Bioelectronics is a perspective future of electronics. The modelling of the protein is an important part that allows to search the appropriate folding structure with applicable conductivity properties. The classical computers struggle from modelling large structures because of number degrees of freedom. The mathematical modelling inside the quantum programming paradigm is a possible way to overcome this factor. This work describes a simplification algorithm of bio material (protein) model used in bioelectronics
Bioelectronics is a perspective future of electronics. The modelling of the protein is an important part that allows to search the appropriate folding structure with applicable conductivity properties. The classical computers struggle from modelling large structures because of number degrees of freedom. The mathematical modelling inside the quantum programming paradigm is a possible way to overcome this factor. This work describes a simplification algorithm of bio material (protein) model used in bioelectronics
Abstract Computational material science aims to simulate substances to understand their physical properties. Bioelectronics is an interdisciplinary field that studies biological material from the conductivity point of view. In case of proteins, the folding is an important feature that directly influences physical and chemical properties. The folding modelling is a hard task. The enormous number of degrees of freedom makes modelling impossible for classical computation due to resource limits. Quantum computations aim to process multidimensional data with logarithmic growth of quantum bits. Quantum operators, gates, form quantum programs, known as circuits, which process the input data. When talking about real quantum computers, the gates are noisy and expensive to execute. Thus, it is essential to reduce the number of quantum gates both for the quality of the result and the cost of computations. This work describes an approach to decrease the number of quantum gates based on their mathematical property.
Computational material science aims to simulate substances to understand their physical properties. Bioelectronics is an interdisciplinary field that studies biological material from the conductivity point of view. In case of proteins, the folding is an important feature that directly influences physical and chemical properties. The folding modelling is a hard task. The enormous number of degrees of freedom makes modelling impossible for classical computation due to resource limits. Quantum computations aim to process multidimensional data with logarithmic growth of quantum bits. Quantum operators (gates) form quantum programs, known as circuits that process the input data. In real quantum computers, the gates are noisy and expensive to execute. Thus, it is essential to reduce the number of quantum gates both for the quality of the result and the cost of computations. This work describes an approach to decrease the number of quantum gates based on their mathematical property. The matrix properties form the first optimization technique. In this case, the optimized quantum circuit predicts precisely the same protein folding as the not optimized circuit predicts. This happens because both of the circuits are mathematically equivalent. The removal of weakly-parametrized gates forms the second optimization technique. In such case the optimized quantum circuit calculates the approximate protein folding. The error depends on parameter’s amplitude of the gates. The first technique allows to decrease the circuit depth from 631 to 629 gates while modelling the part of Azurin peptide. The second technique allows to decrease the depth to 314 gates with the threshold parameter value 0.4 radians.
In computational biology, protein folding continues to be a key challenge with important implications for drug design and biological function comprehension. Using both classical and quantum computing methods, this paper provides an in-depth analysis of various possible lattice configurations and how theyare used in protein folding. To assess the protein design, we investigate classic models including the more intricate Miyazawa-Jernigan (MJ) interaction matrix and the hydrophobic-hydrophilic (HP) lattice model. Furthermore, we use integer programming methods to protein folding problems on lattices, addressing their NP-hardness and proving their effectiveness in obtaining optimal solutions. Expanding upon these conventional techniques, we present sophisticated graph neural network (GNN) models, particularly the RG-MPNN, which integrate pharmacophore ideas to predict chemical properties by using task-related representations. In the latter section of our paper, we examine how protein folding simulations on lattice structures could be transformed using quantum algorithms. Compared to classical methods, quantum computational techniques promise to be more accurate and efficient at handling the enormous diversity and complexity of protein folding.
This paper presents a novel approach to protein structure prediction leveraging the principles of quantum entanglement. Traditional protein structure prediction methods are often limited by the computational complexity of simulating large biomolecular systems. We propose a framework that utilizes quantum entanglement to model the complex correlations inherent in protein folding, potentially overcoming these limitations. The core idea involves translating the amino acid sequence of a protein into a quantum state and employing quantum computation, specifically entanglement-based algorithms, to predict the protein's three-dimensional structure. The theoretical framework outlines the transformation process, the quantum algorithm design, and the methods for interpreting the results. We explore the potential advantages of this approach, focusing on its ability to capture long-range interactions and conformational flexibility that are difficult to model accurately with classical methods. The ultimate goal is to establish a new paradigm for protein structure prediction, offering improved accuracy and efficiency.
This paper proposes a novel approach to protein structure prediction leveraging principles from quantum mechanics, specifically entanglement and superposition. Traditional methods for protein folding, reliant on classical computational techniques, frequently struggle with accuracy and efficiency, particularly when dealing with complex protein structures. We posit that protein folding can be modeled as solving the Schrödinger equation, a problem ideally suited for quantum computation. This work outlines a framework where quantum algorithms are utilized to accelerate the solution of the Schrödinger equation for a given protein, significantly reducing the computational burden. Furthermore, we incorporate biological information, such as sequence data and known structural constraints, to refine the quantum solution and enhance predictive accuracy. The core claim is that utilizing quantum mechanical phenomena can lead to a more accurate protein structure prediction method. The mechanism involves transforming the protein folding problem into a quantum mechanical equation solving task, accelerating the process with quantum computation, and optimizing the solution with biological data. We present a conceptual model and discuss the potential benefits and challenges of this approach, highlighting its potential to surpass the limitations of current classical methods.
Abstract Predicting the three-dimensional structure of a protein from its primary sequence of amino acids is known as the protein folding problem. Due to the central role of proteins’ structures in chemistry, biology and medicine applications, this subject has been intensively studied for over half a century. Although classical algorithms provide practical solutions for the sampling of the conformation space of small proteins, they cannot tackle the intrinsic NP-hard complexity of the problem, even when reduced to the simplest Hydrophobic-Polar model. On the other hand, while fault-tolerant quantum computers are beyond reach for state-of-the-art quantum technologies, there is evidence that quantum algorithms can be successfully used in noisy state-of-the-art quantum computers to accelerate energy optimization in frustrated systems. In this work, we present a model Hamiltonian with O(N4) O ( N 4 ) scaling and a corresponding quantum variational algorithm for the folding of a polymer chain with N monomers on a lattice. The model reflects many physico-chemical properties of the protein, reducing the gap between coarse-grained representations and mere lattice models. In addition, we use a robust and versatile optimization scheme, bringing together variational quantum algorithms specifically adapted to classical cost functions and evolutionary strategies to simulate the folding of the 10 amino acid Angiotensin on 22 qubits. The same method is also successfully applied to the study of the folding of a 7 amino acid neuropeptide using 9 qubits on an IBM 20-qubit quantum computer. Bringing together recent advances in building gate-based quantum computers with noise-tolerant hybrid quantum-classical algorithms, this work paves the way towards accessible and relevant scientific experiments on real quantum processors.