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RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
Solvation is a notoriously difficult and nagging problem for the rigorous theoretical description of chemistry in the liquid phase. Successes and failures of various approaches ranging from implicit solvation modeling through dielectric…
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…
Feature selection from a large number of covariates (aka features) in a regression analysis remains a challenge in data science, especially in terms of its potential of scaling to ever-enlarging data and finding a group of scientifically…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
Knowledge of a protein's atomic conformational ensemble is critical to determining its function, yet state-of-the-art ensemble prediction models are limited by lack of high-quality conformational data from simulation or experiment. Recent…
The structure of an RNA molecule plays a significant role in its biological function. Predicting structure given a one dimensional sequence of RNA nucleotide bases is a difficult and important problem. Many computer programs (known as in…
The Random Walks (RW) algorithm is one of the most e - cient and easy-to-use probabilistic segmentation methods. By combining contrast terms with prior terms, it provides accurate segmentations of medical images in a fully automated manner.…
Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA design framework that leverages evolutionary embeddings from…
The Random Walks (RW) algorithm is one of the most e - cient and easy-to-use probabilistic segmentation methods. By combining contrast terms with prior terms, it provides accurate segmentations of medical images in a fully automated manner.…
Self-avoiding walks (SAW) are the source of very difficult problems in probabilities and enumerative combinatorics. They are also of great interest as they are, for instance, the basis of protein structure prediction in bioinformatics.…
Random sequential adsorption algorithm is a popular tool for modelling structure of monolayers built in irreversible adsorption experiments. However, this algorithm becomes very inefficient when the density of molecules in a layer rises.…
The Ribonucleic Acid (RNA) inverse folding problem, designing nucleotide sequences that fold into specific tertiary structures, is a fundamental computational biology problem with important applications in synthetic biology and…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…