Efe Ali Mert

About CHAOS 2026 (19th Conference on Nonlinear Analysis and Modeling)

Sun, 01 Mar 2026 00:00:00 +0000

Coming soon.

CHAOS2026 Accepted Oral Presentation

Sun, 01 Mar 2026 00:00:00 +0000

Abstract accepted for oral presentation at the Chaotic Modeling and Simulation International Conference (CHAOS2026).

LIPhy's photo exhibition

Fri, 23 Jan 2026 00:00:00 +0000

Transport of water molecules in a microporous polymer

Molecular dynamics simulation showing water molecules (in red and white) adsorbed within a polymer with molecular-sized pores (in gray). These simulations are used to study the collective transport properties of the molecules, and the results can be compared with those obtained from neutron scattering experiments

LAMMPS Tutorials has just been published

Wed, 01 Oct 2025 00:00:00 +0000

The content of lammpstutorials.github.io has just been published in my favorite journal, the Living Journal of Computational Molecular Science (LiveCoMS).

LiveCoMS is a diamond open access journal (free to read and free to publish) that allows articles to evolve over time with updated versions. This was the ideal choice for these LAMMPS tutorials, which have been constantly growing and improving since their creation about 5 years ago.

I’m also glad to see that the number of contributors to LAMMPS tutorials keeps expanding, now even including members of the LAMMPS development team.

See the content here: https://livecomsjournal.org/index.php/livecoms/article/view/v6i1e3037

Marcelle B. M. Spera

Mon, 01 Sep 2025 00:00:00 +0000

Research associate on the MicroSep project since September 2025.

New JCJC ANR project - Fluid separation by microporous material

Wed, 27 Aug 2025 00:00:00 +0000

This marks the official start of the JCJC ANR project `MicroSep’. Our goal is to explore fluid mixtures transport in microporous materials using molecular simulations.

DNA-Based One-Time Pad Encryption with Chaotic Systems

Fri, 01 Aug 2025 00:00:00 +0000

This project explores a novel encryption pipeline that combines classical one-time pad logic with DNA coding and chaos-based key generation.

The system integrates the Mandelbrot set, Logistic map, Lorenz system, and Henon map to improve randomness and key sensitivity.

It was developed and iterated through regional and national competition stages, earning high-level recognition in mathematics-focused research contexts.

Award: TUBITAK 2204A National Silver (Mathematics Category).

ISEF 2026 Selection Stage (Invited)

Fri, 01 Aug 2025 00:00:00 +0000

Invited to the ISEF selection stage with the project titled “An Enhanced DNA-Based One-Time Pad Encryption Method Using Mandelbrot Set and Chaotic Systems.”

TUBITAK 2204A National Finals

Sun, 01 Jun 2025 00:00:00 +0000

In this post, I share my personal experience and observations from the TUBITAK 2204A National Finals.

Before the Presentation

First, I should mention that I did not stay at the hotels arranged by TUBITAK. I stayed in a different hotel with my family, so I cannot comment in detail on official accommodation, though I heard positive things.

I was very excited on the first day because I did not know what to expect, and the exhibition area was much larger than the regional one. For those who do not know, the finals are held in Ankara at the ATO Congresium.

When I arrived, I immediately looked for my stand. In many fields, two regional first-place projects had advanced. In my field, two students named Nil and Ali were also there. We had worked on related topics and both used chaotic systems. In regionals, we were put in direct competition; in the finals, we were placed side by side.

Not much happened on day one, and that actually helped me reduce stress. My main concern was the next day: I had a 35-slide presentation and needed to deliver it clearly in 10 minutes. I practiced with my mother while timing every run, which helped a lot. I also listened to other projects in my field.

Presentation Day

Presentation day was intense. They would evaluate 9 people on the first day and 9 on the second day; I was 17th, so my turn was on day two. People in my field were very supportive. We even shared jury questions with each other.

Apparently this did not happen in every field. For example, one student told me that in psychology people hid details from each other. I personally think that level of competition is unnecessary. Some people win, some do not, but being able to return home with a positive feeling is already valuable.

Normally there are three juries, but this year an additional jury was added in my field. They visited all stands and asked questions. Some questions were difficult and included data I did not have with me; I answered as best as I could.

When my turn came, I was taken to the third floor and waited for the previous students to finish. Staff students there chatted with us and asked questions while we waited.

Inside the jury room, there were four jurors. They gave me a short setup time and started a 10-minute timer when I said I was ready. The unusual part was that they tried to ask questions during the presentation. I asked if I could answer after finishing my flow, and they were understanding.

After the presentation, we moved to Q&A. Unlike regionals, this time the questions felt focused on truly understanding the project. At one point, one juror asked a question and another juror answered it from a different perspective. They were clearly engaged.

At the end, I briefly mentioned the parts we still planned to improve and thanked them for their time.

Days After the Presentation

After my presentation, I visited middle-school projects as well. Many of them were impressive. I also had one odd interaction where a mentor teacher criticized us unfairly; I did not take it seriously.

They also made dismissive comments about other projects, and I ended up defending peers from my field. My advisor suggested we leave, and that was the right choice.

Beyond that, I mainly enjoyed seeing students from all regions of Turkey coming together for science. That atmosphere was genuinely inspiring.

Award Ceremony

At 10 AM, my mother, my advisor, and I were all at the ceremony. I was extremely stressed. First places were announced; my name was not there. Encouragement awards were announced; still not there. Then third places were announced; still not there.

I never truly expected second place. I thought either first or third would happen, if anything. I had invested an enormous amount of effort into this project, and that moment felt emotionally overwhelming.

When second place in mathematics was announced and I heard the beginning of my school name, I realized it was me. I had been selected as the national mathematics runner-up. I could not process the moment; I was laughing and crying at the same time.

One thing that made me sad was that Ali and Nil did not receive an award despite their effort. I was also deeply empathetic toward students who felt disappointed, because I know how heavy that moment can feel.

Closing

Thank you for reading.

I also want to sincerely thank my advisor Tutku Dilara Yilmaz, lecturer Ali Cihan Keles from Yeditepe University, and my family for supporting me throughout this journey.

Running for the CNRS National Committee – Section 08

Sun, 25 May 2025 00:00:00 +0000

I am running as a candidate for the Collège B1 of the new Section 08 of the CoNRS:
Physique de la matière complexe et du vivant (Physics of Complex Matter and Life).

Personal statement (See French version here below)

Recruited at LIPhy in 2023 by the former Section 11, I study soft matter systems (polymers, bio-inspired systems, nanoporous materials), with a focus on the behavior of molecules at interfaces. I primarily use molecular simulation, and my background, which combines simulations and experiments, facilitates my collaborations with experimentalists (NMR, neutrons, X-rays). I also dedicate time to creating open and freely accessible educational content for both beginners and experts.

The CNRS remains one of the few institutions that guarantees independent research that is not subject to trends—an essential condition for producing critical, open, and long-term knowledge. In this regard, the National Committee plays a fundamental role as a space for scientific collegiality, debate, and counterbalance.

As an elected member, I am committed to fully dedicating myself to the National Committee and to contributing to recruitment and evaluation processes in a thoughtful way, not based solely on bibliometric indicators. I will work to equally defend interdisciplinarity, established disciplines, and emerging themes.

Profession de foi (In French)

Recruté au LIPhy en 2023 par l’ancienne Section 11, j’étudie les systèmes de la matière molle (polymères, systèmes bio-inspirés, matériaux nanoporeux), avec un intérêt pour le comportement des molécules aux interfaces. J’utilise principalement la simulation moléculaire, et mon parcours mêlant simulations et expériences facilite mes collaborations avec les expérimentateurs (RMN, neutrons, rayons X). Je consacre aussi du temps à la création de contenus pédagogiques libres et ouverts pour débutants et experts.

Le CNRS reste l’un des rares organismes à garantir une recherche indépendante et non soumise aux effets de mode, conditions indispensables à la production de savoirs critiques, ouverts et de long terme. À ce titre, le Comité National joue un rôle fondamental en tant qu’espace de collégialité scientifique, de débat et de contre-pouvoir.

En tant que membre élu, je m’engage à me consacrer pleinement au Comité National et à contribuer aux recrutements et aux évaluations de façon raisonnée et non fondée uniquement sur des indicateurs bibliométriques, afin de défendre de manière égale l’interdisciplinarité, les disciplines reconnues et les thématiques émergentes.

A Guide to Preparing a TUBITAK 2204A Project

Thu, 15 May 2025 00:00:00 +0000

I wrote this post to help students who are currently preparing a project.

Below, I explain what you should do step by step. I hope this helps you build your own roadmap.

1. Choosing Your Field and Topic

First, decide which field you want to work in. Then comes one of the hardest parts: choosing an original topic. Write down your ideas and investigate them.

Originality is not only about the title; your approach also matters. If you do not add a meaningful original contribution, your project may feel like it was built just to participate. Your project should solve a clearly defined problem.

If you want to increase your project’s impact, interdisciplinary work is a strong option. In my case, my main field was mathematics, and I combined chaotic systems with DNA-inspired ideas to build an encryption method.

2. Literature Review

After choosing your topic, your next step is a solid literature review.

Define good keywords and search them on platforms such as Google Scholar, DergiPark, TRDizin, ScienceDirect, and PubMed. You can also use AI tools to brainstorm keywords. Review what others did, then identify your own contribution.

It helps to archive papers and revisit them multiple times.

3. Project Plan and Method

Once your plan becomes clearer, store all data and references in an organized way (for example, in Drive). You may need them later for analysis, visuals, or your final report.

Find an academic mentor if possible. Do not assume people will not reply. Build a list of academics in your target area (university, expertise, department, contact info) and email them one by one. Platforms like YOKAKADEMIK can help.

4. Report Writing

Be very careful in this stage. I personally wrote my report in an academic-paper style, although styles may vary. I strongly recommend clear academic language.

Do not leave the report to the last minute. Just like a paper, it needs iteration. In my case, I drafted the methods section multiple times before finalizing it.

I recommend starting from the abstract. It helped me set direction for the methods and the rest of the document.

“Should we write the report only after everything is done?” In my experience, the best approach is writing it in parallel with your project.

Even if your project is strong, a poorly structured report can prevent it from being understood. Always follow the latest official TUBITAK guidelines and templates.

Citations are critical. One common mistake is insufficient in-text citation, which can reduce your ethics score.

5. Evaluation Criteria (Summary)

Reports are scored out of 100 using 20 criteria (5 points each). Main dimensions include:

Feasibility (methods and sub-goals)
Creativity
Originality
Ethical compliance
Results and recommendations
Target audience
Intervention/product
Comparison
Output
Time management

6. Presentation and Poster Preparation

Prepare your poster and slide deck carefully. A good flow is: introduction, objective, methods, findings, and conclusions. Do not memorize every word, but do not rely on full improvisation either.

Mastery of your topic makes a huge difference, especially during jury questions. Do not fear questions; they are asked to understand your project. Emphasize applicability and originality.

After regional rounds, present your improvements in the final presentation even if they were not in your initial report.

Personal Tips

This is a long process; 3 months can be short for producing something truly original.
Keep regular communication with your advisor.
Explain your project in a clear, simple, and scientific way.

Good luck!

Sasha (Aleksandra) Ardaševa

Thu, 01 May 2025 00:00:00 +0000

Research associate on the MIAM-CO2 project since May 2025.

TUBITAK 2204-A Mathematics National 2nd Place

Thu, 01 May 2025 00:00:00 +0000

Awarded national 2nd place in the mathematics category at the TUBITAK 2204-A High School Students Research Projects Competition.

Objective ADHD Analysis with EEG and Ensemble Machine Learning

Tue, 01 Apr 2025 00:00:00 +0000

This project investigates objective differentiation of ADHD and healthy control groups using EEG signals and machine learning.

A multi-feature pipeline (including enhanced Higuchi fractal dimensions, spectral features, Hjorth parameters, and statistical descriptors) was combined with ensemble classifiers and cross-validation.

The study focuses on building reproducible, data-driven decision support methods for neurodiagnostic workflows.

I am migrating to the Fediverse

Sat, 01 Mar 2025 00:00:00 +0000

Starting now, I am migrating to the Fediverse and will no longer be publishing on X. This also applies to the communication associated with the LAMMPS Tutorials organization. The main exceptions are my LinkedIn and Youtube accounts that I am keeping (for now).

The Fediverse is a network of social platforms. Its decentralized nature prevents corporate monopolies and censorship.

You can follow me on Mastodon (https://mastodon.social/@simongravelle), where I will primarily post about science, molecular simulations, and open-source projects.

TUBITAK 2204-A Mathematics Regional 1st Place

Sat, 01 Feb 2025 00:00:00 +0000

Awarded regional 1st place in the mathematics category at the TUBITAK 2204-A High School Students Research Projects Competition.

New ANR project - CO₂ capture by foam

Fri, 10 Jan 2025 00:00:00 +0000

This marks the official start of an ANR project led by Elise Lorenceau, in collaboration with the CEA. Together, we aim to demonstrate the feasibility of a foam reactor for CO₂ capture.

Thu, 02 Jan 2025 00:00:00 +0000