Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; ...
2015-10-22
Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholinemore » catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.« less
Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; Huang, Patrick; Lightstone, Felice C.
2015-10-22
Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholine catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.
Fattebert, Jean-Luc; Lau, Edmond Y; Bennion, Brian J; Huang, Patrick; Lightstone, Felice C
2015-12-08
Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale first-principles molecular dynamics simulations and applied them to the study of the enzymatic reaction catalyzed by acetylcholinesterase. We carried out density functional theory calculations for a quantum-mechanical (QM) subsystem consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM subsystem is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite-temperature sampling by first-principles molecular dynamics for the acylation reaction of acetylcholine catalyzed by acetylcholinesterase. Our calculations show two energy barriers along the reaction coordinate for the enzyme-catalyzed acylation of acetylcholine. The second barrier (8.5 kcal/mol) is rate-limiting for the acylation reaction and in good agreement with experiment.
NASA Astrophysics Data System (ADS)
Otsuka, Takao; Taiji, Makoto; Bowler, David R.; Miyazaki, Tsuyoshi
2016-11-01
The recent progress of linear-scaling or O(N) methods in density functional theory (DFT) is remarkable. In this paper, we show that all-atom molecular dynamics simulations of complex biological systems based on DFT are now possible using our linear-scaling DFT code Conquest. We first overview the calculation methods used in Conquest and explain the method introduced recently to realise efficient and robust first-principles molecular dynamics (FPMD) with O(N) DFT. Then, we show that we can perform reliable all-atom FPMD simulations of a hydrated DNA model containing about 3400 atoms. We also report that the velocity scaling method is both reliable and useful for controlling the temperature of the FPMD simulation of this system. From these results, we conclude that reliable FPMD simulations of complex biological systems are now possible with Conquest.
A Scalable O(N) Algorithm for Large-Scale Parallel First-Principles Molecular Dynamics Simulations
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-01
Traditional algorithms for first-principles molecular dynamics (FPMD) simulations only gain a modest capability increase from current petascale computers, due to their O(N^{3}) complexity and their heavy use of global communications. To address this issue, we are developing a truly scalable O(N) complexity FPMD algorithm, based on density functional theory (DFT), which avoids global communications. The computational model uses a general nonorthogonal orbital formulation for the DFT energy functional, which requires knowledge of selected elements of the inverse of the associated overlap matrix. We present a scalable algorithm for approximately computing selected entries of the inverse of the overlap matrix, based on an approximate inverse technique, by inverting local blocks corresponding to principal submatrices of the global overlap matrix. The new FPMD algorithm exploits sparsity and uses nearest neighbor communication to provide a computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic orbitals are confined, and a cutoff beyond which the entries of the overlap matrix can be omitted when computing selected entries of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to O(100K) atoms on O(100K) processors, with a wall-clock time of O(1) minute per molecular dynamics time step.
First Principles Quantitative Modeling of Molecular Devices
NASA Astrophysics Data System (ADS)
Ning, Zhanyu
In this thesis, we report theoretical investigations of nonlinear and nonequilibrium quantum electronic transport properties of molecular transport junctions from atomistic first principles. The aim is to seek not only qualitative but also quantitative understanding of the corresponding experimental data. At present, the challenges to quantitative theoretical work in molecular electronics include two most important questions: (i) what is the proper atomic model for the experimental devices? (ii) how to accurately determine quantum transport properties without any phenomenological parameters? Our research is centered on these questions. We have systematically calculated atomic structures of the molecular transport junctions by performing total energy structural relaxation using density functional theory (DFT). Our quantum transport calculations were carried out by implementing DFT within the framework of Keldysh non-equilibrium Green's functions (NEGF). The calculated data are directly compared with the corresponding experimental measurements. Our general conclusion is that quantitative comparison with experimental data can be made if the device contacts are correctly determined. We calculated properties of nonequilibrium spin injection from Ni contacts to octane-thiolate films which form a molecular spintronic system. The first principles results allow us to establish a clear physical picture of how spins are injected from the Ni contacts through the Ni-molecule linkage to the molecule, why tunnel magnetoresistance is rapidly reduced by the applied bias in an asymmetric manner, and to what extent ab initio transport theory can make quantitative comparisons to the corresponding experimental data. We found that extremely careful sampling of the two-dimensional Brillouin zone of the Ni surface is crucial for accurate results in such a spintronic system. We investigated the role of contact formation and its resulting structures to quantum transport in several molecular
Diebold, Ulrike
2015-01-29
This project has provided an increased understanding of molecular processes and structure-activity relationships in photocatalytic systems. This could ultimately lead to guidelines on how to make TiO_{2}-based photocatalytic systems more efficient. This directly relates to the Program’s mission to develop a mechanistic understanding of chemical reactions that pertain to environmental remediation and pollution control; energy production (photoelectrochemical and production of hydrogen); and novel materials synthesis.
Transport in Molecular Devices from First Principles
NASA Astrophysics Data System (ADS)
di Ventra, Massimiliano
2000-03-01
The simulation of transport properties of Si-based devices has relied on the Boltzmann's equation within a semiclassical framework. When the device dimensions are those of single molecules, however, quantum mechanical simulations are necessary. In particular, it is of fundamental importance to address the following questions: i) are the transport properties of molecular devices dependent only on the molecules electronic structure? ii) Do the contacts play any role? And if so, can we tailor ``better'' contacts? iii) How atoms rearrange when current flows into the device? Can we predict the largest bias at which the device fails to operate? In order to answer all these questions we developed a fully ab initio approach that combines the solution of the Lippman-Schwinger equation[1] with a Hellmann-Feynman-like theorem that applies to steady-state current conditions to calculate forces on atoms.[2] We applied the approach to the study of the transport properties of the benzene-1,4-dithiolate molecule between gold electrodes for which experimental data are available.[3] The theoretical I-V curve has the same overall shape as the experimental curve -- reflecting the electronic structure of the molecule in the presence of the electric field -- but the absolute value of the current is very sensitive to contact chemistry and geometry.[4] In particular the presence of a single gold atom between the molecule and the electrode surface reduces the conductance by more than an order of magnitude. Replacement of the single gold atom by an aluminum atom, whose p orbitals couple more effectively to the molecule's orbitals, increases the conductance by about an order of magnitude. We have also studied the polarization effects induced by a third terminal (gate) on the I-V characteristics of the above device. In particular, we have found that current gain due to the gate bias can be achieved at reasonable gate fields. Finally, we have found that the molecule twists around the axis
First-principles molecular dynamics of metals: A Lagrangian formulation
NASA Astrophysics Data System (ADS)
Stengel, Massimiliano; de Vita, Alessandro
2000-12-01
A set of first-principles molecular-dynamics equations of motion involving fractional orbital occupations is derived from a rotationally invariant time-independent Lagrangian function. All velocity-dependent force terms can be removed from these equations by introducing an additional time-dependent term in the Lagrangian. The resulting scheme is formally equivalent to a recently proposed scheme [J. YandeVondele and A. DeVita, Phys. Rev. B 60, 13 241 (1999)], which is thus put on a firmer theoretical basis, and completed by a constant of motion resulting from the analytical expression of energy conservation.
First-principles simulation of molecular dissociation-recombination equilibrium
NASA Astrophysics Data System (ADS)
Kylänpää, Ilkka; Rantala, Tapio T.
2011-09-01
For the first time, the equilibrium composition of chemical dissociation-recombination reaction is simulated from first-principles, only. Furthermore, beyond the conventional ab initio Born-Oppenheimer quantum chemistry the effects from the thermal and quantum equilibrium dynamics of nuclei are consistently included, as well as, the nonadiabatic coupling between the electrons and the nuclei. This has been accomplished by the path integral Monte Carlo simulations for full NVT quantum statistics of the H_3^+ ion. The molecular total energy, partition function, free energy, entropy, and heat capacity are evaluated in a large temperature range: from below room temperature to temperatures relevant for planetary atmospheric physics. Temperature and density dependent reaction balance of the molecular ion and its fragments above 4000 K is presented, and also the density dependence of thermal ionization above 10 000 K is demonstrated.
Next generation extended Lagrangian first principles molecular dynamics
NASA Astrophysics Data System (ADS)
Niklasson, Anders M. N.
2017-08-01
Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.
Next generation extended Lagrangian first principles molecular dynamics.
Niklasson, Anders M N
2017-08-07
Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.
First principles molecular dynamics without self-consistent field optimization.
Souvatzis, Petros; Niklasson, Anders M N
2014-01-28
We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.
First principles molecular dynamics without self-consistent field optimization
Souvatzis, Petros; Niklasson, Anders M. N.
2014-01-28
We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.
NASA Astrophysics Data System (ADS)
Vladimirov, P. V.; Borodin, V. A.
2017-02-01
Beryllium selected as a neutron multiplier material for the tritium breeding blanket of fusion reactor should withstand high doses of fast neutron irradiation. The damage produced by irradiation is usually evaluated assuming that the number of atomic displacements to the threshold displacement energy, Ed, which is considered as an intrinsic material parameter. In this work the value of Ed for hcp beryllium is estimated simultaneously from classical and first-principles molecular dynamics simulations. Quite similar quantitative pictures of defect production are observed in both simulation types, though the predicted displacement threshold values seem to be approximately two times higher in the first-principles approach. We expect that, after more detailed first-principles investigations, this approach can be used for scaling the damage prediction predictions by classical molecular dynamics, opening a way for more consistent calculations of displacement damage in materials.
A First-principles Molecular Dynamics Investigation of Superionic Conductivity
NASA Astrophysics Data System (ADS)
Wood, Brandon; Marzari, Nicola
2007-03-01
Superionic materials---solids with liquid-like transport properties---have found widespread use in a variety of applications in fuel cells, switches, sensors, and batteries. However, reasons for fast-ion conduction in such materials, as well as the specific atomistic mechanisms involved, remain ill understood. Our work uses first-principles molecular dynamics to illuminate the mechanisms, pathways, and motivations for superionic conductivity in two materials representing different classes of ion conductors: α-AgI, an archetypal Type-I superionic; and CsHSO4, an anhydrous solid-state electrolyte candidate for hydrogen fuel cells. For α-AgI, we trace common pathways for silver ion conduction and discuss how a chemical signature in the electronic structure relates to enhanced silver ion mobility. We also characterize the dynamical lattice structure in the superionic phase and present the likely motivations for its existence. For CsHSO4, we isolate the dominant atomistic mechanisms involved in superprotonic conduction and discuss the effect of correlated diffusive events in enhancing proton transport. We also offer a detailed description of the dynamics of the hydrogen bond network topology in the course of proton diffusion and discuss the relevance of atomistic processes with competing timescales in facilitating proton transport.
First principles molecular dynamics study of filled ice hydrogen hydrate
NASA Astrophysics Data System (ADS)
Zhang, Jingyun; Kuo, Jer-Lai; Iitaka, Toshiaki
2012-08-01
We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C2 by using first principles molecular dynamics simulation. It was found that the experimentally reported "cubic" structure is unstable at low temperature and/or high pressure: The "cubic" structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the "cubic" symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in "cubic" symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules' rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and/or low temperatures.
Thermal conductivity of glassy GeTe4 by first-principles molecular dynamics.
Bouzid, Assil; Zaoui, Hayat; Luca Palla, Pier; Ori, Guido; Boero, Mauro; Massobrio, Carlo; Cleri, Fabrizio; Lampin, Evelyne
2017-03-29
A transient thermal regime is achieved in glassy GeTe4 by first-principles molecular dynamics following the recently proposed "approach-to-equilibrium" methodology. The temporal and spatial evolution of the temperature do comply with the time-dependent solution of the heat equation. We demonstrate that the time scales required to create the hot and the cold parts of the system and observe the resulting approach to equilibrium are accessible to first-principles molecular dynamics. Such a strategy provides the thermal conductivity from the characteristic decay time. We rationalize in detail the impact on the thermal conductivity of the initial temperature difference, the equilibration duration, and the main simulation features.
Extreme Scale Computing for First-Principles Plasma Physics Research
Chang, Choogn-Seock
2011-10-12
World superpowers are in the middle of the “Computnik” race. US Department of Energy (and National Nuclear Security Administration) wishes to launch exascale computer systems into the scientific (and national security) world by 2018. The objective is to solve important scientific problems and to predict the outcomes using the most fundamental scientific laws, which would not be possible otherwise. Being chosen into the next “frontier” group can be of great benefit to a scientific discipline. An extreme scale computer system requires different types of algorithms and programming philosophy from those we have been accustomed to. Only a handful of scientific codes are blessed to be capable of scalable usage of today’s largest computers in operation at petascale (using more than 100,000 cores concurrently). Fortunately, a few magnetic fusion codes are competing well in this race using the “first principles” gyrokinetic equations.These codes are beginning to study the fusion plasma dynamics in full-scale realistic diverted device geometry in natural nonlinear multiscale, including the large scale neoclassical and small scale turbulence physics, but excluding some ultra fast dynamics. In this talk, most of the above mentioned topics will be introduced at executive level. Representative properties of the extreme scale computers, modern programming exercises to take advantage of them, and different philosophies in the data flows and analyses will be presented. Examples of the multi-scale multi-physics scientific discoveries made possible by solving the gyrokinetic equations on extreme scale computers will be described. Future directions into “virtual tokamak experiments” will also be discussed.
Excited-State Properties of Molecular Solids from First Principles.
Kronik, Leeor; Neaton, Jeffrey B
2016-05-27
Molecular solids have attracted attention recently in the context of organic (opto)electronics. These materials exhibit unique charge carrier generation and transport phenomena that are distinct from those of conventional semiconductors. Understanding these phenomena is fundamental to optoelectronics and requires a detailed description of the excited-state properties of molecular solids. Recent advances in many-body perturbation theory (MBPT) and density functional theory (DFT) have made such description possible and have revealed many surprising electronic and optical properties of molecular crystals. Here, we review this progress. We summarize the salient aspects of MBPT and DFT as well as various properties that can be described by these methods. These properties include the fundamental gap and its renormalization, hybridization and band dispersion, singlet and triplet excitations, optical spectra, and excitonic properties. For each, we present concrete examples, a comparison to experiments, and a critical discussion.
Calculating Hugoniots for molecular crystals from first principles.
Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene
2010-03-01
Density Functional Theory (DFT) has over the last few years emerged as an indispensable tool for understanding the behavior of matter under extreme conditions. DFT based molecular dynamics simulations (MD) have for example confirmed experimental findings for shocked deuterium, enabled the first experimental evidence for a triple point in carbon above 850 GPa, and amended experimental data for constructing a global equation of state (EOS) for water, carrying implications for planetary physics. The ability to perform high-fidelity calculations is even more important for cases where experiments are impossible to perform, dangerous, and/or prohibitively expensive. For solid explosives, and other molecular crystals, similar success has been severely hampered by an inability of describing the materials at equilibrium. The binding mechanism of molecular crystals (van der Waals forces) is not well described within traditional DFT. Among widely used exchange-correlation functionals, neither LDA nor PBE balances the strong intra-molecular chemical bonding and the weak inter-molecular attraction, resulting in incorrect equilibrium density, negatively affecting the construction of EOS for undetonated high explosives. We are exploring a way of bypassing this problem by using the new Armiento-Mattsson 2005 (AM05) exchange-correlation functional. The AM05 functional is highly accurate for a wide range of solids, in particular in compression. In addition, AM05 does not include any van der Waals attraction, which can be advantageous compared to other functionals: Correcting for a fictitious van der Waals like attraction with unknown origin can be harder than correcting for a complete absence of all types of van der Waals attraction. We will show examples from other materials systems where van der Waals attraction plays a key role, where this scheme has worked well, and discuss preliminary results for molecular crystals and explosives.
Molecular switches activated by electromagnetic pulses: First-principles calculations
Felicissimo, Viviane Costa; Rocha Martins, Jonathan da; Boldt, Isabel Sager; Chacham, Helio
2009-12-15
In the present work, we investigate, through ab initio molecular dynamics simulations, the molecular switching action (a hydrogen tautomerization reaction) in porphyrazine and phthalocyanine induced by electromagnetic pulses. We find that femtosecond pulses attainable from laser sources can induce the switching mechanism in porphyrazine and phthalocyanine through several reaction pathways. We investigate the dependence of the switching mechanism on the parameters (duration, frequency, and polarization) of the electromagnetic pulse and on isotopic substitutions. We also find that the dynamics of inner hydrogen switching in phthalocyanine can be induced by weaker electromagnetic pulses than in porphyrazine. This indicates that molecules of this class with larger numbers of aromatic rings will be more efficient in displaying the pulse-induced switching.
First principles modelling of contact resistance in molecular electronic devices.
NASA Astrophysics Data System (ADS)
Stokbro, Kurt; Taylor, Jeremy; Brandbyge, Mads
2002-03-01
We have used the TranSIESTA package[1,2] to investigate the contact resistance of gold-thiol bonds. The TranSIESTA package is a new density functional code employing local basis sets[3], combined with a non-equilibrium Greens function transport scheme. With this package we can calculate the selfconsistent electronic structure of a nanostructure coupled to 3-dimensional electrodes with different electrochemical potentials, using the same level of model chemistry for the electrodes as for the nanostructure. We have used the method to calculate the electron transport through DiThiol-Benzene (DTB) connected to gold electrodes. The transport properties have been calculated for a range of different molecule-electrode couplings, and I will discuss the influence of the coupling on the molecular conductance, and compare with experimental data. [1] M. Brandbyge, K. Stokbro, J. Taylor, J. L. Mozos, P. Ordejon, Material Research Society symposium proceedings volume 636, D9.25 (2000). [2] M. Brandbyge, K. Stokbro, J. Taylor, J. L. Mozos, P. Ordejon, Condmat 0110650 [3] SIESTA: D. Sanchez-Portal, P. Ordejon, E. Artacho and J. Soler, Int. J. Quantum Chem. 65, 453 (1997).
A method of orbital analysis for large-scale first-principles simulations.
Ohwaki, Tsukuru; Otani, Minoru; Ozaki, Taisuke
2014-06-28
An efficient method of calculating the natural bond orbitals (NBOs) based on a truncation of the entire density matrix of a whole system is presented for large-scale density functional theory calculations. The method recovers an orbital picture for O(N) electronic structure methods which directly evaluate the density matrix without using Kohn-Sham orbitals, thus enabling quantitative analysis of chemical reactions in large-scale systems in the language of localized Lewis-type chemical bonds. With the density matrix calculated by either an exact diagonalization or O(N) method, the computational cost is O(1) for the calculation of NBOs associated with a local region where a chemical reaction takes place. As an illustration of the method, we demonstrate how an electronic structure in a local region of interest can be analyzed by NBOs in a large-scale first-principles molecular dynamics simulation for a liquid electrolyte bulk model (propylene carbonate + LiBF4).
A method of orbital analysis for large-scale first-principles simulations
NASA Astrophysics Data System (ADS)
Ohwaki, Tsukuru; Otani, Minoru; Ozaki, Taisuke
2014-06-01
An efficient method of calculating the natural bond orbitals (NBOs) based on a truncation of the entire density matrix of a whole system is presented for large-scale density functional theory calculations. The method recovers an orbital picture for O(N) electronic structure methods which directly evaluate the density matrix without using Kohn-Sham orbitals, thus enabling quantitative analysis of chemical reactions in large-scale systems in the language of localized Lewis-type chemical bonds. With the density matrix calculated by either an exact diagonalization or O(N) method, the computational cost is O(1) for the calculation of NBOs associated with a local region where a chemical reaction takes place. As an illustration of the method, we demonstrate how an electronic structure in a local region of interest can be analyzed by NBOs in a large-scale first-principles molecular dynamics simulation for a liquid electrolyte bulk model (propylene carbonate + LiBF4).
Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations
NASA Astrophysics Data System (ADS)
Cole, D. J.; Skylaris, C.-K.; Rajendra, E.; Venkitaraman, A. R.; Payne, M. C.
2010-08-01
A modification of the MM-PBSA technique for calculating binding affinities of biomolecular complexes is presented. Classical molecular dynamics is used to explore the motion of the extended interface between two peptides derived from the BRC4 repeat of BRCA2 and the eukaryotic recombinase RAD51. The resulting trajectory is sampled using the linear-scaling density functional theory code, onetep, to determine from first principles, and with high computational efficiency, the relative free energies of binding of the ~2800 atom receptor-ligand complexes. This new method provides the basis for computational interrogation of protein-protein and protein-ligand interactions within fields ranging from chemical biological studies to small-molecule binding behaviour, with both unprecedented chemical accuracy and affordable computational expense.
Protein-Protein Interactions from Linear-Scaling First Principles Quantum Mechanical Calculations
NASA Astrophysics Data System (ADS)
Cole, Daniel; Skylaris, Chris-Kriton; Rajendra, Eeson; Venkitaraman, Ashok; Payne, Mike
2010-03-01
A modification of the MM-PBSA technique for calculating binding affinities of biomolecular complexes is presented. Classical molecular dynamics is used to explore the motion of the extended interface between two peptides derived from the BRC4 repeat of BRCA2 and the eukaryotic recombinase RAD51. The resulting trajectory is sampled using the linear-scaling density functional theory code, onetep, to determine from first principles, and with high computational efficiency, the relative free energies of binding of the ˜2800 atom receptor-ligand complexes. This new method provides the basis for computational interrogation of protein-protein and protein-ligand interactions, within fields ranging from chemical biological studies to small molecule binding behaviour, with both unprecedented chemical accuracy and affordable computational expense.
Eisenbach, Markus; Perera, Meewanage Dilina N.; Landau, David P; Nicholson, Don M.; Yin, Junqi; Brown, Greg
2015-01-01
We present a unified approach to describe the combined behavior of the atomic and magnetic degrees of freedom in magnetic materials. Using Monte Carlo simulations directly combined with first principles the Curie temperature can be obtained ab initio in good agreement with experimental values. The large scale constrained first principles calculations have been used to construct effective potentials for both the atomic and magnetic degrees of freedom that allow the unified study of influence of phonon-magnon coupling on the thermodynamics and dynamics of magnetic systems. The MC calculations predict the specific heat of iron in near perfect agreement with experimental results from 300K to above Tc and allow the identification of the importance of the magnon-phonon interaction at the phase-transition. Further Molecular Dynamics and Spin Dynamics calculations elucidate the dynamics of this coupling and open the potential for quantitative and predictive descriptions of dynamic structure factors in magnetic materials using first principles-derived simulations.
Declerck, R; Pauwels, E; Speybroeck, V Van; Waroquier, M
2008-02-07
The effect of the molecular environment and the temperature dependence of hyperfine parameters in first principles calculations in alpha-d-glucose and beta-d-fructose crystal radicals have been investigated. More specifically, we show how static (0 K) cluster in vacuo hyperfine calculations, commonly used today, deviate from more advanced molecular dynamics calculations at the experimental temperature using periodic boundary conditions. From the latter approach, more useful information can be extracted, allowing us to ascertain the validity of proposed molecular models.
A method of orbital analysis for large-scale first-principles simulations
Ohwaki, Tsukuru; Otani, Minoru; Ozaki, Taisuke
2014-06-28
An efficient method of calculating the natural bond orbitals (NBOs) based on a truncation of the entire density matrix of a whole system is presented for large-scale density functional theory calculations. The method recovers an orbital picture for O(N) electronic structure methods which directly evaluate the density matrix without using Kohn-Sham orbitals, thus enabling quantitative analysis of chemical reactions in large-scale systems in the language of localized Lewis-type chemical bonds. With the density matrix calculated by either an exact diagonalization or O(N) method, the computational cost is O(1) for the calculation of NBOs associated with a local region where a chemical reaction takes place. As an illustration of the method, we demonstrate how an electronic structure in a local region of interest can be analyzed by NBOs in a large-scale first-principles molecular dynamics simulation for a liquid electrolyte bulk model (propylene carbonate + LiBF{sub 4})
Cold melting of Li under pressure: Perspectives from first-principles molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Xia, Weiyi; Gao, Weiwei; Gao, Xiang; Zhang, Peihong
Despite much work (experiment and theory), the pressure-dependent melting temperature of Li is still under debate. In particular, there is still controversy and significant uncertainty in determining the melting temperature of Li at pressures around 50 GPa. An earlier report suggests that Li melts at as low as 190 K between 40 and 64 GPa. Such a low melting temperature is not likely unless quantum effects of lattice vibration play a significant role. Later experiment, on the other hand, reports that Li melts above 300 K under pressured up to 64 GPa and does not seem to support the view that lattice quantum effects to play any important role. In this talk, we will present results from large-scale (large systems and long simulation times) first-principles molecular dynamics simulations and phonon free energy calculations, aiming at resolving some of the issues. This work is supported by US NSF under Grant No. DMR-0946404 and DMR-1506669. Work at Beijing CSRC is supported by the National Natural Science Foundation of China (Grant No. 11328401).
The melting point of lithium: an orbital-free first-principles molecular dynamics study
Chen, Mohan; Hung, Linda; Huang, Chen; ...
2013-08-25
The melting point of liquid lithium near zero pressure is studied with large-scale orbital-free first-principles molecular dynamics (OF-FPMD) in the isobaric-isothermal ensemble. Here, we adopt the Wang-Govind-Carter (WGC) functional as our kinetic energy density functional (KEDF) and construct a bulk-derived local pseudopotential (BLPS) for Li. Our simulations employ both the ‘heat-until-melts’ method and the coexistence method. We predict 465 K as an upper bound of the melting point of Li from the ‘heat-until-melts’ method, while we predict 434 K as the melting point of Li from the coexistence method. These values compare well with an experimental melting point of 453more » K at zero pressure. Furthermore, we calculate a few important properties of liquid Li including the diffusion coefficients, pair distribution functions, static structure factors, and compressibilities of Li at 470 K and 725 K in the canonical ensemble. This theoretically-obtained results show good agreement with known experimental results, suggesting that OF-FPMD using a non-local KEDF and a BLPS is capable of accurately describing liquid metals.« less
The melting point of lithium: an orbital-free first-principles molecular dynamics study
Chen, Mohan; Hung, Linda; Huang, Chen; Xia, Junchao; Carter, Emily A.
2013-12-01
Abstract The melting point of liquid lithium near zero pressure is studied with large-scale orbital-free first-principles molecular dynamics (OF-FPMD) in the isobaric-isothermal ensemble. We adopt the Wang-Govind-Carter (WGC) functional as our kinetic energy density functional (KEDF) and construct a bulk-derived local pseudopotential (BLPS) for Li. Our simulations employ both the ‘heat-until-melts’ method and the coexistence method. We predict 465 K as an upper bound of the melting point of Li from the ‘heat-until-melts’ method, while we predict 434 K as the melting point of Li from the coexistence method. These values compare well with an experimental melting point of 453 K at zero pressure. Furthermore, we calculate a few important properties of liquid Li including the diffusion coefficients, pair distribution functions, static structure factors, and compressibilities of Li at 470 K and 725 K in the canonical ensemble. Our theoretically-obtained results show good agreement with known experimental results, suggesting that OF-FPMD using a non-local KEDF and a BLPS is capable of accurately describing liquid metals.
The melting point of lithium: an orbital-free first-principles molecular dynamics study
NASA Astrophysics Data System (ADS)
Chen, Mohan; Hung, Linda; Huang, Chen; Xia, Junchao; Carter, Emily A.
2013-12-01
The melting point of liquid lithium near zero pressure is studied with large-scale orbital-free first-principles molecular dynamics (OF-FPMD) in the isobaric-isothermal ensemble. We adopt the Wang-Govind-Carter (WGC) functional as our kinetic energy density functional (KEDF) and construct a bulk-derived local pseudopotential (BLPS) for Li. Our simulations employ both the 'heat-until-melts' method and the coexistence method. We predict 465 K as an upper bound of the melting point of Li from the 'heat-until-melts' method, while we predict 434 K as the melting point of Li from the coexistence method. These values compare well with an experimental melting point of 453 K at zero pressure. Furthermore, we calculate a few important properties of liquid Li including the diffusion coefficients, pair distribution functions, static structure factors, and compressibilities of Li at 470 K and 725 K in the canonical ensemble. Our theoretically-obtained results show good agreement with known experimental results, suggesting that OF-FPMD using a non-local KEDF and a BLPS is capable of accurately describing liquid metals.
Jaramillo-Botero, Andres; Nielsen, Robert; Abrol, Ravi; Su, Julius; Pascal, Tod; Mueller, Jonathan; Goddard, William A
2012-01-01
We expect that systematic and seamless computational upscaling and downscaling for modeling, predicting, or optimizing material and system properties and behavior with atomistic resolution will eventually be sufficiently accurate and practical that it will transform the mode of development in the materials, chemical, catalysis, and Pharma industries. However, despite truly dramatic progress in methods, software, and hardware, this goal remains elusive, particularly for systems that exhibit inherently complex chemistry under normal or extreme conditions of temperature, pressure, radiation, and others. We describe here some of the significant progress towards solving these problems via a general multiscale, multiparadigm strategy based on first-principles quantum mechanics (QM), and the development of breakthrough methods for treating reaction processes, excited electronic states, and weak bonding effects on the conformational dynamics of large-scale molecular systems. These methods have resulted directly from filling in the physical and chemical gaps in existing theoretical and computational models, within the multiscale, multiparadigm strategy. To illustrate the procedure we demonstrate the application and transferability of such methods on an ample set of challenging problems that span multiple fields, system length- and timescales, and that lay beyond the realm of existing computational or, in some case, experimental approaches, including understanding the solvation effects on the reactivity of organic and organometallic structures, predicting transmembrane protein structures, understanding carbon nanotube nucleation and growth, understanding the effects of electronic excitations in materials subjected to extreme conditions of temperature and pressure, following the dynamics and energetics of long-term conformational evolution of DNA macromolecules, and predicting the long-term mechanisms involved in enhancing the mechanical response of polymer-based hydrogels.
First-principles molecular dynamics calculations of the equation of state for tantalum.
Ono, Shigeaki
2009-11-20
The equation of state of tantalum (Ta) has been investigated to 100 GPa and 3,000 K using the first-principles molecular dynamics method. A large volume dependence of the thermal pressure of Ta was revealed from the analysis of our data. A significant temperature dependence of the calculated effective Grüneisen parameters was confirmed at high pressures. This indicates that the conventional approach to analyze thermal properties using the Mie-Grüneisen approximation is likely to have a significant uncertainty in determining the equation of state for Ta, and that an intrinsic anharmonicity should be considered to analyze the equation of state.
NASA Astrophysics Data System (ADS)
Jakse, N.; Pasturel, A.
2007-11-01
We report results of first principles molecular dynamics simulations that confirm early speculations on the presence of liquid-liquid phase transition in undercooled silicon. However, we find that structural and electronic properties of both low-density liquid (LDL) and high-density liquid (HDL) phases are quite different from those obtained by empirical calculations, the difference being more pronounced for the HDL phase. The discrepancy between quantum and classical simulations is attributed to the inability of empirical potentials to describe changes in chemical bonds induced by density and temperature variations.
Energy versus free-energy conservation in first-principles molecular dynamics
NASA Astrophysics Data System (ADS)
Wentzcovitch, Renata M.; Martins, José Luís; Allen, Philip B.
1992-05-01
In applying first-principles molecular dynamics to metals, a fictitious temperature is usefully assigned to the electronic (Fermi-Dirac) occupation functions. This avoids instabilities associated with fluctuations in these occupations during the minimization of the energy density functional. Because these occupations vary with the ionic motion, they give rise to an extra contribution in addition to the usual Hellmann-Feynman forces. If this extra force is omitted, energy is not conserved. We point out, however, that ionic kinetic energy plus electronic free energy is conserved, and argue that this yields a sensible and realistic conservative dynamics.
First-Principles Molecular Dynamics Calculations of the Equation of State for Tantalum
Ono, Shigeaki
2009-01-01
The equation of state of tantalum (Ta) has been investigated to 100 GPa and 3,000 K using the first-principles molecular dynamics method. A large volume dependence of the thermal pressure of Ta was revealed from the analysis of our data. A significant temperature dependence of the calculated effective Grüneisen parameters was confirmed at high pressures. This indicates that the conventional approach to analyze thermal properties using the Mie-Grüneisen approximation is likely to have a significant uncertainty in determining the equation of state for Ta, and that an intrinsic anharmonicity should be considered to analyze the equation of state. PMID:20057949
First principles centroid molecular dynamics simulation of hydride in nanoporous C12A7:H-
NASA Astrophysics Data System (ADS)
Ikeda, Takashi
2017-05-01
Hydrides in nanoporous [Ca24Al28O64]4+(H-)4 (C12A7:H-) were investigated via first principles centroid molecular dynamics (CMD). The quality of our CMD simulations was assessed by examining the temperature dependence of the distribution of hydrides in the cages constituting the C12A7 framework. The vibrational states of C12A7:H- were analyzed by using the trajectories of the centroids generated in our CMD simulations. We find that the rattling motions of H- and D- behave qualitatively differently, resulting in non-trivial isotope effects, which are suggested to be detectable by using infrared and Raman spectroscopy.
Crystalline and liquid Si3 N4 characterization by first-principles molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Mauri, Aurelio; Celino, Massimo; Castellani, Niccoló; Erbetta, Davide
2011-05-01
Silicon nitride (Si3 N4) has a wide range of engineering applications where its mechanical and electronic properties can be effectively exploited. In particular, in the microelectronics field, the amorphous silicon nitride films are widely used as charge storage layer in metal-alumina-nitrideoxide nonvolatile memory devices. Atomic structure of amorphous silicon nitride is characterized by an high concentration of traps that control the electric behavior of the final device by the trappingde-trapping mechanism of the electrical charge occurring in its traps. In order to have a deep understanding of the material properties and, in particular, the nature of the electrical active traps a detailed numerical characterization of the crystalline and liquid phases is mandatory. For these reasons first-principles molecular dynamics simulations are extensively employed to simulate the crystalline Si3 N4 in its crystalline and liquid phases. Good agreement with experimental results is obtained in terms of density and formation entalpy. Detailed characterization of c-Si3 N4 electronic properties is performed in terms of band structure and band gap. Then constant temperature and constant volume first-principles molecular dynamics is used to disorder a stoichiometric sample of Si3 N4 . Extensive molecular dynamics simulations are performed to obtain a reliable liquid sample whose atomic structure does not depend on the starting atomic configuration. Detailed characterization of the atomic structure is achieved in terms of radial distribution functions and total structure factor.
Morari, C.; Buimaga-Iarinca, L.; Rungger, I.; Sanvito, S.; Melinte, S.; Rignanese, G.-M.
2016-01-01
Using first-principles calculations, we study the electronic and transport properties of rutheniumterpyridine molecules sandwiched between two Au(111) electrodes. We analyse both single and packed molecular devices, more amenable to scaling and realistic integration approaches. The devices display all together robust negative differential resistance features at low bias voltages. Remarkably, the electrical control of the spin transport in the studied systems implies a subtle distribution of the magnetisation density within the biased devices and highlights the key role of the Au(111) electrical contacts. PMID:27550064
Implicit solvent model for linear-scaling first-principles electronic structure calculations
NASA Astrophysics Data System (ADS)
Helal, Hatem H.; Payne, Mike; Mostofi, Arash A.
2009-03-01
Density functional theory (DFT) enables first-principles calculations that exhibit cubic scaling of the computational time required with respect to the number of atoms in the system. This presents an unavoidable difficulty when first-principles accuracy is needed for the study of large-scale biological systems. The ONETEP program reformulates DFT so that the required computational effort scales only linearly with system size, recently demonstrated for up to 32,000 atoms on 64 cores.ootnotetextN. D. M. Hine, P. D. Haynes, A. A. Mostofi, C.-K. Skylaris and M. C. Payne, submitted to J. Chem. Phys. (2008). Further complicating DFT based studies of biomolecular systems is the need for an accurate representation of the electrostatic environment. Rather than introducing explicit solvent molecules into the system, which would be computationally prohibitive, we present our recent efforts to integrate an implicit solvent modelootnotetextD. A. Scherlis et al., J. Chem. Phys. 124, 074103 (2006). with ONETEP in order to study systems in solution consisting of many thousands of atoms. We report preliminary results of our methodology with a study of the DNA nucleosome core particle.
NASA Astrophysics Data System (ADS)
Righi, Maria Clelia; Zilibotti, Giovanna; Corni, Stefano; Ferrario, Mauro; Bertoni, Carlo Maria
2016-10-01
Ab initio molecular dynamics offers an unexpected tool to understand many aspects of complex and macroscopic phenomena, like friction, lubrication, and surface passivation through chemical reactions induced by load and confinement, as found in recent works (Zilibotti et al., in Phys. Rev. Lett. 111:146101, 2013; De Barros Bouchet et al., J Phys Chem C 116:6966, 2012). Here we review the results of first-principle molecular dynamics simulations of diamond interfaces interacting with water molecules, at different concentrations. We found that the molecular confinement induced by the applied load promotes water dissociation. The consequent surface passivation prevents the formation of carbon bonds across the interface, reducing adhesion and friction. The possibility to extend the use of an atomistic approach to understand the kinetics of tribochemical reactions and their effects on friction will also be discussed.
A first-principles study of aryloxyanthraquinone-based optical molecular switch
NASA Astrophysics Data System (ADS)
Vakili, Mohamad; Sobhkhizi, Alireza; Darugar, Vahidreza; Kanaani, Ayoub; Ajloo, Davood
2017-10-01
We study the transport properties of 4-((9,10-dioxo-9,10-dihydroanthracen-1-yl)oxy) benzaldehyde molecular optical switch by the first-principles calculations. Our molecule can reversibly switch between trans and ana forms by visible or UV irradiation. We studied many properties such as, I-V characteristics, the effect of electrode materials on electronic transport properties, on-off ratio and spatial distribution of molecular projected self-consistent Hamiltonian orbitals corresponding to both forms. The physical behavior of conductance interpret in terms of the HOMO-LUMO gap, the effective conjugation lengths, and size of the frontier molecular orbitals. Our results show, current through the ana form is higher than that the trans form.
First principles molecular dynamics of Li: Test of a new algorithm
NASA Astrophysics Data System (ADS)
Wentzcovitch, Renata M.; Martins, JoséLuís
1991-06-01
We have tested a new algorithm to perform first-principles molecular dynamics simulations. This new scheme differs from the Car-Parrinello method and is based on the calculation of the self-consistent solutions of the Kohn-Sham equations at each molecular dynamics timestep, using a fast iterative diagonalization algorithm. We do not use a fictitious electron dynamics, and therefore the molecular dynamics timesteps can be considerably larger in our method than in the Car-Parrinello algorithm. Furthermore, the number of basis functions is variable, which makes this method particularly suited to deal with simulations involving a cell with variable shape and volume. Applications of this method to liquid Li offers results which are in excellent agreement with experiment and indicates that it is basically comparable in efficiency to the Car-Parrinello method.
Terahertz spectra of biotin based on first principle, molecular mechanical, and hybrid simulations.
Bykhovski, Alexei; Woolard, Dwight
2013-07-01
Terahertz (THz) absorption of biotin was simulated using the first principle and the density functional theory (DFT) both in the harmonic approximation and with corrections for the anharmonicity. Anharmonicity corrections were calculated using two different approaches. First, the perturbation theory-based first principle calculations were performed to include third- and fourth-order anharmonicity corrections in atomic displacements to harmonic vibrational states. Second, the atom-centered density matrix propagation molecular dynamics model that provides a good energy conservation was used to calculate the atomic trajectories, velocities, and a dipole moment time history of biotin at low and room temperatures. Predicted low-THz lines agree well with the experimental spectra. The influence of the polyethylene (PE) matrix embedment on the THz spectra of biotin at the nanoscale was studied using the developed hybrid DFT/molecular mechanical approach. While PE is almost transparent at THz frequencies, additional low-THz lines are predicted in the biotin/PE system, which reflects a dynamic interaction between biotin and a surrounding PE cavity.
First principles molecular dynamics of metal/water interfaces under bias potential
NASA Astrophysics Data System (ADS)
Pedroza, Luana; Brandimarte, Pedro; Rocha, Alexandre; Fernandez-Serra, Marivi
2014-03-01
Understanding the interaction of the water-metal system at an atomic level is extremely important in electrocatalysts for fuel cells, photocatalysis among other systems. The question of the interface energetics involves a detailed study of the nature of the interactions between water-water and water-substrate. A first principles description of all components of the system is the most appropriate methodology in order to advance understanding of electrochemically processes. In this work we describe, using first principles molecular dynamics simulations, the dynamics of a combined surface(Au and Pd)/water system both in the presence and absence of an external bias potential applied to the electrodes, as one would come across in electrochemistry. This is accomplished using a combination of density functional theory (DFT) and non-equilibrium Green's functions methods (NEGF), thus accounting for the fact that one is dealing with an out-of-equilibrium open system, with and without van der Waals interactions. DOE Early Career Award No. DE-SC0003871.
Quantum Mechanics and First-Principles Molecular Dynamics Selection of Polymer Sensing Materials
NASA Astrophysics Data System (ADS)
Blanco, Mario; Shevade, Abhijit V.; Ryan, Margaret A.
We present two first-principles methods, density functional theory (DFT) and a molecular dynamics (MD) computer simulation protocol, as computational means for the selection of polymer sensing materials. The DFT methods can yield binding energies of polymer moieties to specific vapor bound compounds, quantities that were found useful in materials selection for sensing of organic and inorganic compounds for designing sensors for the electronic nose (ENose) that flew on the International Space Station (ISS) in 2008-2009. Similarly, we present an MD protocol that offers high consistency in the estimation of Hildebrand and Hansen solubility parameters (HSP) for vapor bound compounds and amorphous polymers. HSP are useful for fitting measured polymer sensor responses with physically rooted analytical models. We apply the method to the JPL electronic nose (ENose), an array of sensors with conducting leads connected through thin film polymers loaded with carbon black. Detection relies on a change in electric resistivity of the polymer film as function of the amount of swelling caused by the presence of the analyte chemical compound. The amount of swelling depends upon the chemical composition of the polymer and the analyte molecule. The pattern is unique and it unambiguously identifies the compound. Experimentally determined changes in relative resistivity of fifteen polymer sensor materials upon exposure to ten vapors were modeled with the first-principles HSP model.
Gaigeot, M-P
2009-07-30
First principle DFT-based molecular dynamics simulations are performed in order to bring new insights into the conformational dynamics of the alanine dipeptide analogue Ac-Ala-NHMe (with methyl group caps at the extremities) immersed in liquid water at ambient temperature. Two simulations have been run for a total of 100 ps, which allows for a relevant statistical sampling of the phase space, at the ab initio level. PII-beta equilibrium and (PII-beta)-alphaR conformational interconversions are obtained, without a free-energy barrier for the Phi angle and with a rather low barrier of 2-3 kcal/mol for the Psi angle, easily overcome from solute-solvent energy transfers. We furthermore give first insights into the rather strong zwitterionic character of the peptide bonds of the dipeptide when immersed in the liquid. The structural and zwitterionic properties extracted from first-principle dynamics in the liquid phase will be useful as benchmarks for force field developments.
Length dependence of electron transport through molecular wires--a first principles perspective.
Khoo, Khoong Hong; Chen, Yifeng; Li, Suchun; Quek, Su Ying
2015-01-07
One-dimensional wires constitute a fundamental building block in nanoscale electronics. However, truly one-dimensional metallic wires do not exist due to Peierls distortion. Molecular wires come close to being stable one-dimensional wires, but are typically semiconductors, with charge transport occurring via tunneling or thermally-activated hopping. In this review, we discuss electron transport through molecular wires, from a theoretical, quantum mechanical perspective based on first principles. We focus specifically on the off-resonant tunneling regime, applicable to shorter molecular wires (<∼4-5 nm) where quantum mechanics dictates electron transport. Here, conductance decays exponentially with the wire length, with an exponential decay constant, beta, that is independent of temperature. Different levels of first principles theory are discussed, starting with the computational workhorse - density functional theory (DFT), and moving on to many-electron GW methods as well as GW-inspired DFT + Sigma calculations. These different levels of theory are applied in two major computational frameworks - complex band structure (CBS) calculations to estimate the tunneling decay constant, beta, and Landauer-Buttiker transport calculations that consider explicitly the effects of contact geometry, and compute the transmission spectra directly. In general, for the same level of theory, the Landauer-Buttiker calculations give more quantitative values of beta than the CBS calculations. However, the CBS calculations have a long history and are particularly useful for quick estimates of beta. Comparing different levels of theory, it is clear that GW and DFT + Sigma calculations give significantly improved agreement with experiment compared to DFT, especially for the conductance values. Quantitative agreement can also be obtained for the Seebeck coefficient - another independent probe of electron transport. This excellent agreement provides confirmative evidence of off
Towards first-principles molecular design of liquid crystal-based chemoresponsive systems
NASA Astrophysics Data System (ADS)
Roling, Luke T.; Scaranto, Jessica; Herron, Jeffrey A.; Yu, Huaizhe; Choi, Sangwook; Abbott, Nicholas L.; Mavrikakis, Manos
2016-11-01
Nematic liquid crystals make promising chemoresponsive systems, but their development is currently limited by extensive experimental screening. Here we report a computational model to understand and predict orientational changes of surface-anchored nematic liquid crystals in response to chemical stimuli. In particular, we use first-principles calculations to evaluate the binding energies of benzonitrile, a model for 4'-pentyl-4-biphenylcarbonitrile, and dimethyl methylphosphonate to metal cation models representing the substrate chemical sensing surface. We find a correlation between these quantities and the experimental response time useful for predicting the response time of cation-liquid crystal combinations. Consideration of charge donation from chemical species in the surface environment is critical for obtaining agreement between theory and experiment. Our model may be extended to the design of improved chemoresponsive liquid crystals for selectively detecting other chemicals of practical interest by choosing appropriate combinations of metal cations with liquid crystals of suitable molecular structure.
NASA Astrophysics Data System (ADS)
Loukonen, Ville; Bork, Nicolai; Vehkamäki, Hanna
2013-05-01
The clustering process (sulfuric acid) + (base)→(sulfuric acid)1(base)1 is of fundamental importance in the atmospheric new-particle formation. Especially interesting are the collisions where a proton transfer reaction can happen, as the reaction often leads to relatively strongly bound clusters. Here, we studied the clustering process of (sulfuric acid) + (dimethylamine) → (sulfuric acid)1(dimethylamine)1 using first-principles molecular dynamics simulations. The collision of the two molecules was simulated starting with various spatial orientations and the evolution of the cluster was followed in the NVE ensemble. The simulations suggest that the proton transfer reaction takes place regardless of the intial collision orientation. However, due to the energy released in the process, the newly-formed cluster is not able to reach the minimun energy configuration, which might affect the following growth processes.
von Lilienfeld, O. Anatole
2013-02-26
A well-defined notion of chemical compound space (CCS) is essential for gaining rigorous control of properties through variation of elemental composition and atomic configurations. Here, we give an introduction to an atomistic first principles perspective on CCS. First, CCS is discussed in terms of variational nuclear charges in the context of conceptual density functional and molecular grand-canonical ensemble theory. Thereafter, we revisit the notion of compound pairs, related to each other via “alchemical” interpolations involving fractional nuclear charges in the electronic Hamiltonian. We address Taylor expansions in CCS, property nonlinearity, improved predictions using reference compound pairs, and the ounce-of-gold prize challenge to linearize CCS. Finally, we turn to machine learning of analytical structure property relationships in CCS. Here, these relationships correspond to inferred, rather than derived through variational principle, solutions of the electronic Schrödinger equation.
von Lilienfeld, O. Anatole
2013-02-26
A well-defined notion of chemical compound space (CCS) is essential for gaining rigorous control of properties through variation of elemental composition and atomic configurations. Here, we give an introduction to an atomistic first principles perspective on CCS. First, CCS is discussed in terms of variational nuclear charges in the context of conceptual density functional and molecular grand-canonical ensemble theory. Thereafter, we revisit the notion of compound pairs, related to each other via “alchemical” interpolations involving fractional nuclear charges in the electronic Hamiltonian. We address Taylor expansions in CCS, property nonlinearity, improved predictions using reference compound pairs, and the ounce-of-gold prizemore » challenge to linearize CCS. Finally, we turn to machine learning of analytical structure property relationships in CCS. Here, these relationships correspond to inferred, rather than derived through variational principle, solutions of the electronic Schrödinger equation.« less
First Principles Molecular Modeling of Sensing Material Selection for Hybrid Biomimetic Nanosensors
NASA Astrophysics Data System (ADS)
Blanco, Mario; McAlpine, Michael C.; Heath, James R.
Hybrid biomimetic nanosensors use selective polymeric and biological materials that integrate flexible recognition moieties with nanometer size transducers. These sensors have the potential to offer the building blocks for a universal sensing platform. Their vast range of chemistries and high conformational flexibility present both a problem and an opportunity. Nonetheless, it has been shown that oligopeptide aptamers from sequenced genes can be robust substrates for the selective recognition of specific chemical species. Here we present first principles molecular modeling approaches tailored to peptide sequences suitable for the selective discrimination of small molecules on nanowire arrays. The modeling strategy is fully atomistic. The excellent performance of these sensors, their potential biocompatibility combined with advanced mechanistic modeling studies, could potentially lead to applications such as: unobtrusive implantable medical sensors for disease diagnostics, light weight multi-purpose sensing devices for aerospace applications, ubiquitous environmental monitoring devices in urban and rural areas, and inexpensive smart packaging materials for active in-situ food safety labeling.
First-principles molecular dynamics study of deuterium diffusion in liquid tin
NASA Astrophysics Data System (ADS)
Liu, Xiaohui; Zheng, Daye; Ren, Xinguo; He, Lixin; Chen, Mohan
2017-08-01
Understanding the retention of hydrogen isotopes in liquid metals, such as lithium and tin, is of great importance in designing a liquid plasma-facing component in fusion reactors. However, experimental diffusivity data of hydrogen isotopes in liquid metals are still limited or controversial. We employ first-principles molecular dynamics simulations to predict diffusion coefficients of deuterium in liquid tin at temperatures ranging from 573 to 1673 K. Our simulations indicate faster diffusion of deuterium in liquid tin than the self-diffusivity of tin. In addition, we find that the structural and dynamic properties of tin are insensitive to the inserted deuterium at temperatures and concentrations considered. We also observe that tin and deuterium do not form stable solid compounds. These predicted results from simulations enable us to have a better understanding of the retention of hydrogen isotopes in liquid tin.
Towards first-principles molecular design of liquid crystal-based chemoresponsive systems
Roling, Luke T.; Scaranto, Jessica; Herron, Jeffrey A.; Yu, Huaizhe; Choi, Sangwook; Abbott, Nicholas L.; Mavrikakis, Manos
2016-01-01
Nematic liquid crystals make promising chemoresponsive systems, but their development is currently limited by extensive experimental screening. Here we report a computational model to understand and predict orientational changes of surface-anchored nematic liquid crystals in response to chemical stimuli. In particular, we use first-principles calculations to evaluate the binding energies of benzonitrile, a model for 4′-pentyl-4-biphenylcarbonitrile, and dimethyl methylphosphonate to metal cation models representing the substrate chemical sensing surface. We find a correlation between these quantities and the experimental response time useful for predicting the response time of cation–liquid crystal combinations. Consideration of charge donation from chemical species in the surface environment is critical for obtaining agreement between theory and experiment. Our model may be extended to the design of improved chemoresponsive liquid crystals for selectively detecting other chemicals of practical interest by choosing appropriate combinations of metal cations with liquid crystals of suitable molecular structure. PMID:27804955
First-principles and molecular dynamics studies of twin boundaries in hcp zirconium
Morris, J.R.; Ye, Y.Y.; Ho, K.M.; Chan, C.T.; Yoo, M.H.
1993-12-31
We use a combination of molecular dynamics (MD) and first-principles techniques to study the structure and energies of twin boundaries in hcp zirconium. The empirical many-body potential of Zr is used to test the stability of various possible twin structures, but the final relaxed positions are accurately determined using fully self-consistent ab initio energy and Hellman-Feynman force calculations. This combination of techniques is powerful, as it provides a stringent test of our empirical potential, while producing reliable results for Zr that do not depend upon any empirical parameters. This paper summarizes our work to date on the compression twins, which demonstrates the importance of supporting empirical modeling with more accurate calculations. We also present new results on the empirical modeling of the tension twins of Zr.
Ikeda, Takashi
2014-07-28
From both the polarized and depolarized Raman scattering spectra of supercritical water a peak located at around 1600 cm(-1), attributed normally to bending mode of water molecules, was experimentally observed to vanish, whereas the corresponding peak remains clearly visible in the measured infrared (IR) absorption spectrum. In this computational study a theoretical formulation for analyzing the IR and Raman spectra is developed via first principles molecular dynamics combined with the modern polarization theory. We demonstrate that the experimentally observed peculiar behavior of the IR and Raman spectra for water are well reproduced in our computational scheme. We discuss the origins of a feature observed at 1600 cm(-1) in Raman spectra of ambient water.
First-principles investigation of iron pentacarbonyl molecular solid phases at high pressure
NASA Astrophysics Data System (ADS)
Cong, Kien Nguyen; Steele, Brad A.; Landerville, Aaron C.; Oleynik, Ivan I.
2017-01-01
The polymeric phases of carbon monoxide (p-CO), an extended non-molecular solid, represent a new class of low-Z energetic materials. The presence of transition metal ions is believed to stabilize polymeric carbon monoxide (p-CO) at ambient conditions. Since p-CO forms at high pressures, it becomes important to investigate the high-pressure behavior of one of the potential precursors, iron pentacarbonyl Fe(CO)5. In this work, a first-principles evolutionary structure search method is used to determine the crystal phases of Fe(CO)5 at high pressure. The calculations predict the crystal structure of Phase I in agreement with experiment. Moreover, the previously unidentified crystal structure of Phase II is found. The calculated pressure-dependent Raman spectra are used to demonstrate that the changes in Raman spectra as a function of pressure observed in recent experiment can be explained without invoking a phase transition to a new phase III.
NASA Astrophysics Data System (ADS)
Reeves, Kyle; Yao, Yi; Kanai, Yosuke
Electronic stopping describes the transfer of energy from a highly-energetic charged particle to electrons in a material. This process induces massive electronic excitations via interaction between the material and the highly localized electric field from the charged particle. Understanding this phenomenon in condensed matter systems under proton irradiation has implications in various modern technologies. First-principles simulations, based on our recently-developed large-scale real-time time-dependent density functional theory approach, provide a detailed description of how electrons are excited via a non-equilibrium energy transfer from protons on the attosecond time scale. We apply this computational approach to the important case of liquid water under proton irradiation. Our work reveals several key features of the excitation dynamics at the mesoscopic and molecular levels which support a clearer understanding of the water radiolysis mechanism under proton irradiation. Importantly, we will demonstrate a first-principles determination of the energy transfer rate, (i.e. electronic stopping power) in liquid water, and a comparison to existing empirical models will be presented. We will conclude by discussing how the exchange-correlation approximation influences the calculation of the electronic stopping power.
A First Principles Molecular Dynamics Study Of Calcium Ion In Water
Lightstone, F; Schwegler, E; Allesch, M; Gygi, F; Galli, G
2005-01-28
In this work we report on Car-Parrinello simulations of the divalent calcium ion in water, aimed at understanding the structure of the hydration shell and at comparing theoretical results with a series of recent experiments. Our paper shows some of the progress in the investigation of aqueous solutions brought about by the advent of ab initio molecular dynamics and highlights the importance of accessing subtle details of ion-water interactions from first-principles. Calcium plays a vital role in many biological systems, including signal transduction, blood clotting and cell division. In particular, calcium ions are known to interact strongly with proteins as they tend to bind well to both negatively charged (e.g. in aspartate and glutamate) and uncharged oxygens (e.g. in main-chain carbonyls). The ability of calcium to coordinate multiple ligands (from 6 to 8 oxygen atoms) with an asymmetric coordination shell enables it to cross-link different segments of a protein and induce large conformational changes. The great biochemical importance of the calcium ion has led to a number of studies to determine its hydration shell and its preferred coordination number in water. Experimental studies have used a variety of techniques, including XRD, EXAFS, and neutron diffraction to elucidate the coordination of Ca{sup 2+} in water. The range of coordination numbers (n{sub C}) inferred by X-ray diffraction studies varies from 6 to 8, and is consistent with that reported in EXAFS experiments (8 and 7.2). A wider range of values (6 to 10) was found in early neutron diffraction studies, depending on concentration, while a more recent measurement by Badyal, et al. reports a value close to 7. In addition to experimental measurements, many theoretical studies have been carried out to investigate the solvation of Ca{sup 2+} in water and have also reported a wide range of coordination numbers. Most of the classical molecular dynamics (MD) and QM/MM simulations report n{sub C} in the
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-01
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10^{-4} Ha/Bohr.
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-31
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101,952 atoms on 23,328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7×10(-4) Ha/Bohr.
Consistent first-principles pressure scales for diffraction experiments under extreme conditions
NASA Astrophysics Data System (ADS)
Otero-de-La-Roza, Alberto; Cabal, Victor Lua Na
2012-02-01
Diamond anvil cell (DAC) diffraction experiments are fundamental in geophysics and materials science to explore the behavior of solids under very high pressures and temperatures. A factor limiting the accuracy of DAC experiments is the lack of an accurate pressure scale for the calibration materials that extends to the ever-increasing pressure and temperature limits of the technique. In this communication, we address this problem by applying a newly developed technique that allows the calculation of accurate thermodynamic properties from first-principles calculations [Phys. Rev. B 84 (2011) 024109, 84 (2011) 184103]. Three elements are key in this method: i) the quasiharmonic approximation (QHA) and the static energies and phonon frequencies obtained from an electronic structure calculation ii) the appropriate representation of the equation of state by using averages of strain polynomials and iii) the correction of the systematic errors caused by the exchange-correlation functional approximation. As a result, we propose accurate equations of scale for typical pressure calibrants that can be used in the whole experimental range of pressures and temperatures. The internal consistency and the agreement with the ruby scale based on experimental data is examined.
Tadano, T; Gohda, Y; Tsuneyuki, S
2014-06-04
A systematic method to calculate anharmonic force constants of crystals is presented. The method employs the direct-method approach, where anharmonic force constants are extracted from the trajectory of first-principles molecular dynamics simulations at high temperature. The method is applied to Si where accurate cubic and quartic force constants are obtained. We observe that higher-order correction is crucial to obtain accurate force constants from the trajectory with large atomic displacements. The calculated harmonic and anharmonic force constants are, then, combined with the Boltzmann transport equation (BTE) and non-equilibrium molecular dynamics (NEMD) methods in calculating the thermal conductivity. The BTE approach successfully predicts the lattice thermal conductivity of bulk Si, whereas NEMD shows considerable underestimates. To evaluate the linear extrapolation method employed in NEMD to estimate bulk values, we analyze the size dependence in NEMD based on BTE calculations. We observe strong nonlinearity in the size dependence of NEMD in Si, which can be ascribed to acoustic phonons having long mean-free-paths and carrying considerable heat. Subsequently, we also apply the whole method to a thermoelectric material Mg2Si and demonstrate the reliability of the NEMD method for systems with low thermal conductivities.
Ma, Haibo; Qin, Ting; Troisi, Alessandro
2014-03-11
The electronic excited states of amorphous polymeric semiconductor MEH-PPV are investigated by first principles quantum chemical calculations based on trajectories from classical molecular dynamics simulations. We inferred an average conjugation length of ∼5-7 monomers for lowest vertical excitations of amorphous MEH-PPV at room temperature and verified that the normal definition of a chromophore in a polymer based on purely geometric "conjugation breaks" is not always valid in amorphous polymers and a rigorous definition can be only on the basis of the evaluation of the polymer excited state wave function. The charge transfer character is observed to be nearly invariant for all excited states in low energy window while the exciton delocalization extent is found to increase with energy. The interchain excitonic couplings for amorphous MEH-PPV are shown to be usually smaller than 10 meV suggesting that the transport mechanism across chain can be described by incoherent hopping. All these observations about the energetic and spatial distribution of the excitons in polymer as well as their couplings provide important qualitative insights and useful quantitative information for constructing a realistic model for exciton migration dynamics in amorphous polymer materials.
Water radiolysis by low-energy carbon projectiles from first-principles molecular dynamics.
Kohanoff, Jorge; Artacho, Emilio
2017-01-01
Water radiolysis by low-energy carbon projectiles is studied by first-principles molecular dynamics. Carbon projectiles of kinetic energies between 175 eV and 2.8 keV are shot across liquid water. Apart from translational, rotational and vibrational excitation, they produce water dissociation. The most abundant products are H and OH fragments. We find that the maximum spatial production of radiolysis products, not only occurs at low velocities, but also well below the maximum of energy deposition, reaching one H every 5 Å at the lowest speed studied (1 Bohr/fs), dissociative collisions being more significant at low velocity while the amount of energy required to dissociate water is constant and much smaller than the projectile's energy. A substantial fraction of the energy transferred to fragments, especially for high velocity projectiles, is in the form of kinetic energy, such fragments becoming secondary projectiles themselves. High velocity projectiles give rise to well-defined binary collisions, which should be amenable to binary approximations. This is not the case for lower velocities, where multiple collision events are observed. H secondary projectiles tend to move as radicals at high velocity, as cations when slower. We observe the generation of new species such as hydrogen peroxide and formic acid. The former occurs when an O radical created in the collision process attacks a water molecule at the O site. The latter when the C projectile is completely stopped and reacts with two water molecules.
NASA Astrophysics Data System (ADS)
Ong, Mitchell; Lordi, Vincenzo; Draeger, Erik; Pask, John
2014-03-01
Lithium-ion batteries are commonly used to power many consumer devices. One of the key properties that influence the performance of lithium-ion batteries is the ionic conductivity of the electrolyte. This is dependent on the speed at which Li ions diffuse across the cell and related to the solvation structure of the Li ions. The choice of the electrolyte can greatly impact both solvation and diffusivity of Li ions. In this work, we use first principles molecular dynamics to examine the solvation and diffusion of Li ions in several bulk organic electrolytes. We find that differences in the local environment throughout the liquid can lead to solvation of Li ions by either carbonyl or ether oxygen atoms. In addition, we examine the differences in solvation of associated and dissociated Li(PF6) salts, showing that the bulky PF6 group blocks complete solvation of Li+ by solvent oxygen atoms. Finally, we calculate Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in a linear carbonate such as ethyl methyl carbonate (EMC) compared to a cyclic carbonate like ethylene carbonate (EC). Results from this work can be used to design new bulk electrolytes that will improve the performance of current Li-ion batteries.
High pressure chemistry of thioaldehydes: A first-principles molecular dynamics study
NASA Astrophysics Data System (ADS)
Zhang, Yaoting; Mosey, Nicholas J.
2016-11-01
First-principles molecular dynamics simulations are used to investigate the chemical behavior of bulk thioacetaldehyde (MeC(H)S) in response to changes in pressure, P. The simulations show that these molecules oligomerize in response to applied P. Oligomerization is initiated through C—S bond formation, with constrained dynamics simulations showing that the barrier to this reaction step is lowered significantly by applied P. Subsequent reactions involving the formation of additional C—S bonds or radical processes that lead to S—S and C—C bonds lengthen the oligomers. Oligomerization is terminated through proton transfer or the formation of rings. The mechanistic details of all reactions are examined. The results indicate that the P-induced reactivity of the MeC(H)S-based system differs significantly from that of analogous MeC(H)O-based systems, which have been reported previously. Comparison with the MeC(H)O study shows that replacing oxygen with sulfur significantly lowers the P required to initiate oligomerization (from 26 GPa to 5 GPa), increases the types of reactions in which systems of this type can take part, and increases the variety of products formed through these reactions. These differences can be explained in terms of the electronic structures of these systems, which may be useful for certain high P applications.
Feliciano, Gustavo T; da Silva, Antonio J R; Reguera, Gemma; Artacho, Emilio
2012-08-02
The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved α-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pilin was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's α-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.
Water radiolysis by low-energy carbon projectiles from first-principles molecular dynamics
Kohanoff, Jorge
2017-01-01
Water radiolysis by low-energy carbon projectiles is studied by first-principles molecular dynamics. Carbon projectiles of kinetic energies between 175 eV and 2.8 keV are shot across liquid water. Apart from translational, rotational and vibrational excitation, they produce water dissociation. The most abundant products are H and OH fragments. We find that the maximum spatial production of radiolysis products, not only occurs at low velocities, but also well below the maximum of energy deposition, reaching one H every 5 Å at the lowest speed studied (1 Bohr/fs), dissociative collisions being more significant at low velocity while the amount of energy required to dissociate water is constant and much smaller than the projectile’s energy. A substantial fraction of the energy transferred to fragments, especially for high velocity projectiles, is in the form of kinetic energy, such fragments becoming secondary projectiles themselves. High velocity projectiles give rise to well-defined binary collisions, which should be amenable to binary approximations. This is not the case for lower velocities, where multiple collision events are observed. H secondary projectiles tend to move as radicals at high velocity, as cations when slower. We observe the generation of new species such as hydrogen peroxide and formic acid. The former occurs when an O radical created in the collision process attacks a water molecule at the O site. The latter when the C projectile is completely stopped and reacts with two water molecules. PMID:28267804
Bhatia, Harsh; Gyulassy, Attila; Ong, Mitchell; Lordi, Vincenzo; Draeger, Erik; Pask, John; Pascucci, Valerio; Bremer, Peer -Timo
2016-09-27
The performance of lithium-ion batteries is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact, both, the solvation and diffusivity of Li ions. In this work, we present our application of the topological techniques to extract and predict such behavior in the data generated by the first-principles molecular dynamics simulation of Li ions in an important organic solvent -ethylene carbonate. More specifically, we use the scalar topology of the electron charge density field to analyze the evolution of the solvation structures. This allows us to derive a parameter-free bond definition for lithium-oxygen bonds, to provide a quantitative measure for bond strength, and to understand the regions of influence of each atom in the simulation. This has provided new insights into how and under what conditions certain bonds may form and break. As a result, we can identify and, more importantly, predict, unstable configurations in solvation structures. This can be very useful in understanding when small changes to the atoms' movements can cause significantly different bond structures to evolve. Ultimately, this promises to allow scientists to explore lithium ion solvation and diffusion more systematically, with the aim of new insights and potentially accelerating the calculations themselves.
First-principles molecular-dynamics study of glassy As2Se3
NASA Astrophysics Data System (ADS)
Li, Jun; Drabold, D. A.
2000-05-01
A first-principles molecular-dynamics study of glassy As2Se3, using a 215-atom model, is presented. Our model is in good and uniform agreement with available measurements of the structural, vibrational, and electronic properties. The model reproduces the structure of the experimental static structure factor in the range ~2-6 Å-1. The preferred structural unit is pyramidal AsSe3 loosely coupled by Se. The model mean coordination number is 2.4. The vibrational density of states has two distinct bands. The broadband in the lower-energy range, up to about 20 meV, is dominated by modes extending widely over the network. The localized modes occur at the edges of the bands. The electronic density of states has also two main bands in the valence range. One is from the 4s electrons of As and Se; the other from 4p electrons populates on the upper energy range of the valence band. The calculated fundamental gap is 1.42 eV and the band tail states are localized predominantly on the coordination defects of As.
NASA Astrophysics Data System (ADS)
Liu, Xiandong; Cheng, Jun; Sprik, Michiel; Lu, Xiancai; Wang, Rucheng
2014-09-01
We report a first principles molecular dynamics (FPMD) study of the acid chemistry of 2:1-type dioctahedral phyllosilicates. Using the FPMD based vertical energy gap method, we computed intrinsic acidity constants of phyllosilicate edge sites. The investigated models include both neutral and charged frameworks (i.e., Mg for Al replacement in octahedral sheets and Al for Si replacement in tetrahedral sheets) and the common edge surface types (i.e., (0 1 0) and (1 1 0)). The result of the neutral framework agrees with the experiment of pyrophyllite. For charged frameworks, it is found that tbnd Al(OH) sites in T-sheets (i.e., Al-sub) and tbnd Mg(OH2) sites (i.e., Mg-sub) have extremely high pKas and thus they all keep protonated. Both types of substitutions increase pKas of the apical oxygen sites on (1 1 0) surfaces and Mg substitution also increases the pKas of neighboring silanol sites. With the calculated pKas, we explore the mechanism of heavy metal cations complexation on edge surfaces. As a quantitative basis, the results in this work can be used in future modeling and experimental studies for understanding acid reactivity of phyllosilicates.
NASA Astrophysics Data System (ADS)
Chen, Mohan; Abrams, Tyler; Jaworski, Michael; Carter, Emily
2015-03-01
First-principles molecular dynamics (FPMD) is performed to study liquid lithium (Li) samples with high-concentration deuterium (D) implantation. First, we validate FPMD against experimental properties of solid and liquid Li and LiD. The calculated properties of both Li and LiD include relative stabilities and bulk moduli of several solid phases, melting temperatures, pair distribution functions, and bond angle distribution functions. Excellent agreement is obtained between FPMD and available experimental data. Next, we randomly implant D atoms at four different concentrations into liquid Li at different temperatures. Specifically, the ratios of D:Li atoms studied are 0.25, 0.50, 0.75 and 1.00, and the temperatures range from 400 to 1143 K. FPMD reveals several interesting properties of these liquid Li samples with implanted D atoms. For example, we observe fast nucleation of rock-salt structures of LiD for samples at temperatures lower than the melting point of LiD (960 K). We find that the pure Li component is quickly suppressed with increased concentration of D atoms, and that no D clusters form. Finally, because measured diffusivities of D in liquid Li vary by several orders of magnitude, we predict the diffusivities of both Li and D atoms in all samples.
NASA Astrophysics Data System (ADS)
Zapol, Peter; Karpeyev, Dmitry; Maheshwari, Ketan; Zhong, Xiaoliang; Narayanan, Badri; Sankaranarayanan, Subramanian; Wilde, Michael; Heinonen, Olle; Rungger, Ivan
2015-03-01
The electronic conduction in Hf-oxide heterostructures for use in, e.g., resistive switching devices, depends sensitively on local oxygen stoichiometry and interactions at interfaces with metal electrodes. In order to model the electronic structure of different disordered configurations near interfaces, we have combined molecular dynamics (MD) simulations with first-principle based non-equilibrium Green's functions (NEGF) methods, including self-interaction corrections. We have developed an approach to generating automated workflows that combine MD and NEGF computations over many parameter values using the Swift parallel scripting language. A sequence of software tools transforms the result of one calculation into the input of the next allowing for a high-throughput concurrent parameter sweep. MD simulations generate systems with quenched disorder, which are then directly fed to NEGF and on to postprocessing. Different computations can be run on different computer platforms matching the computational load to the hardware resources. We will demonstrate results for metal-HfO2-metal heterostructures obtained using this workflow. Argonne National Laboratory's work was supported under U.S. Department of Energy Contract DE-AC02-06CH11357.
Far-infrared absorption of water clusters by first-principles molecular dynamics.
Lee, Mal-Soon; Baletto, F; Kanhere, D G; Scandolo, S
2008-06-07
Based on first-principle molecular dynamic simulations, we calculate the far-infrared spectra of small water clusters (H(2)O)(n) (n = 2, 4, 6) at frequencies below 1000 cm(-1) and at 80 K and at atmospheric temperature (T>200 K). We find that cluster size and temperature affect the spectra significantly. The effect of the cluster size is similar to the one reported for confined water. Temperature changes not only the shape of the spectra but also the total strength of the absorption, a consequence of the complete anharmonic nature of the classical dynamics at high temperature. In particular, we find that in the frequency region up to 320 cm(-1), the absorption strength per molecule of the water dimer at 220 K is significantly larger than that of bulk liquid water, while tetramer and hexamer show bulklike strengths. However, the absorption strength of the dimer throughout the far-infrared region is too small to explain the measured vapor absorption continuum, which must therefore be dominated by other mechanisms.
First principles study on the electronic transport properties of C60 and B80 molecular bridges
NASA Astrophysics Data System (ADS)
Zheng, X. H.; Hao, H.; Lan, J.; Wang, X. L.; Shi, X. Q.; Zeng, Z.
2014-08-01
The electronic transport properties of molecular bridges constructed by C60 and B80 molecules which have the same symmetry are investigated by first principles calculations combined with a non-equilibrium Green's function technique. It is found that, like C60, monomer B80 is a good conductor arising from the charge transfer from the leads to the molecule, while the dimer (B80)2 and (C60)2 are both insulators due to the potential barrier formed at the molecule-molecule interface. Our further study shows that, although both the homogeneous dimer (B80)2 and (C60)2 display poor conductivity, the heterogeneous dimer B80C60 shows a very high conductance as a result from the decreased HOMO-LUMO gap and the excess charge redistribution. Finally, we find that the conductivity of both (B80)2 and (C60)2 can be significantly improved by electron doping, for example, by doping C in (B80)2 and doping N in (C60)2.
Nakata, Maho; Shimazaki, Tomomi
2017-06-26
Large-scale molecular databases play an essential role in the investigation of various subjects such as the development of organic materials, in silico drug design, and data-driven studies with machine learning. We have developed a large-scale quantum chemistry database based on first-principles methods. Our database currently contains the ground-state electronic structures of 3 million molecules based on density functional theory (DFT) at the B3LYP/6-31G* level, and we successively calculated 10 low-lying excited states of over 2 million molecules via time-dependent DFT with the B3LYP functional and the 6-31+G* basis set. To select the molecules calculated in our project, we referred to the PubChem Project, which was used as the source of the molecular structures in short strings using the InChI and SMILES representations. Accordingly, we have named our quantum chemistry database project "PubChemQC" ( http://pubchemqc.riken.jp/ ) and placed it in the public domain. In this paper, we show the fundamental features of the PubChemQC database and discuss the techniques used to construct the data set for large-scale quantum chemistry calculations. We also present a machine learning approach to predict the electronic structure of molecules as an example to demonstrate the suitability of the large-scale quantum chemistry database.
Fox, Stephen J; Pittock, Chris; Fox, Thomas; Tautermann, Christofer S; Malcolm, Noj; Skylaris, Chris-Kriton
2011-12-14
Biomolecular simulations with atomistic detail are often required to describe interactions with chemical accuracy for applications such as the calculation of free energies of binding or chemical reactions in enzymes. Force fields are typically used for this task but these rely on extensive parameterisation which in cases can lead to limited accuracy and transferability, for example for ligands with unusual functional groups. These limitations can be overcome with first principles calculations with methods such as density functional theory (DFT) but at a much higher computational cost. The use of electrostatic embedding can significantly reduce this cost by representing a portion of the simulated system in terms of highly localised charge distributions. These classical charge distributions are electrostatically coupled with the quantum system and represent the effect of the environment in which the quantum system is embedded. In this paper we describe and evaluate such an embedding scheme in which the polarisation of the electronic density by the embedding charges occurs self-consistently during the calculation of the density. We have implemented this scheme in a linear-scaling DFT program as our aim is to treat with DFT entire biomolecules (such as proteins) and large portions of the solvent. We test this approach in the calculation of interaction energies of ligands with biomolecules and solvent and investigate under what conditions these can be obtained with the same level of accuracy as when the entire system is described by DFT, for a variety of neutral and charged species.
Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton
2013-08-15
Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.
NASA Astrophysics Data System (ADS)
Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; Schwegler, Eric
2016-10-01
Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na+, K+, and Cl- ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.
Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; Schwegler, Eric
2016-10-17
Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperatures to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na^{+}, K^{+}, and Cl^{-} ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.
Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...
2016-10-17
Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na+, K+, and Cl- ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less
Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric
2016-10-21
Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na(+), K(+), and Cl(-) ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.
Mosey, Nicholas J
2010-04-07
First-principles molecular dynamics simulations are used to investigate the behavior of bulk acetaldehyde (MeCHO) under conditions of increasing pressure. The results demonstrate that increasing pressure causes the aldehydes to polymerize, yielding polyethers through a process involving the rapid formation of C-O bonds between multiple neighboring MeCHO molecules. Attempts to induce polyether formation at different densities through the application of geometric constraints show that polymerization occurs only once a critical density of approximately 1.7 g/cm(3) has been reached. The results of simulations performed at several different temperatures are also consistent with a process that is induced by reaching a critical density. The origins of this effect are rationalized in terms of the structural requirements for the formation of C-O bonds between multiple MeCHO molecules in rapid succession. Specifically, the collective formation of C-O bonds requires the typical distance between the sp(2) carbon atoms and oxygen atoms in neighboring MeCHO molecules to reach a value of approximately 2.5 A. Radial distribution functions calculated at different densities show that this structural requirement is reached when the density is near the observed threshold. The observed reaction may be useful in the context of lubrication, with polyethers being effective lubricants and the extreme conditions experienced in sliding contacts providing the ability to reach the high densities needed to induce the reaction. In this context, the calculations indicate that polyether formation is associated with significant energy dissipation, while energy dissipation is minimal once the polyethers are formed. Furthermore, the polyethers are stable with respect to multiple compression/decompression cycles and pressures of at least 60 GPa.
First-principles study of the switching mechanism of [2]catenane molecular switches
NASA Astrophysics Data System (ADS)
Kim, Yong-Hoon; Jang, Yunhee; Jang, Seung Soon; Goddard, William A., III
2004-03-01
Using large-scale density-functional and matrix Greens function calculations coupled with force-field molecular dynamics, we investigate the coherent charge transport properties of Stoddart--Heath-type [2]catenane molecular devices, which consists of a cyclobis-(paraquat-p-phenylene) ring (CBPQT4+)(PF6)4 encircling a ring-shape backbone with two active sites, tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP). We identify the monolayer packing configuration and present the key swtiching mechanism based on the movement of the frontier molecular orbital levels of TTF or DNP site by ring encircling. According to the switching mechanism, the ring encircling TTF/DNP configuration is the switch off/on state in agreement with the experimental interpretation.
NASA Astrophysics Data System (ADS)
Lee, Hyung-June; Kim, Gunn; Kwon, Young-Kyun
2013-08-01
Using first-principles calculations, we investigate the electronic structures and binding properties of nicotine and caffeine adsorbed on single-walled carbon nanotubes to determine whether CNTs are appropriate for filtering or sensing nicotine and caffeine molecules. We find that caffeine adsorbs more strongly than nicotine. The different binding characteristics are discussed by analyzing the modification of the electronic structure of the molecule-adsorbed CNTs. We also calculate the quantum conductance of the CNTs in the presence of nicotine or caffeine adsorbates and demonstrate that the influence of caffeine is stronger than nicotine on the conductance of the host CNT.
Micoulaut, Matthieu; Le Roux, Sébastien; Massobrio, Carlo
2012-06-14
The structural properties of liquid GeSe(2) have been calculated by first-principles molecular dynamics by using a periodic simulation box containing N = 480 atoms. This has allowed a comparison with previous results obtained on a smaller system size (N = 120) [M. Micoulaut, R. Vuilleumier, and C. Massobrio, Phys. Rev. B 79, 214205 (2009)]. In the domain of first-principles molecular dynamics, we obtain an assessment of system size effects of unprecedented quality. Overall, no drastic differences are found between the two sets of results, confirming that N = 120 is a suitable size to achieve a realistic description of this prototypical disordered network. However, for N = 480, short range properties are characterized by an increase of chemical order, the number of Ge tetrahedra coordinated to four Se atoms being larger. At the intermediate range order level, size effect mostly modify the low wavevector region (k ~1 Å(-1)) in the concentration-concentration partial structure factor.
NASA Astrophysics Data System (ADS)
Owens, Jonathan R.
In this work, we first present two powerful methods for understanding the electronic, structural, conducting, and energetic properties of nano-materials: density functional theory (DFT) and quantum transport. The basics of the theory and background of both methods are discussed thoroughly. After establishing a firm foundation, we turn our attention to using these tools to solve practical problems, often in collaboration with experimental colleagues. The first two projects pertain to nitrogen doping in graphene nanoribbons (GNRs). We study nitrogen doping in two different schema: concentration-based (N_x-doped) and structural based (N_2. {AA}-doped). Concentration based doping is explored in the context of experimental measurements of IV curves on GNRs with differing dopant concentrations. These results show a shift towards semi-conducting behavior with an increase in dopant concentration. We combine first principles calculations (DFT) and transport calculations in the Landauer formalism to compute the density-of-states (DOS) and transport curves for various dopant concentrations (0.46%, 1.39%, 1.89%, and 2.31%), which corroborate the experimental observations. The N_2. {AA}-doped GNR study was inspired by experimental observation of an atomically precise nitrogen doping scheme in bulk graphene. Experimental STM images, combined with simulated STM images, revealed that the majority (80%) of doping sites consist of nitrogen atoms on neighboring sites of the same sublattice (A) in graphene, hence N_2. {AA} doping. We examine this doping scheme applied to zigzag and armchair GNRs under different orientations of the dopants. We present spin-resolved charge densities, energetics, transport, DOS, and simulated STM images for all four systems studied. Our results show the possibility of spin-filtered devices and the STM images provide an aid in helping experimentalist identify the dopant patterns, if these GNRs are fabricated. We next venture to explain different observed
NASA Astrophysics Data System (ADS)
Massobrio, C.; Celino, M.; Pouillon, Y.; Billas, I. M. L.
In both clusters and disordered systems the determination of structural properties often relies on qualitative interpretations of experimental data. First-principles molecular dynamics provides a reliable atomic-scale tool to optimize geometries and follow the dynamical evolution at different temperatures. We present three examples of application of first-principles molecular dynamics to the study of finite systems and disordered, bulk networks. In the first case, devoted to the copper oxide clusters CuO2 and CuO6, the account of temperature effects and a careful search of all isomer allows to complement effectively photoelectron spectroscopy data. In the second example, we analyze the behavior of the C60 fullerene when one or two silicon atoms are inserted in the cage to replace carbon atoms. Silicon atoms correspond to chemically reactive sites of the fullerenes, giving rise to local structural distortions. Then, we describe the determination of the structure for liquid SiSe2 at thermal equilibrium. The microscopic origins of intermediate range order are rationalized in terms of network connectivity and specific features appearing in the structure factors. Overall, first-principles molecular dynamics appears as a convincing method to corroborate experimental work and make reliable predictions based on well-established electronic structure techniques.
A unified electrostatic and cavitation model for first-principles molecular dynamics in solution
Scherlis, D A; Fattebert, J; Gygi, F; Cococcioni, M; Marzari, N
2005-11-14
The electrostatic continuum solvent model developed by Fattebert and Gygi is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. The model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution, and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. They apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.
A first principle particle mesh method for solution SAXS of large bio-molecular systems
NASA Astrophysics Data System (ADS)
Marchi, Massimo
2016-07-01
This paper will show that the solution small angle X-ray scattering (SAXS) intensity of globular and membrane proteins can be efficiently and accurately computed from molecular dynamics trajectories using 3D fast Fourier transforms (FFTs). A suitable particle meshing interpolation, similar to the one used in smooth particle mesh Ewald for electrostatic energies and forces, was combined with a uniform solvent density FFT padding scheme to obtain a convenient SAXS spectral resolution. The CPU time scaling of the method, as a function of system size, is highly favorable and its application to large systems such as solutions of solvated membrane proteins is computationally undemanding. Differently from other approaches, all contributions from the simulation cell are included. This means that the subtraction of the buffer from the solution scattering intensity is straightforward and devoid of artifact due to ad hoc definitions of proximal and distal solvent intensity contributions.
NASA Astrophysics Data System (ADS)
Golovanov, Viacheslav; Golovanova, Viktoria; Rantala, Tapio T.
2016-02-01
First-principles density functional theory calculations in the generalized gradient approximation, with plane wave basis set and pseudopotentials, have been used to investigate the desorption pathways of molecular oxygen species adsorbed on the SnO2 (110) surface. Energetics of the thermodynamically favored precursors is studied in dependence on the surface charge provided either by surface defects or by donor type impurities from the near-surface region. The resonant desorption modes of O2 molecules are examined in the framework of ab initio atomic thermodynamics and relationship of these results to experimental observations is discussed.
NASA Astrophysics Data System (ADS)
Jiang, Jun; Kula, Mathias; Lu, Wei; Luo, Yi
2005-08-01
A generalized Green's function theory is developed to simulate the inelastic electron tunneling spectroscopy (IETS) of molecular junctions. It has been applied to a realistic molecular junction with an octanedithiolate embedded between two gold contacts in combination with the hybrid density functional theory calculations. The calculated spectra are in excellent agreement with recent experimental results. Strong temperature dependence of the experimental IETS spectra is also reproduced. It is shown that the IETS is extremely sensitive to the intra-molecular conformation and to the molecule-metal contact geometry.
Lončarić, Ivor; Alducin, M; Juaristi, J I
2016-10-05
We perform a detailed study of the static and dynamical properties of molecular oxygen adsorption on Ag(110) based on semi-local density functional theory (DFT) calculations and compare the results to experimental studies. For the classical dynamics calculations we use two complementary approaches, ab initio molecular dynamics and dynamics on a precalculated potential energy surface. In contrast to the molecular beam experiments, at low beam incidence energies we obtain high molecular adsorption probabilities that are related to the physisorption-like adsorption wells at the bridge sites of Ag(110). Semi-local DFT seems to overbind O2 in these wells. Based on our dynamics calculations we propose a model for adsorption in the chemisorption wells via initial adsorption in the bridge wells. In this model the measured low adsorption probabilities at low incidence energies are explained by the existence of energy barriers between the physisorption-like and chemisorption wells.
Dal Peraro, Matteo; Ruggerone, Paolo; Raugei, Simone; Gervasio, Francesco Luigi; Carloni, Paolo
2007-04-01
Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.
Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations.
Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei
2017-02-14
Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young's modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young's modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.
First-principles mobility calculations and atomic-scale interface roughness in nanoscale structures.
Evans, M H; Zhang, X-G; Joannopoulos, J D; Pantelides, S T
2005-09-02
Calculations of mobilities have so far been carried out using approximate methods that suppress atomic-scale detail. Such approaches break down in nanoscale structures. Here we report the development of a method to calculate mobilities using atomic-scale models of the structures and density functional theory at various levels of sophistication and accuracy. The method is used to calculate the effect of atomic-scale roughness on electron mobilities in ultrathin double-gate silicon-on-insulator structures. The results elucidate the origin of the significant reduction in mobility observed in ultrathin structures at low electron densities.
First-Principles Mobility Calculations and Atomic-Scale Interface Roughness in Nanoscale Structures
Evans, Matthew H; Zhang, Xiaoguang; Joannopoulos, J. D.; Pantelides, Sokrates T
2005-01-01
Calculations of mobilities have so far been carried out using approximate methods that suppress atomic-scale detail. Such approaches break down in nanoscale structures. Here we report the development of a method to calculate mobilities using atomic-scale models of the structures and density functional theory at various levels of sophistication and accuracy. The method is used to calculate the effect of atomic-scale roughness on electron mobilities in ultrathin double-gate silicon-on-insulator structures. The results elucidate the origin of the significant reduction in mobility observed in ultrathin structures at low electron densities.
Scaling laws for ignition at the National Ignition Facility from first principles.
Cheng, Baolian; Kwan, Thomas J T; Wang, Yi-Ming; Batha, Steven H
2013-10-01
We have developed an analytical physics model from fundamental physics principles and used the reduced one-dimensional model to derive a thermonuclear ignition criterion and implosion energy scaling laws applicable to inertial confinement fusion capsules. The scaling laws relate the fuel pressure and the minimum implosion energy required for ignition to the peak implosion velocity and the equation of state of the pusher and the hot fuel. When a specific low-entropy adiabat path is used for the cold fuel, our scaling laws recover the ignition threshold factor dependence on the implosion velocity, but when a high-entropy adiabat path is chosen, the model agrees with recent measurements.
NASA Astrophysics Data System (ADS)
Wright, Louise B.; Walsh, Tiffany R.
2012-12-01
The ability to exert molecular-level control at the aqueous interface between biomolecules and inorganic substrates is pivotal to advancing applications ranging from sustainable manufacturing to targeted therapeutics. Progress is hindered by a lack of structural information of these interfaces with atomic resolution. Molecular simulation is one approach to obtain such data, but can be limited by the reliability of the force-field used. First-principles simulations, in principle, can provide insights into such aqueous interfaces, but are resource-intensive, limiting previous first-principles studies to approximate the environment of liquid water. Here, we use Car-Parrinello simulations to investigate adsorption of two charged adsorbates that are functional groups common to all amino-acids—ethanoate and ammonium—at the interface between hydroxylated quartz and liquid water, directly incorporating full solvation effects at the interface. Our findings reveal the stable character of carboxylate-quartz binding, as well as the surprisingly indifferent nature of ammonium-quartz interactions, in liquid water.
Wright, Louise B; Walsh, Tiffany R
2012-12-14
The ability to exert molecular-level control at the aqueous interface between biomolecules and inorganic substrates is pivotal to advancing applications ranging from sustainable manufacturing to targeted therapeutics. Progress is hindered by a lack of structural information of these interfaces with atomic resolution. Molecular simulation is one approach to obtain such data, but can be limited by the reliability of the force-field used. First-principles simulations, in principle, can provide insights into such aqueous interfaces, but are resource-intensive, limiting previous first-principles studies to approximate the environment of liquid water. Here, we use Car-Parrinello simulations to investigate adsorption of two charged adsorbates that are functional groups common to all amino-acids--ethanoate and ammonium--at the interface between hydroxylated quartz and liquid water, directly incorporating full solvation effects at the interface. Our findings reveal the stable character of carboxylate-quartz binding, as well as the surprisingly indifferent nature of ammonium-quartz interactions, in liquid water.
First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent
NASA Astrophysics Data System (ADS)
Sánchez, Verónica M.; Sued, Mariela; Scherlis, Damián A.
2009-11-01
Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis et al., J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn-Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car-Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO2-water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model.
Polymorphism and Elastic Response of Molecular Materials from First Principles: How Hard Can it Be?
NASA Astrophysics Data System (ADS)
Reilly, Anthony; Tkatchenko, Alexandre
2014-03-01
Molecular materials are of great fundamental and applied importance in science and industry, with numerous applications in pharmaceuticals, electronics, sensing, and catalysis. A key challenge for theory has been the prediction of their stability, polymorphism and response to perturbations. While pairwise models of van der Waals (vdW) interactions have improved the ability of density functional theory (DFT) to model these systems, substantial quantitative and even qualitative failures remain. In this contribution we show how a many-body description of vdW interactions can dramatically improve the accuracy of DFT for molecular materials, yielding quantitative description of stabilities and polymorphism for these challenging systems. Moreover, the role of many-body vdW interactions goes beyond stabilities to response properties. In particular, we have studied the elastic properties of a series of molecular crystals, finding that many-body vdW interactions can account for up to 30% of the elastic response, leading to quantitative and qualitative changes in elastic behavior. We will illustrate these crucial effects with the challenging case of the polymorphs of aspirin, leading to a better understanding of the conflicting experimental and theoretical studies of this system.
Large-Scale Computations Leading to a First-Principles Approach to Nuclear Structure
Ormand, W E; Navratil, P
2003-08-18
We report on large-scale applications of the ab initio, no-core shell model with the primary goal of achieving an accurate description of nuclear structure from the fundamental inter-nucleon interactions. In particular, we show that realistic two-nucleon interactions are inadequate to describe the low-lying structure of {sup 10}B, and that realistic three-nucleon interactions are essential.
NASA Astrophysics Data System (ADS)
Ishikawa, Takahiro; Nagara, Hitose; Suzuki, Naoshi; Shimizu, Katsuya
2012-12-01
The crystal structure of the simple cubic phase in calcium is investigated by first-principles molecular dynamics simulations at pressure of 40 GPa and at temperatures of 300 and 10 K. For the k-point sampling over the Brillouin zone, at least 3 × 3 × 3 k-points are required to achieve reliable dynamic behavior of the simulation cell consisting of 4 × 4 × 4 simple cubic primitive cells. As a result of the simulation, a dynamically fluctuating simple cubic lattice emerges at 300 K. The dynamic structure is distorted slightly from the cubic lattice at 10 K, which is consistent with previous experimental observations. A static crystal structure obtained by reducing the particle velocities in the course of the simulation becomes an orthorhombic structure, which is far from the simple cubic structure. Our molecular dynamics study indicates that thermal contribution is crucial for a discussion about the emergence of the simple cubic calcium.
Beran, Gregory J O; Hartman, Joshua D; Heit, Yonaton N
2016-11-15
Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties. First, it describes the coupling of fragment electronic structure models with quasi-harmonic techniques for modeling the thermal expansion of molecular crystals, and what effects this expansion has on thermochemical and mechanical properties. Excellent agreement with experiment is demonstrated for the molar volume, sublimation enthalpy, entropy, and free energy, and the bulk modulus of phase I carbon dioxide when large basis second-order Møller-Plesset perturbation theory (MP2) or coupled cluster theories (CCSD(T)) are used. In addition, physical insight is offered into how neglect of thermal expansion affects these properties. Zero-point vibrational motion leads to an appreciable expansion in the molar volume; in carbon dioxide, it accounts for around 30% of the overall volume expansion between the electronic structure energy minimum and the molar volume at the sublimation point. In addition, because thermal expansion typically weakens the intermolecular interactions, neglecting thermal expansion artificially stabilizes the solid and causes the sublimation enthalpy to be too large at higher temperatures. Thermal expansion also frequently weakens the lower-frequency lattice phonon modes; neglecting thermal expansion causes the entropy of sublimation to be overestimated. Interestingly, the sublimation free energy is less significantly affected by neglecting thermal expansion because the systematic
Semiclassical Monte Carlo: a first principles approach to non-adiabatic molecular dynamics.
White, Alexander J; Gorshkov, Vyacheslav N; Wang, Ruixi; Tretiak, Sergei; Mozyrsky, Dmitry
2014-11-14
Modeling the dynamics of photophysical and (photo)chemical reactions in extended molecular systems is a new frontier for quantum chemistry. Many dynamical phenomena, such as intersystem crossing, non-radiative relaxation, and charge and energy transfer, require a non-adiabatic description which incorporate transitions between electronic states. Additionally, these dynamics are often highly sensitive to quantum coherences and interference effects. Several methods exist to simulate non-adiabatic dynamics; however, they are typically either too expensive to be applied to large molecular systems (10's-100's of atoms), or they are based on ad hoc schemes which may include severe approximations due to inconsistencies in classical and quantum mechanics. We present, in detail, an algorithm based on Monte Carlo sampling of the semiclassical time-dependent wavefunction that involves running simple surface hopping dynamics, followed by a post-processing step which adds little cost. The method requires only a few quantities from quantum chemistry calculations, can systematically be improved, and provides excellent agreement with exact quantum mechanical results. Here we show excellent agreement with exact solutions for scattering results of standard test problems. Additionally, we find that convergence of the wavefunction is controlled by complex valued phase factors, the size of the non-adiabatic coupling region, and the choice of sampling function. These results help in determining the range of applicability of the method, and provide a starting point for further improvement.
Wang, Xiaoli; Hou, Dong; Zheng, Xiao; Yan, YiJing
2016-01-21
The magnetic anisotropy and Kondo phenomena in a mechanically stretched magnetic molecular junction are investigated by combining the density functional theory (DFT) and hierarchical equations of motion (HEOM) approach. The system is comprised of a magnetic complex Co(tpy–SH){sub 2} sandwiched between adjacent gold electrodes, which is mechanically stretched in experiments done by Parks et al. [Science 328, 1370 (2010)]. The electronic structure and mechanical property of the stretched system are investigated via the DFT calculations. The HEOM approach is then employed to characterize the Kondo resonance features, based on the Anderson impurity model parameterized from the DFT results. It is confirmed that the ground state prefers the S = 1 local spin state. The structural properties, the magnetic anisotropy, and corresponding Kondo peak splitting in the axial stretching process are systematically evaluated. The results reveal that the strong electron correlations and the local magnetic properties of the molecule magnet are very sensitive to structural distortion. This work demonstrates that the combined DFT+HEOM approach could be useful in understanding and designing mechanically controlled molecular junctions.
NASA Astrophysics Data System (ADS)
Pati, Ranjit; Karna, Shashi P.
2001-03-01
Recent advancements in the experimental measurement of conductance across a single molecule(M. A. Reed et al, Science, 278) , 252 (1997). have generated great deal of interest in the feasibility of molecular electronic devices. A successful realization of molecule based electronic devices rests on a detailed understanding of the physical principles underlying controlled transport of electron/hole across molecular units. In order to develop such a fundamental understanding, we have investigated current-voltage characteristics of metal atom (Ag, Au) substituted 1,4-dithiobenzene within Green's function approach according to Datta and coworkers( W. Tian et al, J. Chem. Phys., 109), 2874 (1998).. Ab initio Hamiltonian matrix elements are used to construct the Green's function. The calculated conductance spectrum for the molecule with S bonded to Au atoms qualitatively agrees with the experiment^1. However, large quantitative difference between the calculated and measured conductance is noted. The Au and Ag bonded 1,4-dithiobenzene molecules exhibit marked difference in their resistance and conductance spectra. The conductance of the Ag-bonded molecule is calculated to be about 1.5 times larger than that bonded with Au.
Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya
2015-02-01
Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications.
NASA Astrophysics Data System (ADS)
Wang, Xiaoli; Hou, Dong; Zheng, Xiao; Yan, YiJing
2016-01-01
The magnetic anisotropy and Kondo phenomena in a mechanically stretched magnetic molecular junction are investigated by combining the density functional theory (DFT) and hierarchical equations of motion (HEOM) approach. The system is comprised of a magnetic complex Co(tpy-SH)2 sandwiched between adjacent gold electrodes, which is mechanically stretched in experiments done by Parks et al. [Science 328, 1370 (2010)]. The electronic structure and mechanical property of the stretched system are investigated via the DFT calculations. The HEOM approach is then employed to characterize the Kondo resonance features, based on the Anderson impurity model parameterized from the DFT results. It is confirmed that the ground state prefers the S = 1 local spin state. The structural properties, the magnetic anisotropy, and corresponding Kondo peak splitting in the axial stretching process are systematically evaluated. The results reveal that the strong electron correlations and the local magnetic properties of the molecule magnet are very sensitive to structural distortion. This work demonstrates that the combined DFT+HEOM approach could be useful in understanding and designing mechanically controlled molecular junctions.
NASA Astrophysics Data System (ADS)
Wang, Wei; Bhandari, Sagar; Yi, Wei; Bell, David; Westervelt, Robert; Kaxiras, Efthimios
2012-02-01
Ultra-thin membranes such as graphene[1] are of great importance for basic science and technology applications. Graphene sets the ultimate limit of thinness, demonstrating that a free-standing single atomic layer not only exists but can be extremely stable and strong [2--4]. However, both theory [5, 6] and experiments [3, 7] suggest that the existence of graphene relies on intrinsic ripples that suppress the long-wavelength thermal fluctuations which otherwise spontaneously destroy long range order in a two dimensional system. Here we show direct imaging of the atomic features in graphene including the ripples resolved using monochromatic aberration-corrected transmission electron microscopy (TEM). We compare the images observed in TEM with simulated images based on an accurate first-principles total potential. We show that these atomic scale features can be mapped through accurate first-principles simulations into high resolution TEM contrast. [1] Geim, A. K. & Novoselov, K. S. Nat. Mater. 6, 183-191, (2007). [2] Novoselov, K. S.et al. Science 306, 666-669, (2004). [3] Meyer, J. C. et al. Nature 446, 60-63, (2007). [4] Lee, C., Wei, X. D., Kysar, J. W. & Hone, J. Science 321, 385-388, (2008). [5] Nelson, D. R. & Peliti, L. J Phys-Paris 48, 1085-1092, (1987). [6] Fasolino, A., Los, J. H. & Katsnelson, M. I. Nat. Mater. 6, 858-861, (2007). [7] Meyer, J. C. et al. Solid State Commun. 143, 101-109, (2007).
NASA Astrophysics Data System (ADS)
Ikeda, Takashi; Boero, Mauro; Terakura, Kiyoyuki
2007-08-01
We studied the solvation structures of the divalent metal cations Mg2+ and Ca2+ in ambient water by applying a Car-Parrinello-based constrained molecular dynamics method. By employing the metal-water oxygen coordination number as a reaction coordinate, we could identify distinct aqua complexes characterized by structural variations of the first coordination shell. In particular, our estimated free-energy profile clearly shows that the global minimum for Mg2+ is represented by a rather stable sixfold coordination in the octahedral arrangement, in agreement with experiments. Conversely, for Ca2+ the free-energy curve shows several shallow local minima, suggesting that the hydration structure of Ca2+ is highly variable. Implications for water exchange reactions are also discussed.
First principles calculation of the mechanical compression of two organic molecular crystals.
Zerilli, Frank J; Kuklja, Maija M
2006-04-20
The mechanical compression curves for the organic molecular crystals 1,1-diamino-2,2-dinitroethylene and beta-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (beta-HMX) are calculated using the Hartree-Fock approximation to the solutions of the many-body Schrödinger equation for a periodic system as implemented in the computer program CRYSTAL. No correction was made for basis set superposition error. The equilibrium lattice parameters are reproduced to within 1% of reported experimental values. Pressure values on the isotherm also agree well with reported experimental values. To obtain accurate results, the relaxation of all the atomic coordinates as well as the lattice parameters under a fixed volume constraint was required.
First-principles and classical molecular dynamics simulation of shocked polymers
NASA Astrophysics Data System (ADS)
Mattsson, Thomas R.; Lane, J. Matthew D.; Cochrane, Kyle R.; Desjarlais, Michael P.; Thompson, Aidan P.; Pierce, Flint; Grest, Gary S.
2010-02-01
Density functional theory (DFT) molecular dynamics (MD) and classical MD simulations of the principal shock Hugoniot are presented for two hydrocarbon polymers, polyethylene (PE) and poly(4-methyl-1-pentene) (PMP). DFT results are in excellent agreement with experimental data, which is currently available up to 80 GPa. Further, we predict the PE and PMP Hugoniots up to 350 and 200 GPa, respectively. For comparison, we studied two reactive and two nonreactive interaction potentials. For the latter, the exp-6 interaction of Borodin showed much better agreement with experiment than OPLS. For the reactive force fields, ReaxFF displayed decidedly better agreement than AIREBO. For shocks above 50 GPa, only the DFT results are of high fidelity, establishing DFT as a reliable method for shocked macromolecular systems.
NASA Astrophysics Data System (ADS)
Sit, P. H.-L.; Marzari, Nicola
2005-05-01
The static and dynamical properties of heavy water have been studied at ambient conditions with extensive Car-Parrinello molecular-dynamics simulations in the canonical ensemble, with temperatures ranging between 325 and 400K. Density-functional theory, paired with a modern exchange-correlation functional (Perdew-Burke-Ernzerhof), provides an excellent agreement for the structural properties and binding energy of the water monomer and dimer. On the other hand, the structural and dynamical properties of the bulk liquid show a clear enhancement of the local structure compared to experimental results; a distinctive transition to liquidlike diffusion occurs in the simulations only at the elevated temperature of 400K. Extensive runs of up to 50ps are needed to obtain well-converged thermal averages; the use of ultrasoft or norm-conserving pseudopotentials and the larger plane-wave sets associated with the latter choice had, as expected, only negligible effects on the final result. Finite-size effects in the liquid state are found to be mostly negligible for systems as small as 32molecules per unit cell.
Solvation of Na^+ in water from first-principles molecular dynamics
NASA Astrophysics Data System (ADS)
White, J. A.; Schwegler, E.; Galli, G.; Gygi, F.
2000-03-01
We have carried out ab initio molecular dynamics (MD) simulations of the Na^+ ion in water with an MD cell containing a single alkali ion and 53 water molecules. The electron-electron and electron-ion interactions were modeled by density functional theory with a generalized gradient approximation for the exchange-correlation functional. The computed radial distribution functions, coordination numbers, and angular distributions are consistent with available experimental data. The first solvation shell contains 5.2±0.6 water molecules, with some waters occasionally exchanging with those of the second shell. The computed Na^+ hydration number is larger than that from calculations for water clusters surrounding an Na^+ ion, but is consistent with that derived from x-ray measurements. Our results also indicate that the first hydration shell is better defined for Na^+ than for K^+ [1], as indicated by the first minimum in the Na-O pair distribution function. [1] L.M. Ramaniah, M. Bernasconi, and M. Parrinello, J. Chem. Phys. 111, 1587 (1999). This work was performed for DOE under contract W-7405-ENG-48.
First principles study on the molecular structure and vibrational spectra of ketoprofen
NASA Astrophysics Data System (ADS)
Liu, Lekun; Gao, Hongwei
2012-11-01
The aim of this work was to compare the performance of different DFT methods at different basis sets in predicting geometry and vibration spectrum of ketoprofen. The molecular geometry and vibrational frequencies of ketoprofen have been calculated using five different density function theory (DFT) methods, including LSDA, B3LYP, mPW1PW91, B3PW91 and HCTH, with various basis sets, including 6-311G, 6-311+G, 6-311++G, 6-311+G (d, p) and 6-311++G (2d, 2p). The results indicate that mPW1PW91/6-311++G (2d, 2p) level is clearly superior to all the remaining density functional methods in predicting the bond lengths and bond angles of ketoprofen. Mean absolute deviations between the calculated harmonic and observed fundamental vibration frequencies for each method shows that LSDA/6-311G method is the best to predict vibrational spectra of ketoprofen comparing other DFT methods.
NASA Astrophysics Data System (ADS)
Mattsson, Ann E.; Mattsson, Thomas R.; Sandberg, Nils; Armiento, Rickard
2009-06-01
A fundamental understanding of thermodynamical properties like specific heat is necessary in order to model shock compression of condensed matter to high fidelity. It is therefore interesting that also central issues remain unsatisfactorily understood for technologically important body centered cubic metals like Mo. For example the long-standing question whether the strong increase of the specific heat of Mo close to the melting point is caused by a high (several percent) concentration of vacancies or by anharmonic lattice and electronic effects. Here we show, through density functional theory (DFT) molecular dynamics simulations of vacancy motion in Mo close to the melting point, using the new AM05 density functional, that a low (fractions of percent) concentration of vacancies does explain experimental observations of specific heat and self-diffusion. We furthermore quantify and discuss the origin of the anharmonicity as well as implications for modeling of shock-processes from an atomistic point of view. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy National Nuclear Security Administration under Contract No. DE-AC04-94AL85000.
Sergey N. Rashkeev; Eric S. Peterson
2011-11-01
Carbon dioxide (CO2)-induced plasticization can significantly decrease the gas separation performance of membranes in high-temperature or high pressure conditions, such as industrial methane (CH4) separations. In this paper, we investigated the crystalline phase of three polymers (polybenzimidazole (PBI), Bis(isobutylcarboxy)polybenzimidazole (PBI-Butyl), and KaptonTM) and interactions between gas molecules (CO2 and N2) and these polymers. A novel, molecular dynamics (MD) based, computational technique was employed to find unknown crystalline structures of these polymer materials. The interaction of CO2 and N2 gases with these crystals was studied by first-principles calculations and by classical MD simulations. The results showed that the packing structure and the interlayer coupling in polymer crystals determine the permeability and diffusivity of gas molecules. This methodology also allows prediction of plastic swelling in these materials caused by gas molecules absorbed in the polymer matrix.
Ion Association in AlCl3 Aqueous Solutions from Constrained First-Principles Molecular Dynamics
Cauet, Emilie L.; Bogatko, Stuart A.; Bylaska, Eric J.; Weare, John H.
2012-10-15
Ab initio molecular dynamics was used to investigate the ion pairing behavior between Cl- and the Al3+ ion in an aqueous AlCl3 solution containing 63 water molecules. A series of constrained simulations was carried out at 300 K for up to 16 ps each, by fixing the inter-nuclear separation (rAl-Cl) between the Al3+ ion and one of the Cl- ions. The calculated potential of mean force of the Al3+-Cl- ion pair shows a pronounced minimum at rAl-Cl = 2.3 Å corresponding to a contact ion pair (CIP). Two local minima assigned to solvent separated ion pairs (SSIP) are identified at rAl-Cl= 4.4 and 6.0 Å. The positions of the free energy minima coincide with the hydration shell intervals of the Al3+ cation suggesting that the Cl- ion is inclined to reside in regions of low concentration of waters, i.e. between the 1st and 2nd shells of Al3+ and between the 2nd shell and bulk. A detailed analysis of solvent structure around the Al3+ and Cl- ions as a function of rAl-Cl is presented. The results are compared to structure data from X-ray measurements and unconstrained AIMD simulations of single ions Al3+ and Cl- and AlCl3 solutions. The dipole moment of the water molecules inside the 1st and 2nd hydration shells of Al3+ and in the bulk region and those of the Clion were calculated as a function of rAl-Cl. Major changes in the electronic structure of the system result from the removal of Cl- from the 1st hydration shell of the Al3+ cation. Finally, two unconstrained AIMD simulations of aqueous AlCl3 solutions corresponding to CIP and SSIP configurations were performed (17 ps, 300 K). Only minor structural changes are observed in these systems, confirming their stability.
NASA Astrophysics Data System (ADS)
Yazyev, Oleg V.; Tavernelli, Ivano; Rothlisberger, Ursula; Helm, Lothar
2007-03-01
Understanding radiation-induced defect formation in carbon materials is crucial for nuclear technology and for the manufacturing of nanostructures with desired properties. Using first-principles molecular dynamics, we perform a systematic study of the nonequilibrium processes of radiation damage in graphite. Our study reveals a rich variety of defect structures (vacancies, interstitials, intimate interstitial-vacancy pairs, and in-plane topological defects) with formation energies of 5-15eV . We clarify the mechanisms underlying their creation and find unexpected preferences for particular structures. Possibilities of controlled defect-assisted engineering of nanostructures are analyzed. In particular, we conclude that the selective creation of two distinct low-energy intimate Frenkel pair defects can be achieved by using a 90-110keV electron beam irradiation.
Tsyshevsky, Roman; Sharia, Onise; Kuklja, Maija
2016-02-19
Our review presents a concept, which assumes that thermal decomposition processes play a major role in defining the sensitivity of organic energetic materials to detonation initiation. As a science and engineering community we are still far away from having a comprehensive molecular detonation initiation theory in a widely agreed upon form. However, recent advances in experimental and theoretical methods allow for a constructive and rigorous approach to design and test the theory or at least some of its fundamental building blocks. In this review, we analyzed a set of select experimental and theoretical articles, which were augmented by our own first principles modeling and simulations, to reveal new trends in energetic materials and to refine known existing correlations between their structures, properties, and functions. Lastly, our consideration is intentionally limited to the processes of thermally stimulated chemical reactions at the earliest stage of decomposition of molecules and materials containing defects.
Tsyshevsky, Roman; Sharia, Onise; Kuklja, Maija
2016-02-19
Our review presents a concept, which assumes that thermal decomposition processes play a major role in defining the sensitivity of organic energetic materials to detonation initiation. As a science and engineering community we are still far away from having a comprehensive molecular detonation initiation theory in a widely agreed upon form. However, recent advances in experimental and theoretical methods allow for a constructive and rigorous approach to design and test the theory or at least some of its fundamental building blocks. In this review, we analyzed a set of select experimental and theoretical articles, which were augmented by our ownmore » first principles modeling and simulations, to reveal new trends in energetic materials and to refine known existing correlations between their structures, properties, and functions. Lastly, our consideration is intentionally limited to the processes of thermally stimulated chemical reactions at the earliest stage of decomposition of molecules and materials containing defects.« less
Tsyshevsky, Roman V; Sharia, Onise; Kuklja, Maija M
2016-02-19
This review presents a concept, which assumes that thermal decomposition processes play a major role in defining the sensitivity of organic energetic materials to detonation initiation. As a science and engineering community we are still far away from having a comprehensive molecular detonation initiation theory in a widely agreed upon form. However, recent advances in experimental and theoretical methods allow for a constructive and rigorous approach to design and test the theory or at least some of its fundamental building blocks. In this review, we analyzed a set of select experimental and theoretical articles, which were augmented by our own first principles modeling and simulations, to reveal new trends in energetic materials and to refine known existing correlations between their structures, properties, and functions. Our consideration is intentionally limited to the processes of thermally stimulated chemical reactions at the earliest stage of decomposition of molecules and materials containing defects.
NASA Astrophysics Data System (ADS)
Torrent, Marc; Geneste, Gregory
2012-02-01
The low-temperature phases of dense hydrogen and deuterium have been investigated using first-principles path-integral molecular dynamics, a technique that we have recently implemented in the ABINIT code and that allows to account for the quantum fluctuations of atomic nuclei. A massively parallelized scheme is applied to produce trajectories of several tens of thousands steps using a 64-atom supercell and a Trotter number of 64. The so-called phases I, II and III are studied and compared to the structures proposed in the literature. The quantum fluctuations produce configurational disorder and are shown to systematically enhance the symmetry of the system: a continuous gain of symmetry in the angular density of probability of the molecules is found from classical particles to quantum D2 and finally to quantum H2. Particular emphasis is made on the ``broken-symmetry'' phase (phase II).
NASA Astrophysics Data System (ADS)
Cammarota, Chiara; Seoane, Beatriz
2016-11-01
As a guideline for experimental tests of the ideal glass transition (random-pinning glass transition, RPGT) that shall be induced in a system by randomly pinning particles, we performed first-principle computations within the hypernetted chain approximation and numerical simulations of a hard-sphere model of a glass former. We obtain confirmation of the expected enhancement of glassy behavior under the procedure of random pinning. We present the analytical phase diagram as a function of c and of the packing fraction ϕ , showing a line of RPGT ending in a critical point. We also obtain microscopic results on cooperative length scales characterizing medium-range amorphous order in hard-sphere glasses and indirect quantitative information on a key thermodynamic quantity defined in proximity to ideal glass transitions, the amorphous surface tension. Finally, we present numerical results of pair correlation functions able to differentiate the liquid and the glass phases, as predicted by the analytic computations.
Mallik, Bhabani S; Kuo, I-F William; Fried, Laurence E; Siepmann, J Ilja
2012-04-14
With the aim to understand the relatively high solubility of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), an important energetic material with a high degree of inter- and intra-molecular hydrogen bonding, in fluoride anion containing ionic liquids (ILs), first principles molecular dynamics simulations in the isobaric-isothermal ensemble were carried out for a system using hydrous tetramethylammonium fluoride as the prototypical solvent. Simulations initiated from both molecular TATB and its Meisenheimer complex (i.e., a σ-complex of the fluoride and the electrophilic ring of TATB) yield a Zundel-type complex where a proton is shared between an amino group and an F(-) ion, whereas the Meisenheimer complex is found to be only transiently stable. An analysis of the electronic structure probing the Wannier function centers supports the finding of a proton-sharing complex with a three-center four-electron like bond. The Zundel-type complex also yields an electronic absorption spectrum consistent with the experimentally observed color change. This study provides evidence that the remarkable solubility of otherwise hard-to-dissolve molecular crystals in ILs can be aided by chemical modification of the solute.
Tamura, Hiroyuki; Huix-Rotllant, Miquel; Burghardt, Irene; Olivier, Yoann; Beljonne, David
2015-09-04
Singlet excitons in π-stacked molecular crystals can split into two triplet excitons in a process called singlet fission that opens a route to carrier multiplication in photovoltaics. To resolve controversies about the mechanism of singlet fission, we have developed a first principles nonadiabatic quantum dynamical model that reveals the critical role of molecular stacking symmetry and provides a unified picture of coherent versus thermally activated singlet fission mechanisms in different acenes. The slip-stacked equilibrium packing structure of pentacene derivatives is found to enhance ultrafast singlet fission mediated by a coherent superexchange mechanism via higher-lying charge transfer states. By contrast, the electronic couplings for singlet fission strictly vanish at the C(2h) symmetric equilibrium π stacking of rubrene. In this case, singlet fission is driven by excitations of symmetry-breaking intermolecular vibrations, rationalizing the experimentally observed temperature dependence. Design rules for optimal singlet fission materials therefore need to account for the interplay of molecular π-stacking symmetry and phonon-induced coherent or thermally activated mechanisms.
Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations
Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei
2017-01-01
Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young’s modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young’s modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions. PMID:28195190
NASA Astrophysics Data System (ADS)
Tamura, Hiroyuki; Huix-Rotllant, Miquel; Burghardt, Irene; Olivier, Yoann; Beljonne, David
2015-09-01
Singlet excitons in π -stacked molecular crystals can split into two triplet excitons in a process called singlet fission that opens a route to carrier multiplication in photovoltaics. To resolve controversies about the mechanism of singlet fission, we have developed a first principles nonadiabatic quantum dynamical model that reveals the critical role of molecular stacking symmetry and provides a unified picture of coherent versus thermally activated singlet fission mechanisms in different acenes. The slip-stacked equilibrium packing structure of pentacene derivatives is found to enhance ultrafast singlet fission mediated by a coherent superexchange mechanism via higher-lying charge transfer states. By contrast, the electronic couplings for singlet fission strictly vanish at the C2 h symmetric equilibrium π stacking of rubrene. In this case, singlet fission is driven by excitations of symmetry-breaking intermolecular vibrations, rationalizing the experimentally observed temperature dependence. Design rules for optimal singlet fission materials therefore need to account for the interplay of molecular π -stacking symmetry and phonon-induced coherent or thermally activated mechanisms.
Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations
NASA Astrophysics Data System (ADS)
Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei
2017-02-01
Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young’s modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young’s modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.
First-principles molecular dynamics study of glassy GeS2: Atomic structure and bonding properties
NASA Astrophysics Data System (ADS)
Celino, M.; Le Roux, S.; Ori, G.; Coasne, B.; Bouzid, A.; Boero, M.; Massobrio, C.
2013-11-01
The structure of glassy GeS2 is studied in the framework of density functional theory, by using a fully self-consistent first-principles molecular dynamics (FPMD) scheme. A comparative analysis is performed with previous molecular dynamics data obtained within the Harris functional (HFMD) total energy approach. The calculated total neutron structure factor exhibits an unprecedented agreement with the experimental counterpart. In particular, the height of the first sharp diffraction peak (FSDP) improves considerably upon the HFMD results. Both the Ge and the S subnetworks are affected by a consistent number of miscoordinations, coexisting with the main tetrahedral structural motif. Glassy GeS2 features a short-range order quite similar to the one found in glassy GeSe2, a notable exception being the larger number of edge-sharing connections. An electronic structure localization analysis, based on the Wannier functions formalism, provides evidence of a more enhanced ionic character in glassy GeS2 when compared to glassy GeSe2.
Kuo, Jer-Lai; Kuhs, Werner F
2006-03-02
We have studied the structure of ice-VI by examining all ice-rule-allowed structures in its primary unit cell of 10 water molecules with first principles methods. A significant amount of static distortions in the oxygen positions away from their crystallographic positions are found, which is in good agreements with significant higher-order terms in the atomic displacement parameters obtained from X-ray and neutron diffraction data. Structural anomalies (such as exceptionally short OH bonds and small H-O-H angles) noted in conventional crystal structure refinements were not seen in our ab initio calculations, and it is evident that these structural anomalies arose from oversimplified models in which static distortions are not properly accounted for. Our results also show that the molecular geometry of water in ice-VI is similar to but richer than those in ice-Ih and ice-VII. Larger distortions in bond lengths/angles and correlation between the molecular geometry and the neighboring environments were found. Different proton-ordering schemes proposed in the literature were examined, and our calculations provide evidence in favor of a ferroelectric phase of the proton-ordered counterpart of ice-VI at about 80 K.
NASA Astrophysics Data System (ADS)
Banerjee, Paramita; Chandrakumar, K. R. S.; Das, G. P.
2016-05-01
To surmount the limitations of bulk MgH2 for the purpose of hydrogen storage, we report here, a detailed first principles density functional theory (DFT) based study on the structure and stability of neutral (Mgm) and positively charged (Mgm+) Mg nanoclusters of different sizes (m = 2, 4, 8 and 12) and their interaction with molecular hydrogen (H2). Our results demonstrate that H2 is weakly bound to the Mg nanoclusters through van der Waals interactions. Incorporation of Grimme's dispersion correction (D3) in the DFT based exchange-correlation functionals leads to improved accuracy of H2 interaction energy (IE) values that fall within an energy window (between physisorption and chemisorption) desirable for hydrogen storage. Energy decomposition analysis reveals the significance of polarization energy for these Mg-H2 binding. Ab-initio molecular dynamics simulation shows that complete dehydrogenation from these Mg nanoclusters occur at ∼100 °C which is a significant improvement over bulk MgH2 (∼300 °C).
Bauchy, M.; Kachmar, A.; Micoulaut, M.
2014-11-21
The structural, vibrational, electronic, and dynamic properties of amorphous and liquid As{sub x}Se{sub 1-x} (0.10
Gu, Bin; Smyth, Maeve; Kohanoff, Jorge
2014-11-28
Using first-principles molecular dynamics simulations, we have investigated the notion that amino acids can play a protective role when DNA is exposed to excess electrons produced by ionizing radiation. In this study we focus on the interaction of glycine with the DNA nucleobase thymine. We studied thymine-glycine dimers and a condensed phase model consisting of one thymine molecule solvated in amorphous glycine. Our results show that the amino acid acts as a protective agent for the nucleobase in two ways. If the excess electron is initially captured by the thymine, then a proton is transferred in a barrier-less way from a neighboring hydrogen-bonded glycine. This stabilizes the excess electron by reducing the net partial charge on the thymine. In the second mechanism the excess electron is captured by a glycine, which acts as a electron scavenger that prevents electron localization in DNA. Both these mechanisms introduce obstacles to further reactions of the excess electron within a DNA strand, e.g. by raising the free energy barrier associated with strand breaks.
Furlan, Sara; La Penna, Giovanni
2012-01-01
The recent discovery of a model compounds of [NiFe] hydrogenase that catalyzes the heterolytic cleavage of the H(2) molecule into a proton and a stable hydride in water solution under room conditions opened up the possibility to understand the mechanism of H(2) uptake by this peculiar class of enzymes. The simplest model compound belongs to the class of NiRu bimetallic cationic complexes mimicking, in water solution and at room conditions, the hydrogenase active site. By using first-principles molecular dynamics computer simulations, in the Car-Parrinello scheme, we investigated models including the water solvent and nitrate counterions. Several simulations, starting from different initial configurations, provided information on the first step of the H(2) cleavage: (1) the pathway of H(2) approach towards the active site; (2) the role of the ruthenium-bonded water molecule in providing a base that extracts the proton from the activated H(2) molecule; (3) the minor role of Ni in activating the H(2) molecule and its role in stabilizing the hydride produced. © SBIC 2011
Ong, Mitchell T.; Verners, Osvalds; Draeger, Erik W.; van Duin, Adri C. T.; Lordi, Vincenzo; Pask, John E.
2014-12-19
We report that lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF _{$\\bar{6}$} anion. Li^{+} prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li^{+} solvation. Corresponding analysis for the PF_{ $\\bar{6}$} anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. In conclusion, these results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.
Ong, Mitchell T.; Verners, Osvalds; Draeger, Erik W.; ...
2014-12-19
We report that lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF more » $$\\bar{6}$$ anion. Li+ prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li+ solvation. Corresponding analysis for the PF $$\\bar{6}$$ anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. In conclusion, these results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.« less
NASA Astrophysics Data System (ADS)
Kong, Xiang-Ping; Wang, Juan
2016-12-01
The adsorption behavior of Cu(II) on the basal hydroxylated kaolinite(001) surface in aqueous environment was investigated by first-principles calculations and molecular dynamics simulations. Structures of possible monodentate and bidentate inner-sphere adsorption complexes of Cu(II) were examined, and the charge transfer and bonding mechanism were analyzed. Combining the binding energy of complex, the radial distribution function of Cu(II) with oxygen and the extended X-ray absorption fine structure data, monodentate complex on site of surface oxygen with "upright" hydrogen and bidentate complex on site of two oxygens (one with "upright" hydrogen and one with "lying" hydrogen) of single Al center have been found to be the major adsorption species of Cu(II). Both adsorption species are four-coordinated with a square planar geometry. The distribution of surface hydroxyls with "lying" hydrogen around Cu(II) plays a key role in the structure and stability of adsorption complex. Upon the Mulliken population analysis and partial density of states, charge transfer occurs with Cu(II) accepting some electrons from both surface oxygens and aqua oxygens, and the bonding Cu 3d-O 2p state filling is primarily responsible for the strong covalent interaction of Cu(II) with surface oxygen.
Zheng, X. H. Hao, H.; Lan, J.; Wang, X. L.; Shi, X. Q.; Zeng, Z.
2014-08-21
The electronic transport properties of molecular bridges constructed by C{sub 60} and B{sub 80} molecules which have the same symmetry are investigated by first principles calculations combined with a non-equilibrium Green's function technique. It is found that, like C{sub 60}, monomer B{sub 80} is a good conductor arising from the charge transfer from the leads to the molecule, while the dimer (B{sub 80}){sub 2} and (C{sub 60}){sub 2} are both insulators due to the potential barrier formed at the molecule-molecule interface. Our further study shows that, although both the homogeneous dimer (B{sub 80}){sub 2} and (C{sub 60}){sub 2} display poor conductivity, the heterogeneous dimer B{sub 80}C{sub 60} shows a very high conductance as a result from the decreased HOMO-LUMO gap and the excess charge redistribution. Finally, we find that the conductivity of both (B{sub 80}){sub 2} and (C{sub 60}){sub 2} can be significantly improved by electron doping, for example, by doping C in (B{sub 80}){sub 2} and doping N in (C{sub 60}){sub 2}.
NASA Astrophysics Data System (ADS)
Zhang, Chi; Liu, Xiandong; Lu, Xiancai; He, Mengjia; Jan Meijer, Evert; Wang, Rucheng
2017-04-01
Aiming at an atomistic mechanism of heavy metal cation complexing on clay surfaces, we carried out systematic first principles molecular dynamics (FPMD) simulations to investigate the structures, free energies and acidity constants of Ni(II) complexes formed on edge surfaces of 2:1 phyllosilicates. Three representative complexes were studied, including monodentate complex on the tbnd SiO site, bidentate complex on the tbnd Al(OH)2 site, and tetradentate complex on the octahedral vacancy where Ni(II) fits well into the lattice. The complexes structures were characterized in detail. Computed free energy values indicate that the tetradentate complex is significantly more stable than the other two. The calculated acidity constants indicate that the tetradentate complex can get deprotonated (pKa = 8.4) at the ambient conditions whereas the other two hardly deprotonate due to extremely high pKa values. By comparing with the 2 Site Protolysis Non Electrostatic Surface Complexation and Cation Exchange (2SPNE SC/CE) model, the vacant site has been assigned to the strong site and the other two to the weak site, respectively. Thus a link has been built between atomistic simulations and macroscopic experiments and it is deduced that this should also apply to other heavy metal cations based on additional simulations of Co(II) and Cu(II) and previous simulations of Fe(II) and Cd(II)). This study forms a physical basis for understanding the transport and fixation of heavy metal elements in many geologic environments.
NASA Astrophysics Data System (ADS)
He, Yang; Chen, Changfeng; Yu, Haobo; Lu, Guiwu
2017-01-01
Formation of the double-layer electric field and capacitance of the water-metal interface is of significant interest in physicochemical processes. In this study, we perform first- principles molecular dynamics simulations on the water/Pt(111) interface to investigate the temperature dependence of the compact layer electric field and capacitance based on the calculated charge densities. On the Pt (111) surface, water molecules form ice-like structures that exhibit more disorder along the height direction with increasing temperature. The Osbnd H bonds of more water molecules point toward the Pt surface to form Ptsbnd H covalent bonds with increasing temperature, which weaken the corresponding Osbnd H bonds. In addition, our calculated capacitance at 300 K is 15.2 mF/cm2, which is in good agreement with the experimental results. As the temperature increases from 10 to 450 K, the field strength and capacitance of the compact layer on Pt (111) first increase and then decrease slightly, which is significant for understanding the water/Pt interface from atomic level.
NASA Astrophysics Data System (ADS)
Kohanoff, Jorge; Artacho, Emilio
2008-12-01
We first present results of first-principles molecular dynamics simulations of the passage of Carbon projectiles through water in the liquid state in the adiabatic regime, where the electrons are always in the instantaneous ground state. We study a range of projectile velocities up to the estimated upper limit for the adiabatic approximation and analyze the different types of collision events. We show that for high projectile velocities collisions are mostly binary, but at lower velocities most trajectories exhibit a continuous energy loss to the medium, which cannot be properly described as a sequence of independent binary collisions. For the slowest projectiles we observe the formation of new chemical species such as hydronium, H5O2+ and hydrogen peroxide. When C-atoms are completely stopped, then we also see the formation of species like formic acid. By analyzing the generation of secondary fragments, we observe that these are mostly hyperthermal and their spatial rate of generation increases with decreasing projectile energy. The two most numerous species are H and OH. In the second part we study, via electronic dynamics with fixed nuclei, the opposite regime of very fast protons producing only electronic excitation in ice, under channeling conditions. We observe the existence of a threshold velocity for electronic excitation of about 0.2 a.u. By monitoring the rate of increase of the total energy, we calculate the electronic stopping power.
Choe, Yoong-Kee; Tsuchida, Eiji; Ikeshoji, Tamio; Yamakawa, Shunsuke; Hyodo, Shi-Aki
2009-05-28
First-principles molecular dynamics simulations have been carried out to investigate the nature of proton dynamics in Nafion, a representative polymer electrolyte membrane (PEM) widely used in PEM fuel cells. From the trajectories of the simulations, diffusion coefficients for the protonic defects were calculated to be 0.3 x 10(-5) cm(2) s(-1) and 7.1 x 10(-5) cm(2) s(-1) for lambda = 4.25 and 12.75, respectively, where lambda denotes hydration levels inside Nafion defined as a number of water molecules per sulfonic group. Our simulations show that proton hopping probability does not depend much on the water content inside Nafion. This finding indicates that the classical vehicular (or en masse) diffusion model, which has been employed to account for the slow diffusion process of protons in low water-content Nafion, is an oversimplification and does not correctly describe proton dynamics. Furthermore, it is found that difference in the value of the proton diffusion coefficient with respect to water content inside Nafion is related to the different character of proton hopping occurring in the water hydrogen bond network. When the water content is low, the proton hopping occurs in a manner that does not contribute constructively to proton mobility, while when the water content is high, it occurs in a manner which is beneficial to overall proton mobility. Such a different nature of proton hoppings arises mainly from the difference in the connectivity of water hydrogen bond network. Our results broadly support earlier simulation studies and provide the molecular level origin of properties arising from the proton dynamics in Nafion.
Han, Yong; Evans, James W.
2015-10-27
Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C6-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom in the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ~0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. Furthermore, this in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001).
Han, Yong; Evans, James W.
2015-10-28
Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C{sub 6}-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom in the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ∼0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. This in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001)
Han, Yong; Evans, James W.
2015-10-27
Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C6-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom inmore » the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ~0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. Furthermore, this in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001).« less
Zhang, Yigang; Yin, Qing-Zhu
2012-01-01
Carbon (C) is one of the candidate light elements proposed to account for the density deficit of the Earth’s core. In addition, C significantly affects siderophile and chalcophile element partitioning between metal and silicate and thus the distribution of these elements in the Earth’s core and mantle. Derivation of the accretion and core–mantle segregation history of the Earth requires, therefore, an accurate knowledge of the C abundance in the Earth’s core. Previous estimates of the C content of the core differ by a factor of ∼20 due to differences in assumptions and methods, and because the metal–silicate partition coefficient of C was previously unknown. Here we use two-phase first-principles molecular dynamics to derive this partition coefficient of C between liquid iron and silicate melt. We calculate a value of 9 ± 3 at 3,200 K and 40 GPa. Using this partition coefficient and the most recent estimates of bulk Earth or mantle C contents, we infer that the Earth’s core contains 0.1–0.7 wt% of C. Carbon thus plays a moderate role in the density deficit of the core and in the distribution of siderophile and chalcophile elements during core–mantle segregation processes. The partition coefficients of nitrogen (N), hydrogen, helium, phosphorus, magnesium, oxygen, and silicon are also inferred and found to be in close agreement with experiments and other geochemical constraints. Contents of these elements in the core derived from applying these partition coefficients match those derived by using the cosmochemical volatility curve and geochemical mass balance arguments. N is an exception, indicating its retention in a mantle phase instead of in the core. PMID:23150591
Zhang, Yigang; Yin, Qing-Zhu
2012-11-27
Carbon (C) is one of the candidate light elements proposed to account for the density deficit of the Earth's core. In addition, C significantly affects siderophile and chalcophile element partitioning between metal and silicate and thus the distribution of these elements in the Earth's core and mantle. Derivation of the accretion and core-mantle segregation history of the Earth requires, therefore, an accurate knowledge of the C abundance in the Earth's core. Previous estimates of the C content of the core differ by a factor of ∼20 due to differences in assumptions and methods, and because the metal-silicate partition coefficient of C was previously unknown. Here we use two-phase first-principles molecular dynamics to derive this partition coefficient of C between liquid iron and silicate melt. We calculate a value of 9 ± 3 at 3,200 K and 40 GPa. Using this partition coefficient and the most recent estimates of bulk Earth or mantle C contents, we infer that the Earth's core contains 0.1-0.7 wt% of C. Carbon thus plays a moderate role in the density deficit of the core and in the distribution of siderophile and chalcophile elements during core-mantle segregation processes. The partition coefficients of nitrogen (N), hydrogen, helium, phosphorus, magnesium, oxygen, and silicon are also inferred and found to be in close agreement with experiments and other geochemical constraints. Contents of these elements in the core derived from applying these partition coefficients match those derived by using the cosmochemical volatility curve and geochemical mass balance arguments. N is an exception, indicating its retention in a mantle phase instead of in the core.
Assary, Rajeev S.; Zhang, Lu; Huang, Jinhua; ...
2016-06-14
First-principles simulations are performed to gain molecular level insights into the factors affecting the stability of seven 1,4-dimethoxybenzene (DMB) derivatives. These molecules are potential catholyte candidates for nonaqueous redox flow battery systems. Computations are performed to predict oxidation potentials in various dielectric mediums, intrinsic-reorganization energies, and structural changes of these representative catholyte molecules during the redox process. In order to understand the stability of the DMB-based radical cations, the thermodynamic feasibility of the following reactions is computed using density functional theory: (a) deprotonation, (b) dimerization, (c) hydrolysis, and (d) demethylation. The computations indicate that radical cations of the 2,3-dimethyl andmore » 2,5-dimethyl derivatives are the most stable among the DMB derivatives considered in this study. In the presence of solvents with high-proton solvating ability (water, DMSO, acetonitrile), degradation of cation radical occurring via deprotonation is the most likely mechanism. In the presence of solvents such as propylene carbonate (PC), demethylation was found to be the most likely reaction that causes degradation of radical cations. From the computed enthalpy of activation (Delta H-double dagger) for a demethylation reaction in PC, the 2,5-dimethyl DMB cation radical would exhibit better kinetic stability in comparison to the other candidates. Finally, this investigation suggests that computational studies of structural properties such as redox potentials, reorganization energies, and the computed reaction energetics (deprotonation and demethylation) of charged species can be used to predict the relative stability of a large set of molecules required for the discovery of novel redox active materials for flow battery applications« less
NASA Astrophysics Data System (ADS)
Huang, F.; Qi, Y.; Liu, X.; He, L.
2016-12-01
Stable isotopes can be fractionated by kinetic chemical diffusion because diffusion coefficients (D) of isotopes are mass-dependent. Diffusive isotopic fractionation recorded in rocks and minerals provide unique temporal constrains on geological processes. The mass dependence of D can be described in the form of Di/Dj= (mj/mi)β, where m denotes masses of isotope i and j, and β is an emperical parameter used to quantify the diffusive transport of isotopes [1]. β values can be estimated by experimental calibration and observation of natural samples, which are still rarely reported because it is challenging to precisely quantify the boundary conditions of diffusion processes [2,3,4]. Recent advances in computation technique provide a new way to theoretically calculate β values. For instance, classical molecular dynamics with empirical potential have been used to simulate interactions between atoms and estimate β of Mg isotopes in MgSiO3 melt [3]. Here, to further consider the effect of bonding and electron properties on β values, we apply first-principles Born-Oppenheimer Molecular Dynamics and pseudo-isotope methods (assuming mj/mi = 1/24, 1/4, 2, and 5) to estimate β for MgSiO3 and Mg2SiO4 melts. Our calculation shows that β of Mg isotopes with pseudo-mass ratios are consistent, indicating the reliability of the pseudo-isotope method. For MgSiO3 melt, β is 0.18 at 4000K and 0 GPa, higher than the value calculatedusing molecular dynamics simulations (0.135) [3]. For Mg2SiO4 melt at 0 GPa, β values are: 0.23 ± 0.04 at 2300K, 0.24 ± 0.07 at 3000K, and 0.24 ± 0.01 at 4000K. Notably, β of MgSiO3 and Mg2SiO4 melts are significantly higher than the value determined by diffusion experiments (0.05) [2]. These results indicate that β values are not sensitive to temperature, but dependent on melt composition.
NASA Astrophysics Data System (ADS)
Wang, J.; Chen, B.
2016-12-01
atomistic scale structure and dynamics on the calculated properties. Such understanding provides invaluable inputs in optimizing the first-principles molecular dynamics simulations. Based on well-benchmarked methods, the liquid properties were calculated to the core pressures.
NASA Astrophysics Data System (ADS)
Shao, Lina; Zhao, Jingfen; Cui, Bin; Fang, Changfeng; Liu, Desheng
2017-06-01
We investigate the electronic transport properties of a molecular motor as an optical molecular switch by using the non-equilibrium Green's function formalism combined with first-principles density functional theory. The two main forms of this molecule during the 360° rotation, named the anti-folded isomer and the syn-folded isomer, have shown a consistent difference in the current. The current of the syn-folded isomer is larger than that of the anti-folded isomer, meaning that the conductivity of the molecules alters four times within a rotary cycle. The merit of the photo-induced conductivity tuning makes the molecule a promising candidate for optical molecular switches.
NASA Astrophysics Data System (ADS)
Pokrovski, Gleb S.; Roux, Jacques; Ferlat, Guillaume; Jonchiere, Romain; Seitsonen, Ari P.; Vuilleumier, Rodolphe; Hazemann, Jean-Louis
2013-04-01
The molecular structure and stability of species formed by silver in aqueous saline solutions typical of hydrothermal settings were quantified using in situ X-ray absorption spectroscopy (XAS) measurements, quantum-chemical modeling of near-edge absorption spectra (XANES) and extended fine structure spectra (EXAFS), and first-principles molecular dynamics (FPMD). Results show that in nitrate-bearing acidic solutions to at least 200 °C, silver speciation is dominated by the hydrated Ag+ cation surrounded by 4-6 water molecules in its nearest coordination shell with mean Ag-O distances of 2.32 ± 0.02 Å. In NaCl-bearing acidic aqueous solutions of total Cl concentration from 0.7 to 5.9 mol/kg H2O (m) at temperatures from 200 to 450 °C and pressures to 750 bar, the dominant species are the di-chloride complex AgCl2- with Ag-Cl distances of 2.40 ± 0.02 Å and Cl-Ag-Cl angle of 160 ± 10°, and the tri-chloride complex AgCl32- of a triangular structure and mean Ag-Cl distances of 2.60 ± 0.05 Å. With increasing temperature, the contribution of the tri-chloride species decreases from ˜50% of total dissolved Ag in the most concentrated solution (5.9m Cl) at 200 °C to less than 10-20% at supercritical temperatures for all investigated solutions, so that AgCl2- becomes by far the dominant Ag-bearing species at conditions typical of hydrothermal-magmatic fluids. Both di- and tri-chloride species exhibit outer-sphere interactions with the solvent as shown by the detection, using FPMD modeling, of H2O, Cl-, and Na+ at distances of 3-4 Å from the silver atom. The species fractions derived from XAS and FPMD analyses, and total AgCl(s) solubilities, measured in situ in this work from the absorption edge height of XAS spectra, are in accord with thermodynamic predictions using the stability constants of AgCl2- and AgCl32- from Akinfiev and Zotov (2001) and Zotov et al. (1995), respectively, which are based on extensive previous AgCl(s) solubility measurements. These data
Ufimtsev, Ivan S; Martinez, Todd J
2009-10-13
We demonstrate that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree-Fock energy + gradient calculations. Such performance makes it possible to run large scale Hartree-Fock and Density Functional Theory calculations, which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born-Oppenheimer molecular dynamics simulations are performed on two molecular systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid molecule solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio molecular dynamics simulation on a single desktop computer for these systems.
Priest, Chad; Li, Bo; Jiang, De-En
2017-08-21
Exploring the structural interplay of ligands with uranyl can provide important knowledge for technology advances in uranium extraction from seawater. However, obtaining such chemical information is not an easy endeavor experimentally. From a plethora of computational methods, this work provides both microscopic insights and free-energy profiles of the binding between uranyl and deprotonated glutardiamidoxime (H2B) for which experimental structural information is not available, despite H2B being an important model ligand with an open-chain conformation for understanding aqueous uranium extraction chemistry. In our molecular dynamics (MD) simulations, we explicitly accounted for the water solvent as well as the Na(+) and Cl(-) ions. We found that hydrogen bonding plays a critical role in dictating the binding configurations of B(2-) and HB(-) with uranyl. Simulated free energies of sequential ligand binding to form UO2B, [UO2B2](2-), and [UO2(HB)B](-) show very good agreement with the experimental values, lending support to our structural insights. The potential of mean force simulations showed the common feature of an important intermediate state where one end of the ligand binds to uranyl while the other end is solvated in water. Bringing the loose end of the ligand to bind with uranyl has a free-energy barrier of 15-25 kJ/mol. The present work shows that the combined simulation approach can reveal key structural and thermodynamic insights toward a better understanding of aqueous complexation chemistry for uranium extraction from the sea.
Drisdell, Walter S.; Leppert, Linn; Sutter-Fella, Carolin M.; ...
2017-04-20
In this paper, we combine high-energy resolution fluorescence detection (HERFD) X-ray absorption spectroscopy (XAS) measurements with first-principles density functional theory (DFT) calculations to provide a molecular-scale understanding of local structure, and its role in defining optoelectronic properties, in CH3NH3Pb(I1–xBrx)3 perovskites. The spectra probe a ligand field splitting in the unoccupied d states of the material, which lie well above the conduction band minimum and display high sensitivity to halide identity, Pb-halide bond length, and Pb-halide octahedral tilting, especially for apical halide sites. The spectra are also sensitive to the organic cation. We find that the halides in these mixed compositionsmore » are randomly distributed, rather than having preferred octahedral sites, and that thermal tilting motions dominate over any preferred structural distortions as a function of halide composition. Finally, these findings demonstrate the utility of the combined HERFD XAS and DFT approach for determining structural details in these materials and connecting them to optoelectronic properties observed by other characterization methods.« less
Park, Jong Hoo; Liu, Tianyuan; Kim, Ki Chul; Lee, Seung Woo; Jang, Seung Soon
2017-04-10
The thermodynamic and electrochemical redox properties for a set of ketone derivatives of phenalenyl and anthracene have been investigated to assess their potential application for positive electrode materials in rechargeable lithium-ion batteries. Using first-principles DFT, it was found that 1) the thermodynamic stabilities of ketone derivatives are strongly dependent on the distribution of the carbonyl groups and 2) the redox potential is increased when increasing the number of the incorporated carbonyl groups. The highest values are 3.93 V versus Li/Li(+) for the phenalenyl derivatives and 3.82 V versus Li/Li(+) for the anthracene derivatives. It is further highlighted that the redox potential of an organic molecule is also strongly correlated with its spin state in the thermodynamically stable form. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Son, Chang Yun; McDaniel, Jesse G; Schmidt, J R; Cui, Qiang; Yethiraj, Arun
2016-04-14
Molecular dynamics study of ionic liquids (ILs) is a challenging task. While accurate fully polarizable atomistic models exist, they are computationally too demanding for routine use. Most nonpolarizable atomistic models predict diffusion constants that are much lower than experiment. Scaled charge atomistic models are cost-effective and give good results for single component ILs but are in qualitative error for the phase behavior of mixtures, due to inaccurate prediction of the IL cohesive energy. In this work, we present an alternative approach for developing computationally efficient models that importantly preserves both the correct dynamics and cohesive energy of the IL. Employing a "top-down" approach, a hierarchy of coarse-grained models for BMIM(+)BF4(-) are developed by systematically varying the polarization/atomic resolution of the distinct functional groups. Parametrization is based on symmetry-adapted perturbation theory (SAPT) calculations involving the homomolecular species; all cross interactions are obtained from mixing rules, and there are no adjustable parameters. We find that enhanced dynamics from a united-atom description counteracts the effect of reduced polarization, enabling computationally efficient models that exhibit quantitative agreement with experiment for both static and dynamic properties. We give explicit suggestions for reduced-description models that are computationally more efficient, more accurate, and more fundamentally sound than existing nonpolarizable atomistic models.
Boero, Mauro; Park, Jung Mee; Hagiwara, Yohsuke; Tateno, Masaru
2007-09-12
First principles molecular dynamics simulations performed on a fully solvated RNA model structure allowed us to investigate the mechanism for enzymatic cleavage reactions, in vitro, of RNA enzymes (ribozymes). The concerted action of two metal catalysts turns out to be the most efficient way to promote, on the one hand, the proton abstraction from 2(')-OH that triggers the nucleophilic attack and, on the other hand, the cleavage of the P-O(5(')) bond. In fact, the elimination of one of the two metal cations leads to an increase in the activation energy of the reaction. The simulated pathway shows that an OH(-) in the coordination shell of the Mg(2+) close to O(2(')) promotes the initial proton abstraction and prevents its transfer to the ribozyme. This suggests that, in a real ribozyme, the double-metal-ion reaction mechanism is preferred with respect to single-metal-ion mechanisms either in the presence or in absence of the OH(-) anion. Finally, an insight into the importance of hybrid quantum mechanics/molecular mechanics (QM/MM) schemes is discussed in view of the modelling of a realistic system carrying all the features of a true ribozyme.
NASA Astrophysics Data System (ADS)
Pal, Partha Pratim; Pati, Ranjit
2010-07-01
We report a first-principles study of quantum transport in a prototype two-terminal device consisting of a molecular nanowire acting as an inter-connect between two gold electrodes. The wire is composed of a series of bicyclo[1.1.1]pentane (BCP) cage-units. The length of the wire (L) is increased by sequentially increasing the number of BCP cage units in the wire from 1 to 3. A two terminal model device is made out of each of the three wires. A parameter free, nonequilibrium Green’s function approach, in which the bias effect is explicitly included within a many body framework, is used to calculate the current-voltage characteristics of each of the devices. In the low bias regime that is considered in our study, the molecular devices are found to exhibit Ohmic behavior with resistances of 0.12, 1.4, and 6.5μΩ for the wires containing one, two, and three cages respectively. Thus the conductance value, Gc , which is the reciprocal of resistance, decreases as e-βL with a decay constant (β) of 0.59Å-1 . This observed variation of conductance with the length of the wire is in excellent agreement with the earlier reported exponential decay feature of the electron transfer rate predicted from the electron transfer coupling matrix values obtained using the two-state Marcus-Hush model and the Koopman’s theorem approximation. The downright suppression of the computed electrical current for a bias up to 0.4 V in the longest wire can be exploited in designing a three terminal molecular transistor; this molecular wire could potentially be used as a throttle to avoid leakage gate current.
Seko, Atsuto; Koyama, Yukinori; Matsumoto, Akifumi; Tanaka, Isao
2012-11-28
Bismuth oxide, Bi(2)O(3), has a cubic structure (δ-phase) at high temperature. High oxygen conductivity of δ-Bi(2)O(3) should be closely related to disordering of the oxygen sublattice. In order to reconstruct the disordered structure in the crystal using first-principles molecular dynamics (FPMD), a sufficiently long simulation time is essentially required. In this study, the FPMD simulation up to 1 ns is performed with special interest given to the convergence of the average structure and the oxygen diffusivity with respect to the simulation time. The obtained average structure and the oxygen diffusivity are in good agreement with those obtained by experimental analysis.
NASA Astrophysics Data System (ADS)
Deekshitha, M.; Nagarajan, V.; Chandiramouli, R.
2015-11-01
The electronic transport properties and trimethylamine adsorption (TMA) characteristics on MoO3 molecular device are explored using density functional theory (DFT) method via GGA/PBE exchange correlation functional. The density of states spectrum visualizes the localization of charges in MoO3 molecular device upon adsorption of TMA. The transport properties of MoO3 molecular device with adsorption of TMA are studied in terms of transmission spectrum. I-V characteristics of MoO3 molecular device reveal the change in the current upon adsorption of TMA. The present work gives an understanding on MoO3 molecular device, which can be used as an efficient TMA sensor.
Migaou, Amani; Sarpi, Brice; Guiltat, Mathilde; Payen, Kevin; Daineche, Rachid; Landa, Georges; Vizzini, Sébastien; Hémeryck, Anne
2016-05-21
First principles calculations, scanning tunneling microscopy, and Auger spectroscopy experiments of the adsorption of Mg on Ag(111) substrate are conducted. This detailed study reveals that an atomic scale controlled deposition of a metallic Mg monolayer perfectly wets the silver substrate without any alloy formation at the interface at room temperature. A liquid-like behavior of the Mg species on the Ag substrate is highlighted as no dot formation is observed when coverage increases. Finally a layer-by-layer growth mode of Mg on Ag(111) can be predicted, thanks to density functional theory calculations as observed experimentally.
Callsen, Martin; Sodeyama, Keitaro; Futera, Zdeněk; Tateyama, Yoshitaka; Hamada, Ikutaro
2017-01-12
The solvation and desolvation of the Li ion play a crucial role in the electrolytes of Li based secondary batteries, and their understanding at the microscopic level is of great importance. Oligoether (glyme) based electrolytes have attracted much attention as electrolytes used in Li based secondary batteries, such as Li-ion, Li-S, and Li-O2 batteries. However, the solvation structure of the Li ion in glyme based electrolytes has not been fully clarified yet. We present a computational study on the solvation structure of lithium ions in the mixture of triglyme and lithium bis(trifluoromethylsulfonyl)-amide (LiTFSA) by means of molecular orbital and molecular dynamics calculations based on density functional theory. We found that, in the electrolyte solution composed of the equimolar mixture of triglyme and LiTFSA, lithium ions are solvated mainly by crown-ether-like curled triglyme molecules and in direct contact with an TFSA anion. We also found the aggregate formed with Li ion and TFSA anions and/or triglyme molecule(s) is equally stable, which has not been reported in the previous classical molecular dynamics simulations, suggesting that in reality a small fraction of Li ions form aggregates and they might have a significant impact on the Li ion transport. Our results demonstrate the importance of performing electronic structure based molecular dynamics of electrolyte solution to clarify the detailed solvation structure of the Li ion.
Multi-scale First-Principles Modeling of Three-Phase System of Polymer Electrolyte Membrane Fuel Cel
Brunello, Giuseppe; Choi, Ji; Harvey, David; Jang, Seung
2012-07-01
The three-phase system consisting of Nafion, graphite and platinum in the presence of water is studied using molecule dynamics simulation. The force fields describing the molecular interaction between the components in the system are developed to reproduce the energies calculated from density functional theory modeling. The configuration of such complicated three-phase system is predicted through MD simulations. The nanophase-segregation and transport properties are investigated from the equilibrium state. The coverage of the electrolyte on the platinum surface and the dissolution of oxygen are analyzed.
Zipoli, Federico; Car, Roberto; Cohen, Morrel H; Selloni, Annabella
2010-11-09
Bacterial di-iron hydrogenases produce hydrogen efficiently from water. Accordingly, we have studied by first-principles molecular-dynamics simulations (FPMD) electrocatalytic hydrogen production from acidified water by their common active site, the [FeFe]H cluster, extracted from the enzyme and linked directly to the (100) surface of a pyrite electrode. We found that the cluster could not be attached stably to the surface via a thiol link analogous to that which attaches it to the rest of the enzyme, despite the similarity of the (100) pyrite surface to the Fe4S4 cubane to which it is linked in the enzyme. We report here a systematic sequence of modifications of the structure and composition of the cluster devised to maintain the structural stability of the pyrite/cluster complex in water throughout its hydrogen production cycle, an example of the molecular design of a complex system by FPMD.
NASA Astrophysics Data System (ADS)
Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele
2016-09-01
Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.
Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele
2016-09-09
Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.
NASA Astrophysics Data System (ADS)
Tamura, Tomoyuki; Kohyama, Masanori; Ogata, Shuji
2017-07-01
We performed a first-principles molecular dynamics (FPMD) simulation of the interfacial reactions between a LiCoO2 electrode and a liquid ethylene carbonate (EC) electrolyte. For configurations during the FPMD simulation, we also performed first-principles Co K-edge x-ray absorption near-edge structure (XANES) simulations, which can properly reproduce the bulk and surface spectra of LiCoO2. We observed strong absorption of an EC molecule on the LiCoO2 {110} surface, involving ring opening of the molecule, bond formation between oxygen atoms in the molecule and surface Co ions, and emission of one surface Li ion, while all the surface Co ions remain Co3 +. The surface Co ions having the bond with an oxygen atom in the molecule showed remarkable changes in simulated K-edge spectra which are similar to those of the in situ observation under electrolyte soaking [D. Takamatsu et al., Angew. Chem., Int. Ed. 51, 11597 (2012), 10.1002/anie.201203910]. Thus, the local environmental changes of surface Co ions due to the reactions with an EC molecule can explain the experimental spectrum changes.
NASA Astrophysics Data System (ADS)
Srivastava, Anurag; Santhibhushan, B.; Sharma, Vikash; Kaur, Kamalpreet; Shahzad Khan, Md.; Marathe, Madura; De Sarkar, Abir; Shahid Khan, Mohd.
2016-04-01
We have investigated the modeling of boron-substituted molecular single-electron transistor (SET), under the influence of a weak coupling regime of Coulomb blockade between source and drain metal electrodes. The SET consists of a single organic molecule (pyridine/pentane/1,2-azaborine/butylborane) placed over the dielectric, with boron (B) as a substituent. The impact of B-substitution on pyridine and pentane molecules in isolated, as well as SET, environments has been analyzed by using density functional theory-based ab initio packages Atomistix toolkit-Virtual NanoLab and Gaussian03. The performance of proposed SETs was analyzed through charging energies, total energy as a function of gate potential and charge stability diagrams. The analysis confirms that the B-substituted pentane (butylborane) and the boron-substituted pyridine (1,2-azaborine) show remarkably improved conductance in SET environment in comparison to simple pyridine and pentane molecules.
Trerayapiwat, Kasidet; Ricke, Nathan; Cohen, Peter; Poblete, Alex; Rudel, Holly; Eustis, Soren N
2016-08-10
This work explores the relationship between theoretically predicted excitation energies and experimental molar absorption spectra as they pertain to environmental aquatic photochemistry. An overview of pertinent Quantum Chemical descriptions of sunlight-driven electronic transitions in organic pollutants is presented. Second, a combined molecular dynamics (MD), time-dependent density functional theory (TD-DFT) analysis of the ultraviolet to visible (UV-Vis) absorption spectra of six model organic compounds is presented alongside accurate experimental data. The functional relationship between the experimentally observed molar absorption spectrum and the discrete quantum transitions is examined. A rigorous comparison of the accuracy of the theoretical transition energies (ΔES0→Sn) and oscillator strength (fS0→Sn) is afforded by the probabilistic convolution and deconvolution procedure described. This method of deconvolution of experimental spectra using a Gaussian Mixture Model combined with Bayesian Information Criteria (BIC) to determine the mean (μ) and standard deviation (σ) as well as the number of observed singlet to singlet transition energy state distributions. This procedure allows a direct comparison of the one-electron (quantum) transitions that are the result of quantum chemical calculations and the ensemble of non-adiabatic quantum states that produce the macroscopic effect of a molar absorption spectrum. Poor agreement between the vertical excitation energies produced from TD-DFT calculations with five different functionals (CAM-B3LYP, PBE0, M06-2X, BP86, and LC-BLYP) suggest a failure of the theory to capture the low energy, environmentally important, electronic transitions in our model organic pollutants. However, the method of explicit-solvation of the organic solute using the quantum Effective Fragment Potential (EFP) in a density functional molecular dynamics trajectory simulation shows promise as a robust model of the hydrated organic
Velizhanin, Kirill A; Kilina, Svetlana; Sewell, Thomas D; Piryatinski, Andrei
2008-10-23
Numerical studies of vibrational energy transport and associated (non)linear infrared and Raman response in polyatomic materials require knowledge of the multidimensional vibrational potential-energy surface and the ability to perform normal-mode analysis on that potential. The presence of translational symmetry, as in crystals, leads to the observed dispersion of the unit cell normal modes and has to be accounted for in calculations of energy transfer rates and other spectroscopic quantities. Here we report on the implementation of a computational approach that combines the generalized supercell method and density functional theory electronic structure calculations to investigate the vibrational structure in translationally symmetric materials containing relatively large numbers of atoms in the unit cell (58 atoms in the present study). The method is applied to calculate the phonon and vibron dispersion relations and the vibrational density of states in pentaerythritol tetranitrate (PETN) molecular crystal which is an important energetic material. The results set the stage for future investigations of vibrational energy transport and associated nonlinear spectroscopic signatures in this class of materials.
First-principles studies on molecular beam epitaxy growth of GaAs1-xBix
Luo, Guangfu; Yang, Shujiang; Li, Jincheng; ...
2015-07-14
We investigate the molecular beam epitaxy (MBE) growth of GaAs1-xBix film using density functional theory with spin-orbit coupling to understand the growth of this film, especially the mechanisms of Bi incorporation. We study the stable adsorption structures and kinetics of the incident molecules (As₂ molecule, Ga atom, Bi atom, and Bi₂ molecule) on the (2 x 1)-Gasub||Bi surface and a proposed q(1 x 1)-Gasub||AsAs surface has a quasi-(1 x 1) As layer above the Ga-terminated GaAs substrate and a randomly oriented As dimer layer on top. We obtain the desorption and diffusion barriers of the adsorbed molecules and also themore » reaction barriers of three key processes related to Bi evolution, namely, Bi incorporation, As/Bi exchange, and Bi clustering. The results help explain the experimentally observed dependence of Bi incorporation on the As/Ga ratio and growth temperature. Furthermore, we find that As₂ exchange with Bi of the (2 x 1)-Gasub||Bi surface is a key step controlling the kinetics of the Bi incorporation. Finally, we explore two possible methods to enhance the Bi incorporation, namely, replacing the MBE growth mode from codeposition of all fluxes with a sequential deposition of fluxes and applying asymmetric in-plane strain to the substrate.« less
Guo, Dezhou; Zybin, Sergey V; An, Qi; Goddard, William A; Huang, Fenglei
2016-01-21
The combustion or detonation of reacting materials at high temperature and pressure can be characterized by the Chapman-Jouguet (CJ) state that describes the chemical equilibrium of the products at the end of the reaction zone of the detonation wave for sustained detonation. This provides the critical properties and product kinetics for input to macroscale continuum simulations of energetic materials. We propose the ReaxFF Reactive Dynamics to CJ point protocol (Rx2CJ) for predicting the CJ state parameters, providing the means to predict the performance of new materials prior to synthesis and characterization, allowing the simulation based design to be done in silico. Our Rx2CJ method is based on atomistic reactive molecular dynamics (RMD) using the QM-derived ReaxFF force field. We validate this method here by predicting the CJ point and detonation products for three typical energetic materials. We find good agreement between the predicted and experimental detonation velocities, indicating that this method can reliably predict the CJ state using modest levels of computation.
NASA Astrophysics Data System (ADS)
Kimizuka, Hajime; Ogata, Shigenobu
We investigated the H diffusivity in face-centered cubic Pd and Al by performing path-integral molecular dynamics (PIMD) modeling in the framework of density functional theory (DFT); in our calculations, we took nuclear quantum effects into consideration. The DFT results showed that the H-migration barriers (Em) in Pd and Al exhibited similar values (approximately 0.16 eV), while the H atoms were stable at octahedral (O) sites for Pd and at tetrahedral (T) sites for Al. The PIMD-based free-energy profiles for H migration between the O-site and T-site were evaluated using the thermodynamic integration of the centroid forces at 150-600 K. We confirmed that the quantum effects significantly affected the Em and the difference between the energies of the H atom at the O-site and the T-site (EO - T); The Em and EO - T values in Pd at 300 K increased by 32% and 98%, respectively, relative to the classical limit. On the other hand, the Em and ET - O (i.e., -EO - T) values in Al at 300 K decreased by 3% and 41%, respectively. This suggested that the quantum nature of H nuclei was essential for understanding the H-diffusion kinetics in these metals even above ambient temperature.
Chen, Mohan; Abrams, T.; Jaworski, M. A.; Carter, Emily A.
2015-12-17
Because of lithium's possible use as a first wall material in a fusion reactor, a fundamental understanding of the interactions between liquid lithium (Li) and deuterium (D) is important. Here, we predict structural and dynamical properties of liquid Li samples with high concentrations of D, as derived from first-principles molecular dynamics simulations. Liquid Li samples with four concentrations of inserted D atoms (LiD$_{\\beta}$ , $\\beta =0.25$ , 0.50, 0.75, and 1.00) are studied at temperatures ranging from 470 to 1143 K. Densities, diffusivities, pair distribution functions, bond angle distribution functions, geometries, and charge transfer between Li and D atoms are calculated and analyzed. The analysis suggests liquid–solid phase transitions can occur at some concentrations and temperatures, forming rock-salt LiD within liquid Li. Finally, we observed the formation of some D_{2} molecules at high D concentrations.
NASA Astrophysics Data System (ADS)
Loukonen, V.; Kuo, I.-F. W.; McGrath, M. J.; Vehkamäki, H.
2014-01-01
The main pathway of new-particle formation in the atmosphere is likely to begin from small sulfuric acid clusters stabilized by other compounds, such as ammonia or amines. Here, we present the results of first-principles molecular dynamics simulations probing the stability and dynamics of (sulfuric acid) (ammonia/dimethylamine) clusters with two, three and four sulfuric acid molecules and a varying number of the bases. In each of the eight simulated clusters, an energetic equilibrium was reached and 35 ps of equilibrium data was collected in the NVT(T=300 K) ensemble. The clusters exhibited pronounced thermal motion including rotations of the molecules within the clusters. Regardless of the continuous movement, the clusters stayed bound together. The calculated electric dipole moments were found to be sensitive to the thermal motion and consequently, large fluctuations were observed. In addition, the vibrational spectra for all the clusters were determined, indicating that the thermal motion differs from purely harmonic motion.
Chen, Mohan; Abrams, T.; Jaworski, M. A.; ...
2015-12-17
Because of lithium's possible use as a first wall material in a fusion reactor, a fundamental understanding of the interactions between liquid lithium (Li) and deuterium (D) is important. Here, we predict structural and dynamical properties of liquid Li samples with high concentrations of D, as derived from first-principles molecular dynamics simulations. Liquid Li samples with four concentrations of inserted D atoms (LiDmore » $$_{\\beta}$$ , $$\\beta =0.25$$ , 0.50, 0.75, and 1.00) are studied at temperatures ranging from 470 to 1143 K. Densities, diffusivities, pair distribution functions, bond angle distribution functions, geometries, and charge transfer between Li and D atoms are calculated and analyzed. The analysis suggests liquid–solid phase transitions can occur at some concentrations and temperatures, forming rock-salt LiD within liquid Li. Finally, we observed the formation of some D2 molecules at high D concentrations.« less
NASA Astrophysics Data System (ADS)
Zhang, Shen; Wang, Hongwei; Kang, Wei; Zhang, Ping; He, X. T.
2016-04-01
An extended first-principles molecular dynamics (FPMD) method based on Kohn-Sham scheme is proposed to elevate the temperature limit of the FPMD method in the calculation of dense plasmas. The extended method treats the wave functions of high energy electrons as plane waves analytically and thus expands the application of the FPMD method to the region of hot dense plasmas without suffering from the formidable computational costs. In addition, the extended method inherits the high accuracy of the Kohn-Sham scheme and keeps the information of electronic structures. This gives an edge to the extended method in the calculation of mixtures of plasmas composed of heterogeneous ions, high-Z dense plasmas, lowering of ionization potentials, X-ray absorption/emission spectra, and opacities, which are of particular interest to astrophysics, inertial confinement fusion engineering, and laboratory astrophysics.
Zhang, Shen; Kang, Wei; Wang, Hongwei; Zhang, Ping; He, X. T.
2016-04-15
An extended first-principles molecular dynamics (FPMD) method based on Kohn-Sham scheme is proposed to elevate the temperature limit of the FPMD method in the calculation of dense plasmas. The extended method treats the wave functions of high energy electrons as plane waves analytically and thus expands the application of the FPMD method to the region of hot dense plasmas without suffering from the formidable computational costs. In addition, the extended method inherits the high accuracy of the Kohn-Sham scheme and keeps the information of electronic structures. This gives an edge to the extended method in the calculation of mixtures of plasmas composed of heterogeneous ions, high-Z dense plasmas, lowering of ionization potentials, X-ray absorption/emission spectra, and opacities, which are of particular interest to astrophysics, inertial confinement fusion engineering, and laboratory astrophysics.
Li, Xuejiao; Song, Jia; Shi, Shuping; Yan, Liuming; Zhang, Zhaochun; Jiang, Tao; Peng, Shuming
2017-01-26
The dynamic fluctuation of the U(3+) coordination structure in a molten LiCl-KCl mixture was studied using first principles molecular dynamics (FPMD) simulations. The radial distribution function, probability distribution of coordination numbers, fluctuation of coordination number and cage volume, self-diffusion coefficient and solvodynamic mean radius of U(3+), dynamics of the nearest U-Cl distances, and van Hove function were evaluated. It was revealed that fast exchange of Cl(-) occurred between the first and second coordination shells of U(3+) accompanied with fast fluctuation of coordination number and rearrangement of coordination structure. It was concluded that 6-fold coordination structure dominated the coordination structure of U(3+) in the molten LiCl-KCl-UCl3 mixture and a high temperature was conducive to the formation of low coordinated structure.
Jung, Hyunwook; Kang, Joonhee; Chun, Hoje; Han, Byungchan
2018-01-05
Using first principles calculations we unveil fundamental mechanism of hydrolysis reactions of two hazardous chemicals PCl3 and POCl3 with explicit molecular water clusters nearby. It is found that the water molecules play a key role as a catalyst significantly lowing activation barrier of the hydrolysis via transferring its protons to reaction intermediates. Interestingly, torsional angle of the molecular complex at transition state is identified as a vital descriptor on the reaction rate. Analysis of charge distribution over the complex further reinforces the finding with atomic level correlation between the torsional angle and variation of the orbital hybridization state of phosphorus (P) in the complex. Electronic charge separation (or polarization) enhances thermodynamic stability of the activated complex and reduces the activation energy through hydrogen bonding network with water molecules nearby. Calculated potential energy surfaces (PES) for the hydrolysis of PCl3 and POCl3 depict their two contrastingly different profiles of double- and triple-depth wells, respectively. It is ascribed to the unique double-bonding O=P in the POCl3. Our results on the activation free energy show well agreements with previous experimental data within 7kcalmol(-1) deviation. Copyright © 2017 Elsevier B.V. All rights reserved.
Wolff, Holger; Dronskowski, Richard
2008-10-01
A series of perovskite-type phases of alkaline-earth-based tantalum and niobium oxynitrides has been studied using both first-principles electronic-structure calculations and molecular-dynamics simulations, in particular by investigating different structural arrangements and anion distributions in terms of total-energy calculations. The structural properties are explained on the basis of COHP chemical bonding analyses and semiempirical molecular orbital calculations. We provide theoretical proof for the surprising result that the local site symmetries of these phases are lower than cubic because density-functional calculations clearly show that all crystallographic unit cells are better described as being orthorhombic with space group Pmc2(1) to optimize metal-nitrogen bonding; nonetheless, there is no contradiction with a macroscopic cubic description of the structures of BaTaO(2)N and BaNbO(2)N adopting space group Pm3m. Additionally, we find that the anionic sublattice is ordered in all compounds studied over a wide temperature range.
Borinaga, Miguel; Riego, P; Leonardo, A; Calandra, Matteo; Mauri, Francesco; Bergara, Aitor; Errea, Ion
2016-12-14
First-principles calculations based on density-functional theory including anharmonicity within the variational stochastic self-consistent harmonic approximation are applied to understand how the quantum character of the proton affects the candidate metallic molecular Cmca - 4 structure of hydrogen in the 400-450 GPa pressure range, where metallization of hydrogen is expected to occur. Anharmonic effects, which become crucial due to the zero-point motion, have a large impact on the hydrogen molecules by increasing the intramolecular distance by approximately a 6%. This induces two new electron pockets at the Fermi surface opening new scattering channels for the electron-phonon interaction. Consequently, the electron-phonon coupling constant and the superconducting critical temperature are approximately doubled by anharmonicity and Cmca - 4 hydrogen becomes a superconductor above 200 K in all the studied pressure range. Contrary to many superconducting hydrides, where anharmoncity tends to lower the superconducting critical temperature, our results show that it can enhance superconductivity in molecular hydrogen.
Rajput, Nav Nidhi; Qu, Xiaohui; Sa, Niya; Burrell, Anthony K; Persson, Kristin A
2015-03-11
In this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg(2+) → Mg(+)), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI(-) exhibits a significant bond weakening while paired with the transient, partially reduced Mg(+). In contrast, BH4(-) and BF4(-) are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.
NASA Astrophysics Data System (ADS)
Borinaga, Miguel; Riego, P.; Leonardo, A.; Calandra, Matteo; Mauri, Francesco; Bergara, Aitor; Errea, Ion
2016-12-01
First-principles calculations based on density-functional theory including anharmonicity within the variational stochastic self-consistent harmonic approximation are applied to understand how the quantum character of the proton affects the candidate metallic molecular Cmca - 4 structure of hydrogen in the 400-450 GPa pressure range, where metallization of hydrogen is expected to occur. Anharmonic effects, which become crucial due to the zero-point motion, have a large impact on the hydrogen molecules by increasing the intramolecular distance by approximately a 6%. This induces two new electron pockets at the Fermi surface opening new scattering channels for the electron-phonon interaction. Consequently, the electron-phonon coupling constant and the superconducting critical temperature are approximately doubled by anharmonicity and Cmca - 4 hydrogen becomes a superconductor above 200 K in all the studied pressure range. Contrary to many superconducting hydrides, where anharmoncity tends to lower the superconducting critical temperature, our results show that it can enhance superconductivity in molecular hydrogen.
Banyai, Douglas R; Murakhtina, Tatiana; Sebastiani, Daniel
2010-12-01
We present (1)H NMR chemical shift calculations of liquid water based on first principles molecular dynamics simulations under periodic boundary conditions. We focus on the impact of computational parameters on the structural and spectroscopic data, which is an important question for understanding how sensitive the computed (1)H NMR resonances are upon variation of the simulation setup. In particular, we discuss the influence of the exchange-correlation functional and the size of the basis set, the choice for the fictitious electronic mass and the use of pseudopotentials for the nuclear magnetic resonance (NMR) calculation on one hand and the underlying Car-Parrinello-type molecular dynamics simulations on the other hand. Our findings show that the direct effect of these parameters on (1)H shifts is not big, whereas the indirect dependence via the structural data is more important. The (1)H NMR chemical shifts clearly reflect the induced structural changes, illustrating once again the sensitivity of (1)H NMR observables on small changes in the local chemical structure of complex hydrogen-bonded liquids.
Chen, X. P.; Liang, Q. H.; Jiang, J. K.; Wong, Cell K. Y.; Leung, Stanley Y. Y.; Ye, H. Y.; Yang, D. G.; Ren, T. L.
2016-01-01
In this paper, we present a first-principles and molecular dynamics study to delineate the functionalization-induced changes in the local structure and the physical properties of amorphous polyaniline. The results of radial distribution function (RDF) demonstrate that introducing -SO3−Na+ groups at phenyl rings leads to the structural changes in both the intrachain and interchain ordering of polyaniline at shorter distances (≤5 Å). An unique RDF feature in 1.8–2.1 Å regions is usually observed in both the interchain and intrachain RDF profiles of the -SO3−Na+ substituted polymer (i.e. Na-SPANI). Comparative studies of the atom-atom pairs, bond structures, torsion angles and three-dimensional structures show that EB-PANI has much better intrachain ordering than that of Na-SPANI. In addition, investigation of the band gap, density of states (DOS), and absorption spectra indicates that the derivatization at ring do not substantially alter the inherent electronic properties but greatly change the optical properties of polyaniline. Furthermore, the computed diffusion coefficient of water in Na-SPANI is smaller than that of EB-PANI. On the other hand, the Na-SPANI shows a larger density than that of EB-PANI. The computed RDF profiles, band gaps, absorption spectra, and diffusion coefficients are in quantitative agreement with the experimental data. PMID:26857962
McGrath, Matthew J; Kuo, I-Feng William; Siepmann, J Ilja
2011-11-28
Using first principles molecular dynamics simulations in the isobaric-isothermal ensemble (T = 300 K, p = 1 atm) with the Becke-Lee-Yang-Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.
Yadav, Sushma; Choudhary, Ashu; Chandra, Amalendu
2017-09-15
A first-principles molecular dynamics study is presented for the structural, dynamical, vibrational, and dipolar properties of the solvation shell of a nitrate ion in deuterated water. A detailed description of the anisotropic structure of the solvation shell is presented through calculations of various structural distributions in different conical shells around the perpendicular axis of the ion. The nitrate ion-water dimer potential energies are also calculated for many different orientations of water. The average vibrational stretch frequency of OD modes in the solvation shell is found to be higher than that of other OD modes in the bulk, which signifies a weakening of hydrogen bonds in the hydration shell. A splitting of the NO stretch frequencies and an associated fast spectral diffusion of the solute are also observed in the current study. The dynamics of rotation and hydrogen bond relaxation are found to be faster in the hydration shell than that in the bulk water. The residence time of water in the hydration shell is, however, found to be rather long. The nitrate ion is found to have a dipole moment of 0.9 D in water which can be attributed to its fluctuating interactions with the surrounding water.
NASA Astrophysics Data System (ADS)
Karthikeyan, S.; Singh, Jiten N.; Park, Mina; Kumar, Rajesh; Kim, Kwang S.
2008-06-01
Important structural isomers of NH4+(H2O)n=4,6 have been studied by using density functional theory, Møller-Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH4+(H2O)n=4,6 because otherwise wrong structures could be assigned for the most probable structures. For NH4+(H2O)6, the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car-Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH4+(H2O)4 and two lowest energy isomers of NH4+(H2O)6 explains each experimental IR spectrum.
Inagaki, Kouji; Kanai, Ryota; Hirose, Kikuji; Yasutake, Kiyoshi
2011-04-01
Chemical reactions between hydrogen terminated Si(001)2 x 1 surface and impinging H radical are investigated by means of first-principles molecular-dynamics simulations. Reaction probabilities of abstraction of surface terminating H atom with H2 formation, adsorption onto Si surface and reflection of impinging H atom are analyzed with respect to the kinetic energy of incident H radical. The probabilities of abstraction and adsorption turn out to be ranging from 0.81 to 0.58 and from 0.19 to 0.42, respectively, while that of reflection almost zero. As initial kinetic energy of the impinging atom increases, the reaction probability of abstraction decreases and that of absorption increases. Metastable H-absorbed atomic configurations are also derived by optimizing the structures obtained in the impinging dynamics calculations. They are candidates of the so-called reservoir site which is a key to understand the unity hydrogen coverage observed after an exposure to gaseous H atom ambient despite existing residual vacant sites due to abstraction.
NASA Astrophysics Data System (ADS)
Zhang, Genghong; Chen, Weijin; Zhu, Jia; Jiang, Gelei; Sheng, Qiang; Wang, Biao; Zheng, Yue
2016-06-01
Piezoelectricity is closely related with the performance and application of piezoelectric devices. It is a crucial issue to understand its detailed fundamental for designing functional devices with more peculiar performances. Basing on the first principles simulations, the ZnO piezoelectric tunnel junction is taken as an example to systematically investigate its piezoelectricity (including the piezopotential energy, piezoelectric field, piezoelectric polarization and piezocharge) and explore their correlation. The comprehensive picture of the piezoelectricity in the ZnO tunnel junction is revealed at atomic scale and it is verified to be the intrinsic characteristic of ZnO barrier, independent of its terminated surface but dependent on its c axis orientation and the applied strain. In the case of the ZnO c axis pointing from right to left, an in-plane compressive strain will induce piezocharges (and a piezopotential energy drop) with positive and negative signs (negative and positive signs) emerging respectively at the left and right terminated surfaces of the ZnO barrier. Meanwhile a piezoelectric polarization (and a piezoelectric field) pointing from right to left (from left to right) are also induced throughout the ZnO barrier. All these piezoelectric physical quantities would reverse when the applied strain switches from compressive to tensile. This study provides an atomic level insight into the fundamental behavior of the piezoelectricity of the piezoelectric tunnel junction and should have very useful information for future designs of piezoelectric devices.
Zhang, Genghong; Zhu, Jia; Jiang, Gelei; Sheng, Qiang; Zheng, Yue; Chen, Weijin; Wang, Biao
2016-06-15
Piezoelectricity is closely related with the performance and application of piezoelectric devices. It is a crucial issue to understand its detailed fundamental for designing functional devices with more peculiar performances. Basing on the first principles simulations, the ZnO piezoelectric tunnel junction is taken as an example to systematically investigate its piezoelectricity (including the piezopotential energy, piezoelectric field, piezoelectric polarization and piezocharge) and explore their correlation. The comprehensive picture of the piezoelectricity in the ZnO tunnel junction is revealed at atomic scale and it is verified to be the intrinsic characteristic of ZnO barrier, independent of its terminated surface but dependent on its c axis orientation and the applied strain. In the case of the ZnO c axis pointing from right to left, an in-plane compressive strain will induce piezocharges (and a piezopotential energy drop) with positive and negative signs (negative and positive signs) emerging respectively at the left and right terminated surfaces of the ZnO barrier. Meanwhile a piezoelectric polarization (and a piezoelectric field) pointing from right to left (from left to right) are also induced throughout the ZnO barrier. All these piezoelectric physical quantities would reverse when the applied strain switches from compressive to tensile. This study provides an atomic level insight into the fundamental behavior of the piezoelectricity of the piezoelectric tunnel junction and should have very useful information for future designs of piezoelectric devices.
NASA Astrophysics Data System (ADS)
Prendergast, David; Pemmaraju, Sri Chaitanya Das
2015-09-01
With the advent of X-ray free electron lasers and table-top high-harmonic-generation X-ray sources, we can now explore changes in electronic structure on ultrafast time scales -- at or less than 1ps. Transient X-ray spectroscopy of this kind provides a direct probe of relevant electronic levels related to photoinitiated processes and associated interfacial electron transfer as the initial step in solar energy conversion. However, the interpretation of such spectra is typically fraught with difficulty, especially since we rarely have access to spectral standards for nonequilibrium states. To this end, direct first-principles simulations of X-ray absorption spectra can provide the necessary connection between measurements and reliable models of the atomic and electronic structure. We present examples of modeling excited states of materials interfaces relevant to solar harvesting and their corresponding X-ray spectra in either photoemission or absorption modalities. In this way, we can establish particular electron transfer mechanisms to reveal detailed working principles of materials systems in solar applications and provide insight for improved efficiency.
Rajput, Nav Nidhi; Qu, Xiaohuui; Sa, Niya; Burrell, Anthony K.; Persson, Kristin A.
2015-02-10
Here in this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg^{2+} -> Mg^{+}), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI exhibits a significant bond weakening while paired with the transient, partially reduced Mg^{+}. In contrast, BH_{4}^{$-$} and BF_{4}^{$-$} are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.
Rajput, Nav Nidhi; Qu, Xiaohuui; Sa, Niya; ...
2015-02-10
Here in this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectricmore » constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg2+ -> Mg+), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI exhibits a significant bond weakening while paired with the transient, partially reduced Mg+. In contrast, BH4$-$ and BF4$-$ are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.« less
NASA Astrophysics Data System (ADS)
Shodja, Hossein M.; Tabatabaei, Maryam; Esfarjani, Keivan
2014-09-01
First principles Kohn-Sham density functional theory (DFT)-based molecular dynamics (MD) is employed to investigate some physical and mechanical properties of amorphous Si (a-Si) samples, as-quenched and annealed containing dangling and floating bonds as well as distorted tetrahedral bonds. The total energy and true stress as functions of the engineering strain for a-Si samples subjected to uniaxial tensile stress as well as uniaxial extension are obtained. It is well-known that the electron density of the state of matters can be determined via ab initio DFT-based MD with high accuracy. Using this technique, such inherent properties as the elastic constants, ideal tensile strength, ultimate tensile strength, and surface and cohesive energies will be calculated. Since the employed ab initio MD, in contrast to the empirical potentials simulations, is capable of providing the evolution of the electronic charge distribution, we can afford to study the chemistry of crack initiation and reconstructed surfaces at final rupture. The calculated cohesive and surface energies are compared with the available theoretical and experimental results; Tyson's empirical relation and universal binding energy relations (UBERs) are also examined. The calculated elastic constants using the symmetry-general scheme satisfy well the isotropic relation ?. To date, the ab initio MD samples of a-Si generated from the completely melted scheme were all free of three-fold-coordinated Si. In contrast, as we will show, by implementing special thermal treatments, generation of all inherent structural defects is possible. Based on the electronic charge distribution, dative bonds and trigonal prisms for, respectively, floating and dangling bonds have been observed.
NASA Astrophysics Data System (ADS)
Zhou, Yanguang; Gong, Xiaojing; Xu, Ben; Hu, Ming
2017-08-01
Electrical and thermal transport in silicon germanium superlattice nanostructures has received extensive attention from scientists for understanding carrier properties at the nanoscale, and the figure-of-merit (ZT) reported in such structures has inspired engineers to develop cost-effective waste heat recovery systems. In this paper, the thermoelectric transport properties of the silicon-based superlattice- and anti-superlattice-nanocrystalline heterostructures are systematically studied by first-principles and molecular dynamics simulations combined with the Boltzmann transport theory. The thermal conductivity, which is thought to be the essential bottleneck for bulk crystalline Si to gain a high ZT value, of such structures is found to be reduced by two orders of magnitude and reaches a level far below the amorphous limit of Si. This is achieved due to the extremely strong phonon-boundary scattering at both grain boundaries and Si-Ge interfaces, which will lead to the phonon mean free path being much smaller than the grain size (Casmir limit): for instance, the dominant phonons are in range of 0.5 to 3 nm for the heterostructures with a grain size of around 8 nm. Meanwhile, the power factor can be preserved at the level comparable to bulk crystalline because of the quantum confinement effect, which resulted from the conduction band minima converge, reduction of band gap, and the short mean free path of carriers. As a result, the ZT of such superlattice based nanomembranes can reach around 0.3 at room temperature, which is two orders of magnitude higher than the bulk crystalline case. The corresponding bulk superlattice-nanocrystalline heterostructures possess a ZT value of 0.5 at room temperature, which is superior to all other bulk silicon-based thermoelectrics. Our results here show that nanostructuring the superlattice structure can further decrease the thermal conductivity while keeping the electrical transport properties at the bulk comparable level, and
NASA Astrophysics Data System (ADS)
An, Zhenlian; Kamezawa, Chihiro; Hirai, Masaaki; Kusaka, Masahiko; Iwami, Motohiro
2002-12-01
A systematic study of the valence band structure of Cu3Si has been performed by soft X-ray emission spectroscopy and a first-principle molecular orbital calculation using the discrete-variational (DV)-Xα cluster model. The existence of Cu 4s, 4p states in the valence band and their important contributions to the valence band as that of Cu 3d are indicated together with previously reported ones. The high-binding energy peak in the Si L2,3 emission spectrum is considered to originate mainly from the Si-Si 3s bonding state but also have a certain contribution of Si 3s bonding state with Cu 4s, 4p. On the other hand, the low-binding energy peaks in the Si L2,3 emission band are attributed to both the antibonding states of Si 3s and the bonding states of Si 3d with Cu 4s, 4p and Cu 3d. The bonding states of Si 3s with Cu 4s, 4p and Cu 3d are expected to exist in the lower part of the valence band for η\\prime-Cu3Si on the basis of the theoretical calculations. As for Si p states, the high-binding energy peak and the low-binding energy peak in the Si Kβ emission spectrum should be attributed to the Si 3p bonding state and antibonding state with Cu 3d and Cu 4s, 4p, respectively, according to the theoretical calculations. A comparison is made between experimental spectra and theoretical density of states.
NASA Astrophysics Data System (ADS)
Bouzid, Assil; Pizzey, Keiron J.; Zeidler, Anita; Ori, Guido; Boero, Mauro; Massobrio, Carlo; Klotz, Stefan; Fischer, Henry E.; Bull, Craig L.; Salmon, Philip S.
2016-01-01
The changes to the topological and chemical ordering in the network-forming isostatic glass GeSe4 are investigated at pressures up to ˜14.4 GPa by using a combination of neutron diffraction and first-principles molecular dynamics. The results show a network built from corner- and edge-sharing Ge(Se1 /2)4 tetrahedra, where linkages by Se2 dimers or longer Sen chains are prevalent. These linkages confer the network with a local flexibility that helps to retain the network connectivity at pressures up to ˜8 GPa, corresponding to a density increase of ˜37 % . The network reorganization at constant topology maintains a mean coordination number n ¯≃2.4 , the value expected from mean-field constraint-counting theory for a rigid stress-free network. Isostatic networks may therefore remain optimally constrained to avoid stress and retain their favorable glass-forming ability over a large density range. As the pressure is increased to around 13 GPa, corresponding to a density increase of ˜49 % , Ge(Se1 /2)4 tetrahedra remain as the predominant structural motifs, but there is an appearance of 5-fold coordinated Ge atoms and homopolar Ge-Ge bonds that accompany an increase in the fraction of 3-fold coordinated Se atoms. The band gap energy decreases with increasing pressure, and midgap states appear at pressures beyond ˜6.7 GPa. The latter originate from undercoordinated Se atoms that terminate broken Sen chains.
Wei, Donghui; Fang, Lei; Tang, Mingsheng; Zhan, Chang-Guo
2013-01-01
Proteasome is the major component of the crucial nonlysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-Oγ. The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-Oγ, followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-Nz. Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-Nz to Thr1-Oγ. According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3b) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally-derived activation free energy of ~18.3–19.4 kcal/mol, suggesting that the computational results are reasonable. PMID:24111489
Ivashchenko, Volodymyr; Veprek, Stan; Pogrebnjak, Alexander; Postolnyi, Bogdan
2014-01-01
The heterostructures of five monolayers B1–TixZr1−xN(111), x = 1.0, 0.6, 0.4 and 0.0 (where B1 is a NaCl-type structure) with one monolayer of a Si3N4-like Si2N3 interfacial layer were investigated by means of first-principles quantum molecular dynamics and a structure optimization procedure using the Quantum ESPRESSO code. Slabs consisting of stoichiometric TiN and ZrN and random, as well as segregated, B1–TixZr1−xN(111) solutions were considered. The calculations of the B1–TixZr1−xN solid solutions, as well as of the heterostructures, showed that the pseudo-binary TiN–ZrN system exhibits a miscibility gap. The segregated heterostructures in which Zr atoms surround the SiyNz interface were found to be the most stable. For the Zr-rich heterostructures, the total energy of the random solid solution was lower compared to that of the segregated one, whereas for the Ti-rich heterostructures the opposite tendency was observed. Hard and super hard Zr–Ti–Si–N coatings with thicknesses from 2.8 to 3.5 μm were obtained using a vacuum arc source with high frequency stimulation. The samples were annealed in a vacuum and in air at 1200 °C. Experimental investigations of Zr–Ti–N, Zr–Ti–Si–N and Ti–Si–N coatings with different Zr, Ti and Si concentrations were carried out for comparison with results obtained from TixZr1−xN(111)/SiNy systems. During annealing, the hardness of the best series samples was increased from (39.6 ± 1.4) to 53.6 GPa, which seemed to indicate that a spinodal segregation along grain interfaces was finished. A maximum hardness of 40.8 GPa before and 55 GPa after annealing in air at 500 °C was observed for coatings with a concentration of elements of Si≽ (7–8) at.%, Ti ≽ 22 at.% and Zr ⩽ 70 at.%. PMID:27877668
NASA Astrophysics Data System (ADS)
Gamba, Aldo; Tabacchi, Gloria; Fois, Ettore
2009-09-01
First principles studies on periodic TS-1 models at Ti content corresponding to 1.35% and 2.7% in weight of TiO2 are presented. The problem of Ti preferential siting is addressed by using realistic models corresponding to the TS-1 unit cell [TiSi95O192] and adopting for the first time a periodic DFT approach, thus providing an energy scale for Ti in the different crystallographic sites in nondefective TS-1. The structure with Ti in site T3 is the most stable, followed by T4 (+0.3 kcal/mol); the less stable structure, corresponding to Ti in T1, is 5.6 kcal/mol higher in energy. The work has been extended to investigate models with two Ti's per unit cell [Ti2Si94O192] (2.7%). The possible existence of Ti-O-Ti bridges, formed by two corner-sharing TiO4 tetrahedra, is discussed. By using cluster models cut from the optimized periodic DFT structures, both vibrational (DFT) and electronic excitation spectra (TDDFT) have been calculated and favorably compared with the experimental data available on TS-1. Interesting features emerged from excitation spectra: (i) Isolated tetrahedral Ti sites show a Beer-Lambert behavior, with absorption intensity proportional to concentration. Such a behavior is gradually lost when two Ti's occupy sites close to each other. (ii) The UV-vis absorption in the 200-250 nm region can be associated with transitions from occupied states delocalized on the framework oxygens to empty d states localized on Ti. Such extended-states-to-local-states transitions may help the interpretation of the photovoltaic activity recently detected in Ti zeolites.
NASA Astrophysics Data System (ADS)
Hong, Liang; Bhatnagar, Kunal; Droopad, Ravi; Klie, Robert F.; Öǧüt, Serdar
2017-07-01
The electronic properties of epitaxial oxide thin films grown on compound semiconductors are largely determined by the interfacial atomic structure, as well as the thermodynamic conditions during synthesis. Ferroelectric polarization and Fermi-level pinning in SrTiO3 films have been attributed to the presence of oxygen vacancies at the oxide/semiconductor interface. Here, we present scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy analyses of GaAs films grown on SrTiO3 combined with first-principles calculations to determine the atomic and electronic structures of the SrTiO3/GaAs interfaces. An atomically abrupt SrO/As interface is observed and the interfacial SrO layer is found to be O-deficient. First-principles density functional theory (DFT) calculations show SrO/Ga and Sr/As interfaces are favorable under O-rich and O-poor conditions, respectively. The SrO/Ga interface is reconstructed via the formation of Ga-Ga dimers while the Sr/As interface is abrupt and consistent with the experiment. DFT calculations further reveal that intrinsic two-dimensional electron gas (2DEG) forms in both SrO/Ga and Sr/As interfaces, and the Fermi level is pinned to the localized 2DEG states. Interfacial O vacancies can enhance the 2DEG density while it is possible for Ga/As vacancies to unpin the Fermi level from the 2DEG states.
First principle thousand atom quantum dot calculations
Wang, Lin-Wang; Li, Jingbo
2004-03-30
A charge patching method and an idealized surface passivation are used to calculate the single electronic states of IV-IV, III-V, II-VI semiconductor quantum dots up to a thousand atoms. This approach scales linearly and has a 1000 fold speed-up compared to direct first principle methods with a cost of eigen energy error of about 20 meV. The calculated quantum dot band gaps are parametrized for future references.
NASA Astrophysics Data System (ADS)
Rani, Shalu; Singh, Poorva
2017-05-01
Hybrid organic/inorganic perovskites have garnered significant research interest due to the extraordinary increase in energy conversion efficiency as witnessed in photovoltaic devices based on CH3NH3PbI3. An experimental report has shown that the substitution of BF4- in the perovskite CH3NH3PbI3 can lead to the high efficiency for solar cell. Employing first-principles calculations based on density functional theory, we have studied several different perovskites CH3NH3PbI3 , CH3NH3PbI2BF4, CH3NH3PbI(BF4)2, CH3NH3Pb(BF4)3 and examined their electronic structure and optical properties.
Ganesh, P.; Kent, P. R. C.; Jiang, De-en
2012-11-26
Understanding the nature and formation of the solid–electrolyte interphase (SEI) formed in electrochemical storage devices, such as Li-ion batteries, is most important for improving functionality. Few experiments exist that adequately probe the SEI, particularly in situ. We perform predictive ab initio molecular dynamics simulations of the anode–electrolyte interface for several electrolytes and interface functionalizations. These show strongly differing effects on the reducibility of the electrolyte. Electrolyte reduction occurs rapidly, on a picosecond time scale. Orientational ordering of electrolyte near the interface precedes reduction. The reduced species depend strongly on surface functionalization and presence of LiPF6 salt. While LiPF6 salt in ethylene carbonate is more stable at a hydrogen-terminated anode, oxygen/hydroxyl termination causes spontaneous dissociation to form LiF and other fluorophosphates. LiF migrates to the interface creating chainlike structures, consistent with experimental observations of LiF agglomeration. Inorganic products such as LiF and Li2CO3 migrate closer to the anode than purely organic components, consistent with their more ionic character. Significantly, we conclude that while the electrolyte reduction occurs at the molecular level near the interface, requiring specific alignments and proximity, the reducibility is governed by the average reduction potential barrier between the electrode (anode) and the electrolyte.
Liu, Song; van Duin, Adri C T; van Duin, Diana M; Liu, Bin; Edgar, James H
2017-04-25
Atomistic-scale insights into the growth of a continuous, atomically thin hexagonal boron nitride (hBN) lattice from elemental boron and nitrogen on Ni substrates were obtained from multiscale modeling combining density functional theory (DFT) and reactive molecular dynamics. The quantum mechanical calculations focused on the adsorption and reaction energetics for the hBN building-block species, i.e., atomic B, N, BxNy (x, y = 1, 2), on Ni(111) and Ni(211), and the diffusion pathways of elemental B and N on these slab model surfaces and in the sublayer. B can diffuse competitively on both the surface and in the sublayer, while N diffuses strictly on the substrate surface. The DFT data were then used to generate a classical description of the Ni-B and Ni-N pair interactions within the formulation of the reactive force field, ReaxFF. Using the potential developed from this work, the elementary nucleation and growth process of an hBN monolayer structure from elemental B and N is shown at the atomistic scale. The nucleation initiates from the growth of linear BN chains, which evolve into branched and then hexagonal lattices. Subsequent DFT calculations confirmed the structure evolution energetically and validate the self-consistency of this multiscale modeling framework. On the basis of this framework, the fundamental aspects regarding crystal quality and the role of temperature and substrates used during hBN growth can also be understood.
First-principles calculations of novel materials
NASA Astrophysics Data System (ADS)
Sun, Jifeng
Computational material simulation is becoming more and more important as a branch of material science. Depending on the scale of the systems, there are many simulation methods, i.e. first-principles calculation (or ab-initio), molecular dynamics, mesoscale methods and continuum methods. Among them, first-principles calculation, which involves density functional theory (DFT) and based on quantum mechanics, has become to be a reliable tool in condensed matter physics. DFT is a single-electron approximation in solving the many-body problems. Intrinsically speaking, both DFT and ab-initio belong to the first-principles calculation since the theoretical background of ab-initio is Hartree-Fock (HF) approximation and both are aimed at solving the Schrodinger equation of the many-body system using the self-consistent field (SCF) method and calculating the ground state properties. The difference is that DFT introduces parameters either from experiments or from other molecular dynamic (MD) calculations to approximate the expressions of the exchange-correlation terms. The exchange term is accurately calculated but the correlation term is neglected in HF. In this dissertation, DFT based first-principles calculations were performed for all the novel materials and interesting materials introduced. Specifically, the DFT theory together with the rationale behind related properties (e.g. electronic, optical, defect, thermoelectric, magnetic) are introduced in Chapter 2. Starting from Chapter 3 to Chapter 5, several representative materials were studied. In particular, a new semiconducting oxytelluride, Ba2TeO is studied in Chapter 3. Our calculations indicate a direct semiconducting character with a band gap value of 2.43 eV, which agrees well with the optical experiment (˜ 2.93 eV). Moreover, the optical and defects properties of Ba2TeO are also systematically investigated with a view to understanding its potential as an optoelectronic or transparent conducting material. We find
Lingerfelt, David B; Lestrange, Patrick J; Radler, Joseph J; Brown-Xu, Samantha E; Kim, Pyosang; Castellano, Felix N; Chen, Lin X; Li, Xiaosong
2017-03-09
Materials and molecular systems exhibiting long-lived electronic coherence can facilitate coherent transport, opening the door to efficient charge and energy transport beyond traditional methods. Recently, signatures of a possible coherent, recurrent electronic motion were identified in femtosecond pump-probe spectroscopy experiments on a binuclear platinum complex, where a persistent periodic beating in the transient absorption signal's anisotropy was observed. In this study, we investigate the excitonic dynamics that underlie the suspected electronic coherence for a series of binuclear platinum complexes exhibiting a range of interplatinum distances. Results suggest that the long-lived coherence can only result when competitive electronic couplings are in balance. At longer Pt-Pt distances, the electronic couplings between the two halves of the binuclear system weaken, and exciton localization and recombination is favored on short time scales. For short Pt-Pt distances, electronic couplings between the states in the coherent superposition are stronger than the coupling with other excitonic states, leading to long-lived coherence.
Katcho, N. A.; Lomba, E.; Urones-Garrote, E.; Otero-Diaz, L. C.; Landa-Canovas, A. R.
2006-06-01
In this work we present an investigation on the composition dependence of the local structure in Se{sub x}Te{sub 1-x} crystalline alloys analyzing their experimental energy-loss spectra with the aid of a real-space multiple-scattering modeling approach and first-principles molecular dynamics. The concourse of this latter technique is essential for a proper modeling of the alloy spectra. From our results, it can be inferred that Se{sub x}Te{sub 1-x} alloys exhibit a high degree of substitutional disorder ruling out the existence of fully ordered alternating copolymer chains of Se and Te atoms.
First-principles simulations of thiophene oligomers
NASA Astrophysics Data System (ADS)
Scherlis, Damian; Marzari, Nicola
2003-03-01
Conducting polymers, extensively investigated for their use in electronic and nanotechnology applications, have recently gained prominence for their possible use as molecular actuators in mechanical and bioengineering devices. We have focused our efforts on thiophene-based compounds, a class of materials that can be designed for high stress generation and large linear displacement (actuation strain), ideally outperforming mammalian muscle. Key features for the development of these materials are the microscopic binding properties of thiophene and thiophene oligomers stacks, where applied electric fields lead to oxidation and enhanced pi-pi bonding. We have completed the structural studies of neutral and charged oligothiophene dimers, in the search for efficient dimerization mechanisms. A comparison between different density-functional and quantum-chemistry approaches is critically presented, as are solvation effects, described in this work with a combination of first-principles molecular dynamics and a QM/MM approach for the solvating medium.
NASA Astrophysics Data System (ADS)
Kim, Yong-Hyun; Zhang, S. B.
2006-03-01
Despite being one of the most important macroscopic measures and a long history even before the quantum mechanics, the concept of pH has rarely been mentioned in microscopic theories, nor being incorporated computationally into first-principles theory of aqueous solutions. Here, we formulate a theory for the pH dependence of solution formation energy by introducing the proton chemical potential as the microscopic counterpart of pH in atomistic solution models. Within the theory, the general acid-base chemistry can be cast in a simple pictorial representation. We adopt density-functional molecular dynamics to demonstrate the usefulness of the method by studying a number of solution systems including water, small solute molecules such as NH3 and HCOOH, and more complex amino acids with several functional groups. For pure water, we calculated the auto- ionization constant to be 13.2 with a 95 % accuracy. For other solutes, the calculated dissociation constants, i.e., the so- called pKa, are also in reasonable agreement with experiments. Our first-principles pH theory can be readily applied to broad solution chemistry problems such as redox reactions.
NASA Astrophysics Data System (ADS)
Peng, Qing; Wang, Guangyu; Liu, G. R.; de, Suvranu
2015-06-01
We investigate the elastic constants and equations of state (EOS) of the β-polymorph of cyclotetramethylene tetranitramine (HMX) energetic molecular crystal using density functional theory (DFT) calculations. The combination of vdW-DF2 van der Waals functionals and PBE exchange-correlation functionals gives optimized results. The DFT results are used to optimize the Reactive Force Field (ReaxFF). The material strength and EOS of beta-HMX at finite temperatures are then predicted from ReaxFF molecular dynamics simulations. Our results suggest that the optimized ReaxFF predicts the mechanics and EOS of beta-HMX well. The authors would like to acknowledge the generous financial support from the Defense Threat Reduction Agency (DTRA) Grant # HDTRA1-13-1-0025.
NASA Astrophysics Data System (ADS)
Bandura, Andrei V.; Evarestov, Robert A.; Lukyanov, Sergey I.; Piskunov, Sergei; Zhukovskii, Yuri F.
2017-08-01
Morphologically reproducible wurtzite-structured zinc oxide nanowires (ZnO NWs) can be synthesized by different methods. Since ZnO NWs have been found to possess piezoelectricity, a comprehensive study of their mechanical properties, e.g. deformations caused by external compression or stretching, is one of the actual tasks of this paper. We have calculated wurtzite-structured [0 0 0 1]-oriented ZnO NWs whose diameters have been varied within 1-5 nm and 1-20 nm ranges when using either ab initio (hybrid DFT-LCAO) or force-field (molecular mechanical) methods, respectively (the minimum diameter d NW of experimentally synthesized NWs has been estimated on average to be ~20 nm). When using both chosen calculation approaches, the values of Young’s moduli determined for the mentioned ranges of NW diameters have been found to be qualitatively compatible (168-169 GPa for 5 nm NW thickness), whereas results of molecular mechanical simulations on Y NW for 20 nm-thick NWs (160-162 GPa) have been qualitatively comparable with those experimentally measured along the [0 0 0 1] direction of NW loading. In all the cases, a gradual increase of the NW diameter has resulted in an asymptotic decrease of Young’s modulus consequently approaching that (Y b) of wurtzite-structured ZnO bulk along its [0 0 0 1] axis. The novelty of this study is that we combine the computation methods of quantum chemistry and molecular mechanics, while the majority of previous studies with the same aim have focused on the application of different classical molecular dynamical methods.
Bucher, Denis; Guidoni, Leonardo; Carloni, Paolo; Rothlisberger, Ursula
2010-05-19
Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K(+) and Na(+) ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, K(+) ions were found to display an average coordination number of 6.6 in the filter, and 6.2 in water. Na(+) ions displayed an average coordination number of 5.2 in the filter, and 5.0 in water. A comparison was made with the average coordination numbers obtained from using classical molecular dynamics (6.7 for K(+) in the filter, 6.6 for K(+) in water, 6.0 for Na(+) in the filter, and 5.2 for Na(+) in water). The observation that different coordination numbers were displayed by the ions in QM/MM simulations and in classical molecular dynamics is relevant to the discussion of selectivity in K-channels.
Bucher, Denis; Guidoni, Leonardo; Carloni, Paolo; Rothlisberger, Ursula
2010-01-01
Abstract Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K+ and Na+ ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, K+ ions were found to display an average coordination number of 6.6 in the filter, and 6.2 in water. Na+ ions displayed an average coordination number of 5.2 in the filter, and 5.0 in water. A comparison was made with the average coordination numbers obtained from using classical molecular dynamics (6.7 for K+ in the filter, 6.6 for K+ in water, 6.0 for Na+ in the filter, and 5.2 for Na+ in water). The observation that different coordination numbers were displayed by the ions in QM/MM simulations and in classical molecular dynamics is relevant to the discussion of selectivity in K-channels. PMID:20483308
NASA Astrophysics Data System (ADS)
Zapp, Edward Neal
Simulation of energetic, colliding nuclear systems at energies between 100 AMeV and 5 AGeV has utility in fields as diverse as the design and construction of fundamental particle physics experiments, patient treatment by radiation exposure, and in the protection of astronaut crews from the risks of exposure to natural radiation sources during spaceflight. Descriptions of these colliding systems which are derived from theoretical principles are necessary in order to provide confidence in describing systems outside the scope of existing data, which is sparse. The system size and velocity dictate descriptions which include both special relativistic and quantum effects, and the currently incomplete state of understanding with respect to the basic processes at work within nuclear matter dictate that any description will exist at some level of approximation. Models commonly found in the literature employ approximations to theory which lead to simulation results which demonstrate departure from fundamental physical principles, most notably conservation of system energy. The HMD (Hamiltonian Molecular Dynamics) mode is developed as a phase-space description of colliding nuclear system on the level of hadrons, inclusive of the necessary quantum and relativistic elements. Evaluation of model simulations shows that the HMD model shows the necessary conservations throughout system simulation. HMD model predictions are compared to both the RQMD (Relativistic Quantum Molecular Dynamics) and JQMD (Jaeri-Quantum Molecular Dynamics) codes, both commonly employed for the purpose of simulating nucleus-nucleus collisions. Comparison is also provided between all three codes and measurement. The HMD model is shown to perform well in light of both measurement and model calculation, while providing for a physically self-consistent description of the system throughout.
Chamber Clearing First Principles Modeling
Loosmore, G
2009-06-09
LIFE fusion is designed to generate 37.5 MJ of energy per shot, at 13.3 Hz, for a total average fusion power of 500 MW. The energy from each shot is partitioned among neutrons ({approx}78%), x-rays ({approx}12%), and ions ({approx}10%). First wall heating is dominated by x-rays and debris because the neutron mean free path is much longer than the wall thickness. Ion implantation in the first wall also causes damage such as blistering if not prevented. To moderate the peak-pulse heating, the LIFE fusion chamber is filled with a gas (such as xenon) to reduce the peak-pulse heat load. The debris ions and majority of the x-rays stop in the gas, which re-radiates this energy over a longer timescale (allowing time for heat conduction to cool the first wall sufficiently to avoid damage). After a shot, because of the x-ray and ion deposition, the chamber fill gas is hot and turbulent and contains debris ions. The debris needs to be removed. The ions increase the gas density, may cluster or form aerosols, and can interfere with the propagation of the laser beams to the target for the next shot. Moreover, the tritium and high-Z hohlraum debris needs to be recovered for reuse. Additionally, the cryogenic target needs to survive transport through the gas mixture to the chamber center. Hence, it will be necessary to clear the chamber of the hot contaminated gas mixture and refill it with a cool, clean gas between shots. The refilling process may create density gradients that could interfere with beam propagation, so the fluid dynamics must be studied carefully. This paper describes an analytic modeling effort to study the clearing and refilling process for the LIFE fusion chamber. The models used here are derived from first principles and balances of mass and energy, with the intent of providing a first estimate of clearing rates, clearing times, fractional removal of ions, equilibrated chamber temperatures, and equilibrated ion concentrations for the chamber. These can be used
NASA Astrophysics Data System (ADS)
Sebbari, Karim; Roques, Jérôme; Domain, Christophe; Simoni, Eric
2012-10-01
The behavior of the UO22+ uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT + U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 Å above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d_{U{-O}_{adsorption}}= 2.39 Å. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.
Sebbari, Karim; Roques, Jérôme; Domain, Christophe; Simoni, Eric
2012-10-28
The behavior of the UO(2)(2+) uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT + U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 Å above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d(U-O(adsorption))=2.39 Å. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.
Sebbari, Karim; Roques, Jerome; Simoni, Eric; Domain, Christophe
2012-10-28
The behavior of the UO{sub 2}{sup 2+} uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT +U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 A above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d{sub U-O{sub a{sub d{sub s{sub o{sub r{sub p{sub t{sub i{sub o{sub n}}}}}}}}}}}=2.39 A. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.
Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan
2016-04-01
In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.
Phonon-phonon interactions: First principles theory
Gibbons, T. M.; Bebek, M. B.; Kang, By.; Stanley, C. M.; Estreicher, S. K.
2015-08-28
We present the details of a method to perform molecular-dynamics (MD) simulations without thermostat and with very small temperature fluctuations ±ΔT starting with MD step 1. It involves preparing the supercell at the time t = 0 in physically correct microstates using the eigenvectors of the dynamical matrix. Each initial microstate corresponds to a different distribution of kinetic and potential energies for each vibrational mode (the total energy of each microstate is the same). Averaging the MD runs over many initial microstates further reduces ΔT. The electronic states are obtained using first-principles theory (density-functional theory in periodic supercells). Three applications are discussed: the lifetime and decay of vibrational excitations, the isotope dependence of thermal conductivities, and the flow of heat at an interface.
Tang, Emilia; Di Tommaso, Devis; de Leeuw, Nora H
2009-06-21
Density functional theory Perdew-Burke-Ernzerhof [Perdew et al., Phys. Rev. Lett. 77, 3865 (1996)] molecular dynamics simulations of aqueous solutions of orthophosphate species H(n)PO(4)(3-n) (n=0-3) provide new insights into hydrogen transfer and intermolecular and hydration properties of these important aqueous species. Extensive Car-Parrinello molecular dynamics simulations of the orthophosphate ion PO(4)(3-), of the hydrogen phosphate anions, HPO(4)(2-) and H(2)PO(4)(-), and of the orthophosphoric acid, H(3)PO(4), in explicit water show that the process of proton transfer from H(n)PO(4)(3-n) to the surrounding water molecules is very fast, less than 1 ps, and indicate that the dehydrogenation occurs through a concerted proton hopping mechanism, which involves H(n)PO(4)(3-n) and three water molecules. Analysis of the intermolecular H(n)PO(4)(3-n)-water structure shows that the PO(4)(3-) anions have a significant effect on the H-bonding network of bulk water and the presence of P-O(-) moieties induce the formation of new types of H-H interactions around this orthophosphate. Calculated probability distributions of the coordination numbers of the first hydration shell of PO(4)(3-), HPO(4)(2-), and H(2)PO(4)(-) show that these phosphate species display a flexible first coordination shell (between 7 and 13 water molecules) and that the flexibility increases on going from PO(4)(3-) to H(2)PO(4)(-). The strength and number of hydrogen bonds of PO(4)(3-), HPO(4)(2-), and H(2)PO(4)(-) are determined through a detailed analysis of the structural correlation functions. In particular, the H-bond interactions between the oxygen atoms of the phosphates and the surrounding water molecules, which decrease on going from PO(4)(3-) to the hydrogenated H(2)PO(4)(-) species, explain the diminished effect on the structure of water with the increasing hydrogenation of the orthophosphate anions.
First-principles studies on molecular beam epitaxy growth of GaAs_{1-x}Bi_{x}
Luo, Guangfu; Yang, Shujiang; Li, Jincheng; Arjmand, Mehrdad; Szlufarska, Izabela; Brown, April S.; Kuech, Thomas F.; Morgan, Dane
2015-07-14
We investigate the molecular beam epitaxy (MBE) growth of GaAs_{1-x}Bi_{x} film using density functional theory with spin-orbit coupling to understand the growth of this film, especially the mechanisms of Bi incorporation. We study the stable adsorption structures and kinetics of the incident molecules (As₂ molecule, Ga atom, Bi atom, and Bi₂ molecule) on the (2 x 1)-Ga_{sub}||Bi surface and a proposed q(1 x 1)-Ga_{sub}||AsAs surface has a quasi-(1 x 1) As layer above the Ga-terminated GaAs substrate and a randomly oriented As dimer layer on top. We obtain the desorption and diffusion barriers of the adsorbed molecules and also the reaction barriers of three key processes related to Bi evolution, namely, Bi incorporation, As/Bi exchange, and Bi clustering. The results help explain the experimentally observed dependence of Bi incorporation on the As/Ga ratio and growth temperature. Furthermore, we find that As₂ exchange with Bi of the (2 x 1)-Ga_{sub}||Bi surface is a key step controlling the kinetics of the Bi incorporation. Finally, we explore two possible methods to enhance the Bi incorporation, namely, replacing the MBE growth mode from codeposition of all fluxes with a sequential deposition of fluxes and applying asymmetric in-plane strain to the substrate.
Umezawa, Naoto; Kalia, Rajiv K; Nakano, Aiichiro; Vashista, Priya; Shimojo, Fuyuki
2007-06-21
We have investigated the decomposition and chemisorption of a 1,3,5-trinitro-1,3,5-triazine (RDX) molecule on Al(111) surface using molecular dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). The real-space DFT calculations are based on higher-order finite difference and norm-conserving pseudopotential methods. Strong attractive forces between oxygen and aluminum atoms break N-O and N-N bonds in the RDX and, subsequently, the dissociated oxygen atoms and NO molecules oxidize the Al surface. In addition to these Al surface-assisted decompositions, ring cleavage of the RDX molecule is also observed. These reactions occur spontaneously without potential barriers and result in the attachment of the rest of the RDX molecule to the surface. This opens up the possibility of coating Al nanoparticles with RDX molecules to avoid the detrimental effect of oxidation in high energy density material applications.
NASA Astrophysics Data System (ADS)
Wang, BinBin; Wang, FengChao; Zhao, YaPu
2012-06-01
In this paper, the possibility of the monatomic chain (MC) formation for ZnO material was studied by molecular dynamics (MD) simulation. The process of MC formation and the effects of temperature, strain rate and size were studied extensively. The tensile process can be divided to be five stages and the ZnO diatomic chain (DC) can be found. The MD results show that most atoms in MC came from the original surface of ZnO nanowires (NWs). Temperature and strain rate are two important factors affecting the process, and both high temperature and low strain rate in a certain range would be beneficial to the formation of DC. Moreover, the effects of strain rate and temperature could attribute to the Arrhenius model and the energy release mechanism. Furthermore, multi-shell structure was found for the samples under tensile strain and the layer-layer distance was about 3 Å. Our studies based on density functional theory showed that the most stable structure of ZnO DC was confirmed to be linear, and the I-V curve was also got using ATK.
Sa, Rongjian; Zhu, Weiliang; Shen, Jianhua; Gong, Zhen; Cheng, Jiagao; Chen, Kaixian; Jiang, Hualiang
2006-03-16
The Car-Parrinello molecular dynamics (CPMD) method was used to study the dynamic characteristics of the cation-pi interaction between ammonium and benzene in gaseous and aqueous media. The results obtained from the CPMD calculation on the cation-pi complex in the gaseous state were very similar to those calculated from the Gaussian98 program with DFT and MP2 algorithms, demonstrating that CPMD is a valid approach for studying this system. Unlike the interaction in the gaseous state, our 12-ps CPMD simulation showed that the geometry of the complex in aqueous solution changes frequently in terms of the interaction angles and distances. Furthermore, the simulation revealed that the ammonium is constantly oscillating above the benzene plane in an aqueous environment and interacts with benzene mostly through three of its hydrogen atoms. In contrast, the interaction of the cation with the aromatic molecule in the gaseous state involves two hydrogen atoms. In addition, the free energy profile in aqueous solution was studied using constrained CPMD simulations, resulting in a calculated binding free energy of -5.75 kcal/mol at an optimum interaction distance of approximately 3.25 A, indicating that the cation-pi interaction between ammonium and benzene is stable even in aqueous solution. Thus, this CPMD study suggested that the cation-pi interaction between an ammonium (group) and an aromatic structure could take place even on surfaces of protein or nucleic acids in solution.
Photoelectron Spectra of Aqueous Solutions from First Principles
Gaiduk, Alex P.; Govoni, Marco; Seidel, Robert; Skone, Jonathan H.; Winter, Bernd; Galli, Giulia
2016-06-08
We present a combined computational and experimental study of the photoelectron spectrum of a simple aqueous solution of NaCl. Measurements were conducted on microjets, and first-principles calculations were performed using hybrid functionals and many-body perturbation theory at the G0W0 level, starting with wave functions computed in ab initio molecular dynamics simulations. We show excellent agreement between theory and experiments for the positions of both the solute and solvent excitation energies on an absolute energy scale and for peak intensities. The best comparison was obtained using wave functions obtained with dielectric-dependent self-consistent and range-separated hybrid functionals. Our computational protocol opens the way to accurate, predictive calculations of the electronic properties of electrolytes, of interest to a variety of energy problems.
First principles approach to ionicity of fragments
NASA Astrophysics Data System (ADS)
Pilania, Ghanshyam; Liu, Xiang-Yang; Valone, Steven M.
2015-02-01
We develop a first principles approach towards the ionicity of fragments. In contrast to the bond ionicity, the fragment ionicity refers to an electronic property of the constituents of a larger system, which may vary from a single atom to a functional group or a unit cell to a crystal. The fragment ionicity is quantitatively defined in terms of the coefficients of contributing charge states in a superposition of valence configurations of the system. Utilizing the constrained density functional theory-based computations, a practical method to compute the fragment ionicity from valence electron charge densities, suitably decomposed according to the Fragment Hamiltonian (FH) model prescription for those electron densities, is presented for the first time. The adopted approach is illustrated using BeO, MgO and CaO diatomic molecules as simple examples. The results are compared and discussed with respect to the bond ionicity scales of Phillips and Pauling.
First principles electrochemistry: Electrons and protons reacting as independent ions
NASA Astrophysics Data System (ADS)
Llano, Jorge; Eriksson, Leif A.
2002-12-01
We here present a first principles approach to calculate standard Gibbs energies and the corresponding observables (standard electrode potentials in the hydrogen scale ESHE0 and pKa values) of stoichiometric reactions involving electrons and/or protons as independent species in solution, from absolute electrochemical potentials defined according to quantum and statistical mechanics. In order to pass from the conventional electrodic and thermodynamic descriptions of electrochemistry to the first principles approach based on estimating absolute electrochemical potentials, we revisit the problem of the absolute and relative electrochemical scales from the macroscopic and microscopic viewpoints. A microscopic definition of the absolute electrochemical potential is presented in order to enable an identical thermodynamic treatment of any species in a given phase, i.e., electrons, protons, atoms, molecules, atomic and molecular ions, and electronically excited species. We show that absolute standard chemical potentials in the mole fraction scale can be easily computed with wave function and density functional theories in conjunction with self-consistent reaction field models. Based on Boltzmann and Fermi-Dirac statistics and experimental solvation data, we estimate an internally compatible set of absolute standard chemical and electrochemical potentials of protons and solvated electrons in the molality and molarity scales in aqueous solution at 298 K and 1 atm, within an absolute error of ±0.5 kcal/mol. This scheme enables a consistent and simultaneous description of the Gibbs energy changes and the observables (ESHE0 and pKa 's) of electron, proton, and proton-coupled electron transfer reactions in aqueous solution at 298 K and 1 atm.
Iron diffusion from first principles calculations
NASA Astrophysics Data System (ADS)
Wann, E.; Ammann, M. W.; Vocadlo, L.; Wood, I. G.; Lord, O. T.; Brodholt, J. P.; Dobson, D. P.
2013-12-01
The cores of Earth and other terrestrial planets are made up largely of iron1 and it is therefore very important to understand iron's physical properties. Chemical diffusion is one such property and is central to many processes, such as crystal growth, and viscosity. Debate still surrounds the explanation for the seismologically observed anisotropy of the inner core2, and hypotheses include convection3, anisotropic growth4 and dendritic growth5, all of which depend on diffusion. In addition to this, the main deformation mechanism at the inner-outer core boundary is believed to be diffusion creep6. It is clear, therefore, that to gain a comprehensive understanding of the core, a thorough understanding of diffusion is necessary. The extremely high pressures and temperatures of the Earth's core make experiments at these conditions a challenge. Low-temperature and low-pressure experimental data must be extrapolated across a very wide gap to reach the relevant conditions, resulting in very poorly constrained values for diffusivity and viscosity. In addition to these dangers of extrapolation, preliminary results show that magnetisation plays a major role in the activation energies for diffusion at low pressures therefore creating a break down in homologous scaling to high pressures. First principles calculations provide a means of investigating diffusivity at core conditions, have already been shown to be in very good agreement with experiments7, and will certainly provide a better estimate for diffusivity than extrapolation. Here, we present first principles simulations of self-diffusion in solid iron for the FCC, BCC and HCP structures at core conditions in addition to low-temperature and low-pressure calculations relevant to experimental data. 1. Birch, F. Density and composition of mantle and core. Journal of Geophysical Research 69, 4377-4388 (1964). 2. Irving, J. C. E. & Deuss, A. Hemispherical structure in inner core velocity anisotropy. Journal of Geophysical
First principles nonequilibrium plasma mixing
NASA Astrophysics Data System (ADS)
Ticknor, C.; Herring, S. D.; Lambert, F.; Collins, L. A.; Kress, J. D.
2014-01-01
We have performed nonequilibrium classical and quantum-mechanical molecular dynamics simulations that follow the interpenetration of deuterium-tritium (DT) and carbon (C) components through an interface initially in hydrostatic and thermal equilibrium. We concentrate on the warm, dense matter regime with initial densities of 2.5-5.5 g/cm3 and temperatures from 10 to 100 eV. The classical treatment employs a Yukawa pair-potential with the parameters adjusted to the plasma conditions, and the quantum treatment rests on an orbital-free density functional theory at the Thomas-Fermi-Dirac level. For times greater than about a picosecond, the component concentrations evolve in accordance with Fick's law for a classically diffusing fluid with the motion, though, described by the mutual diffusion coefficient of the mixed system rather than the self-diffusion of the individual components. For shorter times, microscopic processes control the clearly non-Fickian dynamics and require a detailed representation of the electron probability density in space and time.
First principles nonequilibrium plasma mixing.
Ticknor, C; Herring, S D; Lambert, F; Collins, L A; Kress, J D
2014-01-01
We have performed nonequilibrium classical and quantum-mechanical molecular dynamics simulations that follow the interpenetration of deuterium-tritium (DT) and carbon (C) components through an interface initially in hydrostatic and thermal equilibrium. We concentrate on the warm, dense matter regime with initial densities of 2.5-5.5 g/cm3 and temperatures from 10 to 100 eV. The classical treatment employs a Yukawa pair-potential with the parameters adjusted to the plasma conditions, and the quantum treatment rests on an orbital-free density functional theory at the Thomas-Fermi-Dirac level. For times greater than about a picosecond, the component concentrations evolve in accordance with Fick's law for a classically diffusing fluid with the motion, though, described by the mutual diffusion coefficient of the mixed system rather than the self-diffusion of the individual components. For shorter times, microscopic processes control the clearly non-Fickian dynamics and require a detailed representation of the electron probability density in space and time.
High Pressure Hydrogen from First Principles
NASA Astrophysics Data System (ADS)
Morales, M. A.
2014-12-01
Typical approximations employed in first-principles simulations of high-pressure hydrogen involve the neglect of nuclear quantum effects (NQE) and the approximate treatment of electronic exchange and correlation, typically through a density functional theory (DFT) formulation. In this talk I'll present a detailed analysis of the influence of these approximations on the phase diagram of high-pressure hydrogen, with the goal of identifying the predictive capabilities of current methods and, at the same time, making accurate predictions in this important regime. We use a path integral formulation combined with density functional theory, which allows us to incorporate NQEs in a direct and controllable way. In addition, we use state-of-the-art quantum Monte Carlo calculations to benchmark the accuracy of more approximate mean-field electronic structure calculations based on DFT, and we use GW and hybrid DFT to calculate the optical properties of the solid and liquid phases near metallization. We present accurate predictions of the metal-insulator transition on the solid, including structural and optical properties of the molecular phase. This work was supported by the U.S. Department of Energy at the Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and by LDRD Grant No. 13-LW-004.
Intrinsic ferroelectric switching from first principles.
Liu, Shi; Grinberg, Ilya; Rappe, Andrew M
2016-06-16
The existence of domain walls, which separate regions of different polarization, can influence the dielectric, piezoelectric, pyroelectric and electronic properties of ferroelectric materials. In particular, domain-wall motion is crucial for polarization switching, which is characterized by the hysteresis loop that is a signature feature of ferroelectric materials. Experimentally, the observed dynamics of polarization switching and domain-wall motion are usually explained as the behaviour of an elastic interface pinned by a random potential that is generated by defects, which appear to be strongly sample-dependent and affected by various elastic, microstructural and other extrinsic effects. Theoretically, connecting the zero-kelvin, first-principles-based, microscopic quantities of a sample with finite-temperature, macroscopic properties such as the coercive field is critical for material design and device performance; and the lack of such a connection has prevented the use of techniques based on ab initio calculations for high-throughput computational materials discovery. Here we use molecular dynamics simulations of 90° domain walls (separating domains with orthogonal polarization directions) in the ferroelectric material PbTiO3 to provide microscopic insights that enable the construction of a simple, universal, nucleation-and-growth-based analytical model that quantifies the dynamics of many types of domain walls in various ferroelectrics. We then predict the temperature and frequency dependence of hysteresis loops and coercive fields at finite temperatures from first principles. We find that, even in the absence of defects, the intrinsic temperature and field dependence of the domain-wall velocity can be described with a nonlinear creep-like region and a depinning-like region. Our model enables quantitative estimation of coercive fields, which agree well with experimental results for ceramics and thin films. This agreement between model and experiment suggests
Intrinsic ferroelectric switching from first principles
NASA Astrophysics Data System (ADS)
Liu, Shi; Grinberg, Ilya; Rappe, Andrew M.
2016-06-01
The existence of domain walls, which separate regions of different polarization, can influence the dielectric, piezoelectric, pyroelectric and electronic properties of ferroelectric materials. In particular, domain-wall motion is crucial for polarization switching, which is characterized by the hysteresis loop that is a signature feature of ferroelectric materials. Experimentally, the observed dynamics of polarization switching and domain-wall motion are usually explained as the behaviour of an elastic interface pinned by a random potential that is generated by defects, which appear to be strongly sample-dependent and affected by various elastic, microstructural and other extrinsic effects. Theoretically, connecting the zero-kelvin, first-principles-based, microscopic quantities of a sample with finite-temperature, macroscopic properties such as the coercive field is critical for material design and device performance; and the lack of such a connection has prevented the use of techniques based on ab initio calculations for high-throughput computational materials discovery. Here we use molecular dynamics simulations of 90° domain walls (separating domains with orthogonal polarization directions) in the ferroelectric material PbTiO3 to provide microscopic insights that enable the construction of a simple, universal, nucleation-and-growth-based analytical model that quantifies the dynamics of many types of domain walls in various ferroelectrics. We then predict the temperature and frequency dependence of hysteresis loops and coercive fields at finite temperatures from first principles. We find that, even in the absence of defects, the intrinsic temperature and field dependence of the domain-wall velocity can be described with a nonlinear creep-like region and a depinning-like region. Our model enables quantitative estimation of coercive fields, which agree well with experimental results for ceramics and thin films. This agreement between model and experiment suggests
First principles model of carbonate compaction creep
NASA Astrophysics Data System (ADS)
Keszthelyi, Daniel; Dysthe, Dag Kristian; Jamtveit, Bjørn
2016-05-01
Rocks under compressional stress conditions are subject to long-term creep deformation. From first principles we develop a simple micromechanical model of creep in rocks under compressional stress that combines microscopic fracturing and pressure solution. This model was then upscaled by a statistical mechanical approach to predict strain rate at core and reservoir scale. The model uses no fitting parameter and has few input parameters: effective stress, temperature, water saturation porosity, and material parameters. Material parameters are porosity, pore size distribution, Young's modulus, interfacial energy of wet calcite, the dissolution, and precipitation rates of calcite, and the diffusion rate of calcium carbonate, all of which are independently measurable without performing any type of deformation or creep test. Existing long-term creep experiments were used to test the model which successfully predicts the magnitude of the resulting strain rate under very different effective stress, temperature, and water saturation conditions. The model was used to predict the observed compaction of a producing chalk reservoir.
Heimel, Georg; Romaner, Lorenz; Zojer, Egbert; Brédas, Jean-Luc
2007-04-01
Self-assembled monolayers (SAMs) of organic molecules provide an important tool to tune the work function of electrodes in plastic electronics and significantly improve device performance. Also, the energetic alignment of the frontier molecular orbitals in the SAM with the Fermi energy of a metal electrode dominates charge transport in single-molecule devices. On the basis of first-principles calculations on SAMs of pi-conjugated molecules on noble metals, we provide a detailed description of the mechanisms that give rise to and intrinsically link these interfacial phenomena at the atomic level. The docking chemistry on the metal side of the SAM determines the level alignment, while chemical modifications on the far side provide an additional, independent handle to modify the substrate work function; both aspects can be tuned over several eV. The comprehensive picture established in this work provides valuable guidelines for controlling charge-carrier injection in organic electronics and current-voltage characteristics in single-molecule devices.
Materials Databases Infrastructure Constructed by First Principles Calculations: A Review
Lin, Lianshan
2015-10-13
The First Principles calculations, especially the calculation based on High-Throughput Density Functional Theory, have been widely accepted as the major tools in atom scale materials design. The emerging super computers, along with the powerful First Principles calculations, have accumulated hundreds of thousands of crystal and compound records. The exponential growing of computational materials information urges the development of the materials databases, which not only provide unlimited storage for the daily increasing data, but still keep the efficiency in data storage, management, query, presentation and manipulation. This review covers the most cutting edge materials databases in materials design, and their hot applications such as in fuel cells. By comparing the advantages and drawbacks of these high-throughput First Principles materials databases, the optimized computational framework can be identified to fit the needs of fuel cell applications. The further development of high-throughput DFT materials database, which in essence accelerates the materials innovation, is discussed in the summary as well.
NASA Astrophysics Data System (ADS)
Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi
2015-07-01
In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl- + CH3Cl → ClCH3 + Cl-) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.
Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi
2015-07-07
In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.
Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi
2015-07-07
In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein–Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple S{sub N}2 reaction (Cl{sup −} + CH{sub 3}Cl → ClCH{sub 3} + Cl{sup −}) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.
Description of charge conjugation from first principles
Lujan-Peschard, C.; Napsuciale, M.
2006-09-25
We construct the charge conjugation operator as a unitary automorphism in the spinor space ((1/2), 0) + (0 (1/2)) from first principles. We calculate its eigenspinors and derive the equation of motion they satisfy. The mapping associated to charge conjugation is constructed from parity eigenstates which are considered as particle and antiparticle.
Rediscovering First Principles through Online Learning.
ERIC Educational Resources Information Center
Kidney, Gary W.; Puckett, Edmond G.
2003-01-01
Describes an evaluation of Web-based instruction at the University of Houston-Clear Lake (Texas) that showed that the design team had been distracted from many first principles of instructional design by the creative chaos on the Web and discusses how self-reflection and role definitions allowed the team to overcome these disappointments and…
Coarse graining approach to First principles modeling of structural materials
Odbadrakh, Khorgolkhuu; Nicholson, Don M; Rusanu, Aurelian; Samolyuk, German D; Wang, Yang; Stoller, Roger E; Zhang, X.-G.; Stocks, George Malcolm
2013-01-01
Classical Molecular Dynamic (MD) simulations characterizing extended defects typically require millions of atoms. First principles calculations employed to understand these defect systems at an electronic level cannot, and should not deal with such large numbers of atoms. We present an e cient coarse graining (CG) approach to calculate local electronic properties of large MD-generated structures from the rst principles. We used the Locally Self-consistent Multiple Scattering (LSMS) method for two types of iron defect structures 1) screw-dislocation dipoles and 2) radiation cascades. The multiple scattering equations are solved at fewer sites using the CG. The atomic positions were determined by MD with an embedded atom force eld. The local moments in the neighborhood of the defect cores are calculated with rst-principles based on full local structure information, while atoms in the rest of the system are modeled by representative atoms with approximated properties. This CG approach reduces computational costs signi cantly and makes large-scale structures amenable to rst principles study. Work is sponsored by the USDoE, O ce of Basic Energy Sciences, Center for Defect Physics, an Energy Frontier Research Center. This research used resources of the Oak Ridge Leadership Computing Facility at the ORNL, which is supported by the O ce of Science of the USDoE under Contract No. DE-AC05-00OR22725.
Electronic absorption spectra from first principles
NASA Astrophysics Data System (ADS)
Hazra, Anirban
Methods for simulating electronic absorption spectra of molecules from first principles (i.e., without any experimental input, using quantum mechanics) are developed and compared. The electronic excitation and photoelectron spectra of ethylene are simulated, using the EOM-CCSD method for the electronic structure calculations. The different approaches for simulating spectra are broadly of two types---Frank-Condon (FC) approaches and vibronic coupling approaches. For treating the vibrational motion, the former use the Born-Oppenheimer or single surface approximation while the latter do not. Moreover, in our FC approaches the vibrational Hamiltonian is additively separable along normal mode coordinates, while in vibronic approaches a model Hamiltonian (obtained from ab initio electronic structure theory) provides an intricate coupling between both normal modes and electronic states. A method called vertical FC is proposed, where in accord with the short-time picture of molecular spectroscopy, the approximate excited-state potential energy surface that is used to calculate the electronic spectrum is taken to reproduce the ab initio potential at the ground-state equilibrium geometry. The potential energy surface along normal modes may be treated either in the harmonic approximation or using the full one-dimensional potential. Systems with highly anharmonic potential surfaces can be treated and expensive geometry optimizations are not required, unlike the traditional FC approach. The ultraviolet spectrum of ethylene between 6.2 and 8.7 eV is simulated using vertical FC. While FC approaches for simulation are computationally very efficient, they are not accurate when the underlying approximations are unreasonable. Then, vibronic coupling model Hamiltonians are necessary. Since these Hamiltonians have an analytic form, they are used to map the potential energy surfaces and understand their topology. Spectra are obtained by numerical diagonalization of the Hamiltonians. The
First-principle simulations of electronic structure in semicrystalline polyethylene
NASA Astrophysics Data System (ADS)
Moyassari, A.; Unge, M.; Hedenqvist, M. S.; Gedde, U. W.; Nilsson, F.
2017-05-01
In order to increase our fundamental knowledge about high-voltage cable insulation materials, realistic polyethylene (PE) structures, generated with a novel molecular modeling strategy, have been analyzed using first principle electronic structure simulations. The PE structures were constructed by first generating atomistic PE configurations with an off-lattice Monte Carlo method and then equilibrating the structures at the desired temperature and pressure using molecular dynamics simulations. Semicrystalline, fully crystalline and fully amorphous PE, in some cases including crosslinks and short-chain branches, were analyzed. The modeled PE had a structure in agreement with established experimental data. Linear-scaling density functional theory (LS-DFT) was used to examine the electronic structure (e.g., spatial distribution of molecular orbitals, bandgaps and mobility edges) on all the materials, whereas conventional DFT was used to validate the LS-DFT results on small systems. When hybrid functionals were used, the simulated bandgaps were close to the experimental values. The localization of valence and conduction band states was demonstrated. The localized states in the conduction band were primarily found in the free volume (result of gauche conformations) present in the amorphous regions. For branched and crosslinked structures, the localized electronic states closest to the valence band edge were positioned at branches and crosslinks, respectively. At 0 K, the activation energy for transport was lower for holes than for electrons. However, at room temperature, the effective activation energy was very low (˜0.1 eV) for both holes and electrons, which indicates that the mobility will be relatively high even below the mobility edges and suggests that charge carriers can be hot carriers above the mobility edges in the presence of a high electrical field.
NASA Astrophysics Data System (ADS)
Bahlakeh, Ghasem; Ramezanzadeh, Bahram; Saeb, Mohammad Reza; Terryn, Herman; Ghaffari, Mehdi
2017-10-01
The effect of cerium oxide treatment on the corrosion protection properties and interfacial interaction of steel/epoxy was studied by electrochemical impedance spectroscopy, (EIS) classical molecular dynamics (MD) and first principle quantum mechanics (QM) simulation methods X-ray photoelectron spectroscopy (XPS) was used to verify the chemical composition of the Ce film deposited on the steel. To probe the role of the curing agent in epoxy adsorption, computations were compared for an epoxy, aminoamide and aminoamide modified epoxy. Moreover, to study the influence of water on interfacial interactions the MD simulations were executed for poly (aminoamide)-cured epoxy resin in contact with the different crystallographic cerium dioxide (ceria, CeO2) surfaces including (100), (110), and (111) in the presence of water molecules. It was found that aminoamide-cured epoxy material was strongly adhered to all types of CeO2 substrates, so that binding to ceria surfaces followed the decreasing order CeO2 (111) > CeO2 (100) > CeO2 (110) in both dry and wet environments. Calculation of interaction energies noticed an enhanced adhesion to metal surface due to aminoamide curing of epoxy resin; where facets (100) and (111) revealed electrostatic and Lewis acid-base interactions, while an additional hydrogen bonding interaction was identified for CeO2 (110). Overall, MD simulations suggested decrement of adhesion to CeO2 in wet environment compared to dry conditions. Additionally, contact angle, pull-off test, cathodic delamination and salt spray analyses were used to confirm the simulation results. The experimental results in line with modeling results revealed that Ce layer deposited on steel enhanced substrate surface free energy, work of adhesion, and interfacial adhesion strength of the epoxy coating. Furthermore, decrement of adhesion of epoxy to CeO2 in presence of water was affirmed by experimental results. EIS results revealed remarkable enhancement of the corrosion
Fox, Stephen; Wallnoefer, Hannes G; Fox, Thomas; Tautermann, Christofer S; Skylaris, Chris-Kriton
2011-04-12
The accurate prediction of ligand binding affinities to a protein remains a desirable goal of computational biochemistry. Many available methods use molecular mechanics (MM) to describe the system, however, MM force fields cannot fully describe the complex interactions involved in binding, specifically electron transfer and polarization. First principles approaches can fully account for these interactions, and with the development of linear-scaling first principles programs, it is now viable to apply first principles calculations to systems containing tens of thousands of atoms. In this paper, a quantum mechanical Poisson-Boltzmann surface area approach is applied to a model of a protein-ligand binding cavity, the "tennis ball" dimer. Results obtained from this approach demonstrate considerable improvement over conventional molecular mechanics Poisson-Boltzmann surface area due to the more accurate description of the interactions in the system. For the first principles calculations in this study, the linear-scaling density functional theory program ONETEP is used, allowing the approach to be applied to receptor-ligand complexes of pharmaceutical interest that typically include thousands of atoms.
Electron-phonon interactions from first principles
NASA Astrophysics Data System (ADS)
Giustino, Feliciano
2017-01-01
This article reviews the theory of electron-phonon interactions in solids from the point of view of ab initio calculations. While the electron-phonon interaction has been studied for almost a century, predictive nonempirical calculations have become feasible only during the past two decades. Today it is possible to calculate from first principles many materials properties related to the electron-phonon interaction, including the critical temperature of conventional superconductors, the carrier mobility in semiconductors, the temperature dependence of optical spectra in direct and indirect-gap semiconductors, the relaxation rates of photoexcited carriers, the electron mass renormalization in angle-resolved photoelectron spectra, and the nonadiabatic corrections to phonon dispersion relations. In this article a review of the theoretical and computational framework underlying modern electron-phonon calculations from first principles as well as landmark investigations of the electron-phonon interaction in real materials is given. The first part of the article summarizes the elementary theory of electron-phonon interactions and their calculations based on density-functional theory. The second part discusses a general field-theoretic formulation of the electron-phonon problem and establishes the connection with practical first-principles calculations. The third part reviews a number of recent investigations of electron-phonon interactions in the areas of vibrational spectroscopy, photoelectron spectroscopy, optical spectroscopy, transport, and superconductivity.
First-principles quantum chemistry in the life sciences.
van Mourik, Tanja
2004-12-15
The area of computational quantum chemistry, which applies the principles of quantum mechanics to molecular and condensed systems, has developed drastically over the last decades, due to both increased computer power and the efficient implementation of quantum chemical methods in readily available computer programs. Because of this, accurate computational techniques can now be applied to much larger systems than before, bringing the area of biochemistry within the scope of electronic-structure quantum chemical methods. The rapid pace of progress of quantum chemistry makes it a very exciting research field; calculations that are too computationally expensive today may be feasible in a few months' time! This article reviews the current application of 'first-principles' quantum chemistry in biochemical and life sciences research, and discusses its future potential. The current capability of first-principles quantum chemistry is illustrated in a brief examination of computational studies on neurotransmitters, helical peptides, and DNA complexes.
(Un)folding of a high-temperature stable polyalanine helix from first principles
NASA Astrophysics Data System (ADS)
Blum, Volker; Rossi, Mariana; Tkatchenko, Alex; Scheffler, Matthias
2010-03-01
Peptides in vacuo offer a unique, well-defined testbed to match experiments directly against first-principles approaches that predict the intramolecular interactions that govern peptide and protein folding. In this respect, the polyalanine-based peptide Ac-Ala15-LysH^+ is particularly interesting, as it is experimentally known to form helices in vacuo, with stable secondary structure up to 750 K [1]. Room-temperature folding and unfolding timescales are usually not accessible by direct first-principles simulations, but this high T scale allows a rare direct first-principles view. We here use van der Waals corrected [2] density functional theory in the PBE generalized gradient approximation as implemented in the all-electron code FHI-aims [3] to show by Born-Oppenheimer ab initio molecular dynamics that Ac-Ala15-LysH^+ indeed unfolds rapidly (within a few ps) at T=800 K and 1000 K, but not at 500 K. We show that the structural stability of the α helix at 500 K is critically linked to a correct van der Waals treatment, and that the designed LysH^+ ionic termination is essential for the observed helical secondary structure. [1] M. Kohtani et al., JACS 126, 7420 (2004). [2] A. Tkatchenko, M. Scheffler, PRL 102, 073005 (2009). [3] V. Blum et al, Comp. Phys. Comm. 180, 2175 (2009).
First-principles modelling of Earth and planetary materials at high pressures and temperatures
NASA Astrophysics Data System (ADS)
Gillan, M. J.; Alfè, D.; Brodholt, J.; Vocadlo, L.; Price, G. D.
2006-08-01
Atomic-scale materials modelling based on first-principles quantum mechanics is playing an important role in the science of the Earth and the other planets. We outline the basic theory of this kind of modelling and explain how it can be applied in a variety of different ways to probe the thermodynamics, structure and transport properties of both solids and liquids under extreme conditions. After a summary of the density functional formulation of quantum mechanics and its practical implementation through pseudopotentials, we outline the simplest way of applying first-principles modelling, namely static zero-temperature calculations. We show how calculations of this kind can be compared with static compression experiments to demonstrate the accuracy of first-principles modelling at pressures reached in planetary interiors. Noting that virtually all problems concerning planetary interiors require an understanding of materials at high temperatures as well as high pressures, we then describe how first-principles lattice dynamics gives a powerful way of investigating solids at temperatures not too close to the melting line. We show how such calculations have contributed to important progress, including the recent discovery of the post-perovskite phase of MgSiO3 in the D'' layer at the base of the Earth's mantle. A range of applications of first-principles molecular dynamics are then reviewed, including the properties of metallic hydrogen in Jupiter and Saturn, of water, ammonia and methane in Uranus and Neptune, and of oxides and silicates and solid and liquid iron and its alloys in the Earth's deep interior. Recognizing the importance of phase equilibria throughout the planetary sciences, we review recently developed techniques for the first-principles calculation of solid and liquid free energies, melting curves and chemical potentials of alloys. We show how such calculations have contributed to an improved understanding of the temperature distribution and the chemical
First-principles modeling of electrostatically doped perovskite systems.
Stengel, Massimiliano
2011-04-01
Macroscopically, confined electron gases at polar oxide interfaces are rationalized within the simple "polar catastrophe" model. At the microscopic level, however, many other effects such as electric fields, structural distortions and quantum-mechanical interactions enter into play. Here, we show how to bridge the gap between these two length scales, by combining the accuracy of first-principles methods with the conceptual simplicity of model Hamiltonian approaches. To demonstrate our strategy, we address the equilibrium distribution of the compensating free carriers at polar LaAlO(3)/SrTiO(3) interfaces. Remarkably, a model including only calculated bulk properties of SrTiO(3) and no adjustable parameters accurately reproduces our full first-principles results. Our strategy provides a unified description of charge compensation mechanisms in SrTiO(3)-based systems.
Origin of Spinel Nanocheckerboards via First Principles.
Kornbluth, Mordechai; Marianetti, Chris A
2015-06-05
Self-organizing nanocheckerboards have been experimentally fabricated in Mn-based spinels but have not yet been explained with first principles. Using density-functional theory, we explain the phase diagram of the ZnMn_{x}Ga_{2-x}O_{4} system and the origin of nanocheckerboards. We predict total phase separation at zero temperature and then show the combination of kinetics, thermodynamics, and Jahn-Teller physics that generates the system's observed behavior. We find that the {011} surfaces are strongly preferred energetically, which mandates checkerboard ordering by purely geometrical considerations.
Materials Databases Infrastructure Constructed by First Principles Calculations: A Review
Lin, Lianshan
2015-10-13
The First Principles calculations, especially the calculation based on High-Throughput Density Functional Theory, have been widely accepted as the major tools in atom scale materials design. The emerging super computers, along with the powerful First Principles calculations, have accumulated hundreds of thousands of crystal and compound records. The exponential growing of computational materials information urges the development of the materials databases, which not only provide unlimited storage for the daily increasing data, but still keep the efficiency in data storage, management, query, presentation and manipulation. This review covers the most cutting edge materials databases in materials design, and their hotmore » applications such as in fuel cells. By comparing the advantages and drawbacks of these high-throughput First Principles materials databases, the optimized computational framework can be identified to fit the needs of fuel cell applications. The further development of high-throughput DFT materials database, which in essence accelerates the materials innovation, is discussed in the summary as well.« less
First principles studies on anatase surfaces
NASA Astrophysics Data System (ADS)
Selcuk, Sencer
TiO2 is one of the most widely studied metal oxides from both the fundamental and the technological points of view. A variety of applications have already been developed in the fields of energy production, environmental remediation, and electronics. Still, it is considered to have a high potential for further improvement and continues to be of great interest. This thesis describes our theoretical studies on the structural and electronic properties of anatase surfaces, and their (photo)chemical behavior. Recently much attention has been focused on anatase crystals synthesized by hydrofluoric acid assisted methods. These crystals exhibit a high percentage of {001} facets, generally considered to be highly reactive. We used first principles methods to investigate the structure of these facets, which is not yet well understood. Our results suggest that (001) surfaces exhibit the bulk-terminated structure when in contact with concentrated HF solutions. However, 1x4-reconstructed surfaces, as observed in UHV, become always more stable at the typical temperatures used to clean the as-prepared crystals in experiments. Since the reconstructed surfaces are only weakly reactive, we predict that synthetic anatase crystals with dominant {001} facets should not exhibit enhanced photocatalytic activity. Understanding how defects in solids interact with external electric fields is important for technological applications such as memristor devices. We studied the influence of an external electric field on the formation energies and diffusion barriers of the surface and the subsurface oxygen vacancies at the anatase (101) surface from first principles. Our results show that the applied field can have a significant influence on the relative stabilities of these defects, whereas the effect on the subsurface-to-surface defect migration is found to be relatively minor. Charge carriers play a key role in the transport properties and the surface chemistry of TiO2. Understanding their
Numerical Inductance Calculations Based on First Principles
Shatz, Lisa F.; Christensen, Craig W.
2014-01-01
A method of calculating inductances based on first principles is presented, which has the advantage over the more popular simulators in that fundamental formulas are explicitly used so that a deeper understanding of the inductance calculation is obtained with no need for explicit discretization of the inductor. It also has the advantage over the traditional method of formulas or table lookups in that it can be used for a wider range of configurations. It relies on the use of fast computers with a sophisticated mathematical computing language such as Mathematica to perform the required integration numerically so that the researcher can focus on the physics of the inductance calculation and not on the numerical integration. PMID:25402467
Primordial Black Holes from First Principles (Overview)
NASA Astrophysics Data System (ADS)
Lam, Casey; Bloomfield, Jolyon; Moss, Zander; Russell, Megan; Face, Stephen; Guth, Alan
2017-01-01
Given a power spectrum from inflation, our goal is to calculate, from first principles, the number density and mass spectrum of primordial black holes that form in the early universe. Previously, these have been calculated using the Press- Schechter formalism and some demonstrably dubious rules of thumb regarding predictions of black hole collapse. Instead, we use Monte Carlo integration methods to sample field configurations from a power spectrum combined with numerical relativity simulations to obtain a more accurate picture of primordial black hole formation. We demonstrate how this can be applied for both Gaussian perturbations and the more interesting (for primordial black holes) theory of hybrid inflation. One of the tools that we employ is a variant of the BBKS formalism for computing the statistics of density peaks in the early universe. We discuss the issue of overcounting due to subpeaks that can arise from this approach (the ``cloud-in-cloud'' problem). MIT UROP Office- Paul E. Gray (1954) Endowed Fund.
Numerical inductance calculations based on first principles.
Shatz, Lisa F; Christensen, Craig W
2014-01-01
A method of calculating inductances based on first principles is presented, which has the advantage over the more popular simulators in that fundamental formulas are explicitly used so that a deeper understanding of the inductance calculation is obtained with no need for explicit discretization of the inductor. It also has the advantage over the traditional method of formulas or table lookups in that it can be used for a wider range of configurations. It relies on the use of fast computers with a sophisticated mathematical computing language such as Mathematica to perform the required integration numerically so that the researcher can focus on the physics of the inductance calculation and not on the numerical integration.
First-principles determination of magnetic properties
NASA Astrophysics Data System (ADS)
Wu, Ruqian; Yang, Zongxian; Hong, Jisang
2003-02-01
First-principles density functional theory calculations have achieved great success in the exciting field of low-dimension magnetism, in explaining new phenomena observed in experiments as well as in predicting novel properties and materials. As known, spin-orbit coupling (SOC) plays an extremely important role in various magnetic properties such as magnetic anisotropy, magnetostriction, magneto-optical effects and spin-dynamics. Using the full potential linearized augmented plane wave approach, we have carried out extensive investigations for the effects of SOC in various materials. Results of selected examples, such as structure and magnetic properties of Ni/Cu(001), magnetism and magnetic anisotropy in magnetic Co/Cu(001) thin films, wires and clusters, magnetostriction in FeGa alloys and magneto-optical effects in Fe/Cr superlattices, are discussed.
Anisotropic Spin Hall Effect from First Principles
NASA Astrophysics Data System (ADS)
Freimuth, Frank; Blügel, Stefan; Mokrousov, Yuriy
2011-03-01
We present first principles calculations of the intrinsic non-dissipative spin Hall conductivity (SHC) for 3 d , 4 d and 5 d transition metals focusing in particular on the anisotropy of the SHC in nonmagnetic hcp metals and in antiferromagnetic Cr. For the metals of this study we generally find large anisotropies. We derive the general relation between the SHC vector and the direction of spin-polarization and discuss its consequences for hcp metals. Especially, it is predicted that for systems where the SHC changes sign due to the anisotropy the spin Hall effect may be tuned such that the spin polarization is parallel either to the electric field or to the spin current. Additionally, we describe our computational method [2,3] emphasizing the Wannier interpolation technique and the definition of the conserved spin current. This work is supported by the DFG Project MO 1731/3-1 and HGF-YIG grant VH-NG-513.
Transition Metal Nitrides: A First Principles Study
NASA Astrophysics Data System (ADS)
Pathak, Ashish; Singh, A. K.
2016-04-01
The present work describes the structural stability and electronic and mechanical properties of transition metal nitrides (TmNs: B1 cubic structure (cF8, Fm ‾ overline 3 m)) using first principles density functional theory (DFT) within generalized gradient approximation (GGA). The lattice constant of TmNs increases with increasing the atomic radii of the transition metals. Stability of the TmNs decreases from IVB to VIB groups due to increase in formation energy/atom. The bonding characteristics of these nitrides have been explained based on electronic density of states and charge density. All the TmNs satisfy Born stability criteria in terms of elastic constants except CrN and MoN that do not exist in equilibrium binary phase diagrams. The groups IVB and V-VIB nitrides are associated with brittle and ductile behaviour based on G/B ratios, respectively. The estimated melting temperatures of these nitrides exhibit reasonably good agreement with calculated with B than those of the C11 for all nitrides.
Phonon Engineering in Metals from First Principles
NASA Astrophysics Data System (ADS)
Lanzillo, Nicholas; Thomas, J.; Watson, E. B.; Washington, M.; Nayak, Saroj K.
2013-03-01
The electron-phonon interaction in metallic systems controls the electronic transport properties, including both electrical and thermal resistivity. The effect of compressive strain on the electron-phonon interaction in metals is investigated using first-principles density functional theory, and we propose various ways to ``engineer'' this interaction for various technological applications. In particular, we show that by applying compressive strain on the FCC crystals of Al, Cu, Ag and Au, the net electron-phonon scattering rate decreases and likewise the electrical resistivity decreases with increasing pressure. This trend is corroborated by experimental measurements of the resistance of a 0.5 mm diameter high-purity Al wire pressurized up to 2 GPa in a solid-media pressure apparatus at room temperature. The rate of the decrease in electrical resistivity as a function of pressure as determined by experiment is matched by the rate predicted by theory. Our simulations show that Al nanowires have the same response to strain as the bulk crystal; the net electron-phonon scattering can be reduced through compressive strain. Modifying the electron-phonon interaction in metallic structures shows great promise for future nano-electronic devices.
THERMODYNAMIC MODELING AND FIRST-PRINCIPLES CALCULATIONS
Turchi, P; Abrikosov, I; Burton, B; Fries, S; Grimvall, G; Kaufman, L; Korzhavyi, P; Manga, R; Ohno, M; Pisch, A; Scott, A; Zhang, W
2005-12-15
The increased application of quantum mechanical-based methodologies to the study of alloy stability has required a re-assessment of the field. The focus is mainly on inorganic materials in the solid state. In a first part, after a brief overview of the so-called ab initio methods with their approximations, constraints, and limitations, recommendations are made for a good usage of first-principles codes with a set of qualifiers. Examples are given to illustrate the power and the limitations of ab initio codes. However, despite the ''success'' of these methodologies, thermodynamics of complex multi-component alloys, as used in engineering applications, requires a more versatile approach presently afforded within CALPHAD. Hence, in a second part, the links that presently exist between ab initio methodologies, experiments, and CALPHAD approach are examined with illustrations. Finally, the issues of dynamical instability and of the role of lattice vibrations that still constitute the subject of ample discussions within the CALPHAD community are revisited in the light of the current knowledge with a set of recommendations.
Safeguards First Principle Initiative (SFPI) Cost Model
Mary Alice Price
2010-07-11
The Nevada Test Site (NTS) began operating Material Control and Accountability (MC&A) under the Safeguards First Principle Initiative (SFPI), a risk-based and cost-effective program, in December 2006. The NTS SFPI Comprehensive Assessment of Safeguards Systems (COMPASS) Model is made up of specific elements (MC&A plan, graded safeguards, accounting systems, measurements, containment, surveillance, physical inventories, shipper/receiver differences, assessments/performance tests) and various sub-elements, which are each assigned effectiveness and contribution factors that when weighted and rated reflect the health of the MC&A program. The MC&A Cost Model, using an Excel workbook, calculates budget and/or actual costs using these same elements/sub-elements resulting in total costs and effectiveness costs per element/sub-element. These calculations allow management to identify how costs are distributed for each element/sub-element. The Cost Model, as part of the SFPI program review process, enables management to determine if spending is appropriate for each element/sub-element.
Thermodynamics of magnetic systems from first principles
NASA Astrophysics Data System (ADS)
Eisenbach, Markus; Brown, Gregory; Rusanu, Aurelian; Nicholson, Don M.
2012-02-01
Density functional calculations have proven to be a useful tool in the study of ground state properties of many materials. The investigation of finite temperature magnetism on the other hand has to rely usually on the usage of empirical models that allow the large number of evaluations of the system's Hamiltonian that are required to obtain the phase space sampling needed to obtain the free energy, specific heat, magnetization, susceptibility, and other quantities as function of temperature. We have demonstrated a solution to this problem that harnesses the computational power of today's large massively parallel computers by combining a classical Monte-Carlo calculations with our first principles multiple scattering electronic structure code (LSMS) for constrained magnetic states. Here we will present recent advances in our method that improve the convergence as well as applications to 3d element based ferromagnets. This research was performed at Oak Ridge National Lab and sponsored in parts by the Center for Nanophase Material Sciences, Scientific User Facilities Division, the Center for Defect Physics, an Energy Frontier Research Center funded by the US DOE Office of Basic Energy Sciences and the Division of Materials Science and Engineering, Office of Basic Energy Science of
Dipole strength from first principles calculations
NASA Astrophysics Data System (ADS)
Miorelli, Mirko; Bacca, Sonia; Barnea, Nir; Hagen, Gaute; Jansen, Gustav R.; Papenbrock, Thomas; Orlandini, Giuseppina
2016-09-01
The electric dipole polarizability quantifies the low-energy behavior of the dipole strength. It is related to the proton and neutron distributions of the nucleus, and thereby can be used to constrain the neutron equation of state and the physics of neutron stars. Only recently however, new developments in ab initio methods finally allowed first principles studies of the dipole strength in medium-mass nuclei. Using the Lorentz integral transform coupled cluster method with the newly developed chiral interaction NNLOsat we study the low energy behavior of the dipole strength in 4He, 16O and 22O. For the exotic 22O we observe large contributions to the dipole strength at very low energy, indicating the presence of a pygmy dipole resonance, in agreement with what experimentally found by Leistenschneider et al.. We then study correlations between the electric dipole polarizability and the charge radius in 16O and 40Ca using a variety of realistic Hamiltonians, showing the importance of three-nucleon forces. We aknowledge NRC and NSERC.
Ziegler Natta heterogeneous catalysis by first principles computer experiments
NASA Astrophysics Data System (ADS)
Boero, M.; Parrinello, M.; Terakura, K.
1999-09-01
In this work we present a first attempt to study the polymerization process of ethylene in a realistic Ziegler-Natta heterogeneous system by means of first principles molecular dynamics. In particular, we simulate, in a very unbiased way, both the deposition of the catalyst TiCl 4 on the (110) active surface of a solid MgCl 2 support and the polymer chain formation. By using a constrained molecular dynamics approach, we work out the energetics and the reaction pathway of the polymerization process as it occurs in a laboratory or an industrial plant. The good agreement of the results of our simulations with the available experimental data indicates that these kinds of simulations can be used as a skilful approach to study the details of the reaction mechanism which are not accessible to experimental probes. This offers a tool to improve the production and/or to design reactants and products for practical use.
Simulating fluid-phase equilibria of water from first principles.
McGrath, Matthew J; Siepmann, J Ilja; Kuo, I-Feng W; Mundy, Christopher J; Vandevondele, Joost; Hutter, Jürg; Mohamed, Fawzi; Krack, Matthias
2006-01-19
Efficient Monte Carlo algorithms and a mixed-basis set electronic structure program were used to compute from first principles the vapor-liquid coexistence curve of water. A water representation based on the Becke-Lee-Yang-Parr exchange and correlation functionals yields a saturated liquid density of 900 kg/m3 at 323 K and normal boiling and critical temperatures of 350 and 550 K, respectively. An analysis of the structural and electronic properties of the saturated liquid phase shows an increase of the asymmetry of the local hydrogen-bonded structure despite the persistence of a 4-fold coordination and decreases of the molecular dipole moment and of the spread of the lowest unoccupied molecular orbital with increasing temperature.
First principles study of oxygen diffusion in a α-alumina ? twin grain boundary
NASA Astrophysics Data System (ADS)
Tohei, Tetsuya; Watanabe, Yuito; Takahashi, Nobuaki; Nakagawa, Tsubasa; Shibata, Naoya; Ikuhara, Yuichi
2015-12-01
We have investigated atomistic scale behaviour of oxygen diffusion along the ? twin grain boundary in α-Al2O3 (alumina) using molecular dynamics simulation and first principles total energy calculations. Based on the GB structure model which is verified by atomic-scale STEM observations on the bicrystal sample, quantitative evaluation of migration energies for dominant migration paths were performed by atomistic calculations. The preset calculation results confirmed fast oxygen diffusion behaviour along the GB. Our analysis shows that the dominant migration path or difference in the migration energies can be well correlated with the geometry of local atomic coordination around the migrating oxygen; lower migration energies are generally expected for paths with less change in coordination environment on migration. This trend holds both among gain boundary paths and bulk paths in α-alumina examined in the present study.
Metal decorated graphdiyne: A first principle study
NASA Astrophysics Data System (ADS)
Nayebi, Payman; Zaminpayma, Esmaeil
2017-09-01
In this work, we performed first principles calculations based on self-consistent charge density functional tight-binding to investigate mechanical and electronic properties of the optimized graphdiyne sheet, nanoribbons and transition metal decorated with Ag, Fe and Co atoms in the different sites. Then we calculated electronic properties of the graphdiyne sheet under uniaxial elastic strain in two different crystal directions. It is shown that the carbon bond length values for the graphdiyne structure are agreeable with experimental and other theoretical values. Our results show that the charge transferred to the graphdiyne from Ag and Fe atoms but to the Co decorated charge transferred to the Co atom from the graphdiyne. From the results, it can be seen that the graphdiyne is a direct semiconductor with doubly degenerated for both the valence band maximum and the conduction band minimum in the 6C hole site. Also, by Metal decorated of the graphdiyne, the structures become also direct semiconductor for the Ag decorated and indirect for Co and Fe decorated for the 6C- hole, top and bridge sites while the structure have metallic behavior for the 18C- hole site. Our results from the band structure of the GDY nanoribbons with the size of N = 1, 2, 3 and 4, indicate that all of them are nonzero band gaps at the Γ point. It can be seen that the energy gap decreases with increasing of nanoribbons size. Finally, we found that the gap energy increase with applying strain and also the structure remain direct semiconductor.
Transversity from First Principles in QCD
Brodsky, Stanley J.; /SLAC /Southern Denmark U., CP3-Origins
2012-02-16
Transversity observables, such as the T-odd Sivers single-spin asymmetry measured in deep inelastic lepton scattering on polarized protons and the distributions which are measured in deeply virtual Compton scattering, provide important constraints on the fundamental quark and gluon structure of the proton. In this talk I discuss the challenge of computing these observables from first principles; i.e.; quantum chromodynamics, itself. A key step is the determination of the frame-independent light-front wavefunctions (LFWFs) of hadrons - the QCD eigensolutions which are analogs of the Schroedinger wavefunctions of atomic physics. The lensing effects of initial-state and final-state interactions, acting on LFWFs with different orbital angular momentum, lead to T-odd transversity observables such as the Sivers, Collins, and Boer-Mulders distributions. The lensing effect also leads to leading-twist phenomena which break leading-twist factorization such as the breakdown of the Lam-Tung relation in Drell-Yan reactions. A similar rescattering mechanism also leads to diffractive deep inelastic scattering, as well as nuclear shadowing and non-universal antishadowing. It is thus important to distinguish 'static' structure functions, the probability distributions computed the target hadron's light-front wavefunctions, versus 'dynamical' structure functions which include the effects of initial- and final-state rescattering. I also discuss related effects such as the J = 0 fixed pole contribution which appears in the real part of the virtual Compton amplitude. AdS/QCD, together with 'Light-Front Holography', provides a simple Lorentz-invariant color-confining approximation to QCD which is successful in accounting for light-quark meson and baryon spectroscopy as well as hadronic LFWFs.
NASA Astrophysics Data System (ADS)
Trinkle, Dallas R.; Yasi, Joseph A.; Hector, Louis G.
Predictive modeling of strength from first-principles electronic structure methods offers great promise to inform Mg alloy design. Simulating the mechanical behavior for new alloys requires an understanding of mechanisms for deformation at atomic-length scales, with accurate chemistry, extended to larger length- and time-scales. To design ductile Mg alloys, we identify solutes that strengthen basal slip and increase cross-slip. First-principles modeling of dislocations predict dislocation motion under stress through a field of solutes at a finite temperature. First-principles flexible boundary conditions compute accurate core structures of basal and prismatic dislocations, and dislocation/solute interactions. We develop new models to predict the solute-strengthening for basal dislocations; cross-slip from basal- to prismatic-slip for α-type screw dislocations; and cross-slip stress with solutes. First-principles data provides insight into the response of dislocations to solutes and quantitative data to build new predictive models.
First principles investigation of substituted strontium hexaferrite
NASA Astrophysics Data System (ADS)
Dixit, Vivek
This dissertation investigates how the magnetic properties of strontium hexaferrite change upon the substitution of foreign atoms at the Fe sites. Strontium hexaferrite, SrFe12O19, is a commonly used hard magnetic material and is produced in large quantities (around 500,000 tons per year). For different applications of strontium hexaferrite, its magnetic properties can be tuned by a proper substitution of the foreign atoms. Experimental screening for a proper substitution is a cost-intensive and time-consuming process, whereas computationally it can be done more efficiently. We used the 'density functional theory' a first principles based method to study substituted strontium hexaferrite. The site occupancies of the substituted atoms were estimated by calculating the substitution energies of different configurations. The formation probabilities of configurations were used to calculate the magnetic properties of substituted strontium hexaferrite. In the first study, Al-substituted strontium hexaferrite, SrFe12-x AlxO19 with x=0.5 and x=1.0 were investigated. It was found that at the annealing temperature the non-magnetic Al +3 ions preferentially replace Fe+3 ions from the 12 k and 2a sites. We found that the magnetization decreases and the magnetic anisotropy field increases as the fraction, x of the Al atoms increases. In the second study, SrFe12-xGaxO19 and SrFe12-xInxO19 with x=0.5 and x=1.0 were investigated. In the case of SrFe12-xGaxO19, the sites where Ga+3 ions prefer to enter are: 12 k, 2a, and 4f1. For SrFe12-xInxO19, In+3 ions most likely to occupy the 12k, 4f1 , and 4f2 sites. In both cases the magnetization was found to decrease slightly as the fraction of substituted atom increases. The magnetic anisotropy field increased for SrFe12-xGaxO 19, and decreased for SrFe12-xInxO19 as the concentration of substituted atoms increased. In the third study, 23 elements (M) were screened for their possible substitution in strontium hexaferrite, SrFe12-xMxO 19
Methods for molecular interactions and large-scale simulations
NASA Astrophysics Data System (ADS)
Jeon, Byoungseon
Molecular Dynamics (MD) is one of the powerful methods for studying the complexity of large ensembles of particles in various states of matter. This thesis describes work in advancing selective applications of computational molecular dynamics. First, the detailed interaction between methyl-thiol molecules and a Au(111) surface is investigated through extensive state-of-the-art first principles calculations. The quantum simulation results are used to fit a classical many-body surface potential, which can be conveniently implemented into MD simulations of alkane-thiol ensembles on a Au(111) surface. Also a coarse-grained MD code is developed, and the effect of thiol densities and alkane-chain lengths on self-assembled monolayers is examined. Second, ultracold neutral plasmas with open boundary are investigated with all pair-wise calculations, parallel TREE, and a mean field potential. Using two-component plasma (TCP) analysis and large-scale parallel processing, simulations of realistically large configurations are conducted. In addition to TCP, the mean field theory facilitates the simple description of background electrons, and full scale simulations of ultracold plasma evolution are presented. Finally, two-temperature systems of two-component plasmas with extremely high density and temperatures are examined for thermal mixing and equilibration between the components. Electrostatic interactions are evaluated with periodic boundary conditions, and bare/reduced ion mass simulations are conducted for the balance between numerical efficiency and reliability of simulations. These examples of development and applications of MD methods, such as first-principles calculations, force-field development, efficient algorithm implementation, and large-scale molecular simulations, have provided many valuable experiences in the dynamics and energetics of molecular systems. They have also provided specific new studies and results that are valuable to the communities of surface self
Solubility of nonelectrolytes: a first-principles computational approach.
Jackson, Nicholas E; Chen, Lin X; Ratner, Mark A
2014-05-15
Using a combination of classical molecular dynamics and symmetry adapted intermolecular perturbation theory, we develop a high-accuracy computational method for examining the solubility energetics of nonelectrolytes. This approach is used to accurately compute the cohesive energy density and Hildebrand solubility parameters of 26 molecular liquids. The energy decomposition of symmetry adapted perturbation theory is then utilized to develop multicomponent Hansen-like solubility parameters. These parameters are shown to reproduce the solvent categorizations (nonpolar, polar aprotic, or polar protic) of all molecular liquids studied while lending quantitative rigor to these qualitative categorizations via the introduction of simple, easily computable parameters. Notably, we find that by monitoring the first-order exchange energy contribution to the total interaction energy, one can rigorously determine the hydrogen bonding character of a molecular liquid. Finally, this method is applied to compute explicitly the Flory interaction parameter and the free energy of mixing for two different small molecule mixtures, reproducing the known miscibilities. This methodology represents an important step toward the prediction of molecular solubility from first principles.
Massively parallel first-principles simulation of electron dynamics in materials
Draeger, Erik W.; Andrade, Xavier; Gunnels, John A.; ...
2017-08-01
Here we present a highly scalable, parallel implementation of first-principles electron dynamics coupled with molecular dynamics (MD). By using optimized kernels, network topology aware communication, and by fully distributing all terms in the time-dependent Kohn–Sham equation, we demonstrate unprecedented time to solution for disordered aluminum systems of 2000 atoms (22,000 electrons) and 5400 atoms (59,400 electrons), with wall clock time as low as 7.5 s per MD time step. Despite a significant amount of non-local communication required in every iteration, we achieved excellent strong scaling and sustained performance on the Sequoia Blue Gene/Q supercomputer at LLNL. We obtained up tomore » 59% of the theoretical sustained peak performance on 16,384 nodes and performance of 8.75 Petaflop/s (43% of theoretical peak) on the full 98,304 node machine (1,572,864 cores). Lastly, scalable explicit electron dynamics allows for the study of phenomena beyond the reach of standard first-principles MD, in particular, materials subject to strong or rapid perturbations, such as pulsed electromagnetic radiation, particle irradiation, or strong electric currents.« less
First-principles electrostatic potentials for reliable alignment at interfaces and defects.
Sundararaman, Ravishankar; Ping, Yuan
2017-03-14
The alignment of electrostatic potential between different atomic configurations is necessary for first-principles calculations of band offsets across interfaces and formation energies of charged defects. However, strong oscillations of this potential at the atomic scale make alignment challenging, especially when atomic geometries change considerably from bulk to the vicinity of defects and interfaces. We introduce a method to suppress these strong oscillations by eliminating the deep wells in the potential at each atom. We demonstrate that this method considerably improves the system-size convergence of a wide range of first-principles predictions that depend on the alignment of electrostatic potentials, including band offsets at solid-liquid interfaces, and formation energies of charged vacancies in solids and at solid surfaces in vacuum. Finally, we use this method in conjunction with continuum solvation theories to investigate energetics of charged vacancies at solid-liquid interfaces. We find that for the example of an NaCl (001) surface in water, solvation reduces the formation energy of charged vacancies by 0.5 eV: calculation of this important effect was previously impractical due to the computational cost in molecular-dynamics methods.
Calculating Natural Optical Activity of Molecules from First Principles
NASA Astrophysics Data System (ADS)
Srebro-Hooper, Monika; Autschbach, Jochen
2017-05-01
Computations of natural optical activity (OA) from first principles (ab initio) have become indispensable in chiroptical studies of molecular systems. Calculations are used to assign absolute configurations and to analyze chiroptical data, providing a basis for understanding their origin as well as for assigning and predicting experimental results. In this article, methodology for OA computations is outlined and accompanied by a review of selected, mainly recent (ca. 2010-2016) achievements in optical rotation, electronic and vibrational circular dichroism, and Raman OA calculations. We discuss some important aspects of the computational models and methodological developments, along with recently proposed approaches to analyze and interpret OA parameters. We highlight applications of chiroptical computational methods in studies of helicenes and chiral nanoparticles.
Liquid-state paramagnetic relaxation from first principles
NASA Astrophysics Data System (ADS)
Rantaharju, Jyrki; Vaara, Juha
2016-10-01
We simulate nuclear and electron spin relaxation rates in a paramagnetic system from first principles. Sampling a molecular dynamics trajectory with quantum-chemical calculations produces a time series of the instantaneous parameters of the relevant spin Hamiltonian. The Hamiltonians are, in turn, used to numerically solve the Liouville-von Neumann equation for the time evolution of the spin density matrix. We demonstrate the approach by studying the aqueous solution of the Ni2 + ion. Taking advantage of Kubo's theory, the spin-lattice (T1) and spin-spin (T2) relaxation rates are extracted from the simulations of the time dependence of the longitudinal and transverse magnetization, respectively. Good agreement with the available experimental data is obtained by the method.
First-principles theory, coarse-grained models, and simulations of ferroelectrics.
Waghmare, Umesh V
2014-11-18
CONSPECTUS: A ferroelectric crystal exhibits macroscopic electric dipole or polarization arising from spontaneous ordering of its atomic-scale dipoles that breaks inversion symmetry. Changes in applied pressure or electric field generate changes in electric polarization in a ferroelectric, defining its piezoelectric and dielectric properties, respectively, which make it useful as an electromechanical sensor and actuator in a number of applications. In addition, a characteristic of a ferroelectric is the presence of domains or states with different symmetry equivalent orientations of spontaneous polarization that are switchable with large enough applied electric field, a nonlinear property that makes it useful for applications in nonvolatile memory devices. Central to these properties of a ferroelectric are the phase transitions it undergoes as a function of temperature that involve lowering of the symmetry of its high temperature centrosymmetric paraelectric phase. Ferroelectricity arises from a delicate balance between short and long-range interatomic interactions, and hence the resulting properties are quite sensitive to chemistry, strains, and electric charges associated with its interface with substrate and electrodes. First-principles density functional theoretical (DFT) calculations have been very effective in capturing this and predicting material and environment specific properties of ferroelectrics, leading to fundamental insights into origins of ferroelectricity in oxides and chalcogenides uncovering a precise picture of electronic hybridization, topology, and mechanisms. However, use of DFT in molecular dynamics for detailed prediction of ferroelectric phase transitions and associated temperature dependent properties has been limited due to large length and time scales of the processes involved. To this end, it is quite appealing to start with input from DFT calculations and construct material-specific models that are realistic yet simple for use in
Auger recombination in sodium-iodide scintillators from first principles
McAllister, Andrew; Åberg, Daniel; Schleife, André; Kioupakis, Emmanouil
2015-04-06
Scintillator radiation detectors suffer from low energy resolution that has been attributed to non-linear light yield response to the energy of the incident gamma rays. Auger recombination is a key non-radiative recombination channel that scales with the third power of the excitation density and may play a role in the non-proportionality problem of scintillators. In this work, we study direct and phonon-assisted Auger recombination in NaI using first-principles calculations. Our results show that phonon-assisted Auger recombination, mediated primarily by short-range phonon scattering, dominates at room temperature. We discuss our findings in light of the much larger values obtained by numerical fits to z-scan experiments.
Vibrational and thermophysical properties of PETN from first principles
NASA Astrophysics Data System (ADS)
Gonzalez, Joseph M.; Landerville, Aaron C.; Oleynik, Ivan I.
2017-01-01
Thermophysical properties are urgently sought as input for meso- and continuum-scale modeling of energetic materials (EMs). However, experimental data are often limited as they cover a narrow region of specific pressures and temperatures. Such modeling of EMs can be greatly improved by inclusion of thermophysical properties over a wide range of pressures and temperatures, provided such data could be reliably obtained from theory. We demonstrate such a capability by calculating the PVT equation of state, heat capacities, and coefficients of thermal expansion for pentaerythritol tetranitrate (PETN) using first-principles density functional theory, which includes proper description of van der Waals interactions, zero-point energy and thermal contributions to free energy calculated using the quasi-harmonic approximation. Further, we investigate the evolution of the vibration spectrum of PETN as a function of pressure.
Vibrational and Thermophysical Properties of PETN from First Principles
NASA Astrophysics Data System (ADS)
Gonzalez, Joseph; Landerville, Aaron; Oleynik, Ivan
2015-06-01
Thermophysical properties are urgently sought as input for meso- and continuum-scale modeling of energetic materials (EMs). However, empirical data in this regard are often limited to specific pressures and temperatures. Such modeling of EMs can be greatly improved by inclusion of thermophysical properties over a wide range of pressures and temperatures, provided such data could be reliably obtained from theory. We demonstrate such a capability by calculating the equation of state, heat capacities, coefficients of thermal expansion, and Gruneissen parameters for pentaerythritol tetranitrate (PETN) using first-principles density functional theory, which includes proper description of van der Waals interactions and zero-point and thermal free energy contributions to pressure, the latter being calculated using the quasi-harmonic approximation. Further, we investigate the evolution of the vibration spectrum of PETN as a function of pressure.
Auger recombination in sodium-iodide scintillators from first principles
NASA Astrophysics Data System (ADS)
McAllister, Andrew; Åberg, Daniel; Schleife, André; Kioupakis, Emmanouil
2015-04-01
Scintillator radiation detectors suffer from low energy resolution that has been attributed to non-linear light yield response to the energy of the incident gamma rays. Auger recombination is a key non-radiative recombination channel that scales with the third power of the excitation density and may play a role in the non-proportionality problem of scintillators. In this work, we study direct and phonon-assisted Auger recombination in NaI using first-principles calculations. Our results show that phonon-assisted Auger recombination, mediated primarily by short-range phonon scattering, dominates at room temperature. We discuss our findings in light of the much larger values obtained by numerical fits to z-scan experiments.
Thermodynamics of Magnetic Systems from First Principles: WL-LSMS
Eisenbach, Markus; Zhou, Chenggang; Nicholson, Don M; Brown, Greg; Larkin, Jeffrey M; Schulthess, Thomas C
2010-01-01
Density Functional calculations have proven to be a powerful tool to study the ground state of many materials. For finite temperatures the situation is less ideal and one is often forced to rely on models with parameters either fitted to zero temperature first principles calculations or experimental results. This approach is especially unsatisfacory in inhomogeneous systems, nano particles, or other systems where the model parameters could vary significantly from one site to another. Here we describe a possible solution to this problem by combining classical Monte Carlo calculations the Wang-Landau method in this case with a firs principles electronic structure calculation, specifically our locally selfconsistent multiple scallering code (LSMS). The combined code shows superb scaling behavior on massively parallel computers. The code sustained 1.836 Petaflop/s on 223232 cores of the Cray XT5 jaguar system at Oak Ridge.
First Principles Atomistic Model for Carbon-Doped Boron Suboxide
2014-09-01
First Principles Atomistic Model for Carbon-Doped Boron Suboxide by Amol B Rahane, Jennifer S Dunn, and Vijay Kumar ARL-TR-7106...2014 First Principles Atomistic Model for Carbon-Doped Boron Suboxide Amol B Rahane Dr Vijay Kumar Foundation 1969 Sector 4 Gurgaon...Final 3. DATES COVERED (From - To) October 2013–July 2014 4. TITLE AND SUBTITLE First Principles Atomistic Model for Carbon-Doped Boron Suboxide
NASA Astrophysics Data System (ADS)
Kohno, Yuji; Mori, Kazuki; Hiyoshi, Reiko I.; Takahashi, Osamu; Ueda, Kazuyoshi
2016-06-01
Classical molecular dynamics (MD) calculations were performed to reveal the effect of high pressure on the crystal structure of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), an insensitive energetic material. The primary simulation cell consisted of 54 molecules in a triclinic cell, corresponding to 27 unit cells obtained by replicating the experimentally determined unit cell. Inter- and intra-molecular hydrogen bonds were maintained in the range of 1.0 atm to 20.0 GPa as pressure was incremented by 0.5 GPa. The pressure dependence of the interlayer distances (h1) and farthest intermolecular distance (d1) between nitro groups in the TATB crystal's unit cell was investigated in the same range. h1 decreased monotonously from 3.50 to 2.90 Å as pressure increased to 20.0 GPa. However, d1 increased considerably with pressure up to 4.0 GPa, most remarkably between 2.0 and 4.0 GPa. Thus, a unique structural change occurred in TATB crystal in this range. On the other hand, 1,3-diamino-2,4,6-trinitrobenzene (DATB) crystal showed a unique structural change between 7.0 and 8.0 GPa. These discrepancies are attributed to the different network systems of hydrogen bonding of these two molecules. To validate the MD calculation results, we conducted first-principles calculations. MD and first-principles calculations showed good agreement with previous experimental results.
Designing Interactive Learning Environments: An Approach from First Principles
ERIC Educational Resources Information Center
Scott, Bernard; Cong, Chunyu
2007-01-01
Purpose: Today's technology supports the design of more and more sophisticated interactive learning environments. This paper aims to argue that such design should develop from first principles. Design/methodology/approach: In the paper by first principles is meant: learning theory and principles of course design. These principles are briefly…
The triplet code from first principles.
Trifonov, E N
2004-08-01
Temporal order ("chronology") of appearance of amino acids and their respective codons on evolutionary scene is reconstructed. A consensus chronology of amino acids is built on the basis of 60 different criteria each offering certain temporal order. After several steps of filtering the chronology vectors are averaged resulting in the consensus order: G, A, D, V, P, S, E, (L, T), R, (I, Q, N), H, K, C, F, Y, M, W. It reveals two important features: the amino acids synthesized in imitation experiments of S. Miller appeared first, while the amino acids associated with codon capture events came last. The reconstruction of codon chronology is based on the above consensus temporal order of amino acids, supplemented by the stability and complementarity rules first suggested by M. Eigen and P. Schuster, and on the earlier established processivity rule. At no point in the reconstruction the consensus amino-acid chronology was in conflict with these three rules. The derived genealogy of all 64 codons suggested several important predictions that are confirmed. The reconstruction of the origin and evolutionary history of the triplet code becomes, thus, a powerful research tool for molecular evolution studies, especially in its early stages. Copyright 2004 Adenine Press
First-principles calculations of mobilities in MOSFETs
NASA Astrophysics Data System (ADS)
Hadjisavvas, George; Tsetseris, Leonidas; Evans, Matthew; Pantelides, Sokrates
2007-03-01
Nano-scale MOSFETs demonstrate interesting electron transport behavior. Straining the silicon lattice results in significant increases in carrier mobility up to 100%. Transport properties are known to depend also on the presence of interface traps. Due to their significance, a large number of studies have obtained mobilities, but in an empirical and semi-classical fashion, whereas, in nano-devices quantum mechanical effects and atomic-scale structural details are the key factors of mobility calculations. Here we use a recently developed method[1] for first-principles calculations of mobilites within DFT to probe the effect of strain and interface point defects (e.g., dangling bonds) on mobilities in double gate ultra-thin SOI (UTSOI) MOSFETs. The transport properties are described in a fully self-consistent quantum mechanical fashion and mobilities are calculated within the Born approximation. The results show that biaxial tensile strain is shown to significantly increase carrier mobility in UTSOI devices by suppressing the effective scattering from atomic-scale interface inhomogeneities; the effect of dangling bonds on mobility in a UTSOI channel is weaker than in conventional MOSFETs because the carrier density peaks at the center of the channel. This work was supported in part by NSF Grant ECS-0524655 and by AFOSR Grant 4224224232. [1] M.H. Evans et al., Phys. Rev. Lett. 95, 106802 (2005).
Towards Experimental Accuracy from the First Principles
NASA Astrophysics Data System (ADS)
Polyansky, O. L.; Lodi, L.; Tennyson, J.; Zobov, N. F.
2013-06-01
Producing ab initio ro-vibrational energy levels of small, gas-phase molecules with an accuracy of 0.10 cm^{-1} would constitute a significant step forward in theoretical spectroscopy and would place calculated line positions considerably closer to typical experimental accuracy. Such an accuracy has been recently achieved for the H_3^+ molecular ion for line positions up to 17 000 cm ^{-1}. However, since H_3^+ is a two-electron system, the electronic structure methods used in this study are not applicable to larger molecules. A major breakthrough was reported in ref., where an accuracy of 0.10 cm^{-1} was achieved ab initio for seven water isotopologues. Calculated vibrational and rotational energy levels up to 15 000 cm^{-1} and J=25 resulted in a standard deviation of 0.08 cm^{-1} with respect to accurate reference data. As far as line intensities are concerned, we have already achieved for water a typical accuracy of 1% which supersedes average experimental accuracy. Our results are being actively extended along two major directions. First, there are clear indications that our results for water can be improved to an accuracy of the order of 0.01 cm^{-1} by further, detailed ab initio studies. Such level of accuracy would already be competitive with experimental results in some situations. A second, major, direction of study is the extension of such a 0.1 cm^{-1} accuracy to molecules containg more electrons or more than one non-hydrogen atom, or both. As examples of such developments we will present new results for CO, HCN and H_2S, as well as preliminary results for NH_3 and CH_4. O.L. Polyansky, A. Alijah, N.F. Zobov, I.I. Mizus, R. Ovsyannikov, J. Tennyson, L. Lodi, T. Szidarovszky and A.G. Csaszar, Phil. Trans. Royal Soc. London A, {370}, 5014-5027 (2012). O.L. Polyansky, R.I. Ovsyannikov, A.A. Kyuberis, L. Lodi, J. Tennyson and N.F. Zobov, J. Phys. Chem. A, (in press). L. Lodi, J. Tennyson and O.L. Polyansky, J. Chem. Phys. {135}, 034113 (2011).
Liquid Water from First Principles: Validation of Different Sampling Approaches
Mundy, C J; Kuo, W; Siepmann, J; McGrath, M J; Vondevondele, J; Sprik, M; Hutter, J; Parrinello, M; Mohamed, F; Krack, M; Chen, B; Klein, M
2004-05-20
A series of first principles molecular dynamics and Monte Carlo simulations were carried out for liquid water to assess the validity and reproducibility of different sampling approaches. These simulations include Car-Parrinello molecular dynamics simulations using the program CPMD with different values of the fictitious electron mass in the microcanonical and canonical ensembles, Born-Oppenheimer molecular dynamics using the programs CPMD and CP2K in the microcanonical ensemble, and Metropolis Monte Carlo using CP2K in the canonical ensemble. With the exception of one simulation for 128 water molecules, all other simulations were carried out for systems consisting of 64 molecules. It is found that the structural and thermodynamic properties of these simulations are in excellent agreement with each other as long as adiabatic sampling is maintained in the Car-Parrinello molecular dynamics simulations either by choosing a sufficiently small fictitious mass in the microcanonical ensemble or by Nos{acute e}-Hoover thermostats in the canonical ensemble. Using the Becke-Lee-Yang-Parr exchange and correlation energy functionals and norm-conserving Troullier-Martins or Goedecker-Teter-Hutter pseudopotentials, simulations at a fixed density of 1.0 g/cm{sup 3} and a temperature close to 315 K yield a height of the first peak in the oxygen-oxygen radial distribution function of about 3.0, a classical constant-volume heat capacity of about 70 J K{sup -1} mol{sup -1}, and a self-diffusion constant of about 0.1 Angstroms{sup 2}/ps.
Stavrou, Elissaios Riad Manaa, M. Zaug, Joseph M.; Kuo, I-Feng W.; Pagoria, Philip F.; Crowhurst, Jonathan C.; Armstrong, Michael R.; Kalkan, Bora
2015-10-14
Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C{sub 4}H{sub 4}N{sub 6}O{sub 5} Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. We find very good agreement between the experimental and theoretically derived EOS.
Stavou, Elissaios; Manaa, M. Riad; Zaug, Joseph M.; ...
2015-10-14
Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C4H4N6O5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phasemore » transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. As a result, we find very good agreement between the experimental and theoretically derived EOS.« less
Stavrou, Elissaios; Riad Manaa, M; Zaug, Joseph M; Kuo, I-Feng W; Pagoria, Philip F; Kalkan, Bora; Crowhurst, Jonathan C; Armstrong, Michael R
2015-10-14
Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C4H4N6O5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. We find very good agreement between the experimental and theoretically derived EOS.
Stavou, Elissaios; Manaa, M. Riad; Zaug, Joseph M.; Kuo, I-Feng W.; Pagoria, Philip F.; Crowhurst, Jonathan C.; Armstrong, Michael R.; Kalkan, Bora
2015-10-14
Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C_{4}H_{4}N_{6}O_{5} Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. As a result, we find very good agreement between the experimental and theoretically derived EOS.
Materials corrosion and protection from first principles
NASA Astrophysics Data System (ADS)
Johnson, Donald F.
suggests that alloying Fe with Si can be an effective means to limit uptake of these elements into steel. Spallation of protective layers on jet engine turbine blades is a problem that arises during thermal cycling. An alternative thermal barrier coating system involving MoSi2 is considered and calculations predict strong adhesion at the MoSi2/Ni interface. The interfacial bonding structure reveals a mixture of metallic and covalent cross-interface bonds. The adhesion energy is similar across all three MoSi2 facets studied. Upon exposure to oxygen, this MoSi2 alloy will form a strongly adhered oxide scale, which in turn may strongly adhere the heat shield material (yttria-stabilized zirconia), thereby potentially extending the lifetime of the barrier coating. Lastly, the interaction of hydrogen isotopes (fusion fuel) with tungsten (a proposed fusion reactor wall material) is examined. Exothermic dissociative adsorption is predicted, along with endothermic absorption and dissolution. Surface-to-subsurface diffusion energy barriers for H incorporation into bulk W are large and the corresponding outward diffusion barriers are very small. In bulk W, deep energetic traps (trapping multiple H atoms) are predicted at vacancy defects. Thus, under high neutron fluxes that will produce vacancies in W, H are predicted to collect at these vacancies. In turn, locally high concentrations of H at such vacancies will enhance decohesion of bulk W, consistent with observed blistering under deuterium implantation. Limiting vacancy formation may be key to the survival of W as a fusion reactor wall material.
Predicting catalysis: understanding ammonia synthesis from first-principles calculations.
Hellman, A; Baerends, E J; Biczysko, M; Bligaard, T; Christensen, C H; Clary, D C; Dahl, S; van Harrevelt, R; Honkala, K; Jonsson, H; Kroes, G J; Luppi, M; Manthe, U; Nørskov, J K; Olsen, R A; Rossmeisl, J; Skúlason, E; Tautermann, C S; Varandas, A J C; Vincent, J K
2006-09-14
Here, we give a full account of a large collaborative effort toward an atomic-scale understanding of modern industrial ammonia production over ruthenium catalysts. We show that overall rates of ammonia production can be determined by applying various levels of theory (including transition state theory with or without tunneling corrections, and quantum dynamics) to a range of relevant elementary reaction steps, such as N(2) dissociation, H(2) dissociation, and hydrogenation of the intermediate reactants. A complete kinetic model based on the most relevant elementary steps can be established for any given point along an industrial reactor, and the kinetic results can be integrated over the catalyst bed to determine the industrial reactor yield. We find that, given the present uncertainties, the rate of ammonia production is well-determined directly from our atomic-scale calculations. Furthermore, our studies provide new insight into several related fields, for instance, gas-phase and electrochemical ammonia synthesis. The success of predicting the outcome of a catalytic reaction from first-principles calculations supports our point of view that, in the future, theory will be a fully integrated tool in the search for the next generation of catalysts.
First-principles study of polyacetylene derivatives bearing nitroxide radicals
NASA Astrophysics Data System (ADS)
Bilgiç, Beyza; Kılıç, Çetin; Esat, Burak
2011-09-01
Electrodes made of organic polymers bearing redox-active radical pendant groups have attractive features for use in rechargeable batteries. Electronic structure and electrochemical properties of cathode- and anode-active organic polymers are investigated here by means of first-principles calculations performed in the framework of the density functional theory. We consider organic radical polymers (ORPs) that consist of trans-polyacetylene derivatives bearing a variety of nitroxide radicals. A number of neutral and charged supercells are utilized to compute the ionization potentials and electron affinities as well as the one-electron states of these ORPs. By revealing the polyacetylene-derived highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) as well as the radical-derived singly occupied molecular orbital (SOMO), the variation of the SOMO energy within the HOMO-LUMO gap is determined in the course of the oxidization or reduction of ORPs. Our results indicate that the ionization potential I and electron affinity A of polyacetylene would act as a lower or upper bound in the variation of the electrochemical potential of cathode- or anode-active ORPs in the course of battery discharge or charge owing to pinning of the radical-derived SOMO to the polyacetylene-derived HOMO or LUMO. Accordingly, it is anticipated that the electrochemical “window” [-I,-A] of the polymeric backbone of ORPs will impose certain limitations in accomplishing a high charge/discharge voltage range in a totally organic rechargeable battery with positive and negative electrodes made of cathode- and anode-active ORPs, respectively. On the other hand, our findings suggest that one could, in principle, take advantage of using two different (conducting) polymeric backbones in the anode and cathode with adjusted HOMO and LUMO offsets once the electron transfer is accomplished to take place through the conducting backbones.
First-principles structural design of superhard materials.
Zhang, Xinxin; Wang, Yanchao; Lv, Jian; Zhu, Chunye; Li, Qian; Zhang, Miao; Li, Quan; Ma, Yanming
2013-03-21
We reported a developed methodology to design superhard materials for given chemical systems under external conditions (here, pressure). The new approach is based on the CALYPSO algorithm and requires only the chemical compositions to predict the hardness vs. energy map, from which the energetically preferable superhard structures are readily accessible. In contrast to the traditional ground state structure prediction method where the total energy was solely used as the fitness function, here we adopted hardness as the fitness function in combination with the first-principles calculation to construct the hardness vs. energy map by seeking a proper balance between hardness and energy for a better mechanical description of given chemical systems. To allow a universal calculation on the hardness for the predicted structure, we have improved the earlier hardness model based on bond strength by applying the Laplacian matrix to account for the highly anisotropic and molecular systems. We benchmarked our approach in typical superhard systems, such as elemental carbon, binary B-N, and ternary B-C-N compounds. Nearly all the experimentally known and most of the earlier theoretical superhard structures have been successfully reproduced. The results suggested that our approach is reliable and can be widely applied into design of new superhard materials.
First-principles studies of atomic dynamics in tetrahedrite thermoelectrics
NASA Astrophysics Data System (ADS)
Li, Junchao; Zhu, Mengze; Abernathy, Douglas L.; Ke, Xianglin; Morelli, Donald T.; Lai, Wei
2016-10-01
Cu12Sb4S13-based tetrahedrites are high-performance thermoelectrics that contain earth-abundant and environmentally friendly elements. At present, the mechanistic understanding of their low lattice thermal conductivity (<1 W m-1 K-1 at 300 K) remains limited. This work applies first-principles molecular dynamics simulations, along with inelastic neutron scattering (INS) experiments, to study the incoherent and coherent atomic dynamics in Cu10.5NiZn0.5Sb4S13, in order to deepen our insight into mechanisms of anomalous dynamic behavior and low lattice thermal conductivity in tetrahedrites. Our study of incoherent dynamics reveals the anomalous "phonon softening upon cooling" behavior commonly observed in inelastic neutron scattering data. By examining the dynamic Cu-Sb distances inside the Sb[CuS3]Sb cage, we ascribe softening to the decreased anharmonic "rattling" of Cu in the cage. On the other hand, our study of coherent dynamics reveals that acoustic modes are confined in a small region of dynamic scattering space, which we hypothesize leads to a minimum phonon mean free path. By assuming a Debye model, we obtain a lattice minimum thermal conductivity value consistent with experiments. We believe this study furthers our understanding of the atomic dynamics of tetrahedrite thermoelectrics and will more generally help shed light on the origin of intrinsically low lattice thermal conductivity in these and other structurally similar materials.
DNA translocation through graphene nanopores: a first-principles study
NASA Astrophysics Data System (ADS)
Peng, Shenglin; Yang, Zhixiong; Ni, Xiang; Zhang, Hua; Ouyang, Jun; Fangping, Ouyang
2014-03-01
With first-principles transport simulation, a biosensor device built from a graphene nanoribbon containing a nanopore is designed for DNA sequencing. The four DNA nucleobases can be distinguished from one another by detecting the transverse-currents of this device. To investigate the transport properties and mechanisms of such a device, we examine the motion effects of nucleobases. The analysis of the transmission spectra and frontier orbital energy shows that the transverse-currents variation of the device strongly results from the long-range interaction between nucleobases and the device. This interaction makes transverse-currents ultra-sensitive to the molecule inside the pore. By rotating the nucleotides inside the pore, the transverse-currents of the device vary along with the changes of molecular orientation. Due to the long-range interaction, when nucleobases chain translocates through nanopore of the device, the influences of adjacent nucleobases on transverse-currents cannot be ignored. These novel effects of nucleobases on the transport capacity of the device provide some theoretical guidance for the design of graphene-based nanopore sensor devices.
High-Pressure Hydrogen from First-Principles
NASA Astrophysics Data System (ADS)
Morales, Miguel A.
2014-03-01
The main approximations typically employed in first-principles simulations of high-pressure hydrogen are the neglect of nuclear quantum effects (NQE) and the approximate treatment of electronic exchange and correlation, typically through a density functional theory (DFT) formulation. In this talk I'll present a detailed analysis of the influence of these approximations on the phase diagram of high-pressure hydrogen, with the goal of identifying the predictive capabilities of current methods and, at the same time, making accurate predictions in this important regime. We use a path integral formulation combined with density functional theory, which allows us to incorporate NQEs in a direct and controllable way. In addition, we use state-of-the-art quantum Monte Carlo calculations to benchmark the accuracy of more approximate mean-field electronic structure calculations based on DFT, and we use GW and hybrid DFT to calculate the optical properties of the solid and liquid phases near metallization. We present accurate predictions of the metal-insulator transition on the solid, including structural and optical properties of the molecular phase. MAM was supported by the U.S. Department of Energy at the Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and by LDRD Grant No. 13-LW-004.
First-principles simulations of warm dense lithium fluoride.
Driver, K P; Militzer, B
2017-04-01
We perform first-principles path integral Monte Carlo (PIMC) and density functional theory molecular dynamics (DFT-MD) calculations to explore warm dense matter states of LiF. Our simulations cover a wide density-temperature range of 2.08-15.70gcm^{-3} and 10^{4}-10^{9} K. Since PIMC and DFT-MD accurately treat effects of atomic shell structure, we find a pronounced compression maximum and a shoulder on the principal Hugoniot curve attributed to K-shell and L-shell ionization. The results provide a benchmark for widely used EOS tables, such as SESAME, LEOS, and models. In addition, we compute pair-correlation functions that reveal an evolving plasma structure and ionization process that is driven by thermal and pressure ionization. Finally, we compute electronic density of states of liquid LiF from DFT-MD simulations and find that the electronic gap can remain open with increasing density and temperature to at least 15.7 gcm^{-3}.
First-principles simulations of warm dense lithium fluoride
NASA Astrophysics Data System (ADS)
Driver, K. P.; Militzer, B.
2017-04-01
We perform first-principles path integral Monte Carlo (PIMC) and density functional theory molecular dynamics (DFT-MD) calculations to explore warm dense matter states of LiF. Our simulations cover a wide density-temperature range of 2.08 -15.70 g cm-3 and 104-109 K. Since PIMC and DFT-MD accurately treat effects of atomic shell structure, we find a pronounced compression maximum and a shoulder on the principal Hugoniot curve attributed to K-shell and L-shell ionization. The results provide a benchmark for widely used EOS tables, such as SESAME, LEOS, and models. In addition, we compute pair-correlation functions that reveal an evolving plasma structure and ionization process that is driven by thermal and pressure ionization. Finally, we compute electronic density of states of liquid LiF from DFT-MD simulations and find that the electronic gap can remain open with increasing density and temperature to at least 15.7 g cm-3 .
First-Principles, Physically Motivated Force Field for the Ionic Liquid [BMIM][BF4].
Choi, Eunsong; McDaniel, Jesse G; Schmidt, J R; Yethiraj, Arun
2014-08-07
Molecular simulations play an important role in establishing structure-property relations in complex fluids such as room-temperature ionic liquids. Classical force fields are the starting point when large systems or long times are of interest. These force fields must be not only accurate but also transferable. In this work, we report a physically motivated force field for the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) based on symmetry-adapted perturbation theory. The predictions (from molecular dynamics simulations) of the liquid density, enthalpy of vaporization, diffusion coefficients, viscosity, and conductivity are in excellent agreement with experiment, with no adjustable parameters. The explicit energy decomposition inherent in the force field enables a quantitative analysis of the important physical interactions in these systems. We find that polarization is crucial and there is little evidence of charge transfer. We also argue that the often used procedure of scaling down charges in molecular simulations of ionic liquids is unphysical for [BMIM][BF4]. Because all intermolecular interactions in the force field are parametrized from first-principles, we anticipate good transferability to other ionic liquid systems and physical conditions.
Revising Intramolecular Photoinduced Electron Transfer (PET) from First-Principles.
Escudero, Daniel
2016-09-20
Photoinduced electron transfer (PET) plays relevant roles in many areas of chemistry, including charge separation processes in photovoltaics, natural and artificial photosynthesis, and photoluminescence sensors and switches. As in many other photochemical scenarios, the structural and energetic factors play relevant roles in determining the rates and efficiencies of PET and its competitive photodeactivation processes. Particularly, in the field of fluorescent sensors and switches, intramolecular PET is believed (in many cases without compelling experimental proof) to be responsible of the quench of fluorescence. There is an increasing experimental interest in fluorophore's molecular design and on achieving optimal excitation/emission spectra, excitation coefficients, and fluorescence quantum yields (importantly for bioimaging purposes), but less efforts are devoted to fundamental mechanistic studies. In this Account, I revise the origins of the fluorescence quenching in some of these systems with state-of-the-art quantum chemical tools. These studies go beyond the common strategy of analyzing frontier orbital energy diagrams and performing PET thermodynamics calculations. Instead, the potential energy surfaces (PESs) of the lowest-lying excited states are explored with time-dependent density functional theory (TD-DFT) and complete active space self-consistent field (CASSCF) calculations and the radiative and nonradiative decay rates from the involved excited states are computed from first-principles using a thermal vibration correlation function formalism. With such a strategy, this work reveals the real origins of the fluorescence quenching, herein entitled as dark-state quenching. Dark states (those that do not absorb or emit light) are often elusive to experiments and thus, computational investigations can provide novel insights into the actual photodeactivation mechanisms. The success of the dark-state quenching mechanism is demonstrated for a wide variety of
First Principles Studies of ABO3 Perovskite Surfaces and Nanostructures
NASA Astrophysics Data System (ADS)
Pilania, Ghanshyam
environment and processing conditions on the surface relaxations, local electronic structure and chemical reactivity. By combining our first principles computations with an in-house developed kMC simulation approach, we describe the thermodynamics, steady-state kinetics and the long-time and large-length scale behavior of the catalytically active (001) MnO2-terminated LaMnO3 surface in contact with an oxygen reservoir, as a function of temperature and partial pressure of oxygen. The results obtained are in excellent agreement with available experimental data in the literature.
A First-Principle Kinetic Theory of Meteor Plasma Formation
NASA Astrophysics Data System (ADS)
Dimant, Yakov; Oppenheim, Meers
2015-11-01
Every second millions of tiny meteoroids hit the Earth from space, vast majority too small to observe visually. However, radars detect the plasma they generate and use the collected data to characterize the incoming meteoroids and the atmosphere in which they disintegrate. This diagnostics requires a detailed quantitative understanding of formation of the meteor plasma. Fast-descending meteoroids become detectable to radars after they heat due to collisions with atmospheric molecules sufficiently and start ablating. The ablated material then collides into atmospheric molecules and forms plasma around the meteoroid. Reflection of radar pulses from this plasma produces a localized signal called a head echo. Using first principles, we have developed a consistent collisional kinetic theory of the near-meteoroid plasma. This theory shows that the meteoroid plasma develops over a length-scale close to the ion mean free path with a non-Maxwellian velocity distribution. The spatial distribution of the plasma density shows significant deviations from a Gaussian law usually employed in head-echo modeling. This analytical model will serve as a basis for more accurate quantitative interpretation of the head echo radar measurements. Work supported by NSF Grant 1244842.
First-Principles Monte Carlo Simulations of Reaction Equilibria in Compressed Vapors
2016-01-01
Predictive modeling of reaction equilibria presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions arising from the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. Here we present a novel reactive first-principles Monte Carlo (RxFPMC) approach that allows for investigation of reaction equilibria without the need to prespecify a set of chemical reactions and their ideal-gas equilibrium constants. We apply RxFPMC to investigate a nitrogen/oxygen mixture at T = 3000 K and p = 30 GPa, i.e., conditions that are present in atmospheric lightning strikes and explosions. The RxFPMC simulations show that the solvation environment leads to a significantly enhanced NO concentration that reaches a maximum when oxygen is present in slight excess. In addition, the RxFPMC simulations indicate the formation of NO2 and N2O in mole fractions approaching 1%, whereas N3 and O3 are not observed. The equilibrium distributions obtained from the RxFPMC simulations agree well with those from a thermochemical computer code parametrized to experimental data. PMID:27413785
First-principles Monte Carlo simulations of reaction equilibria in compressed vapors
Fetisov, Evgenii O.; Kuo, I-Feng William; Knight, Chris; ...
2016-06-13
Predictive modeling of reaction equilibria presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions arising from the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. Here we present a novel reactive first-principles Monte Carlo (RxFPMC) approach that allows for investigation of reaction equilibria without the need to prespecify a set of chemical reactions and their ideal-gasmore » equilibrium constants. We apply RxFPMC to investigate a nitrogen/oxygen mixture at T = 3000 K and p = 30 GPa, i.e., conditions that are present in atmospheric lightning strikes and explosions. The RxFPMC simulations show that the solvation environment leads to a significantly enhanced NO concentration that reaches a maximum when oxygen is present in slight excess. In addition, the RxFPMC simulations indicate the formation of NO2 and N2O in mole fractions approaching 1%, whereas N3 and O3 are not observed. Lastly, the equilibrium distributions obtained from the RxFPMC simulations agree well with those from a thermochemical computer code parametrized to experimental data.« less
Monolayer II-VI semiconductors: A first-principles prediction
NASA Astrophysics Data System (ADS)
Zheng, Hui; Li, Xian-Bin; Chen, Nian-Ke; Xie, Sheng-Yi; Tian, Wei Quan; Chen, Yuanping; Xia, Hong; Zhang, S. B.; Sun, Hong-Bo
2015-09-01
A systematic study of 32 honeycomb monolayer II-VI semiconductors is carried out by first-principles methods. While none of the two-dimensional (2D) structures can be energetically stable, it appears that BeO, MgO, CaO, ZnO, CdO, CaS, SrS, SrSe, BaTe, and HgTe honeycomb monolayers have a good dynamic stability. The stability of the five oxides is consistent with the work published by Zhuang et al. [Appl. Phys. Lett. 103, 212102 (2013), 10.1063/1.4831972]. The rest of the compounds in the form of honeycomb are dynamically unstable, revealed by phonon calculations. In addition, according to the molecular dynamic (MD) simulation evolution from these unstable candidates, we also find two extra monolayers dynamically stable, which are tetragonal BaS [P 4 /n m m (129 ) ] and orthorhombic HgS [P 21/m (11 ) ] . The honeycomb monolayers exist in the form of either a planar perfect honeycomb or a low-buckled 2D layer, all of which possess a band gap and most of them are in the ultraviolet region. Interestingly, the dynamically stable SrSe has a gap near visible light, and displays exotic electronic properties with a flat top of the valence band, and hence has a strong spin polarization upon hole doping. The honeycomb HgTe has recently been reported to achieve a topological nontrivial phase under appropriate in-plane tensile strain and spin-orbital coupling (SOC) [J. Li et al., arXiv:1412.2528]. Some II-VI partners with less than 5 % lattice mismatch may be used to design novel 2D heterojunction devices. If synthesized, potential applications of these 2D II-VI families could include optoelectronics, spintronics, and strong correlated electronics.
Nanoflare Statistics from First Principles: Fractal Geometry and Temperature Synthesis
NASA Astrophysics Data System (ADS)
Aschwanden, Markus J.; Parnell, Clare E.
2002-06-01
We derive universal scaling laws for the physical parameters of flarelike processes in a low-β plasma, quantified in terms of spatial length scales l, area A, volume V, electron density ne, electron temperature Te, total emission measure M, and thermal energy E. The relations are specified as functions of two independent input parameters, the power index a of the length distribution, N(l)~l-a, and the fractal Haussdorff dimension D between length scales l and flare areas, A(l)~lD. For values that are consistent with the data, i.e., a=2.5+/-0.2 and D=1.5+/-0.2, and assuming the RTV scaling law, we predict an energy distribution N(E)~E-α with a power-law coefficient of α=1.54+/-0.11. As an observational test, we perform statistics of nanoflares in a quiet-Sun region covering a comprehensive temperature range of Te~1-4 MK. We detected nanoflare events in extreme-ultraviolet (EUV) with the 171 and 195 Å filters from the Transition Region and Coronal Explorer (TRACE), as well as in soft X-rays with the AlMg filter from the Yohkoh soft X-ray telescope (SXT), in a cospatial field of view and cotemporal time interval. The obtained frequency distributions of thermal energies of nanoflares detected in each wave band separately were found to have power-law slopes of α~1.86+/-0.07 at 171 Å (Te~0.7-1.1 MK), α~1.81+/-0.10 at 195 Å (Te~1.0-1.5 MK), and α~1.57+/-0.15 in the AlMg filter (Te~1.8-4.0 MK), consistent with earlier studies in each wavelength. We synthesize the temperature-biased frequency distributions from each wavelength and find a corrected power-law slope of α~1.54+/-0.03, consistent with our theoretical prediction derived from first principles. This analysis, supported by numerical simulations, clearly demonstrates that previously determined distributions of nanoflares detected in EUV bands produced a too steep power-law distribution of energies with slopes of α~2.0-2.3 mainly because of this temperature bias. The temperature-synthesized distributions of
Prediction on technetium triboride from first-principles calculations
NASA Astrophysics Data System (ADS)
Miao, Xiaojia; Xing, Wandong; Meng, Fanyan; Yu, Rong
2017-02-01
Taking the Tc-B binary system as an example, here we report the first-principles prediction on new phases of technetium borides, TcB3, which has an unprecedented stoichiometry. Crystal structures, phase stability, electronic properties and mechanical properties of TcB3 have been investigated using first-principles calculations. The hexagonal P 6 bar m 2 structure (No.187) TcB3 with a high value of hardness (29 GPa) is energetically stable against decomposition into other compounds under pressures above 4 GPa, indicating that TcB3 can be synthesized above this pressure.
Electron Exchange and Conduction in Nontronite from First-Principles
Alexandrov, Vitali Y.; Neumann, Anke; Scherer, Michelle; Rosso, Kevin M.
2013-01-11
Fe-bearing clay minerals serve as an important source and sink for electrons in redox reactions in various subsurface geochemical environments, and electron transfer (ET) properties of the Fe2+/Fe3+ redox couple play a decisive role in a variety of physicochemical processes involving clays. Here, we apply first-principles calculations using both periodic GGA+U planewave and Hartree-Fock molecular-cluster frameworks in conjuction with small polaron hopping approach and Marcus electron transfer theory to examine electron exchange mobilities in an Fe-rich smectite, taking nontronite as a case study. GGA+U calculations of the activation barrier for small-polaron migration provide rates of electron hopping that agree very well with values deduced from variable temperature Mössbauer data (M. V. Schaefer, et. al., Environ. Sci. Technol. 45, 540, (2011)), indicating a surprisingly fast electron mobility at room temperature. Based on molecular cluster calculations, we show that the state with tetrahedral Fe2+ ion in the nontronite lattice is about 0.9 eV higher than the one with octahedral Fe2+. Also, evaluation of the ET rates for the Fe2+/Fe3+ electron hopping in tetrahedral (TS) and octahedral sheets (OS), as well as across the sheets (TS–OS) shows that the dominant contribution to the bulk electronic conductivity should come from the ET within the OS. Deprotonation of structural OH groups mediating ET between the Fe ions in the OS is found to decrease the internal reorganization energy and to increase the magnitude of the electronic coupling matrix element, whereas protonation (to OH2 groups) has the opposite effect. Overall, our calculations suggest that the major factors affecting ET rates are the nature and structure of the nearest-neighbor local environment and the degree of covalency of the bonds between Fe and ligands mediating electron hops. The generally higher reorganization energy and weaker electronic coupling found in Fe-bearing clay minerals leads to
Fermions in d = 1 + 2 dimensions from first principles
Carrillo-Ruiz, Ma. Georgina; Napsuciale, Mauro
2006-09-25
In this work we construct states describing planar electrons ('spin' (1/2) particles with well defined parity) in d = 1 + 2 from first principles and show that they satisfy Dirac equation, which turns out to be the covariant form of the eigenvalue equation for spatial inversion (parity) just like in d = 1 + 3.
First principles calculation of two dimensional antimony and antimony arsenide
Pillai, Sharad Babu Narayan, Som; Jha, Prafulla K.; Dabhi, Shweta D.
2016-05-23
This work focuses on the strain dependence of the electronic properties of two dimensional antimony (Sb) material and its alloy with As (SbAs) using density functional theory based first principles calculations. Both systems show indirect bandgap semiconducting character which can be transformed into a direct bandgap material with the application of relatively small strain.
Encoding First Principles Electronic Structure Information in Classical Potentials: SiO_2
NASA Astrophysics Data System (ADS)
Trickey, S. B.; Al-Derzi, A. R.; Flocke, N.; Zhu, Wuming; Cory, M.; Runge, K.; Zhu, Ting; Li, Ju; Yip, Sidney
2002-03-01
A widely used class of interionic potentials for simulation of the properties of SiO2 is calibrated to a combination of first principles electronic structure results for a small cluster and experimental crystalline data. We test the underlying realism and reliability of this procedure as part of an exploration of the necessary and sufficient transfer of information across the quantum mechanical to molecular dynamical interface in a chemically realistic, multi-scale simulation with no empirical inputs. The approach is to fit the parameters solely to calculated data from each of two clusters (H_4SiO_4, H_6Si_2O_7) versus fits purely to calculated α-quartz. No experimental input is used. This choice probes the significance of short- vs. long-ranged behavior. The fitted parameters exhibit large dependences on the size of cluster, choice of theoretical method (DFT, HF, Many-body Perturbation Theory, Coupled Cluster), level of methodological refinement, and accuracy of implementation (e.g. basis set). By implication, the relatively successful potentials in the literature represent a fortunate set of choices that are not readily improvable in a systematic fashion. After a summary of these findings, we will report studies of the sensitivity of the mechanical behavior of both bulk and nano-rod SiO2 as predicted in MD calculations using the various calculated parameter sets.
First-Principles Investigation of Water Properties at Functionalized Silicon surface
NASA Astrophysics Data System (ADS)
Lee, Donghwa; Schwegler, Eric; Kanai, Yosuke
2013-03-01
Numerous experimental and theoretical investigations have been made to understand the behavior of water molecules under various conditions. Interfacial water behavior at semiconductor interfaces is one of the most important areas of investigation for diverse industrial applications such as crystal growth, lubrication, catalysis, electrochemistry and sensors. Although the terms, hydrophobic and/or hydrophilic, are often used to describe the properties of water in this context at macroscopic level, the effect of hydrophobicity on water behavior at nano-scale interfaces is still not well understood. Computational simulations could offer atomistic basis to build a better foundation for understanding this important dynamics. In this study, first principles molecular dynamics is employed to investigate the water behavior at silicon surfaces that are functionalized with several different molecules. In particular, various analysis methods are used to elucidate the effect of surface polarity on structural and dynamical properties of interfacial water. Our studies show that properties of interfacial water are not always governed by surface polarity alone but also by other atomistic factors. This work is Prepared by LLNL under Contract DE-AC52-07NA27344.
First principle chemical kinetics in zeolites: the methanol-to-olefin process as a case study.
Van Speybroeck, Veronique; De Wispelaere, Kristof; Van der Mynsbrugge, Jeroen; Vandichel, Matthias; Hemelsoet, Karen; Waroquier, Michel
2014-11-07
To optimally design next generation catalysts a thorough understanding of the chemical phenomena at the molecular scale is a prerequisite. Apart from qualitative knowledge on the reaction mechanism, it is also essential to be able to predict accurate rate constants. Molecular modeling has become a ubiquitous tool within the field of heterogeneous catalysis. Herein, we review current computational procedures to determine chemical kinetics from first principles, thus by using no experimental input and by modeling the catalyst and reacting species at the molecular level. Therefore, we use the methanol-to-olefin (MTO) process as a case study to illustrate the various theoretical concepts. This process is a showcase example where rational design of the catalyst was for a long time performed on the basis of trial and error, due to insufficient knowledge of the mechanism. For theoreticians the MTO process is particularly challenging as the catalyst has an inherent supramolecular nature, for which not only the Brønsted acidic site is important but also organic species, trapped in the zeolite pores, must be essentially present during active catalyst operation. All these aspects give rise to specific challenges for theoretical modeling. It is shown that present computational techniques have matured to a level where accurate enthalpy barriers and rate constants can be predicted for reactions occurring at a single active site. The comparison with experimental data such as apparent kinetic data for well-defined elementary reactions has become feasible as current computational techniques also allow predicting adsorption enthalpies with reasonable accuracy. Real catalysts are truly heterogeneous in a space- and time-like manner. Future theory developments should focus on extending our view towards phenomena occurring at longer length and time scales and integrating information from various scales towards a unified understanding of the catalyst. Within this respect molecular
First-principles investigation of anistropic hole mobilities in organic semiconductors.
Wen, Shu-Hao; Li, An; Song, Junling; Deng, Wei-Qiao; Han, Ke-Li; Goddard, William A
2009-07-02
We report a simple first-principles-based simulation model (combining quantum mechanics with Marcus-Hush theory) that provides the quantitative structural relationships between angular resolution anisotropic hole mobility and molecular structures and packing. We validate that this model correctly predicts the anisotropic hole mobilities of ruberene, pentacene, tetracene, 5,11-dichlorotetracene (DCT), and hexathiapentacene (HTP), leading to results in good agreement with experiment.
Mundy, C; Kuo, I W
2005-06-08
successfully applied to studying the complex problems put forth by atmospheric chemists. To date, the majority of the molecular models of atmospherically relevant interfaces have been comprised of two genres of molecular models. The first is based on empirical interaction potentials. The use of an empirical interaction potential suffers from at least two shortcomings. First, empirical potentials are usually fit to reproduce bulk thermodynamic states, or gas phase spectroscopic data. Thus, without the explicit inclusion of charge transfer, it is not at all obvious that empirical potentials can faithfully reproduce the structure at a solid-vapor, or liquid-vapor interface where charge rearrangement is known to occur (see section 5). One solution is the empirical inclusion of polarization effects. These models are certainly an improvement, but still cannot offer insight into charge transfer processes and are usually difficult to parameterize. The other shortcoming of empirical models is that, in general, they cannot describe bond-making/breaking events, i.e. chemistry. In order to address chemistry one has to consider an ab initio (to be referred to as first-principles throughout the remaining text) approach to molecular modeling that explicitly treats the electronic degrees of freedom. First-principles modeling also give a direct link to spectroscopic data and chemistry, but at a large computational cost. The bottle-neck associated with first-principles modeling is usually determined by the level of electronic structure theory that one chooses to study a particular problem. High-level first-principles approaches, such as MP2, provide accurate representation of the electronic degrees of freedom but are only computationally tractable when applied to small system sizes (i.e. 10s of atoms). Nevertheless, this type of modeling has been extremely useful in deducing reaction mechanisms of atmospherically relevant chemistry that will be discussed in this review (see section 4). However
Vibrational spectral diffusion and hydrogen bond dynamics in heavy water from first principles.
Mallik, Bhabani S; Semparithi, A; Chandra, Amalendu
2008-06-12
We present a first-principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in heavy water without using any empirical model potentials. The calculations are based on ab initio molecular dynamics simulations for trajectory generation and a time series analysis using the wavelet method for frequency calculations. It is found that, in deuterated water, although a one-to-one relation does not exist between the instantaneous frequency of an OD bond and the distance of its associated hydrogen bond, such a relation does hold on average. The dynamics of spectral diffusion is investigated by means of frequency-time correlation and spectral hole dynamics calculations. Both of these functions are found to have a short-time decay with a time scale of approximately 100 fs corresponding to dynamics of intact hydrogen bonds and a slower long-time decay with a time constant of approximately 2 ps corresponding to lifetimes of hydrogen bonds. The connection of the slower time scale to the dynamics of local structural relaxation is also discussed. The dynamics of hydrogen bond making is shown to have a rather fast time scale of approximately 100 fs; hence, it can also contribute to the short-time dynamics of spectral diffusion. A damped oscillation is also found at around 150-200 fs, which is shown to have come from underdamped intermolecular vibrations of a hydrogen-bonded water pair. Such assignments are confirmed by independent calculations of power spectra of intermolecular motion and hydrogen bond kinetics using the population correlation function formalism. The details of the time constants of frequency correlations and spectral shifts are found to depend on the frequencies of chosen OD bonds and are analyzed in terms of the dynamics of hydrogen bonds of varying strengths and also of free non-hydrogen-bonded OD groups.
Diagnosis: Reasoning from first principles and experiential knowledge
NASA Technical Reports Server (NTRS)
Williams, Linda J. F.; Lawler, Dennis G.
1987-01-01
Completeness, efficiency and autonomy are requirements for suture diagnostic reasoning systems. Methods for automating diagnostic reasoning systems include diagnosis from first principles (i.e., reasoning from a thorough description of structure and behavior) and diagnosis from experiential knowledge (i.e., reasoning from a set of examples obtained from experts). However, implementation of either as a single reasoning method fails to meet these requirements. The approach of combining reasoning from first principles and reasoning from experiential knowledge does address the requirements discussed above and can possibly ease some of the difficulties associated with knowledge acquisition by allowing developers to systematically enumerate a portion of the knowledge necessary to build the diagnosis program. The ability to enumerate knowledge systematically facilitates defining the program's scope, completeness, and competence and assists in bounding, controlling, and guiding the knowledge acquisition process.
Hybrid first-principles/neural networks model for column flotation
Gupta, S.; Liu, P.H.; Svoronos, S.A.; Sharma, R.; Abdel-Khalek, N.A.; Cheng, Y.; El-Shall, H.
1999-03-01
A new model for phosphate column flotation is presented which for the first time relates the effects of operating variables such as frother concentration on column performance. This is a hybrid model that combines a first-principles model with artificial neural networks. The first-principles model is obtained from material balances on both phosphate particles and gangue (undesired material containing mostly silica). First-order rates of net attachment are assumed for both. Artificial neural networks relate the attachment rate constants to the operating variables. Experiments were conducted in a 6-in.-dia. (152-mm-dia.) laboratory column to provide data for neural network training and model validation. The model successfully predicts the effects of frother concentration, particle size, air flow rate and bubble diameter on grade and recovery.
First-principles modeling of hard and soft matter
NASA Astrophysics Data System (ADS)
Car, Roberto
2013-03-01
Electronic and atomistic processes are key to bio-inspired functional materials and nanocatalysts for energy applications. This talk will review recent simulation studies and discuss the challenges that first-principles quantum mechanical approaches face when addressing these issues. Supported by DOE-DE-FG02-06ER-46344, DOE-DE-SC0008626, DOE-DE-SC0005180, and NSF-CHE-0956500.
Configurational thermodynamics of alloys from first principles: effective cluster interactions
NASA Astrophysics Data System (ADS)
Ruban, A. V.; Abrikosov, I. A.
2008-04-01
Phase equilibria in alloys to a great extent are governed by the ordering behavior of alloy species. One of the important goals of alloy theory is therefore to be able to simulate these kinds of phenomena on the basis of first principles. Unfortunately, it is impossible, even with present day total energy software, to calculate entirely from first principles the changes in the internal energy caused by changes of the atomic configurations in systems with several thousand atoms at the rate required by statistical thermodynamics simulations. The time-honored solution to this problem that we shall review in this paper is to obtain the configurational energy needed in the simulations from an Ising-type Hamiltonian with so-called effective cluster interactions associated with specific changes in the local atomic configuration. Finding accurate and reliable effective cluster interactions, which take into consideration all relevant thermal excitations, on the basis of first-principles methods is a formidable task. However, it pays off by opening new exciting perspectives and possibilities for materials science as well as for physics itself. In this paper we outline the basic principles and methods for calculating effective cluster interactions in metallic alloys. Special attention is paid to the source of errors in different computational schemes. We briefly review first-principles methods concentrating on approximations used in density functional theory calculations, Green's function method and methods for random alloys based on the coherent potential approximation. We formulate criteria for the validity of the supercell approach in the calculations of properties of random alloys. The generalized perturbation method, which is an effective and accurate tool for obtaining cluster interactions, is described in more detail. Concentrating mostly on the methodological side we give only a few examples of applications to the real systems. In particular, we show that the ground
First principles study of ``111'' type iron arsenide superconductors
NASA Astrophysics Data System (ADS)
Murugan, A.; Kanagaprabha, S.; Palanichamy, R. Rajeswara
2013-06-01
First principles calculations are performed using Tight-binding LMTO method with Local density approximation (LDA) and Atomic sphere approximation (ASA) to understand the electronic properties of of iron arsenide compounds. The estimated superconducting transition temperature (Tc) for LiFeAs and NaFeAs are ˜18K, ˜26K respectively and is in agreement with the experimental value. The pressure dependence of superconducting transition temperature is also investigated.
Predictions of the Properties of Water from First Principles
NASA Astrophysics Data System (ADS)
Bukowski, Robert; Szalewicz, Krzysztof; Groenenboom, Gerrit C.; van der Avoird, Ad
2007-03-01
A force field for water has been developed entirely from first principles, without any fitting to experimental data. It contains both pairwise and many-body interactions. This force field predicts the properties of the water dimer and of liquid water in excellent agreement with experiments, a previously elusive objective. Precise knowledge of the intermolecular interactions in water will facilitate a better understanding of this ubiquitous substance.
Evolutionary approach for determining first-principles hamiltonians.
Hart, Gus L W; Blum, Volker; Walorski, Michael J; Zunger, Alex
2005-05-01
Modern condensed-matter theory from first principles is highly successful when applied to materials of given structure-type or restricted unit-cell size. But this approach is limited where large cells or searches over millions of structure types become necessary. To treat these with first-principles accuracy, one 'coarse-grains' the many-particle Schrodinger equation into 'model hamiltonians' whose variables are configurational order parameters (atomic positions, spin and so on), connected by a few 'interaction parameters' obtained from a microscopic theory. But to construct a truly quantitative model hamiltonian, one must know just which types of interaction parameters to use, from possibly 10(6)-10(8) alternative selections. Here we show how genetic algorithms, mimicking biological evolution ('survival of the fittest'), can be used to distil reliable model hamiltonian parameters from a database of first-principles calculations. We demonstrate this for a classic dilemma in solid-state physics, structural inorganic chemistry and metallurgy: how to predict the stable crystal structure of a compound given only its composition. The selection of leading parameters based on a genetic algorithm is general and easily applied to construct any other type of complex model hamiltonian from direct quantum-mechanical results.
User Authorization at the Molecular Scale.
Lustgarten, Omer; Motiei, Leila; Margulies, David
2017-07-05
Electronic user authorization systems help us maintain our privacy in many aspects of everyday life. However, the increasing difficulty to secure access and/or information digitally has inspired chemists to devise alternative, molecular approaches, in which users are identified by chemical means. The potential advantages of using molecular user authentication systems over conventional electronic devices are their versatility and unusual operating principles, which complicate replicating and, consequently, breaking into molecular security devices. Their molecular scale is another unique property that enables hiding such systems and, consequently, applying steganography as an additional layer of protection. Although the area of molecular-based user authorization is still in its infancy, the development of various molecular keypad locks and, more recently, a password-protected molecular cryptographic machine, indicate the possibility of protecting information at the molecular scale. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
First-principles materials applications and design of nonlinear optical crystals
NASA Astrophysics Data System (ADS)
Lin, Zheshuai; Jiang, Xingxing; Kang, Lei; Gong, Pifu; Luo, Siyang; Lee, Ming-Hsien
2014-06-01
With the development of laser technology and related scientific fields, understanding of the structure-property relationships in nonlinear optical (NLO) crystals is becoming more and more important. In this article, first-principles studies based on density functional theory, and their applications to elucidate the microscopic origins of the linear and NLO properties in NLO crystals, are reviewed. The ab initio approaches have the ability to accurately predict the optical properties in NLO crystals, and the developed analysis tools are vital to investigating their intrinsic mechanism. This microscopic understanding has further guided molecular engineering design for NLO crystals with novel structures and properties. It is anticipated that first-principle material approaches will greatly improve the search efficiency and greatly help experiments to save resources in the exploration of new NLO crystals with good performance.
NASA Astrophysics Data System (ADS)
Branicio, Paulo S.; Vastola, Guglielmo; Jhon, Mark H.; Sullivan, Michael B.; Shenoy, Vivek B.; Srolovitz, David J.
2016-10-01
The deformation of graphene due to the chemisorption of hydrogen atoms on its surface and the long-range elastic interaction between hydrogen atoms induced by these deformations are investigated using a multiscale approach based on first principles, empirical interactions, and continuum modeling. Focus is given to the intrinsic low-temperature structure and interactions. Therefore, all calculations are performed at T =0 , neglecting possible temperature or thermal fluctuation effects. Results from different methods agree well and consistently describe the local deformation of graphene on multiple length scales reaching 500 Å . The results indicate that the elastic interaction mediated by this deformation is significant and depends on the deformation of the graphene sheet both in and out of plane. Surprisingly, despite the isotropic elasticity of graphene, within the linear elastic regime, atoms elastically attract or repel each other depending on (i) the specific site they are chemisorbed; (ii) the relative position of the sites; (iii) and if they are on the same or on opposite surface sides. The interaction energy sign and power-law decay calculated from molecular statics agree well with theoretical predictions from linear elasticity theory, considering in-plane or out-of-plane deformations as a superposition or in a coupled nonlinear approach. Deviations on the exact power law between molecular statics and the linear elastic analysis are evidence of the importance of nonlinear effects on the elasticity of monolayer graphene. These results have implications for the understanding of the generation of clusters and regular formations of hydrogen and other chemisorbed atoms on graphene.
Manna, Arun K; Dunietz, Barry D
2014-09-28
We investigate photoinduced charge transfer (CT) processes within dyads consisting of porphyrin derivatives in which one ring ligates a Zn metal center and where the rings vary by their degree of conjugation. Using a first-principles approach, we show that molecular-scale means can tune CT rates through stabilization affected by the polar environment. Such means of CT tuning are important for achieving high efficiency optoelectronic applications using organic semiconducting materials. Our fully quantum mechanical scheme is necessary for reliably modeling the CT process across different regimes, in contrast to the pervading semi-classical Marcus picture that grossly underestimates transfer in the far-inverted regime.
NASA Astrophysics Data System (ADS)
Li, Ying; Mahadevan, Jagan; Wang, Sanwu
2010-03-01
The catalytic reactions of dissociation and oxidation of methane on the copper surfaces play a key role in, for example, the development of high-performance solid oxide fuel cells. We used first-principles quantum theory and large-scale parallel calculations to investigate the atomic-scale mechanism of the catalytic chemical reactions. We report the calculated results, which provide fundamental information and understanding about the atomic-scale dynamics and electronic structures pertinent to the reactions and specifically the catalytic role of the Cu(100) and Cu(111) surfaces. We also report comparison of our results with available experimental data and previous theoretical investigations.
Spin filtering in transition-metal phthalocyanine molecules from first principles
NASA Astrophysics Data System (ADS)
Niu, Li; Wang, Huan; Bai, Lina; Rong, Ximing; Liu, Xiaojie; Li, Hua; Yin, Haitao
2017-08-01
Using first-principles calculations based on density functional theory and the nonequilibrium Green's function formalism, we studied the spin transport through metal-phthalocyanine (MPc, M=Ni, Fe, Co, Mn, Cr) molecules connected to aurum nanowire electrodes. We found that the MnPc, FePc, and CrPc molecular devices exhibit a perfect spin filtering effect compared to CoPc and NiPc. Moreover, negative differential resistance appears in FePc molecular devices. The transmission coefficients at different bias voltages were further presented to understand this phenomenon. These results would be useful in designing devices for future nanotechnology.
Equation of state for technetium from X-ray diffraction and first-principle calculations
NASA Astrophysics Data System (ADS)
Mast, Daniel S.; Kim, Eunja; Siska, Emily M.; Poineau, Frederic; Czerwinski, Kenneth R.; Lavina, Barbara; Forster, Paul M.
2016-08-01
The ambient temperature equation of state (EoS) of technetium metal has been measured by X-ray diffraction. The metal was compressed using a diamond anvil cell and using a 4:1 methanol-ethanol pressure transmitting medium. The maximum pressure achieved, as determined from the gold pressureEquation of state for technetium from X-ray diffraction and first-principle calculations scale, was 67 GPa. The compression data shows that the HCP phase of technetium is stable up to 67 GPa. The compression curve of technetium was also calculated using first-principles total-energy calculations. Utilizing a number of fitting strategies to compare the experimental and theoretical data it is determined that the Vinet equation of state with an ambient isothermal bulk modulus of B0T=288 GPa and a first pressure derivative of B‧=5.9(2) best represent the compression behavior of technetium metal.
First-principle optimal local pseudopotentials construction via optimized effective potential method
NASA Astrophysics Data System (ADS)
Mi, Wenhui; Zhang, Shoutao; Wang, Yanchao; Ma, Yanming; Miao, Maosheng
2016-04-01
The local pseudopotential (LPP) is an important component of orbital-free density functional theory, a promising large-scale simulation method that can maintain information on a material's electron state. The LPP is usually extracted from solid-state density functional theory calculations, thereby it is difficult to assess its transferability to cases involving very different chemical environments. Here, we reveal a fundamental relation between the first-principles norm-conserving pseudopotential (NCPP) and the LPP. On the basis of this relationship, we demonstrate that the LPP can be constructed optimally from the NCPP for a large number of elements using the optimized effective potential method. Specially, our method provides a unified scheme for constructing and assessing the LPP within the framework of first-principles pseudopotentials. Our practice reveals that the existence of a valid LPP with high transferability may strongly depend on the element.
Roy, Tapta Kanchan; Kopysov, Vladimir; Nagornova, Natalia S; Rizzo, Thomas R; Boyarkin, Oleg V; Gerber, R Benny
2015-05-18
Calculated structures of the two most stable conformers of a protonated decapeptide gramicidin S in the gas phase have been validated by comparing the vibrational spectra, calculated from first- principles and measured in a wide spectral range using infrared (IR)-UV double resonance cold ion spectroscopy. All the 522 vibrational modes of each conformer were calculated quantum mechanically and compared with the experiment without any recourse to an empirical scaling. The study demonstrates that first-principles calculations, when accounting for vibrational anharmonicity, can reproduce high-resolution experimental spectra well enough for validating structures of molecules as large as of 200 atoms. The validated accurate structures of the peptide may serve as templates for in silico drug design and absolute calibration of ion mobility measurements.
Diffusion in thorium carbide: A first-principles study
NASA Astrophysics Data System (ADS)
Pérez Daroca, D.; Llois, A. M.; Mosca, H. O.
2015-12-01
The prediction of the behavior of Th compounds under irradiation is an important issue for the upcoming Generation-IV nuclear reactors. The study of self-diffusion and hetero-diffusion is a central key to fulfill this goal. As a first approach, we obtained, by means of first-principles methods, migration and activation energies of Th and C atoms self-diffusion and diffusion of He atoms in ThC. We also calculate diffusion coefficients as a function of temperature.
Error propagation in first-principles kinetic Monte Carlo simulation
NASA Astrophysics Data System (ADS)
Döpking, Sandra; Matera, Sebastian
2017-04-01
First-principles kinetic Monte Carlo models allow for the modeling of catalytic surfaces with predictive quality. This comes at the price of non-negligible errors induced by the underlying approximate density functional calculation. On the example of CO oxidation on RuO2(110), we demonstrate a novel, efficient approach to global sensitivity analysis, with which we address the error propagation in these multiscale models. We find, that we can still derive the most important atomistic factors for reactivity, albeit the errors in the simulation results are sizable. The presented approach might also be applied in the hierarchical model construction or computational catalyst screening.
Hardness of covalent and ionic crystals: first-principle calculations.
Simůnek, Antonín; Vackár, Jirí
2006-03-03
A new concept, the strength of bond, and a new form expressing the hardness of covalent and ionic crystals are presented. Hardness is expressed by means of quantities inherently coupled to the atomistic structure of matter, and, therefore, hardness can be determined by first-principles calculations. Good agreement between theory and experiment is observed in the range of 2 orders of magnitude. It is shown that a lower coordination number of atoms results in higher hardness, contrary to common opinion presented in general literature.
First-Principles Study of the Elastic Properties of Nitrates
NASA Astrophysics Data System (ADS)
Korabel'nikov, D. V.; Zhuravlev, Yu. N.
2017-04-01
Elastic properties of nitrates LiNO3, NaNO3, KNO3 and NH4NO3 are studied from first principles in gradient approximation of the density functional theory by method of linear combination of atomic orbitals using CRYSTAL software complex. Elastic constants and modules, hardness, Poisson coefficient, and anisotropy parameters are calculated. Sound velocity, Debye temperature, thermal conductivity and Gruneisen parameter are evaluated. Mechanical stability, anisotropy and the series dependencies are shown for the examined compounds. Strong elastic anisotropy indicates anisotropy of interatomic interactions. The elastic constants are in good agreement with available experimental data.
First-Principles Calculation of forces and phonons in solid
NASA Astrophysics Data System (ADS)
Ning, Zhenhua; Shelton, William
We have developed a multiple scattering theory approach to calculate Hellmann-Feynman forces and phonons via the calculation of the force constant and dynamical matrix. To demonstrate the accuracy and validity of our approach we compare with the ELK code, which is a full potential Linear Augmented Plane Wave (FLAPW) based method. As we will show our forces and phonon dispersion curves are in good agreement with the FLAPW code. This work lays the foundation for developing a first principles approach for calculation of phonons in substitutionally disordered materials.
First-principles study of blue silicate phosphors.
Ishida, M; Imanari, Y; Isobe, T; Kuze, S; Ezuhara, T; Umeda, T; Ohno, K; Miyazaki, S
2010-09-29
First-principles calculations were performed to investigate the optical property of blue silicate phosphor, CMS:Eu. The optical absorption property is discussed based on electronic band structure and density of states. Our calculation results indicate that hybridization of the wavefunction plays an important role for nonradiative migration of electrons and holes. The calculated optical absorption spectrum could reproduce the optical features of the experimental excitation spectrum. It is also demonstrated that a practical approach using computational materials screening is effective in phosphor materials development.
First-principles study of transition metal carbides
NASA Astrophysics Data System (ADS)
Connétable, Damien
2016-12-01
This study investigates the physical properties of transition metal carbides compounds associated with the Nb-C, Ti-C, Mo-C and W-C alloys systems using first-principles calculations. The ground-state properties (lattice parameters, cohesive energies and magnetism) were analyzed and compared to the experimental and theoretical literature. The simulations are in excellent agreement with experimental findings concerning atomic positions and structures. Elastic properties, computed using a finite-differences approach, are then discussed in detail. To complete the work, their lattice dynamics properties (phonon spectra) were investigated. These results serve to establish that some structures, which are mechanically stable, are dynamically unstable.
Derivation of instanton rate theory from first principles
NASA Astrophysics Data System (ADS)
Richardson, Jeremy O.
2016-03-01
Instanton rate theory is used to study tunneling events in a wide range of systems including low-temperature chemical reactions. Despite many successful applications, the method has never been obtained from first principles, relying instead on the "Im F" premise. In this paper, the same expression for the rate of barrier penetration at finite temperature is rederived from quantum scattering theory [W. H. Miller, S. D. Schwartz, and J. W. Tromp, J. Chem. Phys. 79, 4889 (1983)] using a semiclassical Green's function formalism. This justifies the instanton approach and provides a route to deriving the rate of other processes.
First principle study of PEO-AgI polymer systems
NASA Astrophysics Data System (ADS)
Rao, B. Keshav; Verma, Mohan L.
2017-07-01
First principle calculations based on density functional theory is performed to analyze cation (Ag+) conductivity in polyethylene oxide (PEO) based systems. The relaxed polymer structures are simulated, bond lengths and the charge density distributions around interacting atoms provides the strong bonding nature between higher electro-negative oxygen and silver atoms. Projected density of states and density of states explain s-p hybridization between orbitals, to increase in cation concentration in polymer systems, to reduce in the forbidden energy gap and to increase the ionic conductivity due to gradual increase the number of dispersing AgI molecules in polymer systems.
First principles pseudopotential calculations on aluminum and aluminum alloys
Davenport, J.W.; Chetty, N.; Marr, R.B.; Narasimhan, S.; Pasciak, J.E.; Peierls, R.F.; Weinert, M.
1993-12-31
Recent advances in computational techniques have led to the possibility of performing first principles calculations of the energetics of alloy formation on systems involving several hundred atoms. This includes impurity concentrations in the 1% range as well as realistic models of disordered materials (including liquids), vacancies, and grain boundaries. The new techniques involve the use of soft, fully nonlocal pseudopotentials, iterative diagonalization, and parallel computing algorithms. This approach has been pioneered by Car and Parrinello. Here the authors give a review of recent results using parallel and serial algorithms on metallic systems including liquid aluminum and liquid sodium, and also new results on vacancies in aluminum and on aluminum-magnesium alloys.
Transition metal doped arsenene: A first-principles study
NASA Astrophysics Data System (ADS)
Sun, Minglei; Wang, Sake; Du, Yanhui; Yu, Jin; Tang, Wencheng
2016-12-01
Using first-principles calculations, we investigate the structural, electronic, and magnetic properties of 3d transition metal (TM) atoms substitutional doping of an arsenene monolayer. Based on the binding energy, the TM-substituted arsenene systems were found to be robust. Magnetic states were obtained for Ti, V, Cr, Mn and Fe doping. More importantly, a half-metallic state resulted from Ti and Mn doping, while the spin-polarized semiconducting state occurred with V, Cr and Fe doping. Our studies demonstrated the potential applications of TM-substituted arsenene for spintronics and magnetic storage devices.
Large impurity effects in rubrene crystals: First-principles calculations
Tsetseris, L.; Pantelides, Sokrates T.
2008-01-01
Carrier mobilities of rubrene films are among the highest values reported for any organic semiconductor. Here, we probe with first-principles calculations the sensitivity of rubrene crystals on impurities. We find that isolated oxygen impurities create distinct peaks in the electronic density of states consistent with observations of defect levels in rubrene and that increased O content changes the position and shape of rubrene energy bands significantly. We also establish a dual role of hydrogen as individual H species and H impurity pairs create and annihilate deep carrier traps, respectively. The results are relevant to the performance and reliability of rubrene-based devices.
Value of first principles and phenomenological modeling in mineral processing
Concha, F.
1995-12-31
There is confusion in naming the several models developed in Mineral Processing. The authors often hear of empirical, first principle, mechanistic and phenomenological models. The objective of this paper is to clarify and distinguish between these models, based on a philosophical and linguistic analysis. A state of the art review for mathematical modeling in Mineral Processing is also made. The advantage of considering Mineral Processing as a series of unit operations was recognized by Gaudin a long time ago. He divided the area into four unit operations: (1) comminution, (2) classification, (3) concentration and (4) dewatering.
Collective modes in light nuclei from first principles.
Dytrych, T; Launey, K D; Draayer, J P; Maris, P; Vary, J P; Saule, E; Catalyurek, U; Sosonkina, M; Langr, D; Caprio, M A
2013-12-20
Results for ab initio no-core shell model calculations in a symmetry-adapted SU(3)-based coupling scheme demonstrate that collective modes in light nuclei emerge from first principles. The low-lying states of 6Li, 8Be, and 6He are shown to exhibit orderly patterns that favor spatial configurations with strong quadrupole deformation and complementary low intrinsic spin values, a picture that is consistent with the nuclear symplectic model. The results also suggest a pragmatic path forward to accommodate deformation-driven collective features in ab initio analyses when they dominate the nuclear landscape.
First-principles study of Frenkel pair recombination in tungsten
NASA Astrophysics Data System (ADS)
Qin, Shi-Yao; Jin, Shuo; Li, Yu-Hao; Zhou, Hong-Bo; Zhang, Ying; Lu, Guang-Hong
2017-02-01
The recombination of one Frenkel pair in tungsten has been investigated through first-principles simulation. Two different recombination types have been identified: instantaneous and thermally activated. The small recombination barriers for thermally activated recombination cases indicate that recombination can occur easily with a slightly increased temperature. For both of the two recombination types, recombination occurs through the self-interstitial atom moving towards the vacancy. The recombination process can be direct or through replacement sequences, depending on the vertical distance between the vacancy and the <1 1 1> line of self-interstitial atom pair.
Thermoelastic properties of random alloys from first-principles theory
NASA Astrophysics Data System (ADS)
Huang, L.; Vitos, L.; Kwon, S. K.; Johansson, B.; Ahuja, R.
2006-03-01
We present a first-principles description of the temperature-dependent elastic constants in random alloys. The substitutional disorder is treated using the coherent potential approximation implemented within the frameworks of exact muffin-tin orbitals theory. The temperature effects are approximated as the sum of electronic and thermal expansion contributions. Calculations on pure Nb demonstrate that this approach correctly accounts for the main temperature dependence of cubic elastic constants. When extended to Nb-Zr solid solution, the theoretical results show good agreement with experiments at temperatures ≲300K .
Li, Lesheng; Kanai, Yosuke
2016-04-21
Excited electron dynamics at semiconductor-molecule interfaces is ubiquitous in various energy conversion technologies. However, a quantitative understanding of how molecular details influence the quantum dynamics of excited electrons remains a great scientific challenge because of the complex interplay of different processes with various time scales. Here, we employ first-principles electron dynamics simulations to investigate how molecular features govern the dynamics in a representative interface between the hydrogen-terminated Si(111) surface and a cyanidin molecule. Hot electron transfer to the chemisorbed molecule was observed but was short-lived on the molecule. Interfacial electron transfer to the chemisorbed molecule was found to be largely decoupled from hot electron relaxation within the semiconductor surface. While the hot electron relaxation was found to take place on a time scale of several hundred femtoseconds, the subsequent interfacial electron transfer was slower by an order of magnitude. At the same time, this secondary process of picosecond electron transfer is comparable in time scale to typical electron trapping into defect states in the energy gap.
Coarse graining approach to First principles modeling of radiation cascade in large Fe super-cells
NASA Astrophysics Data System (ADS)
Odbadrakh, Khorgolkhuu; Nicholson, Don; Rusanu, Aurelian; Wang, Yang; Stoller, Roger; Zhang, Xiaoguang; Stocks, George
2012-02-01
First principles techniques employed to understand systems at an atomistic level are not practical for large systems consisting of millions of atoms. We present an efficient coarse graining approach to bridge the first principles calculations of local electronic properties to classical Molecular Dynamics (MD) simulations of large structures. Local atomic magnetic moments in crystalline Fe are perturbed by radiation generated defects. The effects are most pronounced near the defect core and decay with distance. We develop a coarse grained technique based on the Locally Self-consistent Multiple Scattering (LSMS) method that exploits the near-sightedness of the electron Green function. The atomic positions were determined by MD with an embedded atom force field. The local moments in the neighborhood of the defect cores are calculated with first-principles based on full local structure information. Atoms in the rest of the system are modeled by representative atoms with approximated properties. This work was supported by the Center for Defect Physics, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.
First-Principles Simulations of Armchair-Edge Graphene Nanostrips.
NASA Astrophysics Data System (ADS)
Li, Junwen; Mintmire, John W.; Gunlycke, Daniel; White, Carter T.
2007-03-01
We have carried out a series of first-principles, local-density functional band structure calculations of finite-width graphene nanostrips with armchair edges. A simple nearest-neighbor tight-binding model predicts that the band structures of these materials should be directly related to those of zigzag single wall carbon nanotubes, with two-thirds of the structures being small gap semiconductors and one-third of the structures being zero gap systems. The band gap in the semiconducting strips would be expected to decrease monotonically with increasing strip width. In our first-principles results, we find that in addition to the zero gap systems becoming finite gap quasimetallic systems because of symmetry breaking (as in the single-walled nanotubes), we also find that the semiconducting strips split into two families with band gaps that deviate from the simple nearest-neighbor tight binding model. Within the framework of our computational results, we compare the band structures of graphene, single-walled nanotubes, graphene nanostrips, and other carbon nanostructures. This work was supported by the US Office of Naval Research and the DoD HPCMO CHSSI program, both directly and through the US Naval Research Laboratory.
First principles calculations of La2CuO4
NASA Astrophysics Data System (ADS)
Plamada, Andrei; Kozhevnikov, Anton; Haehner, Urs; Jiang, Mi; Staar, Peter; Maier, Thomas; Schulthess, Thomas
We use the DFT+DCA method for a high-end study of the electronic structure properties of La2CuO4. The parameters of a tight-binding model are created using the first-principles electronic structure calculations. The all-electron full-potential linearised augmented plane-wave method is used to solve the non-interacting band problem. Then the set of physically relevant Wannier functions is chosen as a basis for the underlying Hubbard model. The Wannier functions and the corresponding non-interacting Hamiltonian Hnm0 (k) are created using the well-established downfolding approach. The screened Coulomb interaction parameters Unm of the model are computed using the constrained random-phase approximation technique. The double counting term is assumed to be a constant multiplied by the identity operator in the correlated subspace and it is determined based on first-principles considerations. The resulting ab-initio parameterisation of the Hubbard model is solved within dynamical cluster approximation (DCA).
Yang, J. Y.; Liu, L. H.
2016-07-21
The dielectric functions of few-layer graphene and the related temperature dependence are investigated from the atomic scale using first-principles calculations. Compared with ellipsometry experiments in the spectral range of 190–2500 nm, the normalized optical constants of mono-layer graphene demonstrate good agreement and further validate first-principles calculations. To interpret dielectric function of mono-layer graphene, the electronic band structure and density of states are analyzed. By comparing dielectric functions of mono-, bi-, and tri-layer graphene, it shows that interlayer screening strengthens intraband transition and greatly enhances the absorption peak located around 1 eV. The strengthened optical absorption is intrinsically caused by the increasing electron states near the Fermi level. To investigate temperature effect, the first-principles calculations and lattice dynamics are combined. The lattice vibration enhances parallel optical absorption peak around 1 eV and induces redshift. Moreover, it is observed that the van der Waals force plays a key role in keeping the interlayer distance stable during dynamics simulations.
Lee, Byeongno; Stowe, Haley M; Lee, Kyu Hyung; Hur, Nam Hwi; Hwang, Son-Jong; Paek, Eunsu; Hwang, Gyeong S
2017-09-13
Aqueous amines are currently the most promising solution for large-scale CO2 capture from industrial sources. However, molecular design and optimization of amine-based solvents have proceeded slowly due to a lack of understanding of the underlying reaction mechanisms. Unique and unexpected reaction mechanisms involved in CO2 absorption into aqueous hydrazine are identified using (1)H, (13)C, and (15)N NMR spectroscopy combined with first-principles quantum-mechanical simulations. We find production of both hydrazine mono-carbamate (NH2-NH-COO(-)) and hydrazine di-carbamate ((-)OOC-NH-NH-COO(-)), with the latter becoming more populated with increasing CO2 loading. Exchange NMR spectroscopy also demonstrates that the reaction products are in dynamic equilibrium under ambient conditions due to CO2 exchange between mono-carbamate and di-carbamate as well as fast proton transfer between un-protonated free hydrazine and mono-carbamate. The exchange rate rises steeply at high CO2 loadings, enhancing CO2 release, which appears to be a unique property of hydrazine in aqueous solution. The underlying mechanisms of these processes are further evaluated using quantum mechanical calculations. We also analyze and discuss reversible precipitation of carbamate and conversion of bicarbonate to carbamates. The comprehensive mechanistic study provides useful guidance for optimal design of amine-based solvents and processes to reduce the cost of carbon capture. Moreover, this work demonstrates the value of a combined experimental and computational approach for exploring the complex reaction dynamics of CO2 in aqueous amines.
First-Principles Studies of Conformation and Solution Effects on DNA Transport
NASA Astrophysics Data System (ADS)
Tan, Bikan
DNA charge transport (CT) has attracted considerable attention by the scientific community over the past 20 years. This interest reflects the potential of DNA CT to provide a sensitive route for signaling, whether in the construction of a nano-scale biosensor or as an enzymatic tool to detect damage in the genome. Research in DNA CT began as a quest to determine whether the DNA double helix with pi-stacked base pairs might share the conductive characteristics of pi-stacked solids. Physicists carried out sophisticated experiments to measure the conductivity of DNA. But the means to connect DNA to the electrodes, as well as the conditions under which the conductivity was measured are different among many experiments, as the results of the current measurements. DNA CT was seen to depend upon the connection between electrodes and DNA, and coupling between the DNA base pair stacks. Importantly, for those studies that utilized well-characterized connections to the DNA and preserved the duplex native conformation in buffered solution, significant electron conductivities were achieved. Certainly, the debate among researches has shifted from "Is DNA CT possible?" to "How does it work?". To investigate the remarkable characteristics of the double-helix molecule, we use a first-principle technique combined with molecular dynamics simulations to calculate the transport properties of B-DNA sandwiched between carbon nanotubes via alkane linkers. The quantum results using the NEGF method are calculated from snapshots recorded in MD trajectories. In chapter 1, we will go through the basic quantum and classic theories on which our calculations are based. The subject of DNA structure, electronic properties and its potential application in many fields will be introduced in chapter 2. In chapter 3, we discuss our results towards the understanding of the mechanism of DNA charge transport.
First-Principles Informed Thermodynamics of CRUD Deposition
NASA Astrophysics Data System (ADS)
O'Brien, Christopher John
The recent emphasis in the United States on developing abundant domestic sources of energy, together with an increasing awareness of the environmental hazards of fossil fuels, has led to a fresh look at the challenges of nuclear energy within the science and engineering community. One of these challenges is controlling the precipitation of porous oxide deposits onto the nuclear fuel rod cladding from the primary coolant during operation of pressurized light-water reactors (PWRs). These deposits, called CRUD (an acronym for Chalk River Unidentified Deposits), are a major concern to reactor operation because they reduce fuel lifetime and efficiency by reducing heat transfer to the coolant, promote corrosion, and depress neutron flux. This dissertation provides fundamental insights into the process by which CRUD is formed in PWRs by providing a framework linking the results of first-principles calculations to experimental data. The technique developed to facilitate the investigation is referred to as Density Functional Theory (DFT) referenced semi-empirical thermodynamics; It links 0K first-principles calculations with high temperature thermodynamics by redefining the reference chemical potentials of the constituent elements. The technique permits aqueous chemistry to be incorporated into thermodynamic calculations and allows for the prediction of temperature and pressure dependent free energies of materials that are experimentally inaccessible or have not yet been measured. The ability to extend accurate first-principles calculations to high temperatures and aqueous environments allows the stability of crystal surfaces, calculated with DFT techniques, to be predicted at conditions representative of an operating PWR. Accurate values of surface energies are used in fulfilling the principal goal of this dissertation, which is to investigate the aqueous thermodynamics of formation of nickel oxide (NiO) and nickel ferrite (NiFe 2O4) crystallites as representative CRUD
First-principles study of the infrared spectra of the ice Ih (0001) surface
Pham, T. Anh; Huang, P.; Schwegler, E.; Galli, G.
2012-08-22
Here, we present a study of the infrared (IR) spectra of the (0001) deuterated ice surface based on first-principles molecular dynamics simulations. The computed spectra show a good agreement with available experimental IR measurements. We identified the bonding configurations associated with specific features in the spectra, allowing us to provide a detailed interpretation of IR signals. We computed the spectra of several proton ordered and disordered models of the (0001) surface of ice, and we found that IR spectra do not appear to be a sensitive probe of the microscopic arrangement of protons at ice surfaces.
Band gaps and dielectric constants of amorphous hafnium silicates: A first-principles investigation
NASA Astrophysics Data System (ADS)
Broqvist, Peter; Pasquarello, Alfredo
2007-02-01
Electronic band gaps and dielectric constants are obtained for amorphous hafnium silicates using first-principles methods. Models of amorphous (HfO2)x(SiO2)1-x for varying x are generated by ab initio molecular dynamics. The calculations show that the presence of Hf gives rise to low-lying conduction states which explain the experimentally observed nonlinear dependence of the band gap on hafnium content. Static dielectric constants are found to depend linearly on x, supporting recent experimental data.
First-Principles Vibrational Electron Energy Loss Spectroscopy of β -Guanine
NASA Astrophysics Data System (ADS)
Radtke, G.; Taverna, D.; Lazzeri, M.; Balan, E.
2017-07-01
A general approach to model vibrational electron energy loss spectra obtained using an electron beam positioned away from the specimen is presented. The energy-loss probability of the fast electron is evaluated using first-principles quantum mechanical calculations (density functional theory) of the dielectric response of the specimen. The validity of the method is assessed using recently measured anhydrous β -guanine, an important molecular solid used by animals to produce structural colors. The good agreement between theory and experiments lays the basis for a quantitative interpretation of this spectroscopy in complex systems.
First Principles Study on NaxLi1-xFePO4 As Cathode Material for Rechargeable Lithium Batteries
NASA Astrophysics Data System (ADS)
Ouyang, Chu-Ying; Wang, De-Yu; Shi, Si-Qi; Wang, Zhao-Xiang; Li, Hong; Huang, Xue-Jie; Chen, Li-Quan
2006-01-01
The electronic structure and ionic dynamic properties of pure and Na doped (Li site) LiFePO4 have been investigated by first-principles calculations. The band gap of the Na doped material is much narrow than that of the undoped one, indicating of better electronic conductive properties. First-principles based molecular dynamic simulations have been performed to examine the migration energy barriers for the Li ion diffusion. The results shown that the energy barriers for Li diffusion decreased a little along the one-dimensional diffusion pathway, indicating that the ionic conductive property is also improved, as compared with the high valance doping (such as Cr) cases.
NASA Astrophysics Data System (ADS)
Paul, Sujata
In the course of my PhD I have worked on a broad range of problems using simulations from first principles: from catalysis and chemical reactions at surfaces and on nanostructures, characterization of carbon-based systems and devices, and surface and interface physics. My research activities focused on the application of ab-initio electronic structure techniques to the theoretical study of important aspects of the physics and chemistry of materials for energy and environmental applications and nano-electronic devices. A common theme of my research is the computational study of chemical reactions of environmentally important molecules (CO, CO2) using high performance simulations. In particular, my principal aim was to design novel nano-structured functional catalytic surfaces and interfaces for environmentally relevant remediation and recycling reactions, with particular attention to the management of carbon dioxide. We have studied the carbon-mediated partial sequestration and selective oxidation of carbon monoxide (CO), both in the presence and absence of hydrogen, on graphitic edges. Using first-principles calculations we have studied several reactions of CO with carbon nanostructures, where the active sites can be regenerated by the deposition of carbon decomposed from the reactant (CO) to make the reactions self-sustained. Using statistical mechanics, we have also studied the conditions under which the conversion of CO to graphene and carbon dioxide is thermodynamically favorable, both in the presence and in the absence of hydrogen. These results are a first step toward the development of processes for the carbon-mediated partial sequestration and selective oxidation of CO in a hydrogen atmosphere. We have elucidated the atomic scale mechanisms of activation and reduction of carbon dioxide on specifically designed catalytic surfaces via the rational manipulation of the surface properties that can be achieved by combining transition metal thin films on oxide
First-principles study of point defects in thorium carbide
NASA Astrophysics Data System (ADS)
Pérez Daroca, D.; Jaroszewicz, S.; Llois, A. M.; Mosca, H. O.
2014-11-01
Thorium-based materials are currently being investigated in relation with their potential utilization in Generation-IV reactors as nuclear fuels. One of the most important issues to be studied is their behavior under irradiation. A first approach to this goal is the study of point defects. By means of first-principles calculations within the framework of density functional theory, we study the stability and formation energies of vacancies, interstitials and Frenkel pairs in thorium carbide. We find that C isolated vacancies are the most likely defects, while C interstitials are energetically favored as compared to Th ones. These kind of results for ThC, to the best authors' knowledge, have not been obtained previously, neither experimentally, nor theoretically. For this reason, we compare with results on other compounds with the same NaCl-type structure.
First-principles calculations of PuO(2+/-x).
Petit, L; Svane, A; Szotek, Z; Temmerman, W M
2003-07-25
The electronic structure of PuO(2+/-x) was studied using first-principles quantum mechanics, realized with the self-interaction corrected local spin density method. In the stoichiometric PuO2 compound, Pu occurs in the Pu(IV) oxidation state, corresponding to a localized f4 shell. If oxygen is introduced onto the octahedral interstitial site, the nearby Pu atoms turn into Pu(V) (f3) by transferring electrons to the oxygen. Oxygen vacancies cause Pu(III) (f5) to form by taking up electrons released by oxygen. At T = 0, the PuO2 compound is stable with respect to free oxygen, but the delicate energy balance suggests the possible deterioration of the material during long-term storage.
Accurate first principles model potentials for intermolecular interactions.
Gordon, Mark S; Smith, Quentin A; Xu, Peng; Slipchenko, Lyudmila V
2013-01-01
The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.
First-principles prediction of disordering tendencies in pyrochlore oxides
NASA Astrophysics Data System (ADS)
Jiang, Chao; Stanek, C. R.; Sickafus, K. E.; Uberuaga, B. P.
2009-03-01
Using first-principles calculations, we systematically predict the order-disorder energetics of series of zirconate (A2Zr2O7) , hafnate (A2Hf2O7) , titanate (A2Ti2O7) , and stannate (A2Sn2O7) pyrochlores. The disordered defect-fluorite structure is modeled using an 88-atom two-sublattice special quasirandom structure (SQS) that closely reproduces the most relevant near-neighbor intrasublattice and intersublattice pair-correlation functions of the random mixture. The order-disorder transition temperatures of these pyrochlores estimated from our SQS calculations show overall good agreement with existing experiments. We confirm previous studies suggesting that the bonding in pyrochlores is not purely ionic and thus electronic effects also play a role in determining their disordering tendencies. Our results have important consequences for numerous applications, including nuclear waste forms and fast ion conductors.
Electromagnetic response of C12 : A first-principles calculation
Lovato, A.; Gandolfi, S.; Carlson, J.; ...
2016-08-15
Here, the longitudinal and transverse electromagnetic response functions ofmore » $$^{12}$$C are computed in a ``first-principles'' Green's function Monte Carlo calculation, based on realistic two- and three-nucleon interactions and associated one- and two-body currents. We find excellent agreement between theory and experiment and, in particular, no evidence for the quenching of measured versus calculated longitudinal response. This is further corroborated by a re-analysis of the Coulomb sum rule, in which the contributions from the low-lying $$J^\\pi\\,$$=$$\\, 2^+$$, $0^+$ (Hoyle), and $4^+$ states in $$^{12}$$C are accounted for explicitly in evaluating the total inelastic strength.« less
Point defects in thorium nitride: A first-principles study
NASA Astrophysics Data System (ADS)
Pérez Daroca, D.; Llois, A. M.; Mosca, H. O.
2016-11-01
Thorium and its compounds (carbides and nitrides) are being investigated as possible materials to be used as nuclear fuels for Generation-IV reactors. As a first step in the research of these materials under irradiation, we study the formation energies and stability of point defects in thorium nitride by means of first-principles calculations within the framework of density functional theory. We focus on vacancies, interstitials, Frenkel pairs and Schottky defects. We found that N and Th vacancies have almost the same formation energy and that the most energetically favorable defects of all studied in this work are N interstitials. These kind of results for ThN, to the best authors' knowledge, have not been obtained previously, neither experimentally, nor theoretically.
Stability of hydrogenated graphene: a first-principles study
Yi, Ding; Yang, Liu; Xie, Shijie; ...
2015-02-10
In order to explain the disagreement between present theoretical and experimental investigations on the stability of hydrogenated graphene, we have systematically studied hydrogenated graphene with different configurations from the consideration of single-side and double-side adsorption using first-principles calculations. Both binding energy and formation energy are calculated to characterize the stability of the system. It is found that single-side hydrogenated graphene is always unstable. However, for double-side hydrogenation, some configurations are stable due to the increased carbon–carbon sp3 hybridization compared to single-side hydrogenation. Furthermore, it is found that the system is energetically favorable when an equal number of hydrogen atoms aremore » adsorbed on each side of the graphene.« less
Infrared Spectroscopy of Functionalized Graphene Sheets from First Principle Calculations
NASA Astrophysics Data System (ADS)
Zhang, Cui; Dabbs, Daniel; Aksay, Ilhan; Car, Roberto; Selloni, Annabella
2014-03-01
Detailed characterization of the structure of functionalized graphene sheets (FGSs) is an important and challenging task which could help to improve the performance of FGS materials for technological applications. We present here first principles calculations for the infrared (IR) spectra of different FGS models aimed at identifying the IR signatures of different functional groups and defect sites on FGSs. We found that vacancies and edges have significant effects on the IR frequencies of the functional groups on FGSs. In particular, hydroxyl groups close to vacancies have higher stretching and lower bending frequencies in comparison to hydroxyls in defect free regions of FGSs. More interestingly, the OH vibrations of carboxyl groups at edges exhibit unique features in the high frequency IR bands, which originate from the interactions with neighboring groups and the relative orientation of the carboxyl with respect to the FGS plane. Our results are supported by experimental IR measurements on FGS powders.
First-principles study of interface doping in ferroelectric junctions
NASA Astrophysics Data System (ADS)
Wang, Pin-Zhi; Cai, Tian-Yi; Ju, Sheng; Wu, Yin-Zhong
2016-04-01
Effect of atomic monolayer insertion on the performance of ferroelectric tunneling junction is investigated in SrRuO3/BaTiO3/SrRuO3 heterostrucutures. Based on first-principles calculations, the atomic displacement, orbital occupancy, and ferroelectric polarization are studied. It is found that the ferroelectricity is enhanced when a (AlO2)- monolayer is inserted between the electrode SRO and the barrier BTO, where the relatively high mobility of doped holes effectively screen ferroelectric polarization. On the other hand, for the case of (LaO)+ inserted layer, the doped electrons resides at the both sides of middle ferroelectric barrier, making the ferroelectricity unfavorable. Our findings provide an alternative avenue to improve the performance of ferroelectric tunneling junctions.
Electronic Stopping Power in LiF from First Principles
Pruneda, J. M.; Sanchez-Portal, D.; Artacho, Emilio
2007-12-07
Using time-dependent density-functional theory we calculate from first principles the rate of energy transfer from a moving proton or antiproton to the electrons of an insulating material, LiF. The behavior of the electronic stopping power versus projectile velocity displays an effective threshold velocity of {approx}0.2 a.u. for the proton, consistent with recent experimental observations, and also for the antiproton. The calculated proton/antiproton stopping-power ratio is {approx}2.4 at velocities slightly above the threshold (v{approx}0.4 a.u.), as compared to the experimental value of 2.1. The projectile energy loss mechanism is observed to be extremely local.
Two Dimensional Ice from First Principles: Structures and Phase Transitions.
Chen, Ji; Schusteritsch, Georg; Pickard, Chris J; Salzmann, Christoph G; Michaelides, Angelos
2016-01-15
Despite relevance to disparate areas such as cloud microphysics and tribology, major gaps in the understanding of the structures and phase transitions of low-dimensional water ice remain. Here, we report a first principles study of confined 2D ice as a function of pressure. We find that at ambient pressure hexagonal and pentagonal monolayer structures are the two lowest enthalpy phases identified. Upon mild compression, the pentagonal structure becomes the most stable and persists up to ∼2 GPa, at which point the square and rhombic phases are stable. The square phase agrees with recent experimental observations of square ice confined within graphene sheets. This work provides a fresh perspective on 2D confined ice, highlighting the sensitivity of the structures observed to both the confining pressure and the width.
First-principles study of optical excitations in alphaquartz
Chang, Eric K.; Rohlfing, Michael; Louie, Steven G.
1999-06-15
The properties of silicon dioxide have been studied extensively over the years. However, there still remain major unanswered questions regarding the nature of the optical spectrum and the role of excitonic effects in this technologically important material. In this work, we present an ab initio study of the optical absorption spectrum of alpha-quartz, using a newly developed first-principles method which includes self-energy and electron-hole interaction effects. The quasiparticle band structure is computed within the GW approximation to obtain a quantitative description of the single-particle excitations. The Bethe-Salpeter equation for the electron-hole excitations is solved to obtain the optical spectrum and to understand the spatial extent and physical properties of the excitons. The theoretical absorption spectrum is found to be in excellent agreement with the measured spectrum. We show that excitonic effects are crucial in the frequency range up to 5 eV above the absorption threshold.
First-principles studies of native defects in olivine phosphates
NASA Astrophysics Data System (ADS)
Hoang, Khang; Johannes, Michelle
2011-03-01
Olivine phosphates Li M PO4 (M = Mn, Fe, Co, Ni) are promising candidates for rechargeable Li-ion battery electrodes because of their energy storage capacity and electrochemical and thermal stability. It is known that native defects have strong effects on the performance of olivine phosphates. Yet, the formation and migration of these defects are not fully understood, and we expect that once such understanding has been established, one can envisage a solution for improving the materials' performance. In this talk, we present our first-principles density-functional theory studies of native point defects and defect complexes in Li M PO4 , and discuss the implications of these defects on the performance of the materials. Our results also provide guidelines for obtaining different native defects in experiments.
Systematic First-Principles Study of Binary Metal Hydrides.
Bourgeois, Natacha; Crivello, Jean-Claude; Cenedese, Pierre; Joubert, Jean-Marc
2017-08-14
First-principles calculations were systematically performed for 31 binary metal-hydrogen (M-H) systems on a set of 30 potential crystal structures selected on the basis of experimental data and possible interstitial sites. For each M-H system, the calculated enthalpies of formation were represented as functions of H composition. The zero-point energy correction was considered for the most stable hydrides via additional harmonic phonon calculations. The sequence of stable hydrides (ground-state) given by the convex hull was found in satisfactory agreement with the experimental data. In addition, new high pressure dihydrides and trihydrides were predicted, providing orientations for new materials synthesis. The overall results provide a global overview of hydride relative stabilities and relevant input data for thermodynamic modeling methods.
Thermoelectric properties of titanium dioxide polymorphs from first principles
NASA Astrophysics Data System (ADS)
Bayerl, Dylan; Kioupakis, Emmanouil
2014-03-01
Titanium oxides are promising materials for high-temperature thermoelectrics because of their high Seebeck coefficients, thermal stability, and natural abundance. We use first-principles calculations to investigate the thermoelectric transport properties of several titanium dioxide polymorphs. Our methodology is based on density functional and many-body perturbation theory within the GW approximation. The maximally localized Wannier function method is employed to interpolate the GW bands in the Brillouin zone. We use the Boltzmann transport formalism within the constant relaxation time approximation to determine the temperature and carrier-density dependence of the Seebeck coefficient, electron mobility, and electron thermal conductivity from the calculated electronic band structures. We demonstrate agreement with experimentally measured transport parameters and enhanced power factor at high temperature in certain heavily doped phases. This research was supported as part of CSTEC, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science. Computational resources were provided by the DOE NERSC facility.
First-principles study of high explosive decomposition energetics
Wu, C J
1998-08-21
The mechanism of the gas phase unimolecular decomposition of hexahydro-1,3,5,- trinitro- 1,3,5,-triazine (RDX) has been investigated using first principles gradient corrected density functional theory. Our results show that the dominant reaction channel is the N-NO* bond rupture, which has a barrier of 34.2 kcal/mol at the B- PW9 l/cc-pVDZ level and is 18.3 kcal/mol lower than that of the concerted ring fission to three methylenenitramine molecules. In addition, we have carried out a systematic study of homolytic bond dissociation energies of 14 other high explosives at the B-PW91/D95V level. We find that the correlation between the weakest bond strength and high explosive sensitivity is strong
First-principles modeling hydrogenation of bilayered boron nitride
NASA Astrophysics Data System (ADS)
Jing, Wang; Peng, Zhang; Xiang-Mei, Duan
2016-05-01
We have investigated the structural and electronic characteristics of hydrogenated boron-nitride bilayer (H-BNBN-H) using first-principles calculations. The results show that hydrogenation can significantly reduce the energy gap of the BN-BN into the visible-light region. Interestingly, the electric field induced by the interface dipoles helps to promote the formation of well-separated electron-hole pairs, as demonstrated by the charge distribution of the VBM and CBM. Moreover, the applied bias voltage on the vertical direction of the bilayer could modulate the band gap, resulting in transition from semiconductor to metal. We conclude that H-BNBN-H could improve the solar energy conversion efficiency, which may provide a new way for tuning the electronic devices to meet different environments and demands. Project supported by the National Natural Science Foundation of China (Grant No. 11574167).
Principles of silicon surface chemistry from first principles
Doren, D.J.
1996-10-01
First principles theoretical studies of dissociative adsorption of H{sub 2}, H{sub 2}O, SiH{sub 4} and other species on Si(100)-2x1 demonstrate some common principles that permit qualitative understanding of the mechanisms of reactive adsorption on Si. The structures of transition states and the interactions among surface sites can also be understood in terms of correlations between surface structure and local electron density. For example, the transition states for dissociative adsorption involve buckled surface dimers, which present both electrophilic and nucleophilic reaction sites and allow efficient addition across the dimer. A surface Diels-Alder reaction will also be described, in which symmetric addition to an unbuckled surface dimer is allowed by orbital symmetry. The Diets-Alder product establishes novel reactive surface sites that may be useful for subsequent surface modification. This work has been done in collaboration with Sharmila Pai, Robert Konecny and Anita Robinson Brown.
First principles nuclear magnetic resonance signatures of graphene oxide.
Lu, Ning; Huang, Ying; Li, Hai-bei; Li, Zhenyu; Yang, Jinlong
2010-07-21
Nuclear magnetic resonance (NMR) has been widely used in graphene oxide (GO) structure studies. However, the detailed relationship between its spectroscopic features and the GO structural configuration remains elusive. Based on first principles (13)C chemical shift calculations using the gauge including projector augmented waves method, we provide a reliable spectrum-structure connection. The (13)C chemical shift in GO is found to be very sensitive to the atomic environment, even for the same type of oxidation groups. Factors determining the chemical shifts of epoxy and hydroxy groups have been discussed. GO structures previously reported in the literature have been checked from the NMR point of view. The energetically favorable hydroxy chain structure is not expected to be widely existed in real GO samples according to our NMR simulations. The epoxy pair species we proposed previously is also supported by chemical shift calculations.
First principles nuclear magnetic resonance signatures of graphene oxide
NASA Astrophysics Data System (ADS)
Lu, Ning; Huang, Ying; Li, Hai-bei; Li, Zhenyu; Yang, Jinlong
2010-07-01
Nuclear magnetic resonance (NMR) has been widely used in graphene oxide (GO) structure studies. However, the detailed relationship between its spectroscopic features and the GO structural configuration remains elusive. Based on first principles C13 chemical shift calculations using the gauge including projector augmented waves method, we provide a reliable spectrum-structure connection. The C13 chemical shift in GO is found to be very sensitive to the atomic environment, even for the same type of oxidation groups. Factors determining the chemical shifts of epoxy and hydroxy groups have been discussed. GO structures previously reported in the literature have been checked from the NMR point of view. The energetically favorable hydroxy chain structure is not expected to be widely existed in real GO samples according to our NMR simulations. The epoxy pair species we proposed previously is also supported by chemical shift calculations.
Carbon-rich icosahedral boron carbide designed from first principles
Jay, Antoine; Vast, Nathalie; Sjakste, Jelena; Duparc, Olivier Hardouin
2014-07-21
The carbon-rich boron-carbide (B{sub 11}C)C-C has been designed from first principles within the density functional theory. With respect to the most common boron carbide at 20% carbon concentration B{sub 4}C, the structural modification consists in removing boron atoms from the chains linking (B{sub 11}C) icosahedra. With C-C instead of C-B-C chains, the formation of vacancies is shown to be hindered, leading to enhanced mechanical strength with respect to B{sub 4}C. The phonon frequencies and elastic constants turn out to prove the stability of the carbon-rich phase, and important fingerprints for its characterization have been identified.
First principle study of manganese doped cadmium sulphide sheet
Kumar, Sanjeev; Kumar, Ashok; Ahluwalia, P. K.
2014-04-24
First-principle electronic structure calculations for cadmium sulphide (CdS) sheet in hexagonal phase, with Manganese substitution and addition, as well as including the Cd defects, are investigated. The lattice constants calculated for CdS sheet agrees fairly well with results reported for thin films experimentally. The calculations of total spin density of states and partial density of states in different cases shows substantial magnetic dipole moments acquired by the sheet. A magnetic dipole moment 5.00612 μ{sub B} and band gap of the order 1 eV are found when cadmium atom is replaced by Manganese. The magnetism acquired by the sheet makes it functionally important candidate in many applications.
First principles studies of electron tunneling in proteins
Hayashi, Tomoyuki; Stuchebrukhov, Alexei A.
2014-01-01
A first principles study of electronic tunneling along the chain of seven Fe/S clusters in respiratory complex I, a key enzyme in the respiratory electron transport chain, is described. The broken-symmetry states of the Fe/S metal clusters calculated at both DFT and semi-empirical ZINDO levels were utilized to examine both the extremely weak electronic couplings between Fe/S clusters and the tunneling pathways, which provide a detailed atomistic-level description of the charge transfer process in the protein. One-electron tunneling approximation was found to hold within a reasonable accuracy, with only a moderate induced polarization of the core electrons. The method is demonstrated to be able to calculate accurately the coupling matrix elements as small as 10−4 cm−1. A distinct signature of the wave properties of electrons is observed as quantum interferences of multiple tunneling pathways. PMID:25383312
Hydrogen storage in LiH: A first principle study
NASA Astrophysics Data System (ADS)
Banger, Suman; Nayak, Vikas; Verma, U. P.
2014-04-01
First principles calculations have been performed on the Lithium hydride (LiH) using the full potential linearized augmented plane wave (FP-LAPW) method within the framework of density functional theory. We have extended our calculations for LiH+2H and LiH+6H in NaCl structure. The structural stability of three compounds have been studied. It is found that LiH with 6 added Hydrogen atoms is most stable. The obtained results for LiH are in good agreement with reported experimental data. Electronic structures of three compounds are also studied. Out of three the energy band gap in LiH is ˜3.0 eV and LiH+2H and LiH+6H are metallic.
First-principles study on superconductivity of solid oxygen
NASA Astrophysics Data System (ADS)
Ishikawa, Takahiro; Mukai, Kenta; Shimizu, Katsuya
2012-12-01
The superconductivity of solid oxygen in ζ phase was investigated by first-principles calculations based on the density functional theory. Using a monoclinic C2/m structure, we calculated the superconducting transition temperature by the Allen-Dynes formula and obtained 2.4 K at 100 GPa for the effective screened Coulomb repulsion constant μ* of 0.13. The transition temperature slowly decreases with increasing pressure and becomes 1.3 K at 200 GPa. The phonon analysis shows that the electron-phonon coupling is dominantly enhanced by the intermolecular vibrations of O2 rather than the intramolecular ones. The phonon modes showing the strong electron-phonon coupling were found to be concentrated in the phonon frequency range of 100-150 cm-1 at around the M-point in the Brillouin zone.
First-principles investigation of PVDF and its copolymers
NASA Astrophysics Data System (ADS)
Ranjan, V.; Yu, Liping; Buongiorno Nardelli, Marco; Bernholc, J.
2009-03-01
Recently, PVDF and its copolymers have generated significant interest due to their electroactive properties [1] and potential for ultra-high energy-storage applications [2]. In this talk, we present the results of first-principles calculations of stable phases and dielectric properties of different copolymers and terpolymers of PVDF at varying concentrations. Our results show that at very high concentrations of Chloro-trifluoroethylene (CTFE), PVDF/CTFE displays sharp transitions between non-polar (α) and polar (β) phases. On the contrary, the same transitions in copolymers with trifluoroethylene (TrFE) and tetrafluoroethylene (TeFE) are not sharp and happen at lower concentrations. We discuss the interplay of copolymer admixture on the dielectric properties of PVDF and discuss the suitability of copolymers for energy storage and electroactive applications. [1] S. G. Lu et al., App. Phys. Lett. 93, 042905 (2008). [2] V. Ranjan et al., Phys. Rev. Lett. 99, 047801 (2007).
Free-Carrier Absorption in Silicon from First Principles
NASA Astrophysics Data System (ADS)
Shi, Guangsha; Kioupakis, Emmanouil
The absorption of light by free carriers in semiconductors such as silicon results in intraband electron or hole excitations, and competes with optical transitions across the band gap. Free-carrier absorption therefore reduces the efficiency of optoelectronic devices such as solar cells because it competes with the generation of electron-hole pairs. In this work, we use first-principles calculations based on density functional theory to investigate direct and phonon-assisted free-carrier absorption in silicon. We determine the free-carrier absorption coefficient as a function of carrier concentration and temperature and compare to experiment. We also identify the dominant phonon modes that contributing to phonon-assisted free-carrier absorption processes, and analyze the results to evaluate the impact of this loss mechanism on the efficiency of silicon solar cells. This research was supported by the National Science Foundation CAREER award through Grant No. DMR-1254314. Computational resources were provided by the DOE NERSC facility.
NMR shifts for polycyclic aromatic hydrocarbons from first-principles
Thonhauser, Timo; Ceresoli, Davide; Marzari, Nicola N.
2009-09-03
We present first-principles, density-functional theory calculations of the NMR chemical shifts for polycyclic aromatic hydrocarbons, starting with benzene and increasing sizes up to the one- and two-dimensional infinite limits of graphene ribbons and sheets. Our calculations are performed using a combination of the recently developed theory of orbital magnetization in solids, and a novel approach to NMR calculations where chemical shifts are obtained from the derivative of the orbital magnetization with respect to a microscopic, localized magnetic dipole. Using these methods we study on equal footing the 1H and 13C shifts in benzene, pyrene, coronene, in naphthalene, anthracene, naphthacene, and pentacene, and finally in graphene, graphite, and an infinite graphene ribbon. Our results show very good agreement with experiments and allow us to characterize the trends for the chemical shifts as a function of system size.
First-principles study of fluorination of L-Alanine
NASA Astrophysics Data System (ADS)
Sreepad, H. R.; Ravi, H. R.; Ahmed, Khaleel; Dayananda, H. M.; Umakanth, K.; Manohara, B. M.
2013-02-01
First-principles calculations based on Density Functional Theory have been done on effect of fluorination of an important amino acid - L-Alanine. Its structure has been simulated. The unit cell is orthorhombic with lattice parameters a=5.90Å, b=13.85Å and c=5.75Å with volume 470 (Å)3. Bond lengths and bond angles have been estimated. Electronic Density of States calculations show that the material has a band gap of 4.47eV. Electronic band structure indicates that the material can be effectively used for NLO applications. The electronic contribution to the dielectric constant has been calculated and its average value comes out to be 2.165.
First principle study of manganese doped cadmium sulphide sheet
NASA Astrophysics Data System (ADS)
Kumar, Sanjeev; Kumar, Ashok; Ahluwalia, P. K.
2014-04-01
First-principle electronic structure calculations for cadmium sulphide (CdS) sheet in hexagonal phase, with Manganese substitution and addition, as well as including the Cd defects, are investigated. The lattice constants calculated for CdS sheet agrees fairly well with results reported for thin films experimentally. The calculations of total spin density of states and partial density of states in different cases shows substantial magnetic dipole moments acquired by the sheet. A magnetic dipole moment 5.00612 μB and band gap of the order 1 eV are found when cadmium atom is replaced by Manganese. The magnetism acquired by the sheet makes it functionally important candidate in many applications.
Elastic and piezoresistive properties of nickel carbides from first principles
NASA Astrophysics Data System (ADS)
Kelling, Jeffrey; Zahn, Peter; Schuster, Jörg; Gemming, Sibylle
2017-01-01
The nickel-carbon system has received increased attention over the past years due to the relevance of nickel as a catalyst for carbon nanotube and graphene growth, where nickel carbide intermediates may be involved or carbide interface layers form in the end. Nickel-carbon composite thin films comprising Ni3C are especially interesting in mechanical sensing applications. Due to the metastability of nickel carbides, formation conditions and the coupling between mechanical and electrical properties are not yet well understood. Using first-principles electronic structure methods, we calculated the elastic properties of Ni3C ,Ni2C , and NiC , as well as changes in electronic properties under mechanical strain. We observe that the electronic density of states around the Fermi level does not change under the considered strains of up to 1%, which correspond to stresses up to 3 GPa . Relative changes in conductivity of Ni3C range up to maximum values of about 10%.
First-principles study of interface doping in ferroelectric junctions
Wang, Pin-Zhi; Cai, Tian-Yi; Ju, Sheng; Wu, Yin-Zhong
2016-01-01
Effect of atomic monolayer insertion on the performance of ferroelectric tunneling junction is investigated in SrRuO3/BaTiO3/SrRuO3 heterostrucutures. Based on first-principles calculations, the atomic displacement, orbital occupancy, and ferroelectric polarization are studied. It is found that the ferroelectricity is enhanced when a (AlO2)− monolayer is inserted between the electrode SRO and the barrier BTO, where the relatively high mobility of doped holes effectively screen ferroelectric polarization. On the other hand, for the case of (LaO)+ inserted layer, the doped electrons resides at the both sides of middle ferroelectric barrier, making the ferroelectricity unfavorable. Our findings provide an alternative avenue to improve the performance of ferroelectric tunneling junctions. PMID:27063704
First-principles simulations of electrostatic interactions between dust grains
Itou, H. Amano, T.; Hoshino, M.
2014-12-15
We investigated the electrostatic interaction between two identical dust grains of an infinite mass immersed in homogeneous plasma by employing first-principles N-body simulations combined with the Ewald method. We specifically tested the possibility of an attractive force due to overlapping Debye spheres (ODSs), as was suggested by Resendes et al. [Phys. Lett. A 239, 181–186 (1998)]. Our simulation results demonstrate that the electrostatic interaction is repulsive and even stronger than the standard Yukawa potential. We showed that the measured electric field acting on the grain is highly consistent with a model electrostatic potential around a single isolated grain that takes into account a correction due to the orbital motion limited theory. Our result is qualitatively consistent with the counterargument suggested by Markes and Williams [Phys. Lett. A 278, 152–158 (2000)], indicating the absence of the ODS attractive force.
Stability of hydrogenated graphene: a first-principles study
Yi, Ding; Yang, Liu; Xie, Shijie; Saxena, Avadh
2015-02-10
In order to explain the disagreement between present theoretical and experimental investigations on the stability of hydrogenated graphene, we have systematically studied hydrogenated graphene with different configurations from the consideration of single-side and double-side adsorption using first-principles calculations. Both binding energy and formation energy are calculated to characterize the stability of the system. It is found that single-side hydrogenated graphene is always unstable. However, for double-side hydrogenation, some configurations are stable due to the increased carbon–carbon sp^{3} hybridization compared to single-side hydrogenation. Furthermore, it is found that the system is energetically favorable when an equal number of hydrogen atoms are adsorbed on each side of the graphene.
Fundamental limits on transparency: first-principles calculations of absorption
NASA Astrophysics Data System (ADS)
Peelaers, Hartwin
2013-03-01
Transparent conducting oxides (TCOs) are a technologically important class of materials with applications ranging from solar cells, displays, smart windows, and touch screens to light-emitting diodes. TCOs combine high conductivity, provided by a high concentration of electrons in the conduction band, with transparency in the visible region of the spectrum. The requirement of transparency is usually tied to the band gap being sufficiently large to prevent absorption of visible photons. This is a necessary but not sufficient condition: indeed, the high concentration of free carriers can also lead to optical absorption by excitation of electrons to higher conduction-band states. A fundamental understanding of the factors that limit transparency in TCOs is essential for further progress in materials and applications. The Drude theory is widely used, but it is phenomenological in nature and tends to work poorly at shorter wavelengths, where band-structure effects are important. First-principles calculations have been performed, but were limited to direct transitions; as we show in the present work, indirect transitions assisted by phonons or defects actually dominate. Our calculations are the first to address indirect free-carrier absorption in a TCO completely from first principles. We present results for SnO2, but the methodology is general and is also being applied to ZnO and In2O3. The calculations provide not just quantitative results but also deeper insights in the mechanisms that govern absorption processes in different wavelength regimes, which is essential for engineering improved materials to be used in more efficient devices. For SnO2, we find that absorption is modest in the visible, and much stronger in the ultraviolet and infrared. Work performed in collaboration with E. Kioupakis and C.G. Van de Walle, and supported by DOE, NSF, and BAEF.
Leptogenesis from first principles in the resonant regime
Garny, Mathias; Kartavtsev, Alexander; Hohenegger, Andreas
2013-01-15
The lepton asymmetry generated by the out-of-equilibrium decays of heavy Majorana neutrinos with a quasi-degenerate mass spectrum is resonantly enhanced. In this work, we study this scenario within a first-principle approach. The quantum field theoretical treatment is applicable for mass splittings of the order of the width of the Majorana neutrinos, for which the enhancement is maximally large. The non-equilibrium evolution of the mixing Majorana neutrino fields is described by a formal analytical solution of the Kadanoff-Baym equations, that is obtained by neglecting the back-reaction. Based on this solution, we derive approximate analytical expressions for the generated asymmetry and compare them to the Boltzmann result. We find that the resonant enhancement obtained from the Kadanoff-Baym approach is smaller compared to the Boltzmann approach, due to additional contributions that describe coherent transitions between the Majorana neutrino species. We also discuss corrections to the masses and widths of the degenerate pair of Majorana neutrinos that are relevant for very small mass splitting, and compare the approximate analytical result for the lepton asymmetry with numerical results. - Highlights: Black-Right-Pointing-Pointer Treatment of leptogenesis in the resonant regime by a first-principle approach. Black-Right-Pointing-Pointer Applicable for mass differences of the order of the width. Black-Right-Pointing-Pointer Non-equilibrium evolution described by Kadanoff-Baym equations. Black-Right-Pointing-Pointer Analytical solution can be obtained neglecting backreaction. Black-Right-Pointing-Pointer Resonant enhancement is smaller compared to the classical Boltzmann approach.
Emergent symmetries in atomic nuclei from first principles
NASA Astrophysics Data System (ADS)
Launey, K. D.; Dreyfuss, A. C.; Baker, R. B.; Draayer, J. P.; Dytrych, T.
2015-04-01
An innovative symmetry-guided approach and its applications to light and intermediate-mass nuclei is discussed. This approach, with Sp(3, R) the underpinning group, is based on our recent remarkable finding, namely, we have identified the symplectic Sp(3,R) as an approximate symmetry for low-energy nuclear dynamics. This study presents the results of two complementary studies, one that utilizes realistic nucleon-nucleon interactions and unveils symmetries inherent to nuclear dynamics from first principles (or ab initio), and another study, which selects important components of the nuclear interaction to explain the primary physics responsible for emergent phenomena, such as enhanced collectivity and alpha clusters. In particular, within this symmetry-guided framework, ab initio applications of the theory to light nuclei reveal the emergence of a simple orderly pattern from first principles. This provides a strategy for determining the nature of bound states of nuclei in terms of a relatively small fraction of the complete shell-model space, which, in turn, can be used to explore ultra-large model spaces for a description of alpha-cluster and highly deformed structures together with associated rotations. We find that by using only a fraction of the model space extended far beyond current no-core shell-model limits and a long-range interaction that respects the symmetries in play, the outcome reproduces characteristic features of the low-lying 0+ states in 12C (including the elusive Hoyle state of importance to astrophysics) and agrees with ab initio results in smaller spaces. For these states, we offer a novel perspective emerging out of no-core shell-model considerations, including a discussion of associated nuclear deformation, matter radii, and density distribution. The framework we find is also extensible beyond 12C, namely, to the low-lying 0+ states of 8Be as well as the ground-state rotational band of Ne, Mg, and Si isotopes.
First principles theory for surface plasmon generation and decay to hot carriers
NASA Astrophysics Data System (ADS)
Sundararaman, Ravishankar; Narang, Prineha; Jermyn, Adam; Atwater, Harry A.; Goddard, William A., III
2014-03-01
Plasmonic resonances provide a promising pathway for efficiently capturing infrared photons from solar radiation and boosting photo-catalytic activity via local temperature enhancements and hot carrier generation. Previous calculations of plasmon decay to excited carriers employing a fully quantized model Hamiltonian [2] indicate strong plasmon polarization dependence and momentum anisotropy of the generated carriers, in contrast with classical theories. An accurate first principles calculation for this process must account for microscopic details at the atomic scale for the electronic states as well as the effect of the 10-100 nm length scale particle and antennae geometries on the plasmon resonances. Here, we present a first-principles multi-scale model of plasmonics combining electronic density-functional theory with electromagnetic models on longer length-scales, and investigate the role of electronic structure and geometry on plasmonic light absorption, decay and hot carrier generation. This material is based upon work performed by the Joint Center for Artificial Photosynthesis, a DOE Energy Innovation Hub, supported through the Office of Science of the U.S. Department of Energy under Award Number DE-SC0004993.
Molecular scale electronics: syntheses and testing
NASA Astrophysics Data System (ADS)
Reinerth, William A.; Jones, LeRoy, II; Burgin, Timothy P.; Zhou, Chong-wu; Muller, C. J.; Deshpande, M. R.; Reed, Mark A.; Tour, James M.
1998-09-01
This paper describes four significant breakthroughs in the syntheses and testing of molecular scale electronic devices. The 16-mer of oligo(2-dodecylphenylene ethynylene) was prepared on Merrifields resin using the iterative divergent/convergent approach which significantly streamlines the preparation of this molecular scale wire. The formation of self-assembled monolayers and multilayers on gold surfaces of rigid rod conjugated oligomers that have thiol, 0957-4484/9/3/016/img11-dithiol, thioacetyl, or 0957-4484/9/3/016/img11-dithioacetyl end groups have been studied. The direct observation of charge transport through molecules of benzene-1, 4-dithiol, which have been self-assembled onto two facing gold electrodes, has been achieved. Finally, we report initial studies into what effect varying the molecular alligator clip has on the molecule scale wire's conductivity.
Superlubricity of two-dimensional fluorographene/MoS2 heterostructure: a first-principles study.
Wang, Lin-Feng; Ma, Tian-Bao; Hu, Yuan-Zhong; Zheng, Quanshui; Wang, Hui; Luo, Jianbin
2014-09-26
The atomic-scale friction of the fluorographene (FG)/MoS2 heterostructure is investigated using first-principles calculations. Due to the intrinsic lattice mismatch and formation of periodic Moiré patterns, the potential energy surface of the FG/MoS2 heterostructure is ultrasmooth and the interlayer shear strength is reduced by nearly two orders of magnitude, compared with both FG/FG and MoS2/MoS2 bilayers, entering the superlubricity regime. The size dependency of superlubricity is revealed as being based on the relationship between the emergence of Moiré patterns and the lattice mismatch ratio for heterostructures.
Superlubricity of two-dimensional fluorographene/MoS2 heterostructure: a first-principles study
NASA Astrophysics Data System (ADS)
Wang, Lin-Feng; Ma, Tian-Bao; Hu, Yuan-Zhong; Zheng, Quanshui; Wang, Hui; Luo, Jianbin
2014-09-01
The atomic-scale friction of the fluorographene (FG)/MoS2 heterostructure is investigated using first-principles calculations. Due to the intrinsic lattice mismatch and formation of periodic Moiré patterns, the potential energy surface of the FG/MoS2 heterostructure is ultrasmooth and the interlayer shear strength is reduced by nearly two orders of magnitude, compared with both FG/FG and MoS2/MoS2 bilayers, entering the superlubricity regime. The size dependency of superlubricity is revealed as being based on the relationship between the emergence of Moiré patterns and the lattice mismatch ratio for heterostructures.
Interactions between low energy electrons and DNA: a perspective from first-principles simulations
NASA Astrophysics Data System (ADS)
Kohanoff, Jorge; McAllister, Maeve; Tribello, Gareth A.; Gu, Bin
2017-09-01
studying these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.
Interactions between low energy electrons and DNA: a perspective from first-principles simulations.
Kohanoff, Jorge; McAllister, Maeve; Tribello, Gareth A; Gu, Bin
2017-09-27
these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.
First Principles Modeling of Phonon Heat Conduction in Nanoscale Crystalline Structures
Sandip Mazumder; Ju Li
2010-06-30
The inability to remove heat efficiently is currently one of the stumbling blocks toward further miniaturization and advancement of electronic, optoelectronic, and micro-electro-mechanical devices. In order to formulate better heat removal strategies and designs, it is first necessary to understand the fundamental mechanisms of heat transport in semiconductor thin films. Modeling techniques, based on first principles, can play the crucial role of filling gaps in our understanding by revealing information that experiments are incapable of. Heat conduction in crystalline semiconductor films occurs by lattice vibrations that result in the propagation of quanta of energy called phonons. If the mean free path of the traveling phonons is larger than the film thickness, thermodynamic equilibrium ceases to exist, and thus, the Fourier law of heat conduction is invalid. In this scenario, bulk thermal conductivity values, which are experimentally determined by inversion of the Fourier law itself, cannot be used for analysis. The Boltzmann Transport Equation (BTE) is a powerful tool to treat non-equilibrium heat transport in thin films. The BTE describes the evolution of the number density (or energy) distribution for phonons as a result of transport (or drift) and inter-phonon collisions. Drift causes the phonon energy distribution to deviate from equilibrium, while collisions tend to restore equilibrium. Prior to solution of the BTE, it is necessary to compute the lifetimes (or scattering rates) for phonons of all wave-vector and polarization. The lifetime of a phonon is the net result of its collisions with other phonons, which in turn is governed by the conservation of energy and momentum during the underlying collision processes. This research project contributed to the state-of-the-art in two ways: (1) by developing and demonstrating a calibration-free simple methodology to compute intrinsic phonon scattering (Normal and Umklapp processes) time scales with the inclusion
Safeguards First Principles Initiative at the Nevada Test Site
Geneva Johnson
2007-07-08
The Material Control and Accountability (MC&A) program at the Nevada Test Site (NTS) was selected as a test bed for the Safeguards First Principles Initiative (SFPI). The implementation of the SFPI is evaluated using the system effectiveness model and the program is managed under an approved MC&A Plan. The effectiveness model consists of an evaluation of the critical elements necessary to detect, deter, and/or prevent the theft or diversion of Special Nuclear Material (SNM). The modeled results indicate that the MC&A program established under this variance is still effective, without creating unacceptable risk. Extensive performance testing is conducted through the duration of the pilot to ensure the protection system is effective and no material is at an unacceptable risk. The pilot was conducted from January 1, 2007, through May 30, 2007. This paper will discuss the following activities in association with SFPI: 1. Development of Timeline 2. Crosswalk of DOE Order and SFPI 3. Peer Review 4. Deviation 5. MC&A Plan and Procedure changes 6. Changes implemented at NTS 7. Training 8. Performance Test
NMR quadruopole spectra of PZT from first-principles
NASA Astrophysics Data System (ADS)
Mao, Dandan; Walter, Eric J.; Krakauer, Henry
2006-03-01
High performance piezoelectric materials are disordered alloys, so it can be difficult to determine the local atomic geometry. Recently, high field NMR measurements have shown great promise as a microscopic probe of ABO3 perovskite-based alloys by their ability to resolve line-splittings due to nuclear quadrupolar coupling with the electric field gradient (EFG) at the nucleus. We report first-principles LDA calculations of the EFG's in monoclinic and tetragonal Pb(Zr0.5Ti0.5)O3 systems using the linear augmented planewave (LAPW) method, and we compute NMR static powder spectra for ^91Zr, ^47Ti, and ^17O atoms as a function of applied strain. With decreasing c/a ratio PZT converts from tetragonal to monoclinic symmetry. We observe that the calculated NMR spectra show dramatic deviations with decreasing c/a from that in tetragonal P4mm well before the electric polarization begins to rotate away from the [001] direction. This indicates that NMR measurements can be a very accurate probe of local structural changes in perovskite piezoelectrics. G. L. Hoatson, D. H. Zhou, F. Fayon, D. Massiot, and R. L. Vold, Phys. Rev. B, 66, 224103 (2002).
First principles study of O defects in CdSe
NASA Astrophysics Data System (ADS)
T-Thienprasert, J.; Limpijumnong, S.; Du, M.-H.; Singh, D. J.
2012-08-01
Recently, the vibrational signatures related to oxygen defects in oxygen-doped CdSe were measured using ultrahigh resolution Fourier transform infrared (FTIR) spectroscopy by Chen et al.(2008) [1]. They observed two absorption bands centered at ∼1991.77 and 2001.3 cm-1, which they attributed to the LVMs of OCd, in the samples grown with the addition of CdO and excess Se. For the samples claimed to be grown with even more excess Se, three high-frequency modes (1094.11, 1107.45, and 1126.33) were observed and assigned to the LVMs of OSe-VCd complex. In this work, we explicitly calculated the vibrational signatures of OCd and OSe-VCd complex defects based on first principles approach. The calculated vibrational frequencies of OCd and OSe-VCd complex are inconsistent with the frequencies observed by Chen et al., indicating that their observed frequencies are from other defects. Potential defects that could explain the experimentally observed modes are suggested.
Simulation of infrared avalanche photodiodes from first principles
NASA Astrophysics Data System (ADS)
Storebø, Asta Katrine; Goldar, Dara; Brudevoll, Trond
2017-02-01
The present article deals with device physics and modeling of an Hg0.28Cd0.72Te wide-area electron-initiated avalanche photodiode, with main input data extracted from first principles electronic structure codes. Due to the large dimensions of 30 μm x 30 μm x 11 μm a method which combines Monte Carlo transport simulation in the active multiplication layer with `weak conduction' modeling in the charge carrier exit paths is introduced. Consequences resulting from adding perturbative, non-self-consistent small-signal analyses upon a self-consistent, large-signal background bias simulation are briefly examined. Likewise, the issue of ambipolar versus independent electron-hole transport in the absorption layer is discussed. We investigate the effects of alloy scattering on avalanche gain and compare alloy scattering rates used in some recent studies. Alloy scattering is for this particular device and model shown to increase the gain by more than an order of magnitude at typical bias voltages.
Predicted boron-carbide compounds: A first-principles study
Wang, De Yu; Yan, Qian; Wang, Bing; Wang, Yuan Xu Yang, Jueming; Yang, Gui
2014-06-14
By using developed particle swarm optimization algorithm on crystal structural prediction, we have explored the possible crystal structures of B-C system. Their structures, stability, elastic properties, electronic structure, and chemical bonding have been investigated by first-principles calculations with density functional theory. The results show that all the predicted structures are mechanically and dynamically stable. An analysis of calculated enthalpy with pressure indicates that increasing of boron content will increase the stability of boron carbides under low pressure. Moreover, the boron carbides with rich carbon content become more stable under high pressure. The negative formation energy of predicted B{sub 5}C indicates its high stability. The density of states of B{sub 5}C show that it is p-type semiconducting. The calculated theoretical Vickers hardnesses of B-C exceed 40 GPa except B{sub 4}C, BC, and BC{sub 4}, indicating they are potential superhard materials. An analysis of Debye temperature and electronic localization function provides further understanding chemical and physical properties of boron carbide.
First-principles investigation of antiphase boundaries in perovskites
NASA Astrophysics Data System (ADS)
Naumov, Ivan; Rabe, Karin
2002-03-01
The lowering of the dielectric constant of Ba_xSr_1-xTiO3 (BST) films compared to bulk can be attributed, at least in part, to the effects of defects associated with film growth. In BST films grown on MgO substrates, such defects include antiphase boundaries (APBs), which have been clearly observed using electron microscopy. In this work, using a first-principles pseudopotential approach based on variational density functional pertubation theory, we have investigated the structure, lattice dynamics and dielectric properties of two relevant APBs in SrTiO3 (Sr-rich and Ti-rich) using ordered supercells. Comparison with bulk SrTiO3 shows that the Born effective charges and electronic dielectric tensor decrease and the characteristic low-frequency polar mode increases in frequency, leading to a significant lowering of the lattice contribution to the dielectric response. We suggest that this change can be understood as the result of the disruption of the Ti-O chains normal to the APB, and thus that this mechanism is also relevant to the solid solution. This work is supported by U. Maryland/Rutgers NSF-MRSEC DMR-00-80008.
Adsorption of 3-pyrroline on Si(100) from first principles.
Romero, Aldo H; Sbraccia, Carlo; Silvestrelli, Pier Luigi
2004-05-22
The chemisorption of 3-pyrroline (C(4)H(7)N) on Si(100) is studied from first principles. Three different structures can be realized for which, depending on the temperature, the chemisorption process is facile (for two of them it is essentially barrierless); among these configurations the most favored one, from a thermodynamical point of view, is a dissociated structure obtained through an exothermic reaction characterized by the formation of a N-Si bond and a H-Si bond in which the H atom is detached from the molecule. Several other chemisorption structures are possible which, however, require overcoming a significant energy barrier and often breaking multiple bonds. A number of reaction paths going from one stable structure to another have been investigated. We have also generated, for the two basic adsorption structures, theoretical scanning tunneling microscopy images which could facilitate the interpretation of experimental measurements, and we propose a possible reaction mechanism for nitrogen incorporation. (c) 2004 American Institute of Physics.
First-principles prediction of disordering tendencies in pyrochlore oxides
Jiang Chao; Stanek, C. R.; Sickafus, K. E.; Uberuaga, B. P.
2009-03-01
Using first-principles calculations, we systematically predict the order-disorder energetics of series of zirconate (A{sub 2}Zr{sub 2}O{sub 7}), hafnate (A{sub 2}Hf{sub 2}O{sub 7}), titanate (A{sub 2}Ti{sub 2}O{sub 7}), and stannate (A{sub 2}Sn{sub 2}O{sub 7}) pyrochlores. The disordered defect-fluorite structure is modeled using an 88-atom two-sublattice special quasirandom structure (SQS) that closely reproduces the most relevant near-neighbor intrasublattice and intersublattice pair-correlation functions of the random mixture. The order-disorder transition temperatures of these pyrochlores estimated from our SQS calculations show overall good agreement with existing experiments. We confirm previous studies suggesting that the bonding in pyrochlores is not purely ionic and thus electronic effects also play a role in determining their disordering tendencies. Our results have important consequences for numerous applications, including nuclear waste forms and fast ion conductors.
First-principles Simulations and the Criticality of Calving Glaciers
NASA Astrophysics Data System (ADS)
Vallot, D.; Åström, J. A.; Schäfer, M.; Welty, E.; O'Neel, S.; Bartholomaus, T. C.; Liu, Y.; Riikilä, T.; Zwinger, T.; Timonen, J.; Moore, J.
2014-12-01
The algoritm of a first principles calving-simulation computer-code is outlined and demonstrated. The code is particle-based and uses Newtonian dynamics to simulate ice-fracture, motion and calving. The code can simulate real-size glacier but is only able to simualte individual calving events within a few tens of minutes in duration. The code couples to the Elmer/Ice ice flow-simulation code: Elmer is employed to produce various glacier geomteries, which are then tested for stability using the particle code. In this way it is possible to pin-point the location of calving fronts. The particle simulation code and field observations are engaged to investigate the criticality of calving glaciers. The calving mass and inter-event waiting times both have power-law distributions with the same critical exponents as found for Abelian sand-pile models. This indicate that calving glaciers share characteristics with Self-Organized Critical systems (SOC). This would explain why many glacier found in nature may become unstable as a result of even minor changes in their environment. An SOC calving glacier at the critical point will display so large fluctuations in calving rate that it will render the concept 'average calving rate' more or less useless. I.e. 'average calving rate' will depend on measurement time and always have fluctuaions in the range of 100% more or less independent of the averaging time.
Gypsum under pressure: A first-principles study
NASA Astrophysics Data System (ADS)
Giacomazzi, Luigi; Scandolo, Sandro
2010-02-01
We investigate by means of first-principles methods the structural response of gypsum (CaSO4ṡ2H2O) to pressures within and above the stability range of gypsum-I (P≤4GPa) . Structural and vibrational properties calculated for gypsum-I are in excellent agreement with experimental data. Compression within gypsum-I takes place predominantly through a reduction in the volume of the CaO8 polyhedra and through a distortion of the hydrogen bonds. The distance between CaSO4 layers becomes increasingly incompressible, indicating a mechanical limit to the packing of water molecules between the layers. We find that a structure with collapsed interlayer distances becomes more stable than gypsum-I above about 5 GPa. The collapse is concomitant with a rearrangement of the hydrogen-bond network of the water molecules. Comparison of the vibrational spectra calculated for this structure with experimental data taken above 5 GPa supports the validity of our model for the high-pressure phase of gypsum.
First-principles prediction of disordering tendencies in complex oxides
Jiang, Chao; Stanek, Christopher R; Sickafus, Kurt E; Uberuaga, Blas P
2008-01-01
The disordering tendencies of a series of zirconate (A{sub 2}Zr{sub 2}O{sub 7}) , hafnate (A{sub 2}Hf{sub 2}O{sub 7}), titanate (A{sub 2}Ti{sub 2}O{sub 7}), and stannate (A{sub 2} Sn{sub 2}O{sub 7}) pyrochlores are predicted in this study using first-principles total energy calculations. To model the disordered (A{sub 1/2}B{sub 1/2})(O{sub 7/8}/V{sub 1/8}){sub 2} fluorite structure, we have developed an 88-atom two-sublattice special quasirandom structure (SQS) that closely reproduces the most important near-neighbor intra-sublattice and inter-sublattice pair correlation functions of the random alloy. From the calculated disordering energies, the order-disorder transition temperatures of those pyrochlores are further predicted and our results agree well with the existing experimental phase diagrams. It is clearly demonstrated that both size and electronic effects play an important role in determining the disordering tendencies of pyrochlore compounds.
First-principles simulation on Seebeck coefficient in silicon nanowires
NASA Astrophysics Data System (ADS)
Nakamura, Koichi
2017-06-01
The Seebeck coefficients of silicon nanowires (SiNWs) were simulated on the basis of first-principles calculation using various atomistic structure models. The electronic band structures of fully hydrogen-terminated SiNW models give the correct image of quantum mechanical confinement from bulk silicon to SiNW for each axial direction, and the change in the density of states by dimensional reduction to SiNW enhances the thermoelectric performance in terms of the Seebeck coefficient, compared with those of bulk silicon and silicon nanosheets. The uniaxial tensile strain for the SiNW models does not strongly affect the Seebeck coefficient even for the SiNW system with giant piezoresistivity. In contrast, dangling bonds on a wire wall sharply reduce the Seebeck coefficient of SiNW and totally degrade thermoelectric performance from the viewpoint of the power factor. The exclusion of dangling bonds is a key element for the design and application of high-performance thermoelectric nanowires of semiconducting materials.
First principles investigation of the vibrational properties of hydrous wadsleyite
NASA Astrophysics Data System (ADS)
Tsuchiya, Jun
2017-04-01
Wadsleyite is the primary constituent mineral in the upper part of the Earth's transition zone and this phase can be a significant water reservoir in the Earth. There have been large numbers of reports about the structure, stability, and physical properties of hydrous wadsleyite. The vibrational measurements such as FTIR and Raman are the most commonly used for investigating the OH defects in wadsleyite. There are major and minor doublets of OH stretching bands in hydrous wadsleyite, the former exist around 3300 cm-1 with dν/dP˜-10 cm-1 and the latter around 3600 cm-1 with almost no pressure dependence. There is a broad consensus that main absorption band is interpreted as the OH stretching modes existing in the M3 vacancy. On the other hand, the minor OH band is not well constrained so far. Since the stable hydrogen defects are usually less mobile in wadsleyite crystal, the determination of minor and metastable hydrogen defects are more important for investigating the transport properties including the electrical conductivity and the deformation properties. Here I investigated the structural and vibrational properties of hydrous wadsleyite using first principles techniques in order to clarify the minor metastable hydrogen positions under high-pressure.
Mechanical responses of borophene sheets: a first-principles study.
Mortazavi, Bohayra; Rahaman, Obaidur; Dianat, Arezoo; Rabczuk, Timon
2016-10-05
Recent experimental advances for the fabrication of various borophene sheets introduced new structures with a wide range of applications. Borophene is the boron atom analogue of graphene. Borophene exhibits various structural polymorphs all of which are metallic. In this work, we employed first-principles density functional theory calculations to investigate the mechanical properties of five different single-layer borophene sheets. In particular, we analyzed the effect of the loading direction and point vacancy on the mechanical response of borophene. Moreover, we compared the thermal stabilities of the considered borophene systems. Based on the results of our modelling, borophene films depending on the atomic configurations and the loading direction can yield a remarkable elastic modulus in the range of 163-382 GPa nm and a high ultimate tensile strength from 13.5 GPa nm to around 22.8 GPa nm at the corresponding strain from 0.1 to 0.21. Our study reveals the remarkable mechanical characteristics of borophene films.
First-principles reinvestigation of bulk WO3
NASA Astrophysics Data System (ADS)
Hamdi, Hanen; Salje, Ekhard K. H.; Ghosez, Philippe; Bousquet, Eric
2016-12-01
Using first-principles calculations, we analyze the structural properties of tungsten trioxide WO3. Our calculations rely on density functional theory and the use of the B1-WC hybrid functional, which provides very good agreement with experimental data. We show that the hypothetical high-symmetry cubic reference structure combines several ferroelectric and antiferrodistortive (antipolar cation motions, rotations, and tilts of oxygen octahedra) structural instabilities. Although the ferroelectric instability is the largest, the instability related to antipolar W motions combines with those associated to oxygen rotations and tilts to produce the biggest energy reduction, yielding a P 21/c ground state. This nonpolar P 21/c phase is only different from the experimentally reported P c ground state by the absence of a very tiny additional ferroelectric distortion. The calculations performed on a stoichiometric compound so suggest that the low-temperature phase of WO3 is not intrinsically ferroelectric and that the experimentally observed ferroelectric character might arise from extrinsic defects such as oxygen vacancies. Independently, we also identify never observed R 3 m and R 3 c ferroelectric metastable phases with large polarizations and low energies close to the P 21/c ground state, which makes WO3 a potential antiferroelectric material. The relative stability of various phases is discussed in terms of the anharmonic couplings between different structural distortions, highlighting a very complex interplay.
First Principles Thermoelasticity of Tantalum at High Pressures
Orlikowski, D.A.; Soderlind, P.; Moriarty, J.
2002-06-21
The thermoelastic properties of bcc tantalum have been investigated over a broad range of temperatures (up to 12000 K) and pressures (up to 10 Mbar) using first-principles methods that account for cold, electron-thermal, and ion-thermal contributions. Specifically, we have combined ab initio all electron electronic-structure calculations for the cold and electron-thermal contributions to the elastic moduli with phonon contributions for the ion-thermal part calculated using model generalized pseudopotential theory (MGPT). For the latter, a summation of terms over the Brillouin zone is performed within the quasi-harmonic approximation, where each term is composed of a strain derivative of the phonon frequency at a particular k-point. At ambient pressure, the resulting temperature dependence of the elastic moduli is in excellent agreement with ultrasonic measurements. The experimentally observed anomalous behavior of C44 at low temperatures is shown to originate from the electron-thermal contribution. At higher temperatures, the dominant contribution to the temperature dependence of the elastic moduli comes from thermal expansion. Also, the pressure dependence of the moduli compares well with recent diamond and cell measurements up to 105 GPa. The calculated longitudinal and bulk sound velocities at higher pressure and temperature agree well with data obtained from shock experiments. Additionally, the temperature dependence of the Steinberg-Guinan model is examined for ambient pressure.
Thermal conductivity of silicene from first-principles
Xie, Han; Bao, Hua E-mail: hua.bao@sjtu.edu.cn; Hu, Ming E-mail: hua.bao@sjtu.edu.cn
2014-03-31
Silicene, as a graphene-like two-dimensional material, now receives exceptional attention of a wide community of scientists and engineers beyond graphene. Despite extensive study on its electric property, little research has been done to accurately calculate the phonon transport of silicene so far. In this paper, thermal conductivity of monolayer silicene is predicted from first-principles method. At 300 K, the thermal conductivity of monolayer silicene is found to be 9.4 W/mK and much smaller than bulk silicon. The contributions from in-plane and out-of-plane vibrations to thermal conductivity are quantified, and the out-of-plane vibration contributes less than 10% of the overall thermal conductivity, which is different from the results of the similar studies on graphene. The difference is explained by the presence of small buckling, which breaks the reflectional symmetry of the structure. The flexural modes are thus not purely out-of-plane vibration and have strong scattering with other modes.
First-principles study on surface stability of tantalum carbides
NASA Astrophysics Data System (ADS)
Yan, Wen-Li; Sygnatowicz, Michael; Lu, Guang-Hong; Liu, Feng; Shetty, Dinesh K.
2016-02-01
Using first-principles method, surface energies of crystal planes of different tantalum carbide phases have been calculated. Quantum size effects are shown to possibly play a considerable role in determining accurate surface energies of these metallic films, which have been neglected in previous works. The γ-TaC phase has a more stable (0 0 1) surface than the close-packed (1 1 1) surface. In the α-Ta2C phase, (0 0 1) surface with only Ta termination is more stable than that of mixed Ta-C termination because the metallic bonds between Ta atoms are weaker than the Ta-C covalent bonds. The same is true for the ζ-Ta4C3 phase. The introduction of structural vacancies in the ζ-Ta4C3 -x phase creates more direct Ta metallic bonds, making the Ta-terminated surfaces even more stable. This is consistent with the experimental observations of cleavage of the basal planes, lamellae bridging of cracks, and the high fracture toughness of ζ-Ta4C3 -x.
Electrostatic engineering of strained ferroelectric perovskites from first principles
NASA Astrophysics Data System (ADS)
Cazorla, Claudio; Stengel, Massimiliano
2015-12-01
Design of novel artificial materials based on ferroelectric perovskites relies on the basic principles of electrostatic coupling and in-plane lattice matching. These rules state that the out-of-plane component of the electric displacement field and the in-plane components of the strain are preserved across a layered superlattice, provided that certain growth conditions are respected. Intense research is currently directed at optimizing materials functionalities based on these guidelines, often with remarkable success. Such principles, however, are of limited practical use unless one disposes of reliable data on how a given material behaves under arbitrary electrical and mechanical boundary conditions. Here we demonstrate, by focusing on the prototypical ferroelectrics PbTiO3 and BiFeO3 as test cases, how such information can be calculated from first principles in a systematic and efficient way. In particular, we construct a series of two-dimensional maps that describe the behavior of either compound (e.g., concerning the ferroelectric polarization and antiferrodistortive instabilities) at any conceivable choice of the in-plane lattice parameter, a , and out-of-plane electric displacement, D . In addition to being of immediate practical applicability to superlattice design, our results bring new insight into the complex interplay of competing degrees of freedom in perovskite materials and reveal some notable instances where the behavior of these materials depart from what naively is expected.
Electron-hole excitations and optical spectra from first principles
Rohlfing, Michael; Louie, Steven G.
2000-08-15
We present a recently developed approach to calculate electron-hole excitations and the optical spectra of condensed matter from first principles. The key concept is to describe the excitations of the electronic system by the corresponding one- and two-particle Green's function. The method combines three computational techniques. First, the electronic ground state is treated within density-functional theory. Second, the single-particle spectrum of the electrons and holes is obtained within the GW approximation to the electron self-energy operator. Finally, the electron-hole interaction is calculated and a Bethe-Salpeter equation is solved, yielding the coupled electron-hole excitations. The resulting solutions allow the calculation of the entire optical spectrum. This holds both for bound excitonic states below the band gap, as well as for the resonant spectrum above the band gap. We discuss a number of technical developments needed for the application of the method to real systems. To illustrate the approach, we discuss the excitations and optical spectra of spatially isolated systems (atoms, molecules, and semiconductor clusters) and of extended, periodic crystals (semiconductors and insulators). (c) 2000 The American Physical Society.
Lattice thermal conductivity of borophene from first principle calculation
Xiao, Huaping; Cao, Wei; Ouyang, Tao; Guo, Sumei; He, Chaoyu; Zhong, Jianxin
2017-01-01
The phonon transport property is a foundation of understanding a material and predicting the potential application in mirco/nano devices. In this paper, the thermal transport property of borophene is investigated by combining first-principle calculations and phonon Boltzmann transport equation. At room temperature, the lattice thermal conductivity of borophene is found to be about 14.34 W/mK (error is about 3%), which is much smaller than that of graphene (about 3500 W/mK). The contributions from different phonon modes are qualified, and some phonon modes with high frequency abnormally play critical role on the thermal transport of borophene. This is quite different from the traditional understanding that thermal transport is usually largely contributed by the low frequency acoustic phonon modes for most of suspended 2D materials. Detailed analysis further reveals that the scattering between the out-of-plane flexural acoustic mode (FA) and other modes likes FA + FA/TA/LA/OP ↔ TA/LA/OP is the predominant phonon process channel. Finally the vibrational characteristic of some typical phonon modes and mean free path distribution of different phonon modes are also presented in this work. Our results shed light on the fundamental phonon transport properties of borophene, and foreshow the potential application for thermal management community. PMID:28374853
Thermalisation of a quantum system from first principles
NASA Astrophysics Data System (ADS)
Ithier, Gregoire; Benaych-Georges, Florent
2015-03-01
How does a quantum system reach thermodynamical equilibrium? Answering such a question from first principles is, perhaps surprisingly, still an open issue (Popescu Nat. Phys. 2006, Goldstein PRL 2006, Genway PRL 2013). We present here a new model comprising an arbitrary quantum system interacting with a large arbitrary quantum environment, both initially prepared in a quantum pure state. We then demonstrate that thermalisation is an emergent property of the unitary evolution under a Schrödinger equation of this large composite system. The key conceptual tool of our method is the phenomenon of ``measure concentration'' appearing with functions defined on large dimension Hilbert spaces, a phenomenon which cancels out any effect of the microscopic structure of interaction Hamiltonians. Using our model, we first characterize the transient evolution or decoherence of the system and show its universal character. We then focus on the stationary regime and recover the canonical state well known from statistical thermodynamics. This finding leads us to propose an alternative and more general definition of the canonical partition function, that includes, among other things, the possibility of describing partial thermalisation.
Stress dependent defect energetics in Tungsten from first-principles
NASA Astrophysics Data System (ADS)
Hossain, Md.; Marian, Jaime
2013-03-01
Tungsten (W) is an important material for high temperature applications due to its refractory nature. However, like all transition metals from the VI-A group, W suffers from low-temperature brittleness and lack of ductility, which poses serious questions for its use as a structural material. Tungsten's mechanical properties can be enhanced by alloying with elements with d-electrons, such as Re, which has resulted in successful commercial alloys. In this work, we obtain the formation and migration energetics of Re solute atoms in terms of their interaction with vacancies and dislocations. To explore the influence of external stresses on Re transport properties, we examine the role of hydrostatic and shear deformation on the vacancy formation energy (VFE) and migration energy barrier (Em) in BCC W from first-principles calculations by developing a pseudopotential with 6s2, 6p0, 5d4, and 5f0 electronic states for the valence electrons. We find that under hydrostatic deformation, increase or decrease of vacancy formation energy depends on the type of deformation - tensile or compressive, while for shear deformation it decreases irrespective of the magnitude of applied deformation. On the other hand, migration energy barrier always decreases under hydrostatic deformation, but shows path-length dependent behavior under shear deformation. This talk will discuss the underlying principles and possible routes for enhancing mechanical strength from a physics perspective.
Four superhard carbon allotropes: a first-principles study.
He, Chaoyu; Sun, Lizhong; Zhang, Chunxiao; Peng, Xiangyang; Zhang, Kaiwang; Zhong, Jianxin
2012-06-21
Using a generalized genetic algorithm, we propose four new sp(3) carbon allotropes with 5-6-7 (5-6-7-type Z-ACA and Z-CACB) or 4-6-8 (4-6-8-type Z4-A(3)B(1) and A4-A(2)B(2)) carbon rings. Their stability, mechanical and electronic properties are systematically studied using a first-principles method. We find that the four new carbon allotropes show amazing stability in comparison with the carbon phases proposed recently. Both 5-6-7-type Z-ACA and Z-CACB are direct band-gap semiconductors with band gaps of 2.261 eV and 4.196 eV, respectively. However, the 4-6-8-type Z4-A(3)B(1) and A4-A(2)B(2) are indirect band-gap semiconductors with band gaps of 3.105 eV and 3.271 eV, respectively. Their mechanical properties reveal that all the four carbon allotropes proposed in present work are superhard materials, which are comparable to diamond.
Predicted boron-carbide compounds: a first-principles study.
Wang, De Yu; Yan, Qian; Wang, Bing; Wang, Yuan Xu; Yang, Jueming; Yang, Gui
2014-06-14
By using developed particle swarm optimization algorithm on crystal structural prediction, we have explored the possible crystal structures of B-C system. Their structures, stability, elastic properties, electronic structure, and chemical bonding have been investigated by first-principles calculations with density functional theory. The results show that all the predicted structures are mechanically and dynamically stable. An analysis of calculated enthalpy with pressure indicates that increasing of boron content will increase the stability of boron carbides under low pressure. Moreover, the boron carbides with rich carbon content become more stable under high pressure. The negative formation energy of predicted B5C indicates its high stability. The density of states of B5C show that it is p-type semiconducting. The calculated theoretical Vickers hardnesses of B-C exceed 40 GPa except B4C, BC, and BC4, indicating they are potential superhard materials. An analysis of Debye temperature and electronic localization function provides further understanding chemical and physical properties of boron carbide.
Realtime capable first principle based modelling of tokamak turbulent transport
NASA Astrophysics Data System (ADS)
Citrin, Jonathan; Breton, Sarah; Felici, Federico; Imbeaux, Frederic; Redondo, Juan; Aniel, Thierry; Artaud, Jean-Francois; Baiocchi, Benedetta; Bourdelle, Clarisse; Camenen, Yann; Garcia, Jeronimo
2015-11-01
Transport in the tokamak core is dominated by turbulence driven by plasma microinstabilities. When calculating turbulent fluxes, maintaining both a first-principle-based model and computational tractability is a strong constraint. We present a pathway to circumvent this constraint by emulating quasilinear gyrokinetic transport code output through a nonlinear regression using multilayer perceptron neural networks. This recovers the original code output, while accelerating the computing time by five orders of magnitude, allowing realtime applications. A proof-of-principle is presented based on the QuaLiKiz quasilinear transport model, using a training set of five input dimensions, relevant for ITG turbulence. The model is implemented in the RAPTOR real-time capable tokamak simulator, and simulates a 300s ITER discharge in 10s. Progress in generalizing the emulation to include 12 input dimensions is presented. This opens up new possibilities for interpretation of present-day experiments, scenario preparation and open-loop optimization, realtime controller design, realtime discharge supervision, and closed-loop trajectory optimization.
Auger recombination in scintillator materials from first principles
NASA Astrophysics Data System (ADS)
McAllister, Andrew; Kioupakis, Emmanouil; Åberg, Daniel; Schleife, André
2015-03-01
Scintillators convert high energy radiation into lower energy photons which are easier to detect and analyze. One of the uses of these devices is identifying radioactive materials being transported across national borders. However, scintillating materials have a non-proportional light yield in response to incident radiation, which makes this task difficult. One possible cause of the non-proportional light yield is non-radiative Auger recombination. Auger recombination can occur in two ways - direct and phonon-assisted. We have studied both types of Auger recombination from first principles in the common scintillating material sodium iodide. Our results indicate that the phonon-assisted process, assisted primarily by short-range optical phonons, dominates the direct process. The corresponding Auger coefficients are 5 . 6 +/- 0 . 3 ×10-32cm6s-1 for the phonon-assisted process versus 1 . 17 +/- 0 . 01 ×10-33cm6s-1 for the direct process. At higher electronic temperatures the direct Auger recombination rate increases but remains lower than the phonon-assisted rate. This research was supported by the National Science Foundation CAREER award through Grant No. DMR-1254314 and NA-22. Computational Resources provide by LLNL and DOE NERSC Facility.
"Postural first" principle when balance is challenged in elderly people.
Lion, Alexis; Spada, Rosario S; Bosser, Gilles; Gauchard, Gérome C; Anello, Guido; Bosco, Paolo; Calabrese, Santa; Iero, Antonella; Stella, Giuseppe; Elia, Maurizio; Perrin, Philippe P
2014-08-01
Human cognitive processing limits can lead to difficulties in performing two tasks simultaneously. This study aimed to evaluate the effect of cognitive load on both simple and complex postural tasks. Postural control was evaluated in 128 noninstitutionalized elderly people (mean age = 73.6 ± 5.6 years) using a force platform on a firm support in control condition (CC) and mental counting condition (MCC) with eyes open (EO) and eyes closed (EC). Then, the same tests were performed on a foam support. Sway path traveled and area covered by the center of foot pressure were recorded, low values indicating efficient balance. On firm support, sway path was higher in MCC than in CC both in EO and EC conditions (p < 0.001). On foam support, sway path was higher in CC than in MCC in EC condition (p < 0.001), area being higher in CC than in MCC both in EO (p < 0.05) and EC (p < 0.001) conditions. The results indicate that cognitive load alters balance control in a simple postural task (i.e. on firm support), which is highlighted by an increase of energetic expenditure (i.e. increase of the sway path covered) to balance. Awareness may not be increased and the attentional demand may be shared between balance and mental task. Conversely, cognitive load does not perturb the realization of a new complex postural task. This result showed that postural control is prioritized ("postural first" principle) when seriously challenged.
First principle active neutron coincidence counting measurements of uranium oxide
NASA Astrophysics Data System (ADS)
Goddard, Braden; Charlton, William; Peerani, Paolo
2014-03-01
Uranium is present in most nuclear fuel cycle facilities ranging from uranium mines, enrichment plants, fuel fabrication facilities, nuclear reactors, and reprocessing plants. The isotopic, chemical, and geometric composition of uranium can vary significantly between these facilities, depending on the application and type of facility. Examples of this variation are: enrichments varying from depleted (~0.2 wt% 235U) to high enriched (>20 wt% 235U); compositions consisting of U3O8, UO2, UF6, metallic, and ceramic forms; geometries ranging from plates, cans, and rods; and masses which can range from a 500 kg fuel assembly down to a few grams fuel pellet. Since 235U is a fissile material, it is routinely safeguarded in these facilities. Current techniques for quantifying the 235U mass in a sample include neutron coincidence counting. One of the main disadvantages of this technique is that it requires a known standard of representative geometry and composition for calibration, which opens up a pathway for potential erroneous declarations by the State and reduces the effectiveness of safeguards. In order to address this weakness, the authors have developed a neutron coincidence counting technique which uses the first principle point-model developed by Boehnel instead of the "known standard" method. This technique was primarily tested through simulations of 1000 g U3O8 samples using the Monte Carlo N-Particle eXtended (MCNPX) code. The results of these simulations showed good agreement between the simulated and exact 235U sample masses.
First-principles investigation of Ag-doped gold nanoclusters.
Zhang, Xiao-Dong; Guo, Mei-Li; Wu, Di; Liu, Pei-Xun; Sun, Yuan-Ming; Zhang, Liang-An; She, Yi; Liu, Qing-Fen; Fan, Fei-Yue
2011-01-01
Gold nanoclusters have the tunable optical absorption property, and are promising for cancer cell imaging, photothermal therapy and radiotherapy. First-principle is a very powerful tool for design of novel materials. In the present work, structural properties, band gap engineering and tunable optical properties of Ag-doped gold clusters have been calculated using density functional theory. The electronic structure of a stable Au(20) cluster can be modulated by incorporating Ag, and the HOMO-LUMO gap of Au(20-) (n)Ag(n) clusters is modulated due to the incorporation of Ag electronic states in the HOMO and LUMO. Furthermore, the results of the imaginary part of the dielectric function indicate that the optical transition of gold clusters is concentration-dependent and the optical transition between HOMO and LUMO shifts to the low energy range as the Ag atom increases. These calculated results are helpful for the design of gold cluster-based biomaterials, and will be of interest in the fields of radiation medicine, biophysics and nanoscience.
First Principles Structure Calculations Using the General Potential Lapw Method
NASA Astrophysics Data System (ADS)
Wei, Su-Huai
We have developed a completely general first principles self-consistent full-potential linearized-augmented-plane -wave (LAPW) method program within the density functional formalism to calculate electronic band structure, total energy, pressure and other quantities. No symmetry assumptions are used for the crystal structure. Shape unrestricted charge densities and potentials are calculated inside muffin -tin (MT) spheres as well as in the interstitial regions. All contributions to the Hamiltonian matrix elements are completely taken into account. The core states are treated fully relativistically using the spherical part of the potential only. Scalar relativistic effects are included for the band-states, and spin-orbit coupling is included using a second variation procedure. Both core states and valence states are treated self-consistently, the frozen core approximation is not required. The fast Fourier transformation method is used wherever it is applicable, and this greatly improves the efficiency. This state-of-the-art program has been tested extensively to check the accuracy and convergence properties by comparing calculated electronic band structures, ground state properties, equations of state and cohesive energies for bulk W and GaAs with other theoretical calculations and experimental results. It has been successfully applied to calculate and predict structural and metal-insulator phase transitions for close-packed crystal BaSe and BaTe and the geometric structure of the d-band metal W(001) surface. The results are in generally good agreement with experiment.
First principles statistical mechanics of alloys and magnetism
NASA Astrophysics Data System (ADS)
Eisenbach, Markus; Khan, Suffian N.; Li, Ying Wai
Modern high performance computing resources are enabling the exploration of the statistical physics of phase spaces with increasing size and higher fidelity of the Hamiltonian of the systems. For selected systems, this now allows the combination of Density Functional based first principles calculations with classical Monte Carlo methods for parameter free, predictive thermodynamics of materials. We combine our locally selfconsistent real space multiple scattering method for solving the Kohn-Sham equation with Wang-Landau Monte-Carlo calculations (WL-LSMS). In the past we have applied this method to the calculation of Curie temperatures in magnetic materials. Here we will present direct calculations of the chemical order - disorder transitions in alloys. We present our calculated transition temperature for the chemical ordering in CuZn and the temperature dependence of the short-range order parameter and specific heat. Finally we will present the extension of the WL-LSMS method to magnetic alloys, thus allowing the investigation of the interplay of magnetism, structure and chemical order in ferrous alloys. This research was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Science and Engineering Division and it used Oak Ridge Leadership Computing Facility resources at Oak Ridge National Laboratory.
First-principles study of tantalum-arsenic binary compounds
NASA Astrophysics Data System (ADS)
Sun, Jifeng; Singh, David J.
2017-01-01
The electronic properties and phase stability of binary tantalum arsenides are investigated using first-principles calculations. We find strong covalent bonding between Ta and As in TaAs2. In the lower As content compounds, the Ta is less covalent and donates charge to the As backbone. The covalency of other compounds becomes smaller with the increase of Ta composition. Compounds on the convex hull are TaAs2, TaAs, Ta5As4, and Ta3As, while Ta2As is slightly above the hull. Trends in the electronic and other properties are discussed. We identify the space group of TaAs2 to be centrosymmetric C2/m and find semimetallic behavior in TaAs and TaAs2. The other binary compounds are metallic systems with finite density of states at the Fermi level. The plasma energies show moderate conductivity anisotropy in Ta5As4 and Ta2As, which are also the most conductive compounds among the binary phases.
First principles based mean field model for oxygen reduction reaction.
Jinnouchi, Ryosuke; Kodama, Kensaku; Hatanaka, Tatsuya; Morimoto, Yu
2011-12-21
A first principles-based mean field model was developed for the oxygen reduction reaction (ORR) taking account of the coverage- and material-dependent reversible potentials of the elementary steps. This model was applied to the simulation of single crystal surfaces of Pt, Pt alloy and Pt core-shell catalysts under Ar and O(2) atmospheres. The results are consistent with those shown by past experimental and theoretical studies on surface coverages under Ar atmosphere, the shape of the current-voltage curve for the ORR on Pt(111) and the material-dependence of the ORR activity. This model suggests that the oxygen associative pathway including HO(2)(ads) formation is the main pathway on Pt(111), and that the rate determining step (RDS) is the removal step of O(ads) on Pt(111). This RDS is accelerated on several highly active Pt alloys and core-shell surfaces, and this acceleration decreases the reaction intermediate O(ads). The increase in the partial pressure of O(2)(g) increases the surface coverage with O(ads) and OH(ads), and this coverage increase reduces the apparent reaction order with respect to the partial pressure to less than unity. This model shows details on how the reaction pathway, RDS, surface coverages, Tafel slope, reaction order and material-dependent activity are interrelated.
First principles calculation of the activity of cytochrome P450
NASA Astrophysics Data System (ADS)
Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.; Boyes, R. N.
1998-04-01
The cytochrome P450 superfamily of enzymes is of enormous interest in the biological sciences due to the wide range of endogenous and xenobiotic compounds which it metabolises, including many drugs. We describe the use of first principles quantum mechanical modeling techniques, based on density functional theory, to determine the outcome of interactions between an enzyme and a number of compounds. Specifically, we calculate the spin state of an Fe3+ ion present in a haem moiety at the active site of these enzymes. The spin state of this ion indicates if the catalytic reaction will proceed. The computational results obtained compare favorably with experimental data. Only the principle components of the active site of the enzyme are included in the computational models, demonstrating that only a small fragment of the protein needs to be included in the models in order to accurately reproduce this aspect of the enzymes' function. These results open the way for further investigation of this superfamily of enzymes using the methods detailed in this paper.
First-Principle Characterization for Singlet Fission Couplings.
Yang, Chou-Hsun; Hsu, Chao-Ping
2015-05-21
The electronic coupling for singlet fission, an important parameter for determining the rate, has been found to be too small unless charge-transfer (CT) components were introduced in the diabatic states, mostly through perturbation or a model Hamiltonian. In the present work, the fragment spin difference (FSD) scheme was generalized to calculate the singlet fission coupling. The largest coupling strength obtained was 14.8 meV for two pentacenes in a crystal structure, or 33.7 meV for a transition-state structure, which yielded a singlet fission lifetime of 239 or 37 fs, generally consistent with experimental results (80 fs). Test results with other polyacene molecules are similar. We found that the charge on one fragment in the S1 diabatic state correlates well with FSD coupling, indicating the importance of the CT component. The FSD approach is a useful first-principle method for singlet fission coupling, without the need to include the CT component explicitly.
Lattice thermal conductivity of borophene from first principle calculation
NASA Astrophysics Data System (ADS)
Xiao, Huaping; Cao, Wei; Ouyang, Tao; Guo, Sumei; He, Chaoyu; Zhong, Jianxin
2017-04-01
The phonon transport property is a foundation of understanding a material and predicting the potential application in mirco/nano devices. In this paper, the thermal transport property of borophene is investigated by combining first-principle calculations and phonon Boltzmann transport equation. At room temperature, the lattice thermal conductivity of borophene is found to be about 14.34 W/mK (error is about 3%), which is much smaller than that of graphene (about 3500 W/mK). The contributions from different phonon modes are qualified, and some phonon modes with high frequency abnormally play critical role on the thermal transport of borophene. This is quite different from the traditional understanding that thermal transport is usually largely contributed by the low frequency acoustic phonon modes for most of suspended 2D materials. Detailed analysis further reveals that the scattering between the out-of-plane flexural acoustic mode (FA) and other modes likes FA + FA/TA/LA/OP ↔ TA/LA/OP is the predominant phonon process channel. Finally the vibrational characteristic of some typical phonon modes and mean free path distribution of different phonon modes are also presented in this work. Our results shed light on the fundamental phonon transport properties of borophene, and foreshow the potential application for thermal management community.
Electronic and structural reconstruction in titanate heterostructures from first principles
NASA Astrophysics Data System (ADS)
Mulder, Andrew T.; Fennie, Craig J.
2014-03-01
Recent advances in transition metal oxide heterostructures have opened new routes to create materials with novel functionalities and properties. One direction has been to combine a Mott insulating perovskite with an electronic d1 configuration, such as LaTiO3, with a band insulating d0 perovskite, such as SrTiO3. An exciting recent development is the demonstration of interfacial conductivity in GdTiO3/SrTiO3 heterostructures that display a complex structural motif of octahedral rotations and ferromagnetic properties similar to bulk GdTiO3. In this talk we present our first principles investigation of the interplay of structural, electronic, magnetic, and orbital degrees of freedom for a wide range of d1/d0 titanate heterostructures. We find evidence for both rotation driven ferroelectricity and a symmetry breaking electronic reconstruction with a concomitant structural distortion at the interface. We argue that these materials represent an ideal platform to realize novel functionalities such as the electric field control of electronic and magnetic properties.
First-principle studies on the Li-Te system
NASA Astrophysics Data System (ADS)
Wang, Youchun; Tian, Fubo; Li, Da; Duan, Defang; Liu, Yunxian; Liu, Bingbing; Zhou, Qiang; Cui, Tian
2017-01-01
First-principle evolutionary calculation was performed to search for all probable stable lithium tellurium compounds. In addition to the well-known structures of Fm-3m Li2Te and Pnma Li2Te, several novel structures, including those of P4/nmm Li2Te, Imma Li8Te2, and C2/m Li9Te2, were determined under high pressure. The transformation sequence of Li2Te induced by pressure was presented as follows. The phase transition occurred at 7.5 GPa while transforming from Fm-3m phase to Pnma structure, then transformed to P4/nmm phase at 14 GPa. P4/nmm Li2Te can remain stable at least up to 140 GPa. Li8Te2 and Li9Te2 were stable at 8-120 GPa and 80-120 GPa, respectively. Interestingly, Li8Te2 and Li9Te2 were predicted to be metallic under high pressure, Li2Te would metalize on compression. P4/nmm Li2Te is likely a super ionic conductor due to the special characteristic. Metallic P4/nmm Li2Te may be a candidate mixed conductor material under extreme pressure. Charge transfer was studied using Bader charge analysis. Charge transferred from Li to Te, and the relative debilitated ionicity between Li and Te atoms existed at high pressure.
Accurate line intensities of methane from first-principles calculations
NASA Astrophysics Data System (ADS)
Nikitin, Andrei V.; Rey, Michael; Tyuterev, Vladimir G.
2017-10-01
In this work, we report first-principle theoretical predictions of methane spectral line intensities that are competitive with (and complementary to) the best laboratory measurements. A detailed comparison with the most accurate data shows that discrepancies in integrated polyad intensities are in the range of 0.4%-2.3%. This corresponds to estimations of the best available accuracy in laboratory Fourier Transform spectra measurements for this quantity. For relatively isolated strong lines the individual intensity deviations are in the same range. A comparison with the most precise laser measurements of the multiplet intensities in the 2ν3 band gives an agreement within the experimental error margins (about 1%). This is achieved for the first time for five-atomic molecules. In the Supplementary Material we provide the lists of theoretical intensities at 269 K for over 5000 strongest transitions in the range below 6166 cm-1. The advantage of the described method is that this offers a possibility to generate fully assigned exhaustive line lists at various temperature conditions. Extensive calculations up to 12,000 cm-1 including high-T predictions will be made freely available through the TheoReTS information system (http://theorets.univ-reims.fr, http://theorets.tsu.ru) that contains ab initio born line lists and provides a user-friendly graphical interface for a fast simulation of the absorption cross-sections and radiance.
NASA Astrophysics Data System (ADS)
Li, Zi; Zhang, Xu; Lu, Gang
2011-12-01
A Fortran program is developed to calculate charge carrier (electron or hole) mobility in disordered semiconductors from first-principles. The method is based on non-adiabatic ab initio molecular dynamics and static master equation, treating dynamic and static disorder on the same footing. We have applied the method to calculate the hole mobility in disordered poly(3-hexylthiophene) conjugated polymers as a function of temperature and electric field and obtained excellent agreements with experimental results. The program could be used to explore structure-mobility relation in disordered semiconducting polymers/organic semiconductors and aid rational design of these materials. Program summaryProgram title: FPMu Catalogue identifier: AEJV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJV_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.: 788 580 No. of bytes in distributed program, including test data, etc.: 8 433 024 Distribution format: tar.gz Programming language: Fortran 90 Computer: Any architecture with a Fortran 90 compiler Operating system: Linux, Windows RAM: Proportional to the system size, in our example, 1.2 GB Classification: 7.9 Nature of problem: Determine carrier mobility from first-principles in disordered semiconductors as a function of temperature, electric field and carrier concentration. Solution method: Iteratively solve master equation with carrier state energy and transition rates determined from first-principles. Restrictions: Mobility for disordered semiconductors where the carrier wave-functions are localized and the carrier transport is due to phonon-assisted hopping mechanism. Running time: Depending on the system size (about an hour for the example here).
Graphene mechanics: I. Efficient first principles based Morse potential.
Costescu, Bogdan I; Baldus, Ilona B; Gräter, Frauke
2014-06-28
We present a computationally efficient pairwise potential for use in molecular dynamics simulations of large graphene or carbon nanotube systems, in particular, for those under mechanical deformation, and also for mixed systems including biomolecules. Based on the Morse potential, it is only slightly more complex and computationally expensive than a harmonic bond potential, allowing such large or mixed simulations to reach experimentally relevant time scales. By fitting to data obtained from quantum mechanics (QM) calculations to represent bond breaking in graphene patches, we obtain a dissociation energy of 805 kJ mol(-1) which reflects the steepness of the QM potential up to the inflection point. A distinctive feature of our potential is its truncation at the inflection point, allowing a realistic treatment of ruptured C-C bonds without relying on a bond order model. The results obtained from equilibrium MD simulations using our potential compare favorably with results obtained from experiments and from similar simulations with more complex and computationally expensive potentials.
Exploiting periodic first-principles calculations in NMR spectroscopy of disordered solids.
Ashbrook, Sharon E; Dawson, Daniel M
2013-09-17
Much of the information contained within solid-state nuclear magnetic resonance (NMR) spectra remains unexploited because of the challenges in obtaining high-resolution spectra and the difficulty in assigning those spectra. Recent advances that enable researchers to accurately and efficiently determine NMR parameters in periodic systems have revolutionized the application of density functional theory (DFT) calculations in solid-state NMR spectroscopy. These advances are particularly useful for experimentalists. The use of first-principles calculations aids in both the interpretation and assignment of the complex spectral line shapes observed for solids. Furthermore, calculations provide a method for evaluating potential structural models against experimental data for materials with poorly characterized structures. Determining the structure of well-ordered, periodic crystalline solids can be straightforward using methods that exploit Bragg diffraction. However, the deviations from periodicity, such as compositional, positional, or temporal disorder, often produce the physical properties (such as ferroelectricity or ionic conductivity) that may be of commercial interest. With its sensitivity to the atomic-scale environment, NMR provides a potentially useful tool for studying disordered materials, and the combination of experiment with first-principles calculations offers a particularly attractive approach. In this Account, we discuss some of the issues associated with the practical implementation of first-principles calculations of NMR parameters in solids. We then use two key examples to illustrate the structural insights that researchers can obtain when applying such calculations to disordered inorganic materials. First, we describe an investigation of cation disorder in Y2Ti(2-x)Sn(x)O7 pyrochlore ceramics using (89)Y and (119)Sn NMR. Researchers have proposed that these materials could serve as host phases for the encapsulation of lanthanide- and actinide
Performance of arsenene and antimonene double-gate MOSFETs from first principles
Pizzi, Giovanni; Gibertini, Marco; Dib, Elias; Marzari, Nicola; Iannaccone, Giuseppe; Fiori, Gianluca
2016-01-01
In the race towards high-performance ultra-scaled devices, two-dimensional materials offer an alternative paradigm thanks to their atomic thickness suppressing short-channel effects. It is thus urgent to study the most promising candidates in realistic configurations, and here we present detailed multiscale simulations of field-effect transistors based on arsenene and antimonene monolayers as channels. The accuracy of first-principles approaches in describing electronic properties is combined with the efficiency of tight-binding Hamiltonians based on maximally localized Wannier functions to compute the transport properties of the devices. These simulations provide for the first time estimates on the upper limits for the electron and hole mobilities in the Takagi's approximation, including spin–orbit and multi-valley effects, and demonstrate that ultra-scaled devices in the sub-10-nm scale show a performance that is compliant with industry requirements. PMID:27557562
Performance of arsenene and antimonene double-gate MOSFETs from first principles
NASA Astrophysics Data System (ADS)
Pizzi, Giovanni; Gibertini, Marco; Dib, Elias; Marzari, Nicola; Iannaccone, Giuseppe; Fiori, Gianluca
2016-08-01
In the race towards high-performance ultra-scaled devices, two-dimensional materials offer an alternative paradigm thanks to their atomic thickness suppressing short-channel effects. It is thus urgent to study the most promising candidates in realistic configurations, and here we present detailed multiscale simulations of field-effect transistors based on arsenene and antimonene monolayers as channels. The accuracy of first-principles approaches in describing electronic properties is combined with the efficiency of tight-binding Hamiltonians based on maximally localized Wannier functions to compute the transport properties of the devices. These simulations provide for the first time estimates on the upper limits for the electron and hole mobilities in the Takagi's approximation, including spin-orbit and multi-valley effects, and demonstrate that ultra-scaled devices in the sub-10-nm scale show a performance that is compliant with industry requirements.
Towards Bond Selective Chemistry from First Principles: Methane on Metal Surfaces
NASA Astrophysics Data System (ADS)
Shen, X. J.; Lozano, A.; Dong, W.; Busnengo, H. F.; Yan, X. H.
2014-01-01
Controlling bond-selective chemical reactivity is of great importance and has a broad range of applications. Here, we present a molecular dynamics study of bond selective reactivity of methane and its deuterated isotopologues (i.e., CH4-xDx, x =0,1,2,3,4) on Ni(111) and Pt(111) from first principles calculations. Our simulations allow for reproducing the full C-H bond selectivity recently achieved experimentally via mode-specific vibrational excitation and explain its origin. Moreover, we also predict the hitherto unexplored influence of the molecular translational energy on such a selectivity as well as the conditions under which the full selectivity can be realized for the a priori less active C-D bond.
First-principles density-functional theory investigation of FOX-7
NASA Astrophysics Data System (ADS)
Vohaska, Brian; Conroy, Michael; Oleynik, Ivan; White, Carter
2008-03-01
Due to the expense and difficulty of experimental investigation of the chemical and physical properties of energetic materials (EMs), computational methods provide a unique opportunity for accurate determination of the chemical and physical properties of EM molecular crystals based on underlying atomic structure. In this presentation, we discuss the results of first-principles density functional theory (DFT) calculations of hydrostatic and uniaxial compression of the important energetic material, FOX-7. The calculated equilibrium properties, such as lattice parameters, elastic constants, and the bulk modulus will be reported and compared with experiment, as well as the isothermal equation of state. Due to the anisotropic nature of energetic molecular crystals, physical properties such as cohesive energy, band gap, and stress-strain relationships are reported as functions of each uniaxial compression studied. In addition, the shear stress behavior upon uniaxial compression will be discussed, as well as its possible relation to anisotropic shock-sensitivity in FOX-7.
Gaiduk, Alex P; Gygi, François; Galli, Giulia
2015-08-06
We determined the equilibrium density and compressibility of water and ice from first-principles molecular dynamics simulations using gradient-corrected (PBE) and hybrid (PBE0) functionals. Both functionals predicted the density of ice to be larger than that of water, by 15 (PBE) and 35% (PBE0). The PBE0 functional yielded a lower density of both ice and water with respect to PBE, leading to better agreement with experiment for ice but not for liquid water. Approximate inclusion of dispersion interactions on computed molecular-dynamics trajectories led to a substantial improvement of the PBE0 results for the density of liquid water, which, however, resulted to be slightly lower than that of ice.
Hu, S. X. Goncharov, V. N.; Boehly, T. R.; McCrory, R. L.; Skupsky, S.; Collins, L. A.; Kress, J. D.; Militzer, B.
2015-05-15
A comprehensive knowledge of the properties of high-energy-density plasmas is crucial to understanding and designing low-adiabat, inertial confinement fusion (ICF) implosions through hydrodynamic simulations. Warm-dense-matter (WDM) conditions are routinely accessed by low-adiabat ICF implosions, in which strong coupling and electron degeneracy often play an important role in determining the properties of warm dense plasmas. The WDM properties of deuterium–tritium (DT) mixtures and ablator materials, such as the equation of state, thermal conductivity, opacity, and stopping power, were usually estimated by models in hydro-codes used for ICF simulations. In these models, many-body and quantum effects were only approximately taken into account in the WMD regime. Moreover, the self-consistency among these models was often missing. To examine the accuracy of these models, we have systematically calculated the static, transport, and optical properties of warm dense DT plasmas, using first-principles (FP) methods over a wide range of densities and temperatures that cover the ICF “path” to ignition. These FP methods include the path-integral Monte Carlo (PIMC) and quantum-molecular dynamics (QMD) simulations, which treat electrons with many-body quantum theory. The first-principles equation-of-state table, thermal conductivities (κ{sub QMD}), and first principles opacity table of DT have been self-consistently derived from the combined PIMC and QMD calculations. They have been compared with the typical models, and their effects to ICF simulations have been separately examined in previous publications. In this paper, we focus on their combined effects to ICF implosions through hydro-simulations using these FP-based properties of DT in comparison with the usual model simulations. We found that the predictions of ICF neutron yield could change by up to a factor of ∼2.5; the lower the adiabat of DT capsules, the more variations in hydro-simulations. The FP
Hu, S. X.; Goncharov, V. N.; Boehly, T. R.; ...
2015-04-20
In this study, a comprehensive knowledge of the properties of high-energy-density plasmas is crucial to understanding and designing low-adiabat, inertial confinement fusion (ICF) implosions through hydrodynamic simulations. Warm-dense-matter (WDM) conditions are routinely accessed by low-adiabat ICF implosions, in which strong coupling and electron degeneracy often play an important role in determining the properties of warm dense plasmas. The WDM properties of deuterium–tritium (DT) mixtures and ablator materials, such as the equation of state, thermal conductivity, opacity, and stopping power, were usually estimated by models in hydro-codes used for ICF simulations. In these models, many-body and quantum effects were only approximatelymore » taken into account in the WMD regime. Moreover, the self-consistency among these models was often missing. To examine the accuracy of these models, we have systematically calculated the static, transport, and optical properties of warm dense DT plasmas, using first-principles (FP) methods over a wide range of densities and temperatures that cover the ICF “path” to ignition. These FP methods include the path-integral Monte Carlo (PIMC) and quantum-molecular dynamics (QMD) simulations, which treat electrons with many-body quantum theory. The first-principles equation-of-state table, thermal conductivities (KQMD), and first principles opacity table of DT have been self-consistently derived from the combined PIMC and QMD calculations. They have been compared with the typical models, and their effects to ICF simulations have been separately examined in previous publications. In this paper, we focus on their combined effects to ICF implosions through hydro-simulations using these FP-based properties of DT in comparison with the usual model simulations. We found that the predictions of ICF neutron yield could change by up to a factor of –2.5; the lower the adiabat of DT capsules, the more variations in hydro
Hu, S. X.; Goncharov, V. N.; Boehly, T. R.; McCrory, R. L.; Skupsky, S.; Collins, L. A.; Kress, J. D.; Militizer, B.
2015-04-20
In this study, a comprehensive knowledge of the properties of high-energy-density plasmas is crucial to understanding and designing low-adiabat, inertial confinement fusion (ICF) implosions through hydrodynamic simulations. Warm-dense-matter (WDM) conditions are routinely accessed by low-adiabat ICF implosions, in which strong coupling and electron degeneracy often play an important role in determining the properties of warm dense plasmas. The WDM properties of deuterium–tritium (DT) mixtures and ablator materials, such as the equation of state, thermal conductivity, opacity, and stopping power, were usually estimated by models in hydro-codes used for ICF simulations. In these models, many-body and quantum effects were only approximately taken into account in the WMD regime. Moreover, the self-consistency among these models was often missing. To examine the accuracy of these models, we have systematically calculated the static, transport, and optical properties of warm dense DT plasmas, using first-principles (FP) methods over a wide range of densities and temperatures that cover the ICF “path” to ignition. These FP methods include the path-integral Monte Carlo (PIMC) and quantum-molecular dynamics (QMD) simulations, which treat electrons with many-body quantum theory. The first-principles equation-of-state table, thermal conductivities (K_{QMD}), and first principles opacity table of DT have been self-consistently derived from the combined PIMC and QMD calculations. They have been compared with the typical models, and their effects to ICF simulations have been separately examined in previous publications. In this paper, we focus on their combined effects to ICF implosions through hydro-simulations using these FP-based properties of DT in comparison with the usual model simulations. We found that the predictions of ICF neutron yield could change by up to a factor of –2.5; the lower the adiabat of DT capsules, the more variations in hydro
First-principles investigation of hydrous post-perovskite
Townsend, Joshua P.; Tsuchiya, Jun; Bina, Craig R.; ...
2015-04-11
A stable, hydrogen-defect structure of post-perovskite (hy-ppv, Mg1–xSiH2xO3) has been determined by first-principles calculations of the vibrational and elastic properties up to 150 GPa. Among three potential hy-ppv structures analyzed, one was found to be stable at pressures relevant to the lower-mantle D" region. Hydrogen has a pronounced effect on the elastic properties of post-perovskite due to magnesium defects associated with hydration, including a reduction of the zero-pressure bulk (K0) and shear (G0) moduli by 5% and 8%, respectively, for a structure containing ~1 wt.% H2O. However, with increasing pressure the moduli of hy-ppv increase significantly relative to ppv, resultingmore » in a structure that is only 1% slower in bulk compressional velocity and 2.5% slower in shear-wave velocity than ppv at 120 GPa. In contrast, the reduction of certain anisotropic elastic constants (Cij) in hy-ppv increases with pressure (notably, C55, C66, and C23), indicating that hydration generally increases elastic anisotropy in hy-ppv at D" pressures. Calculated infrared absorption spectra show two O–H stretching bands at ~3500 cm–1 that shift with pressure to lower wavenumber by about 2 cm–1/GPa. At 120 GPa the hydrogen bonds in hy-ppv are still asymmetric. Furthermore, the stability of a hy-ppv structure containing 1–2 wt.% H2O at D" pressures implies that post-perovskite may be a host for recycled or primordial hydrogen near the Earth’s core-mantle boundary.« less
First-principles investigation of hydrous post-perovskite
Townsend, Joshua P.; Tsuchiya, Jun; Bina, Craig R.; Jacobsen, Steven D.
2015-04-11
A stable, hydrogen-defect structure of post-perovskite (hy-ppv, Mg_{1–x}SiH_{2x}O_{3}) has been determined by first-principles calculations of the vibrational and elastic properties up to 150 GPa. Among three potential hy-ppv structures analyzed, one was found to be stable at pressures relevant to the lower-mantle D" region. Hydrogen has a pronounced effect on the elastic properties of post-perovskite due to magnesium defects associated with hydration, including a reduction of the zero-pressure bulk (K_{0}) and shear (G_{0}) moduli by 5% and 8%, respectively, for a structure containing ~1 wt.% H_{2}O. However, with increasing pressure the moduli of hy-ppv increase significantly relative to ppv, resulting in a structure that is only 1% slower in bulk compressional velocity and 2.5% slower in shear-wave velocity than ppv at 120 GPa. In contrast, the reduction of certain anisotropic elastic constants (C_{ij}) in hy-ppv increases with pressure (notably, C_{55}, C_{66}, and C_{23}), indicating that hydration generally increases elastic anisotropy in hy-ppv at D" pressures. Calculated infrared absorption spectra show two O–H stretching bands at ~3500 cm^{–1} that shift with pressure to lower wavenumber by about 2 cm^{–1}/GPa. At 120 GPa the hydrogen bonds in hy-ppv are still asymmetric. Furthermore, the stability of a hy-ppv structure containing 1–2 wt.% H_{2}O at D" pressures implies that post-perovskite may be a host for recycled or primordial hydrogen near the Earth’s core-mantle boundary.
First principles modeling of nonlinear incidence rates in seasonal epidemics.
Ponciano, José M; Capistrán, Marcos A
2011-02-01
In this paper we used a general stochastic processes framework to derive from first principles the incidence rate function that characterizes epidemic models. We investigate a particular case, the Liu-Hethcote-van den Driessche's (LHD) incidence rate function, which results from modeling the number of successful transmission encounters as a pure birth process. This derivation also takes into account heterogeneity in the population with regard to the per individual transmission probability. We adjusted a deterministic SIRS model with both the classical and the LHD incidence rate functions to time series of the number of children infected with syncytial respiratory virus in Banjul, Gambia and Turku, Finland. We also adjusted a deterministic SEIR model with both incidence rate functions to the famous measles data sets from the UK cities of London and Birmingham. Two lines of evidence supported our conclusion that the model with the LHD incidence rate may very well be a better description of the seasonal epidemic processes studied here. First, our model was repeatedly selected as best according to two different information criteria and two different likelihood formulations. The second line of evidence is qualitative in nature: contrary to what the SIRS model with classical incidence rate predicts, the solution of the deterministic SIRS model with LHD incidence rate will reach either the disease free equilibrium or the endemic equilibrium depending on the initial conditions. These findings along with computer intensive simulations of the models' Poincaré map with environmental stochasticity contributed to attain a clear separation of the roles of the environmental forcing and the mechanics of the disease transmission in shaping seasonal epidemics dynamics.
A first-principles theoretical approach to heterogeneous nanocatalysis.
Negreiros, Fabio R; Aprà, Edoardo; Barcaro, Giovanni; Sementa, Luca; Vajda, Stefan; Fortunelli, Alessandro
2012-02-21
A theoretical approach to heterogeneous catalysis by sub-nanometre supported metal clusters and alloys is presented and discussed. Its goal is to perform a computational sampling of the reaction paths in nanocatalysis via a global search in the phase space of structures and stoichiometry combined with filtering which takes into account the given experimental conditions (catalytically relevant temperature and reactant pressure), and corresponds to an incremental exploration of the disconnectivity diagram of the system. The approach is implemented and applied to the study of propylene partial oxidation by Ag(3) supported on MgO(100). First-principles density-functional theory calculations coupled with a Reactive Global Optimization algorithm are performed, finding that: (1) the presence of an oxide support drastically changes the potential energy landscape of the system with respect to the gas phase, favoring configurations which interact positively with the electrostatic field generated by the surface; (2) the reaction energy barriers for the various mechanisms are crucial in the competition between thermodynamically and kinetically favored reaction products; (3) a topological database of structures and saddle points is produced which has general validity and can serve for future studies or for deriving general trends; (4) the MgO(100) surface captures some major features of the effect of an oxide support and appears to be a good model of a simple oxide substrate; (5) strong cooperative effects are found in the co-adsorption of O(2) and other ligands on small metal clusters. The proposed approach appears as a viable route to advance the role of predictive computational science in the field of heterogeneous nanocatalysis. This journal is © The Royal Society of Chemistry 2012
First Principles Design of Non-Centrosymmetric Metal Oxides
NASA Astrophysics Data System (ADS)
Young, Joshua Aaron
The lack of an inversion center in a material's crystal structure can result in many useful material properties, such as ferroelectricity, piezoelectricity and non-linear optical behavior. Recently, the desire for low power, high efficiency electronic devices has spurred increased interest in these phenomena, especially ferroelectricity, as well as their coupling to other material properties. By studying and understanding the fundamental structure-property relationships present in non-centrosymmetric materials, it is possible to purposefully engineer new compounds with the desired "acentric" qualities through crystal engineering. The families of ABO3 perovskite and ABO2.5 perovskite-derived brownmillerite oxides are ideal for such studies due to their wide range of possible chemistries, as well as ground states that are highly tunable owing to strong electron-lattice coupling. Furthermore, control over the B-O-B bond angles through epitaxial strain or chemical substitution allows for the rapid development of new emergent properties. In this dissertation, I formulate the crystal-chemistry criteria necessary to design functional non-centrosymmetric oxides using first-principles density functional theory calculations. Recently, chemically ordered (AA')B2O 6 oxides have been shown to display a new form of rotation-induced ferroelectric polarizations. I now extend this property-design methodology to alternative compositions and crystal classes and show it is possible to induce a host of new phenomena. This dissertation will address: 1) the formulation of predictive models allowing for a priori design of polar oxides, 2) the optimization of properties exhibited by these materials through chemical substitution and cation ordering, and 3) the use of strain to control the stability of new phases. Completion of this work has led to a deeper understanding of how atomic structural features determine the physical properties of oxides, as well as the successful elucidation of
First-principles studies of Ni-Ta intermetallic compounds
Zhou Yi; Wen Bin; Ma Yunqing; Melnik, Roderick; Liu Xingjun
2012-03-15
The structural properties, heats of formation, elastic properties, and electronic structures of Ni-Ta intermetallic compounds are investigated in detail based on density functional theory. Our results indicate that all Ni-Ta intermetallic compounds calculated here are mechanically stable except for P21/m-Ni{sub 3}Ta and hc-NiTa{sub 2}. Furthermore, we found that Pmmn-Ni{sub 3}Ta is the ground state stable phase of Ni{sub 3}Ta polymorphs. The polycrystalline elastic modulus has been deduced by using the Voigt-Reuss-Hill approximation. All Ni-Ta intermetallic compounds in our study, except for NiTa, are ductile materials by corresponding G/K values and poisson's ratio. The calculated heats of formation demonstrated that Ni{sub 2}Ta are thermodynamically unstable. Our results also indicated that all Ni-Ta intermetallic compounds analyzed here are conductors. The density of state demonstrated the structure stability increases with the Ta concentration. - Graphical abstract: Mechanical properties and formation heats of Ni-Ta intermetallic compounds are discussed in detail in this paper. Highlights: Black-Right-Pointing-Pointer Ni-Ta intermetallic compounds are investigated by first principle calculations. Black-Right-Pointing-Pointer P21/m-Ni{sub 3}Ta and hc-NiTa{sub 2} are mechanically unstable phases. Black-Right-Pointing-Pointer Pmmn-Ni{sub 3}Ta is ground stable phase of Ni{sub 3}Ta polymorphs. Black-Right-Pointing-Pointer All Ni-Ta intermetallic compounds are conducting materials.
Thermodynamic stability and properties of boron subnitrides from first principles
NASA Astrophysics Data System (ADS)
Ektarawong, A.; Simak, S. I.; Alling, B.
2017-02-01
We use the first-principles approach to clarify the thermodynamic stability as a function of pressure and temperature of three different α -rhombohedral-boron-like boron subnitrides, with the compositions of B6N , B13N2 , and B38N6 , proposed in the literature. We find that, out of these subnitrides with the structural units of B12(N-N), B12(NBN), and [B12(N-N) ] 0.33[B12(NBN)] 0.67 , respectively, only B38N6 , represented by [B12(N-N) ] 0.33[B12(NBN)] 0.67 , is thermodynamically stable. Beyond a pressure of about 7.5 GPa depending on the temperature, also B38N6 becomes unstable, and decomposes into cubic boron nitride and α -tetragonal-boron-like boron subnitride B50N2 . The thermodynamic stability of boron subnitrides and relevant competing phases is determined by the Gibbs free energy, in which the contributions from the lattice vibrations and the configurational disorder are obtained within the quasiharmonic and the mean-field approximations, respectively. We calculate lattice parameters, elastic constants, phonon and electronic density of states, and demonstrate that [B12(N-N) ] 0.33[B12(NBN)] 0.67 is both mechanically and dynamically stable, and is an electrical semiconductor. The simulated x-ray powder-diffraction pattern as well as the calculated lattice parameters of [B12(N-N) ] 0.33[B12(NBN)] 0.67 are found to be in good agreement with those of the experimentally synthesized boron subnitrides reported in the literature, verifying that B38N6 is the stable composition of α -rhombohedral-boron-like boron subnitride.
A digitally reconstructed radiograph algorithm calculated from first principles
Staub, David; Murphy, Martin J.
2013-01-15
Purpose: To develop an algorithm for computing realistic digitally reconstructed radiographs (DRRs) that match real cone-beam CT (CBCT) projections with no artificial adjustments. Methods: The authors used measured attenuation data from cone-beam CT projection radiographs of different materials to obtain a function to convert CT number to linear attenuation coefficient (LAC). The effects of scatter, beam hardening, and veiling glare were first removed from the attenuation data. Using this conversion function the authors calculated the line integral of LAC through a CT along rays connecting the radiation source and detector pixels with a ray-tracing algorithm, producing raw DRRs. The effects of scatter, beam hardening, and veiling glare were then included in the DRRs through postprocessing. Results: The authors compared actual CBCT projections to DRRs produced with all corrections (scatter, beam hardening, and veiling glare) and to uncorrected DRRs. Algorithm accuracy was assessed through visual comparison of projections and DRRs, pixel intensity comparisons, intensity histogram comparisons, and correlation plots of DRR-to-projection pixel intensities. In general, the fully corrected algorithm provided a small but nontrivial improvement in accuracy over the uncorrected algorithm. The authors also investigated both measurement- and computation-based methods for determining the beam hardening correction, and found the computation-based method to be superior, as it accounted for nonuniform bowtie filter thickness. The authors benchmarked the algorithm for speed and found that it produced DRRs in about 0.35 s for full detector and CT resolution at a ray step-size of 0.5 mm. Conclusions: The authors have demonstrated a DRR algorithm calculated from first principles that accounts for scatter, beam hardening, and veiling glare in order to produce accurate DRRs. The algorithm is computationally efficient, making it a good candidate for iterative CT reconstruction techniques
Risk reduction and the privatization option: First principles
Bjornstad, D.J.; Jones, D.W.; Russell, M.; Cummings, R.C.; Valdez, G.; Duemmer, C.L.
1997-06-25
The Department of Energy`s Office of Environmental Restoration and Waste Management (EM) faces a challenging mission. To increase efficiency, EM is undertaking a number of highly innovative initiatives--two of which are of particular importance to the present study. One is the 2006 Plan, a planning and budgeting process that seeks to convert the clean-up program from a temporally and fiscally open-ended endeavor to a strictly bounded one, with firm commitments over a decade-long horizon. The second is a major overhauling of the management and contracting practices that define the relationship between the Department and the private sector, aimed at cost reduction by increasing firms` responsibilities and profit opportunities and reducing DOE`s direct participation in management practices and decisions. The goal of this paper is to provide an independent perspective on how EM should create new management practices to deal with private sector partners that are motivated by financial incentives. It seeks to ground this perspective in real world concerns--the background of the clean-up effort, the very difficult technical challenges it faces, the very real threats to environment, health and safety that have now been juxtaposed with financial drivers, and the constraints imposed by government`s unique business practices and public responsibilities. The approach is to raise issues through application of first principles. The paper is targeted at the EM policy officer who must implement the joint visions of the 2006 plan and privatization within the context of the tradeoff between terminal risk reduction and interim risk management.
First Principles Modeling of Nonlinear Incidence Rates in Seasonal Epidemics
2011-01-01
In this paper we used a general stochastic processes framework to derive from first principles the incidence rate function that characterizes epidemic models. We investigate a particular case, the Liu-Hethcote-van den Driessche's (LHD) incidence rate function, which results from modeling the number of successful transmission encounters as a pure birth process. This derivation also takes into account heterogeneity in the population with regard to the per individual transmission probability. We adjusted a deterministic SIRS model with both the classical and the LHD incidence rate functions to time series of the number of children infected with syncytial respiratory virus in Banjul, Gambia and Turku, Finland. We also adjusted a deterministic SEIR model with both incidence rate functions to the famous measles data sets from the UK cities of London and Birmingham. Two lines of evidence supported our conclusion that the model with the LHD incidence rate may very well be a better description of the seasonal epidemic processes studied here. First, our model was repeatedly selected as best according to two different information criteria and two different likelihood formulations. The second line of evidence is qualitative in nature: contrary to what the SIRS model with classical incidence rate predicts, the solution of the deterministic SIRS model with LHD incidence rate will reach either the disease free equilibrium or the endemic equilibrium depending on the initial conditions. These findings along with computer intensive simulations of the models' Poincaré map with environmental stochasticity contributed to attain a clear separation of the roles of the environmental forcing and the mechanics of the disease transmission in shaping seasonal epidemics dynamics. PMID:21379320
A first-principles theoretical approach to heterogeneous nanocatalysis
NASA Astrophysics Data System (ADS)
Negreiros, Fabio R.; Aprà, Edoardo; Barcaro, Giovanni; Sementa, Luca; Vajda, Stefan; Fortunelli, Alessandro
2012-02-01
A theoretical approach to heterogeneous catalysis by sub-nanometre supported metal clusters and alloys is presented and discussed. Its goal is to perform a computational sampling of the reaction paths in nanocatalysis via a global search in the phase space of structures and stoichiometry combined with filtering which takes into account the given experimental conditions (catalytically relevant temperature and reactant pressure), and corresponds to an incremental exploration of the disconnectivity diagram of the system. The approach is implemented and applied to the study of propylene partial oxidation by Ag3 supported on MgO(100). First-principles density-functional theory calculations coupled with a Reactive Global Optimization algorithm are performed, finding that: (1) the presence of an oxide support drastically changes the potential energy landscape of the system with respect to the gas phase, favoring configurations which interact positively with the electrostatic field generated by the surface; (2) the reaction energy barriers for the various mechanisms are crucial in the competition between thermodynamically and kinetically favored reaction products; (3) a topological database of structures and saddle points is produced which has general validity and can serve for future studies or for deriving general trends; (4) the MgO(100) surface captures some major features of the effect of an oxide support and appears to be a good model of a simple oxide substrate; (5) strong cooperative effects are found in the co-adsorption of O2 and other ligands on small metal clusters. The proposed approach appears as a viable route to advance the role of predictive computational science in the field of heterogeneous nanocatalysis.
First principles explanation of the positive Seebeck coefficient of lithium.
Xu, Bin; Verstraete, Matthieu J
2014-05-16
Lithium is one of the simplest metals, with negative charge carriers and a close reproduction of free-electron dispersion. Experimentally, however, Li is one of a handful of elemental solids (along with Cu, Ag, and Au) where the sign of the Seebeck coefficient (S) is opposite to that of the carrier. This counterintuitive behavior still lacks a satisfactory interpretation. We calculate S fully from first principles, within the framework of Allen's formulation of Boltzmann transport theory. Here it is crucial to avoid the constant relaxation time approximation, which gives a sign for S which is necessarily that of the carriers. Our calculated S are in excellent agreement with experimental data, up to the melting point. In comparison with another alkali metal, Na, we demonstrate that within the simplest nontrivial model for the energy dependency of the electron lifetimes, the rapidly increasing density of states (DOS) across the Fermi energy is related to the sign of S in Li. The exceptional energy dependence of the DOS is beyond the free-electron model, as the dispersion is distorted by the Brillouin zone edge; this has a stronger effect in Li than other alkali metals. The electron lifetime dependency on energy is central, but the details of the electron-phonon interaction are found to be less important, contrary to what has been believed for several decades. Band engineering combined with the mechanism exposed here may open the door to new "ambipolar" thermoelectric materials, with a tunable sign for the thermopower even if either n- or p-type doping is impossible.
First principles investigation of copper and silver intercalated molybdenum disulfide
NASA Astrophysics Data System (ADS)
Guzman, D. M.; Onofrio, N.; Strachan, A.
2017-02-01
We characterize the energetics and atomic structures involved in the intercalation of copper and silver into the van der Waals gap of molybdenum disulfide as well as the resulting ionic and electronic transport properties using first-principles density functional theory. The intercalation energy of systems with formula (Cu,Ag)xMoS2 decreases with ion concentration and ranges from 1.2 to 0.8 eV for Cu; Ag exhibits a stronger concentration dependence from 2.2 eV for x = 0.014 to 0.75 eV for x = 1 (using the fcc metal as a reference). Partial atomic charge analysis indicates that approximately half an electron is transferred per metallic ion in the case of Cu at low concentrations and the ionicity decreases only slightly with concentration. In contrast, while Ag is only slightly less ionic than Cu for low concentrations, charge transfer reduces significantly to approximately 0.1 e for x = 1. This difference in ionicity between Cu and Ag correlates with their intercalation energies. Importantly, the predicted values indicate the possibility of electrochemical intercalation of both Cu and Ag into MoS2 and the calculated activation energies associated with ionic transport within the gaps, 0.32 eV for Cu and 0.38 eV for Ag, indicate these materials to be good ionic conductors. Analysis of the electronic structure shows that charge transfer leads to a shift of the Fermi energy into the conduction band resulting in a semiconductor-to-metal transition. Electron transport calculations based on non-equilibrium Green's function show that the low-bias conductance increases with metal concentration and is comparable in the horizontal and vertical transport directions. These properties make metal intercalated transition metal di-chalcogenides potential candidates for several applications including electrochemical metallization cells and contacts in electronics based on 2D materials.
First principle kinetic studies of zeolite-catalyzed methylation reactions.
Van Speybroeck, Veronique; Van der Mynsbrugge, Jeroen; Vandichel, Matthias; Hemelsoet, Karen; Lesthaeghe, David; Ghysels, An; Marin, Guy B; Waroquier, Michel
2011-02-02
Methylations of ethene, propene, and butene by methanol over the acidic microporous H-ZSM-5 catalyst are studied by means of state of the art computational techniques, to derive Arrhenius plots and rate constants from first principles that can directly be compared with the experimental data. For these key elementary reactions in the methanol to hydrocarbons (MTH) process, direct kinetic data became available only recently [J. Catal.2005, 224, 115-123; J. Catal.2005, 234, 385-400]. At 350 °C, apparent activation energies of 103, 69, and 45 kJ/mol and rate constants of 2.6 × 10(-4), 4.5 × 10(-3), and 1.3 × 10(-2) mol/(g h mbar) for ethene, propene, and butene were derived, giving following relative ratios for methylation k(ethene)/k(propene)/k(butene) = 1:17:50. In this work, rate constants including pre-exponential factors are calculated which give very good agreement with the experimental data: apparent activation energies of 94, 62, and 37 kJ/mol for ethene, propene, and butene are found, and relative ratios of methylation k(ethene)/k(propene)/k(butene) = 1:23:763. The entropies of gas phase alkenes are underestimated in the harmonic oscillator approximation due to the occurrence of internal rotations. These low vibrational modes were substituted by manually constructed partition functions. Overall, the absolute reaction rates can be calculated with near chemical accuracy, and qualitative trends are very well reproduced. In addition, the proposed scheme is computationally very efficient and constitutes significant progress in kinetic modeling of reactions in heterogeneous catalysis.
A digitally reconstructed radiograph algorithm calculated from first principles
Staub, David; Murphy, Martin J.
2013-01-01
Purpose: To develop an algorithm for computing realistic digitally reconstructed radiographs (DRRs) that match real cone-beam CT (CBCT) projections with no artificial adjustments. Methods: The authors used measured attenuation data from cone-beam CT projection radiographs of different materials to obtain a function to convert CT number to linear attenuation coefficient (LAC). The effects of scatter, beam hardening, and veiling glare were first removed from the attenuation data. Using this conversion function the authors calculated the line integral of LAC through a CT along rays connecting the radiation source and detector pixels with a ray-tracing algorithm, producing raw DRRs. The effects of scatter, beam hardening, and veiling glare were then included in the DRRs through postprocessing. Results: The authors compared actual CBCT projections to DRRs produced with all corrections (scatter, beam hardening, and veiling glare) and to uncorrected DRRs. Algorithm accuracy was assessed through visual comparison of projections and DRRs, pixel intensity comparisons, intensity histogram comparisons, and correlation plots of DRR-to-projection pixel intensities. In general, the fully corrected algorithm provided a small but nontrivial improvement in accuracy over the uncorrected algorithm. The authors also investigated both measurement- and computation-based methods for determining the beam hardening correction, and found the computation-based method to be superior, as it accounted for nonuniform bowtie filter thickness. The authors benchmarked the algorithm for speed and found that it produced DRRs in about 0.35 s for full detector and CT resolution at a ray step-size of 0.5 mm. Conclusions: The authors have demonstrated a DRR algorithm calculated from first principles that accounts for scatter, beam hardening, and veiling glare in order to produce accurate DRRs. The algorithm is computationally efficient, making it a good candidate for iterative CT reconstruction techniques
Nomura, Yusuke; Sakai, Shiro; Capone, Massimo; Arita, Ryotaro
2015-01-01
Alkali-doped fullerides A3C60 (A = K, Rb, Cs) are surprising materials where conventional phonon-mediated superconductivity and unconventional Mott physics meet, leading to a remarkable phase diagram as a function of volume per C60 molecule. We address these materials with a state-of-the-art calculation, where we construct a realistic low-energy model from first principles without using a priori information other than the crystal structure and solve it with an accurate many-body theory. Remarkably, our scheme comprehensively reproduces the experimental phase diagram including the low-spin Mott-insulating phase next to the superconducting phase. More remarkably, the critical temperatures Tc’s calculated from first principles quantitatively reproduce the experimental values. The driving force behind the surprising phase diagram of A3C60 is a subtle competition between Hund’s coupling and Jahn-Teller phonons, which leads to an effectively inverted Hund’s coupling. Our results establish that the fullerides are the first members of a novel class of molecular superconductors in which the multiorbital electronic correlations and phonons cooperate to reach high Tc s-wave superconductivity. PMID:26601242
First-principles equation of state and electronic properties of warm dense oxygen.
Driver, K P; Soubiran, F; Zhang, Shuai; Militzer, B
2015-10-28
We perform all-electron path integral Monte Carlo (PIMC) and density functional theory molecular dynamics (DFT-MD) calculations to explore warm dense matter states of oxygen. Our simulations cover a wide density-temperature range of 1-100 g cm(-3) and 10(4)-10(9) K. By combining results from PIMC and DFT-MD, we are able to compute pressures and internal energies from first-principles at all temperatures and provide a coherent equation of state. We compare our first-principles calculations with analytic equations of state, which tend to agree for temperatures above 8 × 10(6) K. Pair-correlation functions and the electronic density of states reveal an evolving plasma structure and ionization process that is driven by temperature and density. As we increase the density at constant temperature, we find that the ionization fraction of the 1s state decreases while the other electronic states move towards the continuum. Finally, the computed shock Hugoniot curves show an increase in compression as the first and second shells are ionized.
Guan, Zhaoyong; Si, Chen; Hu, Shuanglin; Duan, Wenhui
2016-04-28
Based on first-principles calculations, we present the electronic and magnetic properties of a class of line defect-embedded zigzag graphene nanoribbons, with one edge saturated by two hydrogen atoms per carbon atom and the other edge terminated by only one hydrogen atom. Such edge-modified nanoribbons without line defects are found to be typical bipolar magnetic semiconductors (BMS). In contrast, when the line defect is introduced into the ribbons, the ground state is ferromagnetic, and the resulting nanoribbons can be tuned to spin-polarized metal, metal with Dirac point, or half-metal by varying the position of the line defect, owing to the defect-induced self-doping of the BMS. Specifically, when the line defect is far away from the edges of the ribbon, the system shows half-metallicity. We further confirm the structural and magnetic stability at room temperature by first-principles molecular dynamics simulations. Our findings reveal the possibility of building metal-free electronic/spintronic devices with magnetic/half-metallic graphene nanoribbons.
First-principles study on dielectric function of isolated and bundled carbon nanotubes
NASA Astrophysics Data System (ADS)
Yang, J. Y.; Liu, L. H.; Tan, J. Y.
2015-06-01
The dielectric function fundamentally determines the thermal radiative properties of nanomaterials. In this work, the first-principles method is applied to investigate the finite temperature dielectric function of isolated and bundled single-walled carbon nanotubes in the visible-ultraviolet spectral range without empirical models. The effects of diameter, intertube interactions and temperature on dielectric functions are discussed. The calculated extraordinary dielectric functions of four isolated (5,5), (6,6), (7,7) and (8,8) armchair nanotubes with different diameters are compared to study the diameter effect. It shows that the locations of absorption peaks of dielectric functions consistently shift to lower energy with increasing diameter. To analyze the influence of non-local intertube interactions, the dielectric functions of bundled (6,6) armchair nanotubes with varying intertube distance are calculated within the van der Waals theory. As nanotubes bundle together, the intertube interactions become strong and the absorption peaks enhance. The temperature effect is included into computing dielectric function of isolated (5,0) zigzag nanotubes via first-principles molecular dynamics method. It observes that the dominant absorption peak shifts to lower energy as temperature increases from 0 to 600 K. To interpret the temperature influence, the temperature perturbed density of states is presented.
Nomura, Yusuke; Sakai, Shiro; Capone, Massimo; Arita, Ryotaro
2015-08-01
Alkali-doped fullerides A 3C60 (A = K, Rb, Cs) are surprising materials where conventional phonon-mediated superconductivity and unconventional Mott physics meet, leading to a remarkable phase diagram as a function of volume per C60 molecule. We address these materials with a state-of-the-art calculation, where we construct a realistic low-energy model from first principles without using a priori information other than the crystal structure and solve it with an accurate many-body theory. Remarkably, our scheme comprehensively reproduces the experimental phase diagram including the low-spin Mott-insulating phase next to the superconducting phase. More remarkably, the critical temperatures T c's calculated from first principles quantitatively reproduce the experimental values. The driving force behind the surprising phase diagram of A 3C60 is a subtle competition between Hund's coupling and Jahn-Teller phonons, which leads to an effectively inverted Hund's coupling. Our results establish that the fullerides are the first members of a novel class of molecular superconductors in which the multiorbital electronic correlations and phonons cooperate to reach high T c s-wave superconductivity.
First-principles prediction of the softening of the silicon shock Hugoniot curve
Hu, S. X.; Militzer, B.; Collins, L. A.; Driver, K. P.; Kress, J. D.
2016-09-15
Here, whock compression of silicon (Si) under extremely high pressures (>100 Mbar) was investigated by using two first-principles methods of orbital-free molecular dynamics (OFMD) and path integral Monte Carlo (PIMC). While pressures from the two methods agree very well, PIMC predicts a second compression maximum because of 1s electron ionization that is absent in OFMD calculations since Thomas–Fermi-based theories lack inner shell structure. The Kohn–Sham density functional theory is used to calculate the equation of state (EOS) of warm dense silicon for low-pressure loadings (P < 100 Mbar). Combining these first-principles EOS results, the principal Hugoniot curve of silicon for pressures varying from 0.80 Mbar to above ~10 Gbar was derived. We find that silicon is ~20% or more softer than what was predicted by EOS models based on the chemical picture of matter. Existing experimental data (P ≈ 1–2 Mbar) seem to indicate this softening behavior of Si, which calls for future strong-shock experiments (P > 10 Mbar) to benchmark our results.
First-principles equation of state and electronic properties of warm dense oxygen
Driver, K. P. Soubiran, F.; Zhang, Shuai; Militzer, B.
2015-10-28
We perform all-electron path integral Monte Carlo (PIMC) and density functional theory molecular dynamics (DFT-MD) calculations to explore warm dense matter states of oxygen. Our simulations cover a wide density-temperature range of 1–100 g cm{sup −3} and 10{sup 4}–10{sup 9} K. By combining results from PIMC and DFT-MD, we are able to compute pressures and internal energies from first-principles at all temperatures and provide a coherent equation of state. We compare our first-principles calculations with analytic equations of state, which tend to agree for temperatures above 8 × 10{sup 6} K. Pair-correlation functions and the electronic density of states reveal an evolving plasma structure and ionization process that is driven by temperature and density. As we increase the density at constant temperature, we find that the ionization fraction of the 1s state decreases while the other electronic states move towards the continuum. Finally, the computed shock Hugoniot curves show an increase in compression as the first and second shells are ionized.
First-principles prediction of the softening of the silicon shock Hugoniot curve
Hu, S. X.; Militzer, B.; Collins, L. A.; Driver, K. P.; Kress, J. D.
2016-09-15
Here, whock compression of silicon (Si) under extremely high pressures (>100 Mbar) was investigated by using two first-principles methods of orbital-free molecular dynamics (OFMD) and path integral Monte Carlo (PIMC). While pressures from the two methods agree very well, PIMC predicts a second compression maximum because of 1s electron ionization that is absent in OFMD calculations since Thomas–Fermi-based theories lack inner shell structure. The Kohn–Sham density functional theory is used to calculate the equation of state (EOS) of warm dense silicon for low-pressure loadings (P < 100 Mbar). Combining these first-principles EOS results, the principal Hugoniot curve of silicon for pressures varying from 0.80 Mbar to above ~10 Gbar was derived. We find that silicon is ~20% or more softer than what was predicted by EOS models based on the chemical picture of matter. Existing experimental data (P ≈ 1–2 Mbar) seem to indicate this softening behavior of Si, which calls for future strong-shock experiments (P > 10 Mbar) to benchmark our results.
First-principles prediction of the softening of the silicon shock Hugoniot curve
Hu, S. X.; Militzer, B.; Collins, L. A.; ...
2016-09-15
Here, whock compression of silicon (Si) under extremely high pressures (>100 Mbar) was investigated by using two first-principles methods of orbital-free molecular dynamics (OFMD) and path integral Monte Carlo (PIMC). While pressures from the two methods agree very well, PIMC predicts a second compression maximum because of 1s electron ionization that is absent in OFMD calculations since Thomas–Fermi-based theories lack inner shell structure. The Kohn–Sham density functional theory is used to calculate the equation of state (EOS) of warm dense silicon for low-pressure loadings (P < 100 Mbar). Combining these first-principles EOS results, the principal Hugoniot curve of silicon formore » pressures varying from 0.80 Mbar to above ~10 Gbar was derived. We find that silicon is ~20% or more softer than what was predicted by EOS models based on the chemical picture of matter. Existing experimental data (P ≈ 1–2 Mbar) seem to indicate this softening behavior of Si, which calls for future strong-shock experiments (P > 10 Mbar) to benchmark our results.« less
Niu, J. G.; Zhan, Q.; Geng, W. T.
2014-06-15
Despite well documented first-principles theoretical determination of the low migration energy (0.06 eV) of a single He in tungsten, fully quantum mechanical calculations on the migration of a He pair still present a challenge due to the complexity of its trajectory. By identifying the six most stable configurations of the He pair in W and decomposing its motion into rotational, translational, and rotational-translational routines, we are able to determine its migration barrier and trajectory. Our density functional theory calculations demonstrate a He pair has three modes of motion: a close or open circular two-dimensional motion in (100) plane with an energy barrier of 0.30 eV, a snaking motion along [001] direction with a barrier of 0.30 eV, and a twisted-ladder motion along [010] direction with the two He swinging in the plane (100) and a barrier of 0.31 eV. The graceful associative movements of a He pair are related to the chemical-bonding-like He-He interaction being much stronger than its migration barrier in W. The excellent agreement with available experimental measurements (0.24–0.32 eV) on He migration makes our first-principles result a solid input to obtain accurate He-W interatomic potentials in molecular dynamics simulations.