Related papers: Reconstruction of Protein Structures from Single-M…
Gene regulation is a dynamic process that underlies all aspects of human development, disease response, and other key biological processes. The reconstruction of temporal gene regulatory networks has conventionally relied on regression…
We apply a recently proposed method for the analysis of time series from systems with delayed feedback to experimental data generated by a CO_2 laser. The method is able to estimate the delay time with an error of the order of the sampling…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
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…
Molecular dynamics (MD) simulations remain the gold standard for studying protein dynamics, but their computational cost limits access to biologically relevant timescales. Recent generative models have shown promise in accelerating…
This paper examines the reconstruction of a family of dynamical systems with neuromorphic behavior using a single scalar time series. A model of a physiological neuron based on the Hodgkin-Huxley formalism is considered. Single time series…
Molecular dynamics (MD) simulation is widely used to study protein conformations and dynamics. However, conventional simulation suffers from being trapped in some local energy minima that are hard to escape. Thus, most computational time is…
Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the…
The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon…
Simulating large proteins using traditional molecular dynamics (MD) is computationally demanding. To address this challenge, we propose a novel tree-structured coarse-grained model that efficiently captures protein dynamics. By leveraging a…
We report on time dependent Stokes shift measurements of single molecules. Broadband excitation and emission spectroscopy were applied to study the temporal Stokes shift evolution of single perylene diimide molecules (PDI) embedded in a…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
A new and accurate method to determine the time delay and embedding dimension for state space reconstruction of a high dimensional system from a scalar time series using time delay embedding is presented. The time delay is obtained to…
We present an effective method for estimating the motion of proteins from the motion of attached probe particles in single-molecule experiments. The framework naturally incorporates Langevin dynamics to compute the most probable trajectory…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
In several practical applications, particularly healthcare, clinical data of each patient is individually recorded in a database at irregular intervals as required. This causes a sparse and irregularly sampled time series, which makes it…
Takens' Embedding Theorem asserts that when the states of a hidden dynamical system are confined to a low-dimensional attractor, complete information about the states can be preserved in the observed time-series output through the delay…