Publications

A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

Rakesh Vaiwala, K. Ganapathy Ayappa, Soft matter (2021).

Bacterial protein Listeriolysin O induces non-monotonic dynamics due to lipid ejection and crowding

Ilanila. P, Ganapathy Ayappa, Jaydeep K. Basu, Biophysical Journal (2021).

Evaluating Coarse-Grained MARTINI Force-Fields for Capturing the Ripple Phase of Lipid Membranes, Sharma Pradyumn, Desikan Rajat and K. G. Ayappa, Journal of Physical Chemistry B (2021)

Developing a Coarse-Grained Model for Bacterial Cell Walls and Evaluating Mechanical Properties and Free Energy Barriers, Vaiwala  Rakesh, Sharma Pradyumn, Puranik Mrinalini and K. G. Ayappa, Journal of Chemical Theory and Computation (2020).

Assessing Differential Barriers for Penetration of Antimicrobials Through Complex Asymmetric Bacterial Membranes: A case study with thymol, Pradyumn Sharma, Srividhya Parthasarathi, Nivedita Patil, Morris Waskar, Janhavi Raut, Mrinalini Puranik, K. Ganapathy Ayappa and Jaydeep K. Basu, Langmuir (2020).

Investigations on 6FDA/BPDA-DAM Polymer Melt Properties and CO2 Adsorption Using Molecular Dynamics Simulations, Projesh Kumar Roy, Kishant Kumar, Foram M. Thakkar, Amar Deep Pathak Ganapathy Ayappa, Prabal K Maiti,  In Press, Journal of Membrane Science (2020).

Influence of Surface Hydrophilicity and Hydration on the Rotational Relaxation of Supercooled Water on Graphene Oxide Surfaces, M. Rajasekeran, K. G. Ayappa, In Review, Physical Chemistry Chemical Physics (2020).

Dynamical Transitions of Supercooled Water in Graphene Oxide Nanopores: Influence of Surface Hydrophilicity, M. Rajasekeran, K. G. Ayappa,  Journal of Physical Chemistry B, 124, 4805-4820 (2020).

Assessing the Extent of the Structural and Dynamic Modulation of Membrane Lipids due to Pore Forming Toxins: Insights from Molecular Dynamics Simulations, Vadhana Varadarajan, Rajat Desikan and K. G. Ayappa, Soft Matter, 16, 4840-4857 (2020)

Opening of Smaller Toxin Pores by Lipid Micelle Formation, Rajat Desikan, P. Padmanabhan, K.G. Ayappa, Proceedings of the National Academy of Sciences 117 (10), 5107-5108 (2020).

Predicting Interfacial Hot-Spot Residues that Stabilize Protein-Protein Interfaces in Oligomeric Membrane-Toxin Pores through Hydrogen Bonds and Salt Bridges, Rajat Desikan, P.K. Maiti and K.G. Ayappa, Journal of Biomolecular Structure and Dynamics, 1-15 (2020)

Dendrimer: A Novel Nanomaterial, Debabrata Pramanik, Subbarao Kanchi, K. G. Ayappa and Prabal K. Maiti, Springer Series in Materials Science Computational Materials, Chemistry, and Biochemistry: From Bold Initiatives to the Last Mile, Vol 284 (2020)

Correlated protein conformational states and membrane dynamics during attack by pore-forming toxins

Ilanila I. Ponmalar, Ramesh Cheerla, K. Ganapathy Ayappa, and Jaydeep K. Basu- PNAS, 2019

Enhancing Dynamics of Water Confined between Graphene Oxide Surfaces with Janus Interfaces: A Molecular Dynamics Study

R Manokaran, KG Ayappa - The Journal of Physical Chemistry B, 2019 - ACS Publications

Influence of surface commensurability on the structure and relaxation dynamics of a confined monatomic fluid

Vadhana Varadarajan, Chandan Dasgupta and K. G. Ayappa, JCP 149, 064503 (2018).

Cholesterol promotes Cytolysin A activity by stabilizing the intermediates during pore formation

Pradeep Sathyanarayana, Satyaghosh Maurya, Amit Behera, Monisha Ravichandran, Sandhya S. Visweswariah, K. Ganapathy Ayappa, and Rahul Roy​, PNAS (2018).

Dendrimer Interactions with lipid bilayer: comparison of force-field and effect of implicit vs explicit solvation

S Kanchi, M Gosika, KG Ayappa, PK Maiti,Journal of chemical theory and computation (2018).

Assessing the structure and stability of transmembrane oligomeric intermediates of an α-helical toxin

R Desikan, G Ayappa, PK Maiti,Langmuir 33 (42), 11496-11510 (2018).

Complex dynamics at the nanoscale in simple biomembranes

NK Sarangi, KG Ayappa, JK Basu,Scientific Reports 7 (1), 11173 (2017).

Comparison of coarse-grained (MARTINI) and atomistic molecular dynamics simulations of α and β toxin nanopores in lipid membranes

R Desikan, SM Patra, K Sarthak, PK Maiti, KG Ayappa, Journal of Chemical Sciences 129 (7), 1017-1030 (2017).

Transmembrane oligomeric intermediates of pore forming toxin Cytolysin A determine leakage kinetics

Ayush Agrawal, K. Apoorva and K. G. Ayappa, RSC Adv, 7, 51750-51762 (2017).

Capturing the membrane-triggered conformational transition of an α-helical pore-forming toxin

VVH Giri Rao, R Desikan, KG Ayappa, S Gosavi,The Journal of Physical Chemistry B 120 (47), 12064-12078 (2016).

The solvent-exposed c-terminus of the cytolysin a pore-forming toxin directs pore formation and channel function in membranes

P Sathyanarayana, R Desikan, KG Ayappa, SS Visweswariah ,Biochemistry 55 (42), 5952-5961(2016).

Super-resolution stimulated emission depletion-fluorescence correlation spectroscopy reveals nanoscale membrane reorganization induced by pore-forming proteins

Nirod Kumar Sarangi, Ilanila I. P, K. G. Ayappa, Sandhya. S. Visweswariah and Jaydeep Kumar Basu , Langmuir,(2016).

Structure and Dynamics of Octamethylcyclotetrasiloxane Confined between Mica Surfaces

V Vadhana and K. G. Ayappa, Journal of Physical Chemistry B,120(11),2951–2967(2016).

Nanoscale dynamics of phospholipids reveals an optimal assembly mechanism of pore-forming proteins in bilayer membranes

NK Sarangi, KG Ayappa, SS Visweswariah, JK Basu, Physical Chemistry Chemical Physics 18 (43), 29935-29945 (2016).

pH controlled gating of toxic protein pores by dendrimers

Taraknath Mandal, Subbarao Kanchi, Ganapathy Ayappa and Prabal Kumar Maiti, Nanoscale,8,13045 (2016).

Molecular dynamics study of the structure, flexibility, and hydrophilicity of PETIM dendrimers: a comparison with PAMAM dendrimers

Kanchi Subbarao, Suresh Gorle, Priyakumar, U. Deva, K. G. Ayappa and Prabal K Maiti (2015).

Estimation of activation energy for electroporation and pore growth rate in liquid crystalline and gel phases of lipid bilayers using molecular dynamics …

Amit Kumar Majhi, Subbarao Kanchi, V. Venkataraman, K.G.Ayappa,and Prabal K. Maiti, Soft Matter,11,8632-8640 (2015).

Effect of functional groups on separating carbon dioxide from CO2/N2 gas mixtures using edge functionalized graphene nanoribbons

Tonnishtha Das Gupta, Sudeep Punnathan, K.G. Ayappa, Invited Article, Danckwerts Special Issue,Chemical Engineering Science, 121, 279-291(2015).

A new microscopic insight into membrane penetration and reorganization by PETIM dendrimers

R. Bhattacharya, Subbarao Kanchi, C. Roobala, A. Lakshminarayanan, Oliver H. Seeck, Prabal K. Maiti, K. G. Ayappa, N. Jayaraman and J. K. Basu,Soft Matter, 10, 7577-7587(2014).

Laterally structured ripple and square phases with one and two dimensional thickness modulations in a model bilayer system

Ananya Debnath, Foram Thakkar, Prabal K Maiti, V. Kumaran and K.G. Ayappa, Soft Matter, 10, 7630-7637(2014).

Evaluating methane storage targets: from powder samples to onboard storage systems

B. P. Prajwal and K. G. Ayappa, Adsorption,769–776 (2014).

Enhanced gas adsorption on graphitic substrates via defects and local curvature: a density functional theory study

Debosruti Dutta, Brandon C. Wood, Shreyas Y. Bhide, K. Ganapathy Ayappa and Shobhana Narasimhan, Journal of Physical Chemistry C, 118, 7741-7750 (2014).

Influence of exhaust gas heating and L/D ratios on the discharge efficiencies for an activated carbon natural gas storage system

P. K. Sahoo, B. P. Prajwal, Siva Kalyan Dasetty, M. John , B. L. Newalkar, N. V. Choudary and K. G. Ayappa, Applied Energy, 15,190–203 (2014).

Lysis dynamics and membrane oligomerization pathways for Cytolysin A (ClyA) pore-forming toxin

M. S. Vaidyanathan, Pradeep Sathyanarayana, Prabal K.Maiti, Sandhya S. Visweswariah, and K.G. Ayappa, RSC Advances, 4, 4930-4942 (2014).

Filling characteristics for an activated carbon based adsorbed natural gas storage system

Pradeepta K. Sahoo, Mathew John, Bharat L. Newalkar, N. V. Choudhary and K. G. Ayappa, Ind. Eng. Chem. Res., 53, 4522–4523 (2014).

Simulation of influence of bilayer melting on dynamics and thermodynamics of interfacial water

Ananya Debnath, Prabal Maiti, K. G. Ayappa, Physical Review Letters, 110, 018303, (2013).

Adsorption on edge-functionalized bilayer graphene nanoribbons: assessing the role of functional groups in methane uptake

Vinay Kandagal, Amar Deep Pathak, K. G. Ayappa, and Sudeep Punnathanam, Journal of Physical Chemistry C, 116, 23394-23403 (2012).

Methane and carbon dioxide adsorption on edge-functionalized graphene: a comparative DFT study

Brandon C. Wood1, Shreyas Y. Bhide, Debosruti Dutta, Vinay S. Kandagal, Amar Deep Pathak, Sudeep N. Punnathanam, K. G. Ayappa, and Shobhana Narasimhan, J. Chem. Phys. 137, 054702 (2012).

Non-monotonic, distance-dependent relaxation of water in reverse micelles: propagation of surface induced frustration along hydrogen bond networks

Rajib Biswas, Tamaghna Chakraborti, Biman Bagchi, and K. G. Ayappa, J. Chem. Phys. 137, 014515 (2012).

Confined fluids in a Janus pore: influence of surface asymmetry on structure and solvation forces

Ateeque Malani and K. G. Ayappa, Molecular Simulation, DOI:10.1080/08927022.2012.696111 (2012).

Relaxation and jump dynamics of water at the mica interface

Ateeque Malani and K. G. Ayappa, J. Chem. Phys. 136, 194701 (2012).

Glassy dynamics in a confined monatomic fluid

S. H. Krishnan and K. G. Ayappa, Phys. Rev. E 86, 011504 (2012).

Filling characteristics for an activated carbon based adsorbed natural gas storage system

Pradeepta K. Sahoo, Mathew John, Bharat L. Newalkar, N. V. Choudhary and K. G. Ayappa, In Press, I & EC Research (2011).

Verifying scalings for bending rigidity of bilayer membranes using mesoscale models

Foram M. Thakkar, Prabal K. Maiti, V. Kumaran and K. G. Ayappa, Soft Matter, DOI 10.1039/C0SM00876A (2011).

Entropy and dynamics of water in hydration layers of a bilayer

Ananya Debnath, Biswaroop Mukherjee, K. G. Ayappa, Prabal K. Maiti and Shiang-Tai Lin,Journal of Chemical Physics, 133, 174704-174716 (2010).

Investigations on the melting and bending modulus of polymer grafted bilayers using dissipative particle dynamics

Foram Thakkar and K. G. Ayappa, Biomicrofluidics, Special Issue on Surface Modification, Wetting, and Biological Interfaces, 4, 032203 (2010).

Hydration of ions under confinement

Ateeque Malani, K. G. Ayappa and Sohail Murad,Molecular Simulations Special Issue: Recent Developments in Molecular Simulations, 36, 578-579 (2010).

Combined atomic force microscopy and modeling study of the evolution of octadecylamine films on a mica surface

K. G. Patil, V. Santhanam, S. K. Biswas and K. G. Ayappa, J. Phys. Chem. C, 114, 3549-3559 (2010).

Effect of polymer grafting on the bilayer gel to liquid-crystalline transition

Foram Thakkar and K. G. Ayappa, J. Phys. Chem. B 114, 2738 – 2748 (2010). (not showing in google scholar)

Computer simulation of liquid crystals

J. of Indian Institute of Science, A Multidisciplinary Reviews Journal – Special Issue on Liquid Crystals, Prabal K. Maiti, V. Arun Kumar and K. G. Ayappa, 89 (2), 229-241, (2009).

Influence of hydrophilic surface specificity on the structural properties of confined water

Ateeque Malani, K. G. Ayappa, Sohail Murad, J. Phys. Chem. B, 113, 13825 – 13839 (2009).

The influence of bilayer composition on the gel to liquid crystalline transition

Ananya Debnath, K. G. Ayappa, V. Kumaran and Prabal Maiti, J. Phys. Chem. B, 113, 10660-10668 (2009)

Adsorption isotherms of water on mica: redistribution and film growth

Ateeque Malani and K.Ganapathy Ayappa, The Journal of Physical Chemistry B, 113, 1058 – 1067 (2009)

Freezing of fluids confined between mica surfaces

Ayappa, K. G.; Mishra, R. K., J. Phys. Chem. B., 111, 14299-14310 (2007)

Enhancing the hydrophobic effect in confined water nanodrops

Rao, P. V. G.; Gandhi, K. S.; Ayappa, K. G. Langmuir, (Letter), 23, 12795-12798 (2007)

Molecular simulations: probing systems from the nanoscale to mesoscale

J. of Indian Institute of Science, A Multidisciplinary Reviews Journal (Invited), K. G. Ayappa, Ateeque Malani, Patil Kalyan and Foram Thakkar, 87, 35-60 (2007).

Using γ distributions to predict self-diffusivities and density of states of fluids confined in carbon nanotubes

Vinit Choudhary, K. G. Ayappa, Phys. Chem. Chem. Phys., 16, 1952-1961 (2007).

Self-diffusivity and velocity autocorrelation functions for xenon in NaY using memory kernels

Special Issue: Seventh Liblice Conference on the Statistical Mechanics of Liquids, P. Kharat, S. H. Krishnan; K. G. Ayappa, Molecular Physics, 104, 3809 (2006)

Effect of confinement on the hydration and solubility of NaCl in water

A. Malani, K. G. Ayappa and S. Murad, Chemical Physics Letters, 431, 88-93 (2006).

A Model for Liquid State Dynamics: Applications to Bulk and Confined Fluids, J. Chem. Phys., S. H. Krishnan and K. G. Ayappa, 124, 144503-1, 144503-16 (2006).

Relaxation and short time dynamics of bulk liquids and fluids confined in spherical cavities and slit pores

S. H. Krishnan and K. G. Ayappa, J. Phys. Chem. B, 109, 23237-23249, (2005).

Large distinct diffusivity in binary mixtures confined to zeolite NaY

C. R. Kamala, S. Yashonath and K. G. Ayappa, J. Phys. Chem. B (Letter), 109, 22092-22095 (2005)

Thermal Study of Accumulation of Conformational Disorders in the Self-Assembled Monolayers of C8 and C18 Alkanethiols on the Au(111) Surface

Prathima N., Harini M., Neeraj Rai, Chandrashekara R. H., Ayappa K.G., Sampath S., Biswas S.K., Langmuir, 21, 2364-2374 (2005)

Solid/solid phase transitions in confined thin films: A zero temperature approach

H. Bock, K. E. Gubbins and K. G. Ayappa, J. Chem. Phys., 122, 094709 (2005)

Ion exchange in reverse micelles

Sandeep Pal, G. Vishal, K. S. Gandhi and K. G. Ayappa, Langmuir, 21, 767-779 (2005).

Modeling velocity autocorrelation functions for confined fluids using γ distributions

S. H. Krishnan and K. G. Ayappa, J. Chem. Phys., 121, 3197 (2004).

Solvation force, structure and thermodynamics of fluids confined in geometrically rough pores

Chandana Ghatak and K.G. Ayappa, J. Chem. Phys., 120, 9703-9714, (2004).

Distinct diffusion in binary mixtures confined in slit graphite pores

C. R. Kamala, K. G. Ayappa and S. Yashonath, J. Phys. Chem. B., 108, 4411-4421 (2004)

Molecular dynamic simulations of self-assembled alkylthiolate monolayers on an Au (111) surface

Beena Rai, P. Satish, Chetan P Malhotra, Pradip and K. G. Ayappa, Langmuir, 20, 3138-3144, (2004).

Modeling velocity autocorrelation functions of confined fluids: A memory function approach

S. H. Krishnan and K. G. Ayappa, J. Chem. Phys., 118, 690-705 (2003)

The structure of frozen phases in slit nanopores: A grand canonical Monte Carlo study

K. G. Ayappa and Chandana Ghatak, J. Chem. Phys., 117, 5373-5384 (2002).

Mutual diffusion in a binary Ar-Kr mixture confined within zeolite NaY

C. R. Kamala, S. Yashonath and K. G. Ayappa, Phys. Rev. E., 65, 061202-061214 (2002).

Solid–solid transitions in slit nanopores

Chandana Ghatak and K. G. Ayappa, Special Issue Journal of Colloids and Surfaces: Indo-French Workshop, Pune, India, ``Advances in the Understanding of Adsorption Phenomena at Solid/Aqueous Solutions Interfaces", 205, 111-117 (2002)

A fixed-grid finite element based enthalpy formulation for generalized phase change problems: role of superficial mushy region

Madhuchhanda Bhattacharya, Tanmay Basak and K. G. Ayappa, Int. J. of Heat and Mass Transfer, 45, 4881-4898 (2002).

Role of length scales on microwave thawing dynamics in 2D cylinders

Tanmay Basak and K. G. Ayappa, Int. J. of Heat and Mass Transfer, 45, 4543-4559 (2002).

Microwave heating in multiphase systems: evaluation of series solutions

K. G. Ayappa and Tirthankar SenGupta, J. of Eng. Math, 44, 155-171 (2002) (Invited Article)..

Solid-solid transformations in a confined soft sphere fluid

Chandana Ghatak and K. G. Ayappa, Phys. Rev. E., 64, 051507 (2001)..

Structural transitions of nitrogen confined in slit graphite pores

J. Kamakshi and K. G. Ayappa, Langmuir, 17, 5245-5255 (2001)

Influence of internal convection during microwave thawing of cylinders

Tanmay Basak and K. G. Ayappa, AIChE. J., 47, 835-850 (2001).

Molecular dynamics study of vacancy diffusion in a forced Lennard-Jones system

S. Balaji, T. A. Abinandanan, K. G. Ayappa and N. Chandrashekar, Phil. Mag. A., 80, 301-310 (2000).

Statistical thermodynamics of lattice models in zeolites: Implications of local versus global mean field interactions

K. G. Ayappa J. Chem. Phys., 111, 4736-4742 (1999).

Mean field lattice model for adsorption isotherms in zeolite NaA

K. G. Ayappa, C. R. Kamala, and T. A. Abinandanan, J. Chem. Phys., 110, 8714-8721 (1999).

Resonant microwave power absorption in slabs

K. G. Ayappa, Journal of Microwave Power and Electromagnetic Energy, 34, 33-41 (1999).

Analysis of microwave sintering of ceramics

Anindita Chatterjee, Tanmay Basak and K. G. Ayappa, AIChE. J., 44, 2302-2311 (1998).

Density distributions of diatoms in carbon nanotubes: A grand canonical Monte Carlo study

 Ifadat Ali Khan and K. G. Ayappa, Journal of Chemical Physics, 109, 4576-4586 (1998).

Simulations of binary mixture adsorption in carbon nanotubes: Transitions in adsorbed fluid composition

K. G. Ayappa, Langmuir, 14, 880-890 (1998).

Influence of temperature on mixture adsorption in carbon nanotubes: a grand canonical Monte Carlo study

K. G. Ayappa, Chemical Physics Letters, 282, 59-63 (1998).

Analysis of microwave thawing of slabs with effective heat capacity method

Tanmay Basak and K. G. Ayappa, AIChE J., 43, 1662-1674 (1997).

Resonant microwave power absorption in slabs and cylinders

K. G. Ayappa, S. A. Barringer, H. T. Davis and E. A. Davis, AIChE J., 43, 615-624 (1997).

Modelling transport processes during microwave heating: A review

K. G. Ayappa, Reviews in Chemical Engineering, 13, 1-69 (1997).

Binary fluids in planar nanopores: Adsorptive selectivity, heat capacity and self-diffusivity

S. A. Somers, K. G. Ayappa, A. V. McCormick and H. T. Davis, Adsorption, 2, 33-40 (1996).

Microwave‐heating temperature profiles for thin slabs compared to Maxwell and Lambert law predictions

Barringer S. A., K. G. Ayappa, J. Gordon, K. G. Ayappa and H. T. Davis, J. Food Sci., 60, 1137-1142 (1995).

Power absorption during microwave heating of emulsions and layered systems

Barringer S. A., K. G. Ayappa, E. A. Davis, J. Gordon, and H. T. Davis, J. Food Sci., 60, 1132-1136 (1995).

Effect of sample size on the microwave heating rate: oil vs. water

Barringer S. A., E. A. Davis, J. Gordon, K. G. Ayappa and H. T. Davis, AIChE J., 40, 1433-1439 (1994).

Microwave driven convection in a square cavity

K. G. Ayappa, S. Brandon, J. J. Derby, H. T. Davis, E. A. Davis and J. Gordon, AIChE J., 40, 1268 (1994).

Influence of sample width on deducing capillary pressure curves with the centrifuge

Ayappa K. G., H. T. Davis, E. A. Davis, and J. Gordon, Chem. Engng. Sci., 49, 327-333 (1994).


Microwave thawing of lossy dielectric materials

 Pangrle B. P., K. G. Ayappa, E. A. Sutanto, H. T. Davis, E. A. Davis and J. Gordon, Chem. Engng. Comm., 112, 39-53 (1992).

Two‐dimensional finite element analysis of microwave heating

Ayappa K. G., H. T. Davis, E. A. Davis and J. Gordon, 38, 1577-1592 (1992).

Microwave thawing of cylinders

Pangrle B. P., K. G. Ayappa, H. T. Davis, E. A. Davis and J. Gordon, AIChE J., 37, 1789-1800 (1991).

Analysis of microwave heating of materials with temperature‐dependent properties

Ayappa K. G., H. T. Davis, E.A.Davis and J. Gordon, AIChE J., 37, 313-322 (1991).

Microwave heating: an evaluation of power formulations

Ayappa K. G., H. T. Davis, G. Crapiste, E. A. Davis and J. Gordon, Chem. Engng. Sci., 46, 1005-1016 (1991).

Capillary pressure: centrifuge method revisited

Ayappa K. G., H. T. Davis, E. A. Davis and J. Gordon, AIChE J., 35, 365-372 (1989).