11 results on '"Ho, Gregory"'
Search Results
2. Describing metal surfaces and nanostructures with orbital-free density functional theory
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Ho, Gregory S., Huang, Chen, and Carter, Emily A.
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DENSITY functionals , *METALLIC surfaces , *TRANSITION metals , *NANOSTRUCTURES , *QUANTUM theory , *PSEUDOPOTENTIAL method - Abstract
Abstract: Orbital-free density functional theory (OF-DFT) can be made to scale linearly with sample size, allowing thousands of atoms to be treated explicitly with quantum mechanics. State-of-the-art kinetic energy density functionals and ion–electron pseudopotentials are used to obtain accurate structural property predictions for nanoparticles, nanowires, extended surfaces, and nanoindentation of simple metals. [Copyright &y& Elsevier]
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- 2007
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3. Prediction of dislocation nucleation during nanoindentation of Al 3 Mg by the orbital-free density functional theory local quasicontinuum method.
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Hayes, Robin L., Ho, Gregory, Ortiz, Michael, and Carter, Emily A.
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DISLOCATIONS in metals , *DEFORMATIONS (Mechanics) , *NUCLEATION , *MAGNESIUM alloys , *ALUMINUM alloys , *ATOMIC force microscopy , *MICROMECHANICS , *PHYSICAL metallurgy - Abstract
The first-principles prediction of dislocation nucleation in metallic systems subject to realistically sized indenters requires a multiscale approach due to the prohibitive computational expense. The largest empirical atomistic simulations include at most a billion atoms, at the same time requiring the parameterization of new interactions whenever an additional species or crystal structure is added. The multiscale orbital-free density functional theory–local quasicontinuum (OFDFT-LQC) method overcomes these problems by using first-principles OFDFT to capture the atomic interactions while relying upon LQC to evolve the macroscopic system. We use this method to indent the (111) surface of a 2×2×1μm piece of L1 2   Al 3 Mg. Using a localization criterion, the first dislocation is predicted to form off-axis on the slip plane in the direction after the indenter has penetrated 70  nm. Other popular dislocation nucleation criteria give different predictions. These results are strikingly similar to those for indentation into the (111) surface of Al, indicating that the underlying crystal structure, not the atomic identity, is the most important factor in determining the onset of plasticity. [ABSTRACT FROM AUTHOR]
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- 2006
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4. The Cationic Cascade Route to Longifolene.
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Ho, Gregory A., Noun, Dustin H., and Tantillo, Dean J.
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CATIONS , *HARTREE-Fock approximation , *CHEMICAL reactions , *ORGANIC chemistry - Abstract
W. S. Johnson's total synthesis of the sesquiterpenoid longifolene is a classic example of the power of cationic polycyclizations for constructing complex molecular architectures. Herein we revisit the key polycyclization step of this synthesis using hybrid Hartree-Fock/density functional theory calculations and validate the feasibility of Johnson's proposed mechanism. We also explore perturbations to the 3-center 2-electron bonding array in a key intermediate that result from changing the polycyclic framework in which it is embedded. [ABSTRACT FROM AUTHOR]
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- 2005
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5. Introducing PROFESS: A new program for orbital-free density functional theory calculations
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Ho, Gregory S., Lignères, Vincent L., and Carter, Emily A.
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COMPUTER software , *DENSITY functionals , *QUANTUM theory , *BOUNDARY value problems , *ELECTRON distribution , *IONS , *FUNCTIONALS - Abstract
We present PROFESS (PRinceton Orbital-Free Electronic Structure Software), a new software package that performs orbital-free density functional theory (OF-DFT) calculations. OF-DFT is a first principles quantum mechanics method primarily for condensed matter that can be made to scale linearly with system size. We describe the implementation of energy, force, and stress functionals and the methods used to optimize the electron density under periodic boundary conditions. All electronic energy and potential terms scale linearly while terms involving the ions exhibit quadratic scaling in our code. Despite the latter scaling, the program can treat tens of thousands of atoms with quantum mechanics on a single processor, as we demonstrate here. Limitations of the method are also outlined, the most serious of which is the accuracy of state-of-the-art kinetic energy functionals, which limits the applicability of the method to main group elements at present. Program summary: Program title: PROFESS Catalogue identifier: AEBN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEBN_v1_0.html Program obtainable from: CPC Program Library, Queen''s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 35 933 No. of bytes in distributed program, including test data, etc.: 329 924 Distribution format: tar.gz Programming language: Fortran 90 Computer: Intel with ifort; AMD Opteron with pathf90 Operating system: Linux RAM: Problem dependent, but 2 GB is sufficient for up to 10,000 ions Classification: 7.3 External routines: FFTW (http://www.fftw.org), MINPACK-2 Nature of problem: Given a set of coordinates describing the initial ion positions under periodic boundary conditions, recovers the ground state energy, electron density, ion positions, and cell lattice vectors predicted by orbital-free density functional theory. Except for computation of the ion–ion and ion–electron terms, all other terms are effectively linear scaling. Up to ∼10,000 ions may be included in the calculation on just a single processor. Solution method: Computes energies as described in text; minimizes this energy with respect to the electron density, ion positions, and cell lattice vectors. Restrictions: PROFESS cannot use nonlocal (such as ultrasoft) pseudopotentials. Local pseudopotential files for aluminum, magnesium, silver, and silicon are available upon request. Also, due to the current state of the kinetic energy functionals, PROFESS is only reliable for main group metals and some properties of semiconductors. Running time: Problem dependent: the test example provided with the code takes less than a second to run. Timing results for large scale problems are given in the paper. References: [1] Y.A. Wang, N. Govind, E.A. Carter, Phys. Rev. B 58 (1998) 13465; Y.A. Wang, N. Govind, E.A. Carter, Phys. Rev. B 64 (2001) 129901 (erratum). [2] S.C. Watson, E.A. Carter, Comput. Phys. Comm. 128 (2000) 67. [Copyright &y& Elsevier]
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- 2008
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6. Remission-Stage Ovarian Cancer Cell Vaccine with Cowpea Mosaic Virus Adjuvant Prevents Tumor Growth.
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Stump, Courtney T., Ho, Gregory, Mao, Chenkai, Veliz, Frank A., Beiss, Veronique, Fields, Jennifer, Steinmetz, Nicole F., Fiering, Steven, Ksiązek, Krzysztof, and Lopez-Cabrera, Manuel
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MEMORY , *OVARIAN tumors , *ANIMAL experimentation , *TUMOR classification , *DESCRIPTIVE statistics , *CANCER vaccines , *COMBINED modality therapy , *CELL lines , *RNA viruses , *DISEASE remission , *MICE - Abstract
Simple Summary: Ovarian cancer survival rates are poor, with most deaths occurring from cancer recurrence following initial remission. Accordingly, there is a significant need for treatments that prevent relapse. Here, using a therapeutic vaccine against a mouse model of ovarian cancer, we evaluate a personalized vaccine that could be delivered to patients during their remission period. We show that mice that receive a combination of cowpea mosaic virus nanoparticles (CPMV) and irradiated tumor cells overwhelmingly reject tumor challenges in a T cell-dependent manner. Accordingly, we extend the demonstrated potential of CPMV as a vaccine adjuvant. We provide initial evidence that vaccines delivered during periods of clinical remission, using previously resected tumor tissue and an immune adjuvant, may comprise a feasible strategy of ovarian cancer treatment. Ovarian cancer is the deadliest gynecological malignancy. Though most patients enter remission following initial interventions, relapse is common and often fatal. Accordingly, there is a substantial need for ovarian cancer therapies that prevent relapse. Following remission generated by surgical debulking and chemotherapy, but prior to relapse, resected and inactivated tumor tissue could be used as a personalized vaccine antigen source. The patient's own tumor contains relevant antigens and, when combined with the appropriate adjuvant, could generate systemic antitumor immunity to prevent relapse. Here, we model this process in mice to investigate the optimal tumor preparation and vaccine adjuvant. Cowpea mosaic virus (CPMV) has shown remarkable efficacy as an immunostimulatory cancer therapy in ovarian cancer mouse models, so we use CPMV as an adjuvant in a prophylactic vaccine against a murine ovarian cancer model. Compared to its codelivery with tumor antigens prepared in three other ways, we show that CPMV co-delivered with irradiated ovarian cancer cells constitutes an effective prophylactic vaccine against a syngeneic model of ovarian cancer in C57BL/6J mice. Following two vaccinations, 72% of vaccinated mice reject tumor challenges, and all those mice survived subsequent rechallenges, demonstrating immunologic memory formation. This study supports remission-stage vaccines using irradiated patient tumor tissue as a promising option for treating ovarian cancer, and validates CPMV as an antitumor vaccine adjuvant for that purpose. [ABSTRACT FROM AUTHOR]
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- 2021
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7. Author Correction: AI is a viable alternative to high throughput screening: a 318-target study.
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Wallach, Izhar, Bernard, Denzil, Nguyen, Kong, Ho, Gregory, Morrison, Adrian, Stecula, Adrian, Rosnik, Andreana, O'Sullivan, Ann Marie, Davtyan, Aram, Samudio, Ben, Thomas, Bill, Worley, Brad, Butler, Brittany, Laggner, Christian, Thayer, Desiree, Moharreri, Ehsan, Friedland, Greg, Truong, Ha, van den Bedem, Henry, and Ng, Ho Leung
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HIGH throughput screening (Drug development) , *CHILDREN'S hospitals , *CHEMICAL structure , *MEDICAL centers , *INTERNET publishing - Abstract
This document is a correction notice for an article titled "AI is a viable alternative to high throughput screening: a 318-target study" published in Scientific Reports. The correction includes updates to the list of authors and their affiliations, as well as corrections to the affiliation information for certain authors. Additionally, an outdated version of Figure 1 was included in the original article, and the Acknowledgements section contained an error. The original article has been corrected to address these issues. [Extracted from the article]
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- 2024
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8. FeMV is a cathepsin-dependent unique morbillivirus infecting the kidneys of domestic cats.
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Nambulli, Sham, Rennick, Linda J., Acciardo, Andrew S., Tilston-Lunel, Natasha L., Ho, Gregory, Crossland, Nicholas A., Hardcastle, Kathy, Nieto, Betsy, Bainbridge, Graeme, Williams, Tracey, Sharp, Claire R., and Duprex, W. Paul
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CATS , *MORBILLIVIRUSES , *RECOMBINANT viruses , *VIRUS isolation , *REVERSE genetics - Abstract
Feline morbillivirus (FeMV) is a recently discovered pathogen of domestic cats and has been classified as a morbillivirus in the Paramyxovirus family. We determined the complete sequence of FeMVUS5 directly from an FeMV-positive urine sample without virus isolation or cell passage. Sequence analysis of the viral genome revealed potential divergence from characteristics of archetypal morbilliviruses. First, the virus lacks the canonical polybasic furin cleavage signal in the fusion (F) glycoprotein. Second, conserved amino acids in the hemagglutinin (H) glycoprotein used by all other morbilliviruses for binding and/or fusion activation with the cellular receptor CD150 (signaling lymphocyte activation molecule [SLAM]/F1) are absent. We show that, despite this sequence divergence, FeMV H glycoprotein uses feline CD150 as a receptor and cannot use human CD150. We demonstrate that the protease responsible for cleaving the FeMV F glycoprotein is a cathepsin, making FeMV a unique morbillivirus and more similar to the closely related zoonotic Nipah and Hendra viruses. We developed a reverse genetics system for FeMVUS5 and generated recombinant viruses expressing Venus fluorescent protein from an additional transcription unit located either between the phosphoprotein (P) and matrix (M) genes or the H and large (L) genes of the genome. We used these recombinant FeMVs to establish a natural infection and demonstrate that FeMV causes an acute morbillivirus-like disease in the cat. Virus was shed in the urine and detectable in the kidneys at later time points. This opens the door for long-term studies to address the postulated role of this morbillivirus in the development of chronic kidney disease. [ABSTRACT FROM AUTHOR]
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- 2022
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9. Orbital-free density functional theory: Linear scaling methods for kinetic potentials, and applications to solid Al and Si
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Chai, Jeng-Da, Lignères, Vincent L., Ho, Gregory, Carter, Emily A., and Weeks, John D.
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DENSITY functionals , *CHEMICAL kinetics , *ALUMINUM , *SILICON , *LAGRANGE equations , *SOLID state chemistry , *ELECTRON distribution - Abstract
Abstract: In orbital-free density functional theory the kinetic potential (KP), the functional derivative of the kinetic energy density functional, appears in the Euler equation for the electron density and may be more amenable to simple approximations. We study properties of two solid-state systems, Al and Si, using two nonlocal KPs that gave good results for atoms. Very accurate results are found for Al, but results for Si are much less satisfactory, illustrating the general need for a better treatment of extended covalent systems. A different integration pathway in the KP formalism may prove useful in attacking this fundamental problem. [Copyright &y& Elsevier]
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- 2009
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10. Nanoscale structure and local mechanical properties of fiber-reinforced composites containing MWCNT-grafted hybrid glass fibers
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Wood, Charles D., Palmeri, Marc J., Putz, Karl W., Ho, Gregory, Barto, Rick, and Catherine Brinson, L.
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GLASS fibers , *FIBROUS composites , *CARBON nanotubes , *CHEMICAL vapor deposition , *TRANSMISSION electron microscopy , *MECHANICAL behavior of materials - Abstract
Abstract: Carbon nanotubes (CNTs) were grown from the surface of glass fibers by chemical vapor deposition, and these hybrid fibers were individually dispersed in an epoxy matrix to investigate the local composite structure and properties near the fiber surface. High-resolution transmission electron microscopy revealed the influence of infiltration and curing of a liquid epoxy precursor on the morphology of the CNT “forest” region, or region of high CNT density near the fiber surface. Subsequent image analysis highlighted the importance of spatially dependent volume fractions of CNTs in the matrix as a function of distance from the fiber surface, and nanoindentation was used to probe local mechanical properties in the CNT forest region, showing strong correlations between local stiffness and volume fraction. This work represents the first in situ measurements of local mechanical properties of the nano-structured matrix region in hybrid fiber-reinforced composites, providing a means of quantifying the reinforcement provided by the grafted nanofillers. [Copyright &y& Elsevier]
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- 2012
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11. Introducing PROFESS 2.0: A parallelized, fully linear scaling program for orbital-free density functional theory calculations
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Hung, Linda, Huang, Chen, Shin, Ilgyou, Ho, Gregory S., Lignères, Vincent L., and Carter, Emily A.
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LINEAR programming , *DENSITY functionals , *QUANTUM theory , *ELECTRON distribution , *MOLECULAR orbitals , *INTEGRATED software , *ELECTRONIC structure , *MATHEMATICAL optimization - Abstract
Abstract: Orbital-free density functional theory (OFDFT) is a first principles quantum mechanics method to find the ground-state energy of a system by variationally minimizing with respect to the electron density. No orbitals are used in the evaluation of the kinetic energy (unlike Kohn–Sham DFT), and the method scales nearly linearly with the size of the system. The PRinceton Orbital-Free Electronic Structure Software (PROFESS) uses OFDFT to model materials from the atomic scale to the mesoscale. This new version of PROFESS allows the study of larger systems with two significant changes: PROFESS is now parallelized, and the ion–electron and ion–ion terms scale quasilinearly, instead of quadratically as in PROFESS v1 (L. Hung and E.A. Carter, Chem. Phys. Lett. 475 (2009) 163). At the start of a run, PROFESS reads the various input files that describe the geometry of the system (ion positions and cell dimensions), the type of elements (defined by electron–ion pseudopotentials), the actions you want it to perform (minimize with respect to electron density and/or ion positions and/or cell lattice vectors), and the various options for the computation (such as which functionals you want it to use). Based on these inputs, PROFESS sets up a computation and performs the appropriate optimizations. Energies, forces, stresses, material geometries, and electron density configurations are some of the values that can be output throughout the optimization. New version program summary: Program Title: PROFESS Catalogue identifier: AEBN_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEBN_v2_0.html Program obtainable from: CPC Program Library, Queen''s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 68 721 No. of bytes in distributed program, including test data, etc.: 1 708 547 Distribution format: tar.gz Programming language: Fortran 90 Computer: Intel with ifort; AMD Opteron with pathf90 Operating system: Linux Has the code been vectorized or parallelized?: Yes. Parallelization is implemented through domain composition using MPI. RAM: Problem dependent, but 2 GB is sufficient for up to 10,000 ions. Classification: 7.3 External routines: FFTW 2.1.5 (http://www.fftw.org) Catalogue identifier of previous version: AEBN_v1_0 Journal reference of previous version: Comput. Phys. Comm. 179 (2008) 839 Does the new version supersede the previous version?: Yes Nature of problem: Given a set of coordinates describing the initial ion positions under periodic boundary conditions, recovers the ground state energy, electron density, ion positions, and cell lattice vectors predicted by orbital-free density functional theory. The computation of all terms is effectively linear scaling. Parallelization is implemented through domain decomposition, and up to ∼10,000 ions may be included in the calculation on just a single processor, limited by RAM. For example, when optimizing the geometry of ∼50,000 aluminum ions (plus vacuum) on 48 cores, a single iteration of conjugate gradient ion geometry optimization takes ∼40 minutes wall time. However, each CG geometry step requires two or more electron density optimizations, so step times will vary. Solution method: Computes energies as described in text; minimizes this energy with respect to the electron density, ion positions, and cell lattice vectors. Reasons for new version: To allow much larger systems to be simulated using PROFESS. Summary of revisions: [•] PROFESS can run in parallel [1]. Parallelization is implemented through domain decomposition using MPI. (However, copies of all ion positions, which take up a relatively small amount of memory, are saved on all processors.) An updated serial version of PROFESS, with some memory-efficient features specific to the use of a single process, can also be compiled from the same code. [•] Instead of linking to the FFTW3 library, we use FFTW 2.1.5, which is the most recent version of FFTW that supports MPI parallel transforms. [•] Ion–ion and ion–electron calculations can scale as through the use of cardinal B-splines [1–3]. (For ion–ion calculations, this is known as particle-mesh Ewald.) [•] The line search during electron density optimization (when using the square root of electron density as the variational parameter) automatically conserves the total number of electrons in the system, using a similar line search mixing scheme as in Ref. [4]. [•] The square root density CG and TN optimizations are generally more stable. [•] Conjugate gradient ion optimization is improved and stable. [•] Positions of chosen ions can be held fixed during geometry optimization. [•] Variable time steps are used during cell lattice optimization instead of fixed steps. [•] The CAT kinetic energy density functional [5] is available. [•] A cutoff to avoid divergence in vacuum regions is now an option for some kinetic energy and exchange–correlation functionals (keywords WTV, WGV, CAV, PBEC) [6]. [•] The PBE exchange–correlation subroutine is more stable. [•] Calculations of energy and potential for some functionals are more efficient after removing duplicate computations. (Note: CAT, LQ, and HQ functionals have not yet been consolidated.) [•] Density and potential output files have a new format that is more convenient for output from multiple processes. A utility to convert between old and new density formats, as well as Tecplot format, is provided in RhoConvert.f90. [•] The interpolation scheme used when reading in pseudopotentials is more accurate. [•] WGC kernel integration uses the Runge–Kutta method for better accuracy. Restrictions: PROFESS cannot use nonlocal (such as ultrasoft) pseudopotentials. A variety of local pseudopotential files are available at the Carter group website (http://www.princeton.edu/mae/people/faculty/carter/homepage/research/localpseudopotentials/). Also, due to the current state of the kinetic energy functionals, PROFESS is only reliable for main group metals and some properties of semiconductors. Running time: Problem dependent: the test example provided with the code takes less than a second to run. Timing results for large scale problems are given in the PROFESS paper and Ref. [1]. References: [[1]] L. Hung, E.A. Carter, Chem. Phys. Lett. 475 (2009) 163. [[2]] U. Essmann, L. Perera, M. Berkowitz, T. Darden, L. Hsing, L.G. Pedersen, J. Chem. Phys. 103 (1995) 8577. [[3]] N. Choly, E. Kaxiras, Phys. Rev. B 67 (2003) 155101. [[4]] H. Jiang, W. Yang, J. Chem. Phys. 121 (2004) 2030. [[5]] D. Garcìa-Aldea, J.E. Alvarellos, Phys. Rev. A 76 (2007) 052504. [[6]] I. Shin, A. Ramasubramaniam, C. Huang, L. Hung, E.A. Carter, Philos. Mag. 89 (2009) 3195. [Copyright &y& Elsevier]
- Published
- 2010
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