Engineering topics

Perez, Alberto

Publications and source records attributed to Perez, Alberto.

3 records

DOE OSTI2024

A Platform for Ultra-Fast Proton Probing of Matter in Extreme Conditions

Recent developments in ultrashort and intense laser systems have enabled the generation of short and brilliant proton sources, which are valuable for studying plasmas under extreme conditions in high-energy-density physics. However, developing sensors for the energy selection, focusing, transport, and detection of these sources remains challenging. This work presents a novel and simple design for an isochronous magnetic selector capable of angular and energy selection of proton sources, significantly reducing temporal spread compared to the current state of the art. The isochronous selector separates the beam based on ion energy, making it a potential component in new energy spectrum sensors for ions. Analytical estimations and Monte Carlo simulations validate the proposed configuration. Due to its low temporal spread, this selector is also useful for studying extreme states of matter, such as proton stopping power in warm dense matter, where short plasma stagnation time (<100 ps) is a critical factor. The proposed selector can also be employed at higher proton energies, achieving final time spreads of a few picoseconds. This has important implications for sensing technologies in the study of coherent energy deposition in biology and medical physics.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Cryoelectron microscopy requires molecular modeling for refinement of structures. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins. Here, we introduce CryoFold, a pipeline of molecular dynamics simulations that determines ensembles of protein structures by integrating density data of varying sparsity at 3–5 Å resolution with sequence information and coarse-grained topological knowledge of the protein folds. We present six examples, folding proteins between 72 and 2,000 residues, including large membrane and multi-domain systems, and results from two Electron Microscopy Data Bank (EMDB) competitions. Driven by data from a single state, CryoFold discovers ensembles of common low-energy models together with rare low-probability structures that capture the equilibrium distribution of proteins constrained by the density maps. Many of these conformations are experimentally validated and functionally relevant. We arrive at a set of best practices for data-guided protein folding that are controlled using a Python graphical user interface (GUI).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

59 BASIC BIOLOGICAL SCIENCES↗