Related papers: Messenger RNA Design via Expected Partition Functi…
While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
We present a detailed study of the performance and reliability of design procedures based on energy minimization. The analysis is carried out for model proteins where exact results can be obtained through exhaustive enumeration. The…
Nucleic acid sequence design via codon optimization is a fundamental task with applications across synthetic biology, mRNA therapeutics, and vaccine design. Given a target protein, it is a major open challenge to navigate the…
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…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
This paper presents an energy-efficient downlink precoding scheme with the objective of maximizing system energy efficiency in a multi-cell massive MIMO system. The proposed precoding design jointly considers the issues of power control,…
Combinatorial designs provide an interesting source of optimization problems. Among them, permutation codes are particularly interesting given their applications in powerline communications, flash memories, and block ciphers. This paper…
RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA…
We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…
We propose and discuss a novel strategy for protein design. The method is based on recent theoretical advancements which showed the importance to treat carefully the conformational free energy of designed sequences. In this work we show how…
A numerical framework based on network partition and operator splitting is developed to solve nonlinear differential equations of large-scale dynamic processes encountered in physics, chemistry and biology. Under the assumption that those…
Reduction of communication and efficient partitioning are key issues for achieving scalability in hierarchical $N$-Body algorithms like FMM. In the present work, we propose four independent strategies to improve partitioning and reduce…
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 design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which can tremendously impact their cost and…
This thesis is concerned with the design of distributed algorithms for solving optimization problems. We consider networks where each node has exclusive access to a cost function, and design algorithms that make all nodes cooperate to find…
Bayesian optimal design is considered for experiments where the response distribution depends on the solution to a system of non-linear ordinary differential equations. The motivation is an experiment to estimate parameters in the equations…
Real-world problems of operations research are typically high-dimensional and combinatorial. Linear programs are generally used to formulate and efficiently solve these large decision problems. However, in multi-period decision problems, we…
RNA inverse sequence design has broad biological and engineering applications, but computational methods for practical design queries remain limited. Such queries may impose several constraints at once, including target folds or motifs,…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…