Extracting atomic contributions to binding free energy from molecular dynamics simulations with mixed solvents (MDmix)

Background: Mixed solvents MD simulations have proved to be a useful and increasingly accepted technique with several applications in structure-based drug discovery Method: Mixed solvents MD simulations have proved to be a useful and increasingly accepted technique with several applications in structure-based drug discovery Result: As such, they are hardly transferable to different molecules. Conclusion: To achieve transferable energies, we present here a method for decomposing the molecular binding free energy into accurate atomic contributions and we demonstrate with two qualitative visual examples how the corrected energy maps better match known binding hotspots and how they can reveal hidden hotspots with actual drug design potential.

Reducing molecular simulation time for AFM images based on super-resolution methods

Atomic force microscopy (AFM) has been an important tool for nanoscale imaging and characterization with atomic and subatomic resolution. Theoretical investigations are getting highly important for the interpretation of AFM images. Researchers have used molecular simulation to examine the AFM imaging mechanism. With a recent flurry of researches applying machine learning to AFM, AFM images obtained from molecular simulation have also been used as training data. However, the simulation is incredibly time consuming. In this paper, we apply super-resolution methods, including compressed sensing and deep learning methods, to reconstruct simulated images and to reduce simulation time. Several molecular simulation energy maps under different conditions are presented to demonstrate the performance of reconstruction algorithms. Through the analysis of reconstructed results, we find that both presented algorithms could complete the reconstruction with good quality and greatly reduce simulation time. Moreover, the super-resolution methods can be used to speed up the generation of training data and vary simulation resolution for AFM machine learning.

Subsoil Characteristics of Mexico City, acceleration and hysteretic energy spectra for the Mexico Earthquake of September 19, 2017

The September 19, 2017 intraslab earthquake (Mw7.1), whose epicenter was located near the limits between the states of Puebla and Morelos at approximately 120km from Mexico City, caused severe damage in these regions. In Mexico City more than 40 buildings collapsed, and hundreds had moderate to severe damage; dozens of them are to be demolished. This article analyzes the spectral ratios of accelerometric stations in the lake-bed of Mexico City with respect to the average Fourier spectra at hill zone sites in order to study and compare over time the changes in the behavior of local effects and their relationship with the damage presented during this earthquake; these ratios exhibit also the settlement problem in some places in the city due to over exploiting the aquifer for water supply purposes. Finally, pseudoacceleration and hysteretic energy maps for Mexico City with a discussion with a possible correlation with reported damages are presented.

Study of thin, achromatic diffractive structures to focus terahertz radiation on a detector

Thin and lightweight achromatic focusing elements with F-number close to 1 are desirable in many practical applications. We present the idea to use diffractive structures designed to work for the substantially increased THz frequency range. The paper analyses mono- and multi-focal lenses forming point-like foci as well as axicon and light sword optical elements focusing THz radiation into line segments located along the optical axis. We consider diffractive elements in a form of the first and the second order kinoforms having various thicknesses. Designed and fabricated elements were numerically and experimentally examined to verify their achromatic functioning. We present point spread functions (XY scans) and 2D energy maps (XZ scans) for different THz frequencies. Moreover, a diagram of chromatic aberration is created by registering energy distribution along the optical axis for different frequencies. The distance corresponding to the highest energy is chosen for each frequency. Therefore, we can compare broadband working of designed structures. The spherical lens coded as kinoform of the second order provides the best broadband functioning, however it is two times thicker than structures providing extended depth of focus (light sword and axicon) working with slightly smaller efficiency but being much thinner.