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At least 829 records · Page 46

Multiresolution quantum chemistry in multiwavelet bases: excited states from time-dependent Hartree–Fock and density functional theory via linear response

Using the fully numerical method for time-dependent Hartree–Fock and density functional theory (TD-HF/DFT) with the Tamm–Dancoff (TD) approximation we use a multiresolution analysis (MRA) approach to present our findings. From a reformulation with effective use of the density matrix operator, we obtain a general form of the HF/DFT linear response equation in the first quantization formalism. It can be readily rewritten as an integral equation with the bound-state Helmholtz (BSH) kernel for the Green's function. The MRA implementation of the resultant equation permits excited state calculations without virtual orbitals. Moreover, the integral equation is efficiently and adaptively solved using a numerical multiresolution solver with multiwavelet bases. Our implementation of the TD-HF/DFT methods is applied for calculating the excitation energies of H 2 , Be, N 2 , H 2 O, and C 2 H 4 molecules. The numerical errors of the calculated excitation energies converge in proportion to the residuals of the equation in the molecular orbitals and response functions. The energies of the excited states at a variety of length scales ranging from short-range valence excitations to long-range Rydberg-type ones are consistently accurate. It is shown that the multiresolution calculations yield the correct exponential asymptotic tails for the response functions, whereas those computed with Gaussian basis functions are too diffuse or decay too rapidly. Finally, we introduce a simple asymptotic correction to the local spin-density approximation (LSDA) so that in the TDDFT calculations, the excited states are correctly bound.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Layered nested Markov chain Monte Carlo

A configurational sampling algorithm based on nested layerings of Markov chains (Layered Nested Markov Chain Monte Carlo or L-NMCMC) is presented for simulations of systems characterized by rugged free energy landscapes. The layerings are generated using a set of auxiliary potential energy surfaces. The implementation of the method is demonstrated in the context of a rugged, two-dimensional potential energy surface. The versatility of the algorithm is next demonstrated on a simple, many body system, namely, a canonical Lennard-Jones fluid in the liquid state. In that example, different layering schemes and auxiliary potentials are used, including variable cutoff distances and excluded volume tempering. In addition to calculating a variety of properties of the system, it is also shown that L-NMCMC, when combined with a free-energy perturbation formalism, provides a straightforward means to construct approximate free-energy surfaces at no additional computational cost using the sampling distributions of each auxiliary Markov chain. In conclusion, the proposed L-NMCMC scheme is general in that it could be complementary to any number of methods that rely on sampling from a target distribution or methods that exploit a hierarchy of time scales and/or length scales through decomposition of the potential energy.

97 MATHEMATICS AND COMPUTING↗

An interoperable implementation of collective‐variable based enhanced sampling methods in extended phase space within the OpenMM package

Collective variable (CV)-based enhanced sampling techniques are widely used today for accelerating barrier-crossing events in molecular simulations. A class of these methods, which includes temperature accelerated molecular dynamics (TAMD)/driven-adiabatic free energy dynamics (d-AFED), unified free energy dynamics (UFED), and temperature accelerated sliced sampling (TASS), uses an extended variable formalism to achieve quick exploration of conformational space. These techniques are powerful, as they enhance the sampling of a large number of CVs simultaneously compared to other techniques. Extended variables are kept at a much higher temperature than the physical temperature by ensuring adiabatic separation between the extended and physical subsystems and employing rigorous thermostatting. Here, in this work, we present a computational platform to perform extended phase space enhanced sampling simulations using the open-source molecular dynamics engine OpenMM. The implementation allows users to have interoperability of sampling techniques, as well as employ state-of-the-art thermostats and multiple time-stepping. This work also presents protocols for determining the critical parameters and procedures for reconstructing high-dimensional free energy surfaces. As a demonstration, we present simulation results on the high dimensional conformational landscapes of the alanine tripeptide in vacuo, tetra-N-methylglycine (tetra-sarcosine) peptoid in implicit solvent, and the Trp-cage mini protein in explicit water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Efficient Four-Component Dirac–Coulomb–Gaunt Hartree–Fock in the Pauli Spinor Representation

Four-component Dirac Hartree--Fock is an accurate mean-field method for treating molecular systems where relativistic effects are important. However, the computational cost and complexity of the two-electron interaction makes this method less common, even though we can consider the Dirac Hartree--Fock Hamiltonian the ``ground truth" of electronic structure, barring explicit quantum-electrodynamical effects. Being able to calculate these effects is then vital to the design of lower scaling methods for accurate predictions in computational spectroscopy and properties of heavy element complexes that must include relativistic effects for even qualitative accuracy. In this work, we present a Pauli quaternion formalism of maximal component- and spin-separation for computing the Dirac-Coulomb-Gaunt Hartree-Fock ground state, with a minimal floating-point-operation count algorithm. Furthermore, this approach also allows one to explicitly separate different spin physics from the two-body interactions, such as spin-free, spin-orbit, and the spin-spin contributions. Additionally, we use this formalism to examine relativistic trends in the periodic table, and analyze the basis set dependence of atomic gold and gold dimer systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

FDE-vdW: A van der Waals inclusive subsystem density-functional theory

We present a formally exact van der Waals inclusive electronic structure theory, called FDE-vdW, based on the Frozen Density Embedding formulation of subsystem Density-Functional Theory. In subsystem DFT, the energy functional is composed of subsystem additive and non-additive terms. We show that an appropriate definition of the long-range correlation energy is given by the value of the non-additive correlation functional. This functional is evaluated using the fluctuation–dissipation theorem aided by a formally exact decomposition of the response functions into subsystem contributions. FDE-vdW is derived in detail and several approximate schemes are proposed, which lead to practical implementations of the method. We show that FDE-vdW is Casimir-Polder consistent, i.e., it reduces to the generalized Casimir-Polder formula for asymptotic inter-subsystems separations. Pilot calculations of binding energies of 13 weakly bound complexes singled out from the S22 set show a dramatic improvement upon semilocal subsystem DFT, provided that an appropriate exchange functional is employed. The convergence of FDE-vdW with basis set size is discussed, as well as its dependence on the choice of associated density functional approximant.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Energy-Casimir, dynamically accessible, and Lagrangian stability of extended magnetohydrodynamic equilibria

The formal stability analysis of Eulerian extended magnetohydrodynamics (XMHD) equilibria is considered within the noncanonical Hamiltonian framework by means of the energy-Casimir variational principle and the dynamically accessible stability method. Specifically, we find explicit sufficient stability conditions for axisymmetric XMHD and Hall MHD (HMHD) equilibria with toroidal flow and for equilibria with arbitrary flow under constrained perturbations. The dynamically accessible, second-order variation of the Hamiltonian, which can potentially provide explicit stability criteria for generic equilibria, is also obtained. Moreover, we examine the Lagrangian stability of the general quasineutral two-fluid model written in terms of MHD-like variables, by finding the action and the Hamiltonian functionals of the linearized dynamics, working within a mixed Lagrangian-Eulerian framework. Upon neglecting electron mass, we derive a HMHD energy principle, and in addition, the perturbed induction equation arises from Hamilton’s equations of motion in view of a consistency condition for the relation between the perturbed magnetic potential and the canonical variables.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Calculation of spin–orbit couplings using RASCI spinless one-particle density matrices: Theory and applications

Here we present the formalism and implementation for calculations of spin–orbit couplings (SOCs) using the Breit–Pauli Hamiltonian and non-relativistic wave functions described by the restricted active space configuration interaction (RASCI) method with general excitation operators of spin-conserving spin-flipping, ionizing, and electron-attaching types. The implementation is based on the application of the Wigner–Eckart theorem within the spin space, which enables the calculation of the entire SOC matrix based on the explicit calculation of just one transition between the two spin multiplets. Numeric results for a diverse set of atoms and molecules highlight the importance of a balanced treatment of correlation and adequate basis sets and illustrate the overall robust performance of RASCI SOCs. The new implementation is a useful addition to the methodological toolkit for studying spin-forbidden processes and molecular magnetism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The theory of stochastic cosmological lensing

On the scale of the light beams subtended by small sources, e.g. supernovae, matter cannot be accurately described as a fluid, which questions the applicability of standard cosmic lensing to those cases. In this article, we propose a new formalism to deal with small-scale lensing as a diffusion process: the Sachs and Jacobi equations governing the propagation of narrow light beams are treated as Langevin equations. We derive the associated Fokker-Planck-Kolmogorov equations, and use them to deduce general analytical results on the mean and dispersion of the angular distance. This formalism is applied to random Einstein-Straus Swiss-cheese models, allowing us to: (1) show an explicit example of the involved calculations; (2) check the validity of the method against both ray-tracing simulations and direct numerical integration of the Langevin equation. As a byproduct, we obtain a post-Kantowski-Dyer-Roeder approximation, accounting for the effect of tidal distortions on the angular distance, in excellent agreement with numerical results. Besides, the dispersion of the angular distance is correctly reproduced in some regimes.

79 ASTRONOMY AND ASTROPHYSICS↗

On the correspondence between barrier crossing, peak-background split and local biasing

Several, apparently distinct, formalisms exist in the literature for predicting the clustering of dark matter halos. It has been noticed on a case-by-case basis that the predictions of these different methods agree in specific examples, but there is no general proof that they are equivalent. Here, we give a simple proof of the mathematical equivalence of barrier crossing, peak-background split, and local biasing.

79 ASTRONOMY AND ASTROPHYSICS↗

Two- and three-meson scattering amplitudes with physical quark masses from lattice QCD

We study systems of two and three mesons composed of pions and kaons at maximal isospin using four CLS ensembles with 𝑎 ≈ 0.063 fm, including one with approximately physical quark masses. Using the stochastic Laplacian-Heaviside method, we determine the energy spectrum of these systems including many levels in different momentum frames and irreducible representations. Using the relativistic two- and three-body finite-volume formalism, we constrain the two- and three-meson K matrices, including not only the leading 𝑠 wave, but also 𝑝 and 𝑑 waves. By solving the three-body integral equations, we determine, for the first time, the physical-point scattering amplitudes for 3⁢𝜋 + , 3⁢𝐾 + , 𝜋 + ⁢𝜋 + ⁢𝐾 + , and 𝐾 + ⁢𝐾 + ⁢𝜋 + systems. These are determined for total angular momentum 𝐽 𝑃 = 0 − , 1 + , and 2 − . We also obtain accurate results for 2⁢𝜋 + , 𝜋 + ⁢𝐾 + , and 2⁢𝐾 + phase shifts. We compare our results to chiral perturbation theory and to phenomenological fits.

FOS: Physical sciences↗

MO-D-213-07: RadShield: Semi- Automated Calculation of Air Kerma Rate and Barrier Thickness

Purpose: To develop the first Java-based semi-automated calculation program intended to aid professional radiation shielding design. Air-kerma rate and barrier thickness calculations are performed by implementing NCRP Report 147 formalism into a Graphical User Interface (GUI). The ultimate aim of this newly created software package is to reduce errors and improve radiographic and fluoroscopic room designs over manual approaches. Methods: Floor plans are first imported as images into the RadShield software program. These plans serve as templates for drawing barriers, occupied regions and x-ray tube locations. We have implemented sub-GUIs that allow the specification in regions and equipment for occupancy factors, design goals, number of patients, primary beam directions, source-to-patient distances and workload distributions. Once the user enters the above parameters, the program automatically calculates air-kerma rate at sampled points beyond all barriers. For each sample point, a corresponding minimum barrier thickness is calculated to meet the design goal. RadShield allows control over preshielding, sample point location and material types. Results: A functional GUI package was developed and tested. Examination of sample walls and source distributions yields a maximum percent difference of less than 0.1% between hand-calculated air-kerma rates and RadShield. Conclusion: The initial results demonstrated that RadShield calculates air-kerma rates and required barrier thicknesses with reliable accuracy and can be used to make radiation shielding design more efficient and accurate. This newly developed approach differs from conventional calculation methods in that it finds air-kerma rates and thickness requirements for many points outside the barriers, stores the information and selects the largest value needed to comply with NCRP Report 147 design goals. Floor plans, parameters, designs and reports can be saved and accessed later for modification and recalculation. We have confirmed that this software accurately calculates air-kerma rates and required barrier thicknesses for diagnostic radiography and fluoroscopic rooms.

07 ISOTOPE AND RADIATION SOURCES↗

53BP1 Repair Kinetics for Prediction of In Vivo Radiation Susceptibility in 15 Mouse Strains

We present a novel mathematical formalism to predict the kinetics of DNA damage repair after exposure to both low- and high-LET radiation (X rays; 350 MeV/n 40 Ar; 600 MeV/n 56 Fe). Our method is based on monitoring DNA damage repair protein 53BP1 that forms radiation-induced foci (RIF) at locations of DNA double-strand breaks (DSB) in the nucleus and comparing its expression in primary skin fibroblasts isolated from 15 mice strains. We previously reported strong evidence for clustering of nearby DSB into single repair units as opposed to the classic "contact-first" model where DSB are considered immobile. Here we apply this clustering model to evaluate the number of remaining RIF over time. We also show that the newly introduced kinetic metrics can be used as surrogate biomarkers for in vivo radiation toxicity, with potential applications in radiotherapy and human space exploration. In particular, we observed an association between the characteristic time constant of RIF repair measured in vitro and survival levels of immune cells collected from irradiated mice. Moreover, the speed of DNA damage repair correlated not only with radiation-induced cellular survival in vivo, but also with spontaneous cancer incidence data collected from the Mouse Tumor Biology database, suggesting a relationship between the efficiency of DSB repair after irradiation and cancer risk.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Building a Predictive Fission Rate Model

Nuclear fission, and specifically the rate at which fission occurs compared to other types of reactions, is a crucial piece in the puzzle of the origin of the elements in the universe. Fission in astrophysical environments involves rare and exotic nuclei that cannot be studied in the laboratory, and we must therefore rely on model calculations. Yet all fission rates calculated today use a phenomenological (theoretical) model that was formulated in 1939, updated in 1953, and has remained essentially unchanged. Because the model contains many adjustable parameters, it has been successfully used to fit existing data, but in turn has very limited predictive power in cases where the data are poor or nonexistent. The goal of this project was to develop a novel approach that moves away from phenomenology to construct a fission-rate model built from microscopic ingredients: protons, neutrons, and their mutual interactions. The approach adopted in this work relied on the construction of a discrete basis of mean-field states that form paths through scission. The calculations were performed within the framework of the generator coordinate method. The project has produced a methodology for constructing the discrete basis states and identifying likely fission paths, as well as estimates of the energy partition between fragments and a formalism to calculate fission rates based on Fermi’s golden rule.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The evaluation of a 2D diode array in “magic phantom” for use in high dose rate brachytherapy pretreatment quality assurance

Purpose: High dose rate (HDR) brachytherapy is a treatment method that is used increasingly worldwide. The development of a sound quality assurance program for the verification of treatment deliveries can be challenging due to the high source activity utilized and the need for precise measurements of dwell positions and times. This paper describes the application of a novel phantom, based on a 2D 11 × 11 diode array detection system, named “magic phantom” (MPh), to accurately measure plan dwell positions and times, compare them directly to the treatment plan, determine errors in treatment delivery, and calculate absorbed dose. Methods: The magic phantom system was CT scanned and a 20 catheter plan was generated to simulate a nonspecific treatment scenario. This plan was delivered to the MPh and, using a custom developed software suite, the dwell positions and times were measured and compared to the plan. The original plan was also modified, with changes not disclosed to the primary authors, and measured again using the device and software to determine the modifications. A new metric, the “position–time gamma index,” was developed to quantify the quality of a treatment delivery when compared to the treatment plan. The MPh was evaluated to determine the minimum measurable dwell time and step size. The incorporation of the TG-43U1 formalism directly into the software allows for dose calculations to be made based on the measured plan. The estimated dose distributions calculated by the software were compared to the treatment plan and to calibrated EBT3 film, using the 2D gamma analysis method. Results: For the original plan, the magic phantom system was capable of measuring all dwell points and dwell times and the majority were found to be within 0.93 mm and 0.25 s, respectively, from the plan. By measuring the altered plan and comparing it to the unmodified treatment plan, the use of the position–time gamma index showed that all modifications made could be readily detected. The MPh was able to measure dwell times down to 0.067 ± 0.001 s and planned dwell positions separated by 1 mm. The dose calculation carried out by the MPh software was found to be in agreement with values calculated by the treatment planning system within 0.75%. Using the 2D gamma index, the dose map of the MPh plane and measured EBT3 were found to have a pass rate of over 95% when compared to the original plan. Conclusions: The application of this magic phantom quality assurance system to HDR brachytherapy has demonstrated promising ability to perform the verification of treatment plans, based upon the measured dwell positions and times. The introduction of the quantitative position–time gamma index allows for direct comparison of measured parameters against the plan and could be used prior to patient treatment to ensure accurate delivery.

60 APPLIED LIFE SCIENCES↗

SU-G-BRB-15: Verifications of Absolute and Relative Dosimetry of a Novel Stereotactic Breast Device: GammaPodTM

Purpose: A dedicated stereotactic breast radiotherapy device, GammaPod, was developed to treat early stage breast cancer. The first clinical unit was installed and commissioned at University of Maryland. We report our methodology of absolute dosimetry in multiple calibration conditions and dosimetric verifications of treatment plans produced by the system. Methods: GammaPod unit is comprised of a rotating hemi-spherical source carrier containing 36 Co-60 sources and a concentric tungsten collimator providing beams of 15 and 25 mm. Absolute dose calibration formalism was developed with modifications to AAPM protocols for unique geometry and different calibration medium (acrylic, polyethylene or liquid water). Breast cup-size specific and collimator output factors were measured and verified with respect to Monte-Carlo simulations for single isocenter plans. Multiple isocenter plans were generated for various target size, location and cup-sizes in phantoms and 20 breast cancer patients images. Stereotactic mini-farmer chamber, OSL and TLD detectors as well as radio-chromic films were used for dosimetric measurements. Results: At the time of calibration (1/14/2016), absolute dose rate of the GammaPod was established to be 2.10 Gy/min in acrylic for 25 mm for sources installed in March 2011. Output factor for 15 mm collimator was measured to be 0.950. Absolute dose calibration was independently verified by IROC-Houston with a TLD/Institution ratio of 0.99. Cup size specific output measurements in liquid water for single isocenter were found to be within 3.0% of MC simulations. Point-dose measurements of multiple isocenter treatment plans were found to be within −1.0 ± 1.2 % of treatment planning system while 2-dimensional gamma analysis yielded a pass rate of 97.9 ± 2.2 % using gamma criteria of 3% and 2mm. Conclusion: The first GammaPod treatment unit for breast stereotactic radiotherapy was successfully installed, calibrated and commissioned for patient treatments. An absolute dosimetry and dosimetric verification protocols were successfully created.

60 APPLIED LIFE SCIENCES↗

Structural and transport properties of double perovskite Dy{sub 2}NiMnO{sub 6}

Highlights: • Sol–gel citrate method is used to prepare the double perovskite Dy{sub 2}NiMnO{sub 6}. • Structure and dielectric relaxation of the sample are studied for nano and bulk phases. • The relaxation mechanism of the sample is modeled by Cole–Cole equation. • With increasing sintering temperature conductivity increases. • Electronic structures and magnetic properties have been studied by DFT calculations. - Abstract: The double perovskite oxide Dy{sub 2}NiMnO{sub 6} (DNMO) is synthesized in nano and bulk phase by the sol–gel citrate method. The Rietveld refinement of X-ray diffraction pattern of the sample at room temperature shows the monoclinic P2{sub 1}/n phase. Dielectric relaxation of the sample is investigated in the impedance and electric modulus formalisms in the frequency range from 50 Hz to 1 MHz and in the temperature range from 253 to 415 K. The Cole–Cole model is used to explain the relaxation mechanism in DNMO. The frequency-dependent maxima in the imaginary part of impedance are found to obey an Arrhenius law with activation energy of 0.346 and 0.344 eV for nano and bulk DNMO, respectively. A significant increase in conductivity of bulk DNMO has been observed than that of the nanoceramic. Electronic structures and magnetic properties of DNMO have been studied by performing first principles calculation based on density functional theory.

36 MATERIALS SCIENCE↗

Systems and methods for determining optimal parameters for dynamic quantum clustering analyses

In the present work, quantum clustering is extended to provide a dynamical approach for data clustering using a time-dependent Schrodinger equation. To expedite computations, we can approximate the time-dependent Hamiltonian formalism by a truncated calculation within a set of Gaussian wave-functions (coherent states) centered around the original points. This allows for analytic evaluation of the time evolution of all such states, opening up the possibility of exploration of relationships among data points through observation of varying dynamical-distances among points and convergence of points into clusters. This formalism may be further supplemented by preprocessing, such as dimensional reduction through singular value decomposition and/or feature filtering. Additionally, the parameters of the analysis can be modified in order to improve the efficiency of the dynamic quantum clustering processes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Temperature-Dependent Configurational Entropy Calculations for Refractory High-Entropy Alloys

The cluster expansion formalism for alloys is used to construct surrogate models for three refractory high-entropy alloys (NbTiVZr, HfNbTaTiZr, and AlHfNbTaTiZr). These cluster expansion models are then used along with Monte Carlo methods and thermodynamic integration to calculate the configurational entropy of these refractory high-entropy alloys as a function of temperature. Many solid solution alloy design guidelines are based on the ideal entropy of mixing, which increases monotonically with N , the number of elements in the alloy. However, our results show that at low temperatures, the configurational entropy of these materials is largely independent of N , and the assumption described above only holds in the high-temperature limit. This suggests that alloy design guidelines based on the ideal entropy of mixing require further examination.

36 MATERIALS SCIENCE↗