26 papers · ranked by Valyu relevance
Shaji Varghese, Johannes A. A. W. Elemans, Alan E. Rowan, Roeland J. M. Nolte
'Roeland J. M. Nolte'] In this perspective, we highlight some of the recent advances in the development of molecular and biomolecular systems for performing logic operations and computing. We also present a blueprint of a chemical Turing machine using a processive catalytic approach.
Xin Liang, Wen Zhu, Zhibin Lv, Quan Zou
Molecular computing and bioinformatics are two important interdisciplinary sciences that study molecules and computers. Molecular computing is a branch of computing that uses DNA, biochemistry, and molecular biology hardware, instead of traditional silicon-based computer technologies. Research and development in this…
Sahana Gangadharan, Karthik Raman
An astonishingly diverse biomolecular circuitry orchestrates the functioning machinery underlying every living cell. These biomolecules and their circuits have been engineered not only for various industrial applications but also to perform other atypical functions that they were not evolved for—including computation.…
Luca Zammataro
This work is based on the Equivalence between Molecular Dynamics and Neural Network. It provides learning proofs in a Lennard-Jones (LJ) fluid, presented as a network of particles having non-bonded interactions. I describe the fluid’s learning as the property of an order that emerges as an adaptation in establishing…
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…
Yanan Wang, Qi Lv, Yingying Zhang, Luhui Wang + 1 more
Background DNA is a promising candidate for the construction of biological devices due to its unique properties, including structural simplicity, convenient synthesis, high flexibility, and predictable behavior. And DNA has been widely used to construct the advanced logic devices. Results Herein, a molecular probe…
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…
Ehud Shapiro
We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and…
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…
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…
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…
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…
Alan Aspuru-Guzik, Roland Lindh, Markus Reiher
To date, the program for the development of methods and models for atomistic and continuum simulation directed toward chemicals and materials has reached an incredible degree of sophistication and maturity. Currently, one can witness an increasingly rapid emergence of advances in computing, artificial intelligence, 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…
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…
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…
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…
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…
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…
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…
Peter V. Coveney, Roger R. Highfield
Title: Highlights 1. • When machine learning is applied in ignorance of fundamental laws of nature, it is likely to deliver unreliable answers. 2. • With his colleagues, Peter Coveney has described the computational algorithms best suited for deployment on exascale architectures. 3. • In the exascale era, we will…
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…
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…