## 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[126] J.E. Straub, and D. Thirumalai, "Membrane protein interactions are key to understanding amyloid formation,"J. Phys. Chem. Lett. 5, 633-635 (2014).
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[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],"
[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,"
[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,"
[122]
P. Zhang, S. W. Ahn, and J. E. Straub,
"`Strange Kinetics' in the temperature dependence of methionine ligand rebinding dynamics in cytochrome c,"
[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,"
[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,"
[119]
J. Kim, J. E. Straub, and T. Keyes,
"Replica Exchange Statistical Temperature Molecular Dynamics Algorithm,"
[118]
P. Zhang, E. Malolepsza, and J. E. Straub,
"Dynamics of methionine ligand rebinding in cytochrome c,"
[117]
D. Thirumalai, G. Reddy, and J. E. Straub,
``Role of water in protein aggregation and amyloid polymorphism,''
[116]
H. Fujisaki, Y. Zhang, and J.E. Straub,
"Non-Markovian theory of vibrational energy relaxation and its applications to bimolecular systems,"
[115]
T. Komatsuzaki, A. Baba, M. Toda, J. E. Straub, and R. S. Berry,
"Ergodic problems for real complex systems in chemical physics,"
[114] S. S. Cho, G. Reddy, J.E. Straub, and D. Thirumalai, "Entropic stabilization of proteins by TMAO,"
[113] J. Kim, T. Keyes, and J.E. Straub, "Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables,"
[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,"
[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,"
[110] J.E. Straub and D. Thirumalai, "Toward a molecular theory of early and late events in monomer to amyloid fibril formation,"
[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,"
[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,"
[107] J. Kim and J. E. Straub, "Generalized simulated tempering for exploring strong phase transitions,"
[106] J. Kim, T. Keyes, and J. E. Straub, "Generalized Replica Exchange Method,"
[105] J. E. Straub and D. Thirumalai,
"Principles governing oligomer formation in amyloidogenic peptides,"
[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,"
[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,"
[102] H. Fujisaki, K. Yagi, J.E. Straub and G. Stock,
"Quantum and classical vibrational relaxation dynamics of N-methylacetamide on
[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,"
[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,"
[99] J. Kim and J.E. Straub,
"Optimal replica exchange method combined with Tsallis weight sampling,"
[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],"
[97] G. Reddy, J. E. Straub, and D. Thirumalai, "Dynamics of locking of peptides onto growing amyloid fibrils,"
[96] J. Kim and J.E. Straub,
"Relationship between protein folding thermodynamics and the energy landscape,"
[95] J. Kim, T. Keyes and J.E. Straub,
"Replica exchange statistical temperature Monte Carlo,"
[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,"
[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,"
[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,"
[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,"
[90] Y. Zhang and J. E. Straub,
"Diversity of solvent dependent energy transfer pathways in heme proteins,"
[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,"
[88] M. S. Li, D. K. Klimov, J.E. Straub and
D. Thirumalai,
"Probing the mechanisms of fibril formation using lattice models,"
[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,"
[86] N.-V. Buchete, J. E. Straub, D. Thirumalai,
"Dissecting contact potentials for proteins: Relative contributions of individual amino acids,"
[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,"
[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,"
[83] H. Fujisaki, K. Yagi, K. Hirao and J. E. Straub, ``Quantum dynamics of N-methylacetamide studied by the vibrational configuration interaction method,''
[82] J. Kim, J.E. Straub and T. Keyes,
``Statistical temperature molecular dynamics: Application to coarse-grained beta-barrel-forming protein models,''
[81] Y. Zhang, H. Fujisaki, and J. E. Straub, ``Molecular dynamics study on the solvent dependent heme cooling following ligand photolysis in carbonmonoxy myoglobin,''
[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,''
[79] B. Tarus, J. E. Straub and D. Thirumalai, ``Dynamics of Asp23-Lys28 salt-bridge formation in Aβ(10-35) monomers,''
[78] J. Kim, J. E. Straub, and T. Keyes,
``Statistical-temperature Monte Carlo and Molecular Dynamics algorithms,''
[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,''
[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,''
[75] H. Fujisaki, Y. Zhang and J. E. Straub,
``Time-dependent perturbation theory for vibrational energy
relaxation and dephasing in peptides and proteins,''
[74] H. Fujisaki, L. Bu and J. E. Straub,
``Vibrational Energy Relaxation (VER) of a CD stretching mode in cytochrome c,"
[73] H. Fujisaki and J. E. Straub,
``Vibrational energy relaxation in proteins,"
[72] A. van Giessen and J. E. Straub,
``Monte Carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials,''
[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,''
[70] D.K. Klimov, J.E. Straub, and D. Thirumalai,
``Aqueous urea solution destabilizes Aβ
[69] N.-V. Buchete, J. E. Straub, and D. Thirumalai, ``Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases,''
[68] N.-V. Buchete, J. E. Straub, and D. Thirumalai, ``Orientational potentials extracted from protein structures improve native fold recognition,''
[67] N.-V. Buchete, J. E. Straub, and D. Thirumalai, ``Development of novel statistical potentials for protein fold recognition,''
[66] N.-V. Buchete, J. E. Straub, and D. Thirumalai, ``Continuous aniosotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis,''
[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: Met
[64] L. Bu and J. E. Straub, ``Simulating vibrational energy flow in proteins: Relaxation rate and mechanism for heme cooling in cytochrome c,''
[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",''
[62] N.-V. Buchete, J. E. Straub and D. Thirumalai,
``Aniostropic coarse-grained statistical potentials improve the abilitiy
to identify nativelike protein structures,''
[61] L. Bu and J. E. Straub,
``Vibrational frequency shifts and relaxation rates for a selected
vibrational mode in cytochrome c,''
[60] F. Massi and J. E. Straub,
``Structural and dynamical analysis of the hydration of the Alzheimer's
β-amyloid peptide,''
[59] T. W. Whitfield and J. E. Straub,
``Gravitational smoothing as a global optimization strategy,''
[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,''
[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,''
[56] T. W. Whitfield, L. Bu and J. E. Straub,
``Generalized parallel sampling,''
[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,''
[54] I. Andricioaei, J. E. Straub and M. Karplus,
``Simulation of quantum systems using path integrals in a generalized
ensemble,''
[53] T. W. Whitfield and J. E. Straub,
``Uncertainty of path integral averages at low temperature,''
[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,''
[51] N.-V. Buchete and J. E. Straub,
``Mean first-passage time calculations for the coil-to-helix
transition: The active helix Ising model,''
[50] F. Massi and J. E. Straub,
``Probing the origins of increased activity of the E22Q `Dutch' mutant
Alzheimer's β-amyloid peptide,''
[49] I. Andricioaei, A. F. Voter and J. E. Straub,
``Smart Darting Monte Carlo,''
[48] F. Massi and J. E. Straub,
``Energy landscape theory for Alzheimer's amyloid
β-peptide fibril elongation''
[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,''
[46] D. E. Sagnella, J. E. Straub and D. Thirumalai,
``Timescales and pathways for kinetic energy relaxation in solvated proteins:
Application to carbonmonoxy myoglobin,''
[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,''
[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,''
[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,''
[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,''
[41] I. Andricioaei and J. E. Straub,
``Global optimization using bad derivatives:
A derivative-free method for molecular energy minimization,''
[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,''
[39] I. Andricioaei and J. E. Straub,
``An efficient Monte Carlo algorithm for overcoming broken ergodicity
in the simulation of spin systems,''
[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,''
[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,''
[36] B. J. Berne and J. E. Straub,
``Novel methods of sampling phase space in the simulation
of biological systems,''
[35] J. Ma, S. Huo and
J. E. Straub,
``Molecular dynamics simulation study of the B-states of
solvated carbon monoxymyoglobin,''
[34] I. Andricioaei and J. E. Straub,
``Finding the needle in the haystack: Algorithms for
conformational optimization,''
[33] P. Amara and J. E. Straub,
``Energy minimization using the classical density
distribution: Application to sodium chloride clusters,''
[32] I. Andricioaei and J. E. Straub,
[31] P. Amara and J.E. Straub,
"Folding model proteins using kinetic and thermodynamic
annealing of the classical density distribution"
[30] J. Ma, J. E. Straub and E.I. Shakhnovich, "Simulation study of the collapse of linear and ring homopolymers"
[29] J.E. Straub, J. Ma and P. Amara, "Simulated annealing using coarse grained classical dynamics: Smoluchowski dynamics in the Gaussian density approximation"
[28] J.E. Straub, T. Keyes and D. Thirumalai, "Response to `Comment on a proposed method for finding barrier height distributions' [J. Chem. Phys.
[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"
[26] J. Ma and J.E. Straub, "Simulated annealing using the classical density distribution,"
[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,"
[24] J.E. Straub, A. Rashkin and D. Thirumalai, "Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease A,"
[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,"
[22] H. Li, R. Elber and J.E. Straub, "Molecular dynamics simulation of NO recombination to myoglobin mutants,"
[21] P. Amara, D. Hsu and J.E. Straub, "Global energy minimum searches using an approximate solution of the imaginary time Schroedinger equation,"
[20] J.E. Straub and D. Thirumalai, "Theoretical probes of conformational fluctuations in S-peptide and RNase A/3'-UMP enzyme product complex,"
[19] J.E. Straub and D. Thirumalai, "Exploring the energy landscape in proteins,"
[18] J.E. Straub, "Analysis of the role of attractive forces in self-diffusion of a simple fluid,"
[17] J.E. Straub and M. Karplus, "Molecular dynamics study of the photodissociation of carbon monoxide from myoglobin: Ligand dynamics in the first 10ps,"
[16] J.E. Straub and M. Karplus, "Energy equipartitioning in the classical time-dependent Hartree approximation,"
[15] J.E. Straub and M. Karplus, "The interpretation of site-directed mutagenesis experiments by linear free energy relations,"
[14] J.E. Straub, B.J. Berne and B. Roux, "Spatial dependence of time-dependent friction for pair diffusion in a simple fluid,"
[13] B.J. Berne, M. Tuckerman, J.E. Straub and A.L.R. Bug, "Dynamic friction on rigid and flexible bonds,"
[12] J.E. Straub, M. Borkovec and B.J. Berne, "Molecular dynamics study of an isomerizing diatomic in a Lennard-Jones fluid,"
[11] B.J. Berne, M. Borkovec and J.E. Straub,
[10] J.E. Straub and B.J. Berne, "A statistical theory for the effect of nonadiabatic transitions on activated processes,"
[9] J.E. Straub, M. Borkovec and B.J. Berne, "Calculation of dynamic friction on the intramolecular degrees of freedom,"
[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,"
[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,"
[6] M. Borkovec, J.E. Straub and B.J. Berne, "The influence of intramolecular vibrational relaxation on the pressure dependence of unimolecular rate constants,"
[5] J.E. Straub, M. Borkovec and B.J. Berne, "Non-Markovian activated rate processes: Comparison of current theories with numerical simulation data,"
[4] J.E. Straub, M. Borkovec and B.J. Berne, "Shortcomings of current theories of non-Markovian activated rate processes,"
[3] J. E. Straub, D. A. Hsu and B. J. Berne, "On determining reaction kinetics by molecular dynamics using absorbing barriers,"
[2] J.E. Straub and B.J. Berne, "A rapid method for determining rate constants by molecular dynamics,"
[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," ## 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:
[B7] I. Andricioaei and J. E. Straub, ``Simulated annealing methods in
protein folding,'' in:
[B6] J. E. Straub, ``Reaction rates and transition pathways,'' in:
[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:
[B4] J. E. Straub, ``Protein Folding and Optimization Algorithms,''
in:
[B3] J. E. Straub and I. Andricioaei,
"Exploiting Tsallis statistics,'' in:
[B2] P. Amara, J. Ma and J.E. Straub, "Global minimization on rugged energy landscapes" in:
[B1] J.E. Straub, "Optimization Techniques with Applications to Proteins", in: |