The Experts below are selected from a list of 7128 Experts worldwide ranked by ideXlab platform
Luke Shulenburger - One of the best experts on this subject based on the ideXlab platform.
-
An efficient Hybrid Orbital representation for quantum Monte Carlo calculations.
The Journal of chemical physics, 2018Co-Authors: Ye Luo, Kenneth Esler, Paul R. C. Kent, Luke ShulenburgerAbstract:The scale and complexity of the quantum system to which real-space quantum Monte Carlo (QMC) can be applied in part depends on the representation and memory usage of the trial wavefunction. B-splines, the computationally most efficient basis set, can have memory requirements exceeding the capacity of a single computational node. This situation has traditionally forced a difficult choice of either using slow internode communication or a potentially less accurate but smaller basis set such as Gaussians. Here, we introduce a Hybrid representation of the single particle Orbitals that combine a localized atomic basis set around atomic cores and B-splines in the interstitial regions to reduce the memory usage while retaining the high speed of evaluation and either retaining or increasing overall accuracy. We present a benchmark calculation for NiO demonstrating a superior accuracy while using only one eighth of the memory required for conventional B-splines. The Hybrid Orbital representation therefore expands the overall range of systems that can be practically studied with QMC.The scale and complexity of the quantum system to which real-space quantum Monte Carlo (QMC) can be applied in part depends on the representation and memory usage of the trial wavefunction. B-splines, the computationally most efficient basis set, can have memory requirements exceeding the capacity of a single computational node. This situation has traditionally forced a difficult choice of either using slow internode communication or a potentially less accurate but smaller basis set such as Gaussians. Here, we introduce a Hybrid representation of the single particle Orbitals that combine a localized atomic basis set around atomic cores and B-splines in the interstitial regions to reduce the memory usage while retaining the high speed of evaluation and either retaining or increasing overall accuracy. We present a benchmark calculation for NiO demonstrating a superior accuracy while using only one eighth of the memory required for conventional B-splines. The Hybrid Orbital representation therefore expands t...
-
an efficient Hybrid Orbital representation for quantum monte carlo calculations
Journal of Chemical Physics, 2018Co-Authors: Ye Luo, Kenneth Esler, Paul R. C. Kent, Luke ShulenburgerAbstract:The scale and complexity of the quantum system to which real-space quantum Monte Carlo (QMC) can be applied in part depends on the representation and memory usage of the trial wavefunction. B-splines, the computationally most efficient basis set, can have memory requirements exceeding the capacity of a single computational node. This situation has traditionally forced a difficult choice of either using slow internode communication or a potentially less accurate but smaller basis set such as Gaussians. Here, we introduce a Hybrid representation of the single particle Orbitals that combine a localized atomic basis set around atomic cores and B-splines in the interstitial regions to reduce the memory usage while retaining the high speed of evaluation and either retaining or increasing overall accuracy. We present a benchmark calculation for NiO demonstrating a superior accuracy while using only one eighth of the memory required for conventional B-splines. The Hybrid Orbital representation therefore expands the overall range of systems that can be practically studied with QMC.
-
an efficient Hybrid Orbital representation for quantum monte carlo calculations
arXiv: Materials Science, 2018Co-Authors: Ye Luo, Kenneth Esler, Paul R. C. Kent, Luke ShulenburgerAbstract:The scale and complexity of quantum system to which real-space quantum Monte Carlo (QMC) can be applied in part depends on the representation and memory usage of the trial wavefunction. B-splines, the computationally most efficient basis set, can have memory requirements exceeding the capacity of a single computational node. This situation has traditionally forced a difficult choice of either using slow internode communication or a potentially less accurate but smaller basis set such as Gaussians. Here, we introduce a Hybrid representation of the single particle Orbitals that combine a localized atomic basis set around atomic cores and B-splines in the interstitial regions to reduce the memory usage while retaining high speed of evaluation and either retaining or increasing overall accuracy. We present a benchmark calculation for NiO demonstrating a superior accuracy while using only one eighth the memory required for conventional B-splines. The Hybrid Orbital representation therefore expands the overall range of systems that can be practically studied with QMC.
Jaewoon Jung - One of the best experts on this subject based on the ideXlab platform.
-
Improved constrained optimization method for reaction-path determination in the generalized Hybrid Orbital quantum mechanical/molecular mechanical calculations.
The Journal of chemical physics, 2013Co-Authors: Jaewoon Jung, Yuji Sugita, Seiichiro Ten-noAbstract:The nudged elastic band (NEB) and string methods are widely used to obtain the reaction path of chemical reactions and phase transitions. In these methods, however, it is difficult to define an accurate Lagrangian to generate the conservative forces. On the other hand, the constrained optimization with locally updated planes (CO-LUP) scheme defines target function properly and suitable for micro-iteration optimizations in quantum mechanical/molecular mechanical (QM/MM) systems, which uses the efficient second order QM optimization. However, the method does have problems of inaccurate estimation of reactions and inappropriate accumulation of images around the energy minimum. We introduce three modifications into the CO-LUP scheme to overcome these problems: (1) An improved tangent estimation of the reaction path, which is used in the NEB method, (2) redistribution of images using an energy-weighted interpolation before updating local tangents, and (3) reduction of the number of constraints, in particular translation/rotation constraints, for improved convergence. First, we test the method on the isomerization of alanine dipeptide without QM/MM calculation, showing that the method is comparable to the string method both in accuracy and efficiency. Next, we apply the method for defining the reaction paths of the rearrangement reaction catalyzed by chorismate mutase (CM) and of the phosphoryl transfer reaction catalyzed by cAMP-dependent protein kinase (PKA) using generalized Hybrid Orbital QM/MM calculations. The reaction energy barrier of CM is in high agreement with the experimental value. The path of PKA reveals that the enzyme reaction is associative and there is a late transfer of the substrate proton to Asp 166, which is in agreement with the recently published result using the NEB method.
-
improved constrained optimization method for reaction path determination in the generalized Hybrid Orbital quantum mechanical molecular mechanical calculations
Journal of Chemical Physics, 2013Co-Authors: Jaewoon Jung, Yuji Sugita, Seiichiro TennoAbstract:The nudged elastic band (NEB) and string methods are widely used to obtain the reaction path of chemical reactions and phase transitions. In these methods, however, it is difficult to define an accurate Lagrangian to generate the conservative forces. On the other hand, the constrained optimization with locally updated planes (CO-LUP) scheme defines target function properly and suitable for micro-iteration optimizations in quantum mechanical/molecular mechanical (QM/MM) systems, which uses the efficient second order QM optimization. However, the method does have problems of inaccurate estimation of reactions and inappropriate accumulation of images around the energy minimum. We introduce three modifications into the CO-LUP scheme to overcome these problems: (1) An improved tangent estimation of the reaction path, which is used in the NEB method, (2) redistribution of images using an energy-weighted interpolation before updating local tangents, and (3) reduction of the number of constraints, in particular translation/rotation constraints, for improved convergence. First, we test the method on the isomerization of alanine dipeptide without QM/MM calculation, showing that the method is comparable to the string method both in accuracy and efficiency. Next, we apply the method for defining the reaction paths of the rearrangement reaction catalyzed by chorismate mutase (CM) and of the phosphoryl transfer reaction catalyzed by cAMP-dependent protein kinase (PKA) using generalized Hybrid Orbital QM/MM calculations. The reaction energy barrier of CM is in high agreement with the experimental value. The path of PKA reveals that the enzyme reaction is associative and there is a late transfer of the substrate proton to Asp 166, which is in agreement with the recently published result using the NEB method.
-
QM/MM calculation of protein magnetic shielding tensors with generalized Hybrid-Orbital method: A GIAO approach
Physical chemistry chemical physics : PCCP, 2011Co-Authors: Yoshinobu Akinaga, Jaewoon Jung, Seiichiro Ten-noAbstract:A method to compute magnetic shielding tensors with generalized Hybrid-Orbital (GHO) QM/MM scheme is developed at the levels of Hartree–Fock and second-order Moller–Plesset perturbation theory using gauge-including atomic Orbitals. A feature of the GHO method is utilized to ensure gauge-origin independency of GHO shielding tensors in a simple way. The benchmark calculations indicate that the GHO method reproduced full-QM shielding constants nearly quantitatively for atoms not directly coupled to the GHO linking atoms. As an application to a realistic protein, carbon chemical shifts are calculated for the retinal chromophore in visual rhodopsin.
-
a combined quantum mechanical and molecular mechanical method using modified generalized Hybrid Orbitals implementation for electronic excited states
Physical Chemistry Chemical Physics, 2011Co-Authors: Yukio Kawashima, Jaewoon Jung, Haruyuki Nakano, Seiichiro TennoAbstract:The generalized Hybrid Orbital (GHO) method is implemented at the second-order approximate coupled cluster singles and doubles (CC2) level for quantum mechanical (QM)/molecular mechanical (MM) electronic excited state calculations. The linear response function of CC2 in the GHO scheme is derived and implemented. The new implementation is applied to the first singlet excited states of three aromatic amino acids, phenylalanine, tyrosine, and tryptophan, and also bacteriorhodopsin for assessment. The results obtained for aromatic amino acids agreed well with the full QM CC2 calculations, while the calculated excitation energies of bacteriorhodopsin and its chromophore, all-trans retinal, reproduced the environmental shift of the experimental data. For the bacteriorhodopsin case, the environmental shift of GHO also showed good agreements with the experimental data. The contribution of the quantum effect of certain moieties in the excited states is elucidated by changing the partitioning of QM and MM regions.
-
moller plesset perturbation theory gradient in the generalized Hybrid Orbital quantum mechanical and molecular mechanical method
Journal of Chemical Physics, 2010Co-Authors: Jaewoon Jung, Yuji Sugita, Seiichiro TennoAbstract:An analytic gradient expression is formulated and implemented for the second-order Moller–Plesset perturbation theory (MP2) based on the generalized Hybrid Orbital QM/MM method. The method enables us to obtain an accurate geometry at a reasonable computational cost. The performance of the method is assessed for various isomers of alanine dipepetide. We also compare the optimized structures of fumaramide-derived [2]rotaxane and cAMP-dependent protein kinase with experiment.
Donald G Truhlar - One of the best experts on this subject based on the ideXlab platform.
-
Improved direct diabatization and coupled potential energy surfaces for the photodissociation of ammonia
Theoretical Chemistry Accounts, 2007Co-Authors: Rosendo Valero, Donald G TruhlarAbstract:Diabatic potential energy surfaces are a convenient starting point for dynamics calculations of photochemical processes, and they can be calculated by the fourfold way direct diabatization scheme. Here we present an improved definition of the reference Orbital for applying the fourfold way direct diabatization scheme to ammonia. The improved reference Orbital is a geometry-dependent Hybrid Orbital that allows one to define consistent dominant configuration lists at all geometries important for photodissociation. Using diabatic energies calculated with the new reference Orbital and consistent dominant configuration lists, we have refitted the analytical representations of the ground and the first electronically excited singlet-state potential energy surfaces and the diabatic coupling surface. Improved functional forms were used to reproduce the experimental dissociation energies and excitation energies, which will be important for subsequent simulations of photochemical dynamics. We find that the lowest-energy conical intersection point is at 5.16 eV, with C _2v symmetry.
-
Generalized Hybrid-Orbital method for combining density functional theory with molecular mechanicals.
Chemphyschem : a European journal of chemical physics and physical chemistry, 2005Co-Authors: Jiali Gao, Donald G TruhlarAbstract:The generalized Hybrid Orbital (GHO) method has previously been formulated for combining molecular mechanics with various levels of quantum mechanics, in particular semiempirical neglect of diatomic differential overlap theory, ab initio Hartree-Fock theory, and self-consistent charge density functional tight-binding theory. To include electron-correlation effects accurately and efficiently in GHO calculations, we extend the GHO method to density functional theory in the generalized-gradient approximation and Hybrid density functional theory (denoted by GHO-DFT and GHO-HDFT, respectively) using Gaussian-type Orbitals as basis functions. In the proposed GHO-(H)DFT formalism, charge densities in auxiliary Hybrid Orbitals are included to calculate the total electron density. The orthonormality constraints involving the auxiliary Kohn-Sham Orbitals are satisfied by carrying out the Hybridization in terms of a set of Lowdin symmetrically orthogonalized atomic basis functions. Analytical gradients are formulated for GHO-(H)DFT by incorporating additional forces associated with GHO basis transformations. Scaling parameters are introduced for some of the one-electron integrals and are optimized to obtain the correct charges and geometry near the QM/MM boundary region. The GHO-(H)DFT method based on the generalized gradient approach (GGA) (BLYP and mPWPW91) and HDFT methods (B3 LYP, mPW1PW91, and MPW1 K) is tested-for geometries and atomic charges-against a set of small molecules. The following quantities are tested: 1) the C--C stretch potential in ethane, 2) the torsional barrier for internal rotation around the central C--C bond in n-butane, 3) proton affinities for a set of alcohols, amines, thiols, and acids, 4) the conformational energies of alanine dipeptide, and 5) the barrier height of the hydrogen-atom transfer between n-C4H10 and n-C4H9, where the reaction center is described at the MPW1 K/6-31G(d) level of theory.
-
generalized Hybrid Orbital gho method for combining ab initio hartree fock wave functions with molecular mechanics
Journal of Physical Chemistry A, 2004Co-Authors: Jingzhi Pu, Donald G TruhlarAbstract:The generalized Hybrid Orbital (GHO) method provides a way to combine quantum mechanical (QM) and molecular mechanical (MM) calculations on a single molecular system or supramolecular assembly by providing an electrostatically stable connection between the QM portion and the MM portion. The GHO method has previously been developed for semiempirical molecular Orbital calculations, on the basis of neglect of diatomic differential overlap (GHO−NDDO); in the present work, it is extended to the ab initio Hartree−Fock (HF) level (GHO−AIHF). First, the theoretical foundation for the GHO−AIHF extension is discussed, and four different approaches are proposed to overcome the nonorthogonality between active molecular Orbitals (MOs) and auxiliary MOs. In the first scheme, the auxiliary Hybrid basis functions are projected out of the active QM basis. The second scheme neglects the diatomic differential overlap between the auxiliary basis and the active QM basis. In the third scheme, Hybrid Orbitals are constructed fr...
-
Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method
The Journal of Physical Chemistry A, 2004Co-Authors: Jiali Gao, Donald G TruhlarAbstract:In combined quantum mechanical and molecular mechanical (QM/MM) calculations with the QM/MM boundary at a covalent bond, the generalized Hybrid Orbital (GHO) method has been shown to provide a well balanced and stable connection between the QM and MM regions. The GHO method has previously been developed for semiempirical molecular Orbital methods based on neglect of diatomic differential overlap (GHO-NDDO) and for the ab initio Hartree-Fock level (GHO-AIHF). In the present work, we formulate the GHO algorithm and its analytical gradients for treating the QM subsystem by the self-consistent-charge densityfunctional tight-binding (SCC-DFTB) theory. To obtain a good description of the bond length at the QM/ MM boundary, a parametrized empirical correction term involving the GHO boundary atom and its QM frontier neighbor is added. Geometries and Mulliken charges obtained from GHO-SCC-DFTB calculations are compared to the fully QM results for a set of 18 molecules and ions with various functional groups close to the boundary, and we verified that we reproduced the full C-C stretch potential in ethane and in propanoate. The torsion barrier of n-butane around the central C-C bond is studied with the GHO boundary atom placed at different locations. Finally, the energetics of the method are tested for the proton affinities of a series of 15 alcohols, amines, thiols, and acids. The results indicate that the GHO treatment for combining SCCDFTB with molecular mechanics is both theoretically robust and satisfactory for practical use. In Supporting Information we present parameters for boundaries that cut through O-C and S-C bonds.
Seiichiro Tenno - One of the best experts on this subject based on the ideXlab platform.
-
improved constrained optimization method for reaction path determination in the generalized Hybrid Orbital quantum mechanical molecular mechanical calculations
Journal of Chemical Physics, 2013Co-Authors: Jaewoon Jung, Yuji Sugita, Seiichiro TennoAbstract:The nudged elastic band (NEB) and string methods are widely used to obtain the reaction path of chemical reactions and phase transitions. In these methods, however, it is difficult to define an accurate Lagrangian to generate the conservative forces. On the other hand, the constrained optimization with locally updated planes (CO-LUP) scheme defines target function properly and suitable for micro-iteration optimizations in quantum mechanical/molecular mechanical (QM/MM) systems, which uses the efficient second order QM optimization. However, the method does have problems of inaccurate estimation of reactions and inappropriate accumulation of images around the energy minimum. We introduce three modifications into the CO-LUP scheme to overcome these problems: (1) An improved tangent estimation of the reaction path, which is used in the NEB method, (2) redistribution of images using an energy-weighted interpolation before updating local tangents, and (3) reduction of the number of constraints, in particular translation/rotation constraints, for improved convergence. First, we test the method on the isomerization of alanine dipeptide without QM/MM calculation, showing that the method is comparable to the string method both in accuracy and efficiency. Next, we apply the method for defining the reaction paths of the rearrangement reaction catalyzed by chorismate mutase (CM) and of the phosphoryl transfer reaction catalyzed by cAMP-dependent protein kinase (PKA) using generalized Hybrid Orbital QM/MM calculations. The reaction energy barrier of CM is in high agreement with the experimental value. The path of PKA reveals that the enzyme reaction is associative and there is a late transfer of the substrate proton to Asp 166, which is in agreement with the recently published result using the NEB method.
-
a combined quantum mechanical and molecular mechanical method using modified generalized Hybrid Orbitals implementation for electronic excited states
Physical Chemistry Chemical Physics, 2011Co-Authors: Yukio Kawashima, Jaewoon Jung, Haruyuki Nakano, Seiichiro TennoAbstract:The generalized Hybrid Orbital (GHO) method is implemented at the second-order approximate coupled cluster singles and doubles (CC2) level for quantum mechanical (QM)/molecular mechanical (MM) electronic excited state calculations. The linear response function of CC2 in the GHO scheme is derived and implemented. The new implementation is applied to the first singlet excited states of three aromatic amino acids, phenylalanine, tyrosine, and tryptophan, and also bacteriorhodopsin for assessment. The results obtained for aromatic amino acids agreed well with the full QM CC2 calculations, while the calculated excitation energies of bacteriorhodopsin and its chromophore, all-trans retinal, reproduced the environmental shift of the experimental data. For the bacteriorhodopsin case, the environmental shift of GHO also showed good agreements with the experimental data. The contribution of the quantum effect of certain moieties in the excited states is elucidated by changing the partitioning of QM and MM regions.
-
moller plesset perturbation theory gradient in the generalized Hybrid Orbital quantum mechanical and molecular mechanical method
Journal of Chemical Physics, 2010Co-Authors: Jaewoon Jung, Yuji Sugita, Seiichiro TennoAbstract:An analytic gradient expression is formulated and implemented for the second-order Moller–Plesset perturbation theory (MP2) based on the generalized Hybrid Orbital QM/MM method. The method enables us to obtain an accurate geometry at a reasonable computational cost. The performance of the method is assessed for various isomers of alanine dipepetide. We also compare the optimized structures of fumaramide-derived [2]rotaxane and cAMP-dependent protein kinase with experiment.
-
new implementation of a combined quantum mechanical and molecular mechanical method using modified generalized Hybrid Orbitals
Journal of Chemical Physics, 2007Co-Authors: Jaewoon Jung, Yuji Sugita, Cheol Ho Choi, Seiichiro TennoAbstract:Two new techniques are introduced in the generalized Hybrid Orbital (GHO) method [Pu et al., J. Phys. Chem. A 108, 632 (2004)] and tested on small molecules. The first is a way to determine occupation numbers dependent on the molecular mechanical (MM) atoms linked to the boundary. The method takes account of the inhomogeneity in the occupation numbers of the auxiliary Orbitals from different types of MM atoms in such a way that the formal charge condition is fulfilled. The second technique is a rigorous orthogonalization procedure of auxiliary Orbitals for more than two boundary atoms. It is shown that the new implementation widens the realm of the GHO method with flexible quantum mechanical/MM partitionings.
Ye Luo - One of the best experts on this subject based on the ideXlab platform.
-
An efficient Hybrid Orbital representation for quantum Monte Carlo calculations.
The Journal of chemical physics, 2018Co-Authors: Ye Luo, Kenneth Esler, Paul R. C. Kent, Luke ShulenburgerAbstract:The scale and complexity of the quantum system to which real-space quantum Monte Carlo (QMC) can be applied in part depends on the representation and memory usage of the trial wavefunction. B-splines, the computationally most efficient basis set, can have memory requirements exceeding the capacity of a single computational node. This situation has traditionally forced a difficult choice of either using slow internode communication or a potentially less accurate but smaller basis set such as Gaussians. Here, we introduce a Hybrid representation of the single particle Orbitals that combine a localized atomic basis set around atomic cores and B-splines in the interstitial regions to reduce the memory usage while retaining the high speed of evaluation and either retaining or increasing overall accuracy. We present a benchmark calculation for NiO demonstrating a superior accuracy while using only one eighth of the memory required for conventional B-splines. The Hybrid Orbital representation therefore expands the overall range of systems that can be practically studied with QMC.The scale and complexity of the quantum system to which real-space quantum Monte Carlo (QMC) can be applied in part depends on the representation and memory usage of the trial wavefunction. B-splines, the computationally most efficient basis set, can have memory requirements exceeding the capacity of a single computational node. This situation has traditionally forced a difficult choice of either using slow internode communication or a potentially less accurate but smaller basis set such as Gaussians. Here, we introduce a Hybrid representation of the single particle Orbitals that combine a localized atomic basis set around atomic cores and B-splines in the interstitial regions to reduce the memory usage while retaining the high speed of evaluation and either retaining or increasing overall accuracy. We present a benchmark calculation for NiO demonstrating a superior accuracy while using only one eighth of the memory required for conventional B-splines. The Hybrid Orbital representation therefore expands t...
-
an efficient Hybrid Orbital representation for quantum monte carlo calculations
Journal of Chemical Physics, 2018Co-Authors: Ye Luo, Kenneth Esler, Paul R. C. Kent, Luke ShulenburgerAbstract:The scale and complexity of the quantum system to which real-space quantum Monte Carlo (QMC) can be applied in part depends on the representation and memory usage of the trial wavefunction. B-splines, the computationally most efficient basis set, can have memory requirements exceeding the capacity of a single computational node. This situation has traditionally forced a difficult choice of either using slow internode communication or a potentially less accurate but smaller basis set such as Gaussians. Here, we introduce a Hybrid representation of the single particle Orbitals that combine a localized atomic basis set around atomic cores and B-splines in the interstitial regions to reduce the memory usage while retaining the high speed of evaluation and either retaining or increasing overall accuracy. We present a benchmark calculation for NiO demonstrating a superior accuracy while using only one eighth of the memory required for conventional B-splines. The Hybrid Orbital representation therefore expands the overall range of systems that can be practically studied with QMC.
-
an efficient Hybrid Orbital representation for quantum monte carlo calculations
arXiv: Materials Science, 2018Co-Authors: Ye Luo, Kenneth Esler, Paul R. C. Kent, Luke ShulenburgerAbstract:The scale and complexity of quantum system to which real-space quantum Monte Carlo (QMC) can be applied in part depends on the representation and memory usage of the trial wavefunction. B-splines, the computationally most efficient basis set, can have memory requirements exceeding the capacity of a single computational node. This situation has traditionally forced a difficult choice of either using slow internode communication or a potentially less accurate but smaller basis set such as Gaussians. Here, we introduce a Hybrid representation of the single particle Orbitals that combine a localized atomic basis set around atomic cores and B-splines in the interstitial regions to reduce the memory usage while retaining high speed of evaluation and either retaining or increasing overall accuracy. We present a benchmark calculation for NiO demonstrating a superior accuracy while using only one eighth the memory required for conventional B-splines. The Hybrid Orbital representation therefore expands the overall range of systems that can be practically studied with QMC.
