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1

Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials

Nelson, Tammie R., White, Alexander J., Bjorgaard, Josiah A., Sifain, Andrew E., Zhang, Yu, Nebgen, Benjamin, Fernandez-Alberti, Sebastian, Mozyrsky, Dmitry, Roitberg, Adrian E., Tretiak, Sergei

Journal:

Chemical Reviews

Year:

2020

File:

PDF, 19.43 MB

2020

2

Nonadiabatic Excited-State Molecular Dynamics: Modeling Photophysics in Organic Conjugated Materials

Nelson, Tammie, Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Tretiak, Sergei

Journal:

Accounts of Chemical Research

Year:

2014

Language:

english

File:

PDF, 3.29 MB

english, 2014

3

Nonadiabatic excited-state molecular dynamics: Treatment of electronic decoherence

Nelson, Tammie, Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Tretiak, Sergei

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.30 MB

english, 2013

4

Photoexcited Energy Transfer in a Weakly Coupled Dimer

Alfonso Hernandez, Laura, Nelson, Tammie, Tretiak, Sergei, Fernandez-Alberti, Sebastian

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 1.03 MB

english, 2015

5

Nonadiabatic Excited-State Molecular Dynamics Modeling of Photoinduced Dynamics in Conjugated Molecules

Nelson, Tammie, Fernandez-Alberti, Sebastian, Chernyak, Vladimir, Roitberg, Adrian E., Tretiak, Sergei

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 2.73 MB

english, 2011

6

Intermolecular conical intersections in molecular aggregates

De Sio, Antonietta, Sommer, Ephraim, Nguyen, Xuan Trung, GroÃ, Lynn, PopoviÄ, DuÅ¡ko, Nebgen, Benjamin Tyler, Fernandez-Alberti, Sebastian, Pittalis, Stefano, Rozzi, Carlo Andrea, Molinari, Elisa, M

Journal:

Nature Nanotechnology

Year:

2020

File:

PDF, 4.49 MB

2020

7

Identification of unavoided crossings in nonadiabatic photoexcited dynamics involving multiple electronic states in polyatomic conjugated molecules

Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Nelson, Tammie, Tretiak, Sergei

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 1.53 MB

english, 2012

8

Artifacts due to trivial unavoided crossings in the modeling of photoinduced energy transfer dynamics in extended conjugated molecules

Nelson, Tammie, Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Tretiak, Sergei

Journal:

Chemical Physics Letters

Year:

2013

Language:

english

File:

PDF, 775 KB

english, 2013

9

Signature of Nonadiabatic Coupling in Excited-State Vibrational Modes

Soler, Miguel A., Nelson, Tammie, Roitberg, Adrian E., Tretiak, Sergei, Fernandez-Alberti, Sebastian

Journal:

Journal of Physical Chemistry A

Year:

2014

Language:

english

File:

PDF, 428 KB

english, 2014

10

Photoinduced Intra- and Intermolecular Energy Transfer in Chlorophyll a Dimer

Zheng, Fulu, Fernandez-Alberti, Sebastian, Tretiak, Sergei, Zhao, Yang

Journal:

Journal of Physical Chemistry B

Year:

2017

Language:

english

File:

PDF, 1.91 MB

english, 2017

11

Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes

Saldaño, Tadeo E., Tosatto, Silvio C. E., Parisi, Gustavo, Fernandez-Alberti, Sebastian

Journal:

European Biophysics Journal

Year:

2019

Language:

english

File:

PDF, 1.58 MB

english, 2019

12

Non-adiabatic excited state molecular dynamics of phenylene ethynylene dendrimer using a multiconfigurational Ehrenfest approach

Fernandez-Alberti, Sebastian, Makhov, Dmitry V., Tretiak, Sergei, Shalashilin, Dmitrii V.

Journal:

Physical Chemistry Chemical Physics

Year:

2016

Language:

english

File:

PDF, 2.36 MB

english, 2016

13

Modification of Optical Properties and Excited State Dynamics by Linearizing Cyclic Paraphenylene Chromophores

Rodriguez-Hernandez, Beatriz, Ondarse-Alvarez, Dianelys, Oldani, Nicolas, Martinez-Mesa, Aliezer, Uranga-Pina, Llinersy, Tretiak, Sergei, Fernandez-Alberti, Sebastian

Journal:

The Journal of Physical Chemistry C

Year:

2018

Language:

english

File:

PDF, 8.80 MB

english, 2018

14

Electronic Delocalization, Vibrational Dynamics, and Energy Transfer in Organic Chromophores

Nelson, Tammie, Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Tretiak, Sergei

Journal:

The Journal of Physical Chemistry Letters

Year:

2017

Language:

english

File:

PDF, 2.21 MB

english, 2017

15

Photoexcited Nonadiabatic Dynamics of Solvated Push-Pull π-Conjugated Oligomers with the NEXMD Software

Sifain, Andrew E., Bjorgaard, Josiah A., Nelson, Tammie R., Nebgen, Benjamin T., White, Alexander J., Gifford, Brendan J., Gao, David W., Prezhdo, Oleg V., Fernandez-Alberti, Sebastian, Roitberg, Adri

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 6.98 MB

english, 2018

16

Phonon bottleneck and long-lived excited states in π-conjugated pyrene hoop

Franklin-Mergarejo, Ricardo, Nelson, Tammie, Tretiak, Sergei, Fernandez-Alberti, Sebastian

Journal:

Physical Chemistry Chemical Physics

Year:

2017

Language:

english

File:

PDF, 5.97 MB

english, 2017

17

The Antimicrobials Anacardic Acid and Curcumin Are Not-Competitive Inhibitors of Gram-Positive Bacterial Pathogenic Glyceraldehyde-3-Phosphate Dehydrogenase by a Mechanism Unrelated to Human C5a Anaphylatoxin Binding

Gómez, Sara, Querol-García, Javier, Sánchez-Barrón, Gara, Subias, Marta, González-Alsina, Àlex, Franco-Hidalgo, Virginia, Albertí, Sebastián, Rodríguez de Córdoba, Santiago, Fernández, Francisco J., V

Journal:

Frontiers in Microbiology

Year:

2019

Language:

english

File:

PDF, 4.98 MB

english, 2019

18

Vibrational energy redistribution during donor-acceptor electronic energy transfer: criteria to identify subsets of active normal modes

Alfonso-Hernandez, Laura, ATHANASOPOULOS, Stavros, Tretiak, Sergei, Miguel, Beatriz, Bastida, Adolfo, Fernandez-Alberti, Sebastian

Journal:

Physical Chemistry Chemical Physics

Year:

2020

File:

PDF, 2.89 MB

2020

19

Dynamics of exciplex formation in rare gas media

Germán Rojas-Lorenzo, Jesús Rubayo-Soneira, Sebastián Fernández Alberti

Journal:

Chemical Physics

Year:

2009

Language:

english

File:

PDF, 905 KB

english, 2009

20

Exciton Spatial Dynamics and Self-Trapping in Carbon Nanocages

RodrÃguez-HernÃ¡ndez, Beatriz, Nelson, Tammie, Oldani, Nicolas, MartÃnez-Mesa, Aliezer, Uranga-PiÃ±a, Llinersy, Segawa, Yasutomo, Tretiak, Sergei, Itami, Kenichiro, Fernandez-Alberti, Sebastian

Journal:

The Journal of Physical Chemistry Letters

Year:

2020

File:

PDF, 1.45 MB

2020

21

Factors Controlling the Reactivity of Hydrogen Sulfide with Hemeproteins

Pietri, Ruth, Lewis, Ariel, León, Ruth G., Casabona, Gullermina, Kiger, Laurent, Yeh, Syun-Ru, Fernandez-Alberti, Sebastian, Marden, Michael C., Cadilla, Carmen L., López-Garriga, Juan

Journal:

Year:

2009

Language:

english

File:

PDF, 2.83 MB

english, 2009

22

Dynamics fingerprints of active conformers of epidermal growth factor receptor kinase

Barletta, German P., Hasenhuer, Marcia Anahi, Fornasari, Maria Silvina, Parisi, Gustavo, Fernandez-Alberti, Sebastian

Journal:

Journal of Computational Chemistry

Year:

2018

Language:

english

File:

PDF, 1.21 MB

english, 2018

23

Ultrafast Non-Förster Intramolecular Donor–Acceptor Excitation Energy Transfer

Athanasopoulos, Stavros, Alfonso Hernandez, Laura, Beljonne, David, Fernandez-Alberti, Sebastian, Tretiak, Sergei

Journal:

The Journal of Physical Chemistry Letters

Year:

2017

Language:

english

File:

PDF, 8.08 MB

english, 2017

24

Correction to “Dynamics of Energy Transfer in a Conjugated Dendrimer Driven by Ultrafast Localization of Excitations”

Galindo, Johan F., Atas, Evrim, Altan, Aysun, Kuroda, Daniel G., Fernandez-Alberti, Sebastian, Tretiak, Sergei, Roitberg, Adrian E., Kleiman, Valeria D.

Journal:

Journal of the American Chemical Society

Year:

2015

File:

PDF, 121 KB

2015

25

Theoretical study of the solvatochromism of a merocyanine dye

Sebastián Fernández Alberti, Julián Echave

Journal:

Chemical Physics

Year:

1997

Language:

english

File:

PDF, 748 KB

english, 1997

26

Nonadiabatic Molecular Dynamics Simulations of the Energy Transfer between Building Blocks in a Phenylene Ethynylene Dendrimer †

Fernandez-Alberti, Sebastian, Kleiman, Valeria D., Tretiak, Sergei, Roitberg, Adrian E.

Journal:

Journal of Physical Chemistry A

Year:

2009

Language:

english

File:

PDF, 1.63 MB

english, 2009

27

Antioxidant Neolignans from Cordia americana

Fernández, Lucía, Cirigliano, Adriana, Fabani, María, Lima, Beatriz, Alberti, Sebastián, Kramer, Fernando, Tapia, Alejandro, Cabrera, Gabriela, Palermo, Jorge, Sánchez, Marianela

Journal:

Year:

2013

Language:

english

File:

PDF, 175 KB

english, 2013

28

An ab initio multiple cloning approach for the simulation of photoinduced dynamics in conjugated molecules

Freixas, Victor M., Fernandez-Alberti, Sebastian, Makhov, Dmitry V., Tretiak, Sergei, Shalashilin, Dmitrii

Journal:

Physical Chemistry Chemical Physics

Year:

2018

Language:

english

File:

PDF, 3.00 MB

english, 2018

29

Evolutionary Conserved Positions Define Protein Conformational Diversity

Saldaño, Tadeo E., Monzon, Alexander M., Parisi, Gustavo, Fernandez-Alberti, Sebastian, Keskin, Ozlem

Journal:

PLoS Computational Biology

Year:

2016

Language:

english

File:

PDF, 1.68 MB

english, 2016

30

Hybrid Quantum/Classical Simulations of the Vibrational Relaxation of the Amide I Mode of N -Methylacetamide in D 2 O Solution

Bastida, Adolfo, Soler, Miguel A., Zúñiga, José, Requena, Alberto, Kalstein, Adrián, Fernández-Alberti, Sebastián

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 1.50 MB

english, 2012

31

Coherent exciton-vibrational dynamics and energy transfer in conjugated organics

Nelson, Tammie R., Ondarse-Alvarez, Dianelys, Oldani, Nicolas, Rodriguez-Hernandez, Beatriz, Alfonso-Hernandez, Laura, Galindo, Johan F., Kleiman, Valeria D., Fernandez-Alberti, Sebastian, Roitberg, A

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 1.33 MB

english, 2018

32

Electronic Excited State Specific IR Spectra for Phenylene Ethynylene Dendrimer Building Blocks

Galindo, Johan F., Fernandez-Alberti, Sebastian, Roitberg, Adrian E.

Journal:

The Journal of Physical Chemistry C

Year:

2013

Language:

english

File:

PDF, 2.10 MB

english, 2013

33

Photoexcited energy relaxation and vibronic couplings in Ï-conjugated carbon nanorings

Rodriguez-Hernandez, Beatriz, Oldani, A Nicolas, Martinez-Mesa, Aliezer, Uganda-PiÃ±a, Llinersy, Tretiak, Sergei, Fernandez-Alberti, Sebastian

Journal:

Physical Chemistry Chemical Physics

Year:

2020

File:

PDF, 2.36 MB

2020

34

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

Grosso, Marcos, Kalstein, Adrian, Parisi, Gustavo, Roitberg, Adrian E., Fernandez-Alberti, Sebastian

Journal:

The Journal of Chemical Physics

Year:

2015

Language:

english

File:

PDF, 6.17 MB

english, 2015

35

Unraveling Direct and Indirect Energy Transfer Pathways in a Light-Harvesting Dendrimer

Aguilera, Maria Camila, Roitberg, Adrian E., Kleiman, Valeria D., Fernandez-Alberti, Sebastian, Galindo, Johan F.

Journal:

The Journal of Physical Chemistry C

Year:

2020

File:

PDF, 3.19 MB

2020

36

Caging and excited state emission of ICN trapped in cryogenic matrices: experiment and theory

Helbing, Jan, Chergui, Majed, Fernandez-Alberti, Sebastian, Echave, Julian, Halberstadt, Nadine, Alberto Beswick, J.

Journal:

Physical Chemistry Chemical Physics

Year:

2000

Language:

english

File:

PDF, 235 KB

english, 2000

37

Dynamics of Energy Transfer in a Conjugated Dendrimer Driven by Ultrafast Localization of Excitations

Galindo, Johan F., Atas, Evrim, Altan, Aysun, Kuroda, Daniel G., Fernandez-Alberti, Sebastian, Tretiak, Sergei, Roitberg, Adrian E., Kleiman, Valeria D.

Journal:

Journal of the American Chemical Society

Year:

2015

Language:

english

File:

PDF, 1.57 MB

english, 2015

38

Nonadiabatic excited-state molecular dynamics: On-the-fly limiting of essential excited states

Nelson, Tammie, Naumov, Artem, Fernandez-Alberti, Sebastian, Tretiak, Sergei

Journal:

Chemical Physics

Year:

2016

Language:

english

File:

PDF, 868 KB

english, 2016

39

Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin

Querol-García, Javier, Fernández, Francisco J., Marin, Ana V., Gómez, Sara, Fullà, Daniel, Melchor-Tafur, Cecilia, Franco-Hidalgo, Virginia, Albertí, Sebastián, Juanhuix, Jordi, Rodríguez de Córdoba,

Journal:

Frontiers in Microbiology

Year:

2017

Language:

english

File:

PDF, 4.32 MB

english, 2017

40

Internal Conversion and Vibrational Energy Redistribution in Chlorophyll A

Shenai, Prathamesh M., Fernandez-Alberti, Sebastian, Bricker, William P., Tretiak, Sergei, Zhao, Yang

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 2.54 MB

english, 2015

41

Exploring the Common Dynamics of Homologous Proteins. Application to the Globin Family

Maguid, Sandra, Fernandez-Alberti, Sebastian, Ferrelli, Leticia, Echave, Julian

Journal:

Biophysical Journal

Year:

2005

Language:

english

File:

PDF, 635 KB

english, 2005

42

Photoinduced dynamics in cycloparaphenylenes: planarization, electron-phonon coupling, localization and intra-ring migration of the electronic excitation.

Oldani, A Nicolas, Doorn, Stephen, Tretiak, Sergei, Fernandez-Alberti, Sebastian

Journal:

Physical Chemistry Chemical Physics

Year:

2017

Language:

english

File:

PDF, 2.03 MB

english, 2017

43

Nonadiabatic excited-state molecular dynamics: Numerical tests of convergence and parameters

Nelson, Tammie, Fernandez-Alberti, Sebastian, Chernyak, Vladimir, Roitberg, Adrian E., Tretiak, Sergei

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 1.22 MB

english, 2012

44

Nonadiabatic Dynamics of Excited Hg( 3 P 1 ) in Ar Matrixes †

Rojas-Lorenzo, Germán, Rubayo-Soneira, Jesús, Fernández Alberti, Sebastián, Chergui, Majed

Journal:

Journal of Physical Chemistry A

Year:

2003

Language:

english

File:

PDF, 113 KB

english, 2003

45

Protein Fluctuations and Cavity Changes Relationship

Barletta, German P., Fernandez-Alberti, Sebastian

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 4.90 MB

english, 2018

46

Electronic Energy Relaxation in a Photoexcited Fully Fused Edge Sharing Carbon Nanobelt

Freixas, Victor Manuel, Oldani, Nicolas, Franklin-Mergarejo, Ricardo, Tretiak, Sergei, Fernandez-Alberti, Sebastian

Journal:

The Journal of Physical Chemistry Letters

Year:

2020

File:

PDF, 1.76 MB

2020

47

A b initio quantum direct dynamics simulations of ultrafast photochemistry with Multiconfigurational Ehrenfest approach

Makhov, Dmitry, Symonds, Christopher, Fernandez-Alberti, Sebastian, Shalashilin, Dmitrii

Journal:

Chemical Physics

Year:

2017

Language:

english

File:

PDF, 2.33 MB

english, 2017

48

Evolutionary conservation of protein vibrational dynamics

Sandra Maguid, Sebastian Fernandez-Alberti, Julian Echave

Journal:

Year:

2008

Language:

english

File:

PDF, 402 KB

english, 2008

49

Conformational disorder in energy transfer: beyond Förster theory

Nelson, Tammie, Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Tretiak, Sergei

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 3.40 MB

english, 2013

50

Exploring conformational space with thermal fluctuations obtained by normal mode analysis

Saldano, Tadeo Enrique, Freixas, Victor Manuel, Tosatto, Silvio, Parisi, Gustavo, Fernandez-Alberti, Sebastian

Journal:

Journal of Chemical Information and Modeling

Year:

2020

Language:

english

File:

PDF, 1.56 MB

english, 2020

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