Related papers: Counting, Computing, and Pattern Recognition with …
Majumder, Reif and Sahu have presented a stochastic model of reversible, error-permitting, two-dimensional tile self-assembly, and showed that restricted classes of tile assembly systems achieved equilibrium in (expected) polynomial time.…
Self-assembly is ubiquitous in nature, particularly in biology, where it underlies the formation of protein quaternary structure and protein aggregation. Quaternary structure assembles deterministically and performs a wide range of…
The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…
Ordered nanoarrays, i.e. regular patterns of quantum structures at the nanometre scale, have recently been synthesized in a wide range of systems. Here I explore a possible route to technological exploitation: assuming a simple form of…
In recent years there have been a number of proposals to utilize the specificity of DNA based interactions for potential applications in nanoscience. One interesting direction is the self-assembly of micro- and nanoparticle clusters using…
Physical implementations of neural computation now extend far beyond silicon hardware, encompassing substrates such as memristive devices, photonic circuits, mechanical metamaterials, microfluidic networks, chemical reaction systems, and…
Data-Driven Computational Mechanics is a novel computing paradigm that enables the transition from standard data-starved approaches to modern data-rich approaches. At this early stage of development, one can distinguish two mainstream…
Machines enabled the Industrial Revolution and are central to modern technological progress: A machine's parts transmit forces, motion, and energy to one another in a predetermined manner. Today's engineering frontier, building artificial…
The information capacity of double-crossover (DX) tiles was successfully increased beyond a binary representation to higher base representations. By controlling the length and the position of DNA hairpins on the DX tile, ternary and senary…
Natural organisms utilize distributed actuation through their musculoskeletal systems to adapt their gait for traversing diverse terrains or to morph their bodies for varied tasks. A longstanding challenge in robotics is to emulate this…
Many real-world dynamic systems, both natural and artificial, are understood to be performing computations. For artificial dynamic systems, explicitly designed to perform computation - such as digital computers - by construction, we can…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
In order to optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model system for addressable, multicomponent self-assembly based on…
Smartphones, laptops, and data centers are CMOS-based technologies that ushered our world into the information age of the 21st century. Despite their advantages for scalable computing, their implementations come with surprisingly large…
DNA is an ideal candidate to organize matter on the nanoscale, primarily due to the specificity and complexity of DNA based interactions. Recent advances in this direction include the self-assembly of colloidal crystals using DNA grafted…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
We prove the computational weakness of a model of tile assembly that has so far resisted many attempts of formal analysis or positive constructions. Specifically, we prove that, in Winfree's abstract Tile Assembly Model, when restricted to…
As a mathematical model of self-assembling systems, Winfree's abstract Tile Assembly Model (aTAM) is a remarkable platform for studying the behaviors and powers of self-assembling systems. Capable of Turing universal computation, the aTAM…
Multiscale modeling of complex systems is crucial for understanding their intricacies. Data-driven multiscale modeling has emerged as a promising approach to tackle challenges associated with complex systems. On the other hand,…