Related papers: An Efficient Algorithm for Upper Bound on the Part…
Many signal processing problems can be solved by maximizing the fitness of a segmented model over all possible partitions of the data interval. This letter describes a simple but powerful algorithm that searches the exponentially large…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
As the accuracy of machine learning models increases at a fast rate, so does their demand for energy and compute resources. On a low level, the major part of these resources is consumed by data movement between different memory units.…
It has been proven that the accessibility of the target sites has a critical influence for miRNA and siRNA. In this paper, we present a program, rip2.0, not only the energetically most favorable targets site based on the hybrid-probability,…
Modern applications of atomic physics, including the determination of frequency standards, and the analysis of astrophysical spectra, require prediction of atomic properties with exquisite accuracy. For complex atomic systems,…
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…
Recently, collocation based radial basis function (RBF) partition of unity methods (PUM) for solving partial differential equations have been formulated and investigated numerically and theoretically. When combined with stable evaluation…
Utilizing a partitioning method based on equal (or unequal) probabilities -- without incorporating the alpha-cluster ($\alpha$-cluster) model -- allows for the derivation of diverse topological configurations of nuclear fragments resulting…
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…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
In this paper, we introduce the software suite, Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure…
Accurate prediction of protein active-site structures remains a central challenge in structural biology, particularly for short and flexible peptide fragments where conventional and simulation-based methods often fail. Here, we present a…
Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction…
Motivated by the problem of determining the atomic structure of macromolecules using single-particle cryo-electron microscopy (cryo-EM), we study the sample and computational complexities of the sparse multi-reference alignment (MRA) model:…
With the rapid upsurge of deep learning tasks at the network edge, effective edge artificial intelligence (AI) inference becomes critical to provide low-latency intelligent services for mobile users via leveraging the edge computing…
Particle breakage due to collisional interactions plays a vital role in the development of several phenomena in science and engineering. The nonlinear collisional breakage equations (NCBEs) are a significant set of equations in this…
RNA-RNA interaction (RRI) is ubiquitous and has complex roles in the cellular functions. In human health studies, miRNA-target and lncRNAs are among an elite class of RRIs that have been extensively studied. Bacterial ncRNA-target and RNA…
In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various…
Efficient task partitioning plays a crucial role in achieving high performance at multiprocessor plat forms. This paper addresses the problem of energy-aware static partitioning of periodic real-time tasks on heterogeneous multiprocessor…
A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two…