Related papers: PySTACHIO: Python Single-molecule TrAcking stoiCHi…
High-speed tracking of single particles is a gateway to understanding physical, chemical, and biological processes at the nanoscale. It is also a major experimental challenge, particularly for small, nanometer-scale particles. Although…
Focused optical fields are key to a multitude of applications involving light-matter interactions, such as optical microscopy, single-molecule spectroscopy, optical tweezers, lithography, or quantum coherent control. A detailed vectorial…
We have extended the Falkon lightweight task execution framework to make loosely coupled programming on petascale systems a practical and useful programming model. This work studies and measures the performance factors involved in applying…
Optical speckle patterns have been widely used for illumination in computational imaging, optical sectioning microscopy, and super-resolution imaging. However, commonly used speckles satisfy Rayleigh statistics, which are not ideal for…
In numerous systems in biophysics and related fields, scientists measure (with very smart methods) individual molecules (e.g. biopolymers (proteins, DNA, RNA, etc), nano - crystals, ion channels), aiming at finding a model from the data.…
Simulations based on particle methods, such as Smoothed Particle Hydrodynamics (SPH), are known to be computationally demanding. While such methods have for long been executed in parallel on multi-core CPUs, in recent years the increasing…
Scalable atom-based quantum platforms for simulation, computing, and metrology require fast high-fidelity, low-loss imaging of individual atoms. Standard fluorescence detection methods rely on continuous cooling, limiting the detection…
The full understanding of cellular functions requires information about protein numbers for various biomolecular assemblies and their dynamics, which can be partly accessed by super-resolution fluorescence microscopy. Yet, many protein…
Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on…
Particle-in-Cell (PIC) codes are a popular tool to model laser-plasma interactions. Many different PIC codes already exist, and many new PIC codes are being developed constantly. It is therefore important to compare different PIC codes to…
The extraction of information carried by light plays an increasingly important role in optical communication, imaging, and detection. However, the information can only be successfully extracted when the light pulse is comparably strong,…
We explore theoretically the electroluminescence of single molecules. We adopt a local-electrode framework that is appropriate for scanning tunneling microscopy (STM) experiments where electroluminescence originates from individual…
Single-molecule pulling techniques have emerged as versatile tools for probing the noncovalent forces holding together the secondary and tertiary structure of macromolecules. They also constitute a way to study at the single-molecule level…
Imaging individual conformational instances of generic, inhomogeneous, transient or intrinsically disordered protein systems at the single molecule level in situ is one of the notable challenges in structural biology. Present techniques…
Frequentist profile likelihoods have seen a resurgence in cosmology, offering an alternative to Bayesian methods as they can circumvent the impact of prior-volume effects. This paper presents Procoli, a fast and accessible package to obtain…
To be able to resolve molecular-clusters it is crucial to access vital informations (such as, molecule density and cluster-size) that are key to understand disease progression and the underlying mechanism. Traditional single-molecule…
Time resolution is one of the most severe limitations of scanning probe microscopies (SPMs), since the typical image acquisition times are in the order of several seconds or even few minutes. As a consequence, the characterization of…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
Particle tracking is a fundamental task in digital microscopy. Recently, machine-learning approaches have made great strides in overcoming the limitations of more classical approaches. The training of state-of-the-art machine-learning…
We present AngstromPro, a versatile, modular and open-source software built on Python for managing, visualizing and analyzing large datasets acquired via Scanning Tunneling Microscopes (STM). Its robust architecture features a top-level…