select publications
These publications show the work we’ve done over the years, covering different projects and topics we’ve explored. It’s a record of what we’ve learned and shared with the wider scientific community.
Claudin-2 limits pancreatitis development through regulating tight junction-controlled pancreatic ductal transport
Claudin-2 limits pancreatitis development through regulating tight junction-controlled pancreatic ductal transport, S Kesaraju, Y Li, M Tracy, K Wannemo, J Kainov, N Rana, M Sidahmed, S Hyoju, L Smith, J Matthews, S Tay, F Khalili-Araghi, M Rana, SA Oakes, L. Shen, CR Weber, bioRxiv 2023.09.01.555960 (2023)
Molecular dynamics analyses of CLDN15 pore size and charge selectivity
Molecular dynamics analyses of CLDN15 pore size and charge selectivity
S McGuinness, P Li, Y Li, S Fuladi, S Konar, S Bafghi, M Sidahmed, Y Li, L. Shen, F Khalili-Araghi, CR Weber, bioRxiv, 2023.08. 16.553400 (2023)
Phase Separation and Ion Diffusion in Ionic Liquid, Organic Solvent, and Lithium Salt Electrolyte Mixtures
Phase Separation and Ion Diffusion in Ionic Liquid, Organic Solvent, and Lithium Salt Electrolyte Mixtures, H Gholivand, A Salehi-Khojin, F Khalili-Araghi The Journal of Physical Chemistry B 127 (34), 7531-7541 (2023)
Thermodynamics and Kinetics in Anisotropic Growth of One-Dimensional Midentropy Nanoribbons
Thermodynamics and Kinetics in Anisotropic Growth of One-Dimensional Midentropy Nanoribbons, S Wang, T Yang, K Kumar, S Namvar, S Kim, A Ahmadiparidari, H Shahbazi, S Singh, Z Hemmat, V Berry, J Cabana, F Khalili-Araghi, Z Huang, A Salehi-Khojin, ACS nano 17 (15), 15053-15064 (2023)
Molecular mechanism of claudin-15 strand flexibility: a computational study
Molecular mechanism of claudin-15 strand flexibility: a computational study, S Fuladi, S McGuinness, L Shen, CR Weber, F Khalili-Araghi, Journal of General Physiology 154 (12), e202213116 (2022)
Role of TM3 in claudin-15 strand flexibility: a molecular dynamics study
Role of TM3 in claudin-15 strand flexibility: a molecular dynamics study, S Fuladi, S McGuinness, F Khalili-Araghi, Frontiers in Molecular Biosciences 9, 964877 (2022)
Phase-dependent band gap engineering in alloys of metal-semiconductor transition metal dichalgonecides
Phase-dependent band gap engineering in alloys of metal-semiconductor transition metal dichalgonecides, S Wang, J Cavin, Z Hemmat, K Kumar, A Ruckel, L Majidi, H Gholivand, R Dawood, J Cabana, N. Guisinger, RF Klie, F Khalili‐Araghi, R Mishra, A Salehi‐Khojin, Advanced Functional Materials 30 (51), 2004912 (2020)
Multicomponent Phase Separation in Ternary Mixture Ionic Liquid Electrolytes
Multicomponent Phase Separation in Ternary Mixture Ionic Liquid Electrolytes. S Fuladi, H Gholivand, A Ahmadiparidari, LA Curtiss, A Salehi-Khojin, and F Khalili-Araghi, The Journal of Physical Chemistry B 125 (25), 7024-7032 (2021)
Enhancing the performance of lithium oxygen batteries through combining redox mediating salts with a lithium protecting salt
Enhancing the performance of lithium oxygen batteries through combining redox mediating salts with a lithium protecting salt, A. Ahmadiparidari, S Fuladi, L Majidi, S Plunkett, E Sarnello, H Gholivand, Z Hemmat, S Rastegar, SN Misal, N Jimenez, PC Redfern, J Wen, T Li, AT Ngo, F Khalili-Araghi, LA Curtiss, A Salehi-Khojin, Journal of Power Sources 491, 229506 (2021)
Computational modeling of claudin structure and function
Computational modeling of claudin structure and function, S Fuladi, RW Jannat, L Shen, CR Weber, F Khalili-Araghi, Int. J. Mol. Sci. 21 (3), 742 (2020)
Effect of surface termination on the lattice thermal conductivity of monolayer Ti3C2Tz Mxenes
Effect of surface termination on the lattice thermal conductivity of monolayer Ti3C2Tz Mxenes, H Gholivand, S Fuladi, Z Hemmat, A Salehi-Khojin, F Khalili-Araghi, Journal of Applied Physics 126, 065101 (2019)
New Class of Electrocatalysts Based on 2D Transition Metal Dichalcogenides in Ionic Liquid
New Class of Electrocatalysts Based on 2D Transition Metal Dichalcogenides in Ionic Liquid, L Majidi, P Yasaei, RE Warburton, S Fuladi, J Cavin, X Hu, Z Hemmat, SB Cho, P Abbasi, M Vörös, L Cheng, B Sayahpour, IL Bolotin, P Zapol, J Greeley, RF Klie, R Mishra, F Khalili-Araghi, LA Curtiss, A Salehi-Khojin, Advanced Materials, 1804453 (2018)https://onlinelibrary.wiley.com/doi/full/10.1002/adma.201804453
Molecular determination of claudin-15 organization and channel selectivity
Molecular determination of claudin-15 organization and channel selectivity, P Samanta, Y Wang, S Fuladi, J Zou, Y Li, L Shen, CR Weber, F Khalili-Araghi, Journal of General Physiology 150 (7), 949-968 (2018)
A lithium–oxygen battery with a long cycle life in an air-like atmosphere
A lithium–oxygen battery with a long cycle life in an air-like atmosphere, M Asadi, B Sayahpour, P Abbasi, AT Ngo, K Karis, JR Jokisaari, C Liu, B Narayanan, M Gerard, P Yasaei, X Hu, A Mukherjee, KC Lau, RS Assary, F Khalili-Araghi, RF Klie, LA Curtiss, A Salehi-Khojin, Nature 555 (7697), 502-506 (2018)
Interfacial Thermal Transport in Monolayer MoS2‐ and Graphene‐Based Devices
Interfacial Thermal Transport in Monolayer MoS2‐ and Graphene‐Based Devices, P Yasaei, CJ Foss, K Karis, A Behranginia, AI El‐Ghandour, A Fathizadeh, J Olivares, AK Majee, CD Foster, F Khalili‐Araghi, Z Aksamija, A Salehi‐Khojin, Advanced Materials Interfaces 4 (17), 1700334 (2017)
Stable and selective humidity sensing using stacked black phosphorus flakes
Stable and selective humidity sensing using stacked black phosphorus flakes, P Yasaei, A Behranginia, T Foroozan, M Asadi, K Kim, F Khalili-Araghi, A. Salehi-Khojin, ACS nano 9 (10), 9898-9905 (2016)
Modeling and Analysis of Intercalant Effects on Circular DNA Conformation
Modeling and Analysis of Intercalant Effects on Circular DNA Conformation, E Krueger, J Shim, A Fathizadeh, AN Chang, B Subei, KM Yocham, PH Davis, E Graugnard, F Khalili-Araghi, R Bashir, D Estrada, D Fologea, ACS Nano 10 (9), 8910–8917 (2016)
Bimodal phonon scattering in graphene grain boundaries
Bimodal phonon scattering in graphene grain boundaries, P Yasaei, A Fathizadeh, R Hantehzadeh, AK Majee, A El-Ghandour, D Estrada, C Foster, Z Aksamija, F Khalili-Araghi, A Salehi-Khojin, Nano letters 15 (7), 4532-4540 (2015)
A structural rearrangement of the Na+/K+-ATPase traps ouabain within the external ion permeation pathway
A structural rearrangement of the Na+/K+-ATPase traps ouabain within the external ion permeation pathway, JE Sánchez-Rodríguez, F Khalili-Araghi, P Miranda, B Roux, M Holmgren, F Bezanilla, Journal of molecular biology 427 (6), 1335-1344 (2015)
Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations
Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations, F Khalili-Araghi, B Ziervogel, JC Gumbart, B Roux, Journal of General Physiology 142 (4), 465-475 (2013)
An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations
An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations, E Vargas, V Yarov-Yarovoy, F Khalili-Araghi, WA Catterall, ML Klein, M Tarek, E Lindahl, K Schulten, E Perozo, F Bezanilla, B Roux, Journal of General Physiology 140 (6), 587-594 (2012)
Molecular dynamics investigation of the ω-current in the Kv1. 2 voltage sensor domains
Molecular dynamics investigation of the ω-current in the Kv1. 2 voltage sensor domains, F Khalili-Araghi, E Tajkhorshid, B Roux, K Schulten, Biophysical Journal 102 (2), 258-267 (2012)
Constant electric field simulations of the membrane potential illustrated with simple systems
Constant electric field simulations of the membrane potential illustrated with simple systems, J Gumbart, F Khalili-Araghi, M Sotomayor, B Roux, Biochimica et Biophysica Acta (BBA)-Biomembranes 1818 (2), 294-302 (2012)
Ouabain binding site in a functioning Na+/K+ ATPase
Ouabain binding site in a functioning Na+/K+ ATPase, W Sandtner, B Egwolf, F Khalili-Araghi, JE Sánchez-Rodríguez, B Roux, F Bezanilla, M Holmgren, Journal of Biological Chemistry 286 (44), 38177-38183 (2011)
On the sensing mechanism in carbon nanotube chemiresistors
On the sensing mechanism in carbon nanotube chemiresistors, A Salehi-Khojin, F Khalili-Araghi, MA Kuroda, KY Lin, JP Leburton, RI Masel, ACS nano 5 (1), 153-158 (2011)
Calculation of the gating charge for the Kv1. 2 voltage-activated potassium channel
Calculation of the gating charge for the Kv1. 2 voltage-activated potassium channel, F Khalili-Araghi, V Jogini, V Yarov-Yarovoy, E Tajkhorshid, B Roux, K. Schulten, Biophysical journal 98 (10), 2189-2198 (2010)
Molecular dynamics simulations of membrane channels and transporters
Molecular dynamics simulations of membrane channels and transporters, F Khalili-Araghi, J Gumbart, PC Wen, M Sotomayor, E Tajkhorshid, K. Schulten, Current opinion in structural biology 19 (2), 128-137 (2009)
Dynamics of K+ ion conduction through Kv1.2
Dynamics of K+ ion conduction through Kv1. 2, F Khalili-Araghi, E Tajkhorshid, K Schulten, Biophysical journal 91 (6), L72-L74 (2006)
Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality
Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality, S Park, F Khalili-Araghi, E Tajkhorshid, K Schulten, The Journal of chemical physics 119 (6), 3559-3566 (2003)