Publications

Books

“On The Theory Of Activated Processes” J. E. Straub, Doctoral Dissertation (Columbia University, 1987).

“Proteins: Energy, Heat and Signal Flow,” D. M. Leitner and J. E. Straub, Editors, Taylor and Francis Group, CRC Press (Boca Raton, 2009).

“Mathematical Methods for Molecular Science,” J. E. Straub, University Science Books (Melville, 2022).

Journal Articles

2025

[188] “Systematic parameterization of Flory–Huggins models from molecular dynamics simulations for ternary lipid mixtures,” S.P. Nayak, D .Zwicker, and J.E. Straub, J. Chem. Theor. Comp. (2025).

[187] “Efficient sampling of free energy landscapes for the calculation of protein–protein binding affinities in membranes,” A. Majumder, J.E. Straub, J. Phys. Chem. B 129, 9031-9042 (2025).[PDF]

[186] “Kinetics and mechanism of phase separation in ternary lipid mixtures containing APP C99: Atomistic vs coarse-grained MD simulations,” G.A. Pantelopulos, S. Prusty, A. Bandara, and J.E. Straub, J. Chem. Theory Comput. 21, 5291–5303 (2025).[PDF]

[185] “Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins,” M. Mugnai, D. Chakraborty, H.T. Nguyen, F. Maksudov, A. Kumar, W. Zeno, J.C. Stachowiak, J.E. Straub, and D. Thirumalai, Prot. Sci. 34, e70067 (2025). [PDF]

[184] “Elucidating the mechanism of recognition and binding of heparin to amyloid fibrils of Serum Amyloid A,” C.B. Abraham, E. Lewkowicz, O. Gursky, and J.E. Straub, Biochemistry 64, 266-276 (2025).[PDF]

2024

[183] “Exploring free energy landscapes for protein partitioning into membrane domains in all-atom and coarse-grained simulations,” S. Kwon, A. Majumder, and J.E. Straub, J. Chem. Theor. Comp. 20, 9687-9698 (2024).[PDF]

[182] “Probing the origins of the disorder-to-order transition of a modified cholesterol in ternary lipid bilayers,” A. Majumder, Y. Gu, Y.-C. Chen, X. An, B.M. Reinhard and J.E. Straub, J. Am. Chem. Soc. 146, 27725-27735 (2024).[PDF]

[181] “Machine learning derived collective variables for the study of protein homodimerization in membrane,” A. Majumder and J.E. Straub, J. Chem. Theor. Comp. 20, 5774-5783 (2024).[PDF]

[180] “Conformational fluctuations and phases in fused in sarcoma (FUS) low-complexity domain,” D. Thirumalai, A. Kumar, D. Chakraborty, J. E. Straub, M. L. Mugnai, Biopolymers e23558 (2024).[PDF]

[179] “Cholesterol and lipid rafts in the biogenesis of amyloid-β protein and Alzheimer’s disease,” C.B. Abraham, L. Xu, G.A. Pantelopulos, and J.E. Straub, Ann. Rev. Biophys. 53, 455-486 (2024).[PDF]

2023

[178] “Characterizing the transmembrane domains of ADAM10 and BACE1 and the impact of membrane composition,” C.B. Abraham, L. Xu, G.A. Pantelopulos, and J.E. Straub, Biophys. J. 122, 3999-4010 (2023). [PDF]

[177] “Synergistic computational and experimental studies of a phosphoglycosyl transferase membrane/ligand ensemble,” A. Majumder. N. Vuksanovic, L.C. Ray, H.M. Bernstein, K.N. Allen, B. Imperiali, and J.E. Straub, J. Biol. Chem. 299, 105194 (2023). [PDF]

[176] “The role of structural heterogeneity in the homodimerization of transmembrane proteins,” A. Majumder and J.E. Straub, J. Chem. Phys. 159, 134101 (2023).[PDF]

[175] “Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald’a rule of stages,” D.Chakraborty, J.E. Straub, and D. Thirumalai, Sci. Adv. 9, eadd6921 (2023).[PDF]

[174]. “Efficient calculation of the free energy for protein partitioning using restraining potentials,” S. Kwon, G.A. Pantelopulos, and J.E. Straub, Biophys. J. 122, 1914-1925 (2023).[PDF]

2022

[173]. “Formation of extramembrane β-strands controls dimerization of transmembrane helices in amyloid precursor protein C99,” G.A. Pantelopulos, D. Matsuoka, J.M. Hutchison, C.R. Sanders, Y. Sugita, J. E. Straub, and D. Thirumalai, Proc. Natl. Acad. Sci. USA 119, e2212207119 (2022).[PDF]

[172]. “On computing equilibrium binding constants for protein-protein association in membranes,” A. Majumder and J.E. Straub, J. Chem. Theor. Comp. 18, 3961-3971 (2022).[PDF]

[171] “Dynamical models of chemical exchange in nuclear magnetic resonance spectroscopy,” N. Daffern, C. Nordyke, M. Zhang, A.G. Palmer, and J.E. Straub, The Biophysicist 3, 13-34 (2022).[PDF]

2021

[170] “2020 JCP Emerging Investigator Special Collection,” M. Ceriotti, L. Jensen, D.E. Manolopoulos, T.J. Martinez, A. Michaelides, J.P. Ogilvie, D.R. Reichman, Q. Shi, J.E. Straub, C. Vega, L.-S. Wang, E. Weiss, X. Zhu, J.L. Stein, T. Lian, J. Chem. Phys. 155, 230401 (2021).[PDF]

[169] “Sequence determines the switch in the fibril forming regions in the low-complexity FUS protein and its variants,” A. Kumar, D. Chakraborty, M.L. Mugnai, J.E. Straub, and D. Thirumalai, J. Phys. Chem. Lett. 12, 9026-9032 (2021).[PDF]

[168] “Interfacial hydration determines orientational and functional dimorphism of sterol-derived Raman tags in lipid-coated nanoparticles,” X. An, A. Majumder, J. McNeely, J. Yang, T. Puri, Z. He, T. Liang, J.K. Snyder, J.E. Straub, and B.M. Reinhard, Proc. Natl. Acad. Sci. USA 118, e2105913118 (2021).[PDF]

[167] “Finite-size effects and optimal system sizes in simulations of surfactant micelle self-assembly,” J.J. Harris, G.A. Pantelopulos, and J.E. Straub, J. Phys. Chem. B 125, 5068-5077 (2021).[PDF]

[166] “Addressing the excessive aggregation of membrane proteins in the MARTINI model,” A. Majumder and J.E. Straub, J. Chem. Theor. Comp. 17, 2513-2521 (2021).[PDF]

[165] “Direct observation of cholesterol dimers and tetramers in lipid bilayers,” M.R. Elkins, A. Bandara, G.A. Pantelopulos, J.E. Straub, and M. Hong, J. Phys. Chem. B 125, 1825-1837 (2021).[PDF]

[164] “New and notable: A Multiscale coarse-grained model of the SARS-CoV-2 Virion,” J.E. Straub, Biophys. J. 120, 975-976 (2021).[PDF]

[163] “Amyloid oligomers: A joint experimental/computational perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis,” P.H.Nguyen, A. Ramamoorthy, B.R. Sahoo, J. Zheng, P. Faller, J.E. Straub, L. Dominguez, J.-E. Shea, N.V. Dokholyan, A. DeSimone, B. Ma, R. Nussinov, S. Najafi, S.T. Ngo, A. Loquet, M. Chiricotto, P. Ganguly, J. McCarty, M.S. Li, C. Hall, Y. Wang, Y. Miller, S. Melchionna, B. Habenstein, S. Timr, J. Chen, B. Hnath, B. Strodel, R. Kayed, S. Lesn’e, G. Wei, G. Sterpone, A.J. Doig, and P. Derreumaux, Chem. Rev. 121, 2545-2647 (2021).[PDF]

2020

[162] “JCP Emerging Investigator Special Collection 2019,” M.D. Ediger, L. Jensen, D.E. Manolopoulos, T.J. Martinez, A. Michaelides, D.R. Reichman, C.D. Sherrill, Q. Shi, J.E. Straub, C. Vega, L.-S. Wang, E.C. Brigham, T. Lian, J. Chem. Phys. 153, 110402 (2020).[PDF]

[161] “Impact of cholesterol concentration and lipid phase on structure and fluctuation of amyloid precursor protein,” G.A. Pantelopulos, A. Panahi, and J.E. Straub, J. Phys. Chem. B 124, 10173-10185 (2020). [PDF]

[160] “Differences in the free energies between the excited states of Abeta40 and Abeta42 monomers encode their aggregation propensities,” D. Chakraborty, J.E. Straub, and D. Thirumalai, Proc. Natl. Acad. Sci. USA 117, 19926-19937 (2020).[PDF]

[159] “Vibrational spectroscopic map, vibrational spectroscopy, and intermolecular interaction,” C.R. Baiz, B. Błasiak, J. Bredenbeck, M. Cho, J.-H. Choi, S.A. Corcelli, A.G. Dijkstra, C.-J. Feng, S. Garrett-Roe, N.-H. Ge, M.W.D. Hanson-Heine, J.D. Hirst, T.L.C. Jansen, K. Kwac, K.J. Kubarych, C.H. Londergan, H. Maekawa, M. Reppert, S. Saito, S. Roy, J.L. Skinner, G. Stock, J.E. Straub, M.C. Thielges, K. Tominaga, A. Tokmakoff, H. Torii, L. Wang, L.J. Webb, and M.T. Zanni, Chem. Rev. 120, 7152-7218 (2020). [PDF]

[158] “Bicelles rich in both sphingolipids and cholesterol and their use in studies of membrane proteins,”
J. Hutchison, K.-C. Shih, H.A. Scheidt, S. Fantin, K. Parson, G. Pantepoulos, H. Harrington, K. Mittendorf, S. Qian, R.A. Stein, S.E. Collier, M.G. Chambers, J. Katsaras, M.W. Voehler, B.T. Ruotolo, D. Huster, R. McFeeters, J.E. Straub, M.-P. Nieh, and C.R. Sanders, J. Am. Chem. Soc. 142, 12715-12729 (2020). [PDF]

[157] “Structural basis for lipid binding and function by an evolutionarily conserved protein, Serum Amyloid A,” N. M. Frame, M. Kumanan, T.E. Wales, A. Bandara, M. Fändrich, J.E. Straub, J.R. Engen, and O. Gursky, J. Mol. Bio. 432, 1978-1995 (2020). [PDF]

2019

[156] “Sequence effects on size, shape, and structural heterogeneity in intrinsically disordered proteins,” U. Baul, D. Chakraborty, M.L. Mugnai, J.E. Straub, and D. Thirumalai, J. Phys. Chem. B 123, 3462-3474 (2019). [PDF]

[155] “Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture,” A. Bandara, A. Panahi, G.A. Pantelopulos, T.Nagai, and J.E. Straub, J. Chem. Phys. 150, 204702 (2019). [PDF]

[154.] “Aerosol-OT surfactant forms stable reverse micelles in apolar solvent in the absence of water,” R. Urano, G.A. Pantelopulos, and J.E. Straub, J. Phys. Chem. B 123, 2546-2557 (2019). [PDF]

[153.] “Design, synthesis, and biomedical applications of synthetic sulphated polysaccharides,” H.E. Caputo, J.E. Straub, and M.W. Grinstaff, Chem. Soc. Rev. 48, 2338-2365 (2019). [PDF]

[152.] “Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems,” Y. Sakae, J.E. Straub, and Y. Okamoto, J. Comp. Chem. 40, 475-481 (2019). [PDF]

2018

[151.] “Regimes of complex lipid bilayer phases induced by cholesterol concentration in MD simulation,” G.A. Pantelopulos, and J.E. Straub, Biophys. J. 115, 2167-2178 (2018). [PDF]

[150.] “Characterization of dynamics and mechanism in the self-assembly of AOT reverse micelles,” R. Urano, G.A. Pantelopulos, S. Song, and J.E. Straub, J. Chem. Phys. 149, 144901 (2018). [PDF]

[149.] “Membrane-wrapped nanoparticles probe divergent roles of GM3 and phosphatidylserine in lipid-mediated viral entry pathways,” F. Xu, A. Bandara, H. Akiyama, B. Eshaghi, D. Stelter, T. Keyes, J.E. Straub, S. Gummuluru, and B.M. Reinhard, Proc. Natl. Acad. Sci. USA 115, E9041-E9050 (2018). [PDF]

[148.] “Molecular Insights into human hereditary apolipoprotein AI amyloidosis caused by the Glu34Lys mutation,” I. Morgado, A. Panahi, A.G. Burwash, M. Das, J.E. Straub, and O. Gursky, Biochem. 57, 5738-5747 (2018). [PDF]

[147.] “Influence of membrane lipid composition on the structure and activity of γ-secretase,” R. Aguayo-Ortiz, J.E. Straub, and L. Dominguez, Phys. Chem. Chem. Phys. 20, 27294-27304 (2018). [PDF]

[146.] “Structure of APP-C99(1-99) and implications for role of extra-membrane domains in function and oligomerization,” G.A. Pantelopulos, J.E. Straub, D. Thirumalai and Y. Sugita, Biochim. Biophys. Acta 1860, 1698-1708 (2018). [PDF]

2017

[145.] “Cellular prion protein targets amyloid-β fibril ends via its C-terminal domain to prevent elongation,” E. Bove-Fenderson, R. Urano, J.E. Straub, and D.A. Harris, J. Bio. Chem. 292, 16858-16871 (2017). [PDF]

[144] “Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures,” G. A. Pantelopulos, T. Nagai, A. Bandara, A. Panahi, J.E. Straub, J. Chem. Phys. 147, 095101 (2017).[PDF]

[143] “Special Issue: Amyloid Aggregation,” Y. Miller and J.E. Straub, Israel J. Chem. 57, 562-563 (2017).[PDF]

[142] “Exploring the structure and stability of cholesterol dimer formation in multicomponent lipid bilayers,” A. Bandara, A. Panahi, G.A. Pantelopulos, and J.E. Straub, J. Comp. Chem. 38, 1479-1488 (2017); ibid. 40, 2348-2348 (2019).[PDF]

[141] “Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach,” R. Aguayo-Ortiz, C. Chavez-Garcia, J.E. Straub, and L. Dominguez, Chem. Sci. 8, 5576-5584 (2017).[PDF]

2016

[140] “Specific binding of cholesterol to C99 domain of Amyloid Precursor Protein depends critically on charge state of protein,” A. Panahi, A. Bandara, G.A. Pantelopulos, L. Dominguez, and J.E. Straub, J. Phys. Chem. Lett. 7, 3535-3541 (2016).[PDF]

[139] “Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein,” L. Dominguez, L. Foster, J.E. Straub, and D. Thirumalai, Proc. Natl. Acad. Sci. USA 113, E5281-E5287 (2016).[PDF]

[138] “On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics,” T. Nagai, G.A. Pantelopulos, T. Takahashi, and J.E. Straub, J. Comp. Chem. 37, 2017-2028 (2016).[PDF]

[137] “Combined molecular dynamics simulations and experimental studies of the structure and dynamics of polyamidosaccharides,” S.L. Chin, Q. Lu, E.L. Dane, L. Dominguez, C.J. McKnight, J.E. Straub, and M.W. Grinstaff, J. Am. Chem. Soc. 138, 6532-6540 (2016).[PDF]

[136] “Freezing transitions of nanoconfined coarse-grained water show subtle dependence on confining environment,” Q. Lu and J.E. Straub, J. Phys. Chem. B 120, 2517-2525 (2016).[PDF]

2015

[135] “Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization,” S. Viswanath, L. Dominguez, L. S. Foster, J. E. Straub, and R. Elber, Proteins 83, 2170-2185 (2015). [PDF]

[134] “Role of charge and solvation in the structure and dynamics of alanine-rich peptide AKA₂ in AOT reverse micelles,” A.V. Martinez, E. Malolepsza, L. Dominguez, Q. Lu, and J.E. Straub, J. Phys. Chem. B 119, 9084-9090 (2015). [PDF]

2014

[133] “Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ_16-22 and Sup35_7-13 in AOT reverse micelles,” A.V. Martinez, E. Malolepsza, E. Rivera, Q. Lu, and J.E. Straub, J. Chem. Phys. 141, 22D530 (2014). [PDF]

[132] “Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method,” Q. Lu, J. Kim, J. D. Farrell, D. J. Wales, and J.E. Straub, J. Chem. Phys. 141, 18C525 (2014). [PDF]

[131] “Empirical maps for the calculation of amide I vibrational spectra of proteins from classical molecular dynamics simulations,” E. Malolepsza and J.E. Straub, J. Phys. Chem. B 118, 7848-7855 (2014). [PDF]

[130] “Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins,” P.I. Zhuravlev, G. Reddy, J.E. Straub, and D. Thirumalai, J. Mol. Bio. 426, 2653-2666 (2014). [PDF]

[129] “Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection,” L. Dominguez, L. Foster, S.C. Meredith, J.E. Straub, and D. Thirumalai, J. Am. Chem. Soc. 136, 9619-9626 (2014). [PDF]

[128] “Vibrational energy flow across heme-cytochrome c and cytochrome c-water interfaces,” J. K. Agbo, Y. Xu, P. Zhang, J. E. Straub, and D. M. Leitner, Theor. Chem. Acc. 133, 1504 (2014). [PDF]

[127] “Limit of metastability for liquid and vapor phases of water,” W.J. Cho, J. Kim, J. Lee, T. Keyes, J. E. Straub, and K.S. Kim, Phys. Rev. Lett. 112, 157802 (2014). [PDF]

[126] “Membrane protein interactions are key to understanding amyloid formation,” J.E. Straub and D. Thirumalai, J. Phys. Chem. Lett. 5, 633-635 (2014). 2013

[124] “Spatio-temporal hierarchy in the dynamics of a minimalist protein model,” Y. Matsunaga, A. Baba, C.B. Li, J.E. Straub, M. Toda, T. Komatsuzaki, and R. S. Berry, J. Chem. Phys. 139, 215101 (2013). [PDF]

[123] “Probing the structure and dynamics of confined water in AOT reverse micelles,” A.V. Martinez, L. Dominguez, E. Malolepsza, A. Moser, Z. Ziegler, and J.E. Straub, J. Phys. Chem. B 117, 7345-7351 (2013). [PDF]

[122] “‘Strange Kinetics’ in the temperature dependence of methionine ligand rebinding dynamics in cytochrome c,” P. Zhang, S. W. Ahn, and J. E. Straub, J. Phys. Chem. B 117, 7190-7202 (2013). [PDF]

[121] “Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method,” Q. Lu, J. Kim, and J. E. Straub, J. Chem. Phys. 138, 104119 (2013). [PDF]

2012-2011

[120] “Exploring the solid-liquid phase change of an adapted Dzugutov model using Generalized Replica Exchange Method,” Q. Lu, J. Kim, and J.E. Straub, J. Phys. Chem. B 116, 8654-8661 (2012). [PDF]

[119] “Replica Exchange Statistical Temperature Molecular Dynamics Algorithm,” J. Kim, J. E. Straub, and T. Keyes, J. Phys. Chem. B 116, 8646-8653 (2012). [PDF]

[118] “Dynamics of methionine ligand rebinding in cytochrome c,” P. Zhang, E. Malolepsza, and J. E. Straub, J. Phys. Chem. B 116, 6980-6990 (2012). [PDF]

[117] “Role of water in protein aggregation and amyloid polymorphism,” D. Thirumalai, G. Reddy, and J. E. Straub, Acc. Chem. Res. 45, 83-92 (2012). [PDF]

Book Chapters

[B10] “On the development of coarse-grained protein models,” N.-V. Buchete, J. E. Straub and D. Thirumalai, in: Coarse-Graining of Condensed Phase and Biomolecular Systems, edited by G. A. Voth, Taylor & Francis/CRC Press (2009), pp. 141-156.

[B8] “Probing vibrational energy relaxation in protein using normal modes,” H. Fujisaki, L. Bu and J. E. Straub, in: Normal Mode Analysis, edited by Q. Cui and I. Bahar, Chapman and Hall/CRC Press (2005), pp. 301-323. [PDF]

[B4] “Protein Folding and Optimization Algorithms,” J. E. Straub, in: The Encyclopedia of Computational Chemistry, John Wiley & Sons (1998), vol. 3, pp. 2184-2191. [PDF]

[B1] “Optimization Techniques with Applications to Proteins,” J.E. Straub, in: New Developments in Theoretical Studies of Proteins, World Scientific (1996), pp. 137-196. [PDF]