Related papers: QuantumDNA: A Python Package for Analyzing Quantum…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
Microscopic mechanisms of positive charge transfer in DNA remain unclear. A quantum state of electron hole in DNA is determined by the competition of the pi-stacking interaction $b$ sharing a charge between different base pairs and the…
In order to improve the accuracy of molecular dynamics simulations, classical force fields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. As an example application, a…
DNA microarray technology enables the simultaneous measurement of expression levels of thousands of genes, thereby facilitating the understanding of the molecular mechanisms underlying complex diseases such as brain tumors and the…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
We present the Python Tree Tensor Network package (pyTTN) for the evaluation of dynamical properties of closed and open quantum systems that makes use of Tree Tensor Network (TTN), or equivalently the multi-layer multiconfiguration…
Quantum transport for DNA conduction has widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works with concerning the electronic…
Quantum process characterization is a fundamental task in quantum information processing, yet conventional methods, such as quantum process tomography, require prohibitive resources and lack scalability. Here, we introduce an efficient…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
The question of whether DNA conducts electric charges is intriguing to physicists and biologists alike. The suggestion that electron transfer/transport in DNA might be biologically important has triggered a series of experimental and…
The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates…
In the past two decades, many research groups worldwide have tried to understand and categorize simple regimes in the charge transfer of such biological systems as DNA. Theoretically speaking, the lack of exact theories for electron-nuclear…
DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited…
Quantum computing research might lead to "quantum leaps," and it could have unanticipated repercussions in the medical field. This technique has the potential to be used in a broad range of contexts, some of which include the development of…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
Quantum-chemical subsystem and embedding methods require complex workflows that may involve multiple quantum-chemical program packages. Moreover, such workflows require the exchange of voluminous data that goes beyond simple quantities such…
Quantum simulation of chemistry and materials is predicted to be an important application for both near-term and fault-tolerant quantum devices. However, at present, developing and studying algorithms for these problems can be difficult due…
DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is…