Related papers: QuantumDNA: A Python Package for Analyzing Quantum…
In the context of quantum information, a quantum battery refers to a system composed of quantum particles that can store and release energy in a way that is governed by the principles of quantum mechanics. The study of open quantum…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
Lattice Quantum Chromodynamics (QCD) is an approach used by theoretical physicists to model the strong nuclear force. This works at the sub-nuclear scale to bind quarks together into hadrons including the proton and neutron. One of the long…
We present the first open access version of the QMeCha (Quantum MeCha) code, a quantum Monte Carlo (QMC) package developed to study many-body interactions between different types of quantum particles, with a modular and easy-to-expand…
WavePacket is an open-source program package for numerical simulations in quantum dynamics. Building on the previous Part I [Comp. Phys. Comm. 213, 223-234 (2017)] and Part II [Comp. Phys. Comm. 228, 229-244 (2018)] which dealt with quantum…
Binding energy is a fundamental thermodynamic property that governs molecular interactions, playing a crucial role in fields such as healthcare and the natural sciences. It is particularly relevant in drug development, vaccine design, and…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems.…
DNA strand displacement systems have proven themselves to be fertile substrates for the design of programmable molecular machinery and circuitry. Domain-level reaction enumerators provide the foundations for molecular programming languages…
Quantum computing systems depend on the principles of quantum mechanics to perform multiple challenging tasks more efficiently than their classical counterparts. In classical software engineering, the software life cycle is used to document…
Effective and accurate diagnosis of diseases such as cancer, diabetes, and heart failure is crucial for timely medical intervention and improving patient survival rates. Machine learning has revolutionized diagnostic methods in recent years…
Computing the similarity between two DNA sequences is of vital importance in bioscience, yet it can be computationally expensive on classical hardware. For example, the edit distance with move operations (EDM), a DNA similarity measure of…
WavePacket is an open-source program package for numeric simulations in quantum dynamics. It can solve time-independent or time-dependent linear Schr\"odinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled…
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves…
DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between…
QmeQ is an open-source Python package for numerical modeling of transport through quantum dot devices with strong electron-electron interactions using various approximate master equation approaches. The package provides a framework for…
With the overwhelming success in the field of quantum information in the last decades, the "quest" for a Quantum Neural Network (QNN) model began in order to combine quantum computing with the striking properties of neural computing. This…
The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA…
The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and…