Straub Group 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

[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).

[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).

[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).

[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 investi- gation 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 carbonmonoxy myoglobin,'' 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 abilitiy 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]