Related papers: Orientation before destruction. A multiscale molec…
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
A novel technique was demonstrated that overcome important drawbacks to crosslink cells by irradiation with ultrashort UV laser pulses (L-crosslinking). To use this technique coupled to Chromatin ImmunoPrecipitation (ChIP) in a high…
Single particle cryo-electron microscopy is a vital tool for 3D characterization of protein structures. A typical workflow involves acquiring projection images of a collection of randomly oriented particles, picking and classifying…
The performance of organic optoelectronic devices is critically dependent on how molecules orient within organic thin films. Yet, standard characterization techniques only reveal the first and second moments of the molecular orientation…
We show that field-free molecular orientation induced by a half-cycle pulse may be considerably enhanced by an additional laser pulse inducing molecular anti-alignment. Two qualitatively different enhancement mechanisms are identified…
Precise control and study of molecules is challenging due to the variety of internal degrees of freedom and local coordinates that are typically not controlled in an experiment. Employing quantum gas microscopy to position and resolve the…
By folding into particular 3D structures, proteins play a key role in living beings. To learn meaningful representation from a protein structure for downstream tasks, not only the global backbone topology but the local fine-grained…
Single-pixel imaging, originally developed in light optics, facilitates fast three-dimensional sample reconstruction, as well as probing with light wavelengths undetectable by conventional multi-pixel detectors. However, the spatial…
Optoplasmonic methods capable of single protein detection so far rely on analyte immobilization in order to facilitate detection [1-6]. These detection schemes, even if they facilitate transient single-molecule detection [7,8] via…
The analysis of proteins in the gas phase benefits from detectors that exhibit high efficiency and precise spatial resolution. Although modern secondary electron multipliers already address numerous analytical requirements, new methods are…
Single-particle electron microscopy is a modern technique that biophysicists employ to learn the structure of proteins. It yields data that consist of noisy random projections of the protein structure in random directions, with the added…
Accurate estimation of mutational effects on protein-protein binding energies is an open problem with applications in structural biology and therapeutic design. Several deep learning predictors for this task have been proposed, but,…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
The Single Particles, Clusters and Biomolecules (SPB) instrument at the European XFEL is located behind the SASE1 undulator, and aims to support imaging and structure determination of biological specimen between about 0.1 micrometer and 1…
Speckle patterns manifesting from the interaction of coherent X-rays with matter offer a glimpse into the dynamics of nanoscale domains that underpin many emergent phenomena in quantum materials. While the dynamics of the average structure…
During the last five years, serial femtosecond crystallography using x-ray laser pulses has developed into a powerful technique for determining the atomic structures of protein molecules from micrometer and sub-micrometer sized crystals.…
Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Prior work focused on supervised learning methods using a large set of binding affinity data for small molecules, but it is hard to apply the same…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
We explore the role of laser induced anti-alignment in enhancing molecular orientation. A field-free enhanced orientation via anti-alignment scheme is presented, which combines a linearly polarized femtosecond laser pulse with a half-cycle…