Related papers: QuantumDNA: A Python Package for Analyzing Quantum…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
Quantum biology is an emerging field of research that concerns itself with the experimental and theoretical exploration of non-trivial quantum phenomena in biological systems. In this tutorial overview we aim to bring out fundamental…
Computer simulations are indispensable for analyzing complex systems, yet high-fidelity models often incur prohibitive computational costs. Multi-fidelity frameworks address this challenge by combining inexpensive low-fidelity simulations…
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which…
Measurements of electron transfer rates as well as of charge transport characteristics in DNA produced a number of seemingly contradictory results, ranging from insulating behaviour to the suggestion that DNA is an efficient medium for…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
Transfection of an anionic polynucleotide through a negatively charged membrane is an important problem in genetic engineering. The direct association of cationic surfactant to DNA decreases the effective negative charge of the nucleic…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
Quantum computing promises substantial speedups by exploiting quantum mechanical phenomena such as superposition and entanglement. Corresponding design methods require efficient means of representation and manipulation of quantum…
During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation…
Quantum nuclear dynamics with wavepacket time-evolution is classically intractable and viewed as a promising avenue for quantum information processing. Here, we use an IonQ 11-qubit trapped-ion quantum computer, Harmony, to study the…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
Charge migration along DNA molecules has attracted scientific interest for over half a century. Reports on possible high rates of charge transfer between donor and acceptor through the DNA, obtained in the last decade from solution…
DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced…
Accurate and efficient methods to simulate nonadiabatic and quantum nuclear effects in high-dimensional and dissipative systems are crucial for the prediction of chemical dynamics in condensed phase. To facilitate effective development,…
The scientific community shows a great interest in the study of DNA damage induction, DNA damage repair and the biological effects on cells and cellular systems after exposure to ionizing radiation. Several in-silico methods have been…
Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…