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Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most phenomenological models of the unfolding process are two-state and/or one dimensional, with the details of the…
We apply a time-dependent perturbation theory based on unitary transformations combined with averaging techniques, on molecular orientation dynamics by ultrashort pulses. We test the validity and the accuracy of this approach on LiCl…
Materials with large second-order nonlinearities are crucial for next-generation integrated photonics. Spontaneously oriented organic thin films prepared by physical vapor deposition offer a promising poling-free and scalable approach. This…
The orientation and stability of the reconnection x-line in asymmetric geometry is studied using three-dimensional (3D) particle-in-cell simulations. We initiate reconnection at the center of a large simulation domain to minimize the…
We present a systematic study of the unbinned, photon-by-photon likelihood technique which can be used as an alternative method to analyse phase-dependent, X-ray spectro-polarimetric observations obtained with IXPE and other photo-electric…
For efficient application of protons and light ions in radiotherapy, detailed knowledge and realistic models of the corresponding radiobiological mechanism are necessary. Basic characteristics of this mechanism have been represented within…
Directed evolution of proteins has been the most effective method for protein engineering. However, a new paradigm is emerging, fusing the library generation and screening approaches of traditional directed evolution with computation…
Single molecule X-ray scattering experiments using free electron lasers hold the potential to resolve both single structures and structural ensembles of biomolecules. However, molecular electron density determination has so far not been…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
Imaging single proteins has been a long-standing ambition for advancing various fields in natural science, as for instance structural biology, biophysics and molecular nanotechnology. In particular, revealing the distinct conformations of…
Using fully kinetic simulations, we study the x-line orientation of magnetic reconnection in an asymmetric configuration. A spatially localized perturbation is employed to induce a single x-line, that has sufficient freedom to choose its…
Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…
Experimentally obtained X-ray diffraction (XRD) patterns can be difficult to solve, precluding the full characterization of materials, pharmaceuticals, and geological compounds. Herein, we propose a method based upon a multi-objective…
This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…
In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing…
Molecular dynamics simulations provide detailed trajectories at the atomic level, but extracting interpretable and robust insights from these high-dimensional data remains challenging. In practice, analyses typically rely on a single…
Recent advancements in deep learning for predicting 3D protein structures have shown promise, particularly when leveraging inputs like protein sequences and Cryo-Electron microscopy (Cryo-EM) images. However, these techniques often fall…
X-ray single particle imaging involves the measurement of a large number of noisy diffraction patterns of isolated objects in random orientations. The missing information about these patterns is then computationally recovered in order to…
Accurate quantification of protein-nanoparticle interactions is essential for applications in nanobiotechnology, nanomedicine, and drug delivery. Motivated by recent computational and experimental work, we combine coarse-grained united-atom…
Predicting changes in binding free energy ($\Delta\Delta G$) is a vital task in protein engineering and protein-protein interaction (PPI) engineering for drug discovery. Previous works have observed a high correlation between $\Delta\Delta…