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Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
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…
Recent years have witnessed the growing scholarly interest in the next-generation general-purpose computers. Various innovative computing modes have been proposed, such as optical, quantum phenomena, and DNA-based modes. Sequential logic…
Over the last century, a large number of physical and mathematical developments paired with rapidly advancing technology have allowed the field of quantum chemistry to advance dramatically. However, the lack of computationally efficient…
Quantum computers can in principle solve certain problems exponentially more quickly than their classical counterparts. We have not yet reached the advent of useful quantum computation, but when we do, it will affect nearly all scientific…
Quantum simulation of chemical systems is one of the most promising near-term applications of quantum computers. The variational quantum eigensolver, a leading algorithm for molecular simulations on quantum hardware, has a serious…
Optimization strategies driven by machine learning, such as Bayesian optimization, are being explored across experimental sciences as an efficient alternative to traditional design of experiment. When combined with automated laboratory…
While most work on the quantum simulation of chemistry has focused on computing energy surfaces, a similarly important application requiring subtly different algorithms is the computation of energy derivatives. Almost all molecular…
DNA computing is an unconventional approach to computing that harnesses the parallelism and information storage capabilities of DNA molecules. It has emerged as a promising field with potential applications in solving a variety of…
Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…
Transformers generate valid and diverse chemical structures, but little is known about the mechanisms that enable these models to capture the rules of molecular representation. We present a mechanistic analysis of autoregressive…
We review algorithms for protein design in general. Although these algorithms have a rich combinatorial, geometric, and mathematical structure, they are almost never covered in computer science classes. Furthermore, many of these algorithms…
The difficulty of simulating quantum systems, well-known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on…
Quantum computation based on quantum cellular automata (QCA) can greatly reduce the control and precision necessary for experimental implementations of quantum information processing. A QCA system consists of a few species of qubits in…
Current quantum computing hardware is restricted by the availability of only few, noisy qubits which limits the investigation of larger, more complex molecules in quantum chemistry calculations on quantum computers in the near-term. In this…
The last decade has witnessed a swiftly increasing interest in the design and production of novel multivalent molecules as powerful alternatives for conventional antibodies in the fight against cancer and infectious diseases. However, while…
The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics…
DNA-mediated computing is a novel technology that seeks to capitalize on the enormous informational capacity of DNA and has tremendous computational ability to compete with the current silicon-mediated computing, due to massive parallelism…
Recent advances in high-throughput genomic technologies coupled with exponential increases in computer processing and memory have allowed us to interrogate the complex aberrant molecular underpinnings of human disease from a genome-wide…
If the 20th century was known for the computational revolution, what will the 21st be known for? Perhaps the recent strides in the nascent fields of molecular programming and biological computation will help bring about the 'Coming Era of…