Related papers: First-principles molecular structure search with a…
Conjugated organic molecules represent an important area of materials chemistry for both fundamental scientific exploration and technological applications. Using a genetic algorithm to computationally screen up to ~25-50 million molecules…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
Finding low-energy molecular conformers is challenging due to the high dimensionality of the search space and the computational cost of accurate quantum chemical methods for determining conformer structures and energies. Here, we combine…
A genetic algorithm is suitable for exploring large search spaces as it finds an approximate solution. Because of this advantage, genetic algorithm is effective in exploring vast and unknown space such as molecular search space. Though the…
We present the implementation of GAtor, a massively parallel, first principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…
Discovering the low-energy conformations of a molecule is of great interest to computational chemists, with applications in {\em in silico} materials design and drug discovery. In this paper, we propose a variable neighbourhood search…
Many proteins carry out their biological functions by forming the characteristic tertiary structures. Therefore, the search of the stable states of proteins by molecular simulations is important to understand their functions and…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
The discovery of molecules with tailored optoelectronic properties such as specific frequency and intensity of absorption or emission is a major challenge in creating next-generation organic light-emitting diodes (OLEDs) and photovoltaics.…
We present a method for reliably determining the lowest energy structure of an atomic cluster in an arbitrary model potential. The method is based on a genetic algorithm, which operates on a population of candidate structures to produce new…
Grover's algorithm is one of the most famous algorithms which explicitly demonstrates how the quantum nature can be utilized to accelerate the searching process. In this work, Grover's quantum search problem is mapped to a time-optimal…
Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database…
The computation of the global minimum energy conformation (GMEC) is an important and challenging topic in structure-based computational protein design. In this paper, we propose a new protein design algorithm based on the AND/OR…
We introduce the concepts of Grover operators and Grover kernels to systematically analyse Grover's searching algorithms. Then, we investigate a one-parameter family of quantum searching algorithms of Grover's type and we show that the…
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…
We present a continuous time quantum search algorithm analogous to Grover's. In particular, the optimal search time for this algorithm is proportional to $\sqrt{N}$, where $N$ is the database size. This search algorithm can be implemented…
Functions of chemical composition are complex and discrete in nature making it impossible to optimize them with gradient methods. Genetic algorithms, which do not use derivative information, are used to maximize the thermal conductivity of…
Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino…
Given two sets A and B and two oracles O(A) and O(B) that can identify the elements of these sets respectively, the goal is to find an element common to both sets using minimum number of oracle queries. Each application of either O(A) or…