Related papers: QuantumDNA: A Python Package for Analyzing Quantum…
Recent genomic foundation models largely adopt large language model architectures that treat DNA as a one-dimensional token sequence. However, exhaustive sequential reading is structurally misaligned with sparse and discontinuous genomic…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
Characterizing the temporal variability of astrophysical sources is key to understanding the underlying physical processes driving their emissions. This work introduces a gammapy_SyLC, a Python package that offers tools to simulate and fit…
Scientific progress is tightly coupled to the emergence of new research tools. Today, machine learning (ML)-especially deep learning (DL)-has become a transformative instrument for quantum science and technology. Owing to the intrinsic…
The DNA cryptography is a new and very promising direction in cryptography research. DNA can be used in cryptography for storing and transmitting the information, as well as for computation. Although in its primitive stage, DNA cryptography…
DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a…
The advent of hybrid computing platforms consisting of quantum processing units integrated with conventional high-performance computing brings new opportunities for algorithm design. By strategically offloading select portions of the…
The incorporation of quantum ansatz with machine learning classification models demonstrates the ability to extract patterns from data for classification tasks. However, taking advantage of the enhanced computational power of quantum…
Transcription factors regulate gene expression, but how these proteins recognize and specifically bind to their DNA targets is still debated. Machine learning models are effective means to reveal interaction mechanisms. Here we studied the…
Quantum computing offers the promise of speedups for scientific computations, but its application to reacting flows is hindered by nonlinear source terms, the challenges of time-dependent simulations, and the difficulty of extracting…
Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
Molecular ecology uses molecular genetic data to answer traditional ecological questions in biogeography and biodiversity among others. Several ecological principles, such as the niche hypothesis and the competitive exclusions, are based on…
In this methods article, we provide a flexible but easy-to-use implementation of Direct Coupling Analysis (DCA) based on Boltzmann machine learning, together with a tutorial on how to use it. The package \texttt{adabmDCA 2.0} is available…
The combined quantum electron-nuclear dynamics is often associated with the Born-Huang expansion of the molecular wave function and the appearance of nonadiabatic effects as a perturbation. On the other hand, native multicomponent…
We study an intermediate quantum coherent-incoherent charge transport mechanism in metal-molecule-metal junctions using B\"uttiker's probe technique. This tool allows us to include incoherent effects in a controlled manner, and thus to…
In this article we propose a dynamic quantum tomography model for open quantum systems with evolution given by phase-damping channels. Mathematically, these channels correspond to completely positive trace-preserving maps defined by the…
We investigate quantum transport characteristics of a ladder model, which effectively mimics the topology of a double-stranded DNA molecule. We consider the interaction of tunneling charges with a selected internal vibrational degree of…
Quantum engineering seeks to create novel technologies based on the exploitation of distinctly nonclassical behaviors such as quantum superposition. The vast majority of currently pursued applications fall into the domain of quantum…
The DNA molecule, apart from carrying the genetic information, plays a crucial role in a variety of biological processes and find applications in drug design, nanotechnology and nanoelectronics. The molecule undergoes significant structural…