Related papers: DNA nanotechnology for building artificial dynamic…
In recent years, several studies have provided insight on the functioning of the brain which consists of neurons and form networks via interconnection among them by synapses. Neural networks are formed by interconnected systems of neurons,…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…
Grand efforts in neuroscience are working toward mapping the connectomes of many new species, including the near completion of the Drosophila melanogaster. It is important to ask whether these models could benefit artificial intelligence.…
We investigate the salt-dependent current modulation of bundled DNA nanostructures in a nanopore. To this end, we developed four simulation models for a 2x2 origami structure with increasing level of detail: from the mean-field level to an…
Artificial Intelligence (AI) and Machine Learning (ML) are weaving their way into the fabric of society, where they are playing a crucial role in numerous facets of our lives. As we witness the increased deployment of AI and ML in various…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
DNA monolayers with inherent chirality play a pivotal role across various domains, including biosensors, DNA chips, and bioelectronics. Nonetheless, conventional DNA chiral monolayers, typically constructed from single-stranded DNA (ssDNA)…
Long range charge transfer experiments in DNA oligomers and the subsequently measured -- and very diverse -- transport response of DNA wires in solid state experiments exemplifies the need for a thorough theoretical understanding of charge…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that…
The cells and tissues that make up our body juggle contradictory mechanical demands. It is crucial for their survival to be able to withstand large mechanical loads, but it is equally crucial for them to produce forces and actively change…
Functions of chemical composition are complex and discrete in nature making it impossible to optimize them with gradient methods. Genetic algorithms, which do not use derivative information, are used to maximize the thermal conductivity of…
DNA origami is an interdisciplinary area where DNA can be used as a building block for making useful stuff at nanoscale. This work presents an open source software DNA pen (based on the recent work of Peng Yin and his group) which can be…
Neural Cellular Automata (NCA) represent a powerful framework for modeling biological self-organization, extending classical rule-based systems with trainable, differentiable (or evolvable) update rules that capture the adaptive…
In this paper we propose a biomolecular implementation of the push-down automaton (one of theoretical models of computing device with unbounded memory) using DNA molecules. The idea of this improved implementation was inspired by Cavaliere…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Direct mechanical coupling is known to be critical for establishing synchronization among cilia. However, the actual role of the connections is still elusive - partly because controlled experiments in live samples are challenging. Here, we…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…