divide-and-conquer density functional tight-binding program for huge-system quantum mechanical molecular dynamics simulations (Molecular Dynamics Inc)
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Molecular Dynamics Inc
divide-and-conquer density functional tight-binding program for huge-system quantum mechanical molecular dynamics simulations
Divide And Conquer Density Functional Tight Binding Program For Huge System Quantum Mechanical Molecular Dynamics Simulations, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/divider+function/divide+and+conquer+density+functional+tight+binding+program+for+huge+system+quantum+mechanical+molecular+dynamics+simulations/pm37972315-414-8-18
Average 90 stars, based on 1 article reviews
Divide And Conquer Density Functional Tight Binding Program For Huge System Quantum Mechanical Molecular Dynamics Simulations, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/divider+function/divide+and+conquer+density+functional+tight+binding+program+for+huge+system+quantum+mechanical+molecular+dynamics+simulations/pm37972315-414-8-18
Average 90 stars, based on 1 article reviews
divide-and-conquer density functional tight-binding program for huge-system quantum mechanical molecular dynamics simulations - by Bioz Stars,
2026-10
90/100 stars
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Functional Assay:Article Title: Nanoscale and Real-Time Nuclear-Electronic Dynamics Simulation Study of Charge Transfer at the Donor-Acceptor Interface in Organic Photovoltaics. Article Snippet: Charge-transfer (CT) processes in donor−acceptor interfaces of organic photovoltaics have been challenging targets for computational chemistry owing to their nanoscale and ultrafast nature.. Herein, we report real-time nuclear−electronic dynamics simulations of CT processes in a nanometer-scale donor−acceptor interface model composed of a donor poly(3-hexylthiophene-2,5diyl) crystal and an acceptor [6,6]-phenyl-C61-butyric acid methyl ester aggregate.. The simulations were realized using our original reduced-scaling computational technique, namely, patchworkapproximation-based Ehrenfest dynamics. Article Title: Investigating the Accuracy of Water Models through the Van Hove Correlation Function. Article Snippet: 2016, 37, 1983−1992. (75) Nishimura, Y.; Nakai, H. Dcdftbmd: Divide-and-Conquer Density Functional Tight- Binding Program for Article Title: Modeling the Conformational Preference of the Lignocellulose Interface and Its Interaction with Weak Acids. Article Snippet: We have examined the conformational space of model systems for the hydrogen-bonded and covalent linkages between the sugar and lignin components of lignocellulose.. Specifically, glucose and paracoumaryl alcohol moieties are used in our models.. Multistage screening protocols are used to identify and validate a set of lowestenergy isomers. Article Title: Hybrid Density Functional Tight Binding (DFTB)─Molecular Mechanics Approach for a Low-Cost Expansion of DFTB Applicability. Article Snippet: The density functional-based tight binding (DFTB) method has seen a rise in adoption for materials modeling, as it offers significant improvement in scalability with accuracy comparable to the density functional theory (DFT) when good parameterizations exist.. The cost reduction in DFTB compared to DFT is achieved by the pre-parameterization of the elements of the Hamiltonian matrix as well as the repulsion potential between all pairs of atoms.. Parameterization for new systems with accuracies competitive with DFT in specific applications requires specialized manpower and computational resources. Article Title: Scalable Ehrenfest Molecular Dynamics Exploiting the Locality of Density-Functional Tight-Binding Hamiltonian. Article Snippet: To explore the science behind excited-state dynamics in high-complexity chemical systems, a scalable nonadiabatic molecular dynamics (MD) technique is indispensable.. In this study, by treating the electronic degrees of freedom at the density-functional tight-binding level, we developed and implemented a reduced scaling and multinode-parallelizable Ehrenfest MD method.. To achieve this goal, we introduced a concept called patchwork approximation (PA), where the effective Hamiltonian for real-time propagation of the electronic density matrix is partitioned into a set of local parts. Article Title: Divide-and-Conquer Linear-Scaling Quantum Chemical Computations. Article Snippet: Fragmentation and embedding schemes are of great importance when applying quantum-chemical calculations to more complex and attractive targets.. The divide-and-conquer (DC)-based quantum-chemical model is a fragmentation scheme that can be connected to embedding schemes.. This feature article explains several DC-based schemes developed by the authors over the last two decades, which was inspired by the pioneering study of DC self-consistent field (SCF) method by Yang and Lee (J. Chem. Article Title: Quantum-Mechanical Molecular Dynamics Simulations on Secondary Proton Transfer in Bacteriorhodopsin Using Realistic Models. Article Snippet: Bacteriorhodopsin (BR) transports a proton from intracellular to extracellular (EC) sites through five proton transfers.. The second proton transfer is the release of an excess proton stored in BR into the EC medium, and an atomistic understanding of this whole process has remained unexplored due to its ubiquitous environment.. Here, fully quantum mechanical (QM) molecular dynamics (MD) and metadynamics (MTD) simulations for this process were performed at the divide-and-conquer density-functional tight-binding level using realistic models (∼50000 and ∼20000 atoms) based on the time-resolved photointermediate structures from an X-ray free electron laser. Article Title: Theoretical Examination of the Hydroxide Transport in Cobaltocenium-Containing Polyelectrolytes. Article Snippet: Polymers incorporating cobaltocenium groups have received attention as promising components of anion-exchange membranes (AEMs), exhibiting a good balance of chemical stability and high ionic conductivity.. In this work, we analyze the hydroxide diffusion in the presence of cobaltocenium cations in an aqueous environment based on the molecular dynamics of model systems confined in one dimension to mimic the AEM channels.. In order to describe the proton hopping mechanism, the forces are obtained from the electronic structure computed at the density-functional tight-binding level. Binding Assay:Article Title: Nanoscale and Real-Time Nuclear-Electronic Dynamics Simulation Study of Charge Transfer at the Donor-Acceptor Interface in Organic Photovoltaics. Article Snippet: Charge-transfer (CT) processes in donor−acceptor interfaces of organic photovoltaics have been challenging targets for computational chemistry owing to their nanoscale and ultrafast nature.. Herein, we report real-time nuclear−electronic dynamics simulations of CT processes in a nanometer-scale donor−acceptor interface model composed of a donor poly(3-hexylthiophene-2,5diyl) crystal and an acceptor [6,6]-phenyl-C61-butyric acid methyl ester aggregate.. The simulations were realized using our original reduced-scaling computational technique, namely, patchworkapproximation-based Ehrenfest dynamics. Article Title: Investigating the Accuracy of Water Models through the Van Hove Correlation Function. Article Snippet: 2016, 37, 1983−1992. (75) Nishimura, Y.; Nakai, H. Dcdftbmd: Divide-and-Conquer Density Functional Tight- Binding Program for Article Title: Modeling the Conformational Preference of the Lignocellulose Interface and Its Interaction with Weak Acids. Article Snippet: We have examined the conformational space of model systems for the hydrogen-bonded and covalent linkages between the sugar and lignin components of lignocellulose.. Specifically, glucose and paracoumaryl alcohol moieties are used in our models.. Multistage screening protocols are used to identify and validate a set of lowestenergy isomers. Article Title: Hybrid Density Functional Tight Binding (DFTB)─Molecular Mechanics Approach for a Low-Cost Expansion of DFTB Applicability. Article Snippet: The density functional-based tight binding (DFTB) method has seen a rise in adoption for materials modeling, as it offers significant improvement in scalability with accuracy comparable to the density functional theory (DFT) when good parameterizations exist.. The cost reduction in DFTB compared to DFT is achieved by the pre-parameterization of the elements of the Hamiltonian matrix as well as the repulsion potential between all pairs of atoms.. Parameterization for new systems with accuracies competitive with DFT in specific applications requires specialized manpower and computational resources. Article Title: Scalable Ehrenfest Molecular Dynamics Exploiting the Locality of Density-Functional Tight-Binding Hamiltonian. Article Snippet: To explore the science behind excited-state dynamics in high-complexity chemical systems, a scalable nonadiabatic molecular dynamics (MD) technique is indispensable.. In this study, by treating the electronic degrees of freedom at the density-functional tight-binding level, we developed and implemented a reduced scaling and multinode-parallelizable Ehrenfest MD method.. To achieve this goal, we introduced a concept called patchwork approximation (PA), where the effective Hamiltonian for real-time propagation of the electronic density matrix is partitioned into a set of local parts. Article Title: Divide-and-Conquer Linear-Scaling Quantum Chemical Computations. Article Snippet: Fragmentation and embedding schemes are of great importance when applying quantum-chemical calculations to more complex and attractive targets.. The divide-and-conquer (DC)-based quantum-chemical model is a fragmentation scheme that can be connected to embedding schemes.. This feature article explains several DC-based schemes developed by the authors over the last two decades, which was inspired by the pioneering study of DC self-consistent field (SCF) method by Yang and Lee (J. Chem. Article Title: Quantum-Mechanical Molecular Dynamics Simulations on Secondary Proton Transfer in Bacteriorhodopsin Using Realistic Models. Article Snippet: Bacteriorhodopsin (BR) transports a proton from intracellular to extracellular (EC) sites through five proton transfers.. The second proton transfer is the release of an excess proton stored in BR into the EC medium, and an atomistic understanding of this whole process has remained unexplored due to its ubiquitous environment.. Here, fully quantum mechanical (QM) molecular dynamics (MD) and metadynamics (MTD) simulations for this process were performed at the divide-and-conquer density-functional tight-binding level using realistic models (∼50000 and ∼20000 atoms) based on the time-resolved photointermediate structures from an X-ray free electron laser. Article Title: Theoretical Examination of the Hydroxide Transport in Cobaltocenium-Containing Polyelectrolytes. Article Snippet: Polymers incorporating cobaltocenium groups have received attention as promising components of anion-exchange membranes (AEMs), exhibiting a good balance of chemical stability and high ionic conductivity.. In this work, we analyze the hydroxide diffusion in the presence of cobaltocenium cations in an aqueous environment based on the molecular dynamics of model systems confined in one dimension to mimic the AEM channels.. In order to describe the proton hopping mechanism, the forces are obtained from the electronic structure computed at the density-functional tight-binding level. |