Related papers: A Jump Distance-based Bayesian analysis method to …
Molecular dynamics simulations yield large amounts of trajectory data. For their durable storage and accessibility an efficient compression algorithm is paramount. State of the art domain-specific algorithms combine quantization, Huffman…
We propose an approach to analysing single trajectories of a particle, which moves randomly on a landscape distinct parts of which result in sufficiently various diffusion coefficients. The method based on the mapping the cumulative sum of…
The modelling of data on a spherical surface requires the consideration of directional probability distributions. To model asymmetrically distributed data on a three-dimensional sphere, Kent distributions are often used. The moment…
Diffusion coefficient measurements are important for many biological and material investigations, such as particle dynamics, kinetics, and size determinations. Amongst current measurement methods, single particle tracking (SPT) offers the…
Stochastic sampling based trackers have shown good performance for abrupt motion tracking so that they have gained popularity in recent years. However, conventional methods tend to use a two-stage sampling paradigm, in which the search…
Single-molecule break junction measurements deliver a huge number of conductance vs.\ electrode separation traces. Along such measurements the target molecules may bind to the electrodes in different geometries, and the evolution and…
This paper introduces the Gene Mover's Distance, a measure of similarity between a pair of cells based on their gene expression profiles obtained via single-cell RNA sequencing. The underlying idea of the proposed distance is to interpret…
Molecular systems can exhibit a complex, chemically tailorable inner structure which allows for targeting of specific mechanical, electronic and optical properties. At the single-molecule level, two major complementary ways to explore these…
Recent technological advances in cutting-edge ultrasensitive fluorescence microscopy have allowed single-molecule imaging experiments in living cells across all three domains of life to become commonplace. Single-molecule live-cell data is…
Single-molecule localization microscopy allows practitioners to locate and track labeled molecules in biological systems. When extracting diffusion coefficients from the resulting trajectories, it is common practice to perform a linear fit…
We show how one can measure the signal from slow jumps of a single molecule between metastable positions using a setup where the molecule is fixed to one lead, and one of the coupling strengths is controlled externally. Such a measurement…
In the past decades, advances in microscopy have made it possible to study the dynamics of individual biomolecules in vitro and resolve intramolecular kinetics that would otherwise be hidden in ensemble averages. More recently,…
This paper develops a novel sequential Monte Carlo (SMC) approach for joint state and parameter estimation that can deal efficiently with abruptly changing parameters which is a common case when tracking maneuvering targets. The approach…
We show how to speed up Sequential Monte Carlo (SMC) for Bayesian inference in large data problems by data subsampling. SMC sequentially updates a cloud of particles through a sequence of distributions, beginning with a distribution that is…
A near-field motion parameter estimation method is proposed. In contract to far-field sensing systems, the near-field sensing system leverages spherical-wave characteristics to enable full-vector location and velocity estimation. Despite…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
We derived a number of numerical methods to treat biomolecular systems with multiple time scales. Based on the splitting of the operators associated with the slow-varying and fast-varying forces, new multiple time-stepping (MTS) methods are…
In a stochastic reaction network setting we consider the problem of tracking the fate of individual molecules. We show that using the classical large volume limit results, we may approximate the dynamics of a single tracked molecule in a…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
Current advances in next generation sequencing techniques have allowed researchers to conduct comprehensive research on microbiome and human diseases, with recent studies identifying associations between human microbiome and health outcomes…