arXiv subjects

Tomasz Skóra

Publications and source records attributed to Tomasz Skóra.

3 recordsLinked to original sources

arXiv2025

GPU-accelerated FREDopt package for simultaneous dose and LETd proton radiotherapy plan optimization via superiorization methods

This study presents FREDopt, a newly developed GPU-accelerated open-source optimization software for simultaneous proton dose and dose-averaged LET (LETd) optimization in IMPT treatment planning. FREDopt was implemented entirely in Python, leveraging CuPy for GPU acceleration and incorporating fast Monte Carlo (MC) simulations from the FRED code. The treatment plan optimization workflow includes pre-optimization and optimization, the latter equipped with a novel superiorization of feasibility-seeking algorithms. Feasibility-seeking requires finding a point that satisfies prescribed constraints. Superiorization interlaces computational perturbations into iterative feasibility-seeking steps to steer them toward a superior feasible point, replacing the need for costly full-fledged constrained optimization. The method was validated on two treatment plans of patients treated in a clinical proton therapy center, with dose and LETd distributions compared before and after reoptimization. Simultaneous dose and LETd optimization using FREDopt led to a substantial reduction of LETd and (dose)x(LETd) in organs at risk (OARs) while preserving target dose conformity. Computational performance evaluation showed execution times of 14-50 minutes, depending on the algorithm and target volume size-satisfactory for clinical and research applications while enabling further development of the well-tested, documented open-source software.

physics.med-ph↗

arXiv2024

Crowding-Regulated Binding of Divalent Biomolecules

Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding. Herein, we use scaled particle theory and develop a molecular simulation method to investigate the binding of monovalent to divalent biomolecules. We find that crowding can increase or reduce cooperativity--the extent to which the binding of a second molecule is enhanced after binding a first molecule--by orders of magnitude, depending on the sizes of the involved molecular complexes. Cooperativity generally increases when a divalent molecule swells and then shrinks upon binding two ligands. Our calculations also reveal that, in some cases, crowding enables binding that does not occur otherwise. As an immunological example, we consider Immunoglobulin G-antigen binding and show that crowding enhances its cooperativity in bulk but reduces it when an Immunoglobulin G binds antigens on a surface.

cond-mat.soft↗

arXiv2023

Feasibility of the J-PET to monitor range of therapeutic proton beams

Objective: The aim of this work is to investigate the feasibility of the Jagiellonian Positron Emission Tomography (J-PET) scanner for intra-treatment proton beam range monitoring. Approach: The Monte Carlo simulation studies with GATE and PET image reconstruction with CASToR were performed in order to compare six J-PET scanner geometries (three dual-heads and three cylindrical). We simulated proton irradiation of a PMMA phantom with a Single Pencil Beam (SPB) and Spread-Out Bragg Peak (SOBP) of various ranges. The sensitivity and precision of each scanner were calculated, and considering the setup's cost-effectiveness, we indicated potentially optimal geometries for the J-PET scanner prototype dedicated to the proton beam range assessment. Main results: The investigations indicate that the double-layer cylindrical and triple-layer double-head configurations are the most promising for clinical application. We found that the scanner sensitivity is of the order of 10$^{-5}$ coincidences per primary proton, while the precision of the range assessment for both SPB and SOBP irradiation plans was found below 1 mm. Among the scanners with the same number of detector modules, the best results are found for the triple-layer dual-head geometry. Significance: We performed simulation studies demonstrating that the feasibility of the J-PET detector for PET-based proton beam therapy range monitoring is possible with reasonable sensitivity and precision enabling its pre-clinical tests in the clinical proton therapy environment. Considering the sensitivity, precision and cost-effectiveness, the double-layer cylindrical and triple-layer dual-head J-PET geometry configurations seem promising for the future clinical application. Experimental tests are needed to confirm these findings.

physics.med-ph↗