Selected Publications of the Center's Research
Publications for 2011
Journal articles
- Min Yu and Dallas Trinkle, "Accurate and efficient algorithm for Bader charge integration", Journal of Chemical Physics, p. 064111, vol. 134,
(2011).
- Teck L. Tan and D.D. Johnson, "Topologically correct phase boundaries and transition temperatures for Ising Hamiltonians via self-consistent
coarse-grained cluster-lattice models", Phys. Rev. B, p. 144427, vol. 83, (2011). Published, 10.1103/PhysRevB.83.144427
- Min Yu and Dallas Trinkle, "Au/TiO2(110) Interfacial Reconstruction Stability from ab Initio", Journal of Physical Chemistry C, p. 17799, vol.
115, (2011). Published, dx.doi.org/10.1021/jp2017133
- David Lyon and Alfred Hubler, "Nanoscale Electrostatic Capacitors", Journal of Vacuum Science & Technology B, p. , vol. , (2011).
Submitted.
- YEHUDA BEN-ZION, KARIN A. DAHMEN and JONATHAN T. UHL, "A Unifying Phase Diagram for the Dynamics of Sheared Solids and
Granular Materials", Pure Appl. Geophys., p. , vol. , (2011). Published, DOI 10.1007/s00024-011-0273-7
- Karin A. Dahmen, Yehuda Ben-Zion, and Jonathan T. Uhl, "A simple analytic theory for the statistics of avalanches in sheared granular
materials", Nature Physics, p. 554, vol. 7, (2011). 10.1038/nphys1957
Publications for 2010
Journal articles
- Shun Wang, Eric de Sturler, and Glaucio H. Paulino, "Dynamic Adaptive Mesh Refinement for Topology Optimization", International Journal
for Numerical Methods in Engineering, p. , vol. , (2010). Under revision.
- Glaucio H. Paulino, Eric de Sturler, Shun Wang, and Chau Le;, "Continuum Topology optimization with preconditioned Krylov subspace
recycling", Journal for Structural and Multidisciplinary Optimization, p. , vol. , (2010). Under revision.
- Ondrej Hovorka, Y. Liu, Karin A. Dahmen, Andreas Berger;, "On the ability to determine intrinsic switching-h field distributions from
hysteresis loops in the partially correlated magnetization reversal regime", Journal of Magnetism and Magnetic Materials, p. 459, vol.
322, (2010).
Y.L. Loh, E.W. Carlson, and K.A. Dahmen;, "Noise Predictions for STM in Systems with Local Electron Nematic Order", Physical Review B,
p. 224207, vol. 81, (2010). Published, 10.1103/PhysRevB.81.224207
- Pak Yuen Chan, Georgios Tsekenis, Jonathan Dantzig, Karin Dahmen, and Nigel Goldenfeld, "Plasticity and dislocation dynamics in a phase
field crystal model", Physical Review Letters, p. 015502, vol. 105, (2010).
- M. Singleton, G. Heiss, A. Huebler,, "The optimal shape of roots", Complexity, p. 9, vol. 15, (2010). Published, 10.1002/cplx.20312
- A. Huebler and O. Osuagwu, "Digital quantum batteries: Energy and information storage in nano vacuum tube arrays", Complexity, p. 48, vol.
15, (2010). Published, 10.1002/cplx.20306
- A. Hubler and J. Crutchfield, "Order and disorder in open systems", Complexity, p. , vol. , (2010). Accepted.
- Anant Kulkarni, Lin-Lin Wang, Duane D. Johnson, David Sholl, Karl Johnson, "First-Principles Characterization of Amorphous Phases of
MB12H12, M=Mg, Ca", J. Phys. Chem. C, p. 14601, vol. 114, (2010). 10.1021/jp101326g
- Teck L. Tan and D.D. Johnson, "Unique Cluster Expansions for Alloy Thermodynamics via Subspace Projection", Phys. Rev. B, p. , vol. ,
(2010). In preparation.
- Luis A. Motta Mello, Eric de Sturler, Glaucio H. Paulino, and Emilio C. Nelli Silva, "Recycling Krylov subspaces for efficient large-scale
electrical impedance tomography", Computer Methods in Applied Mechanics and Engineering, p. , vol. , (2010). Accepted,
10.1016/j.cma.2010.06.001
Publications for 2009
Chapters in books
- K.A. Dahmen and Y. Ben-Zion, “The physics of jerky motion in slowly driven magnetic and earthquake fault systems”, Encyclopedia of Complexity and Systems Science (in press 2009) Springer.
- D. V. Melnikov and J.P. Leburton, “Self-consistent simulation of quantum dot spin transistor”, Encyclopedia of Complexity and Systems Science (2009) Springer.
Journal articles
- Karin A. Dahmen, Yehuda Ben-Zion, and Jonathan T. Uhl, “A micromechanical model for deformation in solids with universal predictions for stress strain curves and slip avalanches”, Physical Review Letters (102), 175501 (2009) http://dx.doi.org/10.1103/PhysRevLett.102.175501
- Karin A. Dahmen, Y. Ben-Zion, and J.T. Uhl, “A Lattice Model for Sheared Granular Materials with Detail Independent Predictions for Slip Avalanche Statistics”, Nature Materials (2009)
- Ondrej Hovorka, Y. Liu, Karin A. Dahmen, Andreas Berger, “On the ability to determine intrinsic switchingÊ field distributions from hysteresis loops in the partially correlated magnetization reversal regime”, Journal of Magnetism and Magnetic Materials (2009) (Submitted not published)
- S. Kibey, L-L. Wang, J. B. Liu, H.T. Johnson, H. Sehitoglu, and D. D. Johnson, “Prediction of twinning stresses in fcc alloys: application to Cu-Al alloys”, Physical Review B (2009) http://dx.doi.org/10.1103/PhysRevB.79.214202
- Brent Kraczek, Scott Miller, R.B. Haber, and D.D. Johnson, “Spacetime, balance-law formulation of coupled atomistic-continuum dynamics for solids”, Journal of Computational Physics (2009)
- Y. Liu and Karin A. Dahmen, “Random Field Ising model in and out of equilibrium”, Europhysics Letters (2009) http://dx.doi.org/10.1209/0295-5075/86/56003 (Submitted not published)
- Y. Liu and Andrew Missel, Karin A. Dahmen, Pierre Le Doussal, Kay Joerg Wiese, “Measuring functional renormalization group fixed-point functions in the random field Ising model”, Physical Review E (2009) (Submitted not published)
- J.B. Liu and D.D. Johnson, “bcc-to-hcp Transformation Pathways in Iron versus Hydrostatic Pressure: Coupled Shuffle and Shear Modes,”, Physical Review B 79 (13), 134113-9 (2009)
- Y.L. Loh, E.W. Carlson, and K.A. Dahmen, “Noise Predictions for STM in Systems with Local Electron Nematic Order”, Physical Review B (2009) (Submitted not published)
- D.V. Melnikov, J. Kim, L-X Zhang and J.P. Leburton, “Few-electron Quantum Dot Spintronics”, Frontiers in Nanoscience and Nanotechnology (in press 2009)
- Scott Miller, Brent Kraczek, R.B. Haber, and D.D. Johnson, “Multi-field spacetime discontinuous Galerkin methods for linearized elastodynamics,”, Computer Methods in Applied Mechanics and Engineering (2009) (Submitted not published)
- A.R. Missel, and K.A. Dahmen, Phys. Rev. E, “Hopping Transport in Hostile Reaction-Diffusion Systems”, Physical Review E 79 (21126) (2009) http://dx.doi.org/10.1103/PhysRevE.79.021126
- Luis A. Motta Mello, Emilio C. Nelli Silva, Eric de Sturler, and Glaucio H. Paulino, “Recycling Krylov subspaces for efficient electrical impedance tomography: toward large-scale topology”, IEEE Transactions on Medical Imaging (2009) (Submitted not published)
- Glaucio H. Paulino, Eric de Sturler, Shun Wang, and Chau Le, “Continuum Topology optimization with preconditioned Krylov subspace recycling”, Structural and Multidisciplinary Optimization (2009) (Submitted not published)
- L-L. Wang and D. D. Johnson, “Predicted Trends of Core-Shell Preferences for 132 Late Transition-Metal Binary Alloyed anoparticles”, Journal of American Chemical Society (2009) (Submitted not published)
- L.-X. Zhang, D. V. Melnikov, and J.-P. Leburton, “Non-monotonic variation of the exchange energy in double elliptic quantum dots”, Journal of Physics: Condensed Matter 21, 95502 (2009) http://dx.doi.org/10.1088/0953-8984/21/9/095502
Theses
- Yang Liu, “Unexpected Universality in Disordered Systems and Modeling Perpendicular Recording Media” (2009) PDF
Publications for 2008
Journal articles
- Todd D. Beaudet, Michele Casula, Jeongnim Kim, Sandro Sorella, and Richard M. Martin, “Molecular hydrogen adsorbed on benzene: Insights from a quantum Monte Carlo study”, Journal of Chemical Physics 129, 164711 (2008) http://dx.doi.org/10.1063/1.2987716
- D. M. Ceperley, “Path Integrals and Supersolids”, Computer Physics Communications, 307-14 (2008)
- Clark, B. K. and D. M. Ceperley, “Path Integral Calculations of Vacancies in Solid Helium”, Computer Physics Communications 179, 82-8 (2008)
- S. Kibey, H. Sehitoglu, and D. D. Johnson, “Energy landscape for martensitic phase transformation in shape memory NiTi”, Acta Materialia 57 (5), 1624-9 (2008) http://dx.doi.org/10.1016/j.actamat.2008.12.008
- J. Kim, D.V. Melnikov and J.P. Leburton, “Tunable many-body effects in triple quantum dot”, Physical Review B (in press 2008)
- B. Kraczek, D. D. Johnson, R. B. Haber, “A spacetime, balance-law formulation of coupled atomistic and continuum dynamics for solids” (2008) (Submitted not published)
- Y. Liu, Karin A. Dahmen, and A. Berger, “The role of dipolar interactions for the determination of intrinsic switching field distributions”, Applied Physics Letters 92, 222503 (2008) http://dx.doi.org/10.1063/1.2938695
- Y. Liu, Karin A. Dahmen, and A. Berger, “Intrinsic switching field distribution in perpendicular recording media: numerical study of the DeltaH(M, DeltaM) method”, Physical Review B 77 (54422) (2008)
- Y. Liu, Karin A. Dahmen, and A. Berger, “Comparative Study of the DeltaH(M, DeltaM) method reliability for square and triangular lattices”, Journal of Applied Physics 103 (07F504) (2008) http://dx.doi.org/0.1063/1.2828810
- D.V. Melnikov, T. Fijisawa, D.G. Austing, S. Tarucha and J.P. Leburton, “Many-body excitations in the tunneling current spectra of a few-electron quantum dots”, Physical Review B 77, 165340 (2008) http://dx.doi.org/10.1103/PhysRevB.77.165340
- S. T. Miller, R. B. Haber, “A spacetime discontinuous Galerkin method for hyperbolic heat conduction” (2008) (Submitted not published)
- Andrew Missel and Karin A. Dahmen, “Hopping Conduction and Bacteria: Transport in Disordered Reaction Diffusion Systems”, Physical Review Letters 100 (58301) (2008) http://dx.doi.org/10.1103/PhysRevLett.100.058301
- J. Palaniappan, S. T. Miller, R. B. Haber, “Sub-cell shock capturing and spacetime discontinuity tracking for nonlinear conservation laws”, International Journal for Numerical Methods in Fluids (accepted 2008)
- Ivan S. Ufimtsev and Todd J. Martinez, “Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation”, Journal of Chemical Theory and Computation (2008) Abstract http://dx.doi.org/10.1021/ct700268q
- I. S. Ufimtsev and T. J. Martinez, “Graphical Processing Units for Quantum Chemistry”, Computing in Science and Engineering 10 (6), 26 (2008)
- L-L. Wang and D.D. Johnson, “Electrocatalytic Properties of PtBi and PtPb Line Compounds via DFT: CO and H adsorption”, Journal of Physical Chemistry C (112), 8266 (2008) http://dx.doi.org/10.1021/jp7110956
- J. Xu and A. W. Huebler, “Detecting quasiperiodic structures with double diffraction”, Europhysics Letters 81, 16002 (in press 2008) http://dx.doi.org/10.1209/0295-5075/81/16002
- N.A. Zarkevich, Teck L. Tan, L-L. Wang and D.D. Johnson, “Low-energy antiphase boundaries, degenerate superstructures, and phase stability in frustrated Ising model and Ag-Au alloys”, Physical Review B (77), 144208 (2008) http://dx.doi.org/10.1103/PhysRevB.77.144208
- L.-X. Zhang, D. V. Melnikov, and J.-P. Leburton, “The von Neumann-Wigner theorem in quantum dot molecules”, Physical Review B 78, 85310 (2008) http://dx.doi.org/10.1103/PhysRevB.78.085310
- L-X Zhang, D.V Melnikov, S. Agrawal and J.P. Leburton, “Size effects in the exchange coupling between two electrons in quantum wire quantum dots”, Physical Review B 78, 35418 (2008) http://dx.doi.org/10.1103/PhysRevB.78.035418
Theses
- Andrew Royce Missel, “Noisy Transport in Reaction-diffusion Systems with Quenched Disorder” (2008) PDF
Journal articles
- Todd D. Beaudet, Michele Casula, Jeongnim Kim, Sandro Sorella, and Richard M. Martin, “Molecular hydrogen adsorbed on benzene: Insights from a quantum Monte Carlo study”, Journal of Chemical Physics 129, 164711 (2008) http://dx.doi.org/10.1063/1.2987716
- D. M. Ceperley, “Path Integrals and Supersolids”, Computer Physics Communications, 307-14 (2008)
- Clark, B. K. and D. M. Ceperley, “Path Integral Calculations of Vacancies in Solid Helium”, Computer Physics Communications 179, 82-8 (2008)
- S. Kibey, H. Sehitoglu, and D. D. Johnson, “Energy landscape for martensitic phase transformation in shape memory NiTi”, Acta Materialia 57 (5), 1624-9 (2008) http://dx.doi.org/10.1016/j.actamat.2008.12.008
- J. Kim, D.V. Melnikov and J.P. Leburton, “Tunable many-body effects in triple quantum dot”, Physical Review B (in press 2008)
- B. Kraczek, D. D. Johnson, R. B. Haber, “A spacetime, balance-law formulation of coupled atomistic and continuum dynamics for solids” (2008) (Submitted not published)
- Y. Liu, Karin A. Dahmen, and A. Berger, “The role of dipolar interactions for the determination of intrinsic switching field distributions”, Applied Physics Letters 92, 222503 (2008) http://dx.doi.org/10.1063/1.2938695
- Y. Liu, Karin A. Dahmen, and A. Berger, “Intrinsic switching field distribution in perpendicular recording media: numerical study of the DeltaH(M, DeltaM) method”, Physical Review B 77 (54422) (2008)
- Y. Liu, Karin A. Dahmen, and A. Berger, “Comparative Study of the DeltaH(M, DeltaM) method reliability for square and triangular lattices”, Journal of Applied Physics 103 (07F504) (2008) http://dx.doi.org/0.1063/1.2828810
- D.V. Melnikov, T. Fijisawa, D.G. Austing, S. Tarucha and J.P. Leburton, “Many-body excitations in the tunneling current spectra of a few-electron quantum dots”, Physical Review B 77, 165340 (2008) http://dx.doi.org/10.1103/PhysRevB.77.165340
- S. T. Miller, R. B. Haber, “A spacetime discontinuous Galerkin method for hyperbolic heat conduction” (2008) (Submitted not published)
- Andrew Missel and Karin A. Dahmen, “Hopping Conduction and Bacteria: Transport in Disordered Reaction Diffusion Systems”, Physical Review Letters 100 (58301) (2008) http://dx.doi.org/10.1103/PhysRevLett.100.058301
- J. Palaniappan, S. T. Miller, R. B. Haber, “Sub-cell shock capturing and spacetime discontinuity tracking for nonlinear conservation laws”, International Journal for Numerical Methods in Fluids (accepted 2008)
- Ivan S. Ufimtsev and Todd J. Martinez, “Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation”, Journal of Chemical Theory and Computation (2008) Abstract http://dx.doi.org/10.1021/ct700268q
- I. S. Ufimtsev and T. J. Martinez, “Graphical Processing Units for Quantum Chemistry”, Computing in Science and Engineering 10 (6), 26 (2008)
- L-L. Wang and D.D. Johnson, “Electrocatalytic Properties of PtBi and PtPb Line Compounds via DFT: CO and H adsorption”, Journal of Physical Chemistry C (112), 8266 (2008) http://dx.doi.org/10.1021/jp7110956
- J. Xu and A. W. Huebler, “Detecting quasiperiodic structures with double diffraction”, Europhysics Letters 81, 16002 (in press 2008) http://dx.doi.org/10.1209/0295-5075/81/16002
- N.A. Zarkevich, Teck L. Tan, L-L. Wang and D.D. Johnson, “Low-energy antiphase boundaries, degenerate superstructures, and phase stability in frustrated Ising model and Ag-Au alloys”, Physical Review B (77), 144208 (2008) http://dx.doi.org/10.1103/PhysRevB.77.144208
- L.-X. Zhang, D. V. Melnikov, and J.-P. Leburton, “The von Neumann-Wigner theorem in quantum dot molecules”, Physical Review B 78, 85310 (2008) http://dx.doi.org/10.1103/PhysRevB.78.085310
- L-X Zhang, D.V Melnikov, S. Agrawal and J.P. Leburton, “Size effects in the exchange coupling between two electrons in quantum wire quantum dots”, Physical Review B 78, 35418 (2008) http://dx.doi.org/10.1103/PhysRevB.78.035418
Patents
- Jean-Pierre Leburton, Jeanlex Soares De Sousa,Gil De Aquino Farias, Valder Nogueira Freire, “Memory Device” (2008) Abstract
Press coverage
- “Game consoles reveal their hidden power”, New Scientist (2008)
Theses
- Andrew Royce Missel, “Noisy Transport in Reaction-diffusion Systems with Quenched Disorder” (2008) PDF
Publications for 2007
Journal articles
- M. V. Butz, D. E. Goldberg, P. L. Lanzi, K. Sastry, “Problem solution sustenance in XCS: Markov chain analysis of niche support distributions and the impact on computational complexity.”, Genetic and Evolutionary Computation Conference 8 (1), 5-37 (2007) Abstract PDF Springer link
- Glenn Foster, Alfred W. Hubler, Karin Dahmen, “Resonant forcing of multi-dimensional chaotic map dynamics”, Physical Review E 75, 036212, 9 pages (2007) Abstract http://server10.how-why.com/papers/glenn_pre.pdf
- Gerig, Austin; Hubler, Alfred, “Chaos in a one-dimensional compressible flow”, Physical Review E, 4 pages (2007) Abstract http://dx.doi.org/10.1103/PhysRevE.75.045202
- S. Kibey, J. B. Liu, D. D. Johnson and H. Sehitoglu, “Predicting twinning stress in fcc metals: linking twin-energy pathways to twin nucleation”, Acta Materialia (55), 6843 (2007) http://dx.doi.org/10.1016/j.actamat.2007.08.042
- Dmitriy V. Melnikov and Jean-Pierre Leburton, “Single-particle state mixing in two-electron double quantum dots”, Physical Review B 73, 155301-1-5, 5 pages (2007) Abstract
- Dmitriy V. Melnikov, Jean-Pierre Leburton,Ahmed Taha, and Nahil Sobh, “Coulomb localization and exchange modulation in two-electron coupled quantum dots”, Physical Review B 74, 041309-1-4, 4 pages (2007) Abstract
- M. Pelikan, K. Sastry, D. E. Goldberg, “Sporadic model building for efficiency enhancementof the hierarchical BOA”, Genetic Programming and Evolvable Machines (accepted 2007)
- Nichols A. Romero, Jeongnim Kim, and Richard M. Martin, “Electronic structures and superconductivity of endohedrally doped C28 solids from first principles”, Physical Review B 76 (205405), 6 pages (2007) 10.1103/PhysRevB.76.205405
- K. Sastry, D.D. Johnson, D. E. Goldberg, “Scalability of a hybrid extended compact genetic algorithm for ground state optimization of clusters.”, Materials and Manufacturing Processes 22, 570, 7 pages (2007) Abstract http://dx.doi.org/10.1080/10426910701319654
- K. Sastry, D.D. Johnson, A. L. Thompson, D. E. Goldberg, T. J. Martinez, J. Leiding, J. Owens, “Optimization of Semiempirical Quantum Chemistry Methods via Multiobjective Genetic Algorithms: Accurate Photochemistry for Larger Molecules and Longer Time Scales”, Materials and Manufacturing Processes 22, 9 pages (2007) Abstract http://dx.doi.org/10.1080/10426910701319506
- Martin S. Singleton, Alfred W. Huebler, “Learning rate and attractor size of the single-layer perceptron”, Physical Review E 75, 026704, 13 pages (2007) Abstract http://link.aps.org/abstract/PRE/v75/e026704
- Jordan E. Vincent, Jeongnim Kim, and Richard M. Martin, “Quantum Monte Carlo calculations of the optical gaps of Ge nanoclusters using core-polarization potentials”, Physical Review B 75, 045302, 10 pages (2007) Abstract http://dx.doi.org/10.1103/PhysRevB.75.045302
- Shun Wang, Eric de Sturler, and Glaucio H. Paulino, “Large-Scale Topology Optimization using Preconditioned Krylov Subspace Methods with Recycling”, International Journal for Numerical Methods in Engineering 69 (12), 2441-68, 28 pages (2007) Abstract PDF http://dx.doi.org/10.1002/nme.1798
- LinLin Wang and D.D. Johnson, “Shear instabilities in metallic nanoparticles: hydrogen-stabilized structure of Pt37 on carbon”, Journal of American Chemical Society 129, 3658-64, 7 pages (2007) Abstract PDF http://dx.doi.org/10.1021/ja068750h
- L-L Wang and D.D. Johnson, “Density functional study of structural trends for late-transition-metal 13-atom clusters”, Physical Review B 75 (23), 235405 (2007) http://dx.doi.org/10.1103/PhysRevB.75.235405
- L-L Wang and D.D. Johnson, “Shear instabilities in metallic nanoparticles: hydrogen-stabilized structure of Pt37 on carbon,”, Journal of American Chemical Society 129 (12), 3658 (2007) http://dx.doi.org/10.1021/ja068750h
- N. A. Zarkevich, Teck L. Tan, and D. D. Johnson, “First-principles prediction of phase-segregating alloy phase diagrams and a rapid design estimates of their transition temperatures”, Physical Review B 75, 104203-1-2 (2007) Abstract PDF http://dx.doi.org/10.1103/PhysRevB.75.104203
- L.-X. Zhang, D. V. Melnikov and J.P. Leburton, “Exchange interaction and stability diagram of coupled quantum dots in magnetic fields”, Physical Review B 74, 205306-1-6, 6 pages (2007) Abstract
Articles in proceedings
- D. V. Melnikov and J.P. Leburton, “Transport Spectroscopy in Vertical Quantum Dots”, Eds. G. Guizzetti, L. C. Andreani , F. Marabelli and M. Patrini, Highlights on Spectroscopies of Semiconductors and Nanostructure; Festschrift in honour of Angiolino Stella : Pavia, 13 June 2007, Aula Foscolo, Università degli studi di Pavia, 327 (2007)
- J. Bacardit, M. Stout, J.D. Hirst, K. Sastry, X. Llorà, N. Krasnogor, “Automated alphabet reduction method with evolutionary algorithms for protein structure prediction”, Genetic and Evolutionary Computation Conference, 346 (2007) Abstract http://doi.acm.org/10.1145/1276958.1277033
- X. Llorà, K. Sastry, T.-L. Yu, D. E. Goldberg, “Do not match, Inherit: Fitness surrogates for genetics-based machine learning techniques”, Genetic and Evolutionary Computation Conference, 1798 (2007) http://doi.acm.org/10.1145/1276958.1277319
- Dmitriy V. Melnikov and Jean-Pierre Leburton, “Single-Paticle State Mixing and Coulomb Localization in Two- Electron Realistic Coupled Quantum Dots”, physica status solidi (c) 4 (2), 578-81, 4 pages (2007) Abstract http://dx.doi.org/10.1002/pssc.200673206
- A. Orriols-Puig, D. E. Goldberg, K. Sastry, E. Bernadó-Mansilla, “Modeling XCS in class imbalances: Population sizing and parameter settings”, Genetic and Evolutionary Computation Conference, 1838 (2007) Abstract PDF http://doi.acm.org/10.1145/1276958.1277324
- A. Orriols-Puig, K. Sastry, P. L. Lanzi, D. E. Goldberg, E. Bernadó-Mansilla E, “Modeling selection pressure in XCS for proportionate and tournament selection”, Genetic and Evolutionary Computation Conference, 1846 (2007) PDF http://doi.acm.org/10.1145/1276958.1277325
- K. Sastry, D. E. Goldberg, X. Llorà, “Towards billion-bit optimization via a parallel estimation of distribution algorithm”, Genetic and Evolutionary Computation Conference, 577 (2007) Abstract PDF http://doi.acm.org/10.1145/1276958.1277077
- K. Sastry, M. Pelikan, D. E. Goldberg, “Empirical Analysis of Ideal Recombination on Random Decomposable Problems”, Genetic and Evolutionary Computation Conference, 1388 (2007) Abstract http://doi.acm.org/10.1145/1276958.1277216
- T.-L. Yu, K. Sastry, D. E. Goldberg, M. Pelikan, “Let's get ready to rumble redux: Crossover versus mutation head to head on exponentially scaled problems”, Genetic and Evolutionary Computation Conference, 1380 (2007) Abstract PDF http://doi.acm.org/10.1145/1276958.1277215
- L-X Zhang, D. V. Melnikov and J.P. Leburton, “Engineering Exchange Coupling in Double Elliptic Quantum Dots”, IEEE Transactions on Nanotechnology 6 (2), 250-6, 6 pages (2007) Abstract
Theses
Publications for 2006
Journal articles
- Salvador Barraza-Lopez, Peter M Albrecht, Nichols A. Romero, and Karl Hess, “Ab initio study of semiconducting carbon nanotubes adsorbed on the Si(100) surface: Diameter- and registration-dependent atomic configurations and electronic properties”, Journal of Applied Physics 100 (124304), 10 pages (2006) Abstract PDF
- E.W. Carlson, K.A. Dahmen, E. Fradkin, “Hysteresis and Noise from Electronic Nematicity in High Temperature Superconductors”, Physical Review Letters 96, 097003/1-4 (2006) Abstract http://arxiv.org/abs/cond-mat/0510259
- B. Clark and D. M. Ceperley, “Off-Diagonal Long-Range Order in Solid 4He”, Physical Review Letters 96, 105301 (2006) http://arxiv.org//abs/cond-mat/0512547
- D. Coe and T. J. Martínez, “Ab Initio Molecular Dynamics of Excited State Intramolecular Proton Transfer Around a Three-State Conical Intersection in Malonaldehyde”, Journal of Physical Chemistry A 110 (2), 618-30 (2006) DOI link
- D. Das, R. M. Martin, and M. Kalos, “Quantum Monte Carlo using a Stochastic Poisson Solver”, Physical Review E 73 (4), 046702 (accepted 2006)
- K. Delaney, C. Pierleoni and D. M. Ceperley, “Quantum Monte Carlo Simulation of the High Pressure Molecular-Atomic Transition in Fluid Hydrogen”, Physical Review Letters 97, 235702 (2006) PDF http://dx.doi.org/10.1103/PhysRevLett.97.235702
- Daniel Finkenstadt and D.D. Johnson, “Solute/Defect-Mediated Pathway for Rapid anoprecipitation in Solid-Solutions: Gamma-Surface Analysis in fcc Al-Ag”, Physical Review B 73, 024101-10 (2006) Abstract DOI Download
- Glenn Foster, Alfred W. Hubler, Karin Dahmen, “Resonance Spectroscopy with Chaotic Forcing Functions”, Physical Review E (2006) Abstract PDF
- Subhradip Ghosh, D.A. Biava, W.A. Shelton, and D.D. Johnson, “Systematically exact, integrated density of states Lloyd's formula for disordered alloys with short-range order”, Physical Review B 73, 085106-12 (2006) Abstract DOI Download
- Misha Kilmer and Eric de Sturler, “Recycling Subspace Information for Diffuse Optical Tomography”, SIAM Journal on Scientific Computing, SIAM Journal on Scientific Computing 27 (6), 2140-66, 27 pages (2006) Abstract PDF http://epubs.siam.org/SISC/volume-27/art_61027.html
- B. G. Levine, C. Ko, J. Quenneville, and T. J. Martinez, “Conical Intersections and Double Excitations in Time Dependent Density Functional Theory”, Molecular Physics 104 (05-07), 1039-51 (2006) DOI link
- T. J. Martinez, “Insights for Light-Driven Molecular Devices from Ab Initio Multiple Spawning Dynamics”, Accounts of Chemical Research 39 (2), 119-26 (2006) DOI link
- Michael L. Parks, Eric de Sturler, Greg Mackey, Duane D. Johnson, and Spandan Maiti, “Recycling Krylov Subspaces for Sequences of Linear Systems”, SIAM Journal on Scientific Computing 28 (5), 1651-74, 24 pages (accepted 2006) Abstract PDF http://huygens.math.vt.edu/~sturler/Papers/SeqLinSys_FinalDraft.pdf
- Chris Siefert and Eric de Sturler, “Probing Methods for Saddle-Point Problems”, Electronic Transactions on Numerical Analysis 22, 163-8, 21 pages (2006) Abstract PDF http://etna.mcs.kent.edu/vol.22.2006/pp163-183.dir/pp163-183.pdf
- Chris Strelioff, Alfred Hübler, “Medium-Term Prediction of Chaos”, Physical Review Letters 9, 044101-1-4 (2006) Abstract
- L-L Wang, S.V. Khare, V. Chirita, D.D. Johnson, A.A. Rockett, A.I. Frenkel, N.H. Mack, and R.G. Nuzzo, “Origin of bulk-like structure and bond distributions of Pt37 and Pt6Ru31 clusters on carbon: comparison of theory and experiment”, Journal of American Chemical Society 128 (1), 131-42 (2006) Abstract DOI Download
- Jia Ye and Pascal Bellon, “Nanoscale patterning of chemical order introduced by displacement cascades in irradiated L10 alloys: Scaling analysis of the fluctuations of order”, Physical Review B 73, 224121-1-1, 11 pages (2006) Abstract http://dx.doi.org/10.1103/PhysRevB.73.224121
Articles in proceedings
- Lei Guo and Erik Luijten, “Langevin Dynamics Study of Polymer Translocation through a anopore”, edited by D.P. Landau, S.P. Lewis and H.B. Schüttler, Computer Simulation Studies in Condensed-Matter Physics XVIII (2006) Springer's book information
- M. Pelikan, K. Sastry, D. E. Goldberg, “Sporadic Model Building for Efficiency Enhancement of hBOA”, Genetic and Evolutionary Computation Conference, 405-12 (2006) Abstract PDF
- K. Sastry, D.D. Johnson, A. L. Thompson, D. E. Goldberg, T. J. Martinez, J. Leiding, J. Owens, “Multiobjective Genetic Algorithms for Multiscaling Excited State Direct Dynamics in Photochemistry”, *Chosen as Best Paper in Track.
*Won 2006 "Silver Humie" in Human Competitive Results Awards at Genetic and Evolutionary Computation Conference, Genetic and Evolutionary Computation Conference, 1745-52, 8 pages (2006) Abstract PDF
- K. Sastry, C. F. Lima, D. E. Goldberg, “Evaluation Relaxation Using Substructural Information and Linear Estimation”, Genetic and Evolutionary Computation Conference, 419-26 (2006) Abstract PDF
- K. Sastry, P. Winward, D. E. Goldberg, C. F. Lima, “Fluctuating Crosstalk as a Source of Deterministic oise and its Effects on GA Scalability”, Applications of Evolutionary Computing: EvoWorkshops 2006, 740-51 (2006) Abstract http://dx.doi.org/10.1007/11732242_72
Theses
Publications for 2005
Journal articles
- A. Barr and A. Hubler, “Adaptation to the Edge of Chaos in a on-Isothermal Autocatalator”, Journal of Chemical Physics (2005) (Submitted not published)
- D.A. Biava, Subhradip Ghosh, D.D. Johnson, W.A. Shelton, and A.V. Smirnov, “Systematic, multisite short-range-order corrections to the electronic structure of disordered alloys from a first-principles KKR nonlocal CPA dynamical cluster approximation”, Physical Review B 72, 113105-1-4 (2005) Abstract PRB download
- John H. Carpenter, Karin A. Dahmen, Andrea C. Mills, Michael B. Weissman, Andreas Berger, Olav Hellwig, “History-Induced Critical Behavior in Disordered Systems”, Physical Review B 72, 052410/1-4 (2005)
- Karin A. Dahmen, “Universal Clues in Noisy Skews”, Nature Physics 1, 14-5 (2005)
- Dene Farrell, A. Hubler, Joseph Brewer, and I. Hubler, “Acceleration Beyond the Wave Speed in Dissipative Wave-Particle Systems”, Physical Review Letters (2005) (Submitted not published)
- Lei Guo and Erik Luijten, “Reversible gel formation of triblock copolymers studied by molecular dynamics simulation”, Journal of Polymer Science B: Polymer Physics 43 (8), 959-6 (2005) Abstract PDF
- Lei Guo and Erik Luijten, “Critical polymer-polymer phase separation in ternary solutions”, Journal of Chemical Physics 123, 074907 (2005) Abstract PDF http://link.aip.org/link/?JCP/123/074907
- Alfred W. Hubler, “Predicting Complex Systems with a Holistic Approach”, Complexity 10, 11-6 (2005)
- Joseph K. Jun and Alfred W. Hubler, “Formation and structure of ramified charge transportation networks in an electromechanical system”, Proceedings of the National Academy of Sciences 102, 536-40 (2005)
- Khairallah, S.A., Ceperley, D.M., “Superfluidity of dense /sup 4/He in Vycor”, Physical Review Letters 95 (18), 185301 (2005)
- J. Kim, P. Matagne, J.P. Leburton, R.M. Martin and S. Tarucha, “Engineering Quantum Confinement and Orbital Coupling in Laterally-Coupled Vertical Quantum Dots for Spintronic Applications”, IEEE Transactions on Nanotechnology (in press 2005) Abstract
- Jian-Bo Liu, D.D. Johnson and A.V. Smirnov, “Predicting Yield-Stress Anomalies in L12 Alloys: i3Ge-Fe3Ge Pseudo-Binaries”, Acta Materialia 53, 3601-12 (2005) Abstract DOI download
- X. Luo and R. M. Martin, “Jahn-Teller Distortion and Ferromagnetism in the Dilute Magnetic Semiconductors GaAs:Mn and Cubic GaN:Mn”, Physical Review B (72), 035212, 6 pages (2005) http://link.aps.org/abstract/PRB/v72/e035212
- P. Melby, N. Weber, A. Hubler, “Dynamics of Self-Adjusting System with Noise”, Chaos 15 (033902), 7 pages (2005) Abstract PDF
- G. A. Narvaez, J. Kim and J. W. Wilkins, “Effects of morphology on phonons in nanoscopic silver grains”, Physical Review B 72, 155411 (2005)
- Kumara Sastry, D.D. Johnson, D.E. Goldberg, and P. Bellon, “Genetic programming for multitimescale modeling”, Physical Review B 72, 085438-1-9 (2005) Abstract DOI download
- Kumara Sastry, D.D. Johnson, D.E. Goldberg, and P. Bellon, “Genetic Programming for MultiScale Modeling”, International Journal of MultiScale Computational Engineering 2 (2), 239-56 (2005)
- A.V. Smirnov, W.A. Shelton, and D.D. Johnson, “Importance of Thermal Disorder on the Properties of Alloys: Origin of Paramagnetism and Structural Anomalies in Iron-Aluminum”, Physical Review B 71, 064408-6 (2005)
- L-L Wang and D.D. Johnson, “Removing critical errors for DFT application to transition-metal nanoclusters: correct ground-state structures of Ru clusters”, Journal of Physical Chemistry B 109 (49), L23113-2317 (2005) Abstract DOI download
- G.J. Xu, N.A. Zarkevich, A. Agrawal, A.W. Signor, B.R. Trenhaile, D.D. Johnson, and J.H. Weaver, “Cross-over Energetics for Halogenated Si(100): Vacancy Line Defects, Dimer Vacancy Lines, and Atom Vacancy Lines”, Physical Review B 71, 115332-7 (2005)
- Nikolai Zarkevich and D.D. Johnson, “Energy Scaling and Surface Patterning of Halogen-Terminated Si(001) Surfaces”, Surface Science Letters 591, L292-298 (2005) Abstract
- L-X Zhang, D. Melnikov and J.P. Leburton, “Simulation of Spin-Qubit Quantum Dot Circuit with Integrated Quantum Point Contact Read-Out”, Journal of Computational Electronics 4, 111 (2005)
Articles in proceedings
- J. D. Coe and T. J. Martìnez, “Competitive Decay at Two and Three-State Conical Intersections in Excited State Intramolecular Proton Transfer”, Journal of American Chemical Society 127, 4560-1 (2005)
- Kumara Sastry, Hussein A. Abbass, David E. Goldberg, D. D. Johnson, “Sub-structural Niching in Estimation Distribution Algorithms”, Genetic and Evolutionary Computation Conference, 671-8 (2005) Abstract PDF
Articles in books
- S. Olsen, A. Toniolo, C. Ko, L. Manohar, K. Lamothe, and T. J. Martìnez, “Computation of Reaction Mechanisms and Dynamics in Photobiology”, M. Olivucci, Computational Photochemistry (2005) Elsevier.
- James P. Sethna, Karin A. Dahmen, Olga Perkovic, “Random-Field Ising Models of Hysteresis”, Giorgio Bertotti and I. Mayergoyz, Science of Hysteresis (2005) Elsevier.
- A. Toniolo, B. Levine, A. Thompson, J. Quenneville, M. Ben-Nun, J. Owens, S. Olsen, L. Manohar, and T. J. Martìnez, “Photodynamics from First Principles”, ed. A. Kutateladze, Computational Methods in Organic Photochemistry (2005) CRC Press book description
Theses
- Robert Allen White, “Sweeprate and Temperature Effects on Crackling Noise” (2005) PDF
- Amit Pankaj Mehta, “Higher Order Spectra and Universal Shape Functions in Avalanche Models” (2005) PDF
- Dyutiman Das, “Quantum Monte Carlo with a stochastic potential solver” (2005) Abstract PDF
- Nichols Anthony Romero, “Density functional study of fullerene-based solids: crystal structure, doping, and electron-phonon interaction” (2005) Abstract PDF
Publications for 2004
Journal articles
- Chiesa, S., D. M. Ceperley and S.-W. Zhang, “Accurate, efficient and simple forces with quantum Monte Carlo methods”, Physical Review Letters 94, 036404, 4 pages (2004) http://arxiv.org/abs/physics/0409087
- William D. Mattson, Daniel Sanchez-Portal, Simone Chiesa and Richard M. Martin, “Prediction of new phases of nitrogen at high pressure from first-principles simulations”, Physical Review Letters 93, 125501 (2004) Abstract
- Morales J, Martinez TJ, “A ew Approach to Reactive Potentials with Fluctuating Charges: The Quadratic Valence Bond Model”, Journal of Physical Chemistry 108A, 3076-84 (2004) Abstract PDF
- R. Ravishankar, P. Matagne, J. P. Leburton and R. M. Martin, “Three-dimensional self-consistent simulations of symmetric and asymmetric laterally coupled vertical quantum dots”, Physical Review B 69, 035326 (2004)
- D. A. Richie, Jeongnim Kim, Stephen A. Barr, Kaden R. A. Hazzard, Richard Hennig, and John W. Wilkins, “Complexity of Small Silicon Self-Interstitial Defects”, Physical Review Letters 92, 045501 (2004)
- Nichols A. Romero, Jeongnim Kim and Richard M. Martin, “Electron-Phonon Interactions in C28-derived Molecular Solids”, Physical Review B 70, 140504, 4 pages (2004)
- Toniolo A, Olsen S, Manohar L, Martinez TJ, “Conical Intersection Dynamics in Solution: The Chromophore of Green Fluorescent Protein"”, Faraday Discussions 127, 149-63 (2004) Abstract PDF
- I. Vasiliev, and R. M. Martin, “Time-dependent density-functional calculations with asymptotically correct exchange-correlation potentials”, Physical Review A 69, 052508 (2004)
- Jia Ye and Pascal Bellon, “Nanoscale patterning of chemical order induced by displacement cascades in irradiated alloys. I. A kinetic Monte Carlo study”, Physical Review B 70, 094104, 11 pages (2004) Abstract
- Nikolai Zarkevich and D.D. Johnson, “Reliable First-Principles Alloy Thermodynamics via Truncated Cluster Expansions”, Physical Review Letters 92, 255702-1/4 (2004)
- L.-X. Zhang, J. P. Leburton, R. Hanson, and L. P., “Engineering the quantum point contact response to single-electron charging in a few-electron quantum-dot circuit”, Applied Physics Letters 85, 2628, 4 pages (2004)
- L.-X Zhang and J.P. Leburton, “Electrostatic cross-talk between quantum dot and quantum point contact charge read-out in few-electron quantum dot circuits”, Journal of Applied Physics, 7352 (2004)
Articles in proceedings
- B. Levine and T. J. MartÃŒnez, “First Principles Ab Initio Multiple Spawning Dynamics of Electronically Excited trans-1,3-Butadiene with Wavefunction and Density Functional Theory”, G. A. Worth and S. C. Allthorpe, Quantum Dynamics and Conical Intersections (2004)
Articles in books
- T. Schultz, S. Ullrich, J. Quenneville, T. J. MartÃŒnez, M. Z. Zgierski, and A. Stolow, “Azobenzene photoisomerization: Two states and two relaxation pathways explain the violation of Kasha’s rule”, M. Martin and J. T. Hynes, Femtochemistry and Femtobiology: Ultrafast Events in Molecular Science (2004) Elsevier, Amsterdam.
- Toniolo A, Olsen S, Manohar L, Martinez TJ, “Ultrafast Excited State Dynamics in Green Fluorescent Protein Chromophore”, Eds. M. Martin and J. T. Hynes, Femtochemistry and Femtobiology: Ultrafast Events in Molecular Science (2004) Elsevier, Amsterdam.
Theses
- John Halsey Carpenter, “History Induced Critical Scaling in Disordered Media and Super Diffusive Growth in Highly Advective Random Environments” (2004) PDF
Books
- Richard M. Martin, Electronic Structure: Basic Theory and Practical Methods (2004) Cambridge University Press. Book link
Publications for 2003
Chapters in books
- Toniolo A, Levine B, Thompson A, Quenneville J, Ben-Nun M, Owens J, Olsen S, Manohar L, Martinez TJ, “Photochemistry from First Principles and Direct Dynamics”, ed. A. Kutateladze, Marcel-Dekker, Computational Methods in Organic Photochemistry (in press 2003)
Journal articles
- Carpenter JH, Dahmen KA, “Barkhausen noise and critical scaling in the demagnetization curve”, Physical Review B 67, 020412-R (2003) PDF
- M. D. Deshpande, D. G. Kanhere, I. Vasiliev, and R. M. Martin, “Ab initio absorption spectra of Aln (n=2-13) clusters”, Physical Review B 68, 035428 (2003)
- Lei Guo and Erik Luijten, “Shape variation of linear polymers upon phase separation in a ternary solution”, Macromolecules 36, 8201 (2003) Abstract HTML
- S.V. Khare, S. Kodambaka, D.D. Johnson, I. Petrov and J.E. Greene, “Determining Absolute Orientation-Dependent Step Energies: A General Theory for Wulff construction and for Anisotropic Two-Dimensional Island Shape Fluctuations”, Surface Science 522, 75-83 (2003)
- S. Kodambaka, V. Petrov, S.V. Khare, D.D. Johnson, I. Petrov and J.E. Greene, “Absolute Orientation-Dependent Anisotropic Ti (111) Island Step Energies and Stiffnesses from Shape Fluctuation Analyses”, Physical Review B 67, 035409 (2003)
- White R, Dahmen K, “Driving rate effects on crackling noise”, Physical Review Letters 91, 085702/1-4 (2003) PDF
- Nikolai Zarkevich and D.D. Johnson, “The predicted hcp Al-Ag metastable phase diagram, ground states and precipitate structure”, Physical Review B 67, 064104-8 (2003)
Reports
- Ruyi Yu, Eric de Sturler, D.D. Johnson and A.V. Smirnov, “A block GCROT method for Complex, non-Hermitian matrices: Application to Large-Scale Electronic-Structure Calculations” (2003)
