The Center for Nanoscience and Nanotechnology of UNAM invites you to
VII COLLOQUIUM ON COMPUTATIONAL
SIMULATION IN SCIENCES
VIRTUAL
- August 26 - 30, 2024
Students session.
Hands-on workshops: Python for IA, Non Covalent Interactions, and Optical Properties of Materials.
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Organizing committee.
Local committee
External committee
- Jonathan Guerrero Sanchez
- Sergio A. Aguila Puentes
- Maria Guadalupe Moreno Armenta
- Armando Reyes Serrato
- Rodrigo Ponce Pérez
- Aldo Rodriguez Guerrero
- Carlos A. Corona García
- Mirna Burciaga Flores
- Oscar Ruiz Galindo
- Etienne I. Palos, UCSD
- Héctor Noé Fernández, UANL
- Reyes García Díaz, UAdeC
Acknowledgments: Project DGAPA-PAPIIT IG101124
General Program
- Monday 08/26
- Tuesday 08/27
- Wednesday 08/28
- Thursday 08/29
- Friday 08/30
Student Session 1 - Monday, August 26
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Student Session 2 - Tuesday, August 27
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Session 1 - Wednesday, August 28
– Fernando Rojas Íñiguez – Director Centro de Nanociencias y Nanotecnología, UNAM.
AI-driven Fully Quantum (Bio)Molecular Simulations: From Dream to Reality
– Alex Tkatchenko – University of Luxembourg
Abstract
The convergence between accurate quantum-mechanical (QM) models (and codes) with efficient machine learning (ML) methods seem to promise a paradigm shift in molecular simulations. Many challenging applications are now being tackled by increasingly powerful QM/ML methodologies. These include modeling covalent materials, molecules, molecular crystals, surfaces, and even whole proteins in explicit water (https://www.science.org/doi/abs/10.1126/sciadv.adn4397). In this talk, I attempt to provide a reality check on these recent advances and on the developments required to enable fully quantum dynamics of complex functional (bio)molecular systems. Multiple challenges are highlighted that should keep theorists in business for the foreseeable future:
(1) Ensuring the accuracy of high-level QM methods (https://doi.org/10.1038/s41467-021-24119-3; https://doi.org/10.1038/s41586-023-06587-3),
(2) Describing intricate QM long-range interactions (https://doi.org/10.1126/sciadv.aax0024; https://doi.org/10.1126/science.aae0509; https://doi.org/10.1103/PhysRevLett.128.106101),
(3) Treating quantum electrodynamic effects that become relevant for complex molecules (https://doi.org/10.1021/acs.jpclett.1c04222; https://doi.org/10.1103/PhysRevResearch.4.013011).
(4) Developing increasingly accurate, efficient, scalable, and transferable ML architectures for molecules and materials (https://doi.org/10.1038/s41467-022-31093-x; https://arxiv.org/abs/2209.14865; https://arxiv.org/abs/2209.03985).
(5) Accounting for the quantum nature of the nuclei and the influence of external environments (https://doi.org/10.1038/s41467-020-20212-1; https://doi.org/10.1038/s41467-022-28461-y).
I argue that only a conjunction of all these developments will enable the long-held dream of fully quantum (bio)molecular simulations.
Strategies to boost electrical conductivity in porous materials: a computational perspective
– Joaquin Calbo – Universitat de València
Abstract
Despite being traditionally considered as insulators, (metal)-organic frameworks are porous crystalline structures that have proved to be efficient for the transport of electrical charge upon suitable chemical design for next-generation applications.[1] Among the most promising strategies to infuse charge conductivity in porous crystals, we emphasize the π-π stacking of electroactive ligands, the incorporation of guest molecules within the pores, or the exploitation of mixed valency in chemically available metal redox pairs. These porous conductors are meant to unlock new avenues in the design of novel materials for efficient energy conversion and storage.[2]
Herein, we showcase the theoretical modelling of advanced porous materials that take advantage of each of these chemical strategies to boost charge conductivity. First, the charge transport of a series of purely organic porous frameworks based on H-bonding (HOFs) is described in terms of a through-space hopping of charge carriers between stacked electroactive TTF-based ligands in a zwitterionic form (Figure 1a).[3] Second, one of the first examples of perylene-based MOFs with semiconductivity is presented based on the partial oxidation of the ligand upon inclusion of I2 dopant, and promoted by a herringbone CH···π perylene-perylene stacking (Figure 1b).[4] Last, the record 3D conducting MOF based on Fe(II)/Fe(III) redox pair and tetrazole ligand Fe2(BDT)3 (Figure 1c)[5] is characterized theoretically, and compared with its polymorphs, to unveil the origin of its striking high charge transport.
Figure 1. Crystal structure of a) TTF-based MUV-20a, b) perylene-based Per-MOF, and c) tetrazole-based Fe2(BDT)3 frameworks.
References
(1) Calbo, J.; Golomb, M. J.; Walsh, A. J. Mater. Chem. A 2019, 7, 16571-16597.
(2) Xie, L. S.; Skorupskii, G.; Dincă, M. Chem. Rev. 2020, 120, 8536–8580.
(3) Vicent-Morales, M.; Esteve-Rochina, M.; Calbo, J.; Ortí, E.; Vitórica-Yrezábal, I. J.; Mínguez Espallargas, G. J. Am. Chem. Soc. 2022, 144, 9074–9082.
(4) Valente, G.; Esteve-Rochina, M.; Paracana, A.; Rodríguez-Diéguez, A.; Choquesillo-Lazarte, D.; Ortí, E.; Calbo, J.; Ilkaeva, M.; Mafra, L.; Hernández-Rodríguez, M. A.; Rocha, J.; Alves, H.; Souto, M. Mol. Syst. Des. Eng. 2022, 7, 1065-1072.
(5) Xie, L. S.; Sun, L.; Wan, R.; Park, S. S.; DeGayner, J. A.; Hendon, C. H.; Dinca, M. J. Am. Chem. Soc. 2018, 140, 7411-7414.
Elevating the Accuracy of Density Functional Theory for Condensed Phase Simulations through Machine Learning and Many-Body Techniquesvited
– Saswata Dasgupta – University of California, San Diego
Abstract
Accurately depicting the electronic structure and dynamics of condensed phases is crucial for understanding their phase behavior and reactivity. Among the quantum chemistry techniques, Density Functional Theory (DFT) is extensively employed to model the properties of condensed-phase systems, despite its high computational demands that hinder the use of more accurate modern density functionals. To address this, we introduce innovative data-driven many-body potential energy functions trained with arbitrary DFT functionals (MB-DFT), which preserve the accuracy of the parent functionals consistently from gas to condensed phases. Despite these advancements, no existing density functional has achieved the necessary accuracy to predict the properties of hydrated systems across their full phase diagram. To bridge this gap, we present the Density-Corrected SCAN (DC-SCAN) method that elevates the accuracy of the SCAN functional to the level of coupled-cluster theory, the gold standard for chemical accuracy. This method allows for accurate descriptions of aqueous systems from gas to condensed phases within our data-driven many-body DFT framework. However, like most polarizable force fields, these MB-DFT potentials cannot participate in chemical reactions. To model chemical reactions in the condensed phase, we have combined the accuracy of DC-SCAN with the capabilities of neural network potentials. This integration has resulted in the development of reactive machine-learned potentials capable of studying phenomena such as water autoionization and proton transport within confinement, facilitated by advanced enhanced-sampling techniques. Our findings provide not only an accurate estimation of the autoionization constant but also emphasize the significant role of the Grotthuss mechanism in acid/base equilibria.
Molecular Simulations of Extraterrestrial Organic Minerals
– Richard Remsing – Rutgers University
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Titan, Saturn’s largest moon, has a thick atmosphere rich in organic molecules and a cold surface temperature of 94 K. As a result, many of the organic molecules produced by photochemistry in the atmosphere condense onto the surface as organic liquids and solids. The resulting crystalline organic solids coat Titan’s surface and are referred to as cryominerals, in analogy to minerals on Earth. Cryominerals can play important roles in Titan’s surface geology, geochemistry, and even potential prebiotic chemistry. To fully understand chemical processes in these unique environments, a molecular-level picture is needed, which we are working towards using a combination of ab initio simulations and machine learning models. I will discuss our recent work modeling structure and dynamics in several Titan cryominerals, including the potential for these solids to exist in plastic crystal phases, in which molecules are translationally ordered but rotationally disordered. The disorder present in plastic crystals generally impacts important thermodynamic and mechanical properties relevant to surface processes, such as reducing elastic moduli. I will also discuss the implications of our work for understanding the properties of Titan’s surface and for understanding driving forces for prebiotic chemistry in Titan-like non-aqueous environments.
Invited 4
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Plenary 2
– Marivi Fernandez-Serra – Stony Brook University
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Sesión 2 - Thursday, August 29
More-predictive density functionals, symmetry breaking, and strong correlation
– John P. Perdew – Tulane University
Abstract
Approximate density functionals constructed to satisfy known mathematical
properties of the exact density functional for the exchange-correlation energy of a many-electron system can be predictive over a wide range of materials and molecules. The strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation [1] satisfies 17 exact constraints, and nicely describes some systems that were formerly thought to be beyond the reach of density functional theory, such as the cuprates [2]. Ground states that break the symmetry of a Coulomb-interacting Hamiltonian can be understood as dynamic density or spin-density fluctuations that drop to low or zero frequency [3,4] and so persist over long times. In many cases, symmetry breaking transforms the strong correlation in a symmetry-unbroken wavefunction into moderate correlation like that found in the uniform electron gas of high or valence-electron density (an “appropriate norm” for constraint-based approximations).
Supported by NSF DMR-1939528 and DE-SC0018331
[1] J. Sun, A. Ruzsinszky, and J.P. Perdew, Phys. Rev. Lett. 115, 036402 (2015)
[2] J.W. Furness, Y. Zhang, C. Lane, I.G. Buda, B. Barbiellini, R.S. Markiewicz, A.
Bansil, and J. Sun, Commun. Phys. 1, 11 (2018)
[3] P.W. Anderson, Science 177, 393 (1972)
[4] J.P. Perdew, A. Ruzsinszky, J. Sun, N.K. Nepal, and A.D. Kaplan, Proc. Nat.
Acad. Sci. USA 118, e2017850118 (2021).
Invited 5
– Rodrigo A. Vargas-Hernandez – McMaster University
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Invited 6
– Stefan Vuckovic – University of Fribourg
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Aplicaciones de aprendizaje automático a la ciencia de materiales
– Luis Pellegrin – Universidad Autónoma de Baja California
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Se llevará a cabo una revisión de trabajos recientes que han aplicado aprendizaje automático a la ciencia de materiales. El objetivo de la charla se centrará en conocer las ventajas, características y oportunidades que representa la sinergia entre estas dos áreas de estudio.
Machine learning electronic structures
– Michele Pavanello – Rutgers University-Newark
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Multiscale Biomolecular Simulations: From Mechanistic Insights to Cancer
– G. Andrés Cisneros – University of Texas at Dallas
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Computational biomolecular simulations based on molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) methods have become sufficiently accurate to be able to predict specific features of protein systems. We have developed various programs and tools to perform QM/MM simulations with advanced potentials, and to assess various features of biomolecular systems. We have also developed a comprehensive approach to find and characterize the impact of cancer mutants on target proteins, Our approach employs a new method for discovery and statistical validation of single nucleotide polymorphisms (SNPs) on specific genes called HyDn–SNP–S, followed by atomistic simulations via. We will present examples of the use of these approaches to investigate the structural, dynamic and mechanistic features of five DNA transaction enzymes and how they can be used for various applications including the development of new drugs or uncovering how mutations affect enzymatic catalysis.
Session 3 - Friday, August 30
Plenary 5
– Jorge Sofo – PennState University
Abstract
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Current vortices in aromatic carbon molecules
– Yenny Priscila Ortiz Acero – Universidad de Barcelona
Abstract
The local current flow through three small aromatic carbon molecules, namely, benzene, naphthalene, and anthracene, is studied. Applying density functional theory and the nonequilibrium Green’s function method for transport, we demonstrate that pronounced current vortices exist at certain electron energies for these molecules. The intensity of these circular currents, which appear not only at the antiresonances of the transmission but also in the vicinity of its maxima, can exceed the total current flowing through the molecular junction and generate considerable magnetic fields. The π electron system of the molecular junctions is emulated experimentally by a network of macroscopic microwave resonators. The local current flows in these experiments confirm the existence of current vortices as a robust property of ring structures. The circular currents can be understood in terms of a simple nearest-neighbor tight-binding Hückel model. Current vortices are caused by the interplay of the complex eigenstates of the open system which have energies close to the considered electron energy. Degeneracies, as observed in benzene and anthracene, can thus generate strong circular currents, but also nondegenerate systems like naphthalene exhibit current vortices. Small imperfections and perturbations can couple otherwise uncoupled states and induce circular currents.
Invited 10
– Andreas Goetz – University of California San Diego
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Spin Topology in Insulating Materials
– Rafael Gonzalez-Hernandes – Universidad del Norte
Abstract
In this work, we study the role of electron spin in establishing topological invariants in insulating materials. We explore how the spin valence operator, induced by the spin operator, provides crucial information about spin Chern class phases. Gapped spin valence spectra denote constant spin Chern numbers, defining materials as spin Chern insulators [1]. Conversely, changes in spin Chern numbers occur at zero spin spectrum values, characterizing materials as spin Weyl topological insulators [2]. We also introduce the average spin Chern number [3] to classify non-trivial spin transport properties in 3D topological insulators, which closely correlates with the spin Hall conductivity within the
bandgap.
[1] E. Prodan, Phys. Rev. B 80, 125327 (2009), https://link.aps.org/doi/10.1103/PhysRevB.80.125327
[2] R. González-Hernández and B. Uribe, Phys. Rev. B 109, 045126 (2024),
https://link.aps.org/doi/10.1103/PhysRevB.109.045126.
[3] R. González-Hernández and B. Uribe, arxiv: 2404.08595 (2024).
https://doi.org/10.48550/arXiv.2404.08595.
Invited 12
– Author – Adscription
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Experimental and Computational Studies of 2D Carbides and Carbonitrides (MXenes)
– Yury Gogotsi – Drexel University
Abstract
2D carbides, nitrides, and carbonitrides of early transition metals known as MXenes are among the few nanomaterials that have jumped into the limelight not only because of their exotic structure or attractive properties but also because of numerous practical applications [1]. The family of MXenes has been expanding rapidly since the discovery of Ti3C2 at Drexel University in 2011. Close to 50 different stoichiometric MXenes, dozens of solid solutions, high-entropy materials and MXenes with various surface terminations have been reported. The structure and properties of numerous other MXenes have been predicted by DFT. We are working to synthesize some of the predicted MXene compositions. The availability of solid solutions on M and X sites, multi-element high-entropy MXenes, control of surface terminations, and the discovery of out-of-plane ordered double-M o-MXenes (e.g., Mo2TiC2), as well as in-plane ordered i-MAX phases and their i-MXenes offer the potential for producing an infinite number of new 2D materials. This presentation will describe the state of the art in the field of MXene synthesis [2,3]. Synthesis-structure-properties relations of MXenes will be described [4]. The versatile chemistry of the MXene family renders their properties tunable for a large variety of energy-related, electronic, optical, biomedical, and other applications. In particular, the applications of MXenes in electrochemical energy storage and harvesting, electrocatalytic water splitting and water purification/desalination are promising [1]. However, MXene antennas, sensors, actuators, as well as coatings for EMI shielding and thermal regulation are equally attractive.
- A. VahidMohammadi, J. Rosen, Y. Gogotsi, The World of Two-Dimensional Carbides and Nitrides (MXenes), Science, 372, eabf1581 (2021).
- H. Ding, Y. et al, Chemical-scissor-mediated structural editing of layered transition metal carbides, Science, 379, 1130–1135 (2023).
- H. Shao, S. Luo, A. Descamps-Mandine, K. Ge, Z. Lin, P.-L. Taberna, Y. Gogotsi, P. Simon, Synthesis of MAX phase nanofibers and nanoflakes and the resulting MXenes, Advanced Science, 10 (1) 2205509 (2023).
- K. R. G. Lim, M. Shekhirev, B. C. Wyatt, B. Anasori, Y. Gogotsi, Z. W. Seh, Fundamentals of MXene synthesis, Nature Synthesis, 1 (8) 601-614 (2022).
Plenary Speakers
Distinguished University and Charles T. and Ruth M. Bach Professor
Drexel University
Professor
Tulane University
Professor and Department Head-Physics
University of Texas
Professor
University of Luxembourg
Professor
Stony Brook University
PennState University
Invited Speakers
Professor
Rutgers University-Newark
Principal Investigator
University of California San Diego
Professor
University of Valencia
Postdoctoral Researcher
University of California San Diego
Assistant Professor
University of Valencia
Postdoctoral Researcher
Universidad de Barcelona
Assistant Professor
University of Fribourg
Assistant Professor
Universidad Autónoma de Baja California
Professor
Universidad del Norte
Assistant Professor
Rutgers University-New Brunswick
Short Courses
Hands-on workshops (from 15:00 to 19:00 hrs, Pacific Standard Time).
Introduction to Python for IA
Dr. Luis García, CNyN-UNAM
Known for its simplicity and versatility, Python has become the language of choice for many developers and data scientists working in the field of AI. This course explores the basic AI concepts and algorithms for creating a QSAR model using Python. After completing the course students will be able to prepare data (analyze and clean), select the best features using different strategies and build classification models. As example problem we will build a QSAR model for predict activities in small compounds.
Content:
- Environment setting
- Python scientific libraries
- Data analysis
- Feature selection algorithms
- Modeling algorithms
For taking the workshop, It is desired to have basic knowledge of Python
Non-Covalent Interactions
Dr. Rodrigo Ponce Pérez, CNyN-UNAM
The non-covalent interactions (NCI) are weak interactions present in several processes that help stabilize the systems and favor chemical reactions such as hydrogen bonds, Van der Waals forces, or steric effects, among others. In this short course, we focus on studying the NCI from the point of view of the Density Functional Theory (DFT) framework. We will start with the basic concept of DFT, the origin of the NCI within the DFT, and the use of computational codes devoted to visualizing the non-covalent interactions.
The short course aims to teach the assistants the use of the critic2 software to visualize the NCI. We focus on how to graph and understand the s(ρ) vs sig(λ2)ρ plots and their corresponding NCI isosurfaces. This is with the purpose of visualize, understanding, and interpret properly the results. In the course, we address several systems where NCI appears from two molecules interacting to more complex systems.
What do we need?
-A PC with Linux software
for taking the workshop, it desired to have basic knowledge of:
-Basic Linux commands.
-Preinstall the VESTA visualization software.
-Preinstall some plotting software, such as Gnuplot.
Optical properties of materials
Dr. Jose Mario Galicia Hernandez, CNyN-UNAM
In this workshop, we will learn about the so-called “beyond-DFT” theoretical techniques used to correctly describe the excited states of systems. It is well known that standard DFT lacks accuracy when computing the electronic and optical properties of systems out of the ground state. For this reason, several approximations based on Green’s function have been developed to overcome the standard DFT limitations.
The workshop will focus on teaching the basic concepts of the GW approach to computing the electronic band gap. On the other hand, we will learn about the RPA theory for computing some optical properties, such as the real and imaginary parts of the dielectric function, as well as some other useful quantities for linear optical analysis, such as the real and imaginary parts of the refractive index, the absorption coefficient, the energy loss function, and the reflectivity. Finally, we will learn about the BSE approach, which allows us to compute the dielectric function by considering the excitonic effects.
Workshop content
- Basic concepts of DFT.
- Computation of electronic band structures within standard DFT approach.
- Basic concepts of systems out of ground state.
- Basics concepts of GW approximation.
- Exercises for computing the band gap within the GW approximations.
- Basic concepts of optical properties.
- Computation of linear optical properties within the RPA theory.
- Exercises for computing the dielectric function by using the BSE approximation.
For taking the workshop, it desired to have basic knowledge on:
- Density Functional Theory.
- Basic Linux commands.
- Preinstall the VESTA visualization software.
- Preinstall some plotting software, such as Origin Lab, Magic Plot, and Gnuplot.
- Preinstall a Worksheet software such as Excel or Open Office.
Registration
Please remember that you must specify which course you will attend.
If you are interested in the students’ session, please attach your abstract in the following form.
To attend the conference series, please wait for the Zoom link through which you will register.