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). [Download PDF]

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).

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). [Download PDF]

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).

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).

J. Kim, J. E. Straub, and T. Keyes, ``Statistical-temperature Monte Carlo and Molecular Dynamics algorithms,'' Phys. Rev. Lett. 97, 050601 (2006). [Download PDF]

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). [Download PDF]

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). [Download PDF]

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). [Download PDF]

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. [Download PDF]

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

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

D.K. Klimov, J.E. Straub, and D. Thirumalai, ``Aqueous urea solution destabilizes Aβ_16-22 oligomers,'' Proc. Natl. Acad. Sci. USA 101, 14760-14765 (2004).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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). [Download PDF]

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). [Download PDF]

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).[Download PDF]

T. W. Whitfield and J. E. Straub, ``Gravitational smoothing as a global optimization strategy,'' J. Comp. Chem. 23, 1100-1103 (2002).[Download PDF]

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).[Download PDF]

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).[Download PDF]

T. W. Whitfield, L. Bu and J. E. Straub, ``Generalized parallel sampling,'' Physica A 305, 157-171 (2002).[Download PDF]

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).[Download PDF]

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).[Download PDF]

T. W. Whitfield and J. E. Straub, ``Uncertainty of path integral averages at low temperature,'' J. Chem. Phys. 115, 6834-6840 (2001). [Download PDF]

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).[Download PDF]

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). [Download PDF]

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).[Download PDF]

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

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.

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).[Download PDF]

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). [Download PDF]

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.

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.

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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. [Download PDF]

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.[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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

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).[Download PDF]

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).[Download PDF]

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.[Download PDF]

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).[Download PDF]

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).[Download PDF]

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.[Download PDF]

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).[Download PDF]

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).[Download PDF] [Download original comment PDF]

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).[Download PDF]

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

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).[Download PDF]

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).[Download PDF]

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).[Download PDF]

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

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).[Download PDF]

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).[Download PDF]

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

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

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).[Download PDF]

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

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

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).[Download PDF]

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). [Download PDF]

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).[Download PDF]

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). [Download PDF]

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). [Download PDF]

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). [Download PDF]

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).[Download PDF]

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). [Download PDF]

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). [Download PDF]

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). [Download PDF]

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).[Download PDF]

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). [Download PDF]

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

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). [Download PDF]