Related papers: DNA nanotechnology for building artificial dynamic…
Vital to primary visual processing, retinal circuitry shows many similar structures across a very broad array of species, both vertebrate and non-vertebrate, especially functional components such as lateral inhibition. This surprisingly…
Artificial Neural Networks (ANNs) are one of the most widely employed forms of bio-inspired computation. However the current trend is for ANNs to be structurally homogeneous. Furthermore, this structural homogeneity requires the application…
Learning from nature's amazing molecular machines, globular proteins, we present a framework for the predictive design of nano-machines. We show that the crucial ingredients for a chain molecule to behave as a machine are its inherent…
DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures…
This technical report deals with the concept of an artificial DNA which contains a blueprint of the structure and organization of an embedded system. This blueprint can be used to build up the embedded system in a self-organizing manner at…
In soft matter science, it is often the goal to design new materials with targeted properties. These materials can be used in many applications, each requiring specific features to be optimized for maximum fitness. The use of self-assembly…
We introduce and train distributed neural architectures (DNA) in vision and language domains. DNAs are initialized with a proto-architecture that consists of (transformer, MLP, attention, etc.) modules and routers. Any token (or patch) can…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
Structural DNA nanotechnology has advanced to the extent that extremely complex structures can be designed. Much of this advancement has been due to the development of automated DNA design and simulation tools. Typically, the tools (e.g.…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
Dynamical systems see widespread use in natural sciences like physics, biology, chemistry, as well as engineering disciplines such as circuit analysis, computational fluid dynamics, and control. For simple systems, the differential…
Synthetic biology is the engineering of cellular networks. It combines principles of engineering and the knowledge of biological networks to program the behavior of cells. Computational modeling techniques in conjunction with molecular…
While the autonomous assembly of hard nanoparticles with different shapes has been studied extensively both in experiment and simulations, little is known about systems where particle shape can be dynamically altered. DNA origami…
Chronic diseases can greatly benefit from bioelectronic medicine approaches. Neuromorphic electronic circuits present ideal characteristics for the development of brain-inspired low-power implantable processing systems that can be…
Spontaneous directed motion, a hallmark of cell biology, is unusual in classical statistical physics. Here we study, using both numerical and analytical methods, organized motion in models of the cytoskeleton in which constituents are…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and…
The combination of self-assembly and electronic properties as well as its true nanoscale dimensions make DNA a promising candidate for a building block of single molecule electronics. We argue that the intrinsic double helix conformation of…
All known life forms are based upon a hierarchy of interwoven feedback loops, operating over a cascade of space, time and energy scales. Among the most basic loops are those connecting DNA and proteins. For example, in genetic networks, DNA…