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The design of solid state batteries with lithium anodes is attracting attention for the prospect of high capacity and improved safety over liquid electrolyte systems. The nature of transport with lithium as the current carrier has as a consequence the accretion or stripping away of the anode with every charge-discharge cycle. While this poses challenges from the growth of protrusions (dendrites) to loss of contact, there lurks an opportunity: Morphogenesis at the anode-electrolyte interface layer can be studied, and may ultimately be controlled as a factor in solid state battery design. The accessible interface morphologies, the dynamic paths to them, and mechanisms to control them expand considerably if lithium alloys are introduced in the anode. The thermodynamics and kinetics of lithium intermetallics present principled approaches for morphogenic interface design. In this communication we adopt a computational approach to such an exploration. With phase field models that are parameterized by a combination of first principles atomistic calculations and experiments, we present phenomenological studies of two lithium intermetallics: Li-Mg and Li-Zn. An array of parametric investigations follows on the influence of kinetics, charge-discharge rate, cycling, transport mechanisms and grain structure. The emphasis across these computations is on the dynamic morphogenesis of the intermetallic interface. Specifically, the plating, segregation and smooth distribution of Li, Mg and Zn, the growth and disappearance of voids, evolution of solid electrolyte-anode contact area, and grain boundary structure are investigated. The computational platform is a framework for future studies of morphogenic electrolyte-anode interfaces with more extensive inputs from first principles atomistics and experiments.

Coronary Artery Disease (CAD) is one of the most common forms of heart disease, which is caused by a buildup of atherosclerotic plaque (known as stenosis) in the coronary arteries, leading to insufficient supplement of blood, oxygen, and nutrients to the heart. Fractional Flow Reserve (FFR), measuring the pressure ratio between the aorta and distal coronary artery, is an invasive physiologic gold standard for assessing the severity of coronary artery stenosis. Despite its benefits, invasive FFR assessment is still underutilized due to its high cost, time-consuming, experimental variability, and increased risk to patients. In this study, an attention-based multi-fidelity machine learning model (AttMulFid) is proposed for computationally efficient and accurate FFR assessment with uncertainty measurement. Within AttMulFid, an autoencoder is utilized to intelligently select geometric features from coronary arteries, with additional attention on the key area. Results show that the geometric features are able to represent the entirety of the geometric information and intelligently allocate attention based on crucial properties of geometry. Furthermore, the AttMulFid is a feasible approach for non-invasive, rapid, and accurate FFR assessment (with 0.002s/simulation).

Reaction-diffusion systems have been proposed as a model for pattern formation and morphogenesis. The Fickian diffusion typically employed in these constructions model the Brownian motion of particles. The biological and chemical elements that form the basis of this process, like cells and proteins, occupy finite mass and volume and interact during migration. We propose a Reaction-diffusion system with Maxwell-Stefan formulation to construct the diffusive flux. This formulation relies on inter-species force balance and provides a more realistic model for interacting elements. We also present a variational system inference-based technique to extract these models from spatiotemporal data for these processes. We show that the inferred models can capture the characteristics of local Turing instability that instigates the pattern formation process. Moreover, the equilibrium solutions of the inferred models form similar patterns to the observed data.

In this work, we present a computational framework for coupled electro-chemo-(nonlinear) mechanics at the particle scale for solid-state batteries. The framework accounts for interfacial fracture between the active particles and solid electrolyte due to intercalation stresses. We extend discontinuous finite element methods for a sharp interface treatment of discontinuities in concentrations, fluxes, electric fields and in displacements, the latter arising from active particle-solid electrolyte interface fracture. We model the degradation in the charge transfer process that results from the loss of contact due to fracture at the electrolyte-active particle interfaces. Additionally, we account for the stress-dependent kinetics that can influence the charge transfer reactions and solid state diffusion. The discontinuous finite element approach does not require a conformal mesh. This offers the flexibility to construct arbitrary particle shapes and geometries that are based on design, or are obtained from microscopy images. The finite element mesh, however, can remain Cartesian, and independent of the particle geometries. We demonstrate this computational framework on micro-structures that are representative of solid-sate batteries with single and multiple anode and cathode particles.

Inverse Reinforcement Learning (IRL) is a compelling technique for revealing the rationale underlying the behavior of autonomous agents. IRL seeks to estimate the unknown reward function of a Markov decision process (MDP) from observed agent trajectories. However, IRL needs a transition function, and most algorithms assume it is known or can be estimated in advance from data. It therefore becomes even more challenging when such transition dynamics is not known a-priori, since it enters the estimation of the policy in addition to determining the system's evolution. When the dynamics of these agents in the state-action space is described by stochastic differential equations (SDE) in It^{o} calculus, these transitions can be inferred from the mean-field theory described by the Fokker-Planck (FP) equation. We conjecture there exists an isomorphism between the time-discrete FP and MDP that extends beyond the minimization of free energy (in FP) and maximization of the reward (in MDP). We identify specific manifestations of this isomorphism and use them to create a novel physics-aware IRL algorithm, FP-IRL, which can simultaneously infer the transition and reward functions using only observed trajectories. We employ variational system identification to infer the potential function in FP, which consequently allows the evaluation of reward, transition, and policy by leveraging the conjecture. We demonstrate the effectiveness of FP-IRL by applying it to a synthetic benchmark and a biological problem of cancer cell dynamics, where the transition function is inaccessible.

Targeting signaling pathways that drive cancer cell migration or proliferation is a common therapeutic approach. A popular experimental technique, the scratch assay, measures the migration and proliferation-driven cell closure of a defect in a confluent cell monolayer. These assays do not measure dynamic effects. To improve analysis of scratch assays, we combine high-throughput scratch assays, video microscopy, and system identification to infer partial differential equation (PDE) models of cell migration and proliferation. We capture the evolution of cell density fields over time using live cell microscopy and automated image processing. We employ weak form-based system identification techniques for cell density dynamics modeled with first-order kinetics of advection-diffusion-reaction systems. We present a comparison of our methods to results obtained using traditional inference approaches on previously analyzed 1-dimensional scratch assay data. We demonstrate the application of this pipeline on high throughput 2-dimensional scratch assays and find that low levels of trametinib inhibit wound closure primarily by decreasing random cell migration by approximately 20%. Our integrated experimental and computational pipeline can be adapted for quantitatively inferring the effect of biological perturbations on cell migration and proliferation in various cell lines.

The most promising solid electrolytes for all-solid-state Li batteries are oxide and sulfide ceramics. Current ceramic solid electrolytes are brittle and lack the toughness to withstand the mechanical stresses of repeated charge and discharge cycles. Solid electrolytes are susceptible to crack propagation due to dendrite growth from Li metal anodes and to debonding processes at the cathode/electrolyte interface due to cyclic variations in the cathode lattice parameters. In this perspective, we argue that solutions to the mechanics challenges of all-solid-state batteries can be borrowed from the aerospace industry, which successfully overcame similar hurdles in the development of thermal barrier coatings of superalloy turbine blades. Their solution was to exploit ferroelastic and transformation toughening mechanisms to develop ceramics that can withstand cyclic stresses due to large variations in temperature. This perspective describes fundamental materials design principles with which to search for solid electrolytes that are ferroelastically toughened., Comment: 8 pages, 8 figures

Traditional, numerical discretization-based solvers of partial differential equations (PDEs) are fundamentally agnostic to domains, boundary conditions and coefficients. In contrast, machine learnt solvers have a limited generalizability across these elements of boundary value problems. This is strongly true in the case of surrogate models that are typically trained on direct numerical simulations of PDEs applied to one specific boundary value problem. In a departure from this direct approach, the label-free machine learning of solvers is centered on a loss function that incorporates the PDE and boundary conditions in residual form. However, their generalization across boundary conditions is limited and they remain strongly domain-dependent. Here, we present a framework that generalizes across domains, boundary conditions and coefficients simultaneously with learning the PDE in weak form. Our work explores the ability of simple, convolutional neural network (CNN)-based encoder-decoder architectures to learn to solve a PDE in greater generality than its restriction to a particular boundary value problem. In this first communication, we consider the elliptic PDEs of Fickean diffusion, linear and nonlinear elasticity. Importantly, the learning happens independently of any labelled field data from either experiments or direct numerical solutions. Extensive results for these problem classes demonstrate the framework's ability to learn PDE solvers that generalize across hundreds of thousands of domains, boundary conditions and coefficients, including extrapolation beyond the learning regime. Once trained, the machine learning solvers are orders of magnitude faster than discretization-based solvers. We place our work in the context of recent continuous operator learning frameworks, and note extensions to transfer learning, active learning and reinforcement learning., Comment: 5 figures. Supplementary Information included. This work is the next in the series beginning with arXiv:2101.04879. arXiv admin note: substantial text overlap with arXiv:2101.04879

New criteria for energy stability of multi-step, multi-stage, and mixed schemes are introduced in the context of evolution equations that arise as gradient flow with respect to a metric. These criteria are used to exhibit second and third order consistent, energy stable schemes, which are then demonstrated on several partial differential equations that arise as gradient flow with respect to the 2-Wasserstein metric.

Modeling crack initiation and propagation in brittle materials is of great importance to be able to predict sudden loss of load-carrying capacity and prevent catastrophic failure under severe dynamic loading conditions. Second-order phase-field fracture models have gained wide adoption given their ability to capture the formation of complex fracture patterns, e.g. via crack merging and branching, and their suitability for implementation within the context of the conventional finite element method. Higher-order phase-field models have also been proposed to increase the regularity of the exact solution and thus increase the spatial convergence rate of its numerical approximation. However, they require special numerical techniques to enforce the necessary continuity of the phase field solution. In this paper, we derive a fourth-order phase-field model of fracture in two independent ways; namely, from Hamilton's principle and from a higher-order micromechanics-based approach. The latter approach is novel, and provides a physical interpretation of the higher-order terms in the model. In addition, we propose a continuous/discontinuous Galerkin (C/DG) method for use in computing the approximate phase-field solution. This method employs Lagrange polynomial shape functions to guarantee $C^0$-continuity of the solution at inter-element boundaries, and enforces the required $C^1$ regularity with the aid of additional variational and interior penalty terms in the weak form. The phase-field equation is coupled with the momentum balance equation to model dynamic fracture problems in hyper-elastic materials. Two benchmark problems are presented to compare the numerical behavior of the C/DG method with mixed finite element methods.

We present an approach to reduced-order modelling that builds off recent graph-theoretic work for representation, exploration, and analysis of computed states of physical systems (Banerjee et al., Comp. Meth. App. Mech. Eng., 351, 501-530, 2019). We extend a non-local calculus on finite weighted graphs to build such models by exploiting polynomial expansions and Taylor series. In the general framework for non-local calculus on graphs, the graph edge weights are intricately linked to the embedding of the graph, and consequently to the definition of the derivatives. In a previous communication (Duschenes and Garikipati, arXiv:2105.01740), we have shown that radially symmetric, continuous edge weights derived from, for example Gaussian functions, yield inconsistent results in the resulting non-local derivatives when compared against the corresponding local, differential derivative definitions. Taking inspiration from finite difference methods, we algorithmically compute edge weights, considering the embedding of the local neighborhood of each graph vertex. Given this procedure, we ensure the consistency of the non-local derivatives in this setting, a crucial requirement for numerical applications. We show that we can achieve any desired orders of accuracy of derivatives, in a chosen number of dimensions without symmetry assumptions in the underlying data. Finally, we present two example applications of extracting reduced-order models using this non-local calculus, in the form of ordinary differential equations from parabolic partial differential equations of progressively greater complexity., Comment: 68 pages, 23 figures

Contemporary material characterisation techniques that leverage deformation fields and the weak form of the equilibrium equations face challenges in the numerical solution procedure of the inverse characterisation problem. As material models and descriptions differ, so too must the approaches for identifying parameters and their corresponding mechanisms. The widely-used Ogden material model can be comprised of a chosen number of terms of the same mathematical form, which presents challenges of parsimonious representation, interpretability, and stability. Robust techniques for system identification of any material model are important to assess and improve experimental design, in addition to their centrality to forward computations. Using fully 3D displacement fields acquired in silicone elastomers with our recently-developed magnetic resonance cartography (MR-u) technique on the order of $>20,000$ points per sample, we leverage PDE-constrained optimisation as the basis of variational system identification of our material parameters. We incorporate the statistical F-test to maintain parsimony of representation. Using a new, local deformation decomposition locally into mixtures of biaxial and uniaxial tensile states, we evaluate experiments based on an analytical sensitivity metric, and discuss the implications for experimental design., Comment: 19 pages, 8 figures

The "Workshop on Machine learning in heterogeneous porous materials" brought together international scientific communities of applied mathematics, porous media, and material sciences with experts in the areas of heterogeneous materials, machine learning (ML) and applied mathematics to identify how ML can advance materials research. Within the scope of ML and materials research, the goal of the workshop was to discuss the state-of-the-art in each community, promote crosstalk and accelerate multi-disciplinary collaborative research, and identify challenges and opportunities. As the end result, four topic areas were identified: ML in predicting materials properties, and discovery and design of novel materials, ML in porous and fractured media and time-dependent phenomena, Multi-scale modeling in heterogeneous porous materials via ML, and Discovery of materials constitutive laws and new governing equations. This workshop was part of the AmeriMech Symposium series sponsored by the National Academies of Sciences, Engineering and Medicine and the U.S. National Committee on Theoretical and Applied Mechanics., Comment: The workshop link is: https://amerimech.mech.utah.edu

In this work we employ an encoder-decoder convolutional neural network to predict the failure locations of porous metal tension specimens based only on their initial porosities. The process we model is complex, with a progression from initial void nucleation, to saturation, and ultimately failure. The objective of predicting failure locations presents an extreme case of class imbalance since most of the material in the specimens do not fail. In response to this challenge, we develop and demonstrate the effectiveness of data- and loss-based regularization methods. Since there is considerable sensitivity of the failure location to the particular configuration of voids, we also use variational inference to provide uncertainties for the neural network predictions. We connect the deterministic and Bayesian convolutional neural networks at a theoretical level to explain how variational inference regularizes the training and predictions. We demonstrate that the resulting predicted variances are effective in ranking the locations that are most likely to fail in any given specimen., Comment: 40 pages, 12 figures

Material produced by current metal additive manufacturing processes is susceptible to variable performance due to imprecise control of internal porosity, surface roughness, and conformity to designed geometry. Using a double U-notched specimen, we investigate the interplay of nominal geometry and porosity in determining ductile failure characteristics during monotonic tensile loading. We simulate the effects of distributed porosity on plasticity and damage using a statistical model based on populations of pores visible in computed tomography scans and additional sub-threshold voids required to match experimental observations of deformation and failure. We interpret the simulation results from a physical viewpoint and provide statistical models of the probability of failure near stress concentrations. We provide guidance for designs where material defects could cause unexpected failures depending on the relative importance of these defects with respect to features of the nominal geometry.

We present an approach to studying and predicting the spatio-temporal progression of infectious diseases. We treat the problem by adopting a partial differential equation (PDE) version of the Susceptible, Infected, Recovered, Deceased (SIRD) compartmental model of epidemiology, which is achieved by replacing compartmental populations by their densities. Building on our recent work (Computational Mechanics, 66, 1177, 2020), we replace our earlier use of global polynomial basis functions with those having local support, as epitomized in the finite element method, for the spatial representation of the SIRD parameters. The time dependence is treated by inferring constant parameters over time intervals that coincide with the time step in semi-discrete numerical implementations. In combination, this amounts to a scheme of field inversion of the SIRD parameters over each time step. Applied to data over ten months of 2020 for the pandemic in the US state of Michigan and to all of Mexico, our system inference via field inversion infers spatio-temporally varying PDE SIRD parameters that replicate the progression of the pandemic with high accuracy. It also produces accurate predictions, when compared against data, for a three week period into 2021. Of note is the insight that is suggested on the spatio-temporal variation of infection, recovery and death rates, as well as patterns of the population's mobility revealed by diffusivities of the compartments.

Partial differential equation-based numerical solution frameworks for initial and boundary value problems have attained a high degree of complexity. Applied to a wide range of physics with the ultimate goal of enabling engineering solutions, these approaches encompass a spectrum of spatiotemporal discretization techniques that leverage solver technology and high performance computing. While high-fidelity solutions can be achieved using these approaches, they come at a high computational expense and complexity. Systems with billions of solution unknowns are now routine. The expense and complexity do not lend themselves to typical engineering design and decision-making, which must instead rely on reduced-order models. Here we present an approach to reduced-order modelling that builds off of recent graph theoretic work for representation, exploration, and analysis on computed states of physical systems (Banerjee et al., Comp. Meth. App. Mech. Eng., 351, 501-530, 2019). We extend a non-local calculus on finite weighted graphs to build such models by exploiting first order dynamics, polynomial expansions, and Taylor series. Some aspects of the non-local calculus related to consistency of the models are explored. Details on the numerical implementations and the software library that has been developed for non-local calculus on graphs are described. Finally, we present examples of applications to various quantities of interest in mechano-chemical systems., Comment: 72 pages, 19 figures

Li$_xTM$O$_2$ (TM={Ni, Co, Mn}) are promising cathodes for Li-ion batteries, whose electrochemical cycling performance is strongly governed by crystal structure and phase stability as a function of Li content at the atomistic scale. Here, we use Li$_x$CoO$_2$ (LCO) as a model system to benchmark a scale-bridging framework that combines density functional theory (DFT) calculations at the atomistic scale with phase field modeling at the continuum scale to understand the impact of phase stability on microstructure evolution. This scale bridging is accomplished by incorporating traditional statistical mechanics methods with integrable deep neural networks, which allows formation energies for specific atomic configurations to be coarse-grained and incorporated in a neural network description of the free energy of the material. The resulting realistic free energy functions enable atomistically informed phase-field simulations. These computational results allow us to make connections to experimental work on LCO cathode degradation as a function of temperature, morphology and particle size.

Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging of nutrients, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo significant morphological changes through deformation, scission, and fusion. Modeling the underlying mechanics of such morphological changes has traditionally relied on reduced order axisymmetric representations of membrane geometry and deformation. Axisymmetric representations, while robust and extensively deployed, suffer from their inability to model symmetry breaking deformations and structural bifurcations. To address this limitation, a 3D computational mechanics framework for high fidelity modeling of biomembrane deformation is presented. The proposed framework brings together Kirchhoff-Love thin-shell kinematics, Helfrich-energy based mechanics, and state-of-the-art numerical techniques for modeling deformation of surface geometries. Lipid bilayers are represented as spline-based surfaces immersed in a 3D space; this enables modeling of a wide spectrum of membrane geometries, boundary conditions, and deformations that are physically admissible in a 3D space. The mathematical basis of the framework and its numerical machinery are presented, and their utility is demonstrated by modeling 3 classical, yet non-trivial, membrane problems: formation of tubular shapes and their lateral constriction, Piezo1-induced membrane footprint generation and gating response, and the budding of membranes by protein coats during endocytosis. For each problem, the full 3D membrane deformation is captured, potential symmetry-breaking deformation paths identified, and various case studies of boundary and load conditions are presented. Using the endocytic vesicle budding as a case study, we also present a "phase diagram" for its symmetric and broken-symmetry states.

Solving partial differential equations (PDEs) is the canonical approach for understanding the behavior of physical systems. However, large scale solutions of PDEs using state of the art discretization techniques remains an expensive proposition. In this work, a new physics-constrained neural network (NN) approach is proposed to solve PDEs without labels, with a view to enabling high-throughput solutions in support of design and decision-making. Distinct from existing physics-informed NN approaches, where the strong form or weak form of PDEs are used to construct the loss function, we write the loss function of NNs based on the discretized residual of PDEs through an efficient, convolutional operator-based, and vectorized implementation. We explore an encoder-decoder NN structure for both deterministic and probabilistic models, with Bayesian NNs (BNNs) for the latter, which allow us to quantify both epistemic uncertainty from model parameters and aleatoric uncertainty from noise in the data. For BNNs, the discretized residual is used to construct the likelihood function. In our approach, both deterministic and probabilistic convolutional layers are used to learn the applied boundary conditions (BCs) and to detect the problem domain. As both Dirichlet and Neumann BCs are specified as inputs to NNs, a single NN can solve for similar physics, but with different BCs and on a number of problem domains. The trained surrogate PDE solvers can also make interpolating and extrapolating (to a certain extent) predictions for BCs that they were not exposed to during training. Such surrogate models are of particular importance for problems, where similar types of PDEs need to be repeatedly solved for many times with slight variations. We demonstrate the capability and performance of the proposed framework by applying it to steady-state diffusion, linear elasticity, and nonlinear elasticity., Comment: 37 pages, 25 figures

Presently, models for the parameterization of cross sections for nodal diffusion nuclear reactor calculations at different conditions using histories and branches are developed from reactor physics expertise and by trial and error. In this paper we describe the development and application of a novel graph theoretic approach (GTA) to develop the expressions for evaluating the cross sections in a nodal diffusion code. The GTA generalizes existing nodal cross section models into a ``non-orthogonal'' and extensible dimensional parameter space. Furthermore, it utilizes a rigorous calculus on graphs to formulate partial derivatives. The GTA cross section models can be generated in a number of ways. In our current work we explore a step-wise regression and a complete Taylor series expansion of the parameterized cross sections to develop expressions to evaluate them. To establish proof-of-principle of the GTA, we compare numerical results of GTA generated cross section evaluations with traditional models for canonical PWR case matrices and the AP1000 lattice designs., Comment: 15 pages, 7 figures

We introduce a class of high order accurate, semi-implicit Runge-Kutta schemes in the general setting of evolution equations that arise as gradient flow for a cost function, possibly with respect to an inner product that depends on the solution, and we establish their energy stability. This class includes as a special case high order, unconditionally stable schemes obtained via convexity splitting. The new schemes are demonstrated on a variety of gradient flows, including partial differential equations that are gradient flow with respect to the Wasserstein (mass transport) distance., Comment: arXiv admin note: text overlap with arXiv:1908.10246

We extend the classical SIR model of infectious disease spread to account for time dependence in the parameters, which also include diffusivities. The temporal dependence accounts for the changing characteristics of testing, quarantine and treatment protocols, while diffusivity incorporates a mobile population. This model has been applied to data on the evolution of the COVID-19 pandemic in the US state of Michigan. For system inference, we use recent advances; specifically our framework for Variational System Identification (Wang et al., Comp. Meth. App. Mech. Eng., 356, 44-74, 2019; arXiv:2001.04816 [cs.CE]) as well as Bayesian machine learning methods.

The free energy plays a fundamental role in descriptions of many systems in continuum physics. Notably, in multiphysics applications, it encodes thermodynamic coupling between different fields. It thereby gives rise to driving forces on the dynamics of interaction between the constituent phenomena. In mechano-chemically interacting materials systems, even consideration of only compositions, order parameters and strains can render the free energy to be reasonably high-dimensional. In proposing the free energy as a paradigm for scale bridging, we have previously exploited neural networks for their representation of such high-dimensional functions. Specifically, we have developed an integrable deep neural network (IDNN) that can be trained to free energy derivative data obtained from atomic scale models and statistical mechanics, then analytically integrated to recover a free energy density function. The motivation comes from the statistical mechanics formalism, in which certain free energy derivatives are accessible for control of the system, rather than the free energy itself. Our current work combines the IDNN with an active learning workflow to improve sampling of the free energy derivative data in a high-dimensional input space. Treated as input-output maps, machine learning accommodates role reversals between independent and dependent quantities as the mathematical descriptions change with scale bridging. As a prototypical system we focus on Ni-Al. Phase field simulations using the resulting IDNN representation for the free energy density of Ni-Al demonstrate that the appropriate physics of the material have been learned. To the best of our knowledge, this represents the most complete treatment of scale bridging, using the free energy for a practical materials system, that starts with electronic structure calculations and proceeds through statistical mechanics to continuum physics.

We present two approaches to system identification, i.e. the identification of partial differential equations (PDEs) from measurement data. The first is a regression-based Variational System Identification procedure that is advantageous in not requiring repeated forward model solves and has good scalability to large number of differential operators. However it has strict data type requirements needing the ability to directly represent the operators through the available data. The second is a Bayesian inference framework highly valuable for providing uncertainty quantification, and flexible for accommodating sparse and noisy data that may also be indirect quantities of interest. However, it also requires repeated forward solutions of the PDE models which is expensive and hinders scalability. We provide illustrations of results on a model problem for pattern formation dynamics, and discuss merits of the presented methods.

Many important multi-component crystalline solids undergo mechanochemical spinodal decomposition: a phase transformation in which the compositional redistribution is coupled with structural changes of the crystal, resulting in dynamically evolving microstructures. The ability to rapidly compute the macroscopic behavior based on these detailed microstructures is of paramount importance for accelerating material discovery and design. Here, our focus is on the macroscopic, nonlinear elastic response of materials harboring microstructure. Because of the diversity of microstructural patterns that can form, there is interest in taking a purely computational approach to predicting their macroscopic response. However, the evaluation of macroscopic, nonlinear elastic properties purely based on direct numerical simulations (DNS) is computationally very expensive, and hence impractical for material design when a large number of microstructures need to be tested. A further complexity of a hierarchical nature arises if the elastic free energy and its variation with strain is a small-scale fluctuation on the dominant trajectory of the total free energy driven by microstructural dynamics. To address these challenges, we present a data-driven approach, which combines advanced neural network (NN) models with DNS to predict the homogenized, macroscopic, mechanical free energy and stress fields arising in a family of multi-component crystalline solids that develop microstructure. The hierarchical structure of the free energy's evolution induces a multi-resolution character to the machine learning paradigm: We construct knowledge-based neural networks (KBNNs) with either pre-trained fully connected deep neural networks (DNNs), or pre-trained convolutional neural networks (CNNs) that describe the dominant characteristic of the data to fully represent the hierarchically evolving free energy., Comment: 24 pages, 15 figures

Machine learning is increasingly recognized as a promising technology in the biological, biomedical, and behavioral sciences. There can be no argument that this technique is incredibly successful in image recognition with immediate applications in diagnostics including electrophysiology, radiology, or pathology, where we have access to massive amounts of annotated data. However, machine learning often performs poorly in prognosis, especially when dealing with sparse data. This is a field where classical physics-based simulation seems to remain irreplaceable. In this review, we identify areas in the biomedical sciences where machine learning and multiscale modeling can mutually benefit from one another: Machine learning can integrate physics-based knowledge in the form of governing equations, boundary conditions, or constraints to manage ill-posted problems and robustly handle sparse and noisy data; multiscale modeling can integrate machine learning to create surrogate models, identify system dynamics and parameters, analyze sensitivities, and quantify uncertainty to bridge the scales and understand the emergence of function. With a view towards applications in the life sciences, we discuss the state of the art of combining machine learning and multiscale modeling, identify applications and opportunities, raise open questions, and address potential challenges and limitations. We anticipate that it will stimulate discussion within the community of computational mechanics and reach out to other disciplines including mathematics, statistics, computer science, artificial intelligence, biomedicine, systems biology, and precision medicine to join forces towards creating robust and efficient models for biological systems.

The threshold dynamics algorithm of Merriman, Bence, and Osher is only first order accurate in the two-phase setting. Its accuracy degrades further to half order in the multi-phase setting, a shortcoming it has in common with other related, more recent algorithms such as the equal surface tension version of the Voronoi implicit interface method. As a first, rigorous step in addressing this shortcoming, we present two different second order accurate versions of two-phase threshold dynamics. Unlike in previous efforts in this direction, we present careful consistency calculations for both of our algorithms. The first algorithm is consistent with its limit (motion by mean curvature) up to second order in any space dimension. The second achieves second order accuracy only in dimension two, but comes with a rigorous stability guarantee (unconditional energy stability) in any dimension -- a first for high order schemes of its type.

Fueled by breakthrough technology developments, the biological, biomedical, and behavioral sciences are now collecting more data than ever before. There is a critical need for time- and cost-efficient strategies to analyze and interpret these data to advance human health. The recent rise of machine learning as a powerful technique to integrate multimodality, multifidelity data, and reveal correlations between intertwined phenomena presents a special opportunity in this regard. However, classical machine learning techniques often ignore the fundamental laws of physics and result in ill-posed problems or non-physical solutions. Multiscale modeling is a successful strategy to integrate multiscale, multiphysics data and uncover mechanisms that explain the emergence of function. However, multiscale modeling alone often fails to efficiently combine large data sets from different sources and different levels of resolution. We show how machine learning and multiscale modeling can complement each other to create robust predictive models that integrate the underlying physics to manage ill-posed problems and explore massive design spaces. We critically review the current literature, highlight applications and opportunities, address open questions, and discuss potential challenges and limitations in four overarching topical areas: ordinary differential equations, partial differential equations, data-driven approaches, and theory-driven approaches. Towards these goals, we leverage expertise in applied mathematics, computer science, computational biology, biophysics, biomechanics, engineering mechanics, experimentation, and medicine. Our multidisciplinary perspective suggests that integrating machine learning and multiscale modeling can provide new insights into disease mechanisms, help identify new targets and treatment strategies, and inform decision making for the benefit of human health.

We introduce a class of unconditionally energy stable, high order accurate schemes for gradient flows in a very general setting. The new schemes are a high order analogue of the minimizing movements approach for generating a time discrete approximation to a gradient flow by solving a sequence of optimization problems. In particular, each step entails minimizing the associated energy of the gradient flow plus a movement limiter term that is, in the classical context of steepest descent with respect to an inner product, simply quadratic. A variety of existing unconditionally stable numerical methods can be recognized as (typically just first order accurate in time) minimizing movement schemes for their associated evolution equations, already requiring the optimization of the energy plus a quadratic term at every time step. Therefore, our approach gives a painless way to extend these to high order accurate in time schemes while maintaining their unconditional stability. In this sense, it can be viewed as a variational analogue of Richardson extrapolation.

Membrane neck formation is essential for scission, which, as recent experiments on tubules have demonstrated, can be location dependent. The diversity of biological machinery that can constrict a neck such as dynamin, actin, ESCRTs and BAR proteins, and the range of forces and deflection over which they operate, suggest that the constriction process is functionally mechanical and robust to changes in biological environment. In this study, we used a mechanical model of the lipid bilayer to systematically investigate the influence of location, symmetry constraints, and helical forces on membrane neck constriction. Simulations from our model demonstrated that the energy barriers associated with constriction of a membrane neck are location-dependent. Importantly, if symmetry restrictions are relaxed, then the energy barrier for constriction is dramatically lowered and the membrane buckles at lower values of forcing parameters. Our simulations also show that constriction due to helical proteins further reduces the energy barrier for neck formation compared to cylindrical proteins. These studies establish that despite different molecular mechanisms of neck formation in cells, the mechanics of constriction naturally leads to a loss of symmetry that can lower the energy barrier to constriction., Comment: Soft Matter (2019)