Saranya Vasudevan

Saranya Vasudevan
Istituto Italiano di Tecnologia | IIT · Computational mOdelling of NanosCalE and bioPhysical sysTems (CONCEPT) Lab

Doctor of Philosophy

About

14
Publications
3,111
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96
Citations
Introduction
Experienced Senior Researcher with a demonstrated history of working in Biophysics. Skilled in Computational Physics, Molecular Dynamics, Virtual Screening, Peptide and Protein designing, Density Functional Theory, Molecular Docking and modelling. Strong research professional with a Doctor of Philosophy (Ph.D.) focused in Molecular Quantum Mechanics from Bharathiar University.
Additional affiliations
September 2015 - June 2021
Bharathiar University
Position
  • PhD Student
Education
November 2012 - November 2013
Bharathiar University
Field of study
  • Molecular Quantum Mechanics
March 2010 - April 2012
P.K.R. Arts College for Women
Field of study
  • Physics
March 2007 - April 2010

Publications

Publications (14)
Article
Full-text available
The drug target protein β-secretase 1 (BACE1) is one of the promising targets in the design of the drugs to control Alzheimer’s disease (AD). Patients with neurodegenerative diseases are increasing in number globally due to the increase in the average lifetime. Neuro modulation is the only remedy for overcoming these age related diseases. In recent...
Article
Full-text available
In these studies, we designed and investigated the potential anticancer activity of five iron(II) cyclopentadienyl complexes bearing different phosphine and phosphite ligands. All complexes were characterized with spectroscopic analysis viz. NMR, FT–IR, ESI–MS, UV–Vis, fluorescence, XRD (for four complexes) and elemental analyses. For biological st...
Article
Full-text available
Cognitive functions are lost due to the rapid hydrolysis of acetylcholine including Acetylcholinesterase (AChE) and Butyrylcholinesterase (BChE). Marine algae-derived compounds were reported for their neuroprotective activities and hence they can be utilised for treating neurodegenerative ailments like Alzheimer’s Disease and Parkinson’s Disease wh...
Article
Full-text available
Marine algae-derived compounds were reported for their neuroprotective activities, hence they can be utilised for treating neurodegenerative ailments like Alzheimer’s Disease and Parkinson’s Disease. Marine algae are potential sources of useful compounds for the pharmaceutical, medical and cosmetics industries. Molecular Docking study has been perf...
Article
Full-text available
In these studies, we designed and investigated cyto- and genotoxic potential of five ruthenium cyclopentadienyl complexes bearing different phosphine and phosphite ligands. All of the complexes were characterized with spectroscopic analysis (NMR, FT-IR, ESI-MS, UV-vis, fluorescence and XRD (for two compounds)). For biological studies, we used three...
Article
Full-text available
The quest to find new inhibitors of biologically relevant targets is considered an important strategy to introduce new drug candidates for the treatment of neurodegenerative diseases. A series of (aminomethyl)benzylphosphonates 8a–c and their metallocarbonyl iron 9a–c and ruthenium 10a–c complexes were designed, synthesized, and evaluated for their...
Article
The interaction of two stereoisomeric flavanols (+) catechin (CT) and (-) epicatechin (ECT) with bovine serum albumin (BSA) has been studied using UV-Vis absorption and fluorescence spectroscopy. The binding affinity between flavanols and BSA is investigated through fluorescence quenching. Fluorescence study shows that both flavanols exhibit a stro...
Article
One of the main causes for Alzheimer disease is the abnormal self-assembly of the amyloid-beta (Aβ) peptide, which in turn forms a toxic β-rich aggregation. A recent study suggests that gold nanoparticles (AuNPs) can inhibit the Aβ aggregation. Nevertheless, the effects of AuNPs on Aβ peptide system are still ambiguous and needs exploration that is...
Article
Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO2, SO2 and NO2 that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin trigg...
Article
Dengue virus is becoming a major global disease; the envelope protein is the major target for vaccine development against Dengue. Nowadays, the attention has focused on developing inhibitors based on Papain is a promising target for treating Dengue. In the present work, the theoretical studies of E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 a...
Article
A quantum chemical investigation is performed to understand the adsorption behaviour of DNA/RNA base pairs onto the defective (Di-Vacancy (DV) and Stone-Wales (SW)), boron (B) and silicon (Si) defect-dopant graphene (B-DV, Si-DV, B-SW, and Si-SW) sheets using density functional theory (DFT). The stability of DNA/RNA base pairs on the Si-SW sheet is...
Article
Full-text available
Here, a theoretical and comprehensive study of the structural features and interaction properties of viral protein 40 is being briefed out to understand the mechanism of Ebola virus (EV) with structural and orbital analysis. In general, viral protein 40 is the key protein for the oligomerization, the N-terminal loop region in the viral protein 40 a...

Questions

Questions (6)
Question
Which laptop should I buy (latest model) for working in computational physics?
For performing molecular dynamics simulation, docking, DFT and modelling etc
Question
Hi users,  I want to create an itp file for my ligand (ligand with ruthenium) complex, im using MCPB.Py for generating itp for my structure during the process i got the following error kindly please help. MCPB.py -i dna.in -s 3 The input file you are using is : dna.in The following is the input variable you have: The variable ion_ids is :  [1201] The variable ion_info is :  [] The variable ion_mol2files is :  ['Ru.mol2'] The variable original_pdb is :  complex_fixed_h.pdb The variable add_bonded_pairs is :  [] The variable add_redcrd is :  0 The variable additional_resids is :  [] The variable anglefc_avg is :  0 The variable bondfc_avg is :  0 The variable chgfix_resids is :  [] The variable cut_off is :  2.8 The variable force_field is :  ff19SB The variable frcmod_files is :  ['LIG.frcmod'] The variable gaff is :  1 The variable group_name is :  dna The variable ion_paraset is :  12_6 (Only for the ions using the nonbonded model). The variable large_opt is :  1 The variable lgmodel_chg is :  -99 The variable lgmodel_spin is :  -99              -99 means program will assign a charge automatically. The variable naa_mol2files is :  ['LIG.mol2'] The variable scale_factor is :  1.0              ATTENTION: This is the scale factor of frequency. The              force constants will be scaled by multiplying the square              of scale_factor. The variable smmodel_chg is :  -99 The variable smmodel_spin is :  -99              -99 means program will assign a charge automatically. The variable software_version is :  gau The variable sqm_opt is :  0 The variable water_model is :  OPC The variable xstru is :  0 ****************************************************************** *                                                                * *======================RESP Charge fitting=======================* *                                                                * ****************************************************************** ***Generating the 1st stage resp charge fitting input file... ***Generating the 2nd stage resp charge fitting input file... ***Doing the RESP charge fiting... =========================Checking models========================== ***Check the large model... Good. The charges and atom numbers are match for the large model. Good. There are 27 atoms in the large model. ***Check the standard model... Traceback (most recent call last):   File "/home/saranya/amber20/bin/MCPB.py", line 692, in <module>     resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids, ff_choice,   File "/home/saranya/amber20/lib/python3.9/site-packages/pymsmt/mcpb/resp_fitting.py", line 521, in resp_fitting     raise pymsmtError('Error: the charges and atom numbers are mismatch ' pymsmt.exp.pymsmtError: Error: the charges and atom numbers are mismatch for the standard model!
Question
I am trying to do MD simulation for DNA-ruthenium (Ru) complex. Does anyone know how to generate itp file for this metal.
Question
I am performing NeB calculations using vasp. I have performed the calculations and plotted the graph for reaction coordinates vs energy and obtained the Saddle point. Say, the saddle point occurs at reaction coordinate 6 which is supposed to be the TS. I need to perform frequency calculations to confirm the TS. What parameters should be set in the incar to obtain the frequencies ?
Question
Hi
I am calculating bader charge for a molecule in HSE06 hybrid functional using vasp. I find the the bader charge (339) is higher than the actual net charge (331) of the molecule. Is there something wrong with the input and how to rectify it?
Question
I have performed a simulation for a protein-metal cluster complex system for 500ns. while calculating MMPBSA analysis for the system, I had selected two ranges of Trajectory period (100-110 ns; 290-300 ns) based on RMSD profile of protein-metal cluster 500 ns simulation period and executed the commands for a single range of trajectory period. In the result of the binding energy of my system, values are void. Hence, I Kindly need your valuable suggestions in this regard. Herewith I have attached the obtained results of my system,
#Complex Number: 1 =============== SUMMARY ===============
van der Waal energy = -1144.250 +/- 28.405 kJ/mol
Electrostattic energy = 0.000 +/- 0.000 kJ/mol
Polar solvation energy = nan +/- nan kJ/mol
SASA energy = -25.841 +/- 1.107 kJ/mol
SAV energy = 0.000 +/- 0.000 kJ/mol
WCA energy = 0.000 +/- 0.000 kJ/mol
Binding energy = nan +/- nan kJ/mol
=============== END ===============

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