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At least 397 records · Page 22

Impact of Surface Chemistry of Ultrasmall Superparamagnetic Iron Oxide Nanoparticles on Protein Corona Formation and Endothelial Cell Uptake, Toxicity, and Barrier Function

Ultrasmall superparamagnetic iron oxide nanoparticles (USPIONs) have been investigated for biomedical applications, including novel contrast agents, magnetic tracers for tumor imaging, targeted drug delivery vehicles, and magneto-mechanical actuators for hyperthermia and thrombolysis. Despite significant progress, recent clinical reports have raised concerns regarding USPION safety related to endothelial cell dysfunction; however, there is limited information on factors contributing to these clinical responses. The influence of USPION surface chemistry on nanoparticle interactions with proteins may impact endothelial cell function leading to adverse responses. Therefore, the goal of this study was to assess the effects of carboxyl-functionalized USPION (CU) or amine-functionalized USPION (AU) (approximately 30 nm diameter) on biological responses in human coronary artery endothelial cells. Increased protein adsorption was observed for AU compared with CU after exposure to serum proteins. Exposure to CU, but not AU, resulted in a concentration-dependent decrease in cell viability and perinuclear accumulation inside cytoplasmic vesicles. Internalization of CU was correlated with endothelial cell functional changes under non-cytotoxic conditions, as evidenced by a marked decreased expression of endothelial-specific adhesion proteins (eg, vascular endothelial-cadherin and platelet endothelial cell adhesion molecule-1) and increased endothelial permeability. Evaluation of downstream signaling indicated endothelial permeability is associated with actin cytoskeleton remodeling, possibly elicited by intracellular events involving reactive oxygen species, calcium ions, and the nanoparticle cellular uptake pathway. This study demonstrated that USPION surface chemistry significantly impacts protein adsorption and endothelial cell uptake, viability, and barrier function. This information will advance the current toxicological profile of USPION and improve development, safety assessment, and clinical outcomes of USPION-enabled medical products.

Toxicology↗

Ground state wave functions for single-band Hubbard models from the Gutzwiller conjugate gradient minimisation theory

The Gutzwiller conjugate gradient minimisation (GCGM) theory is an ab initio quantum many-body theory for computing the ground-state properties of infinite systems. Previous applications of GCGM provides satisfying accuracy of ground-state energy of Hubbard models. In the current work, we address the problem of whether the obtained wave function is a good approximation for the true ground state by comparing the correlation functions with the benchmark data. Additionally, our results confirms the accuracy of the reproduced ground state of the regular Hubbard model, but with some exception for the frustrated Hubbard model.

74 ATOMIC AND MOLECULAR PHYSICS↗

Evaluating the Feasibility of Measuring and Analyzing Strain Caused by Changes in Barometric Pressure in the Vadose Zone

Changes in barometric pressure propagate into the subsurface where they can affect water level measurements in wells and cause vertical strain. Previous strain sensors were developed to measure vertical strain, but they were limited to measurements at a single depth, making it difficult to evaluate strains from a migrating pressure wave. Technology known as Coherence-length-gated Microwave Photonics Interferometry (CMPI) uses optical fiber sensors to measure strain at multiple locations. It has the potential to detect strain caused by variations in barometric pressure at multiple depths in the subsurface. The goal of this study is to evaluate the feasibility of using this technology to record the changes in vertical strain in the vadose zone from small fluctuations in air pressure. Propagation of these air pressure fluctuations is affected by hydrogeological properties such as water content and permeability. A second goal of this study is to evaluate how these properties affect the air pressure distribution, strain, and gas-phase diffusivity with a long-term goal of using strain to monitor the vadose zone. The focus of this study is on a suite of laboratory experiments that used a sand-filled column with an open head space. The CMPI fiber was packaged and embedded along the axis of the column to measure the strain at multiple locations while air pressure transducers were installed through the wall of the column. Small periodic fluctuations in air pressure, similar to barometric pressure fluctuations, were created in the head space of the column using an audio driven speaker driven at 4 Hz using a sinusoidal signal created by a function generator. Then, the fluctuations propagated along the column where they were measured by the transducers and recorded as functions of time. Initial tests were conducted using dry sand, but then additional tests were conducted after injecting water into the column, which changed the hydrologic and mechanical properties. Another experiment was conducted after creating a thin barrier to air flow, which was designed to simulate a thin layer of saturated ground during rainfall. A final experiment was conducted by changing the grain size of the material to create a heterogeneity in the upper half of the column. The suite of six experiments was conducted to highlight effects of variations in water content and heterogeneities on air pressure and vertical strain. Numerical simulations were also created to evaluate the laboratory data and to provide a baseline analysis for the results. The numerical simulations used the governing equations to linear poroelasticity and two-phase flow with boundary conditions representing the experiments. The conceptual model for strain caused by barometric pressure recognizes that a fluctuating barometric pressure causes fluctuations in the air pore pressure that decrease in amplitude and lag in time with increase depth. The pressure distribution results in two different loads that cause strain: 1.) a mechanical load as the barometric pressure acts on the ground surface; and 2.) pressure loading in the pore space. The results show that the total vertical strain is a contribution of both of these loads, and this is the strain that was observed in the laboratory. The lab experiments show that both air pressure and strain vary as sinusoids that propagate with depth. The amplitude of the air pressure and strain decrease as a function of depth in all the conditions that were evaluate. For example, in the dry sand, the amplitude of the air pressure decreases from 25 Pa at the head space to 5 Pa at a depth of 70 cm, whereas the amplitude of the strain decreases from 0.15 to 0.06 µε over the same depth interval. In many cases the amplitudes decrease is approximately negative exponential functions of depth. When water was injected into the sand and the saturation increased, the amplitude of the air pressure increased in the partially saturated sand but decreased sharply to zero where the soil was saturated. The strain decreased with depth, but the transition from partially to fully saturated conditions had little effect on the strain profile, even though it had a major effect on the air pressure. This apparently is because strain is caused by variations in both water and air pressure. The fluctuating air pressure caused the water pressure to fluctuate, which caused strain throughout the column. Phase delay of the air pressure and the strain both increase as linear to bi-linear functions of depth. The phase delays indicate that pressure propagates at a velocity of 7 to 8 m/s in dry or partially saturated sand, but it drops by more than an order of magnitude in the vicinity of the capillary fringe. The phase delays indicate the strain propagates faster than the pressure. The data indicate that the strain propagates from 1.2 to more than 4x faster than the pressure. Switching from sand to silt in the column caused the velocity of the pressure to drop by roughly half for both pressures, but curiously, it had little effect on the velocity of the strain.

54 ENVIRONMENTAL SCIENCES↗

Quasi-Stochastic Approximation and Off-Policy Reinforcement Learning: Preprint

The Robbins-Monro stochastic approximation algorithm is a foundation of many algorithmic frameworks for reinforcement learning and often an efficient approach to solving (or approximating the solution to) complex optimal control problems. In many cases, however, practitioners are unable to apply these techniques because of an inherent high variance. This paper aims to provide a general foundation for 'quasi-stochastic approximation,' in which all of the processes under consideration are deterministic, much like quasi-Monte Carlo for variance reduction in simulation. The variance reduction can be substantial, subject to tuning of pertinent parameters in the algorithm. This paper introduces a new coupling argument to establish the optimal rate of convergence provided the gain is sufficiently large. These results are established for linear models and tested also in nonideal settings. A major application of these general results is a new class of reinforcement learning algorithms for deterministic state space models. In this setting, the main contribution is a class of algorithms for approximating the value function for a given policy, using a different policy designed to introduce exploration.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Injection data analysis using material balance time for CO 2 storage capacity estimation in deep closed saline aquifers

Estimating the ultimate storage capacity of deep saline aquifers is important to address the formation potential to store the envisioned large volumes of CO 2 . Injection data (i.e. injection rate, bottomhole pressure, and cumulative injected volume of CO 2 ) are routinely recorded during storage operations. These data contain valuable information on the subsurface (e.g. the reservoir pore volume and the formation storage capacity) that can be extracted. In this paper, we present a two-step graphical technique to infer the pore volume and the ultimate storage capacity of closed saline aquifers by analyzing the available injection data. First, the pore volume is inferred through adapting the concept of the material balance time. Material balance time is an approximate superposition time function developed to interpret production data from oil and gas wells operating at variable pressure/rate conditions during the boundary-dominated flow period. Using material balance techniques, the ultimate storage capacity is then estimated through linear extrapolation of the average pressure trend to the maximum allowable pressure the formation can withstand. The average pressure is not available in practice, but is can be obtained from the injection data. Two approaches are presented in this study to calculate the average pressure; namely the rigorous and the approximate approaches. Unlike the rigorous approach, the approximate approach does not require a prior knowledge of some reservoir properties (e.g. relative permeability, absolute permeability, formation porosity and thickness) to calculate the average pressure. To investigate its potential and reliability in analyzing CO 2 injection data, the proposed technique is applied to four synthetic cases representing different well operating conditions. Results indicate that the approximate approach consistently overestimates the actual (simulated) storage capacity as compared to the rigorous approach. The agreement - between the inferred and the simulated reservoir pore volume, and between the analytical and numerical estimates of storage capacity - validates the potential application of the technique to CO 2 storage in closed saline aquifers. The technique is further substantiated through application to a field data set utilized from a commercial-scale geological storage (CGS) project. Finally, field data interpretation shows that the proposed technique can be utilized to identify the degree of hydraulic continuity and reservoir compartmentalization within a target formation by interpreting the corresponding pressure and rate responses.

02 PETROLEUM↗

Neutrino-Nucleus Cross Section within the Extended Factorization Scheme

The factorization scheme, based on the impulse approximation and the spectral function formalism, has been recently generalized to allow the description of electromagnetic nuclear interactions driven by two-nucleon currents. We have extended this framework to the case of weakly charged and neutral currents, and carried out calculations of the double-differential neutrino-carbon and neutrino-oxygen cross sections using two different models of the target spectral functions. The results, showing a moderate dependence on the input spectral function, confirm that our approach provides a consistent treatment of all reaction mechanisms contributing to the signals detected by accelerator-based neutrino experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

HomPINNs: Homotopy physics-informed neural networks for learning multiple solutions of nonlinear elliptic differential equations

Physics-informed neural networks (PINNs) based machine learning is an emerging framework for solving nonlinear differential equations. However, due to the implicit regularity of neural network structure, PINNs can only find the flattest solution in most cases by minimizing the loss functions. In this paper, we combine PINNs with the homotopy continuation method, a classical numerical method to compute isolated roots of polynomial systems, and propose a new deep learning framework, named homotopy physics-informed neural networks (HomPINNs), for solving multiple solutions of nonlinear elliptic differential equations. The implementation of an HomPINN is a homotopy process that is composed of the training of a fully connected neural network, named the starting neural network, and training processes of several PINNs with different tracking parameters. The starting neural network is to approximate a starting function constructed by the trivial solutions, while other PINNs are to minimize the loss functions defined by boundary condition and homotopy functions, varying with different tracking parameters. These training processes are regraded as different steps of a homotopy process, and a PINN is initialized by the well-trained neural network of the previous step, while the first starting neural network is initialized using the default initialization method. Finally, several numerical examples are presented to show the efficiency of our proposed HomPINNs, including reaction-diffusion equations with a heart-shaped domain.

97 MATHEMATICS AND COMPUTING↗

Updates to R-matrix Evaluations of Fissile Actinides: 233,235 U, 239 Pu [Slides]

This presentation begins by discussing the importance and significance of cross section fluctuations. It also discusses the motivation and overarching goals which are to establish the highest fidelity nuclear evaluated data. In conclusion, a procedure to accurately model the measured cross section fluctuations for inclusion into evaluated nuclear data files was developed and tested on 239 Pu total cross sections. The procedure consisted of defining population of levels as well as related amplitudes extrapolated from the systematics of the resonance parameters in the resolved resonance region. By using realistic population of extrapolated levels, the fit of measured total cross section produced a continuous S-matrix function S( E ) in Reich-Moore approximation. The S-matrix function averaged over a suitable energy interval was used to obtain averaged cross sections consistent with the measured data. Transmittable formatted files (ENDF, GNDS) with LSSF=1 will consist of File 3 which are smoothed cross sections and File 2 which are average resonance parameters fitted to the energy bins defined in File 3. The capability to store probability tables is a way to show the fluctuating cross sections.

07 ISOTOPE AND RADIATION SOURCES↗

Partition Density Functionals: Theory and Applications. Final Technical Report

Partition Density Functional Theory is a method to calculate the energy and density of a molecule via self-consistent calculations on isolated fragments. At the start of this project, Partition Density Functional Theory (PDFT) had only been applied to one-dimensional model systems of non-interacting electrons. Its most appealing feature (the reason why PDFT was born in the first place) was that it allowed one to construct an internally-consistent Density Functional Theory (DFT) valid for non-integer electron numbers to be used in the context of Chemical Reactivity Theory. Many formal properties of the quantities entering the theory, such as partition potentials, were unknown when the project started. The connections with other fragment-based electronic structure methods, and especially with embedding theories, were unclear, and the potential of PDFT for fixing problems of approximate exchange-correlation functionals was unanticipated. Supported by grant DE-SC0005031, we made progress in developing, understanding, implementing, and applying PDFT. We discovered its potential for applications in situations where approximate DFT fails, such as when stretching bonds or when calculating the energy of weakly-interacting systems, both cases of importance for energy research applications. We extended PDFT in several directions (spin-densities, current densities, external electric and magnetic fields), and carried out many calculations on diatomic molecules and small clusters to test ideas for approximate non-additive functionals. As a result, we were able to propose physically-motivated fragment-density approximations for both covalent and weak bonds. Because many applications will increasingly benefit from efficient and accurate electronic-structure calculations via density-embedding techniques, the research results enabled by this grant should prove useful for addressing complex problems in a wide variety of fields, from chemistry to molecular biology and materials engineering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Kohn-Sham Solver (KSSOLV) v2.0

KSSOLV is a MATLAB toolbox for solving Kohn-Sham density functional theory based electronic structure eigenvalue problems. It uses an object oriented features of MATLAB to represent atom, molecules, wavefunctions and Hamiltonians and their operations. It is designed to make it easier for users to prototype and test new algorithms for solving the Kohn-Sham problem. KSSOLV2.0 contains significant improvement over the original KSSOLV described in a paper published in ACM Transaction on Mathematical Software (attached). In addition to performing ground state calculation for small molecules, it can also perform geometry optimization for both molecules and solids. It uses standard pseudopotentials and implements local density approximation, generalized gradient approximation and hybrid functionals. Future releases will also include time-dependent DFT and post DFT calculations such as the GW quasi-particle energy calculation and Bethe-Salpeter equation solver for optical absorption.

Yang, Chao↗

First-Principles-Based Machine Learning Models for Phase Behavior and Transport Properties of CO 2

In this work, we construct distinct first-principles-based machine-learning models of CO 2 , reproducing the potential energy surface of the PBE-D3, BLYP-D3, SCAN and SCAN-rvv10 approximations of density functional theory. Here we employ the Deep Potential methodology to develop the models and consequently achieve a significant computational efficiency over ab initio molecular dynamics (AIMD) that allows for larger system sizes and time scales to be explored. Although our models are trained only with liquid phase configurations, they are able to simulate a stable interfacial system and predict vapor-liquid equilibrium properties, in good agreement with results from the literature. Because of the computational efficiency of the models, we are also able to obtain transport properties, such as viscosity and diffusion coefficients. We find that the SCAN-based model presents a temperature shift in the position of the critical point, while the SCAN-rvv10-based model shows improvement but still exhibits a temperature shift that remains approximately constant for all properties investigated in this work. We find that the BLYP-D3-based model generally performs better for liquid phase and vapor-liquid equilibrium properties, but the PBE-D3-based model is better suited for predicting transport properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spectral-density estimation with the Gaussian integral transform

The spectral-density operator $\hat{ρ}(ω) = δ(ω–\hat{H})$ plays a central role in linear response theory as its expectation value, the dynamical response function, can be used to compute scattering cross sections. In this work, we describe a near optimal quantum algorithm providing an approximation to the spectral density with energy resolution $\Delta$ and error $\epsilon$ using $O(\sqrt{\text{log}_2 (1/ε)[\text{log}_2 (1 / Δ) + \text{log}_2 (1/ε)]/ Δ)}$ operations. This is achieved without using expensive approximations to the time-evolution operator, but instead exploiting qubitization to implement an approximate Gaussian integral transform of the spectral density. Finally, we also describe appropriate error metrics to assess the quality of the spectral function approximations more generally.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A primal–dual algorithm for risk minimization

In this paper, we develop an algorithm to efficiently solve risk-averse optimization problems posed in reflexive Banach space. Such problems often arise in many practical applications as, e.g., optimization problems constrained by partial differential equations with uncertain inputs. Unfortunately, for many popular risk models including the coherent risk measures, the resulting risk-averse objective function is nonsmooth. Here, this lack of differentiability complicates the numerical approximation of the objective function as well as the numerical solution of the optimization problem. To address these challenges, we propose a primal–dual algorithm for solving large-scale nonsmooth risk-averse optimization problems. This algorithm is motivated by the classical method of multipliers and by epigraphical regularization of risk measures. As a result, the algorithm solves a sequence of smooth optimization problems using derivative-based methods. We prove convergence of the algorithm even when the subproblems are solved inexactly and conclude with numerical examples demonstrating the efficiency of our method.

97 MATHEMATICS AND COMPUTING↗

Alternative CNDOL Fockians for fast and accurate description of molecular exciton properties

CNDOL is an a priori, approximate Fockian for molecular wave functions. In this study, we employ several modes of singly excited configuration interaction (CIS) to model molecular excitation properties by using four combinations of the one electron operator terms. Those options are compared to the experimental and theoretical data for a carefully selected set of molecules. The resulting excitons are represented by CIS wave functions that encompass all valence electrons in the system for each excited state energy. The Coulomb–exchange term associated to the calculated excitation energies is rationalized to evaluate theoretical exciton binding energies. This property is shown to be useful for discriminating the charge donation ability of molecular and supermolecular systems. Multielectronic 3D maps of exciton formal charges are showcased, demonstrating the applicability of these approximate wave functions for modeling properties of large molecules and clusters at nanoscales. This modeling proves useful in designing molecular photovoltaic devices. Our methodology holds potential applications in systematic evaluations of such systems and the development of fundamental artificial intelligence databases for predicting related properties.

Chemistry↗

Green’s function coupled cluster formulations utilizing extended inner excitations

Here, we analyze new approximations of the Green’s function coupled cluster (GFCC) method where locations of poles are improved by extending the excitation level of inner auxiliary operators. These new GFCC approximations can be categorized as the GFCC-i( n, m ) method, where the excitation level of the inner auxiliary operators ( m ) used to describe the ionization potential and electron affinity effects in the N-1 and N+1 particle spaces is higher than the excitation level ( n ) used to correlate the ground-state coupled cluster wave function for the N-electron system. Furthermore, we reveal the so-called “n + 1” rule in this category [or the GFCC-i( n, n + 1) method], which states that in order to maintain size-extensivity of the Green’s function matrix elements, the excitation level of inner auxiliary operators X p (ω) and Y q (ω) cannot exceed n + 1. We also discuss the role of the moments of coupled cluster equations that in a natural way assures these properties. Our implementation in the present study is focused on the first approximation in this GFCC category, i.e., the GFCC-i(2,3) method. As our first practice, we use the GFCC-i(2,3) method to compute the spectral functions for the N 2 and CO molecules in the inner and outer valence regimes. Lastly, in comparison with the Green’s function coupled cluster singles, doubles results, the computed spectral functions from the GFCC-i(2,3) method exhibit better agreement with the experimental results and other theoretical results, particularly in terms of providing higher resolution of satellite peaks and more accurate relative positions of these satellite peaks with respect to the main peak positions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charting C–C coupling pathways in electrochemical CO 2 reduction on Cu(111) using embedded correlated wavefunction theory

The electrochemical CO 2 reduction reaction (CO 2 RR) powered by excess zero-carbon-emission electricity to produce especially multicarbon (C 2+ ) products could contribute to a carbon-neutral to carbon-negative economy. Foundational to the rational design of efficient, selective CO 2 RR electrocatalysts is mechanistic analysis of the best metal catalyst thus far identified, namely, copper (Cu), via quantum mechanical computations to complement experiments. Here, we apply embedded correlated wavefunction (ECW) theory, which regionally corrects the electron exchange-correlation error in density functional theory (DFT) approximations, to examine multiple C–C coupling steps involving adsorbed CO (*CO) and its hydrogenated derivatives on the most ubiquitous facet, Cu(111). We predict that two adsorbed hydrogenated CO species, either *COH or *CHO, are necessary precursors for C–C bond formation. The three kinetically feasible pathways involving these species yield all three possible products: *COH–CHO, *COH–*COH, and *OCH–*OCH. The most kinetically favorable path forms *COH–CHO. In contrast, standard DFT approximations arrive at qualitatively different conclusions, namely, that only *CO and *COH will prevail on the surface and their C–C coupling paths produce only *COH–*COH and *CO–*CO, with a preference for the first product. This work demonstrates the importance of applying qualitatively and quantitatively accurate quantum mechanical method to simulate electrochemistry in order ultimately to shed light on ways to enhance selectivity toward C 2+ product formation via CO 2 RR electrocatalysts.

30 DIRECT ENERGY CONVERSION↗

Weak entanglement approximation for nuclear structure

The interacting shell model, a configuration-interaction method, is a venerable approach for low-lying nuclear structure calculations, but it is hampered by the exponential growth of its basis dimension as one increases the single-particle space and/or the number of active particles. Recent, quantum-information-inspired work has demonstrated that the proton and neutron sectors of a nuclear wave function are weakly entangled. Furthermore, the entanglement is smaller for nuclides away from N = Z, such as heavy, neutron-rich nuclides. Here, in this study, we implement a weak entanglement approximation to bipartite configuration-interaction wave functions, approximating low-lying levels by coupling a relatively small number of many-proton and many-neutron states. This truncation scheme, which we present in the context of past approaches, reduces the basis dimension by many orders of magnitude while preserving essential features of nuclear spectra.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Closed-Form Approximation of the Total Variation Proximal Operator

Total variation (TV) is a widely used function for regularizing imaging inverse problems that is particularly appropriate for images whose underlying structure is piecewise constant. TV regularized optimization problems are typically solved using proximal methods, but the way in which they are applied is constrained by the absence of a closed-form expression for the proximal operator of the TV function. A closed-form approximation of the TV proximal operator has previously been proposed, but its accuracy was not theoretically explored in detail. Here, we address this gap by making several new theoretical contributions, proving that the approximation leads to a proximal operator of some convex function, it is equivalent to a gradient descent step on a smoothed version of TV, and that its error can be fully characterized and controlled with its scaling parameter. We experimentally validate our theoretical results on image denoising and sparse-view computed tomography (CT) image reconstruction.

97 MATHEMATICS AND COMPUTING↗