arXiv subjects

Tomas André

Publications and source records attributed to Tomas André.

7 recordsLinked to original sources

arXiv2026

Protein eXplosion Imaging (PXI): Protein Structures from Laser-Driven Explosions

We investigate the structural information retained in the distribution of explosion ion trajectories from proteins subjected to strong ionization. Using molecular-dynamics simulations and machine-learning analysis benchmarked against an analytical approach, we show that low-resolution structural information can be retrieved from the explosion distributions alone. An ensemble of convolutional neural networks trained on simulated spherical ion maps recovers the radius of gyration and the three semi-axes of an ellipsoidal molecular envelope with prediction errors of 1.2 Å and 1.5 Å, respectively, while an analytical ellipsoid charge model returns similar estimates and performs best for globular structures. We further investigate how higher-level structural information and symmetries can be extrapolated from ion measurements. This study supports the viability for structural determination of single proteins without large-scale X-ray facilities.

physics.bio-ph↗

arXiv2026

MolDStruct: benchmarking a hybrid Monte Carlo/Molecular Dynamics model for X-ray free-electron laser ionisation and fragmentation dynamics

Single Particle Imaging with intense X-ray free-electron laser pulses requires modelling of the resulting ionisation and Coulomb explosion dynamics of biomolecules to optimise experimental parameters and enable correct structural reconstruction, yet simulating the complete dynamics at protein scale is beyond the reach of quantum-mechanical methods. To address this, we developed \moldstruct, a hybrid Monte Carlo/Molecular Dynamics code built on GROMACS that couples high intense X-ray ionisation dynamics modelled through a Monte Carlo module with classical Molecular Dynamics for atomic propagation. Benchmarked against quantum mechanical calculations for di-alanine, MolDStruct agrees in fragmentation patterns above a mean charge per atom of $\bar{z} \approx 1.35$. Compared with Coulomb explosion imaging experimental data for 2-iodopyridine, simulated momentum distributions reproduce the experimental Newton plots in fragment direction and fall within the range of experimental absolute momenta, with a moderate overestimation. We further apply MolDStruct to Protein Explosion Imaging, a method that classifies molecular structures from explosion ion maps recorded on a detector, demonstrating via dimensionality reduction that conformers of the 16-residue peptide $\mathrm{Ala}_16$ and five chromophore-labelled ubiquitin mutants are distinguishable. These results establish MolDStruct as a practical tool for simulating radiation damage and Coulomb explosion dynamics of biomolecules at protein scale, where quantum-mechanical methods are computationally infeasible.

physics.bio-ph↗

arXiv2026

Orientation Reconstruction of Proteins using Coulomb Explosions

We solve the orientation recovery of a tumbling protein in the gas phase from single-event measurements of the spatial positions of its ions after an X-ray laser induced explosion. We simulate diffracted X-ray signal and ion dynamics under experimental conditions and compare our method to conventional orientation recovery in single-particle imaging with X-ray free-electron lasers using only diffraction data. We reconstruct 3D diffraction intensities using orientations recovered from the ion signatures and retrieve the electron density with established phase-retrieval algorithms. We test our orientation recovery procedure on 56 proteins ranging from 14 to 52 kDa (1800 to 6500 atoms), achieving roughly an angular error of around 5°. The resulting 3D electron-density reconstructions are compared to ground-truth volumes simulated at the same nominal resolution, and achieve the resolution at the edge of the detector in conditions similar to current single-particle imaging setups. We investigate the reconstruction quality and demonstrate that ion data can be used for reliable orientation recovery of particles in single-particle imaging, achieving orientation on par or better than currently used recovery techniques. This work shows the potential of ion detection for retrieving additional information from the sample fragmentation, and boost single particle imaging with X-ray lasers in the cases where the diffraction signal is a limiting factor.

physics.chem-ph↗

arXiv2024

Partial Orientation Retrieval of Proteins From Coulomb Explosions

Single Particle Imaging techniques at X-ray lasers have made significant strides, yet the challenge of determining the orientation of freely rotating molecules during delivery remains. In this study, we propose a novel method to partially retrieve the relative orientation of proteins exposed to ultrafast X-ray pulses by analyzing the fragmentation patterns resulting from Coulomb explosions. We simulate these explosions for 45 proteins in the size range 100 -- 4000 atoms using a hybrid Monte Carlo/Molecular Dynamics approach and capture the resulting ion ejection patterns with virtual detectors. Our goal is to exploit information from the explosion to infer orientations of proteins at the time of X-ray exposure. Our results demonstrate that partial orientation information can be extracted, particularly for larger proteins. Our findings can be integrated into existing reconstruction algorithms such as Expand-Maximize-Compress, to improve their efficiency and reduce the need for high-quality diffraction patterns. This method offers a promising avenue for enhancing Single Particle Imaging by leveraging measurable data from the Coulomb explosion to provide valuable insights about orientation.

physics.chem-ph↗

arXiv2024

Protein structure classification based on X-ray laser induced Coulomb explosion

We simulated the Coulomb explosion dynamics due to the fast ionization induced by high-intensity X-rays in six proteins that share similar atomic content and shape. We followed and projected the trajectory of the fragments onto a virtual detector, providing a unique explosion footprint. After collecting 500 explosion footprints for each protein, we utilized principal component analysis and t-distributed stochastic neighbor embedding to classify these. The results show that the classification algorithms were able to separate proteins on the basis of explosion footprints from structurally similar proteins into distinct groups. The explosion footprints, therefore, provide a unique identifier for each of the proteins. We envision that method could be used concurrently with single particle coherent imaging experiments to provide additional information on shape, mass, or conformation.

physics.chem-ph↗

arXiv2024

MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics

We describe a method to compute photon-matter interaction and atomic dynamics with X-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically computed based on changes to their electronic occupations and the free electron cloud created due to the irradiation of photons in the X-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, which reduces the number of non-bonded interactions required to compute. In combination with parallelisation through domain decomposition, large-scale molecular dynamics and ionisation induced by X-ray lasers can be followed. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters and crystals) that when exposed to an X-ray laser pulse turn into a plasma in the first few femtoseconds of the interaction. We show several examples of the applicability of the method and we quantify the sizes that the method is suitable for. For large systems, we investigate non-thermal heating and scattering of bulk water, which we compare to previous experiments. We simulate molecular dynamics of a protein crystal induced by an X-ray pump, X-ray probe scheme, and find good agreement of the damage dynamics with experiments. For single particle imaging, we simulate ultrafast dynamics of a methane cluster exposed to a femtosecond X-ray laser. In the context of coherent diffractive imaging we study the fragmentation as given by an X-ray pump X-ray probe setup to understand the evolution of radiation damage.

physics.chem-ph↗

arXiv2022

Dark path holonomic qudit computation

Non-adiabatic holonomic quantum computation is a method used to implement high-speed quantum gates with non-Abelian geometric phases associated with paths in state space. Due to their noise tolerance, these phases can be used to construct error resilient quantum gates. We extend the holonomic dark path qubit scheme in [M.-Z. Ai {\t et al.}, Fundam. Res. {\bf 2}, 661 (2022)] to qudits. Specifically, we demonstrate one- and two-qudit universality by using the dark path technique. Explicit qutrit ($d=3$) gates are demonstrated and the scaling of the number of loops with the dimension $d$ is addressed. This scaling is linear and we show how any diagonal qudit gate can be implemented efficiently in any dimension.

quant-ph↗