M3 - Publications

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2020     
A comprehensive theoretical picture of E centers in silicon: from optical properties to vacancy-mediated dopant diffusion
Gabriela Herrero Saboya, Layla Martin Samos, Anne Hémeryck, Nicolas Richard
Journal of Applied Physics 127 (2020) 085703 doi: 10.1063/1.5140724

Simulation of Single Particle Displacement Damage in Si_1-xGe_x alloys – Interaction of Primary Particles with the Material and Generation of the Damage Structure
Thomas Jarrin, Antoine Jay, Mélanie Raine, Normand Mousseau, Anne Hémeryck, Nicolas Richard
published in IEEE Transactions on Nuclear Science XX (2020) X-X doi: 10.1109/TNS.2020.2970488

Ionic transport under electric fields: equivalent polarization-work charge from Modern Theory of Polarization and connection with the classical picture
Nicolas Salles, Layla Martin Samos,  Stefano de Gironcoli, Luigi Giacomazzi, M. Valant, Anne Hémeryck, Philippe Blaise, Benoit Sklénard, Nicolas Richard
accepted in Nature Communications (2020)

2019     

Hybrid QM/MM vs Pure MM Molecular Dynamics for Evaluating Water Distribution within p21N-ras and the Resulting GTP Electronic Density
Ruth Tichauer, Gilles Favre, Stéphanie Cabantous, Marie Brut
J. Phys. Chem. B 123 (2019) 3935-3944  - doi: 10.1021/acs.jpcb.9b02660

Insight of Surfaces Treatments for CMOS Compatibility of InAs Nanowires
Daya Dhungana, Anne Hemeryck, Nicolo Sartori, Pier-Francesco Fazzini, Fuccio Cristiano, Sébastien Plissard
Nano Research 12 (2019) 581–586  - link: https://link.springer.com/article/10.1007%2Fs12274-018-2257-8

(Book Chapter) - Basics of semiconducting metal oxide–based gas sensors. Gas Sensors Based on Conducting Metal Oxides,
Alexandru Oprea, David Degler, Nicolae Barsan, Anne Hémeryck, Julia Rebholz
Elsevier, pp.61-165, 2019 - doi: 10.1016/B978-0-12-811224-3.00003-2

Defect creation and diffusion under electric fields from first-principles: the prototypical case of silicon dioxide
Nicolas Salles, Layla Martin Samos,  Stefano de Gironcoli, Luigi Giacomazzi, M. Valant, Anne Hémeryck, Philippe Blaise, Benoit Sklénard, Nicolas Richard
Conference paper - 2019 International Conference on Simulation of Semiconductor Processes and Devices (SISPAD), Sept 2019, Udine, Italy. pp.1-4 - doi: 10.1109/SISPAD.2019.8870555

Electronic and structural properties of interstitial titanium in crystalline silicon from first-principles simulations
Gabriela Herrero-Saboya, Layla Martin-Samos, Anne Hémeryck, Denis Rideau, Nicolas Richard
Conference paper - 2019 International Conference on Simulation of Semiconductor Processes and Devices (SISPAD), Sep 2019, Udine, Italy. pp.1-4. doi: 10.1109/SISPAD.2019.8870382

Simulation of Single Particle Displacement Damage in Si_1-xGe_x alloys – Interaction of Primary Particles with the Material and Generation of the Damage Structure
Thomas Jarrin, Antoine Jay, Mélanie Raine, Normand Mousseau, Anne Hémeryck, Nicolas Richard
Conference paper - 2019 European Conference on Radiation and its Effects on Components and Systems (RADECS), Sept 2019, Montpellier, France. pp.1-9. (available on request)

2018     

Water distribution within wild type NRas protein and Q61 mutants during unrestrained QM/MM dynamics
Ruth Tichauer, Gilles Favre, Stéphanie Cabantous, Georges Landa, Anne Hémeryck, Marie Brut
Biophysical Journal 115 (2018) 1417-1430  - doi: 10.1016/j.bpj.2018.07.042

Simulation of Single Particle Displacement Damage in Silicon – Part III: Generation and Long-Time Relaxation of Damage Structure
Antoine Jay, Anne Hémeryck, Nicolas Richard, Layla Martin Samos, Mélanie Raine, Alexandre Le Roch, Normand Mousseau, Vincent Goiffon, Philippe Paillet, Marc Gaillardin, Pierre Magnan
IEEE Transactions on Nuclear Science 65 (2018) 724-731- doi: 10.1109/TNS.2018.2790843

Insight into the Bonding of Silanols to Oxidized Aluminum Surfaces
Matic Poberznik, Dominique Costa, Anne Hemeryck, Anton Kokalj
The Journal of Physical Chemistry C  122 (2018) 9417 - doi: 10.1021/acs.jpcc.7b12552

Growth stability and decomposition of Mg2Si ultra-thin films on Si(100)
Brice Sarpi, Rachid Zirmi, Magali Putero, Mohammed Bouslama, Anne Hemeryck, Sébastien Vizzini
Applied Surface Science 427 (2018) 522 - doi: 10.1016/j.apsusc.2017.09.027

Spatial analysis of nanofluidic-embedded biosensors for wash-free single-nucleotide difference discrimination
Jean Cacheux, Marie Brut, Aurélien Bancaud, Pierre Cordelier, Thierry Leichlé 
ACS Sensors 3 (2018) 606 doi: 10.1021/acssensors.7b00667

2017     

MgO monolayer epitaxy on Ni(100)
Brice Sarpi, Magali Putero, Anne Hemeryck, Sébastien Vizzini
Applied Physics Letters 111 (2017) 211604 - doi: https://doi.org/10.1063/1.5000119

Ambient humidity influence of CO detection with SnO2 gas sensing materials - a DRIFTS/DFT investigation
Susanne Wicker, Mathilde Guiltat, Udo Weimar, Anne Hemeryck, Nicolae Barsan
Journal of Physical Chemistry C 121  (2017) 25064–25073 - doi: 10.1021/acs.jpcc.7b06253

Strain-driven diffusion process during silicon oxidation investigated by coupling Density Functional Theory and Activation Relaxation Technique
Nicolas Salles, Nicolas Richard, Normand Mousseau and Anne Hemeryck
Journal of Chemical Physics 147 (2017) 054701 - doi: 10.1063/1.4996206

DFT-D Study of Adsorption of Diaminoethane and Propylamine Molecules on TiO₂-Anatase (101) Surface
Anne Hemeryck, Alessandro Motta, Corinne Lacaze-Dufaure, Dominique Costa and Philippe Marcus
Applied Surface Science 426 (2017) 107-115 - doi: 10.1016/j.apsusc.2017.07.161

Modeling Of The Interface Formation During CuO Deposition On Al(111) Substrate: Linking Material Design and Elaboration Process Parameters Through Multi-Levels Approach
Mathilde Guiltat, Nicolas Salles, Marie Brut, Georges Landa,Nicolas Richard, Sébastien Vizzini, Anne Hémeryck
submitted in Modelling and Simulation in Materials Science and Engineering - Proceedings of MMM 2016

Dioxygen molecule adsorption and oxygen atom diffusion on clean and defective Aluminum (111) surface using first principles calculations
Mathilde Guiltat, Marie Brut, Sébastien Vizzini, Anne Hémeryck
Surface Science 657 (2017) 79-89 - doi: 10.1016/j.susc.2016.11.010

Simulation of Single Particle Displacement Damage in Silicon – Part II: Generation and Long-Time Relaxation of Damage Structure
Antoine Jay, Mélanie Raine, Nicolas Richard, Normand Mousseau, Vincent Goiffon, Anne Hémeryck, Pierre Magnan
IEEE Transactions on Nuclear Science 64 (2017) 141-148 - doi: 10.1109/TNS.2016.2628089

2016     

Atomic scale modeling to understand how matter organizes during growth of ultrathin materials in close relation with elaboration process parameters: Climbing the scales
Anne Hémeryck, Mathilde Guiltat, Nicolas Salles, Nicolas Richard
Conference Paper - 2016 IEEE Nanotechnology Materials and Devices Conference (NMDC) - doi: 10.1109/NMDC.2016.7777119

A perfect wetting of Mg monolayer on Ag(111) under atomic scale investigation: first principles calculations, scanning tunneling microscopy and Auger spectroscopy
Amani Migaou, Brice Sarpi, Mathilde Guiltat, Kevin Payen, Rachid Daineche, Georges Landa, Sébastien Vizzini, Anne Hémeryck
The Journal of Chemical Physics 144 (2016) 194708 - doi: 10.1063/1.4949764

Ultra-thin MgO(111)-polar sheets grown onto Ag(111)
B. Sarpi, R. Daineche, C. Girardeaux, A. Hemeryck, S. Vizzini
Applied Surface Science 361 (2016) 259 - doi: 10.1016/j.apsusc.2015.11.176

2015     

Role of Alumina Coatings for Selective and Controlled Bonding of DNA on Technologically Relevant Oxide Surfaces
T. Calais, Theo, B. Playe, J.-M. Ducere, J.-F. Veyan, S. Rupich, A. Hemeryck, M. Djafari Rouhani, C. Rossi, Y. Chabal, A. Esteve,
The Journal of Physical Chemistry C 119 (2015) 23527 - doi: 10.1021/acs.jpcc.5b06820

Oxidation of Mg atomic monolayer onto silicon: A road toward MgOx/Mg₂Si (11–1)/Si (100) heterostructure
B. Sarpi, N. Rochdi, R. Daineche, M. Bertoglio, C. Girardeaux, A. Baronnet, J. Perrin-Toinin, M. Bocquet, M. Djafari-Rouhani, A. Hemeryck, S. Vizzini
Surface Science 642 (2015) L1 - doi: 10.1016/j.susc.2015.08.003

Surface-interface exploration of Mg deposited on Si(100) and oxidation effect on interfacial layer
B. Sarpi, R. Daineche, C. Girardeaux, M. Bertoglio, F. Derivaux, J.P. Biberian, A. Hemeryck, S. Vizzini
Applied Physics Letters 106 (2015) 021604 - doi: 10.1063/1.4905592

Binding modes of thrombin binding aptamers investigated by simulations and experiments
A. Trapaidze, A. Bancaud, M. Brut
Applied Physics Letters 106 (2015) 043702 - doi: 10.1063/1.4906594

Thrombin detection in murine plasma using engineered fluorescence resonance energy transfer aptadimers
A. Trapaidze, M. Brut, S. Mazères, D. Estève, A-M. Gué, A. Bancaud
Applied Physics Letters 107 (2015) 233701 - doi: 10.1063/1.4937351

2014     

Elementary surface chemistry during CuO/Al nanothermites synthesis: copper and oxygen deposition on aluminium (111) surfaces
C. Lanthony, M. Guiltat, J.-M. Ducéré, A. Verdier, A. Hémeryck, M. Djafari-Rouhani, C. Rossi, Y.J. Chabal, A. Estève
ACS Applied Materials & Interfaces 6 (2014) 15086 - doi: 10.1021/am503126k

Toward in Silico Biomolecular Manipulation through Static Modes : Atomic Scale Characterization of HIV-1 Protease Flexibility
M. Brut, A. Estève, G. Landa, M. Djafari Rouhani
Journal of Physical Chemistry B 118 (2014) 2821 - doi: 10.1021/jp4113156

Nanoindentation of NiAl and Ni3Al crystals on (100), (110), and (111) surfaces: a molecular dynamics study
R. Seymour, A. Hémeryck, K. Nomura, W. Wang, R.K. Kalia, A. Nakano, P. Vashishta
Applied Physics Letters 104 (2014) 141904 - doi: 10.1063/1.4867168

2013     

Bottom-up modeling of Al/Ni multilayer combustion: effect of intermixing and role of vacancy defects on the ignition process
A. Hémeryck, J.-M. Ducéré, C. Lanthony, A. Estève, C. Rossi, M. Djafari Rouhani, D. Estève
Journal of Applied Physics 113 (2013) 204301 - doi: 10.1063/1.4807164

Diaminoethane adsorption and water substitution on hydrated TiO2: a thermochemical study based on first-principles calculations
A. Hémeryck, A. Motta, C. Pereira Nabais, J. Swiatowska, P. Marcus, D. Costa
Physical Chemistry Chemical Physics - 15 (2013) 10824 - doi: 10.1039/c3cp44498h

2012

Oxidation of Germanium and Silicon Surfaces (100): a comparative study through DFT methodology
C. Mastail, I. Bourennane, A. Estève, G. Landa, M. Djafari Rouhani, N. Richard, A. Hémeryck
IOP Conference Series: Materials Science and Engineering 41 (2012) 012007 - doi: 10.1088/1757-899X/41/1/012007

On the early stage of aluminum oxidation: An extraction mechanism via oxygen cooperation
C. Lanthony, J.M. Ducéré, M. Djafari Rouhani, A. Hémeryck, A. Estève, C. Rossi
Journal of Chemical Physics 137 (2012) 094707 - doi: 10.1063/1.4746943

Mimicking DNA stretching with the Static Mode method: Shear stress versus transverse pulling stress 
M. Brut, A. Estève, G. Landa, M. Djafari Rouhani 
European Physical Journal E 35 (2012) 75

A computational chemist approach to gas sensors: Modeling the response of SnO2 to CO, O2 and H2O gases
J-M. Ducéré, A. Hémeryck, A. Estève, M. Djafari Rouhani, G. Landa, P. Menini, C. Tropis, A. Maisonnat, P. Fau, B. Chaudret
Journal of Computational Chemistry 33 (2012) 247 - doi: 10.1002/jcc.21959

Bringing aptamers into technologies: Impact of spacer terminations
M. Brut, A. Trapaidze, A. Estève, A. Bancaud, D. Estève, G. Landa, M. Djafari Rouhani
Applied Physics Letters 100 (2012) 163702

Defect generation during silicon oxidation: a kinetic Monte Carlo study
A. Ali Messaoud  A. Chikouche, A. Estève, A. Hémeryck, C. Lanthony, C. Mastail, M. Djafari Rouhani, N. Richard
Thin Solid Films 520 (2012) 4734 - doi: 10.1016/j.tsf.2011.10.207

2011

Atomic scale determination of enzyme flexibility and active site stability through static modes: case of Dihydrofolate Reductase
M. Brut, A. Estève, G. Landa, M. Djafari Rouhani, M. Vaisset
Journal of Physical Chemistry B 115 (2011) 1616

The electrostatic probe: a tool for the investigation of the αβ(1-16) peptide deformations using the Static Modes
G. Renvez, A. Estève, M. Brut, G., M. Djafari Rouhani, A. Dkhissi
Physical Chemistry Chemical Physics 13 (2011) 14611

Effects of solvation shells and cluster size on the reaction of aluminium clusters with water
W. Mou, S. Ohmura, A. Hémeryck, F. Shimojo, R.K. Kalia, A. Nakano, P. Vashista
AIP Advances 1 (2011) 042149  - doi: 10.1063/1.3664751

2010

Atomic scale determination of DNA conformational rsponse to strained furanose: a static mode approach
M. Brut, A. Estève, G. Landa, A. Dkhissi, G. Renvez, M. Djafari Rouhani, D. Gauchard 
Tetrahedron 66 (2010) 9123
 
Periodic boundary versus quantum cluster approaches in the simulation of a nanoenergetic model-system: Ni/Al (111) surface reactions
M. Petrantoni, A. Hémeryck, J.M. Ducéré, A. Estève, C. Rossi, M. Djafari Rouhani, D. Estève, G. Landa
Journal of Physics and Chemistry of Solids 71 (2010) 130 - doi: 10.1016/j.jpcs.2009.08.010

A mesoscopic model of the intermixing during nanoenergetic materials processing
A. Hémeryck, M. Petrantoni, A. Estève, C. Rossi, M. Djafari Rouhani, D. Estève, G. Landa
Journal of Physics and Chemistry of Solids 71 (2010) 125 - doi: 10.1016/j.jpcs.2009.07.019
 
Deformation of thiolated nucleic acid deposited on a silicon surface: a static mode approach
M. Brut, A. Estève, G. Landa, G. Renvez, M. Djafari Rouhani, D. Gauchard
Materials Science and Engineering B 169 (2010) 23
 
Asymmetric diffusion as a key mechanism in Ni/Al energetic multilayer processing
M. Petrantoni, A. Hémeryck, J.M. Ducéré, A. Estève, C. Rossi, M. Djafari Rouhani, D. Estève, G. Landa
Journal of Vacuum Science & Technology A: Vacuum Surfaces and Films 28 (2010) L15 - doi: 10.1116/1.3491182

2009

The Static Modes : An alternative approach for the treatment of macro- and bio-molecular induced-fit flexibility
M. Brut, A. Estève, G. Landa, G. Renvez, M. Djafari Rouhani
The European Physical Journal E 28 (2009) 17 (on cover)
 
Evidence of the non reactivity of Ge during the initial stage of SiGe oxidation
A. Dkhissi, A.K. Upadhyay, A. Hémeryck, A. Estève, G. Landa, M. Djafari Rouhani
Applied Physics Letters 94 (2009) 041912 - doi: 10.1063/1.3076092

Fundamental steps towards interface amorphization during silicon oxidation
A. Hémeryck, A. Estève, N. Richard, M. Djafari Rouhani, Y.J. Chabal
Physical Review B 79 (2009) 035317 - doi: 10.1103/PhysRevB.79.035317
 
A kinetic Monte Carlo study of the initial stage of silicon oxidation: basic mechanisms-induced partial ordering of the oxide interfacial layer
A. Hémeryck, A. Estève, N. Richard, M. Djafari Rouhani, G. Landa
Surface Science 603 (2009) 2132 - doi: 10.1016/j.susc.2009.04.014
 
Logiciel Hikad : modéliser l’organisation atomique durant la croissance de HfO2 sur silicium
A. Estève, M. Djafari Rouhani, A. Dkhissi, C. Mastail, G. Landa, A. Hémeryck, N. Richard
Les Techniques de l’Ingénieur RE123 (2009)
 
Étude ab initio des premières étapes de l’oxydation du silicium
A. Hémeryck, A. Estève, N. Richard, M. Djafari Rouhani and Y.J. Chabal
Chocs Avancées (2009) 24

2007

Difficulty for oxygen to incorporate into the silicon network during initial O2 oxidation of Si(100)-(2x1)
A. Hémeryck, A. Mayne, N. Richard, A. Estève, Y.J. Chabal, M. Djafari Rouhani, G. Dujardin, G. Comtet
Journal of Chemical Physics 126 (2007) 114707 - doi: 10.1063/1.2566299
 
A new insight into the understanding of the collapsed form of poly(N-isopropylacrylamide) molecules
A. Estève, A. Bail, G. Landa, A. Dkhissi, M. Brut, M. Djafari Rouhani, J. Sudor, A-M. Gué
Chemical Physics 340 (2007) 12

Diffusion of oxygen atom in the topmost layer of the Si(100) surface: Structures and oxidation kinetics
A. Hémeryck, N. Richard, A. Estève, M. Djafari Rouhani
Surface Science 601 (2007) 2339- doi : 10.1016/j.susc.2007.03.038
 
Active oxidation: silicon etching and oxide decomposition basic mechanisms using Density Functional Theory
A. Hémeryck, N. Richard, A. Estève, M. Djafari Rouhani
Surface Science 601 (2007) 2082 - doi : 10.1016/j.susc.2007.03.008

Multi-scale modeling of oxygen molecule adsorption on a Si(100)-p(2x2) surface
A. Hémeryck, N. Richard, A. Estève, M. Djafari Rouhani
Journal of Non-Crystalline Solids 353 (2007) 594
 
Oxidation of silicon: how to deal with a Kinetic Monte Carlo approach
A. Ali Messaoud, A. Hémeryck, A. Estève, M. Djafari Rouhani, G. Landa
Material Research Society Symposium Proceedings 996 (2007)