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At least 1,117 records · Page 62

Bayesian calibration of thermodynamic models for the uptake of CO{sub 2} in supported amine sorbents using ab initio priors

A statistical methodology was applied to the simultaneous calibration and validation of thermodynamic models for the uptake of CO{sub 2} in mesoporous silica-supported amines. The methodology is Bayesian, and follows the procedure introduced by Kennedy and O'Hagan. One key aspect of the application presented is the use of quantum chemical calculations to define prior probability distributions for physical model parameters. Inclusion of this prior information proved to be crucial to the identifiability of model parameters against experimental thermogravimetric data. Through the statistical analysis, a quantitative assessment of the accuracy of various quantum chemical methods is produced. Another important aspect of the current approach is the conditioning of the model form discrepancy – a critical component of the Kennedy and O'Hagan methodology – to the experimental data in such a manner that it becomes an implicit function of the model parameters and thereby connected with the posterior distribution. It is shown that the inclusion of prior information in the analysis leads to a shifting of uncertainty from the posterior distribution for model parameters to this conditioned model form discrepancy. Prospects for more accurate model predictions and propagation of uncertainty in upscaling and extrapolation through a “model-plus-discrepancy” approach are discussed. The synthesis methods and thermogravimetric characterization of hybrid grafted/impregnated mesoporous silica-supported amine sorbents are presented, along with the details of the quantum chemical study, which shows that a carbamic acid–base acceptor complex is the most stable form of adsorbed CO{sub 2} in both alkanol- and ethyleneamines.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analytical nuclear gradients for the range-separated many-body dispersion model of noncovalent interactions

An accurate treatment of the long-range electron correlation energy, including van der Waals (vdW) or dispersion interactions, is essential for describing the structure, dynamics, and function of a wide variety of systems. Among the most accurate models for including dispersion into density functional theory (DFT) is the range-separated many-body dispersion (MBD) method [A. Ambrosetti et al., J. Chem. Phys., 2014, 140, 18A508], in which the correlation energy is modeled at short-range by a semi-local density functional and at long-range by a model system of coupled quantum harmonic oscillators. In this work, we develop analytical gradients of the MBD energy with respect to nuclear coordinates, including all implicit coordinate dependencies arising from the partitioning of the charge density into Hirshfeld effective volumes. To demonstrate the efficiency and accuracy of these MBD gradients for geometry optimizations of systems with intermolecular and intramolecular interactions, we optimized conformers of the benzene dimer and isolated small peptides with aromatic side-chains. We find excellent agreement with the wavefunction theory reference geometries of these systems (at a fraction of the computational cost) and find that MBD consistently outperforms the popular TS and D3(BJ) dispersion corrections. To demonstrate the performance of the MBD model on a larger system with supramolecular interactions, we optimized the C 60 @C 60 H 28 buckyball catcher host–guest complex. In our analysis, we also find that neglecting the implicit nuclear coordinate dependence arising from the charge density partitioning, as has been done in prior numerical treatments, leads to an unacceptable error in the MBD forces, with relative errors of ~20% (on average) that can extend well beyond 100%.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coarse-grained molecular dynamics simulation of the interface behaviour and self-assembly of CTAB cationic surfactants

Here, we study the behaviour at interfaces and the micelle self-assembly of a cationic surfactant (CTAB) by Molecular Dynamics (MD) simulations of coarse-grained models. We consider both the standard (with explicit water) Martini force field and the implicit solvent version of the Martini force field (Dry Martini). First, we study the behaviour of CTAB at a water/vacuum interface, at a water/organic solvent interface and in a pre-assembled CTAB micelle using both standard and Dry Martini and all-atomic simulations. Our results indicate that there are significant quantitative differences between the predictions of the two models. Interestingly, implicit solvent simulations with Dry Martini show good quantitative agreement with all-atomic MD simulations, better than explicit solvent Martini MD simulations. The computational efficiency of the Martini and Dry Martini models allowed us to study the self-assembly of CTAB in a large system with many micelles. We observe the self-assembly of CTAB into micelles and also the exchange of CTAB molecules between micelles by events such as micelle fusion and fission which are difficult to observe in all-atomic MD simulations due to the time and length scales involved. Under the studied conditions, both Martini models predict a rather different self-assembly behaviour. The standard Martini model predicts a final equilibrium state with spherical micelles with an average size of ≈70 CTAB molecules. In contrast, the Dry Martini model predicts the formation of large tubular micelles with ≈330 CTAB molecules. Compared with experiments, standard Martini and Dry Martini underestimate and overestimate, respectively, the micelle size.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Aqueous-phase effects on ethanol decomposition over Ru-based catalysts

The effects of an aqueous phase on ethanol decomposition for hydrogen production over a Ru(0001) catalyst surface model have been investigated from first principles. Solvent effects on the reaction mechanism and kinetic parameters have been quantified with the help of a microkinetic reactor model, density functional theory, and an implicit solvation scheme (iSMS). Our calculations indicate that in both vapor- and aqueous-phase reaction environments, the ethanol decomposition starts with acetaldehyde formation on the surface, some of which further dehydrogenates to ketenyl species (CHCO), where the C–C bond cleaves to form methylidyne (CH) and CO. In the vapor phase, adsorbed CH gets hydrogenated to methane, and CO desorbs or undergoes methanation reducing the amount of hydrogen produced. In contrast, under aqueous phase reaction conditions, the methanation is inhibited, and the water–gas shift (WGS) reaction is accelerated, leading to complete conversion of CO to CO 2 and H 2 . Furthermore, calculations indicate that the observed reaction behavior under aqueous phase reforming conditions originates primarily from the higher water chemical potential, and implicit solvent models predict only a small solvation effect.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Parallelised ROOT for Future HEP Data Processing

In the coming years, HEP data processing will need to exploit parallelism on present and future hardware resources to sustain the bandwidth requirements. As one of the cornerstones of the HEP software ecosystem, ROOT embraced an ambitious parallelisation plan which delivered compelling results. In this contribution the strategy is characterised as well as its evolution in the medium term. The units of the ROOT framework are discussed where task and data parallelism have been introduced, with runtime and scaling measurements. We will give an overview of concurrent operations in ROOT, for instance in the areas of I/O (reading and writing of data), fitting / minimization, and data analysis. This paper introduces the programming model and use cases for explicit and implicit parallelism, where the former is explicit in user code and the latter is implicitly managed by ROOT internally.

97 MATHEMATICS AND COMPUTING↗

Modeling time-coincident ultrafast electron transfer and solvation processes at molecule-semiconductor interfaces

Kinetic models based on Fermi's Golden Rule are commonly employed to understand photoinduced electron transfer dynamics at molecule-semiconductor interfaces. Implicit in such second-order perturbative descriptions is the assumption that nuclear relaxation of the photoexcited electron donor is fast compared to electron injection into the semiconductor. This approximation breaks down in systems where electron transfer transitions occur on 100-fs time scale. Here, we present a fourth-order perturbative model that captures the interplay between time-coincident electron transfer and nuclear relaxation processes initiated by light absorption. The model consists of a fairly small number of parameters, which can be derived from standard spectroscopic measurements (e.g., linear absorbance, fluorescence) and/or first-principles electronic structure calculations. Insights provided by the model are illustrated for a two-level donor molecule coupled to both (i) a single acceptor level and (ii) a density of states (DOS) calculated for TiO{sub 2} using a first-principles electronic structure theory. These numerical calculations show that second-order kinetic theories fail to capture basic physical effects when the DOS exhibits narrow maxima near the energy of the molecular excited state. Overall, we conclude that the present fourth-order rate formula constitutes a rigorous and intuitive framework for understanding photoinduced electron transfer dynamics that occur on the 100-fs time scale.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Issues in measure-preserving three dimensional flow integrators: Self-adjointness, reversibility, and non-uniform time stepping

Properties of integration schemes for solenoidal fields in three dimensions are studied, with a focus on integrating magnetic field lines in a plasma using adaptive time stepping. It is shown that implicit midpoint (IM) and a scheme we call three-dimensional leapfrog (LF) can do a good job (in the sense of preserving KAM tori) of integrating fields that are reversible, or (for LF) have a “special divergence-free” (SDF) property. We review the notion of a self-adjoint scheme, showing that such schemes are at least second order accurate and can always be formed by composing an arbitrary scheme with its adjoint. We also review the concept of reversibility, showing that a reversible but not exactly volume-preserving scheme can lead to a fractal invariant measure in a chaotic region, although this property may not often be observable. We also show numerical results indicating that the IM and LF schemes can fail to preserve KAM tori when the reversibility property (and the SDF property for LF) of the field is broken. We discuss extensions to measure preserving flows, the integration of magnetic field lines in a plasma and the integration of rays for several plasma waves. The main new result of this paper relates to non-uniform time stepping for volume-preserving flows. We investigate two potential schemes, both based on the general method of Feng and Shang [Numer. Math. 71, 451 (1995)], in which the flow is integrated in split time steps, each Hamiltonian in two dimensions. The first scheme is an extension of the method of extended phase space, a well-proven method of symplectic integration with non-uniform time steps. This method is found not to work, and an explanation is given. The second method investigated is a method based on transformation to canonical variables for the two split-step Hamiltonian systems. This method, which is related to the method of non-canonical generating functions of Richardson and Finn [Plasma Phys. Controlled Fusion 54, 014004 (2012)], appears to work very well.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

On the representation of many-body interactions in water

Recent work has shown that the many-body expansion of the interaction energy can be used to develop analytical representations of global potential energy surfaces (PESs) for water. In this study, the role of short- and long-range interactions at different orders is investigated by analyzing water potentials that treat the leading terms of the many-body expansion through implicit (i.e., TTM3-F and TTM4-F PESs) and explicit (i.e., WHBB and MB-pol PESs) representations. It is found that explicit short-range representations of 2-body and 3-body interactions along with a physically correct incorporation of short- and long-range contributions are necessary for an accurate representation of the water interactions from the gas to the condensed phase. Similarly, a complete many-body representation of the dipole moment surface is found to be crucial to reproducing the correct intensities of the infrared spectrum of liquid water.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Solvent controlled ion association in structured copolymers: Molecular dynamics simulations in dilute solutions

Tailoring the nature of individual segments within ion containing block co-polymers is one critical design tool to achieve desired properties. The local structure including the size and distribution of the ionic blocks, as well as the long range correlations, are crucial for their transport ability. Here, we present molecular dynamics simulations on the effects of varying the concentrations of the ionizable groups on the conformations of pentablock ionomer that consist of a center block of ionic sulfonated styrene tethered to polyethylene and terminated by a bulky substituted styrene in dilute solutions. Sulfonation fractions f (0 ≤ f ≤ 0.55), spanning the range from ionomer to polyelectrolytes, were studied. Results for the equilibrium conformation of the chains in water and a 1:1 mixture of cyclohexane and heptane are compared to that in implicit poor solvents with dielectric constants ε = 1.0 and 77.73. In water, the pentablock collapses with the sulfonated groups on the outer surface. As f increases, the ionic, center block increasingly segregates from the hydrophobic regions. In the 1:1 mixture of cyclohexane and heptane, the flexible blocks swell, while the center ionic block collapses for f > 0. For f = 0, all blocks swell. In both implicit poor solvents, the pentablock collapses into a nearly spherical shape for all f . In conclusion, the sodium counterions disperse widely throughout the simulation cell for both water and ε = 77.73, whereas for ε = 1.0 and mixture of cyclohexane and heptane, the counterions largely condense onto the collapsed pentablock.

74 ATOMIC AND MOLECULAR PHYSICS↗

Electronic coupling through natural amino acids

Myriad scientific domains concern themselves with biological electron transfer (ET) events that span across vast scales of rate and efficiency through a remarkably fine-tuned integration of amino acid (AA) sequences, electronic structure, dynamics, and environment interactions. Within this intricate scheme, many questions persist as to how proteins modulate electron-tunneling properties. To help elucidate these principles, we develop a model set of peptides representing the common α-helix and β-strand motifs including all natural AAs within implicit protein-environment solvation. Using an effective Hamiltonian strategy with density functional theory, we characterize the electronic coupling through these peptides, furthermore considering side-chain dynamics. For both motifs, predictions consistently show that backbone-mediated electronic coupling is distinctly sensitive to AA type (aliphatic, polar, aromatic, negatively charged and positively charged), and to side-chain orientation. The unique properties of these residues may be employed to design activated, deactivated, or switch-like superexchange pathways. Electronic structure calculations and Green’s function analyses indicate that localized shifts in the electron density along the peptide play a role in modulating these pathways, and further substantiate the experimentally observed behavior of proline residues as superbridges. The distinct sensitivities of tunneling pathways to sequence and conformation revealed in this electronic coupling database help improve our fundamental understanding of the broad diversity of ET reactivity and provide guiding principles for peptide design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Determination of the critical micelle concentration in simulations of surfactant systems

Alternative methods for determining the critical micelle concentration (cmc) are investigated using canonical and grand canonical Monte Carlo simulations of a lattice surfactant model. A common measure of the cmc is the “free” (unassociated) surfactant concentration in the presence of micellar aggregates. Many prior simulations of micellizing systems have observed a decrease in the free surfactant concentration with overall surfactant loading for both ionic and nonionic surfactants, contrary to theoretical expectations from mass-action models of aggregation. In the present study, we investigate a simple lattice nonionic surfactant model in implicit solvent, for which highly reproducible simulations are possible in both the canonical (NVT) and grand canonical (μVT) ensembles. We confirm the previously observed decrease of free surfactant concentration at higher overall loadings and propose an algorithm for the precise calculation of the excluded volume and effective concentration of unassociated surfactant molecules in the accessible volume of the solution. We find that the cmc can be obtained by correcting the free surfactant concentration for volume exclusion effects resulting from the presence of micellar aggregates. We also develop an improved method for determination of the cmc based on the maximum in curvature for the osmotic pressure curve determined from μVT simulations. Excellent agreement in cmc and other micellar properties between NVT and μVT simulations of different system sizes is observed. The methodological developments in this work are broadly applicable to simulations of aggregating systems using any type of surfactant model (atomistic/coarse grained) or solvent description (explicit/implicit)

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

One-baryon spectrum and analytical properties of one-baryon dispersion curves in 3 + 1 dimensional strongly coupled lattice QCD with three flavors

Considering a 3 + 1 dimensional lattice quantum chromodynamics (QCD) model defined with the improved Wilson action, three flavors, and 4 × 4 Dirac spin matrices, in the strong coupling regime, we reanalyze the question of the existence of the eightfold way baryons and complete our previous work where the existence of isospin octet baryons was rigorously solved. Here, we show the existence of isospin decuplet baryons which are associated with isolated dispersion curves in the subspace of the underlying quantum mechanical Hilbert space with vectors constructed with an odd number of fermion and antifermion basic quark and antiquark fields. Moreover, smoothness properties for these curves are obtained. The present work deals with a case for which the traditional method to solve the implicit equation for the dispersion curves, based on the use of the analytic implicit function theorem, cannot be applied. We do not have only one but two solutions for each one-baryon decuplet sector with fixed spin third component. Instead, we apply the Weierstrass preparation theorem, which also provides a general method for the general degenerate case. This work is completed by analyzing a spectral representation for the two-baryon correlations and providing the leading behaviors of the field strength normalization and the mass of the spectral contributions with more than one-particle. These are needed results for a rigorous analysis of the two-baryon and meson-baryon particle spectra.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Varying stopping and self-focusing of intense proton beams as they heat solid density matter

Transport of intense proton beams in solid-density matter is numerically investigated using an implicit hybrid particle-in-cell code. Both collective effects and stopping for individual beam particles are included through the electromagnetic fields solver and stopping power calculations utilizing the varying local target conditions, allowing self-consistent transport studies. Two target heating mechanisms, the beam energy deposition and Ohmic heating driven by the return current, are compared. The dependences of proton beam transport in solid targets on the beam parameters are systematically analyzed, i.e., simulations with various beam intensities, pulse durations, kinetic energies, and energy distributions are compared. The proton beam deposition profile and ultimate target temperature show strong dependence on intensity and pulse duration. A strong magnetic field is generated from a proton beam with high density and tight beam radius, resulting in focusing of the beam and localized heating of the target up to hundreds of eV.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Knowledge represented using RDF semantic network in the concept of semantic web

The RDF(S) model has been declared as the basic model to capture knowledge of the semantic web. It provides a common and flexible way to decompose composed knowledge to elementary statements, which can be represented by RDF triples or by RDF graph vectors. From the logical point of view, elements of knowledge can be expressed using at most binary predicates, which can be converted to RDF-triples or graph vectors. However, it is not able to capture implicit knowledge representable by logical formulas. This contribution shows how existing approaches (semantic networks and clausal form logic) can be combined together with RDF to obtain RDF-compatible system with ability to represent implicit knowledge and inference over knowledge base.

97 MATHEMATICS AND COMPUTING↗

Full particle orbit effects in regular and stochastic magnetic fields

Here we present a numerical study of charged particle motion in a time-independent magnetic field in cylindrical geometry. The magnetic field model consists of an unperturbed reversed-shear (non-monotonic q-profile) helical part and a perturbation consisting of a superposition of modes. Contrary to most of the previous studies, the particle trajectories are computed by directly solving the full Lorentz force equations of motion in a six-dimensional phase space using a sixth-order, implicit, symplectic Gauss-Legendre method. The level of stochasticity in the particle orbits is diagnosed using averaged, effective Poincare sections. It is shown that when only one mode is present, the particle orbits can be stochastic even though the magnetic field line orbits are not stochastic (i.e., fully integrable). The lack of integrability of the particle orbits in this case is related to separatrix crossing and the breakdown of the global conservation of the magnetic moment. Some perturbation consisting of two modes creates resonance overlapping, leading to Hamiltonian chaos in magnetic field lines. Then, the particle orbits exhibit a nontrivial dynamics depending on their energy and pitch angle. It is shown that the regions where the particle motion is stochastic decrease as the energy increases. The non-monotonicity of the q-profile implies the existence of magnetic ITBs (internal transport barriers) which correspond to shearless flux surfaces located in the vicinity of the q-profile minimum. It is shown that depending on the energy, these magnetic ITBs might or might not confine particles. That is, magnetic ITBs act as an energy-dependent particle confinement filter. Magnetic field lines in reversed-shear configurations exhibit topological bifurcations (from homoclinic to heteroclinic) due to separatrix reconnection. Finally, we show that a similar but more complex scenario appears in the case of particle orbits that depend in a non-trivial way on the energy and pitch angle of the particles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

Here, we develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules, to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two-dimensional Turing-like pattern and examine the effect of fluctuations on three-dimensional chemical front propagation. Furthermore, by comparing stochastic simulations to deterministic reaction-diffusion simulations, we show that fluctuations accelerate pattern formation in spatially homogeneous systems and lead to a qualitatively different disordered pattern behind a traveling wave.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Combining the ensemble and Franck-Condon approaches for calculating spectral shapes of molecules in solution

The correct treatment of vibronic effects is vital for the modeling of absorption spectra of many solvated dyes. Vibronic spectra for small dyes in solution can be easily computed within the Franck-Condon approximation using an implicit solvent model. However, implicit solvent models neglect specific solute-solvent interactions on the electronic excited state. On the other hand, a straightforward way to account for solute-solvent interactions and temperature-dependent broadening is by computing vertical excitation energies obtained from an ensemble of solute-solvent conformations. Ensemble approaches usually do not account for vibronic transitions and thus often produce spectral shapes in poor agreement with experiment. Here we address these shortcomings by combining zero-temperature vibronic fine structure with vertical excitations computed for a room-temperature ensemble of solute-solvent configurations. In this combined approach, all temperature-dependent broadening is treated classically through the sampling of configurations and quantum mechanical vibronic contributions are included as a zero-temperature correction to each vertical transition. In our calculation of the vertical excitations, significant regions of the solvent environment are treated fully quantum mechanically to account for solute-solvent polarization and charge-transfer. For the Franck-Condon calculations, a small amount of frozen explicit solvent is considered in order to capture solvent effects on the vibronic shape function. We test the proposed method by comparing calculated and experimental absorption spectra of Nile red and the green fluorescent protein chromophore in polar and non-polar solvents. For systems with strong solute-solvent interactions, the combined approach yields significant improvements over the ensemble approach. For systems with weak to moderate solute-solvent interactions, both the high-energy vibronic tail and the width of the spectra are in excellent agreement with experiments

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On the molecular correlations that result in field-dependent conductivities in electrolyte solutions

Employing recent advances in response theory and nonequilibrium ensemble reweighting, we study the dynamic and static correlations that give rise to an electric field-dependent ionic conductivity in electrolyte solutions. We consider solutions modeled with both implicit and explicit solvents, with different dielectric properties, and at multiple concentrations. Implicit solvent models at low concentrations and small dielectric constants exhibit strongly field-dependent conductivities. We compare these results to Onsager-Wilson theory of the Wien effect, which provides a qualitatively consistent prediction at low concentrations and high static dielectric constants but is inconsistent away from these regimes. The origin of the discrepancy is found to be increased ion correlations under these conditions. Explicit solvent effects act to suppress nonlinear responses, yielding a weakly field-dependent conductivity over the range of physically realizable field strengths. By decomposing the relevant time correlation functions, we find that the insensitivity of the conductivity to the field results from the persistent frictional forces on the ions from the solvent. Our findings illustrate the utility of nonequilibrium response theory in rationalizing nonlinear transport behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗