Pooja Sarngadharan- PhD student
- Constructor University
Pooja Sarngadharan
- PhD student
- Constructor University
About
5
Publications
871
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46
Citations
Introduction
Current institution
Education
August 2014 - June 2019
Field of study
- Major Chemistry and minor biology
Publications
Publications (5)
In this study, the site energy fluctuations, energy transfer dynamics, and some spectroscopic properties of the minor light-harvesting complex CP24 in a membrane environment were determined. For this purpose, a 3 μs-long classical molecular dynamics simulation was performed for the CP24 complex. Furthermore, using the density functional tight bindi...
Besides absorbing light, the core antenna complex CP43 of photosystem II is of great importance in transferring excitation energy from the antenna complexes to the reaction center. Excitation energies, spectral densities and linear absorption spectra of the complex have been evaluated by a multiscale approach. In this scheme, quantum mechanics/mole...
Light harvesting as the first step in photosynthesis is of prime importance for life on earth. For a theoretical description of photochemical processes during light harvesting, spectral densities are key quantities. They serve as input functions for modeling the excitation energy transfer dynamics and spectroscopic properties. Herein, a recently de...
Light harvesting as the first step in photosynthesis is of prime importance for life on earth. For a theoretical description of photochemical processes during light harvesting, spectral densities are key quantities. They serve as input functions for modeling the excitation energy transfer dynamics and spectroscopic properties. Herein, a recently de...
SxIP is a microtubule tip localizing signal found in many +TIP proteins that bind to the hydrophobic cavity of C-terminal domain of End binding protein 1 (EB1), and then positively regulate the microtubule plus-end tracking of EBs. However, the exact mechanism of microtubule activation of EBs in the presence of SxIP signaling motif is not known. He...
Questions
Question (1)
I was trying to model a system with several chlorophyll molecules and carotenoids. For adding hydrogens, I used chimera which is working perfectly well for carotenoids. However, the chlorophyll molecules are not getting pronated in the desired manner. There are discrepancies in the number of hydrogen atoms. Sometimes, these packages fails to identify the valencies correctly. The results were even worse when Pymol is used. Previously, I used HAAD for this purpose. Unfortunately, HAAD is not giving any outputs this time (only getting 0 KB files). I need to add hydrogens to these molecules before setting up a system in GROMACS. How can I model these chlorophyll molecules accurately?
