Related papers: QuantumDNA: A Python Package for Analyzing Quantum…
Trajectories, sequentially measured quantities that form a path, are an important presence in many different fields, from hadronic beams in physics to electrocardiograms in medicine. Trajectory anal-ysis requires the quantification and…
Quantum computing harnesses quantum laws of nature to enable new types of algorithms, not efficiently possible on traditional computers, that may lead to breakthroughs in crucial areas like materials science and chemistry. There is rapidly…
Understanding astrophysical and cosmological processes can be challenging due to their complexity and lack of intuitive analogies. To address this, we present \texttt{AstronomyCalc}, a Python package specifically designed to aid…
Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…
The Geant4-DNA project proposes to develop an open-source simulation software based and fully included in the general-purpose Geant4 Monte Carlo simulation toolkit. The main objective of this software is to simulate biological damages…
Dynamo is a full-stack software solution for scientific data management. Dynamo's architecture is modular, extensible, and customizable, making the software suitable for managing data in a wide range of installation scales, from a few…
Recent advances in machine learning (ML) have accelerated progress in calibrating and operating quantum dot (QD) devices. However, most ML approaches rely on access to large, representative datasets designed to capture the full spectrum of…
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased simulation is slow, limiting applications…
We propose a multi-scale approach to understand the physics related to ion-beam cancer therapy. It allows the calculation of the probability of DNA damage as a result of irradiation of tissues with energetic ions, up to 430 MeV/u. This…
Charge transfer can take place along double helical DNA over distances as long as 30 nanometers. However, given the active role of the thermal environment surrounding charge carriers in DNA, physical mechanisms driving the transfer process…
Dynamic convolution enhances model capacity by adaptively combining multiple kernels, yet faces critical trade-offs: prior works either (1) incur significant parameter overhead by scaling kernel numbers linearly, (2) compromise inference…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
We describe how Python can be leveraged to streamline the curation, modelling and dissemination of drug discovery data as well as the development of innovative, freely available tools for the related scientific community. We look at various…
A number of tools have been developed to detect topological phase transitions in strongly correlated quantum systems. They apply under different conditions, but do not cover the full range of many-body models. It is hence desirable to…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…
Low-energy electrons offer a unique possibility for long exposure imaging of individual biomolecules without significant radiation damage. In addition, low-energy electrons exhibit high sensitivity to local potentials and thus can be…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
DNA has been proposed as a chemical platform for computing and data storage, paving the way for building DNA-based computers. Recently, DNA has been hypothesized as an ideal quantum computer with the base pairs working as Josephson…