Related papers: Interpreting NMR dynamic parameters via the separa…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
A novel algorithm for real-time modal identification in linear vibrating systems with complex modes is introduced, utilizing a combination of first order eigen-perturbation and second order separation techniques. In practical settings,…
Numerical simulations are commonly used to understand the parameter dependence of given spatio-temporal phenomena. Sampling a multi-dimensional parameter space and running the respective simulations leads to an ensemble of a large number of…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
Calculating the values of nuclear correlation functions is computationally intensive due to the fact that the number of terms in a nuclear wave function scales exponentially with atomic number. To speed up this computation, we represent a…
Ion adsorption and dynamics in porous carbons is crucial for many technologies such as energy storage and desalination. Nuclear Magnetic Resonance (NMR) spectroscopy is a key method to investigate such systems thanks to the possibility to…
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…
We propose a two-dimensional model for a complete description of the dynamics of molecular motors, including both the processive movement along track filaments and the dissociation from the filaments. The theoretical results on the…
The Dynamic-Mode Decomposition (DMD) is a well established data-driven method of finding temporally evolving linear-mode decompositions of nonlinear time series. Traditionally, this method presumes that all relevant dimensions are sampled…
Molecular dynamics (MD) simulation predicts the trajectory of atoms by solving Newton's equation of motion with a numeric integrator. Due to physical constraints, the time step of the integrator need to be small to maintain sufficient…
Molecular simulations as well as single molecule experiments have been widely analyzed in terms order parameters, the latter representing candidate probes for the relevant degrees of freedom. Notwithstanding this approach is very intuitive,…
Modeling biological processes is a highly demanding task because not all processes are fully understood. Mathematical models allow us to test hypotheses about possible mechanisms of biological processes. The mathematical mechanisms…
Permutation tests have been proposed by Albert et al. (2015) to detect dependence between point processes, modeling in particular spike trains, that is the time occurrences of action potentials emitted by neurons. Our present work focuses…
Motion blur can adversely affect a number of vision tasks, hence it is generally considered a nuisance. We instead treat motion blur as a useful signal that allows to compute the motion of objects from a single image. Drawing on the success…
Tethered particle motion is an experimental technique to monitor conformational changes in single molecules of DNA in real time, by observing the position fluctuations of a micrometer-size particle attached to the DNA. This article reviews…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
Motion planning under uncertainty is essential for reliable robot operation. Despite substantial advances over the past decade, the problem remains difficult for systems with complex dynamics. Most state-of-the-art methods perform search…
Statistical properties of Brownian motion that arise by analyzing, separately, trajectories over which the system energy increases (upside) or decreases (downside) with respect to a threshold energy level, are derived. This selective…
We demonstrate the use of spatially encoded magnetic resonance to quantify ensemble dynamics of microscopic particles below the spatial resolution. By evaluating time series of k-space data-points, k-dependent motion patterns can be…
The collective motion of a finite nuclear system is investigated by numerical simulation and by linear response theory. Using a pseudo-particle simulation technique we analyze the giant resonances with a multipole decomposition scheme. We…