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Communication Techniques and Technology Transfer
2016-2017
10 X 10
IMAGES SECONDS
Sílvia Escayola Gordils
Developing	
  New	
  Tools	
  to	
  Study	
  Excited	
  
States	
  in	
  DNA
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  
DNA	
  is	
  an	
  essen6al	
  molecule	
  and	
  it	
  is	
  composed	
  of	
  small	
  organic	
  molecules,	
  the	
  
nucleobases,	
  which	
  can	
  undergo	
  photochemical	
  reac6ons	
  
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  
To	
  study	
  photochemical	
  reac6ons	
  we	
  have	
  to	
  take	
  into	
  account	
  the	
  excited	
  states	
  of	
  the	
  
molecule	
  and	
  the	
  crossings	
  between	
  different	
  states	
  
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  
The	
  crossing	
  points	
  between	
  different	
  PES	
  (Poten6al	
  Energy	
  Surface)	
  are	
  known	
  as	
  conical	
  
intersec6ons,	
  and	
  are	
  very	
  important	
  in	
  order	
  to	
  determine	
  the	
  reac6vity	
  of	
  the	
  molecule	
  
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  
The	
  treatment	
  of	
  these	
  elements	
  of	
  the	
  poten6al	
  energy	
  surface	
  only	
  can	
  be	
  done	
  
computa6onally	
  using	
  methods	
  based	
  on	
  quantum	
  mechanics	
  
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  
But	
  even	
  we	
  have	
  the	
  tools	
  to	
  do	
  it,	
  nowadays	
  there	
  is	
  not	
  enough	
  computa6onal	
  power	
  
to	
  treat	
  big	
  systems	
  like	
  DNA,	
  and	
  we	
  have	
  to	
  find	
  simplified	
  models	
  instead	
  
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  
For	
  this	
  reason	
  there	
  are	
  combined	
  methods	
  that	
  allow	
  us	
  to	
  divide	
  the	
  system	
  in	
  
different	
  layers,	
  like	
  an	
  onion.	
  And	
  treat	
  each	
  part	
  at	
  different	
  levels	
  of	
  theory	
  
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  
Using	
  this	
  strategy,	
  the	
  most	
  relevant	
  part	
  for	
  the	
  reac6vity	
  can	
  be	
  treated	
  with	
  a	
  
quantum	
  mechanics	
  method	
  and	
  the	
  environment	
  with	
  a	
  cheaper	
  method	
  	
  
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  
However,	
  these	
  combined	
  methods	
  do	
  not	
  include	
  all	
  the	
  tools	
  needed	
  to	
  op6mize	
  
conical	
  intersec6ons	
  and	
  some	
  implementa6ons	
  of	
  the	
  code	
  have	
  to	
  be	
  made	
  
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  
The	
  modifica6ons	
  of	
  the	
  code	
  have	
  to	
  be	
  tested	
  using	
  some	
  simplified	
  models	
  like	
  
nucleobases	
  or	
  nucleo6des	
  and	
  also	
  with	
  more	
  demanding	
  models	
  like	
  DNA	
  strands	
  
Energy	
  Difference	
  (S1-­‐S0)	
  
in	
  hartree	
  
No.	
  of	
  Microitera6ons	
  cycle	
  
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  
Finally,	
  we	
  analyze	
  the	
  results	
  obtained,	
  which	
  indicates	
  that	
  there	
  is	
  an	
  improvement	
  of	
  the	
  
conical	
  intersec6on	
  op6miza6on	
  process.	
  So,	
  we	
  have	
  achieved	
  a	
  good	
  tool	
  to	
  study	
  DNA	
  systems	
  
Thanks
for your
attention
10 X 10
IMAGES SECONDS
Sílvia	
  Escayola	
  Gordils	
  	
  Ÿ 	
  @silviaescayola	
  	
  Ÿ 	
  	
  	
  	
  	
  www.silviaescayola.wordpress.com	
  

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Pechakucha silvia notes

  • 1. Communication Techniques and Technology Transfer 2016-2017 10 X 10 IMAGES SECONDS Sílvia Escayola Gordils Developing  New  Tools  to  Study  Excited   States  in  DNA Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com  
  • 2. Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com   DNA  is  an  essen6al  molecule  and  it  is  composed  of  small  organic  molecules,  the   nucleobases,  which  can  undergo  photochemical  reac6ons  
  • 3. Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com   To  study  photochemical  reac6ons  we  have  to  take  into  account  the  excited  states  of  the   molecule  and  the  crossings  between  different  states  
  • 4. Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com   The  crossing  points  between  different  PES  (Poten6al  Energy  Surface)  are  known  as  conical   intersec6ons,  and  are  very  important  in  order  to  determine  the  reac6vity  of  the  molecule  
  • 5. Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com   The  treatment  of  these  elements  of  the  poten6al  energy  surface  only  can  be  done   computa6onally  using  methods  based  on  quantum  mechanics  
  • 6. Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com   But  even  we  have  the  tools  to  do  it,  nowadays  there  is  not  enough  computa6onal  power   to  treat  big  systems  like  DNA,  and  we  have  to  find  simplified  models  instead  
  • 7. Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com   For  this  reason  there  are  combined  methods  that  allow  us  to  divide  the  system  in   different  layers,  like  an  onion.  And  treat  each  part  at  different  levels  of  theory  
  • 8. Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com   Using  this  strategy,  the  most  relevant  part  for  the  reac6vity  can  be  treated  with  a   quantum  mechanics  method  and  the  environment  with  a  cheaper  method    
  • 9. Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com   However,  these  combined  methods  do  not  include  all  the  tools  needed  to  op6mize   conical  intersec6ons  and  some  implementa6ons  of  the  code  have  to  be  made  
  • 10. Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com   The  modifica6ons  of  the  code  have  to  be  tested  using  some  simplified  models  like   nucleobases  or  nucleo6des  and  also  with  more  demanding  models  like  DNA  strands  
  • 11. Energy  Difference  (S1-­‐S0)   in  hartree   No.  of  Microitera6ons  cycle   Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com   Finally,  we  analyze  the  results  obtained,  which  indicates  that  there  is  an  improvement  of  the   conical  intersec6on  op6miza6on  process.  So,  we  have  achieved  a  good  tool  to  study  DNA  systems  
  • 12. Thanks for your attention 10 X 10 IMAGES SECONDS Sílvia  Escayola  Gordils    Ÿ  @silviaescayola    Ÿ          www.silviaescayola.wordpress.com