A resource dependent protein synthesis model for evaluating synthetic circuits
Reliable in-silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the Ribosome Flow Model and among other things describes the movement of RNA-polymerase and Ribosomes on mRNA and DNA templates respectively. By analyzing the convergence properties of this model based upon geometric considerations we present additional insights into the dynamic mechanisms of the process of protein synthesis. Further, we exemplarily show how this model can be used to evaluate the performance of synthetic gene circuits under different loading scenarios.
Code (0)
등록된 구현이 없습니다.
Similar Papers 제목 키워드 기반
Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species
Protein synthesis is an important determinant of microbial growth and response that demands a high amount of metabolic and biosynthetic resources. Despite these costs, microbial species from different taxa and habitats m…
Paradoxical LTP maintenance with inhibition of protein synthesis and the proteasome suggests a novel protein synthesis requirement for early LTP reversal
The transition from early long-term potentiation (E-LTP) to late LTP (L-LTP) involves protein synthesis and degradation. L-LTP is blocked by inhibiting either protein synthesis or proteasome-dependent degradation prior t…
SynClaimEval: A Framework for Evaluating the Utility of Synthetic Data in Long-Context Claim Verification
Large Language Models (LLMs) with extended context windows promise direct reasoning over long documents, reducing the need for chunking or retrieval. Constructing annotated resources for training and evaluation, however,…
CogMol: Target-Specific and Selective Drug Design for COVID-19 Using Deep Generative Models
The novel nature of SARS-CoV-2 calls for the development of efficient de novo drug design approaches. In this study, we propose an end-to-end framework, named CogMol (Controlled Generation of Molecules), for designing ne…
AttributeDrug DesignRetrosynthesisSpecificitySynthFormer: Equivariant Pharmacophore-based Generation of Synthesizable Molecules for Ligand-Based Drug Design
Drug discovery is a complex, resource-intensive process requiring significant time and cost to bring new medicines to patients. Many generative models aim to accelerate drug discovery, but few produce synthetically acces…
Drug DesignDrug DiscoveryGraph Neural Network