Related papers: mRNA Folding Algorithms for Structure and Codon Op…
Messenger RNA-based medicines hold immense potential, as evidenced by their rapid deployment as COVID-19 vaccines. However, worldwide distribution of mRNA molecules has been limited by their thermostability, which is fundamentally limited…
The optimization of dynamic problems is both widespread and difficult. When conducting dynamic optimization, a balance between reinitialization and computational expense has to be found. There are multiple approaches to this. In parallel…
We present analysis of a novel tool for protein secondary structure prediction using the recently-investigated Neural Machine Translation framework. The tool provides a fast and accurate folding prediction based on primary structure with…
We explore the potential application of quantum annealing to address the protein structure problem. To this end, we compare several proposed ab initio protein folding models for quantum computers and analyze their scaling and performance…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
When a fault occurs in nuclear facilities, accurately reconstructing gamma radiation fields through measurements from the mobile radiation detection (MRD) system becomes crucial to enable access to internal facility areas for essential…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy…
Background: We study the sparsification of dynamic programming folding algorithms of RNA structures. Sparsification applies to the mfe-folding of RNA structures and can lead to a significant reduction of time complexity. Results: We analyze…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…
2. In Section 3, we used some vague statements to affirm the training process of the neural network, which cannot support others to reproduce the results of the paper. In addition, this section does not show the difference between this…
Chance-constrained problems involve stochastic components in the constraints which can be violated with a small probability. We investigate the impact of different types of chance constraints on the performance of iterative search…
This review explores the application of intelligent optimization algorithms to Multi-Objective Optimal Power Flow (MOPF) in enhancing modern power systems. It delves into the challenges posed by the integration of renewables, smart grids,…
The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics…
Medical imaging is key in modern medicine. From magnetic resonance imaging (MRI) to microscopic imaging for blood cell detection, diagnostic medical imaging reveals vital insights into patient health. To predict diseases or provide…
Evolutionary crystal structure prediction proved to be a powerful approach for studying a wide range of materials. Here, we present a specifically designed algorithm for the prediction of the structure of complex crystals consisting of…
Nuclear magnetic resonance (NMR) spectroscopy is one of the leading techniques for protein studies. The method features a number of properties, allowing to explain macromolecular interactions mechanistically and resolve structures with…
Across many disciplines, chemical reaction networks (CRNs) are an established population model defined as a system of coupled nonlinear ordinary differential equations. In many applications, for example, in systems biology and epidemiology,…