Related papers: Decoding Single Molecule Time Traces with Dynamic …
Single-molecule experiments provide insight into the motion (conformational dynamics) of individual protein molecules. Usually, a well-defined but coarse-grained intramolecular coordinate is measured and subsequently analysed with the help…
Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule F\"orster Resonance Energy Transfer (smFRET) is a powerful approach to inform on the structure and the dynamics of labeled molecules.…
State space models (SSMs) have recently achieved strong performance on long sequence modeling tasks while offering improved memory and computational efficiency compared to transformer based architectures. However, their evaluation has been…
Bayesian nonparametric methods have recently transformed emerging areas within data science. One such promising method, the infinite hidden Markov model (iHMM), generalizes the HMM which itself has become a workhorse in single molecule data…
Analyzing disease progression patterns can provide useful insights into the disease processes of many chronic conditions. These analyses may help inform recruitment for prevention trials or the development and personalization of treatments…
We propose a Dynamical Boolean Network (DBN), which is a Virtual Boolean Network (VBN) whose set of states is fixed but whose transition matrix can change from one discrete time step to another. The transition matrix $T_{k}$ of our DBN for…
Motivated by high-throughput single-cell cytometry data with applications to vaccine development and immunological research, we consider statistical clustering in large-scale data that contain multiple rare clusters. We propose a new…
Formation, maintenance and physiology of high-density protein-enriched organized nanodomains, first observed in electron microscopy images, remains challenging to investigate due to their small sizes. However, these regions regulate…
Single-molecule experimental techniques track the real-time dynamics of molecules by recording a small number of experimental observables. Following these observables provides a coarse-grained, low-dimensional representation of the…
Single polymer dynamics offers a powerful approach to study molecular-level interactions and dynamic microstructure in materials. Direct visualization of single chain dynamics has uncovered new ideas regarding the rheology and…
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…
Clinical researchers use disease progression models to understand patient status and characterize progression patterns from longitudinal health records. One approach for disease progression modeling is to describe patient status using a…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…
The bacterial transcription factor LacI loops DNA by binding to two separate locations on the DNA simultaneously. Despite being one of the best-studied model systems for transcriptional regulation, the number and conformations of loop…
Membrane proteins move in heterogeneous environments with spatially (sometimes temporally) varying friction and with biochemical interactions with various partners. It is important to reliably distinguish different modes of motion to…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
General discrete one-dimensional stochastic models to describe the transport of single molecules along coupled parallel lattices with period $N$ are developed. Theoretical analysis that allows to calculate explicitly the steady-state…
Biomolecular condensates provide distinct chemical environments, which control various cellular processes. The diffusive dynamics and chemical kinetics inside phase-separated condensates can be studied experimentally by fluorescently…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…