Caltech Asci Technical Report 105 (2008)
S. B. Sane, T. Cagin, W. A. Goddard, W. G. Knauss
The results of molecular dynamics computations and corresponding values of laboratory measurements are compared to assess the efficacy of the numerical method. Details are presented on the modeling...
Y. Qi, T. Cagin, W. A. Goddard, Yue Qi, Tahir Cag N, ...
The new M-SC many body potentials for Cu, Ni, Ag have been applied to investigate the melting, glass formation and crystallization processes in Cu-Ag, Cu-Ni and pure Ni systems. The melting...
"Studies of Fullerenes and Carbon Nanotubes by an Extended Bond Order Potential" (2007)
J. Che, T. Cagin, W. A. Goddard, Jianwei Che, Tahir Ça ˘gın
nanotubes by an extended bond order potential
Abstract Molecular Dynamics Simulations to Compute the Bulk Response of Amorphous PMMA (2007)
S. B. Sane, T. Cagin, W. A. Goddard, W. G. Knauss
The results of molecular dynamics computations and corresponding values of laboratory measurements are compared to assess the efficacy of the numerical method. Details are presented on the modeling...
Theoretical approaches to the thermochemistry of silicate anions have so far focused on gas-phase molecular orbital and density functional theory (DFT) calculations. These calculations predict that...
Theoretical approaches to the thermochemistry of silicate anions have so far focused on gas-phase molecular orbital and density functional theory (DFT) calculations. These calculations predict that...
Theoretical approaches to the thermochemistry of silicate anions have so far focused on gas-phase molecular orbital and density functional theory (DFT) calculations. These calculations predict that...
W. A. Goddard, T. Cagin, M. Blanco, N. Vaidehi, S. Dasgupta, W. Floriano, ...
Advances in theory and methods making it practical to consider fully first principles (de novo) predictions of structures, properties and processes for organic materials. However despite the progress...
A Multiscale Approach for Modeling Crystalline Solids (2001)
A. M. Cuitino, L. Stainier, G. Wang, A. Strachan, T. Cagin, W. A. Goddard, ...
In this paper we present a modeling approach to bridge the atomistic with macroscopic scales in crystalline materials. The methodology combines identification and modeling of the controlling unit...
Arakawa, H., Aresta, M., Armor, J.N., Barteau, M.A., Beckman, E.J., Bell, A.T., ...
Chemical Reviews, 101(2001) S.953-96
Y. Zhou, S. Jiang, T. Cagin, E. S. Yamaguchi, R. Frazier, A. Ho, ...
In previous studies of dithiophosphate [DTP = S 2 P(OR) 2 ] wear inhibitors bound to an oxidized iron surface, we found that the cohesive energy of the self-assembled monolayers (SAM) for DTP...
Strain Rate Induced Amorphization in Metallic Nanowires (1999)
H. Ikeda, Y. Qi, T. Cagin, K. Samwer, W. L. Johnson, W. A. Goddard, ...
Using molecular dynamics simulations with a many-body force field, we studied the deformation of metal alloy nanowires subjected to various strain rates. For all strain rates, the Ni nanowire is...
The 1998 Center for Simulation of Dynamic Response in Materials Annual Technical Report (1998)
Goddard, W. A., Meiron, D. I., Ortiz, M., Shepherd, J. E.
Introduction: This annual report describes research accomplishments for FY 98 of the Center for Simulation of Dynamic Response of Materials. The Center is constructing a virtual shock physics...
Youngquist, M. G., Driscoll, R. J., Coley, T. R., Goddard, W. A., Baldeschwieler, J. D.
We have shown that it is possible to image DNA with atomic resolution using scanning tunneling microscopy (STM), [R. J. Driscoll, M. G. Youngquist, and J. D. Baldeschwieler, Nature 346, 294 (1990)]....
Mechanism of superconductivity in K3C60.
Using electronic states and phonon states from the first-principles calculations and including both conventional electron-phonon charge coupling and Jahn-Teller coupling, we predict Tc and other...
Park, C, Campbell, J L, Goddard, W A
Using protein stitchery with appropriate attachment of cysteines linking to either C or N termini of the basic region of the v-Jun leucine zipper gene-regulatory protein, we constructed three...
The one-dimensional three-band Hubbard Hamiltonian is shown to be equivalent to an effective Hamiltonian that has independent spinon and holon quasiparticle excitations plus a weak coupling of the...
Protein stitchery: design of a protein for selective binding to a specific DNA sequence.
Park, C, Campbell, J L, Goddard, W A
We present a general strategy for designing proteins to recognize DNA sequences and illustrate this with an example based on the "Y-shaped scissors grip" model for leucine-zipper gene-regulatory...
Predictions of structural elements for the binding of Hin recombinase with the hix site of DNA.
Plaxco, K W, Mathiowetz, A M, Goddard, W A
Molecular dynamics simulations were coupled with experimental data from biochemistry and genetics to generate a theoretical structure for the binding domain of Hin recombinase complexed with the hix...
Molecular description of dioxygen bonding in hemoglobin.
From ab initio quality calculations on model systems, we conclude that in unliganded Fe-porphyrin the FE lies in the plane for both the high-spin (q) and intermediate-spin (t) states. Thus, the...
Mechanism of superconductivity in K3C60.
Using electronic states and phonon states from the first-principles calculations and including both conventional electron-phonon charge coupling and Jahn-Teller coupling, we predict Tc and other...
Park, C, Campbell, J L, Goddard, W A
Using protein stitchery with appropriate attachment of cysteines linking to either C or N termini of the basic region of the v-Jun leucine zipper gene-regulatory protein, we constructed three...
The one-dimensional three-band Hubbard Hamiltonian is shown to be equivalent to an effective Hamiltonian that has independent spinon and holon quasiparticle excitations plus a weak coupling of the...
Protein stitchery: design of a protein for selective binding to a specific DNA sequence.
Park, C, Campbell, J L, Goddard, W A
We present a general strategy for designing proteins to recognize DNA sequences and illustrate this with an example based on the "Y-shaped scissors grip" model for leucine-zipper gene-regulatory...
Predictions of structural elements for the binding of Hin recombinase with the hix site of DNA.
Plaxco, K W, Mathiowetz, A M, Goddard, W A
Molecular dynamics simulations were coupled with experimental data from biochemistry and genetics to generate a theoretical structure for the binding domain of Hin recombinase complexed with the hix...
Molecular description of dioxygen bonding in hemoglobin.
From ab initio quality calculations on model systems, we conclude that in unliganded Fe-porphyrin the FE lies in the plane for both the high-spin (q) and intermediate-spin (t) states. Thus, the...
Evans, J. S., Chan, S. I., Goddard, W. A.
Many interesting proteins possess defined sequence stretches containing negatively charged amino acids. At present, experimental methods (X-ray crystallography, NMR) have failed to provide structural...
Building proteins from C alpha coordinates using the dihedral probability grid Monte Carlo method.
Mathiowetz, A. M., Goddard, W. A.
Dihedral probability grid Monte Carlo (DPG-MC) is a general-purpose method of conformational sampling that can be applied to many problems in peptide and protein modeling. Here we present the DPG-MC...
Evans, J. S., Mathiowetz, A. M., Chan, S. I., Goddard, W. A.
We tested the dihedral probability grid Monte Carlo (DPG-MC) methodology to determine optimal conformations of polypeptides by applying it to predict the low energy ensemble for two peptides whose...
Floriano, W. B., Nascimento, M. A., Domont, G. B., Goddard, W. A.
We investigated the pathway for pressure unfolding of metmyoglobin using molecular dynamics (MD) for a range of pressures (0.1 MPa to 1.2 GPa) and a temperature of 300 K. We find that the unfolding...