I'm Cahit Dalgicdir

Computational Researcher

Focused on Molecular Dynamics Techniques on

Chemical and Biological Experimental Systems

Hello, I am Cahit Dalgicdir

Born and grew up in Istanbul, Turkey. Postdoctoral computational researcher working on polymers and peptides using molecular dynamics and other computational methods.

I currently work at Thermo-Fluids & Interfaces (previously Center of Smart Interfaces) in Technical University of Darmstadt, in Germany with Prof. van der Vegt in the Computational Physical Chemistry group.

I am interested in conformational transitions, understanding mechanisms and driving forces for such transitions through computational techniques such as molecular dynamics, or advanced sampling techniques. I also develop working coarse-grain models that can reproduce such behaviors.

Currently, I am working on cononsolvency of PNIPAM in water/methanol solutions with Dr. Francísco Rodriguez Ropero.

Selected Projects

Here's a list of some of my studies.

Cononsolvency of PNIPAM in Aqueous Methanol Solutions

Folding of an LK Peptide

Aggregation of LK Peptides

Coarse-Graining EALA Peptide

Two-state Coarse-Grain Model of Diphenylalanine

Two-state Coarse-Grain Model of LK Peptide

Decreasing Oxygen Permeability of PET/EVOH bottles

Curing of Epoxy Resin via Ultraviolet light

Research Topics

My work can be grouped in a number of subjects.

Polymer Solution Behavior

Cononsolvency of Poly-(N-isopropylacrylamide) in water/methanol solution

           

Protein/Peptide Folding

Folding mechanisms of proteins & peptides

Model Building

Building working models for environment dependent conformational transition

Surface Effects & Ions

Effects of charged ions on aqueous surfaces & interfaces

Coarse-Graining

Building low resolution coarse-grain models of polymers & peptides that exhibit similar structural and thermodynamic behaviors compared to their all atomistic references

Supervision

Research advice to bachelor & master students

Skills & Expertise

Learning is the new skill. Imagination, creation and asking new questions are at its core.

— Sugata Mitra

Molecular Dynamics

Python

Shell Scripting

Linux

Data Analysis

C, C++, Java

RESUME

Work Experience
2006 - Now

2015 - Now

Postdoctoral Fellow - TU Darmstadt

With Prof. Nico van der Vegt at Center of Smart Interfaces
Working on cononsolvency of PNIPAM in water/methanol solutions, ion effects at aqueous surfaces, coarse-grain models of polymer transitions

Teaching: Computer Applications in Chemistry, Physical Chemistry Supervision: 1 master thesis, 2 bachelor theses, and 3 master practicals

2014 - 2015

Postdoctoral Fellow - University of Konstanz

With Prof. Christine Peter in Department of Chemistry
Studied peptide folding in different environments, and analyzed the underlying driving forces, developed working two-state coarse-grain models for short peptides that adopt different secondary structures in different environments

Teaching: Computational Chemistry

2009 - 2014

Teaching Assistant -Koc University

Teaching: Introduction to Probability and Statistics, Statistics for Engineers, Introduction to Computational Science and Engineering (using Python), Intermolecular and Surface Forces, Introduction to Programming (using Java), Introduction to Computer Programming with C

2007 - 2009

Teaching Assistant - SABANCI UNIVERSITY

Teaching: Computational Techniques for Materials Science, Polymer Synthesis, Polymer Engineering, Composite Materials, Material Characterization

Education
2002 - 2012

2009 - 2014

Computational Sciences and Engineering

Studied environment dependent structural behavior of short peptides, developed working models of environment-induced conformational transition displayed folding mechanism of a synthetic leucine-lysine peptide

2007 - 2009

Materials Science and Engineering

Developed PET films with enhanced barrier properties using, processed them using twin screw extrusion and film casting, applied a number of material characterization techniques to determine their physical and chemical properties .

2002 - 2006

BACHELOR - SABANCI UNIVERSITY

Materials Science and Engineering

Developed an epoxy resin with clay mixture with enhanced mechanical properties for paint coatings that can be cured by ultraviolet light to save energy, measured the mechanical and optical properties of the coating using a number of characterization techniques.

Publications

A multi-state coarse grained modeling approach for an intrinsically disordered peptide

F Ramezanghorbani, C Dalgicdir, M Sayar The Journal of Chemical Physics 2017

Computational Calorimetry of PNIPAM Cononsolvency in Water/Methanol Mixtures

C Dalgicdir, F Rodríguez-Ropero, NFA van der Vegt The Journal of Physical Chemistry B 2017

Representing environment-induced helix-coil transitions in a coarse grained peptide model

C Dalgicdir, C Globisch, M Sayar, C Peter The European Physical Journal Special Topics 2016

Conformation and Aggregation of LKα14 Peptide in Bulk Water and at the Air/Water Interface

C Dalgicdir, M Sayar The Journal of Physical Chemistry B 2015

Tipping the scale from disorder to alpha-helix: folding of amphiphilic peptides in the presence of macroscopic and molecular interfaces

C Dalgicdir, C Globisch, M Sayar, C Peter PLoS computational biology 2015

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

C Dalgicdir, C Peter, M Sayar The Journal of Chemical Physics 2013

Oxygen Gas and Water Vapor Permeability of Biaxially Stretched Poly (ethylene terephthalate)/Poly (ethylene-co-vinyl alcohol) and Poly (ethylene terephthalate-co-isophthalate)/Poly (ethylene-co-vinyl alcohol) Blend Films

I, Ozen, C Dalgicdir Polymer-Plastics Technology and Engineering 2012

Improvement in gas permeability of biaxially stretched PET films blended with high barrier polymers: The role of chemistry and processing conditions

İ Özen, G Bozoklu, C Dalgıçdir, O Yücel, E Ünsal, M Çakmak, YZ Menceloglu European Polymer Journal 2010

Effect of Organoclay on the Physical Properties of UV-Curable Coatings

F Inceoglu, C Dalgicdir, YZ Menceloglu ACS Book Chapter 2009

Contact Me

Have a project you'd like to discuss?

Say
Hello

CahitDalgicdir

dalgicdir@cpc.tu-darmstadt.de