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At least 703 records · Page 39

Formulation of the Multi-Hit Model With a Non-Poisson Distribution of Hits

Purpose: We proposed a formulation of the multi-hit single-target model in which the Poisson distribution of hits was replaced by a combination of two distributions: one for the number of particles entering the target and one for the number of hits a particle entering the target produces. Such an approach reflects the fact that radiation damage is a result of two different random processes: particle emission by a radiation source and interaction of particles with matter inside the target. Methods and Materials: Poisson distribution is well justified for the first of the two processes. The second distribution depends on how a hit is defined. To test our approach, we assumed that the second distribution was also a Poisson distribution. The two distributions combined resulted in a non-Poisson distribution. We tested the proposed model by comparing it with previously reported data for DNA single- and double-strand breaks induced by protons and electrons, for survival of a range of cell lines, and variation of the initial slopes of survival curves with radiation quality for heavy-ion beams. Results: Analysis of cell survival equations for this new model showed that they had realistic properties overall, such as the initial and high-dose slopes of survival curves, the shoulder, and relative biological effectiveness (RBE) In most cases tested, a better fit of survival curves was achieved with the new model than with the linear-quadratic model. The results also suggested that the proposed approach may extend the multi-hit model beyond its traditional role in analysis of survival curves to predicting effects of radiation quality and analysis of DNA strand breaks. Conclusions: Our model, although conceptually simple, performed well in all tests. The model was able to consistently fit data for both cell survival and DNA single- and double-strand breaks. It correctly predicted the dependence of radiation effects on parameters of radiation quality.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Preclinical Evaluation of Promitil, a Radiation-Responsive Liposomal Formulation of Mitomycin C Prodrug, in Chemoradiotherapy

Purpose: To examine the effect of radiation on in vitro drug activation and release of Promitil, a pegylated liposomal formulation of a mitomycin C (MMC) lipid-based prodrug; and examine the efficacy and toxicity of Promitil with concurrent radiation in colorectal cancer models. Methods and Materials: Promitil was obtained from Lipomedix Pharmaceuticals (Jerusalem, Israel). We tested the effects of radiation on release of active MMC from Promitil in vitro. We next examined the radiosensitization effect of Promitil in vitro. We further evaluated the toxicity of a single injection of free MMC or Promitil when combined with radiation by assessing the effects on blood counts and in-field skin and hair toxicity. Finally, we compared the efficacy of MMC and Promitil in chemoradiotherapy using mouse xenograft models. Results: Mitomycin C was activated and released from Promitil in a controlled-release profile, and the rate of release was significantly increased in medium from previously irradiated cells. Both Promitil and MMC potently radiosensitized HT-29 cells in vitro. Toxicity of MMC (8.4 mg/kg) was substantially greater than with equivalent doses of Promitil (30 mg/kg). Mice treated with human-equivalent doses of MMC (3.3 mg/kg) experienced comparable levels of toxicity as Promitil-treated mice at 30 mg/kg. Promitil improved the antitumor efficacy of 5-fluorouracil–based chemoradiotherapy in mouse xenograft models of colorectal cancer, while equitoxic doses of MMC did not. Conclusions: We demonstrated that Promitil is an attractive agent for chemoradiotherapy because it demonstrates a radiation-triggered release of active drug. We further demonstrated that Promitil is a well-tolerated and potent radiosensitizer at doses not achievable with free MMC. These results support clinical investigations using Promitil in chemoradiotherapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Extended FFT-based micromechanical formulation to consider general non-periodic boundary conditions

Here, this paper presents a new approach for applying non-periodic boundary conditions in the context of FFT-based methods to solve micromechanical problems in heterogeneous solids. The domain of the original problem is extended to satisfy the periodicity requirements at the boundary of the extended domain. The velocity constraint on the boundary of the original domain is replaced by a corresponding constraint on the velocity gradient in the extended volume, and a two-level augmented Lagrangian method is used to enforce the constraint. The proposed method is implemented as an extension of the large-strain elasto-viscoplastic FFT-based (LS-EVPFFT) model of Zecevic et al. (2022). The proposed method is verified in the cases of fully imposed velocity boundary conditions and mixed velocity/traction-free boundary conditions. The accuracy and convergence of the method are studied next, followed by applications to bending and indentation of polycrystals that illustrate the extended capabilities of the proposed formulation.

36 MATERIALS SCIENCE↗

A 2.5D boundary element formulation for modeling damped waves in arbitrary cross-section waveguides and cavities

Highlights: •Dispersive properties of viscoelastic waveguides and cavities are computed using a regularized 2.5D BEM. •Linear viscoelasticity is introduced at the constitutive level by means of frequency dependent complex moduli. •A contour integral algorithm is used to solve the nonlinear eigenvalue problem. •The Sommerfeld radiation condition is used to select the permissible Riemann sheets. •Attenuation of surface waves in cavities approaches the attenuation of Rayleigh waves. -- Abstract: A regularized 2.5D boundary element method (BEM) is proposed to predict the dispersion properties of damped stress guided waves in waveguides and cavities of arbitrary cross-section. The wave attenuation, induced by material damping, is introduced using linear viscoelastic constitutive relations and described in a spatial manner by the imaginary component of the axial wavenumber. The discretized dispersive wave equation results in a nonlinear eigenvalue problem, which is solved obtaining complex axial wavenumbers for a fixed frequency using a contour integral algorithm. Due to the singular characteristics and the multivalued feature of the wave equation, the requirement of holomorphicity inside the contour region over the complex wavenumber plane is fulfilled by the introduction of the Sommerfeld branch cuts and by the choice of the permissible Riemann sheets. A post processing analysis is developed for the extraction of the energy velocity of propagative guided waves. The reliability of the method is demonstrated by comparing the results obtained for a rail and a bar with square cross-section with those obtained from a 2.5D Finite Element formulation also known in literature as Semi Analytical Finite Element (SAFE) method. Next, to show the potential of the proposed numerical framework, dispersion properties are predicted for surface waves propagating along cylindrical cavities of arbitrary cross-section. It is demonstrated that the attenuation of surface waves approaches asymptotically the attenuation of Rayleigh waves.

97 MATHEMATICS AND COMPUTING↗

Multilayer shallow shelf approximation: Minimisation formulation, finite element solvers and applications

In this paper, a multilayer generalisation of the Shallow Shelf Approximation (SSA) is considered. In this recent hybrid ice flow model, the ice thickness is divided into thin layers, which can spread out, contract and slide over each other in such a way that the velocity profile is layer-wise constant. Like the SSA (1-layer model), the multilayer model can be reformulated as a minimisation problem. However, unlike the SSA, the functional to be minimised involves a new penalisation term for the interlayer jumps of the velocity, which represents the vertical shear stresses induced by interlayer sliding. Taking advantage of this reformulation, numerical solvers developed for the SSA can be naturally extended layer-wise or column-wise. Numerical results show that the column-wise extension of a Newton multigrid solver proves to be robust in the sense that its convergence is barely influenced by the number of layers and the type of ice flow. In addition, the multilayer formulation appears to be naturally better conditioned than the one of the first-order approximation to face the anisotropic conditions of the sliding-dominant ice flow of ISMIP-HOM experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Finite element formulation of fluctuating hydrodynamics for fluids filled with rigid particles using boundary fitted meshes

In this paper, we present a finite element implementation of fluctuating hydrodynamics with a moving boundary fitted mesh for treating the suspended particles. The thermal fluctuations are incorporated into the continuum equations using the Landau and Lifshitz approach [1]. The proposed implementation fulfills the fluctuation–dissipation theorem exactly at the discrete level. Since we restrict the equations to the creeping flow case, this takes the form of a relation between the diffusion coefficient matrix and friction matrix both at the particle and nodal level of the finite elements. Brownian motion of arbitrarily shaped particles in complex confinements can be considered within the present formulation. A multi-step time integration scheme is developed to correctly capture the drift term required in the stochastic differential equation (SDE) describing the evolution of the positions of the particles. The proposed approach is validated by simulating the Brownian motion of a sphere between two parallel plates and the motion of a spherical particle in a cylindrical cavity. The time integration algorithm and the fluctuating hydrodynamics implementation are then applied to study the diffusion and the equilibrium probability distribution of a confined circle under an external harmonic potential.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An integral equation formulation for rigid bodies in Stokes flow in three dimensions

Here we present a new derivation of a boundary integral equation (BIE) for simulating the three-dimensional dynamics of arbitrarily-shaped rigid particles of genus zero immersed in a Stokes fluid, on which are prescribed forces and torques. Our method is based on a single-layer representation and leads to a simple second-kind integral equation. It avoids the use of auxiliary sources within each particle that play a role in some classical formulations. We use a spectrally accurate quadrature scheme to evaluate the corresponding layer potentials, so that only a small number of spatial discretization points per particle are required. The resulting discrete sums are computed in $\mathscr{O}(n)$ time, where n denotes the number of particles, using the fast multipole method (FMM). The particle positions and orientations are updated by a high-order time-stepping scheme. We illustrate the accuracy, conditioning and scaling of our solvers with several numerical examples.

97 MATHEMATICS AND COMPUTING↗

Physics-informed neural networks for solving forward and inverse flow problems via the Boltzmann-BGK formulation

We report the Boltzmann equation with the Bhatnagar-Gross-Krook collision model (Boltzmann-BGK equation) has been employed to describe multiscale flows, i.e., from the hydrodynamic limit to free molecular flow. In this study we employ physics-informed neural networks (PINNs) to solve forward and inverse problems via the Boltzmann-BGK formulation (PINN-BGK), enabling PINNs to model flows in both the continuum and rarefied regimes. In particular, the PINN-BGK is composed of three sub-networks, i.e., the first for approximating the equilibrium distribution function, the second for approximating the non-equilibrium distribution function, and the third one for encoding the Boltzmann-BGK equation as well as the corresponding boundary/initial conditions. By minimizing the residuals of the governing equations and the mismatch between the predicted and provided boundary/initial conditions, we can approximate the Boltzmann-BGK equation for both continuous and rarefied flows. For forward problems, the PINN-BGK is utilized to solve various benchmark flows given boundary/initial conditions, e.g. Kovasznay flow, Taylor-Green flow, cavity flow, and micro Couette flow for Knudsen number up to 5. For inverse problems, we focus on rarefied flows in which accurate boundary conditions are difficult to obtain. We employ the PINN-BGK to infer the flow field in the entire computational domain given a limited number of interior scattered measurements on the velocity without using the (unknown) boundary conditions. Results for the two-dimensional micro Couette and micro cavity flows with Knudsen numbers ranging from 0.1 to 10 indicate that the PINN-BGK can infer the velocity field in the entire domain with good accuracy. Finally, we also present some results on using transfer learning to accelerate the training process. Specifically, we can obtain a three-fold speedup comparted to the standard training process (e.g., Adam plus L-BFG-B) for the two-dimensional flow problems considered in our work.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A unified formulation of splitting-based implicit time integration schemes

Splitting-based time integration approaches such as fractional step, alternating direction implicit, operator splitting, and locally one dimensional methods partition the system of interest into components, and solve individual components implicitly in a cost-effective way. Here this work proposes a unified formulation of splitting time integration schemes in the framework of general-structure additive Runge–Kutta (GARK) methods. Specifically, we develop implicit-implicit (IMIM) GARK schemes, provide the order conditions for this class, and explain their application to partitioned systems of ordinary differential equations. We show that classical splitting methods belong to the IMIM GARK family, and therefore can be studied in this unified framework. New IMIM-GARK splitting methods are developed and tested using parabolic systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A three dimensional field formulation, and isogeometric solutions to point and line defects using Toupin's theory of gradient elasticity at finite strains

In this study, we present a field formulation for defects that draws from the classical representation of the cores as force dipoles. We write these dipoles as singular distributions. Exploiting the key insight that the variational setting is the only appropriate one for the theory of distributions, we arrive at universally applicable weak forms for defects in nonlinear elasticity. Remarkably, the standard, Galerkin finite element method yields numerical solutions for the elastic fields of defects that, when parameterized suitably, match very well with classical, linearized elasticity solutions. The true potential of our approach, however, lies in its easy extension to generate solutions to elastic fields of defects in the regime of nonlinear elasticity, and even more notably for Toupin's theory of gradient elasticity at finite strains (Toupin Arch. Ration. Mech. Anal., 11 (1962) 385). In computing these solutions we adopt recent numerical work on an isogeometric analytic framework that enabled the first three-dimensional solutions to general boundary value problems of Toupin's theory (Rudraraju et al. Comput. Methods Appl. Mech. Eng., 278 (2014) 705). We first present exhaustive solutions to point defects, edge and screw dislocations, and a study on the energetics of interacting dislocations. Then, to demonstrate the generality and potential of our treatment, we apply it to other complex dislocation configurations, including loops and low-angle grain boundaries.

36 MATERIALS SCIENCE↗

A single crystal plasticity finite element formulation with embedded deformation twins

Deformation twinning is an important plastic deformation mechanism in some polycrystalline metals such as titanium and magnesium. In this paper, we present a novel crystal plasticity finite element framework that accounts for deformation twinning explicitly, in addition to crystallographic slip. Within this computational framework, deformation twins are treated as weak discontinuities embedded within individual finite elements, such that a jump in the velocity gradient field is introduced (via the discretized gradient operator) between the twinned and untwinned crystalline regions, taking into account compatibility and traction continuity conditions at the interface between these two regions. The deformation gradient is multiplicatively split into elastic and plastic parts in the untwinned region, as is customary in finite-deformation crystal plasticity formulations. A different multiplicative decomposition of the deformation gradient into elastic, plastic (slip), and twinning parts is adopted in the twinned region, allowing deformation twinning to be accounted for as an additional mode of plastic deformation. Here, a stochastic model is used to predict twin nucleation at grain boundaries, and the evolution of the length and thickness of the twinned region under subsequent deformation is taken into account.

36 MATERIALS SCIENCE↗

Thermodynamic theory of crystal plasticity: Formulation and application to polycrystal fcc copper

We present a thermodynamic description of crystal plasticity. Our formulation is based on the Langer-Bouchbinder-Lookman thermodynamic dislocation theory (TDT), which asserts the fundamental importance of an effective temperature that describes the state of configurational disorder and therefore the dislocation density of the crystalline material. We extend the TDT description from isotropic plasticity to crystal plasticity with many slip systems. Finite-element simulations show favourable comparison with experiments on polycrystal fcc copper under uniaxial compression, tension, and simple shear. Here, the thermodynamic theory of crystal plasticity thus provides a thermodynamically consistent and physically rigorous description of dislocation motion in crystals. We also discuss new insights about the interaction of dislocations belonging to different slip systems.

36 MATERIALS SCIENCE↗

Generalized grain boundary constitutive description implemented in a strain-gradient large-strain FFT-based formulation: Application to nano-metallic laminates

Herein this paper presents a general treatment of grain boundary constitutive behavior in the context of strain-gradient (SG) plasticity, and its numerical implementation in a large-strain (LS) elasto-viscoplastic (EVP) fast Fourier transform (FFT)-based micromechanical model. Two novel grain boundary constitutive equations are proposed, allowing for more accurate description of the Burgers vector flow at the grain boundary. The capabilities of the generalized SG-LS-EVPFFT formulation are illustrated for the case of kink-band formation during layer-parallel compression of nano-metallic laminates (NMLs), requiring consideration of the interaction between dislocations and interfaces.

36 MATERIALS SCIENCE↗

A phase-field fracture formulation for generalized standard materials: The interplay between thermomechanics and damage

Accurately modeling fracture of ductile materials poses open challenges in the field of computational mechanics due to the multiphysics nature of their failure processes. Integrating the interplay between thermodynamics and damage into ductile fracture models is vital for predicting critical failure modes. Here, in this paper, we develop a versatile phase-field (PF) framework for modeling ductile fracture, taking into account finite-strain elasto-plasticity. The framework stems from a variational formulation of constitutive relations for generalized standard materials (GSMs), whose response is described by a Helmholtz free energy and a dissipation pseudo-potential. Its variational structure is based on a minimum principle for a functional that expresses the sum of power densities for reversible and irreversible processes. By minimizing this functional with a constraint on a von Mises yield function, we derive the evolution equation for the equivalent plastic strain and an associative flow rule. This constrained optimization problem is analytically solved for a wide class of thermo-viscoplasticity models. The key innovations of the current work include (i) a cubic plastic degradation function that accounts for a non-vanishing damage-dependent yield stress, (ii) closed-form expressions of the Helmholtz free energy and dissipation pseudo-potential for three thermo-viscoplasticity models, (iii) an extended Johnson–Cook plasticity model with a nonlinear hardening law, and (iv) a plastic work heat source that depends on the plastic degradation function and a variable Taylor–Quinney (TQ) coefficient. The capabilities of the proposed framework are tested with the aid of four ductile fracture problems, including the Sandia Fracture Challenge. In each of these problems, we examine the evolution of relevant field variables such as the PF order parameter, the equivalent plastic strain, the temperature, and the internal power dissipation density, in addition to the overall structural response quantified by the force–displacement curve. These numerical studies demonstrate that the proposed framework effectively represents ductile fracture, yielding computational results that exhibit good agreement with experimental data.

36 MATERIALS SCIENCE↗

Next-generation poly-L-histidine formulations for miRNA mimic delivery

Many diseases, especially cancer, are caused by the abnormal expression of non-coding microRNAs (miRNAs), which regulate gene expression, leading to the development of miRNA-based therapeutics. Synthetic miRNA inhibitors have shown promising efficacy in blocking the activity of aberrant miRNAs that are upregulated in disease-specific pathologies. On the other hand, miRNAs that aid in preventing certain diseases and are reduced in expression in the disease state need different strategies. To tackle this, miRNA mimics, which mimic the activity of endogenous miRNAs, can be delivered for those miRNAs downregulated in different disease states. However, the delivery of miRNA mimics remains a challenge. Here, we report a cationic polylactic-co-glycolic acid (PLGA)-poly-L-histidine delivery system to deliver miRNA mimics. We chose miR-34a mimics as a proof of concept for miRNA delivery. miR-34a-loaded PLGA-poly-L-histidine nanoparticles (NPs) were formulated and biophysically characterized to analyze the structural properties of miRNA mimic-loaded NPs. In vitro efficacy was determined by investigating miR-34a and downstream target levels and performing cell viability and apoptosis assays. We confirmed in vivo efficacy through prolonged survival of miR-34a NP-treated A549-derived xenograft mice treated intratumorally. The results of these studies establish PLGA-poly-L-histidine NPs as an effective delivery system for miRNA mimics for treating diseases characterized by downregulated miRNAs.

60 APPLIED LIFE SCIENCES↗

A matrix-algebraic formulation of distributed-memory maximal cardinality matching algorithms in bipartite graphs

We describe parallel algorithms for computing maximal cardinality matching in a bipartite graph on distributed-memory systems. Unlike traditional algorithms that match one vertex at a time, our algorithms process many unmatched vertices simultaneously using a matrix-algebraic formulation of maximal matching. This generic matrix-algebraic framework is used to develop three efficient maximal matching algorithms with minimal changes. The newly developed algorithms have two benefits over existing graph-based algorithms. First, unlike existing parallel algorithms, cardinality of matching obtained by the new algorithms stays constant with increasing processor counts, which is important for predictable and reproducible performance. Second, relying on bulk-synchronous matrix operations, these algorithms expose a higher degree of parallelism on distributed-memory platforms than existing graph-based algorithms. We report high-performance implementations of three maximal matching algorithms using hybrid OpenMP-MPI and evaluate the performance of these algorithm using more than 35 real and randomly generated graphs. On real instances, our algorithms achieve up to 200 × speedup on 2048 cores of a Cray XC30 supercomputer. Even higher speedups are obtained on larger synthetically generated graphs where our algorithms show good scaling on up to 16,384 cores.

97 MATHEMATICS AND COMPUTING↗

HPC formulations of optimization algorithms for tensor completion

Tensor completion is a powerful tool used to estimate or recover missing values in multi-way data. It has seen great success in domains such as product recommendation and healthcare. Tensor completion is most often accomplished via low-rank sparse tensor factorization, a computationally expensive non-convex optimization problem which has only recently been studied in the context of parallel computing. In this work, we study three optimization algorithms that have been successfully applied to tensor completion: alternating least squares (ALS), stochastic gradient descent (SGD), and coordinate descent (CCD++). We explore opportunities for parallelism on shared- and distributed-memory systems and address challenges such as memory- and operation-efficiency, load balance, cache locality, and communication. Among our advancements are a communication-efficient CCD++ algorithm, an ALS algorithm rich in level-3 BLAS routines, and an SGD algorithm which combines stratification with asynchronous communication. Furthermore, we show that introducing randomization during ALS and CCD++ can accelerate convergence. We evaluate our parallel formulations on a variety of real datasets on a modern supercomputer and demonstrate speedups through 16384 cores. Further, these improvements reduce time-to-solution from hours to seconds on real-world datasets. We show that after our optimizations, ALS is advantageous on parallel systems of small-to-moderate scale, while both ALS and CCD++ provide the lowest time-to-solution on large-scale distributed systems.

97 MATHEMATICS AND COMPUTING↗

Ability of Particulate Matter Index to describe sooting tendency of various gasoline formulations in a stratified-charge spark-ignition engine

This study investigates the ability of Particulate Matter Index (PMI) to describe the sooting behavior of various gasoline formulations in a stratified-charge (SC) spark-ignition engine. Specifically, the engine was operated at 2000 rpm with an intake pressure of 130 kPa where soot formation is known to primarily occur in the bulk gases. Exhaust soot emissions were measured for nine test fuels at various exhaust gas recirculation levels. A comparison between measured soot levels and PMI shows that PMI is a relatively poor predictor of the sooting tendency of the tested fuels under lean SC combustion. Among the fuels, three fuels, namely the diisobutylene blend, High Olefin, and E30 fuels exhibit measured soot behavior opposite of that predicted by PMI. Optical diagnostics were utilized to further investigate the in-cylinder phenomena for these three fuels. Analysis of natural luminosity and diffused back-illumination extinction imaging suggests that fuel-induced differences in the amount of soot formed are responsible for a majority of the discrepancy in measured versus predicted sooting tendency. Fuel-induced differences in soot oxidation and spray development seem to play minor roles. Because the combustion and air-fuel mixing processes for lean SC combustion are different from conventional stoichiometric operation it is hypothesized that the PMI correlation needs to be modified to account for differences in stoichiometric air-fuel ratio and level of oxygenation between fuels. Furthermore, the role of fuel volatility in PMI possibly needs to be de-emphasized for SC operation with fuel injection into compression-heated gases.

42 ENGINEERING↗