Itzel Perez Trejo
About me
My research background includes performing molecular dynamics simulations of biomolecular systems, quantum molecular calculations for elucidation of mechanisms of reactions, and enhanced sampling techniques for the study of structures of nanoparticles. I have primarily focused on understanding protein–protein and protein–solvent interactions through atomistic simulations, exploring the effect of environmental changes on the conformational
ensemble of disordered proteins. Additionally, I have developed Python scripts to analyze and process simulation data, demonstrating my proficiency in computational tools and programming. I have acquired experience using several computational technics for the study of molecular interactions and structural properties, and for that reason I could contribute to the study of the role of water availability in biological systems, where hydration dynamics are critical to conformation and stability.
My teaching experience reflects a strong commitment to science education, particularly at the undergraduate level. I have consistently adapted to the pedagogical values and academic standards of the diverse institutions where I have work. Also, I co-developed instructional materials for the course Basic Mathematics for Chemical Problems through Python and for chemistry courses at the Faculty of Chemistry, UNAM. Additionally, I contributed to the creation of a faculty guide for university instructors focused on designing and delivering effective online lessons.
Computational chemist with expertise in molecular dynamic simulations, enhanced sampling and excited state calculations. Skilled in using AMBER, GROMACS, Gaussian, and Python for studying biomolecular and nanomaterial systems. Demonstrated experience in exploring protein-solvent interactions, structural stability of nanomaterials, catalysis process, and contributing to collaborative research.
Ph.D. research
Project Title: “Effect of environmental changes on the structure and dynamics of intrinsically disordered proteins from the LEA family”
This research focuses on the theoretical analysis of the effects of physicochemical environment conditions, such as: water availability, solvent polarity, and the charged state on the structure and dynamics of LEA (Late Embryogenesis Abundant) proteins and peptide derived from Arabidospis thaliana, by performing molecular dynamics (MD) and gaussian accelerated molecular dynamics (GaMD) simulations.
Force fields and water models were validated to reproduce the experimental behavior of the secondary structure of AtLEA4-2 protein both in aqueous solution and in trifluoroethanol–water mixtures. Once the methodology that better reproduce experimental data was established, the behavior of the model peptide PILEA-22 was analyzed in water and under two dehydration-mimicking conditions: trifluoroethanol–water and glycerol–water mixtures.
Finally, the impact of water availability was explored in a disordered system unrelated to the LEA protein family. For this purpose, a disordered fragment of calcitonin was randomly selected.
Project Title: “GaMD simulation as alternative in the TFE-water mixture description”
The behavior of TFE-water mixtures was studied under different model descriptions of the interactions to determine the most suitable conditions that reproduce experimentally reported properties of TFE-water mixtures. Also, we compared the employment of conventional molecular dynamics (MD) and gaussian accelerated molecular dynamics (GaMD) simulations. Our results verify that the parameters that better reproduce the experimental reports are the combination of the TIP4PD water model and GaMD simulations.
M.Sc. research
Project Title: “Stability Study of NimAgn Bimetallic Nanocluster (N= m+n and 13≤ N ≤ 127)”
This theoretical study explored the stability and preferred configurations of medium-sized NiₘAgₙ bimetallic nanoclusters. Clusters in the size range of 13 to 127 atoms were examined combining the Basin Hopping Monte Carlo algorithm with the Gupta potential. This method enabled global structure optimization and evaluation of total energies to determine the most stable atomic arrangements and compositions of these nanostructures. Therefore, stable compositions and sizes were identified by using stability parameters, such as the excess energy, stability function and difference energy between isomers, showed that binary particles are energetically favored over pure clusters for every composition, and as the cluster size increase as well the Ni fraction does in the most stable compositions.
B.Sc. research
Project Title: “Catalytic Activity and Substitution Effect of Ru[(5,5’-R-Sal2en)(PPH3)]Cl in the Hydrogenation of Cyclohexene”
The theoretical study examined the electronic effects of different R substituents on the catalytic efficiency of the Ru[(5,5'-R-sal2en)(PPh3)2] complex in the cyclohexene reduction cycle, both R substituents with electron-donating and electron-accepting were evaluated. The mechanism of reaction was purposed and supported by structural optimization as well as frequency calculations using density functional theory (DFT).
Teaching Experience:
National Autonomous University of Mexico (UNAM)
Faculty of Chemistry - Department of Theoretical Physics and Chemistry
Teacher of Structure of Matter
Teaching Assistant of Physics
University of the Valley of Mexico (UVM)
Department of Health Science
Teacher of Calculus
Teacher of Thermodynamics
Technological University of Mexico (UniTEC)
Teacher of General Chemistry