Related papers: Single-molecule experiments in biological physics:…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
Scanning probe microscopy (SPM) is a valuable technique by which one can investigate the physical characteristics of the surfaces of materials. However, its widespread use is hampered by the time-consuming nature of running an experiment…
Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…
We introduce Spline Moment Equations (SME) for kinetic equations using a new weighted spline ansatz of the distribution function and investigate the ansatz, the model, and its performance by simulating the one-dimensional Boltzmann-BGK…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…
Non-invasive light scattering methods provide data on biological macromolecules (i.e. proteins, nucleic acids, as well as assemblies and larger entities composed of them) that are complementary with those of size exclusion chromatography,…
Spectroscopic ellipsometry is a widely used optical technique both in industry and research for determining the optical properties and thickness of thin films. The effective use of spectroscopic ellipsometry on micro-structures is inhibited…
Electromechanical coupling is ubiquitous in biological systems with examples ranging from simple piezoelectricity in calcified and connective tissues to voltage-gated ion channels, energy storage in mitochondria, and electromechanical…
The ability to inject dopant atoms with high spatial resolution, flexibility in dopant species and high single ion detection fidelity opens opportunities for the study of dopant fluctuation effects and the development of devices in which…
To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist to obtain the thermodynamic functions for such systems. But…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
The advent of single molecule optics has had a profound impact in fields ranging from biophysics to material science, photophysics, and quantum optics. However, all existing room-temperature single molecule methods have been based on…
The Bethe-Salpeter equation (BSE) combined with the Green's function GW method has successfully transformed into a robust computational tool to describe light-matter interactions and excitation spectra for molecules, solids, and materials…
Vibrational spectroscopy is a ubiquitous technology that derives the species, constituents, and morphology of an object from its natural vibrations. However, the vibrational spectra of mesoscopic particles - including most biological cells…
Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular…
Cells within biological tissue are constantly subjected to dynamic mechanical forces. Measuring the internal stress of tissues has proven crucial for our understanding of the role of mechanical forces in fundamental biological processes…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
Multiscale models allow for the treatment of complex phenomena involving different scales, such as remodeling and growth of tissues, muscular activation, and cardiac electrophysiology. Numerous numerical approaches have been developed to…
Single-molecule F\"orster Resonance Energy Transfer (smFRET) is ideally suited to resolve the dynamics of biomolecules. A significant challenge to date is capturing and quantifying the exchange between multiple conformational states, mainly…