Related papers: Dynamic polarizability of macromolecules for singl…
The optical properties of molecules close to plasmonic nanostructures greatly differ from their isolated molecule counterparts. To theoretically investigate such systems in a Quantum Chemistry perspective, one has to take into account that…
We investigate the influence of thermally activated internal molecular dynamics on the phase shifts of matter waves inside a molecule interferometer. While de Broglie physics generally describes only the center-of-mass motion of a quantum…
The overall goal of this thesis is to investigate the connection between the dynamics and structure of molecular glass formers, by testing different scaling laws for both. The inspiration for this work is the Isomorph theory because it…
Proteins are made of atoms constantly fluctuating, but can occasionally undergo large-scale changes. Such transitions are of biological interest, linking the structure of a protein to its function with a cell. Atomic-level simulations, such…
Photoactive proteins absorb light and undergo structural changes that enable them to perform essential biological functions. These proteins are critical for understanding light-induced biological processes, making them important in…
The short and intense pulses of the new X-ray free electron lasers, now operational or under construction, may make possible diffraction experiments on single molecule-sized objects with high resolution, before radiation damage destroys the…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single molecule and single cell level can add…
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…
The use of probe molecules to extract the local dynamical and structural properties of complex dynamical systems is an age-old technique both in simulations and experiments. A lot of important information which is not immediately accessible…
In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules.While the effects of electronic polarization are highly…
The application of molecular dynamics (MD) simulations to the interpretation of Raman scattering spectra is hindered by inability of atomistic simulations to account for the dynamic evolution of electronic polarizability, requiring the use…
Microtubules are stiff filamentary proteins that constitute an important component of the cytoskeleton of cells. These are known to exhibit a dynamic instability. A steadily growing microtubule can suddenly start depolymerizing very…
Laser-induced alignment of particles and molecules was long envisioned to support three-dimensional structure determination using "single-molecule diffraction" with x-ray free-electron lasers [PRL 92, 198102 (2004)]. However, the alignment…
Electrostatic interactions involving proteins depend not just on the ionic charges involved but also on their chemical identities. Here we examine the origins of incompletely understood differences in the strength of association of…
We report on measurements of the anisotropic dynamical polarizability of Dy near the 626-nm intercombination line, employing modulation spectroscopy in a one-dimensional optical lattice. To eliminate large systematic uncertainties resulting…
X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to…