Fifty Years of Molecular Simulations at UAM and in Mexico
Bibliographic record
Abstract
Molecular simulation methods are the bridge between molecular interactions and the macroscopic properties of matter. The equations of statistical mechanics give the probabilistic method of Monte Carlo while those of Newton are the bases of Molecular Dynamics, which is deterministic. A molecular simulation predicts the movement of molecules and hundreds of physicochemical properties can be obtained to understand its behavior at different thermodynamic conditions. The molecular simulation methods were developed in the 1950s in United States of America and in the 1980s in Mexico, where Universidad Autónoma Metropolitana (UAM) was a pioneer. It is a multidisciplinary field that involves mathematicians, chemists, physicists, engineers from different disciplines, biologists, computer scientists, etc. Supercomputers have played an important role in its development. Currently, the United States, China and the European Community have everyone more than 100 supercomputers in the TOP500 ranking, while Canada and Brazil have 10, Spain 3, Argentina 1 and Mexico none. These resources allow increasing the training capabilities, the production of research articles, the organization of academic events, etc. In this work, we make a review of the development of molecular simulations at UAM and in Mexico. The diffusion and promotion of this research field has been undertaken by academic leaders from several universities. We have organized 12 Molecular Dynamics Workshops nationwide to teach and put the basic concepts into practice and 13 international Meetings on Molecular Simulations to discuss the state of the art in research projects. The number of articles in molecular dynamics grows exponentially over time; in 2023, more than 250,000 were published worldwide. Mexico contributed 10 % and the UAM 10 % of those published in Mexico. There are more than 32 Mexican leaders living in Mexico who have published around 120 articles with at least 100 citations, according to Web of Science. About 70 % belong to the National System of Researchers at levels III and Emeritus. The research lines range equations of state in liquids, phase equilibrium, development of simulation methods and force fields, polar fluids, electrolytes, colloids, polymers, drug/protein interaction, protein folding, among others. Resumen. Los métodos de simulación molecular son el puente entre las interacciones moleculares y las propiedades macroscópicas de la materia. Las ecuaciones de la mecánica estadística dan el método probabilístico de Montecarlo mientras que las de Newton son las bases de la Dinámica Molecular, que es determinista. Una simulación molecular predice el movimiento de las moléculas y se pueden obtener cientos de propiedades fisicoquímicas para comprender su comportamiento en diferentes condiciones termodinámicas. Los métodos de simulación molecular se desarrollaron en la década de 1950 en Estados Unidos de América y en la década de 1980 en México, donde la Universidad Autónoma Metropolitana (UAM) fue pionera. Es un campo multidisciplinario que involucra a matemáticos, químicos, físicos, ingenieros de diferentes disciplinas, biólogos, informáticos, etc. Las supercomputadoras han jugado un papel importante en su desarrollo. Actualmente, Estados Unidos, China y la Comunidad Europea cuentan con más de 100 supercomputadoras en el ranking TOP500, mientras que Canadá y Brasil tienen 10, España 3, Argentina 1 y México ninguno. Estos recursos permiten incrementar las capacidades de formación, la producción de artículos de investigación, la organización de eventos académicos, etc. En este trabajo hacemos una revisión del desarrollo de simulaciones moleculares en la UAM y en México. La difusión y promoción de este campo de investigación ha sido llevada a cabo por líderes académicos de varias universidades. Hemos organizado 12 Talleres de Dinámica Molecular a nivel nacional para enseñar y poner en práctica los conceptos básicos y 13 Simposios internacionales sobre Simulación Molecular para discutir el estado del arte en proyectos de investigación. El número de artículos sobre dinámica molecular crece exponencialmente con el tiempo; en 2023, se publicaron más de 250.000 en todo el mundo. México aportó el 10 % y la UAM el 10 % de los publicados en México. Hay más de 32 líderes mexicanos viviendo en México que han publicado alrededor de 120 artículos con al menos 100 citas, según Web of Science. Alrededor del 70 % pertenece al Sistema Nacional de Investigadores en los niveles III y Eméritos. Las líneas de investigación abarcan ecuaciones de estado en líquidos, equilibrio de fases, desarrollo de métodos de simulación y campos de fuerza, fluidos polares, electrolitos, coloides, polímeros, interacción fármaco/proteína, plegamiento de proteínas, entre otras.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".