Research Paper/Article:
Mondal M, Gao YQ, Sequence dependent clustering properties of nucleotides fragments in ionic solution, J Chin Chem Soc.,70(3):297-316, 2023
Mondal M, Chakrabarty S, Gao YQ, Bhattacharyya D, Chakrabarti J, Microscopic model on indoor propagation of respiratory droplets, Comput Biol Chem. 102:107806, 2023
Mondal M, Gao YQ, Microscopic insight into pH-dependent conformational dynamics and noncanonical base pairing in telomeric i-motif DNA, J Phys Chem Lett.,13(23):5109-5115, 2022
Mondal M, Yang L, Cai Z, Patra P, Gao, YQ, Perspective on Molecular Simulation of DNA from structural and functional aspect, Chemical Science, 12, 5390-5409, 2021
Mandal C S, Maganti L, Mondal M, Chakrabarti J, Microscopic insight to specificity of metal ion cofactor in DNA cleavage by restriction endonuclease EcoRV, Biopolymers, DOI: 10.1002/bip.23396, 2020
Mondal M, Bhattacharyya D, Gao YQ, Structural properties and influence of solvent in the stability of telomeric four-stranded i-motif DNA, Phys. Chem. Chem. Phys., 21:21549-21560,2019
Zeng H*, Mondal M*, Song R*, Zhang J, Xia B, Liu M, Zhu C, He B,Gao YQ and Yi C Unnatural cytosine bases recognized as thymines by DNA polymerases via the formation of the Watson-Crick geometry. Angew. Chem. Int. Ed., 58, 130-133, 2019 [* Joint first author]
Mondal M, Yang Y, Yang L, Yang W and Gao YQ Role of Conformational Fluctuations of Protein toward Methylation in DNA by Cytosine-5-methyltransferase. J Chem Theory Comput, 14(12)6679-6689, 2018.
Mondal M, Chakrabarti J, Ghosh M. Molecular dynamics simulations on interaction between bacterial proteins: Implication on pathogenic activities. Proteins. 86(3):370-378, 2018.
Mazumder A, Batabyal S, Mondal M, Mondol T, Choudhury S, Ghosh R, Chatterjee T, Bhattacharyya D, Pal SK and Roy S. Specific DNA sequences allosterically enhance protein-protein interaction in a transcription factor through modulation of protein dynamics: implications for specificity of gene regulation. Phys Chem Chem Phys, 19(22):14781-92, 2017.
Naiya G, Raha P, Mondal M, Pal U, Saha R, Chaudhuri S, Batabyal S, Pal S, Bhattacharyya D, Maiti N and Roy S. Conformational selection underpins recognition of multiple DNA sequences by proteins and consequent functional actions. Phys Chem Chem Phys, 18(31):21618-28, 2016.
Mondal M, Halder S, Chakrabarti J and Bhattacharyya D. Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs. Biopolymers, 105(4):212-26, 2016.
Mondal M, Mukherjee S, Halder S and Bhattacharyya D. Stacking geometry for non-Canonical G:U wobble base pair containing dinucleotide sequences in RNA: Dispersion Corrected DFT-D study. Biopolymers, 103(6):328-38, 2015.
Mondal M, Choudhury D, Chakrabarti J and Bhattacharyya D. Role of indirect readout mechanism in TATA box binding protein-DNA interaction. J Comput Aided Mol Des, 29(3):283-95, 2015.
Mondal M, Mukherjee S and Bhattacharyya D. Contribution of Phenylalanine side chain intercalation in TATA-box binding protein-DNA interaction: molecular dynamics and dispersion corrected density functional theory studies. J Mol Modeling, 20(11):2499, 2014.
Journal Cover:
Mondal M, Chakrabarti J, Ghosh M. Molecular dynamics simulations on interaction between bacterial proteins: Implication on pathogenic activities. Proteins Structure Function and Bioinformatics 86(3):C4-C4, DOI: 10.1002/prot.25463, 2018.
Book Chapter:
Mukherjee S, Mondal M, Bhattacharyya D. Variation of stacking interactions along with twist parameter in DNA and RNA: DFT-D Studies. Advs in Intelligent Syst., Computing, Vol. 452, Advanced Computing and Communication Technologies, 978-981-10-1021-7, Springer, 2016.
Conference Proceeding:
Mondal M, Bose N, Patra P, Das Rajkumar and Mukherjee S. Synthesis and characterization of CuO nanoparticles in SiO2 matrices. Conference Proceeding, National Conference on Advanced Nanomaterials and its Application, Jadavpur University, Kolkata, India, August, 2008.