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First-principles simulations of the interaction of ionic projectiles with water and ice

First-principles simulations of the interaction of ionic projectiles with water and ice. Jorge Kohanoff Atomistic Simulation Centre Queen’s University Belfast. Toulouse, 2-4 December 2009. Contents. Introduction Main questions General framework Computational methods Results:

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First-principles simulations of the interaction of ionic projectiles with water and ice

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  1. First-principles simulations of the interaction of ionic projectiles with water and ice Jorge Kohanoff Atomistic Simulation Centre Queen’s University Belfast Toulouse, 2-4 December 2009

  2. Contents • Introduction • Main questions • General framework • Computational methods • Results: • C through water • C through solvated guanine • H+ through ice • H+ through metals, self-irradiation in metals. • Conclusions and Outlook

  3. IntroductionWhat does radiation do to biomolecules? • Radiation causes lesions to biomolecules, especially DNA (but also proteins) • Directly by interacting with DNA components (bases, sugars or backbone) • Indirectly by interacting with matter around DNA and generating reactive species that cause the damage, e.g. • electrons by ionization • free radicals (OH˙), e.g. from water

  4. SSB DSB IntroductionConsequences of DNA damage Mainly two effects: • To alter of eliminate the ability of cells to replicate • Senescence (dormancy) • Apoptosis (cell suicide) • To induce potentially harmful mutations • Cancerous tumors • Strand damage (backbone): cosmic rays, UV, X and -rays, ions, electrons): • Single strand beaks (SSB) • Double strand breaks (DSB, less than 10 units apart) DNA damage occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day SSB: easy to repair DSB: can go wrong in many ways ACCUMULATION OF DSB TRIGGERS CYCLE CELL ARREST USEFUL IN CANCER THERAPY

  5. IntroductionEnergy deposition and radiotherapies X-rays and electrons deposit energy along the way with decreasing intensity Ions deposit mostly at the Bragg peak X-ray therapy: LINAC Hadrontherapy

  6. Established radiotherapies Attachment to DNA and strand breaking Transport through water / biological matter Electrons generated by ionization X-rays Secondary electrons Radicals Ions fragments Cellular membrane Electrons generated by ionization DNA Ions (p+,C+)

  7. Main questions • Which particles cause DNA damage? • Where do they come from? • Primary events (high energy): • Direct DNA ionization • Direct impact fragmentation • Secondary events (low energy): • Electrons generated by ionization of surrounding material • Radicals (e.g. OH˙, H˙) generated in collision processes • Fragments (ions/neutrals) generated in primary processes • What is the origin of double strand breaks?

  8. Radical / ion dynamics Adiabatic TDDFT Ehrenfest Electron-molecule / condensed phase simulations First-principles MD Ehrenfest dynamics Generation of radicals, ions, neutrals Biological end-point effects Radical /ion transport Modelling

  9. Electron dynamics Experiment TDDFT Ehrenfestsimulations Ion scattering (loss) Ehrenfest dynamics and beyond Electron spectroscopy X-ray diffraction Mass spectroscopy Molecular calculations Electron-molecule / condensed phase simulations Electro-phoresis Biological end-point effects Generation of electrons Electron transport Modelling electron-phonon interactions

  10. Generation of reactive species Electron energy distribution: Peak at ~ 50 eV Gustavo Garcia (Madrid) Other species: radicals, ions, etc. Abundance and energy distribution

  11. Inelastic transport of electrons and radicals • How far do electrons/radicals travel in water? (Mean free path) • How far do electrons/radical travel in intracellular matter • water/protein/ions mixture -- histones • What type of processes stop electrons? • impact ionization, electron-phonon interactions • What type of processes stop radicals? • What secondary species are generated along the tracks? • What is their frequency and energy distribution?

  12. End-point biological effectsStrand breaks by low energy electrons and ions B. Boudaïffa et al, Science 287, 1659 (2000) P. Swiderek, Angew. Chem. Int.. Ed. 45, 4056 (2006) B. Liu et al., J. Chem. Phys. 128, 075102 (2008) Low energy electrons (1-20 eV) cause SSB and DSB in plasmid DNA Dissociative electron attachment to DNA components or hydration waters (electronic resonances) Low energy C+ ions (1-6 keV) also cause SSB and DSB in plasmid DNA [A. Hunniford et al., Phys. Med. Biol. 52, 3729 (2007)]

  13. Ionic projectiles

  14. electronic nuclear Schiefermuller et al., Phys. Rev. A 48, 4467 (1993) Cabrera-Trujillo et al., Phys. Rev. Lett. 84, 5300 (2000) Ionic projectileselectronic vs nuclear stopping • Stopping power: energy deposited per unit length (S=dE/dx) • Nuclear: dominates at low energies • Electronic: • Metals: for v0, S  v (e-h pairs). Decrease a large v (Bethe) • Insulators: Threshold due to band gap vth 0.10.2 a.u. [First-principles on LiF: M. Pruneda et al., Phys. Rev. Lett. 99, 235501 (2007)]

  15. Ionic projectilesRegions of interest for biomolecular systems • Water is an electronic insulator -- Eg (water)  10 eV. • Threshold effects separate nuclear from electronic stopping. Low and high energy regimes can be treated separately • Low energy (v < 0.1 a.u., or 4 keV for C): adiabatic regime (GS electrons) • High energy (v > 0.1 a.u.): sudden regime (purely electronic dynamics) • Depending on the energy levels of the projectile: • Electronic excitation, capture and ionization by low-energy ions is possible. • Intermediate energy: impact fragmentation coexists with electronic excitation. Combined electron-nuclear dynamics required.

  16. Computational methodsFirst-principles molecular dynamics • Adiabatic regime • First-principles molecular dynamics (Car-Parrinello) • Electronic structure described within DFT-GGA • Pseudopotentials for core electrons • Slab geometry to avoid PBC in the incidence direction • Charge state of projectile not relevant under adiabatic conditions • SIESTA code[ J. M. Soler, E. Artacho, J. D. Gale, A. Garcia, J. Junquera, P. Ordejon & D. Sanchez-Portal, J. Phys.: Condens. Matter14, 2745 (2002)] • Basis set for electronic wave functions: numerical atomic orbitals • Numerical evaluation of matrix elements • Nuclear motion described by Newton’s equations:

  17. Computational methodsReal-time electronic dynamics • Sudden regime • Real-time electronic dynamics via TDDFT • Adiabatic GGA (AGGA) approximation to time-dependent XC • Fixed nuclei • Incident ion treated as a moving external potential • Channeling to avoid direct impact • Time-dependent Kohn-Sham equations implemented in SIESTA • [A. Tsolakidis, D. Sanchez-Portal and R. M. Martin, Phys. Rev. B 66, 235416 (2002)] with Kohn-Sham orbitals expanded in atomic orbital basis

  18. Computational methodsEhrenfest dynamics • Sudden regime • Real-time electronic dynamics via TDDFT • Adiabatic GGA (AGGA) approximation to time-dependent XC • Classical MD for the nuclei • Incident ion treated as another classical particle • No channeling restrictions • Ehrenfest equations implemented in SIESTA [D. Sanchez-Portal, J. Kohanoff and E. Artacho (unpublished)] V-1/2 r0=r1+V-1/2 V1/2=V-1/2+ F1/m Leap-frog Crank-Nic. Projections t-/2 t t t+/2 t+

  19. Systems studied • Adiabatic • C passing through water slab (128 water molecules) • C passing through guanine solvated in water slab (methylguanine + 136 water molecules) • Sudden • H+ shooting through channels in hexagonal ice (24 and 40 water molecules)

  20. C through water slabv=0.1 a.u.

  21. C through water slabv=0.1 a.u. (2.8 keV) H2OOH+H Multiple dissociation Head-on H2OO+2H

  22. C through water slabv=0.075 a.u.

  23. C through water slabv=0.05 a.u.

  24. C through water slabv=0.05 a.u. (700 eV) 2H2O  OH- + H3O+ Continuous energy transfer

  25. C through water slabv=0.025 a.u. Non-dissociative collisions. Energy transferred to vibrations.

  26. C through water slabv=0.025 a.u. (175 eV) Non-dissociative collisions. Energy transfer to vibrations. Complete stopping trajectories

  27. C through water slabv=0.025 a.u. Formation of new species: H2O2

  28. C+ in watergeneration of new chemical species

  29. Adiabatic stopping (nuclear)Final kinetic energy distributions • Average loss of kinetic energy (nuclear stopping) peaks at about 0.08 a.u. • Mostly elastic. Interplay between cross section and energy transfer. • At low energies also vibrational excitation of OH stretching.

  30. Adiabatic stopping Fragment distributions as a function of time H3O+ H˙/H+ O˙/O- OH˙/OH-

  31. Adiabatic stoppingFragment distributions as a function of position H˙/H+ H3O+ 1 H every 5 Å to 1 H every 20 Å OH˙/OH- O˙/O- 1 OH every 7 Å to 1 OH every 30 Å Low-energy projectiles cause more damage !

  32. C through solvated guaninev=0.1 a.u.

  33. C through solvated guaninev=0.025 a.u.

  34. Electronic stopping in ice • H+ shooting through channels in hexagonal ice • (24 and 40 water molecules – 3 and 5 units)

  35. Non-adiabatic stoppingchanneling of H+ through hexagonal ice Energy transferred to electrons

  36. Electronic stopping power channeling of H+ through hexagonal ice • Se through center of channel is about half that of LiF • Channels in ice are more open • Se increases by a factor of 3 when proton travels closer to water molecules

  37. Electronic stopping power channeling of H+ through hexagonal ice Experiment: P. Bauer et al., NIMB 93, 132 (1994) Peak at 90 keV/nucleon

  38. Non-adiabatic stoppingCharge state of the proton • At low speed the proton drags the electronic charge with it, forming H. • At higher speed, electrons respond to the proton, but too late, creating a wake. • Eventually, the electronic wake detaches and the proton travels as H+.

  39. Electronic stopping in metals SRIM stopping tables reproduced !

  40. Nuclear materials: stopping of Fe in Fe It is possible to compute Se for heavier projectiles FM vs PM: influence of EDOS apart from 

  41. Conclusions • Nuclear and electronic stopping in water separated in energy. Nuclear stopping becomes unimportant at v  0.15 - 0.2 a.u., where electronic stopping begins. • Peak in nuclear stopping • Formation of new chemical species (e.g. formic acid) • H, O and OH species are created by water radiolysis. Also hydrogen peroxide (H2O2 ) observed. • Spatial rate of production increases with decreasing speed. • Hyperthermal fragments. No thermalization of the medium. • Charge state: hyperthermal H•, otherwise H+ • Threshold of 0.2 a.u. for electronic stopping in ice. Maximum at 80 kev/n • Strong channeling effects.

  42. Wish list: radicals and ions • Generation of reactive species (radicals, ions) by ions, X-rays and electrons. Ehrenfest dynamics, R. Vuilleumiere. • How do radicals and ions make it to DNA? First-principles Molecular Dynamics (Car-Parrinello). SIC functional. • Radical attack to DNA (Mundy, Eriksson)

  43. Wish list: electrons • Inelastic transport of electrons through water and biological matter at energies below 50 eV (beyond Ehrenfest dynamics) • Electron impact ionization • Electronic excitation • Capture of electrons in resonant states of biomolecules in realistic environments: nucleic acids, sugars, nucleosides, nucleotides and DNA fragments, solvated or wrapped around histones. • Electron transport to other regions in DNA, e.g. phosphate bonds. • Weakening of bonds and strand breaks: Dynamics of dissociative electron attachment. • Exchange-correlation functionals: hybrids vs SIC (Suraud, Gervasio) M. Smyth Thanks to: YOU FOR YOUR ATTENTION Wellcome Trust for financial support and Clare Hall for visiting fellowship Department of Earth Sciences (University of Cambridge) for hospitality

  44. Collaborators • Emilio Artacho (Cambridge, UK) • Daniel Sanchez-Portal (San Sebastian, Spain) … and thanks to • Pablo Dans Puiggrós (Montevideo, Uruguay) • Mariví Fernández-Serra (Stonybrook, USA) • Tristan Youngs (QUB, Northern Ireland) • Kostya Trachenko (Cambridge, UK)

  45. IntroductionThe origins of radiation damage and therapy • Wilhelm Röntgen (Würzburg, 1895): discovers X-rays and proposes medical uses. • John Hall-Edwards (Birmingham, 1896): first radiograph for diagnostic purposes. Experiments on his own arm and contracts dermatitis. If they cause harm, they can also cure • L. Freund (Vienna, 1898): first therapeutic use of X-rays (birthmark removal). • J. E. Gilman (Chicago, 1901): first use of X-rays in cancer therapy. • Widespread use of radiotherapy for cancer only after WW2

  46. IntroductionConsequences of DNA damage • Mainly two effects: • To alter of eliminate the ability of cells to replicate • Senescence (dormancy) • Apoptosis (cell suicide) • Cancerous tumours • To induce potentially harmful mutations DNA damage, due to environmental factors and normal metabolic processes, occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day Something has to be done! SSB: easy to repair DSB: can go wrong in many ways. ACCUMULATION OF DSB triggers multiple pathways such as cell cycle arrest and inhibition of cell division: USEFUL IN CANCER THERAPY.

  47. SSB DSB IntroductionMorphology and sources of DNA damage • Types of damage • Bases • loss or changes (thermal) • Dimerization (UV-B, direct) • Inter-strand • H-bond breakage • Cross-linking (chemicals) • Intra-strand (backbone) cosmic rays, UV-A indirectly, X and -rays, ions, electrons): • Single strand beaks (SSB, thermal) • Double strand breaks (DSB, less than 10 units apart)

  48. IONS ELECTRONS PHOTONS NEUTRONS IntroductionSources of radiation

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