Related papers: DNA-based chemical compiler
Quantum simulation can beat current classical computers with minimally a few tens of qubits and will likely become the first practical use of a quantum computer. One promising application of quantum simulation is to attack challenging…
Background: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main…
This paper presents a comprehensive workflow for generating and validating a synthetic dataset designed for robotic surgery instrument segmentation. A 3D reconstruction of the Da Vinci robotic arms was refined and animated in Autodesk Maya…
Large language models (LLMs) are changing the way researchers interact with code and data in scientific computing. While their ability to generate general-purpose code is well established, their effectiveness in producing scientifically…
Nearly thirty years after its inception, the field of DNA-programmed colloidal self-assembly has begun to realize its initial promise. In this review, we summarize recent developments in designing effective interactions and understanding…
The Turing completeness of continuous Chemical Reaction Networks (CRNs) states that any computable real function can be computed by a continuous CRN on a finite set of molecular species, possibly restricted to elementary reactions, i.e.…
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 Chemical Reaction Network (CRN) is a well-studied model that describes the interaction of molecules in well-mixed solutions. In 2014, Qian and Winfree [22] proposed the abstract surface chemical reaction network model (sCRN), which…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…
With the rapid development of quantum technology, one of the leading applications is the simulation of chemistry. Interestingly, even before full scale quantum computers are available, quantum computer science has exhibited a remarkable…
In Compiler Design courses, students learn how a program written in high level programming language and designed for humans understanding is systematically converted into low level assembly language understood by machines, through different…
The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…
Quantum computers are expected to be considerably more efficient than classical computers for the execution of some specific tasks. The difficulty in the practical implementation of thoose computers is to build a microscopic quantum system…
The problem of synthesis in computer sciences, including cybernetics, artificial intelligence and system analysis, is analyzed. Main methods of realization this problem are discussed. Ways of search universal method of creation universal…
Simulations of chemical dynamics are a powerful means for understanding chemistry. However, classical computers struggle to simulate many chemical processes, especially non-adiabatic ones, where the Born-Oppenheimer approximation breaks…
In the current world due to the huge demand for storage, DNA-based storage solution sounds quite promising because of their longevity, low power consumption, and high capacity. However in real life storing data in the form of DNA is quite…
We present KinetiX, a software toolkit to generate computationally efficient fuel-specific routines for the chemical source term, thermodynamic and mixture-averaged transport properties for use in combustion simulation codes. The C++…
The ability to detect whether a species (or dimension) is zero in Chemical Reaction Networks (CRN), Vector Addition Systems, or Petri Nets is known to increase the power of these models -- making them capable of universal computation. While…
The potential number of drug like small molecules is estimated to be between 10^23 and 10^60 while current databases of known compounds are orders of magnitude smaller with approximately 10^8 compounds. This discrepancy has led to an…