相关论文: A domain-level DNA strand displacement reaction en…
DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a broad set of design frameworks has emerged to accommodate…
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…
We propose novel chemical reaction networks to translate levels of concentration into unique DNA strand species, which we call concentration translators. Our design of the concentration translators is based on combination of two chemical…
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…
DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…
DNA strand displacement (DSD) reactions have been used to construct chemical reaction networks in which species act catalytically at the level of the overall stoichiometry of reactions. These effective catalytic reactions are typically…
We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of DNA strand displacement. The design is scalable: all species of DNA strands can in principle be mixed and prepared in a single test…
DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent…
Several technological limitations of traditional silicon based computing are leading towards the paradigm shift, from silicon to carbon, in computational world. Among the unconventional modes of computing evolved in past several decades,…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
DNA nanostructures are made using synthetic DNA strands, the sequences of which are designed such that they will self-assemble into the desired form by hybridization of complementary domains. Various structures and devices have been…
A nonlinear Tracking-Differentiator is one-input-two-output system that can generate smooth approximation of measured signals and get the derivatives of the signals. The nonlinear tracking-Differentiator is explored to denoise and generate…
DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited…
We present a general method for rendering representations of multi-stranded DNA complexes from textual descriptions into 2D diagrams. The complexes can be arbitrarily pseudoknotted, and if a planar rendering is possible, the method will…
The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…