26 papers · ranked by Valyu relevance
Boya Wang, Cameron Chalk, David Doty, David Soloveichik
Synthetic molecular information processing is typically designed through programming kinetic pathways, so that molecules bind, unbind, or incur conformational changes in some desired order. In DNA nanotechnology, this paradigm is exemplified by strand displacement cascades that control signal transmission through…
Phillip W. K. Jensen, Lasse Bjørn Kristensen, Cyrille Lavigne, Alán Aspuru‐Guzik
'Alán Aspuru‐Guzik'] In this study, we explore the use of molecules and molecular electronics for quantum computing. We construct one-qubit gates using one-electron scattering in molecules, and two-qubit controlled-phase gates using electron-electron scattering along metallic leads. Furthermore, we propose a class of…
Ryan C. Lee, Ariel Corsano, Chung Yi Tseng, Leo Y. T. Chou
Deep learning algorithms, such as neural networks, enable the processing of complex datasets with many related variables, and have applications in disease diagnosis, cell profiling, and drug discovery. Beyond its use in electronic computers, neural networks have been implemented using programmable biomolecules such as…
Hongbin Liu, Guang Hao Low, Damian S. Steiger, Thomas Häner + 2 more
'Markus Reiher' 'Matthias Troyer'] Molecular science is governed by the dynamics of electrons and atomic nuclei, and by their interactions with electromagnetic fields. A faithful physicochemical understanding of these processes is crucial for the design and synthesis of chemicals and materials of value for our society…
Takeru Kameda, Akinori Awazu, Yuichi Togashi
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important topic, where physicochemical properties of nucleotides are important as well as…
Panagiotis Mougkogiannis, Andrew Adamatzky
Proteinoid are thermal proteins which swell into microspheres in aqueous solution. Ensembles of proteinoids produce electrical spiking activity similar to that of neurons. We introduce a novel method for implementing logical gates in the ensembles of proteinoid microspheres using chronoamperometry. Chronoamperometry is…
Alberto Baiardi, Matthias Christandl, Markus Reiher
Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these interactions are very well established, the computational solution of the…
Małgorzata Borówko
Molecular simulation and modeling have a huge and growing impact on scientific progress. We are witnessing a kind of “transfer of experience to cyberspace moving”. This became possible thanks to the development of advanced theories, new computational methods, and, above all, thanks to the unimaginable increase in the…
Natarajan Arul Murugan, Artur Podobas, Davide Gadioli, Emanuele Vitali + 3 more
Drug discovery is the most expensive, time-demanding, and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high-affinity binding and specificity for a target associated with a…
Renée A. Sirbu, Luciano Floridi
Biological computing (biocomputing) leverages biologically derived materials and processes, such as DNA and protein synthesis, to perform computational tasks. Biocomputing offers significant advantages over traditional silicon-based systems in terms of scalability, energy efficiency, computational flexibility, and…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
Arnav Solanki, Zak Griffin, Purab Ranjan Sutradhar, Karisha Pradhan + 3 more
'Caiden Merritt' 'Amlan Ganguly' 'Marc D. Riedel'] DNA has been discussed as a potential medium for data storage. Potentially it could be denser, could consume less energy, and could be more durable than conventional storage media such as hard drives, solid-state storage, and optical media. However, computing on data…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
Jing Li, Leyi Wei, Henry H Y Tong, Quan Zou
In early drug discovery, virtual screening based on deep learning, virtual screening based on molecular docking, and molecular dynamics are three widely used computational strategies, but they always face a trade-off between throughput, search stability, and physical fidelity. This article discusses how quantum…
Ashar J. Malik, Chandra S. Verma
Quantum computers have demonstrated advantage in tackling problems considered hard for classical computers and hold promise for tackling complex problems in molecular mechanics such as mapping the conformational landscapes of biomolecules. This work attempts to explore a few ways in which classical data, relating to…
Eric Hartmann, Jannik Buhr, Kai Riedmiller, Evgeni Ulanov + 5 more
Molecular simulations have become indispensable in biological research. Their accuracy continues to improve, but directly modelling biochemical reactions – central to all life processes – remains computationally challenging. Here, we present a biomolecular reaction emulator that models reactions across conformational…
Authors not listed
We describe a collaborative research project spanning the disciplines of quantum hardware, quantum algorithms, conventional computational chemistry, synthetic medicinal chemistry and life sciences. Our project seeks to demonstrate an impact of quantum computing on human health. It is one of several funded by Wellcome…
Kevin V. Bigting, Shubhadeep Nag, Yaxin An
Coarse-graining (CG) reduces molecular details to extend the time and length scales of molecular dynamics simulations to microseconds and micrometers. However, the CG approaches have long been limited by the difficulty of constructing both accurate and transferable models efficiently, considering the large diversity of…
Ignasi Puch-Giner, Alexis Molina, Martí Municoy, Carles Pérez + 3 more
'Victor Guallar' 'Asia Fernandez Carvajal' 'Gerard Pujadas'] Computer simulation techniques are gaining a central role in molecular pharmacology. Due to several factors, including the significant improvements of traditional molecular modelling, the irruption of machine learning methods, the massive data generation, or…
Authors not listed
Imagine a computer capable of solving currently unsolvable problems. Quantum computing leverages the principles of quantum mechanics to tackle complex challenges that would take classical computers centuries to complete. In this Commentary, we explore the current state of quantum computing development and how it will…
Authors not listed
Computational chemistry has entered a new era where machine learning (ML) models—particularly graph neural networks and machine learning force fields—routinely deliver quantum mechanical accuracy at classical speeds, scaling to millions of atoms and reshaping workflows in drug discovery, catalysis, and materials…
Arit Kumar Bishwas, Arish Pitchai, Anuraj Som
Molecular docking is a crucial phase in drug discovery, involving the precise determination of the optimal spatial arrangement between two molecules when they bind. In such analysis, the 3D structure of molecules is a fundamental consideration, involving the manipulation of molecular representations based on their…
Weitang Li, Zhi Yin, Xiaoran Li, Dongqiang Ma + 8 more
Quantum computing, with its superior computational capabilities compared to classical approaches, holds the potential to revolutionize numerous scientific domains, including pharmaceuticals. However, the application of quantum computing for drug discovery has primarily been limited to proof-of-concept studies, which…
Weitang Li, Zhi Yin, Xiaoran Li, Dongqiang Ma + 9 more
'Zhenxing Zhang' 'Chenji Zou' 'Kunliang Bu' 'Maochun Dai' 'Jie Yue' 'Yuzong Chen' 'Xiaojin Zhang' 'Shengyu Zhang'] Quantum computing, with its superior computational capabilities compared to classical approaches, holds the potential to revolutionize numerous scientific domains, including pharmaceuticals. However, the…
Authors not listed
For decades, computational theoretical chemistry has provided critical insights into molecular behavior, often anticipating experimental discoveries. This review surveys twenty notable examples from the past fifteen years in which computational chemistry successfully predicted molecular structures, reaction mechanisms…
Georg Schusteritsch, David W. Wright, Andrew G. Green, Vid Stojevic
Quantum computing promises to revolutionise a range of scientific fields by providing solutions to previously intractable problems. The link between the technology and applications in chemistry has made drug discovery a natural place to look for ‘low-hanging fruit’. However, until recently, the lack of accessible…