Related papers: First-principles molecular structure search with a…
Molecular geometry prediction of flexible molecules, or conformer search, is a long-standing challenge in computational chemistry. This task is of great importance for predicting structure-activity relationships for a wide variety of…
Isomer search or molecule enumeration refers to the problem of finding all the isomers for a given molecule. Many classical search methods have been developed in order to tackle this problem. However, the availability of quantum computing…
All living organisms use the same genetic languages in their molecular biology machinery. They can be understood as the optimal solutions to the replication tasks involving DNA and proteins. These solutions perfectly fit the pattern…
Motif finding is an important step for the detection of rare events occurring in a set of DNA or protein sequences. Extraction of information about these rare events can lead to new biological discoveries. Motifs are some important patterns…
We propose a family of very efficient hierarchical indexing schemes for ungapped, score matrix-based similarity search in large datasets of short (4-12 amino acid) protein fragments. This type of similarity search has importance in both…
Global Optimization with First-principles Energy Expressions (GOFEE) is an efficient method for identifying low energy structures in computationally expensive energy landscapes such as the ones described by density functional theory (DFT),…
In this work we address two questions concerning Grover's algorithm. In the first we give an answer to the question how to employ Grover's algorithm for actual search over database. We introduce a quantum model of an unordered phone book…
One of the most powerful techniques to study protein structures is to look for recurrent fragments (also called substructures or spatial motifs), then use them as patterns to characterize the proteins under study. An emergent trend consists…
As the structural databases continue to expand, efficient methods are required to search similar structures of the query structure from the database. There are many previous works about comparing protein 3D structures and scanning the…
We propose a scheme for global optimization with first-principles energy expressions (GOFEE) of atomistic structure. While unfolding its search, the method actively learns a surrogate model of the potential energy landscape on which it…
Genetic algorithms are considered as one of the most efficient search techniques. Although they do not offer an optimal solution, their ability to reach a suitable solution in considerably short time gives them their respectable role in…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years,…
Generating a novel and optimized molecule with desired chemical properties is an essential part of the drug discovery process. Failure to meet one of the required properties can frequently lead to failure in a clinical test which is costly.…
Unstructured search remains as one of the significant challenges in computer science, as classical search algorithms become increasingly impractical for large-scale systems due to their linear time complexity. Quantum algorithms, notably…
The computational models for geophysical flows are computationally very expensive to employ in multi-query tasks such as data assimilation, uncertainty quantification, and hence surrogate models sought to alleviate the computational burden…
Grover's algorithm, orginally conceived as a means of searching an unordered database, can also be used to extract solutions from the result sets generated by quantum computations. The Grover algorithm exploits the concept of an oracle…
Protein structure prediction is considered as one of the most challenging and computationally intractable combinatorial problem. Thus, the efficient modeling of convoluted search space, the clever use of energy functions, and more…
Grover's algorithm is normally presented as a method of searching a database, however it would be more accurately described as a method of identifying elements of an interval of the integers which satisfy some logical clause - an example…
This paper proposes a machine learning (ML) method to predict stable molecular geometries from their chemical composition. The method is useful for generating molecular conformations which may serve as initial geometries for saving time…