Related papers: PySTACHIO: Python Single-molecule TrAcking stoiCHi…
In the past one hundred years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years,…
In the past few decades, the development of fluorescent technologies and microscopic techniques has greatly improved scientists' ability to observe real-time single-cell activities. In this paper, we consider the filtering problem associate…
Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the…
Current single-molecule imaging techniques are incapable of providing stochastic information of individual chemical reactions. We have developed an optical imaging method for stochastic analysis of individual electrochemical reactions. The…
Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To…
Single-molecule tracking is a powerful way to look at the dynamic organization of plasma membranes. However, there are some limitations to its use. For example, it was recently observed, using numerical simulation, that time-averaging…
Particle-in-cell methods with stochastic collision models are commonly used to simulate collisional plasma dynamics, with applications ranging from hypersonic flight to semiconductor manufacturing. Code verification of such methods is…
There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the…
A scanning tunneling microscope (STM) can do more than atomic imaging and manipulation. Its tunneling current can also be used for the excitation of light, converting electron energy to photon energy. STM based single-molecule…
Time course measurement of single molecules on a cell surface provides detailed information on the dynamics of the molecules, which is otherwise inaccessible. To extract the quantitative information, single particle tracking (SPT) is…
StocHy is a software tool for the quantitative analysis of discrete-time stochastic hybrid systems (SHS). StocHy accepts a high-level description of stochastic models and constructs an equivalent SHS model. The tool allows to (i) simulate…
We combine stroboscopic laser excitation with stochastic photoactivation and super-resolution fluorescence imaging. This makes it possible to record hundreds of diffusion trajectories of small protein molecules in single bacterial cells…
Single-molecule RNA imaging has been made possible with the recent advances in microscopy methods. However, systematic analysis of these images has been challenging due to the highly variable background noise, even after applying…
Particle-in-Cell Monte Carlo simulations on large-scale systems play a fundamental role in understanding the complexities of plasma dynamics in fusion devices. Efficient handling and analysis of vast datasets are essential for advancing…
Single-molecule experiments are a unique tool to characterize the structural dynamics of biomolecules. However, reconstructing molecular details from noisy single-molecule data is challenging. Simulation-based inference (SBI) integrates…
We present PyAtoms, an interactive open-source software that rapidly simulates atomic-scale scanning tunneling microscopy (STM) and other scanning probe microscopy (SPM) images of two-dimensional (2D) layered materials, moir\'{e} systems,…
Single molecule X-ray scattering experiments using free electron lasers hold the potential to resolve both single structures and structural ensembles of biomolecules. However, molecular electron density determination has so far not been…
This work-in-progress paper presents results on the feasibility of single-shot object detection on microcontrollers using YOLO. Single-shot object detectors like YOLO are widely used, however due to their complexity mainly on larger…
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…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…