Related papers: DNA-based chemical compiler
The self-assembly of DNA-coated colloids controlled by enzymatic reactions has the potential to enable the formation of materials with hierarchical organization and switchable configurations. However, the problem of designing such…
Most molecular diagram parsers recover chemical structure from raster images (e.g., PNGs). However, many PDFs include commands giving explicit locations and shapes for characters, lines, and polygons. We present a new parser that uses these…
Chemically reacting flows are common in engineering, such as hypersonic flow, combustion, explosions, manufacturing processes and environmental assessments. For combustion, the number of reactions can be significant (over 100) and due to…
Polynomial dynamical systems (DSs) can model a wide range of physical processes. A special subset of these DSs that can model chemical reactions under mass-action kinetics is called chemical dynamical systems (CDSs). A fundamental problem,…
DNA sequence classification is a fundamental task in computational biology with vast implications for applications such as disease prevention and drug design. Therefore, fast high-quality sequence classifiers are significantly important.…
Computing-in-memory (CIM) architectures demonstrate superior performance over traditional architectures. To unleash the potential of CIM accelerators, many compilation methods have been proposed, focusing on application scheduling…
We describe a visual programming language for defining behaviors manifested by reified actors in a 2D virtual world that can be compiled into programs comprised of sequences of combinators that are themselves reified as actors. This makes…
Astrochemical modeling is needed for understanding the formation and evolution of interstellar molecules, and for extracting physical information from spectroscopic observations of interstellar clouds. The modeling usually involves handling…
The difficulty of simulating quantum systems, well-known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on…
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…
Chemical reaction networks (CRNs) are a standard formalism used in chemistry and biology to reason about the dynamics of molecular interaction networks. In their interpretation by ordinary differential equations, CRNs provide a…
In the last few years, we have seen the transformative impact of deep learning in many applications, particularly in speech recognition and computer vision. Inspired by Google's Inception-ResNet deep convolutional neural network (CNN) for…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
We introduce ppsim, a software package for efficiently simulating population protocols, a widely-studied subclass of chemical reaction networks (CRNs) in which all reactions have two reactants and two products. Each step in the dynamics…
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…
Chemists now routinely use software as part of their work. For example, virtual chemistry allows chemical reactions to be simulated. In particular, a selection of software is available for the visualisation of complex 3-dimensional…
Computational screening of naturally occurring proteins has the potential to identify efficient catalysts among the hundreds of millions of sequences that remain uncharacterized. Current experimental methods remain time, cost and labor…
Molecular structures are always depicted as 2D printed form in scientific documents like journal papers and patents. However, these 2D depictions are not machine-readable. Due to a backlog of decades and an increasing amount of these…
Computer Aided Design systems provide tools for building and manipulating models of solid objects. Some also provide access to programming languages so that parametrised designs can be expressed. There is a sharp distinction, therefore,…
We develop a tool that enables domain experts to quickly generate numerical solvers for emerging multi-physics phenomena starting from a high-level description based on ordinary/partial differential equations and their initial and boundary…