arXiv subjects

Mahdi Tavakol

Publications and source records attributed to Mahdi Tavakol.

4 recordsLinked to original sources

arXiv2026

An Efficient Approach for Calculating Free Energy in Molecular Dynamics: Demineralization of Hydroxyapatite as a Case Study

Despite the strength of Molecular Dynamics simulations in providing insights into the microscopic details of phenomenon in many fields in materials science, physics and biology, the biggest barrier is its limited timescale which is several orders of magnitude lower than the timescale of the real-world processes and phenomena being modeled. Free energy calculations are designed as a remedy to this problem that in theory can overcome this barrier. This is particularly relevant for biomineralisation processes such as tooth mineral formation and dissolution, while reflecting a broader challenge in accurately modelling rare events and long-timescale phenomena across complex molecular systems. However, due to the novelty of the field, a number of questions remain outstanding pertaining to the best practice of applying this method. The non-equilibrium work approach based on the Jarzynski equation is one of the most promising free energy calculation methods. However, the biggest challenge for the broader use of this method is the question of how many simulations are required for an accurate free energy estimation. Comparing the free energy results with very long reversible pulling simulations of atom clusters from the surface, each taking 75 days on the 48-core Intel Xeon Platinum 8268 CPUs, in this study we showed that this question is irrelevant and higher quality and better equilibrated initial structures is the proper approach than simply based on the number of simulations. We designed a new adaptive free energy calculation methodology which combines high quality, high computational cost free energy values with lower quality, lower cost values to build up the entire free energy profile. In the best case scenario this method lowers manifold the computational cost required for the non-equilibrium work free energy calculations compared to both the regular method and the reversible simulation.

cond-mat.mtrl-sci↗

arXiv2026

Uncovering the role of ionic doping in hydroxyapatite: The building blocks of tooth enamel and bones

Hydroxyapatite (HAp) is the primary mineral component of various mineralized tissues in the human body, including bone and teeth, where it performs critical roles of structural support and load transmission. In the context of dental health, the two most crucial properties of HAp are mechanical stability, which ensures resistance to forces, and chemical stability, which preserves surface integrity in acidic environments. During early stages of human evolution, e.g. when teeth were used to crush uncooked food, mechanical stability was of paramount importance. However, with changes in diet and lifestyle, the principal origins of tooth damage and loss shifted towards bacterially mediated chemical attack, known as tooth decay, or caries. To enhance the chemical stability, ion doping has emerged as a particularly significant approach, and it lies at the focus of the present study. A Molecular Dynamics (MD) framework was developed to investigate the effects of ion doping on the chemical and mechanical stability of HAp and to identify optimal doping candidates. The framework combines conventional MD with Steered Molecular Dynamics (SMD), Thermodynamic Integration (TI) and uniaxial compression test simulations to provide comprehensive insights into the doping process. The findings revealed surface atoms as the most viable candidates for doping, as demonstrated by SMD and conventional MD simulations. Notably, TI calculations have identified magnesium ions as a better candidate among the ions considered here for enhancing the chemical stability of HAp. The results presented in this study offer valuable guidelines for synthesizing HAp-based substituent materials with properties tailored to meet the demands of modern dental applications such as implant coatings, enamel remineralization agents and restorative materials.

cond-mat.mtrl-sci↗

arXiv2025

Comparative molecular dynamics simulations of charged solid-liquid interfaces with different water models

Aqueous solid-liquid interfaces (SLI) are ubiquitous in nature and technology, often hosting molecular-level processes with macroscopic consequences. Molecular dynamics (MD) simulations offer a tool of choice to investigate interfacial phenomena with atomistic precision, but there exists a large number of water models, each optimised for a different purpose. Here we compare the ability of common water models to accurately simulate the interface between a charged silica surface and an aqueous solution containing NaCl. We first compare the bulk dielectric constant of water and its dependence on salt concentration for SPC/Fw, SPC/e, TIPS3p, H2O/DC, TIP3P-Fw, OPC3, TIP3P, TIP3P-FB, TIP3P-ST, FBA/e, and TIPS3p-PPPM, revealing large variations between models. Simulating the interface with silica for the most suitable water models (SPC/Fw, H2O/DC, TIP3-ST and TIPS3p-PPPM) show some intrinsic consistency with continuum predictions (Poisson-Boltzmann) whereby the free energy minima obtained from MD and the analytical model are in agreement, provided the latter includes the MD-determined total charge of ions in the Stern layer and dielectric constant. This consistency stands even for water models with a dielectric constant off by 100%. For salt concentrations higher than 0.21 M NaCl, the formation of random ion-ion pairs limits the reproducibility of the MD results and the applicability of the analytical method. The results highlight the applicability of the analytical model down to the nanoscale, provided a priory knowledge of the Stern layer charge is available. The findings could have significant implications for MD simulations of SLIs, especially at charged or electrified interfaces.

cond-mat.soft↗

arXiv2020

Mechanical properties of graphene oxide: the impact of functional groups

In the current study, mechanical characteristics of graphene oxide (GO) as a promising substitute of graphene are systematically studied through molecular dynamics simulation. For this purpose, several GO samples having different concentrations of epoxide and hydroxyl functional groups are considered. The results reveal that increasing the epoxide coverage causes a noticeable deterioration in the mechanical characteristics of GO systems. This change is correlated with the increase of the formation of ripples in the structure upon increasing the epoxide coverage. Moreover, investigating the bond lengths in the system, it is concluded that the higher epoxide percentage leads to an increase in the length of single and hybrid resonance bonds leading to an overall deterioration of the mechanical properties of GO samples. Additionally, our results demonstrate that high concentration of functional groups can lead to a negative Poisson ratio. Increasing the amount of hydroxyl groups shows the same declining effect on the Young modulus. In a graphene system containing both epoxide and hydroxyl groups, it is deduced that a higher percentage of the former can result in a higher residual strain because of the formation of more ripples within the system.

cond-mat.mtrl-sci↗