Related papers: Orientation before destruction. A multiscale molec…
We propose a criterion for identifying the orientation of the X-line when two regions of plasma with arbitrary densities, temperatures, and magnetic fields undergo reconnection. The X-line points in the direction that maximizes the…
Serial femtosecond X-ray crystallography (SFX) captures the structure and dynamics of biological macromolecules at high spatial and temporal resolutions. The ultrashort pulse produced by an X-ray free electron laser (XFEL) 'outruns' much of…
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid…
Feynman once asked physicists to build better electron microscopes to be able to watch biology at work. While electron microscopes can now provide atomic resolution, electron beam induced specimen damage precludes high resolution imaging of…
Quantum mechanical calculations are performed on the proteins that constitute the ubiquitin-Dsk2 complex whose atomic structure has been experimentally determined by NMR spectroscopy (PDB id 1WR1). The results indicate that the dipole…
Two mechanisms of two-color (\omega + 2\omega) laser-induced field-free molecular orientation, based on the hyperpolarizability and ionization depletion, are explored and compared. The CO molecule is used as a computational example. While…
The dynamic of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally…
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motions. Model-free types…
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…
Electric field-assisted chemistry has attracted much attention in recent years, particularly in the context of oriented external electric fields for controlling molecular structure and reactivity. Such fields have been explored in a wide…
The oxygen stoichiometry is an essential key to tune functional properties of advanced oxide materials and thus has motivated numerous studies of the oxygen off-stoichiometry diagram, with the aim to determine and control structural,…
We investigated experimentally and theoretically angular momentum alignment-to-orientation conversion created by the joint interaction of laser radiation and an external magnetic field with atomic rubidium at room temperature. In particular…
Ultrafast diffraction imaging is a powerful tool to retrieve the geometric structure of gas-phase molecules with combined picometre spatial and attosecond temporal resolution. However, structural retrieval becomes progressively difficult…
The rich information content of measurements in the molecular frame rather than the laboratory frame has motivated the development of several methods for aligning gas phase molecules in space. Even so, for asymmetric tops the problem of…
The mixed-field orientation of an asymmetric-rotor molecule with its permanent dipole moment non-parallel to the principal axes of polarizability is investigated experimentally and theoretically. We find that for the typical case of a…
The X-ray free electron lasers (XFEL) can enable diffractive structural determination of protein crystals or single molecules that are too radiation-sensitive for conventional X-ray analysis. However the electronic form factor could have…
X-ray free-electron lasers (XFELs) with megahertz repetition rate can provide novel insights into structural dynamics of biological macromolecule solutions. However, very high dose rates can lead to beam-induced dynamics and structural…
Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…