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Desikan, R and Behera, A and Maiti, PK and Ayappa, KG (2021) Using multiscale molecular dynamics simulations to obtain insights into pore forming toxin mechanisms. [Book Chapter]
Dasgupta, S and Arun, KS and Ayappa, KG and Maiti, PK (2023) Trajectory-Extending Kinetic Monte Carlo Simulations to Evaluate Pure and Gas Mixture Diffusivities through a Dense Polymeric Membrane. In: Journal of Physical Chemistry B, 127 (45). pp. 9841-9849.
Kulshrestha, A and Punnathanam, SN and Roy, R and Ayappa, KG (2023) Cholesterol catalyzes unfolding in membrane-inserted motifs of the pore forming protein cytolysin A. In: Biophysical Journal, 122 (20). pp. 4068-4081.
Vaiwala, R and Ayappa, KG (2023) Martini-3 Coarse-Grained Models for the Bacterial Lipopolysaccharide Outer Membrane of Escherichia coli. In: Journal of Chemical Theory and Computation .
Ronghe, A and Ayappa, KG (2023) Graphene Nanopores Enhance Water Evaporation from Salt Solutions: Exploring the Effects of Ions and Concentration. In: Langmuir, 39 (25). pp. 8787-8800.
Kulshrestha, A and Maurya, S and Gupta, T and Roy, R and Punnathanam, SN and Ayappa, KG (2022) Conformational Flexibility Is a Key Determinant for the Lytic Activity of the Pore-Forming Protein, Cytolysin A. In: Journal of Physical Chemistry B, 127 (1). pp. 69-84.
Dasgupta, S and Rajasekaran, M and Roy, PK and Thakkar, FM and Pathak, AD and Ayappa, KG and Maiti, PK (2022) Influence of chain length on structural properties of carbon molecular sieving membranes and their effects on CO2, CH4 and N2 adsorption: A molecular simulation study. In: Journal of Membrane Science, 664 .
Sharma, P and Vaiwala, R and Parthasarathi, S and Patil, N and Verma, A and Waskar, M and Raut, JS and Basu, JK and Ayappa, KG (2022) Interactions of Surfactants with the Bacterial Cell Wall and Inner Membrane: Revealing the Link between Aggregation and Antimicrobial Activity. In: Langmuir, 38 (50). pp. 15714-15728.
Sharma, P and Ayappa, KG (2022) A Molecular Dynamics Study of Antimicrobial Peptide Interactions with the Lipopolysaccharides of the Outer Bacterial Membrane. In: Journal of Membrane Biology .
Choudhury, S and Ananthanarayanan, V and Ayappa, KG (2022) Coupling of mitochondrial population evolution to microtubule dynamics in fission yeast cells: a kinetic Monte Carlo study. In: Soft Matter, 18 . pp. 4483-4492.
M, R and Ayappa, KG (2022) Influence of the extent of hydrophobicity on water organization and dynamics on 2D graphene oxide surfaces. In: Physical Chemistry Chemical Physics, 24 . pp. 14909-14923.
Sathyanarayana, P and Visweswariah, SS and Ayappa, KG (2021) Mechanistic Insights into Pore Formation by an α-Pore Forming Toxin: Protein and Lipid Bilayer Interactions of Cytolysin A. In: Accounts of Chemical Research, 54 (1). pp. 120-131.
Ilangumaran Ponmalar, I and Ayappa, KG and Basu, JK (2021) Bacterial protein listeriolysin O induces nonmonotonic dynamics because of lipid ejection and crowding. In: Biophysical Journal, 120 (15). pp. 3040-3049.
Sharma, P and Desikan, R and Ayappa, KG (2021) Evaluating Coarse-Grained MARTINI Force-Fields for Capturing the Ripple Phase of Lipid Membranes. In: Journal of Physical Chemistry B, 124 (24). pp. 6587-6599.
Yamini, G and Kanchi, S and Kalu, N and Momben Abolfath, S and Leppla, SH and Ayappa, KG and Maiti, PK and Nestorovich, EM (2021) Hydrophobic Gating and 1/f Noise of the Anthrax Toxin Channel. In: The journal of physical chemistry. B, 125 (21). pp. 5466-5478.
Ilangumaran Ponmalar, I and Sarangi, NK and Basu, JK and Ayappa, KG (2021) Pore Forming Protein Induced Biomembrane Reorganization and Dynamics: A Focused Review. In: Frontiers in Molecular Biosciences, 8 .
Vaiwala, R and Ayappa, KG (2021) A generic force field for simulating native protein structures using dissipative particle dynamics. In: Soft Matter, 17 (42). pp. 9772-9785.
Cheerla, R and Ayappa, KG (2020) Molecular Dynamics Study of Lipid and Cholesterol Reorganization Due to Membrane Binding and Pore Formation by Listeriolysin O. In: Journal of Membrane Biology .
Vaiwala, R and Sharma, P and Puranik, M and Ayappa, KG (2020) Developing a Coarse-Grained Model for Bacterial Cell Walls: Evaluating Mechanical Properties and Free Energy Barriers. In: Journal of Chemical Theory and Computation, 16 (8). pp. 5369-5384.
Sharma, P and Parthasarathi, S and Patil, N and Waskar, M and Raut, JS and Puranik, M and Ayappa, KG and Basu, JK (2020) Assessing Barriers for Antimicrobial Penetration in Complex Asymmetric Bacterial Membranes: A Case Study with Thymol. In: Langmuir, 36 (30). pp. 8800-8814.
Varadarajan, V and Desikan, R and Ayappa, KG (2020) Assessing the extent of the structural and dynamic modulation of membrane lipids due to pore forming toxins: Insights from molecular dynamics simulations. In: Soft Matter, 16 (20). pp. 4840-4857.
Desikan, R and Maiti, PK and Ayappa, KG (2020) Predicting interfacial hot-spot residues that stabilize protein-protein interfaces in oligomeric membrane-toxin pores through hydrogen bonds and salt bridges. In: Journal of Biomolecular Structure and Dynamics .
Roy, PK and Kumar, K and Thakkar, FM and Pathak, AD and Ayappa, KG and Maiti, PK (2020) Investigations on 6FDA/BPDA-DAM polymer melt properties and CO2 adsorption using molecular dynamics simulations. In: Journal of Membrane Science, 613 .
Varadarajan, Vadhana and Dasgupta, Chandan and Ayappa, KG (2018) Influence of surface commensurability on the structure and relaxation dynamics of a confined monatomic fluid. In: JOURNAL OF CHEMICAL PHYSICS, 149 (6).
Sathyanarayana, Pradeep and Maurya, Satyaghosh and Behera, Amit and Ravichandran, Monisha and Visweswariah, Sandhya S and Ayappa, KG and Roy, Rahul (2018) Cholesterol promotes Cytolysin A activity by stabilizing the intermediates during pore formation. In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115 (31). E7323-E7330.
Kanchi, Subbarao and Gosika, Mounika and Ayappa, KG and Maiti, Prabal K (2018) Dendrimer Interactions with Lipid Bilayer: Comparison of Force Field and Effect of Implicit vs Explicit Solvation. In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 14 (7). pp. 3825-3839.
Desikan, Rajat and Patra, Swarna M and Sarthak, Kumar and Maiti, Prabal K and Ayappa, KG (2017) Comparison of coarse-grained (MARTINI) and atomistic molecular dynamics simulations of and toxin nanopores in lipid membranes. In: JOURNAL OF CHEMICAL SCIENCES, 129 (7, SI). pp. 1017-1030.
Sarangi, Nirod Kumar and Ayappa, KG and Basu, Jaydeep Kumar (2017) Complex dynamics at the nanoscale in simple biomembranes. In: SCIENTIFIC REPORTS, 7 .
Agrawal, Ayush and Apoorva, K and Ayappa, KG (2017) Transmembrane oligomeric intermediates of pore forming toxin Cytolysin A determine leakage kinetics. In: RSC ADVANCES, 7 (82). pp. 51750-51762.
Sarangi, Nirod Kumar and Ayappa, KG and Visweswariah, Sandhya S and Basu, Jaydeep Kumar (2016) Nanoscale dynamics of phospholipids reveals an optimal assembly mechanism of pore-forming proteins in bilayer membranes. In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18 (43). pp. 29935-29945.
Vadhana, V and Ayappa, KG (2016) Structure and Dynamics of Octamethylcyclotetrasiloxane Confined between Mica Surfaces. In: JOURNAL OF PHYSICAL CHEMISTRY B, 120 (11). pp. 2951-2967.
Sarangi, Nirod Kumar and Ilanila, IP and Ayappa, KG and Visweswariah, Sandhya S and Basu, Jaydeep Kumar (2016) Super-resolution Stimulated Emission Depletion-Fluorescence Correlation Spectroscopy Reveals Nanoscale Membrane Reorganization Induced by Pore-Forming Proteins. In: LANGMUIR, 32 (37). pp. 9649-9657.
Sarangi, Nirod Kumar and Ilanila, IP and Ayappa, KG and Visweswariah, Sandhya S and Basu, Jaydeep Kumar (2016) Super-resolution Stimulated Emission Depletion-Fluorescence Correlation Spectroscopy Reveals Nanoscale Membrane Reorganization Induced by Pore-Forming Proteins. In: LANGMUIR, 32 (37). pp. 9649-9657.
Mandal, Taraknath and Kanchi, Subbarao and Ayappa, KG and Maiti, Prabal K (2016) pH controlled gating of toxic protein pores by dendrimers. In: NANOSCALE, 8 (26). pp. 13045-13058.
Kanchi, Subbarao and Suresh, Gorle and Priyakumar, Deva U and Ayappa, KG and Maiti, Prabal K (2015) Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers. In: JOURNAL OF PHYSICAL CHEMISTRY B, 119 (41). pp. 12990-13001.
Dasgupta, Tonnishtha and Punnathanam, Sudeep N and Ayappa, KG (2014) Effect of functional groups on separating carbon dioxide from CO2/N-2 gas mixtures using edge functionalized graphene nanoribbons. In: CHEMICAL ENGINEERING SCIENCE, 121 . pp. 279-291.
Prajwal, BP and Ayappa, KG (2014) Evaluating methane storage targets: from powder samples to onboard storage systems. In: ADSORPTION-JOURNAL OF THE INTERNATIONAL ADSORPTION SOCIETY, 20 (5-6). pp. 769-776.
Debnath, Ananya and Thakkar, Foram M and Maiti, Prabal K and Kumaran, V and Ayappa, KG (2014) Laterally structured ripple and square phases with one and two dimensional thickness modulations in a model bilayer system. In: SOFT MATTER, 10 (38). pp. 7630-7637.
Vaidyanathan, MS and Sathyanarayana, Pradeep and Maiti, Prabal K and Visweswariah, Sandhya S and Ayappa, KG (2014) Lysis dynamics and membrane oligomerization pathways for Cytolysin A (ClyA) pore-forming toxin. In: RSC ADVANCES, 4 (10). pp. 4930-4942.
Bhattacharya, R and Kanchi, Subbarao and Roobala, C and Lakshminarayanan, A and Seeck, Oliver H and Maiti, Prabal K and Ayappa, KG and Jayaraman, N and Basu, JK (2014) A new microscopic insight into membrane penetration and reorganization by PETIM dendrimers. In: SOFT MATTER, 10 (38). pp. 7577-7587.
Debnath, Ananya and Ayappa, KG and Maiti, Prabal K (2013) Simulation of Influence of Bilayer Melting on Dynamics and Thermodynamics of Interfacial Water. In: PHYSICAL REVIEW LETTERS, 110 (1).
Krishnan, SH and Ayappa, KG (2012) Glassy dynamics in a confined monatomic fluid. In: PHYSICAL REVIEW E, 86 (1, Par).
Biswas, Rajib and Chakraborti, Tamaghna and Bagchi, Biman and Ayappa, KG (2012) Non-monotonic, distance-dependent relaxation of water in reverse micelles: Propagation of surface induced frustration along hydrogen bond networks. In: JOURNAL OF CHEMICAL PHYSICS, 137 (1).
Malani, Ateeque and Ayappa, KG (2012) Relaxation and jump dynamics of water at the mica interface. In: JOURNAL OF CHEMICAL PHYSICS, 136 (19).
Kandagal, Vinay S and Pathak, Amardeep and Ayappa, KG and Punnathanam, Sudeep N (2012) Adsorption on Edge-Functionalized Bilayer Graphene Nanoribbons: Assessing the Role of Functional Groups in Methane Uptake. In: JOURNAL OF PHYSICAL CHEMISTRY C, 116 (44). pp. 23394-23403.
Malani, Ateeque and Ayappa, KG (2012) Confined fluids in a Janus pore: influence of surface asymmetry on structure and solvation forces. In: Molecular Simulation, 38 (13). pp. 1114-1123.
Wood, Brandon C and Bhide, Shreyas Y and Dutta, Debosruti and Kandagal, Vinay S and Pathak, Amar Deep and Punnathanam, Sudeep N and Ayappa, KG and Narasimhan, Shobhana (2012) Methane and carbon dioxide adsorption on edge-functionalized graphene: a comparative DFT study. In: Journal of Chemical Physics, 137 (5). 054702-1.
Ayappa, KG and Davis, HT and Barringer, SA and Davis, EA (1997) Resonant microwave power absorption in slabs and cylinders. In: AIChE Journal, 43 (3). pp. 615-624.
Desikan, Rajat and Agrawal, Ayush and Ayappa, KG and Basu, JK (2014) Novel Lipid Dynamics Around the Cytolysin-A Membrane-Pore Complex and its Intermediates. In: BIOPHYSICAL JOURNAL, 106 (2, 1). 292A.
Agrawal, Ayush and Desikan, Rajat and Pradeep, S and Ayappa, KG and Basu, JK and Visweswariah, Sandhya (2014) Pore Formation and Dynamics of Cytolysin-A on Supported Lipid Bilayer Membranes. In: BIOPHYSICAL JOURNAL, 106 (2, 1). 88A.
