Related papers: Two-dimensional tile displacement can simulate cel…
In this paper, we propose applying semantic embedding to learn the range of behaviors exhibited by molecular swarms, thereby providing a richer set of features to optimize such systems. Specifically, we consider a standard molecular swarm…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
Neural Cellular Automata (NCA) are a powerful combination of machine learning and mechanistic modelling. We train NCA to learn complex dynamics from time series of images and PDE trajectories. Our method is designed to identify underlying…
Biological materials are self-assembled with near-atomic precision in living cells, whereas synthetic 3D structures generally lack such precision and controllability. Recently, DNA nanotechnology, especially DNA origami technology, has been…
The Besicovitch pseudo-metric is a shift-invariant pseudo-metric on the set of infinite sequences, that enjoys interesting properties and is suitable for studying the dynamics of cellular automata. They correspond to the asymptotic behavior…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
We develop a multi-dimensional, parallelized domain decomposition strategy (DDC) for mass-transfer particle tracking (MTPT) methods. These methods are a type of Lagrangian algorithm for simulating reactive transport and are able to be…
Traveling-wave modulation is a form of space-time modulation which has been shown to enable unique electromagnetic phenomena such as non-reciprocity, beam-steering, frequency conversion, and amplification. In practice, traveling-wave…
The fast multipole method (FMM) performs fast approximate kernel summation to a specified tolerance $\epsilon$ by using a hierarchical division of the domain, which groups source and receiver points into regions that satisfy local…
The use of buried dopants to construct quantum-dot cellular automata is investigated as an alternative to conventional electronic devices for information transport and elementary computation. This provides a limit in terms of…
Plastic deformation In crystalline materials is controlled by the motion and interactions of dislocations [AND 17]. Discrete Dislocation Dynamics (DDD) simulations have now existed for about 25 years to investigate plastic flow at the…
We investigate theoretically how single-molecule spectroscopy techniques can be used to perform fast and high resolution displacement detection and manipulation of nanomechanical oscillators, such as singly clamped carbon nanotubes. We…
The Pattern self-Assembly Tile set Synthesis (PATS) problem, which arises in the theory of structured DNA self-assembly, is to determine a set of coloured tiles that, starting from a bordering seed structure, self-assembles to a given…
The DNA molecules were controllable deposited on graphene and thin graphite films and visualized using AFM. The mechanical micro- and nanotools, such as nanotweezers with shape memory effect controlled by heating were designed and tested. A…
We investigate the mechanisms of histone sliding and detachment with a stochastic model that couples thermally-induced, passive histone sliding with active motor-driven histone unwrapping. Analysis of a passive loop or twist defect-mediated…
A new class of deterministic dynamical systems, termed semipredictable dynamical systems, is presented. The spatiotemporal evolution of these systems have both predictable and unpredictable traits, as found in natural complex systems. We…
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…
Cells in tissues can organize into a broad spectrum of structures according to their function. Drastic changes of organization, such as epithelial-mesenchymal transitions or the formation of spheroidal aggregates, are often associated…
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…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…