Related papers: Quantitative evaluation of methods to analyze moti…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
We developed a new approach comprised of different visualizations for the comparative spatio-temporal analysis of displacement processes in porous media. We aim to analyze and compare ensemble datasets from experiments to gain insight into…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
Keratin are among the most abundant proteins in epithelial cells. Functions of the keratin network in cells are shaped by their dynamical organization. Using a collection of experimentally-driven mathematical models, different hypotheses…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Molecular transport maintains cellular structures and functions. For example, lipid and protein diffusion sculpts the dynamic shapes and structures on the cell membrane that perform essential cellular functions, such as cell signaling.…
To recover the long-time behavior and the statistics of molecular trajectories from the large number (tens of thousands) of their short fragments, obtained by super-resolution methods at the single molecule level, data analysis based on a…
Exploring the use of individual molecules as active components in electronic devices has been at the forefront of nanoelectronics research in recent years. Compared to semiconductor microelectronics, modeling transport in single-molecule…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
We have extended our recent molecular-dynamic simulations of memristors to include the effect of thermal inhomogeneities on mobile ionic species appearing during operation of the device. Simulations show a competition between an attractive…
To explain the observed dynamics in equilibrium single-molecule measurements of biomolecules, the experimental observable is often chosen as a putative reaction coordinate along which kinetic behavior is presumed to be governed by diffusive…
In addressing the origins of Darwinian evolution, recent experimental work has been focussed on the discovery of simple physical effects which would provide a relevant selective advantage to protocells competing with each other for a…
Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
Hypothesis A prototypical modelling approach is required for a full characterisation of the static and equilibrium dynamical properties of confined ionic liquids (ILs), in order to gain predictive power of properties that are difficult to…
Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output.…
Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and…
Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater opportunities to understand cellular states and biological processes.…
A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are…
Recent advances in human mobility research have revealed consistent pairwise characteristics in movement behavior, yet existing mobility models often overlook the spatial and topological structure of mobility networks. By analyzing millions…