A5106668072- Advanced Chemical Physics Studies
- Mass Spectrometry Techniques and Applications
- Atomic and Molecular Physics
- Ion-surface interactions and analysis
- Spectroscopy and Quantum Chemical Studies
- Electron Spin Resonance Studies
- Immunotherapy and Immune Responses
- vaccines and immunoinformatics approaches
- DNA and Nucleic Acid Chemistry
- Antimicrobial Peptides and Activities
- DNA Repair Mechanisms
- Atomic and Subatomic Physics Research
- Radiation Effects and Dosimetry
- Electronic and Structural Properties of Oxides
- Enzyme Structure and Function
- Inorganic Chemistry and Materials
- Laser-Matter Interactions and Applications
- Luminescence Properties of Advanced Materials
- Analytical chemistry methods development
- Nanocluster Synthesis and Applications
- Parallel Computing and Optimization Techniques
- Synthesis and Characterization of Heterocyclic Compounds
- Photochromic and Fluorescence Chemistry
- Advanced NMR Techniques and Applications
- Free Radicals and Antioxidants
Netherlands eScience Center
2023-2024
Donostia International Physics Center
2020
Material Physics Center
2020
Vrije Universiteit Amsterdam
2017-2019
École Polytechnique Fédérale de Lausanne
2012-2018
Universidad Autónoma de Madrid
2009-2013
A review of the present status, recent enhancements, and applicability SIESTA program is presented. Since its debut in mid-nineties, SIESTA's flexibility, efficiency free distribution has given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, a real-space grid for representation charge density potentials computation their associated matrix...
A combination of time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods is used to investigate fragmentation doubly charged gas-phase uracil in collisions with 100 keV protons. The results are good agreement ion-ion coincidence measurements. Orbitals similar energy and/or localized bonds lead very different patterns, thus showing the importance intramolecular chemical environment. In general, observed fragments do not correspond energetically most favorable...
First-principles electronic structure calculations are very widely used thanks to the many successful software packages available. Their traditional coding paradigm is monolithic, i.e., regardless of how modular its internal may be, code built independently from others, compiler up, with exception linear-algebra and message-passing libraries. This model has been quite for decades. The rapid progress in methodology, however, resulted an ever increasing complexity those programs, which implies...
Coulombic explosion of uracil: Ionizing radiation is used in cancer therapy to induce molecular damage cells. Ab initio dynamics were probe the early dissociation processes and ensuing chemical reactions following selective ionization either uracil or surrounding water molecules (see scheme; C gray, N blue, O red, H white).
Coinage metal clusters are of great importance for a wide range scientific fields, ranging from microscopy to catalysis. Despite their clear fundamental and technological importance, the experimental structural determination copper has attracted little attention. We fill this gap by elucidating structure cationic through infrared (IR) photodissociation spectroscopy Cun+–Arm complexes. Structures Cun+ (n = 3–10) unambiguously assigned based on comparison IR spectra in 70–280 cm–1 spectral...
We present a combined experimental and computational study of the relaxation dynamics ethylene cation. In experiment, we apply an extreme-ultraviolet-pump/infrared-probe scheme that permits us to resolve time scales on order 10 fs. The photoionization followed by infrared (IR) probe pulse leads rich structure in fragment ion yields reflecting fast response molecule its nuclei. temporal resolution our setup enables pinpoint upper bound previously defined ethylene–ethylidene isomerization 30 ±...
We investigate the coulomb coupling interactions of natural chromophores in solubilised light harvesting complex II (LHCII) using DFT quantum chemistry calculations.
We study the dissociative ionization of water clusters by impact 12 MeV/u Ni25+ ions. Cold target recoil ion momentum spectroscopy (COLTRIMS) is used to obtain information about stability, energetics and charge mobility ionized clusters. An unusual stability H9O+4 observed, which could be signature so-called Eigen structure in gas-phase From analysis coincidences between charged fragments, we conclude that very high responsible for formation protonated clusters, (H2O)nH+, dominate mass...
Abstract The interaction between peptides and major histocompatibility complex (MHC) molecules is pivotal in autoimmunity, pathogen recognition tumor immunity. Recent advances cancer immunotherapies demand for more accurate computational prediction of MHC-bound peptides. We address the generalizability challenge peptide predictions, revealing limitations current sequence-based approaches. Our structure-based methods leveraging geometric deep learning (GDL) demonstrate promising improvement...
The interaction between peptides and major histocompatibility complex (MHC) molecules is pivotal in autoimmunity, pathogen recognition tumor immunity. Recent advances cancer immunotherapies demand for more accurate computational prediction of MHC-bound peptides. We address the generalizability challenge peptide predictions, revealing limitations current sequence-based approaches. Our structure-based methods leveraging geometric deep learning (GDL) demonstrated promising improvement across...
The Minnesota family of exchange-correlation (xc) functionals are among the most popular, accurate, and abundantly used available to date. However, their use in plane-wave based first-principles MD has been limited by sparse availability. Here, we present an implementation M05, M06, M11 families xc within a plane wave/pseudopotential framework allowing for comprehensive analysis basis set dependence. While it reported that Gaussian bases some members only converge slowly limit, (1) show...
Abstract We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states dication are obtained by removing electrons from different inner-shell orbitals neutral species. show that shape-equivalent lead very patterns revealing importance intramolecular chemical environment. The results good agreement with ionion coincidence measurements collision...
Fragmentation of doubly charged biomolecules, uracil and amino acids, has been investigated using different ab inito Molecular Dynamics Methods. Time-Dependent Density Functional Theory give a description the non-adiabatic effects, charge redistributions that occur in first few femtoseconds reveal importance chemical environment. The combination techniques allow us to interpret complex multicoincident spectra obtained experimentally when molecules collides with ions or are excited...
Coulomb-Explosion an Uracil: Ionisierende Strahlung kann im Zuge der Krebstherapie gezielt molekulare Schäden in Zellen hervorrufen. Frühe Dissoziationsprozesse und chemische Folgereaktionen nach einer selektiven Ionisierung von Uracil oder umgebenden Wassermolekülen (siehe Schema: C grau, N blau, O rot, H weiß) wurden mithilfe Ab-initio-Moleküldynamik untersucht.
To experimentally investigate the role of hydration in initial process decomposition 2-deoxy-d-ribose (dR), which is a major component DNA backbone, we used mass spectrometry to monitor ions desorbing from hydrated dR films exposed monochromatic soft X rays (560 eV). The X-ray photons preferentially ionize K-shell electrons oxygen atoms DNA. Hydrated samples were prepared under vacuum by exposing cooled (∼150 K) film deposited on Si substrate water vapor. Using quadrupole spectrometer,...
Abstract The interaction between peptides and major histocompatibility complex (MHC) molecules is pivotal for tissue transplantation, pathogen recognition autoimmune disease treatments. Recent advances in cancer immunotherapies demand more accurate computational prediction of MHC-bound peptides. We address the generalizability challenge peptide predictions, revealing limitations current sequence-based approaches. Our solution employs structure-based methods leveraging geometric deep learning...
We have studied the fragmentation of uracil in both gas phase and water environments. applied a combination time-dependent density functional theory Born-Oppenheimer molecular dynamics methods to investigate doubly-charged uracil. also present results new ion/ion coincidence measurements which fragments are produced collisions with 100 keV protons. Breaking molecule more than two mainly arises from inner shell two-electron vacancies. Orbitals similar energy and/or localized bonds can lead...
Kosmische Primärstrahlung besteht zu 99 % aus Kernen der häufigsten Atome (H, He, Fe). Diese Ionen induzieren in biologischen Materialien mehrfache Ionisationen bis hin zur Coulomb-Explosion von Biomolekülen. In ihrer Zuschrift auf S. 3242 ff. untersuchen M.-A. Hervé du Penhoat, M.-F. Politis et al. die Hydroxylierung Uracil durch ein ionisiertes Wassermolekül mit “First-principle”-Moleküldynamikstudien. Der Filmstreifen zeigt Schnappschüsse Reaktion Pikosekunden-Zeitskala.