Publications

Books

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

Journal Articles

2017

[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).[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. Grinsta ff, J. Am. Chem. Soc. 138, 6532-6540 (2016).[PDF]

[136] “Freezing transitions of nanocon fined coarse-grained water show subtle dependence on con fining 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 Aβ16-22 and Sup357-13 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 nano films 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] L. Dominguez, L. Foster, S.C. Meredith, J.E. Straub, and D. Thirumalai, “Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection,” J. Am. Chem. Soc. 136, 9619-9626 (2014). [PDF]

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

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

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

[125] L. Dominguez, S.C. Meredith, J.E. Straub, and D. Thirumalai, “Transmembrane fragment structures of Amyloid Precursor Protein depend on membrane surface curvature [Communication],” J. Am. Chem. Soc. 136, 854-857 (2014). [PDF]

2013

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

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

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

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

2012

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

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

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

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

2011

[116] H. Fujisaki, Y. Zhang, and J.E. Straub, “Non-Markovian theory of vibrational energy relaxation and its applications to bimolecular systems,” Adv. Chem. Phys. 145, 1-33 (2011). [PDF]

[115] T. Komatsuzaki, A. Baba, M. Toda, J. E. Straub, and R. S. Berry, “Ergodic problems for real complex systems in chemical physics,” Adv. Chem. Phys. 145, 171-220 (2011). [PDF]

[114] S. S. Cho, G. Reddy, J.E. Straub, and D. Thirumalai, “Entropic stabilization of proteins by TMAO,” J. Phys. Chem. B 115, 13401-13407 (2011). [PDF]

[113] J. Kim, T. Keyes, and J.E. Straub, “Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables,” J. Chem. Phys. 135, 061103 (2011). [PDF]

[112] E.P. O’Brien, J.E. Straub, B.R. Brooks, and D. Thirumalai, “Influence of nanoparticle size and shape on oligomer formation of an amyloidogenic peptide,” J. Phys. Chem. Lett. 2, 1171-1177 (2011). [PDF]

[111] A.V. Martinez, S.C. DeSensi, L. Dominguez, E. Rivera, and J.E. Straub, “Protein folding in a reverse micelle environment: The role of confinement and dehydration,” J. Chem. Phys. 134, 055107 (2011). [PDF]

[110] J.E. Straub and D. Thirumalai, “Toward a molecular theory of early and late events in monomer to amyloid fibril formation,” Ann. Rev. Phys. Chem. 62, 437-463 (2011). [PDF]

2010

[109] G. Reddy, J.E. Straub, and D. Thirumalai, “Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires,”Proc. Natl. Acad. Sci. USA 107, 21459-21464 (2010). [PDF]

[108] M. S. Li, N. T. Co, G. Reddy, C.K. Hu, J.E. Straub, and D. Thirumalai, “Factors governing fibrillogenesis of polypeptide chains revealed by lattice models,” Phys. Rev. Lett. 105 218101 (2010). [PDF]

[107] J. Kim and J. E. Straub, “Generalized simulated tempering for exploring strong phase transitions,” J. Chem. Phys. 133 154101 (2010). [PDF]

[106] J. Kim, T. Keyes, and J. E. Straub, “Generalized Replica Exchange Method,” J. Chem. Phys. 132, 224107 (2010). [PDF]

[105] J. E. Straub and D. Thirumalai, “Principles governing oligomer formation in amyloidogenic peptides,” Curr. Opin. Struc. Bio. 20, 187-195 (2010). [PDF]

2009

[104] N. Miyashita, J.E. Straub, and D. Thirumalai, “Structures of β-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with γ-secretase,” J. Am. Chem. Soc. 131, 17843-17852 (2009). [PDF]

[103] E.P. O’Brien, Y. Okamoto, J.E. Straub, B.R. Brooks and D. Thirumalai, “Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibris,” J. Phys. Chem. B 113, 14421-14430 (2009). [PDF]

[102] H. Fujisaki, K. Yagi, J.E. Straub and G. Stock, “Quantum and classical vibrational relaxation dynamics of N-methylacetamide on ab initio potential energy surfaces,” Int. J. Quant. Chem. 109, 2047-2057 (2009). [PDF]

[101] E. Rivera, J.[E.] Straub and D. Thirumalai, “Sequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide,” Biophys. J. 96, 4552-4560 (2009). [PDF]

[100] Y. Zhang and J.E. Straub, “Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. III. The ν4 and ν7 modes of nonplanar nickel porphyrin models,” J. Chem. Phys. 130, 215101 (2009). [PDF]

[99] J. Kim and J.E. Straub, “Optimal replica exchange method combined with Tsallis weight sampling,” J. Chem. Phys. 130, 144114 (2009). [PDF]

[98] N. Miyashita, J.E. Straub, D. Thirumalai and Y. Sugita, “Transmembrane structures of amyloid precursor protein dimer predicted by Replica-Exchange Molecular Dynamics simulations [Communication],” J. Am. Chem. Soc. 131, 3438-3439 (2009). [PDF]

[97] G. Reddy, J. E. Straub, and D. Thirumalai, “Dynamics of locking of peptides onto growing amyloid fibrils,” Proc. Natl. Acad. Sci. USA 106, 11948-11953 (2009). [PDF]

[96] J. Kim and J.E. Straub, “Relationship between protein folding thermodynamics and the energy landscape,” Phys. Rev. E 79, 030902 (2009). [PDF]

[95] J. Kim, T. Keyes and J.E. Straub, “Replica exchange statistical temperature Monte Carlo,” J. Chem. Phys. 130, 124112 (2009). [PDF]

[94] Y. Zhang, H. Fujisaki and J.E. Straub, “Mode-specific vibrational energy relaxation of amide I’ and II’ modes in N-methylacetamide/water clusters: Intra- and intermolecular energy transfer mechanisms,” J. Phys. Chem. A 113, 3051-3060 (2009). [PDF]

[93] Y. Zhang, H. Fujisaki and J.E. Straub, “Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. II. The ν4 and ν7 modes of iron-protoporphyrin IX and iron porphine,” J. Chem. Phys. 130, 095102 (2009). [PDF]

[92] Y. Zhang, H. Fujisaki and J.E. Straub, “Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model,” J. Chem. Phys. 130, 025102 (2009). [PDF]

[91] G. Reddy, J. E. Straub and D. Thirumalai, “Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Aβ peptides with implications for rates of fibril formation,” J. Phys. Chem. B 113, 1162-1172 (2009). [PDF]

[90] Y. Zhang and J. E. Straub, “Diversity of solvent dependent energy transfer pathways in heme proteins,” J. Phys. Chem. B 113, 825-830 (2009). [PDF]

2008

[89] B.M. Leu, Y. Zhang, L.T. Bu, J. E. Straub, J.Y. Zhao, W. Sturhahn, E. E. Alp and J. T. Sage, “Resilience of the iron environment in heme proteins,” Biophys. J. 95, 5874-5899 (2008). [PDF]

[88] M. S. Li, D. K. Klimov, J.E. Straub and D. Thirumalai, “Probing the mechanisms of fibril formation using lattice models,” J. Chem. Phys. 129, 175101 (2008). [PDF]

[87] B. Tarus, J.E. Straub, and D. Thirumalai, “Structures and free-energy landscapes of the wild type and mutants of the Aβ(21-30) peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions,” J. Mol. Bio. 379, 815-829 (2008). [PDF]

[86] N.-V. Buchete, J. E. Straub, D. Thirumalai, “Dissecting contact potentials for proteins: Relative contributions of individual amino acids,” Proteins 70, 119-130 (2008). [PDF]

2007

[85] H. Fujisaki and J.E. Straub, “Vibrational energy relaxation of isotopically labeled amide I modes in cytochrome c: Theoretical investigation of vibrational energy relaxation rates and pathways,”J. Phys. Chem. B 111, 12017-12023 (2007).[PDF]

[84] J. Kim, J.E. Straub and T. Keyes, “Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing,” Phys. Rev. E 76, 011913 (2007). [PDF]

[83] H. Fujisaki, K. Yagi, K. Hirao and J. E. Straub, “Quantum dynamics of N-methylacetamide studied by the vibrational configuration interaction method,” Chem. Phys. Lett. 443, 6-11 (2007). [PDF]

[82] J. Kim, J.E. Straub and T. Keyes, “Statistical temperature molecular dynamics: Application to coarse-grained beta-barrel-forming protein models,” J. Chem. Phys. 126, 135101 (2007). [PDF]

[81] Y. Zhang, H. Fujisaki, and J. E. Straub, “Molecular dynamics study on the solvent dependent heme cooling following ligand photolysis in carbonmonoxymyoglobin,” J. Phys. Chem. B 111, 3243-3250 (2007). [PDF]

[80] P.H. Phuong, M.S. Li, G. Stock, J.E. Straub, and D. Thirumalai, “Monomer adds to preformed structured oligomers of A beta-peptides by a two-stage dock-lock mechanism,” Proc. Natl. Acad. Sci. USA 104, 111-116 (2007). [PDF]

2006

[79] B. Tarus, J. E. Straub and D. Thirumalai, “Dynamics of Asp23-Lys28 salt-bridge formation in Aβ(10-35) monomers,” J. Am. Chem. Soc. 128, 16159-16168 (2006). [PDF]

[78] J. Kim, J. E. Straub, and T. Keyes, “Statistical-temperature Monte Carlo and Molecular Dynamics algorithms,” Phys. Rev. Lett. 97, 050601 (2006). [PDF]

[77] A. E. van Giessen and J. E. Straub, “Coarse-grained model of coil-to-helix kinetics demonstrates the importance of multiple nucleation sites in helix folding,” J. Chem. Theor. Comp. 2, 674 – 684 (2006). [PDF]

[76] M. E. Cremeens, H. Fujisaki, Y. Zhang, J. Zimmerman, L. B. Sagle, S. Matsuda, P. E. Dawson, J. E. Straub and F. E. Romesberg, “Efforts toward developing direct probes of protein dynamics,” J. Am. Chem. Soc. 128, 6028-6029 (2006). [PDF]

[75] H. Fujisaki, Y. Zhang and J. E. Straub, “Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins,” J. Chem. Phys. 124, 144910 (2006). [PDF]

2005

[74] H. Fujisaki, L. Bu and J. E. Straub, “Vibrational Energy Relaxation (VER) of a CD stretching mode in cytochrome c,” Adv. Chem. Phys. 130, 179-203 (2005).[PDF]

[73] H. Fujisaki and J. E. Straub, “Vibrational energy relaxation in proteins,” Proc. Natl. Acad. Sci. USA 102, 6726-6731 (2005). [PDF]

[72] A. van Giessen and J. E. Straub, “Monte Carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials,” J. Chem. Phys. 122, 024904 (2005). [PDF]

[71] B. Tarus, J. E. Straub and D. Thirumalai, “Probing the initial stage of aggregation of the Aβ(10-35)-protein: Assessing the propensity of peptide dimerization,” J. Mol. Bio. 345, 1141-1156 (2005). [PDF]

2004

[70] D.K. Klimov, J.E. Straub, and D. Thirumalai, “Aqueous urea solution destabilizes Aβ16-22 oligomers,” Proc. Natl. Acad. Sci. USA 101, 14760-14765 (2004).[PDF]

[69] N.-V. Buchete, J. E. Straub, and D. Thirumalai, “Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases,” Polymer 45, 597-608 (2004). [PDF]

[68] N.-V. Buchete, J. E. Straub, and D. Thirumalai, “Orientational potentials extracted from protein structures improve native fold recognition,” Prot. Sci. 13, 862-874 (2004). [PDF]

[67] N.-V. Buchete, J. E. Straub, and D. Thirumalai, “Development of novel statistical potentials for protein fold recognition,” Curr. Opin. Struct. Bio. 14, 225-232 (2004). [PDF]

[66] N.-V. Buchete, J. E. Straub, and D. Thirumalai, “Continuous aniosotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis,” J. Mol. Graph. 22, 441-450 (2004). [PDF]

2003

[65] G. Bitan, B. Tarus, S. S. Vollers, H. A. Lashuel, M. M. Condron, J. E. Straub, and D. B. Teplow, “A molecular switch in amyloid assembly: Met35 and amyloid β-protein oligomerization,” J. Am. Chem. Soc. 125, 15359-15365 (2003). [PDF]

[64] L. Bu and J. E. Straub, “Simulating vibrational energy flow in proteins: Relaxation rate and mechanism for heme cooling in cytochrome c,” J. Phys. Chem. B 107, 12339-12345 (2003). [PDF]

[63] L. Bu and J. E. Straub, “Vibrational energy relaxation of ‘tailored’ hemes in myoglobin following ligand photolysis supports energy funneling mechanism of heme ‘cooling’,” J. Phys. Chem. B 107, 10634-10639 (2003). [PDF]

[62] N.-V. Buchete, J. E. Straub and D. Thirumalai, “Aniostropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures,” J. Chem. Phys. 118, 7658-7671 (2003). [PDF]

[61] L. Bu and J. E. Straub, “Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome c,” Biophys. J. 85, 1429-1439 (2003). [PDF]

[60] F. Massi and J. E. Straub, “Structural and dynamical analysis of the hydration of the Alzheimer’s β-amyloid peptide,” J. Comp. Chem. 24, 143-153 (2003).[PDF]

2002

[59] T. W. Whitfield and J. E. Straub, “Gravitational smoothing as a global optimization strategy,”J. Comp. Chem. 23, 1100-1103 (2002). [PDF]

[58] J. E. Straub, J. Guevara, S. H. Huo and J. P. Lee, “Long time dynamic simulations: Exploring the folding pathways of an Alzheimer’s amyloid β-peptide,” Acc. Chem. Res. 35, 473-481 (2002). [PDF]

[57] F. Massi, D. Klimov, D. Thirumalai and J. E. Straub, “Charge states rather than propensity for β-structure determine enhanced fibrillogenesis in wild-type Alzheimer’s β-amyloid peptide compared to E22Q Dutch mutant,” Prot. Sci. 11, 1639-1647 (2002). [PDF]

[56] T. W. Whitfield, L. Bu and J. E. Straub, “Generalized parallel sampling,” Physica A 305, 157-171 (2002). [PDF]

2001

[55] T. W. Whitfield and J. E. Straub, “Enhanced sampling in numerical path integration: An approximation for the quantum statistical density matrix based on the nonextensive thermostatistics,” Phys. Rev. E 64, 66115-11 (2001). [PDF]

[54] I. Andricioaei, J. E. Straub and M. Karplus, “Simulation of quantum systems using path integrals in a generalized ensemble,” Chem. Phys. Lett. 346, 274-282 (2001). [PDF]

[53] T. W. Whitfield and J. E. Straub, “Uncertainty of path integral averages at low temperature,” J. Chem. Phys. 115, 6834-6840 (2001). [PDF]

[52] D. E. Sagnella and J. E. Straub, “Directed energy ‘funneling’ mechanism for heme cooling following ligand photolysis or direct excitation in solvated carbonmonoxy myoglobin,” J. Phys. Chem. 105, 7057-7063 (2001). [PDF]

[51] N.-V. Buchete and J. E. Straub, “Mean first-passage time calculations for the coil-to-helix transition: The active helix Ising model,” J. Phys. Chem. 105, 6684-6697 (2001). [PDF]

[50] F. Massi and J. E. Straub, “Probing the origins of increased activity of the E22Q `Dutch’ mutant Alzheimer’s β-amyloid peptide,” Biophys. J. 81, 697-709 (2001). [PDF]

[49] I. Andricioaei, A. F. Voter and J. E. Straub, “Smart Darting Monte Carlo,” J. Chem. Phys. 114, 6994-7000 (2001).[PDF]

[48] F. Massi and J. E. Straub, “Energy landscape theory for Alzheimer’s amyloid β-peptide fibril elongation” Proteins: Structure, Function and Genetics 42, 217-229 (2001). [PDF]

[47] F. Massi, J. W. Peng, J. P. Lee and J. E. Straub, “Simulation study of the structure and dynamics of the Alzheimer’s amyloid peptide congener in solution,” Biophys. J. 80, 31-44 (2001). [PDF]

2000

[46] D. E. Sagnella, J. E. Straub and D. Thirumalai, “Timescales and pathways for kinetic energy relaxation in solvated proteins: Application to carbonmonoxy myoglobin,” J. Chem. Phys. 113, 7702-7711 (2000). [PDF]

1999

[45] D. E. Sagnella, J. E. Straub, T. A. Jackson, M. Lim, and P. A. Anfinrud, “Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carbonmonoxy myoglobin: Comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations,” Proc. Natl. Acad. Sci. USA 96, 14324-14329 (1999). [PDF]

[44] D. E. Sagnella and J. E. Straub, “A study of vibrational relaxation of B-state carbon monoxide in the heme pocket of photolyzed carboxymyoglobin,” Biophys. J. 77, 70-84 (1999). [PDF]

[43] S. Huo and J. E. Straub, “Direct computation of long time processes in proteins: Reaction path study of the coil-to-helix transition in polyalanine,” Proteins: Structure, Function and Genetics 36, 249-261 (1999). [PDF]

[42] J. E. Straub and I. Andricioaei, “Computational methods inspired by Tsallis statistics: Monte Carlo and molecular dynamics algortihms for the simulation of classical and quantum systems,” Brazilian J. Phys. 29, 179-186 (1999). [PDF]

1998

[41] I. Andricioaei and J. E. Straub, “Global optimization using bad derivatives: A derivative-free method for molecular energy minimization,” J. Comput. Chem. 19, 1445-1455 (1998). [PDF]

[40] A.D. Mackerell, Jr., D. Bashford, M. Bellott, R.L. Dunbrack, Jr., J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher, III, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. [E.] Straub, M. Watanabe, J. Wiokiewicz-Kuczera, D. Yin, and M. Karplus, “All-atom empirical potential for molecular modeling and dynamics studies of proteins,” J. Phys. Chem. B 102, 3586-3616 (1998).[PDF]

1997

[39] I. Andricioaei and J. E. Straub, “An efficient Monte Carlo algorithm for overcoming broken ergodicity in the simulation of spin systems,” Physica A 247, 553-558 (1997).[PDF]

[38] I. Andricioaei and J. E. Straub, “On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters,” J. Chem. Phys. 107, 9117-9124 (1997).[PDF]

[37] S. Huo and J. E. Straub, “The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature,” J. Chem. Phys. 107, 5000-5006 (1997).[PDF]

[36] B. J. Berne and J. E. Straub, “Novel methods of sampling phase space in the simulation of biological systems,” Curr. Opin. Struc. Bio. 7, 181-189 (1997). [PDF]

[35] J. Ma, S. Huo and J. E. Straub, “Molecular dynamics simulation study of the B-states of solvated carbon monoxymyoglobin,” J. Am. Chem. Soc. 119, 2541-2551 (1997); ibid. 119, 6454 (1997).[PDF]

1996

[34] I. Andricioaei and J. E. Straub, “Finding the needle in the haystack: Algorithms for conformational optimization,” Computers in Physics 10, 449-454 (1996). [PDF]

[33] P. Amara and J. E. Straub, “Energy minimization using the classical density distribution: Application to sodium chloride clusters,” Phys. Rev. B 53, 13857-13863 (1996).[PDF]

[32] I. Andricioaei and J. E. Straub, Rapid Communication Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide,” Phys. Rev. E 53, R3055-3058 (1996). [PDF]

1995

[31] P. Amara and J.E. Straub, “Folding model proteins using kinetic and thermodynamic annealing of the classical density distribution” J. Phys. Chem. 99, 14840-14853 (1995). [PDF]

[30] J. Ma, J. E. Straub and E.I. Shakhnovich, “Simulation study of the collapse of linear and ring homopolymers” J. Chem. Phys. 103, 2615-2624 (1995).[PDF]

[29] J.E. Straub, J. Ma and P. Amara, “Simulated annealing using coarse grained classical dynamics: Smoluchowski dynamics in the Gaussian density approximation” J. Chem. Phys. 103, 1574-1581 (1995).[PDF]

[28] J.E. Straub, T. Keyes and D. Thirumalai, “Response to `Comment on a proposed method for finding barrier height distributions’ [J. Chem. Phys. 103, 1235 (1995)]” J. Chem. Phys. 103, 1237-1238 (1995).[PDF][R. Zwanzig original comment PDF]

1994

[27] J.E. Straub and J.-K. Choi, “Extracting the energy barrier distribution of a disordered system from the instantaneous normal mode density of states: Applications to peptides and proteins” J. Phys. Chem. 98, 10978-10987 (1994).[PDF]

[26] J. Ma and J.E. Straub, “Simulated annealing using the classical density distribution,” J. Chem. Phys. 101, 533-541 (1994); ibid. 103, 9113 (1995).[PDF]

[25] J.E. Straub, C. Lim and M. Karplus, “Simulation analysis of the binding interactions in the RNase A/3′-UMP enzyme/product complex as a function of pH,” J. Am. Chem. Soc. 116, 2591-2599 (1994).[PDF]

[24] J.E. Straub, A. Rashkin and D. Thirumalai, “Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease A,” J. Am. Chem. Soc. 116, 2049-2063 (1994).[PDF]

1993

[23] J. Ma, D. Hsu and J.E. Straub, “Approximate solution of the classical Liouville equation using Gaussian phase packet dynamics: Application to enhanced equilibrium averaging and global optimization,” J. Chem. Phys. 99, 4024-4035 (1993).[PDF]

[22] H. Li, R. Elber and J.E. Straub, “Molecular dynamics simulation of NO recombination to myoglobin mutants,” J. Biol. Chem. 268, 17908-17916 (1993).[PDF]

[21] P. Amara, D. Hsu and J.E. Straub, “Global energy minimum searches using an approximate solution of the imaginary time Schroedinger equation,” J. Phys. Chem. 97, 6715-6721 (1993).[PDF]

[20] J.E. Straub and D. Thirumalai, “Theoretical probes of conformational fluctuations in S-peptide and RNase A/3′-UMP enzyme product complex,” Proteins 15, 360-373 (1993).[PDF]

[19] J.E. Straub and D. Thirumalai, “Exploring the energy landscape in proteins,” Proc. Natl. Acad. Sci. USA 90, 809-813 (1993).[PDF]

1992

[18] J.E. Straub, “Analysis of the role of attractive forces in self-diffusion of a simple fluid,” Mol. Phys. 76, 373-385 (1992).[PDF]

1991

[17] J.E. Straub and M. Karplus, “Molecular dynamics study of the photodissociation of carbon monoxide from myoglobin: Ligand dynamics in the first 10ps,” Chem. Phys. 158, 221-248 (1991).[PDF]

[16] J.E. Straub and M. Karplus, “Energy equipartitioning in the classical time-dependent Hartree approximation,” J. Chem. Phys. 94, 6737-6739 (1991). [PDF]

1990

[15] J.E. Straub and M. Karplus, “The interpretation of site-directed mutagenesis experiments by linear free energy relations,” Protein Engineering 3, 673-675 (1990).[PDF]

[14] J.E. Straub, B.J. Berne and B. Roux, “Spatial dependence of time-dependent friction for pair diffusion in a simple fluid,” J. Chem. Phys. 93, 6804-6812 (1990).[PDF]

[13] B.J. Berne, M. Tuckerman, J.E. Straub and A.L.R. Bug, “Dynamic friction on rigid and flexible bonds,” J. Chem. Phys. 93, 5084-5095 (1990). [PDF]

1988

[12] J.E. Straub, M. Borkovec and B.J. Berne, “Molecular dynamics study of an isomerizing diatomic in a Lennard-Jones fluid,” J. Chem. Phys. 89, 4833-4847 (1988).[PDF]

[11] B.J. Berne, M. Borkovec and J.E. Straub, Feature Article “Classical and modern methods in reaction rate theory,” J. Phys. Chem. 92, 3711-3725 (1988). [PDF]

1987

[10] J.E. Straub and B.J. Berne, “A statistical theory for the effect of nonadiabatic transitions on activated processes,” J. Chem. Phys. 87, 6111-6116 (1987). [PDF]

[9] J.E. Straub, M. Borkovec and B.J. Berne, “Calculation of dynamic friction on the intramolecular degrees of freedom,” J. Phys. Chem. 91, 4995-4998 (1987). [PDF]

[8] J.E. Straub, M. Borkovec and B.J. Berne, “Numerical simulation of rate constants for a two degree of freedom system in the weak collision limit,” J. Chem. Phys. 86, 4296-4297 (1987).[PDF]

1986

[7] J.E. Straub and B.J. Berne, “Energy diffusion in many-dimensional Markovian systems: The consequences of competition between inter- and intramolecular vibrational energy transfer,” J. Chem. Phys. 85, 2999-3006 (1986); ibid. 86, 5223 (1987). [PDF]

[6] M. Borkovec, J.E. Straub and B.J. Berne, “The influence of intramolecular vibrational relaxation on the pressure dependence of unimolecular rate constants,” J. Chem. Phys. 85, 146-149 (1986). [PDF]

[5] J.E. Straub, M. Borkovec and B.J. Berne, “Non-Markovian activated rate processes: Comparison of current theories with numerical simulation data,” J. Chem. Phys. 84, 1788-1794 (1986); ibid. 86, 1079 (1987). [PDF] [R.Zwanzig subsequent comment PDF]

1985

[4] J.E. Straub, M. Borkovec and B.J. Berne, “Shortcomings of current theories of non-Markovian activated rate processes,” J. Chem. Phys. 83, 3172-3174 (1985).[PDF]

[3] J. E. Straub, D. A. Hsu and B. J. Berne, “On determining reaction kinetics by molecular dynamics using absorbing barriers,” J. Phys. Chem. 89, 5188-5191 (1985). [PDF]

[2] J.E. Straub and B.J. Berne, “A rapid method for determining rate constants by molecular dynamics,” J. Chem. Phys. 83, 1138-1139 (1985). [PDF]

1983

[1] M.H. Alexander, T. Orlikowski and J.E. Straub, “Theoretical study of intramultiplet transitions in collisions of atoms in 3P electronic states with structureless targets: Ca(eP) + He,” Phys. Rev. A 28, 73-82 (1983). [PDF]

Book Chapters

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

[B9] R. Dima, B. Tarus, G. Reddy, J. E. Straub and D. Thirumalai, “Scenarios for protein aggregation: Molecular Dynamics simulations and bioinformatics analysis,” R. Dima, B. Tarus, G. Reddy, J. E. Straub and D. Thirumalai, in: Protein Folding, Misfolding and Aggregation: Classical Themes and Novel Approaches, edited by V. Muñoz, Royal Society of Chemistry Publishing (Cambridge, United Kingdom, 2008), pp. 241-265.

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

[B7] I. Andricioaei and J. E. Straub, “Simulated annealing methods in protein folding,” in: Encyclopedia of Optimization, edited by C.A. Floudas and P.M. Pardalos, Kluwer Academic Publishers (The Netherlands, 2001), vol. 5, pp. 219-224.

[B6] J. E. Straub, “Reaction rates and transition pathways,” in: Computational Biochemistry and Biophysics, edited by O. Becker, A. D. MacKerell Jr., B. Roux and M. Watanabe, Marcel Dekker (New York, 2001), Chapter 10, pp. 199-220.

[B5] J. E. Straub and I. Andricioaei, “Computational methods for the simulation of classical and quantum many body systems sprung from non-extensive thermostatistics,” in: Nonextensive Statistical Mechanics and Its Application, edited by S. Abe and Y. Okamoto, Lecture Notes in Physics, Springer Verlag (Berlin, 2001), Chapter IV, pp. 195-235.

[B4] J. E. Straub, “Protein Folding and Optimization Algorithms,” in: The Encyclopedia of Computational Chemistry, edited by P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Schaefer III, P. R. Schreiner, John Wiley & Sons (Chichester, 1998), vol. 3, pp. 2184-2191. [PDF]

[B3] J. E. Straub and I. Andricioaei, “Exploiting Tsallis statistics,” in: Computational Molecular Dynamics: Challenges, Methods, Ideas, edited by P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, S. Reich and R. D. Skeel, Lecture Notes in Computational Science and Engineering, Springer-Verlag, Berlin (1999), vol. 4, pp. 197-211. [PDF]

[B2] P. Amara, J. Ma and J.E. Straub, “Global minimization on rugged energy landscapes” in: Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, edited by P.M. Pardalos, D. Shalloway and G. Xue, American Mathematical Society (Providence, 1996), pp. 1-13.[PDF]

[B1] J.E. Straub, “Optimization Techniques with Applications to Proteins”, in: New Developments in Theoretical Studies of Proteins, edited by Ron Elber, World Scientific (Singapore1996), pp. 137-196. [PDF]