Related papers: An Efficient Algorithm for Upper Bound on the Part…
New high-throughput sequencing technologies have made it possible to pursue the advent of genome-wide transcriptomics. That progress combined with the recent discovery of regulatory non-coding RNAs (ncRNAs) has necessitated fast and…
In this paper we present a selfcontained analysis and description of the novel {\it ab initio} folding algorithm {\sf cross}, which generates the minimum free energy (mfe), 3-noncrossing, $\sigma$-canonical RNA structure. Here an RNA…
The minimum degree algorithm is one of the most widely-used heuristics for reducing the cost of solving large sparse systems of linear equations. It has been studied for nearly half a century and has a rich history of bridging techniques…
Makespan scheduling on identical machines is one of the most basic and fundamental packing problems studied in the discrete optimization literature. It asks for an assignment of $n$ jobs to a set of $m$ identical machines that minimizes the…
In this article, we present our recent experiments on fission fragment rocket propulsion, and on an innovative new design for an alpha particle detection system that has been inspired by these rocketry results. Our test platform, which…
Recent advancements in quantum computing have opened new avenues for tackling long-standing complex combinatorial optimization problems that are intractable for classical computers. Predicting secondary structure of mRNA is one such…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
We propose a new algorithm for the fast solution of large, sparse, symmetric positive-definite linear systems, spaND -- sparsified Nested Dissection. It is based on nested dissection, sparsification and low-rank compression. After…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
We present a tight RMR complexity lower bound for the recoverable mutual exclusion (RME) problem, defined by Golab and Ramaraju \cite{GR2019a}. In particular, we show that any $n$-process RME algorithm using only atomic read, write,…
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…
Finding Minimum Energy Configurations (MECs) is essential in fields such as physics, chemistry, and materials science, as they represent the most stable states of the systems. In particular, identifying such MECs in multi-component alloys…
Mutual exclusion (ME) is one of the most commonly used techniques to handle conflicts in concurrent systems. Traditionally, mutual exclusion algorithms have been designed under the assumption that a process does not fail while…
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…
The secondary structure that maximizes the number of non-crossing matchings between complimentary bases of an RNA sequence of length n can be computed in O(n^3) time using Nussinov's dynamic programming algorithm. The Four-Russians method…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
Partitioning algorithms play a key role in many scientific and engineering disciplines. A partitioning algorithm divides a set into a number of disjoint subsets or partitions. Often, the quality of the resulted partitions is measured by the…
A widely used strategy to reduce the computational cost in quantum-chemical calculations is to partition the system into an active subsystem, which is the focus of the computational efforts and an environment that is treated at a lower…
The random phase approximation (RPA) as formulated as an orbital-dependent, fifth-rung functional within the density functional theory (DFT) framework offers a promising approach for calculating the ground-state energies and the derived…
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…