Related papers: pyFRET: A Python Library for Single Molecule Fluor…
Advanced microscopy techniques are essential in biomedical research for visualising and tracking biomolecules within living cells and their compartments. Conventional fluorescence microscopy methods, however, often struggle with accurately…
diffpy$.$morph addresses a need to gain scientific insights from 1D scientific spectra in model independent ways. A powerful approach for this is to take differences between pairs of spectra and look for meaningful changes that might…
F\"orster's theory of resonant energy transfer (FRET) predicts the strength and range of exciton transport between separated molecules. We introduce an exactly soluble model for FRET which reproduces F\"orster's results as well as…
We report high time-resolution measurements of photon statistics from pairs of dye molecules coupled by fluorescence resonance energy transfer (FRET). In addition to quantum-optical photon antibunching, we observe photon bunching on a…
Over the past decade, the Python-based Simulations of Chemistry Framework (PySCF) has developed into a widely used open-source platform for electronic structure theory and quantum chemical method development. This article reviews the major…
The wavelet scattering transform is an invariant signal representation suitable for many signal processing and machine learning applications. We present the Kymatio software package, an easy-to-use, high-performance Python implementation of…
pyspeckit is a toolkit and library for spectroscopic analysis in Python. We describe the pyspeckit package and highlight some of its capabilities, such as interactively fitting a model to data, akin to the historically widely-used splot…
Determining molecular abundances in astrophysical environments is crucial for interpreting observational data and constraining physical conditions in these regions. Chemical modelling tools are essential for simulating the complex processes…
Fourier transforms are an often necessary component in many computational tasks, and can be computed efficiently through the fast Fourier transform (FFT) algorithm. However, many applications involve an underlying continuous signal, and a…
I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize…
Applications of Fluorescence Resonance Energy Transfer (FRET) in biology have expanded tremendously in the last 25 years. This technique has become a staple technique in many biological and biophysical fields. FRET based chemical sensors…
HIPSTER (Heavily Ionising Particle Standard Toolkit for Event Recognition) is an open source Python package designed to facilitate the use of TensorFlow in a high energy physics analysis context. The core functionality of the software is…
pyforce is a Python package implementing Data-Driven Reduced Order Modelling techniques for applications to multi-physics problems, mainly set in the Nuclear Engineering world. The package is part of the ROSE (Reduced Order modelling with…
Resonant energy transfers, i.e. the non-radiative redistribution of an electronic excitation between two particles coupled by the dipole-dipole interaction, lie at the heart of a variety of chemical and biological phenomena, most notably…
We present PrismSSL, a Python library that unifies state-of-the-art self-supervised learning (SSL) methods across audio, vision, graphs, and cross-modal settings in a single, modular codebase. The goal of the demo is to show how researchers…
We review methods of data analysis for biophysical data with a special emphasis on single molecule applications. Our review is intended for anyone, from student to established researcher. For someone just getting started, we focus on…
Despite image reconstruction becoming more widespread when interpreting OIFITS Data, model fitting in u,v space often remains the best way to interpret data, either because of the sparsity of the data, or because a quantitative measurement…
Fluorescence spectroscopy and modeling provide powerful means to characterize biomacromolecular structures, dynamics, and interactions. F\"orster resonance energy transfer serves as a key technique for this due to its nanometer-scale…
We introduce a Python package that provides simply and unified access to a collection of datasets from fundamental physics research - including particle physics, astroparticle physics, and hadron- and nuclear physics - for supervised…
Zero-mode waveguides (ZMW) nanoapertures milled in metal films were proposed to improve the FRET efficiency and enable single molecule FRET detection beyond the 10 nm barrier, overcoming the restrictions of diffraction-limited detection in…