Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

X-ray free electron lasers (XFEL) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges both in terms of experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classification tasks using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering (FXS) algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. We envision skopi as a resource to aid the development of on-the-fly feedback during non-crystalline experiments at XFEL facilities, which will provide critical insights into biomolecular structure and function.

MONTE-CARLO SIMULATION OF QUASI-INFINITE DEPLETED URANIUM TARGET IRRADIATED BY 1…10 GeV DEUTERON AND PROTON BEAM

Simulation of a ~21 t depleted uranium target irradiated by 1…10 GeV proton and deuteron particles with the help of FLUKA simulation package was carried out. Neutron spectra and neutron flux in a target volume were obtained. Total number of 235U (n,f), 238U(n,f) reactions occurred in a target were determined. Beam particle power multiplication are calculated. The calculations were performed for the purpose of planning experiments on irradiation of a uranium target (22 tons of depleted uranium) at JINR (Dubna) within the framework of the international project “Energy and Transmutation of RAW”.

Improving Weather Simulations Through Increased Generality

By adding support for spatially variable velocity fields and anisotropy, the CoSMoS simulation package can more accurately reproduce physical phenomena.

MONTE CARLO SIMULATIONS OF ENERGY RESOLUTION OF THE ELECTROMAGNETIC CALORIMETER PROTOTYPE FOR ELECTRON–ION COLLIDER

In this article, we present energy resolution studies of an electromagnetic calorimeter prototype for Electron–Ion Collider. The results of energy resolution for various configurations of lead tungstate crystals were obtained based on the Geant4 simulation package. The energy resolution was studied as a function of the polar angle of incident electrons in a momentum range of 1 to 10 GeV.

Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free Energy Calculations

<div><div><div><p>The quantum mechanical bespoke (QUBE) force field approach has been developed to facilitate the automated derivation of potential energy function parameters for modelling protein-ligand binding. To date the approach has been validated in the context of Monte Carlo simulations of protein-ligand complexes. We describe here the implementation of the QUBE force field in the alchemical free energy calculation molecular dynamics simulation package SOMD. The implementation is validated by demonstrating the reproducibility of absolute hydration free energies computed with the QUBE force field across the SOMD and GROMACS software packages. We further demonstrate, by way of a case study involving two series of non-nucleoside inhibitors of HIV-1 reverse transcriptase, that the availability of QUBE in a modern simulation package that makes efficient use of GPU acceleration will facilitate high-throughput alchemical free energy calculations.</p></div></div></div>

The Effect of the Design of Surgical Electrodes On the Formation of Sparking Enhanced Burns

Electrocautery is a safe and effective method of hemostasis during cutaneous surgery. Despite the unquestionable benefits, electrocautery sparks in the surgical field represent a significant fire risk that can be eliminated by clarifying the causation and conditions of their development. Apart from the experimental methods, computer modeling is proven to be an effective approach to improve the performance of electrocautery. This paper is dealing with the design of electrodes to prevent burns during standard procedures. Simulations were carried out by using the COMSOL simulation package for various electrode configurations (cylinder-cylinder, sphere-sphere, sphere-cylinder, and cylinder-sphere) representing shapes of surgical electrodes. The primary goal was to determine the location where sparking starts. The obtained simulation results agree well with the experimental data taken from the literature supporting that the sparking formation is strongly affected by the electrode configuration. It was found that sparking occurs most easily when both electrodes are cylindrical. Also, the sparking mechanism depends on electrical asymmetry that results in undesirable direct current burns. Results presented here can be used to establish practices for the safe use of the electrocautery devices and to prevent injury to patients and staff.