoshi Arai

Synthetic biology and bioengineering provide the opportunity to create novel embodied cognitive systems (otherwise known as minds) in a very wide variety of chimeric architectures combining evolved and designed material and software. These…

Tissues and Organs · Quantitative Biology 2022-01-26 Michael Levin

The amoebot model abstracts active programmable matter as a collection of simple computational elements called amoebots that interact locally to collectively achieve tasks of coordination and movement. Since its introduction at SPAA 2014, a…

Distributed, Parallel, and Cluster Computing · Computer Science 2022-09-20 Joshua J. Daymude , Andréa W. Richa , Christian Scheideler

Addressing a fundamental problem in programmable matter, we present the first deterministic algorithm to elect a unique leader in a system of connected amoebots assuming only that amoebots are initially contracted. Previous algorithms…

Distributed, Parallel, and Cluster Computing · Computer Science 2019-05-03 Yuval Emek , Shay Kutten , Ron Lavi , William K. Moses

Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…

Soft Condensed Matter · Physics 2020-02-17 Santi Prestipino , Domenico Gazzillo , Gianmarco Munaò , Dino Costa

The Agent Based Model community has a rich and diverse ecosystem of libraries, platforms, and applications to help modelers develop rigorous simulations. Despite this robust and diverse ecosystem, the complexity of life from microbial…

Computers and Society · Computer Science 2021-11-16 Thomas Pike , Samantha Golden , Daniel Lowdermilk , Brandon Luong , Benjamin Rosado

MoleMOD is a heterogeneous self-reconfigurable modular robotic system to be employed in architecture and civil engineering. In this paper we present two components of the MoleMOD infrastructure - a test environment and a planning algorithm.…

Robotics · Computer Science 2020-07-21 Michaela Brejchová , Miroslav Kulich , Jan Petrš , Libor Přeučil