Zhen Li

Elham Kiyani, Mahdi Kooshkbaghi, Khemraj Shukla et al.

The molten sand, a mixture of calcia, magnesia, alumina, and silicate, known as CMAS, is characterized by its high viscosity, density, and surface tension. The unique properties of CMAS make it a challenging material to deal with in high-temperature applications, requiring innovative solutions and materials to prevent its buildup and damage to critical equipment. Here, we use multiphase many-body dissipative particle dynamics (mDPD) simulations to study the wetting dynamics of highly viscous molten CMAS droplets. The simulations are performed in three dimensions, with varying initial droplet sizes and equilibrium contact angles. We propose a coarse parametric ordinary differential equation (ODE) that captures the spreading radius behavior of the CMAS droplets. The ODE parameters are then identified based on the Physics-Informed Neural Network (PINN) framework. Subsequently, the closed form dependency of parameter values found by PINN on the initial radii and contact angles are given using symbolic regression. Finally, we employ Bayesian PINNs (B-PINNs) to assess and quantify the uncertainty associated with the discovered parameters. In brief, this study provides insight into spreading dynamics of CMAS droplets by fusing simple parametric ODE modeling and state-of-the-art machine learning techniques.

Yuan Lan, Zhen Li, Jie Sun et al.

Deep neural networks (DNNs) recently emerged as a promising tool for analyzing and solving complex differential equations arising in science and engineering applications. Alternative to traditional numerical schemes, learning-based solvers utilize the representation power of DNNs to approximate the input-output relations in an automated manner. However, the lack of physics-in-the-loop often makes it difficult to construct a neural network solver that simultaneously achieves high accuracy, low computational burden, and interpretability. In this work, focusing on a class of evolutionary PDEs characterized by having decomposable operators, we show that the classical ``operator splitting'' numerical scheme of solving these equations can be exploited to design neural network architectures. This gives rise to a learning-based PDE solver, which we name Deep Operator-Splitting Network (DOSnet). Such non-black-box network design is constructed from the physical rules and operators governing the underlying dynamics contains learnable parameters, and is thus more flexible than the standard operator splitting scheme. Once trained, it enables the fast solution of the same type of PDEs. To validate the special structure inside DOSnet, we take the linear PDEs as the benchmark and give the mathematical explanation for the weight behavior. Furthermore, to demonstrate the advantages of our new AI-enhanced PDE solver, we train and validate it on several types of operator-decomposable differential equations. We also apply DOSnet to nonlinear Schrödinger equations (NLSE) which have important applications in the signal processing for modern optical fiber transmission systems, and experimental results show that our model has better accuracy and lower computational complexity than numerical schemes and the baseline DNNs.

Minglei Lu, Ali Mohammadi, Zhaoxu Meng et al.

Additive manufacturing has been recognized as an industrial technological revolution for manufacturing, which allows fabrication of materials with complex three-dimensional (3D) structures directly from computer-aided design models. The mechanical properties of interpenetrating phase composites (IPCs), especially response to dynamic loading, highly depend on their 3D structures. In general, for each specified structural design, it could take hours or days to perform either finite element analysis (FEA) or experiments to test the mechanical response of IPCs to a given dynamic load. To accelerate the physics-based prediction of mechanical properties of IPCs for various structural designs, we employ a deep neural operator (DNO) to learn the transient response of IPCs under dynamic loading as surrogate of physics-based FEA models. We consider a 3D IPC beam formed by two metals with a ratio of Young's modulus of 2.7, wherein random blocks of constituent materials are used to demonstrate the generality and robustness of the DNO model. To obtain FEA results of IPC properties, 5,000 random time-dependent strain loads generated by a Gaussian process kennel are applied to the 3D IPC beam, and the reaction forces and stress fields inside the IPC beam under various loading are collected. Subsequently, the DNO model is trained using an incremental learning method with sequence-to-sequence training implemented in JAX, leading to a 100X speedup compared to widely used vanilla deep operator network models. After an offline training, the DNO model can act as surrogate of physics-based FEA to predict the transient mechanical response in terms of reaction force and stress distribution of the IPCs to various strain loads in one second at an accuracy of 98%. Also, the learned operator is able to provide extended prediction of the IPC beam subject to longer random strain loads at a reasonably well accuracy.

Elham Kiyani, Amit Makarand Deshpande, Madhura Limaye et al.

Fiber reinforcement and polymer matrix respond differently to manufacturing conditions due to mismatch in coefficient of thermal expansion and matrix shrinkage during curing of thermosets. These heterogeneities generate residual stresses over multiple length scales, whose partial release leads to process-induced deformation (PID), requiring accurate prediction and mitigation via optimized non-isothermal cure cycles. This study considers a unidirectional AS4 carbon fiber/amine bi-functional epoxy prepreg and models PID using a two-mechanism framework that accounts for thermal expansion/shrinkage and cure shrinkage. The model is validated against manufacturing trials to identify initial and boundary conditions, then used to generate PID responses for a diverse set of non-isothermal cure cycles (time-temperature profiles). Building on this physics-based foundation, we develop a data-driven surrogate based on Deep Operator Networks (DeepONets). A DeepONet is trained on a dataset combining high-fidelity simulations with targeted experimental measurements of PID. We extend this to a Feature-wise Linear Modulation (FiLM) DeepONet, where branch-network features are modulated by external parameters, including the initial degree of cure, enabling prediction of time histories of degree of cure, viscosity, and deformation. Because experimental data are available only at limited time instances (for example, final deformation), we use transfer learning: simulation-trained trunk and branch networks are fixed and only the final layer is updated using measured final deformation. Finally, we augment the framework with Ensemble Kalman Inversion (EKI) to quantify uncertainty under experimental conditions and to support optimization of cure schedules for reduced PID in composites.

Xuhui Meng, Zhen Li, Dongkun Zhang et al.

Physics-informed neural networks (PINNs) encode physical conservation laws and prior physical knowledge into the neural networks, ensuring the correct physics is represented accurately while alleviating the need for supervised learning to a great degree. While effective for relatively short-term time integration, when long time integration of the time-dependent PDEs is sought, the time-space domain may become arbitrarily large and hence training of the neural network may become prohibitively expensive. To this end, we develop a parareal physics-informed neural network (PPINN), hence decomposing a long-time problem into many independent short-time problems supervised by an inexpensive/fast coarse-grained (CG) solver. In particular, the serial CG solver is designed to provide approximate predictions of the solution at discrete times, while initiate many fine PINNs simultaneously to correct the solution iteratively. There is a two-fold benefit from training PINNs with small-data sets rather than working on a large-data set directly, i.e., training of individual PINNs with small-data is much faster, while training the fine PINNs can be readily parallelized. Consequently, compared to the original PINN approach, the proposed PPINN approach may achieve a significant speedup for long-time integration of PDEs, assuming that the CG solver is fast and can provide reasonable predictions of the solution, hence aiding the PPINN solution to converge in just a few iterations. To investigate the PPINN performance on solving time-dependent PDEs, we first apply the PPINN to solve the Burgers equation, and subsequently we apply the PPINN to solve a two-dimensional nonlinear diffusion-reaction equation. Our results demonstrate that PPINNs converge in a couple of iterations with significant speed-ups proportional to the number of time-subdomains employed.

Zhen Li, Sheng Wang, Yizhou Yu et al.

Computational prediction of membrane protein (MP) structures is very challenging partially due to lack of sufficient solved structures for homology modeling. Recently direct evolutionary coupling analysis (DCA) sheds some light on protein contact prediction and accordingly, contact-assisted folding, but DCA is effective only on some very large-sized families since it uses information only in a single protein family. This paper presents a deep transfer learning method that can significantly improve MP contact prediction by learning contact patterns and complex sequence-contact relationship from thousands of non-membrane proteins (non-MPs). Tested on 510 non-redundant MPs, our deep model (learned from only non-MPs) has top L/10 long-range contact prediction accuracy 0.69, better than our deep model trained by only MPs (0.63) and much better than a representative DCA method CCMpred (0.47) and the CASP11 winner MetaPSICOV (0.55). The accuracy of our deep model can be further improved to 0.72 when trained by a mix of non-MPs and MPs. When only contacts in transmembrane regions are evaluated, our method has top L/10 long-range accuracy 0.62, 0.57, and 0.53 when trained by a mix of non-MPs and MPs, by non-MPs only, and by MPs only, respectively, still much better than MetaPSICOV (0.45) and CCMpred (0.40). All these results suggest that sequence-structure relationship learned by our deep model from non-MPs generalizes well to MP contact prediction. Improved contact prediction also leads to better contact-assisted folding. Using only top predicted contacts as restraints, our deep learning method can fold 160 and 200 of 510 MPs with TMscore>0.6 when trained by non-MPs only and by a mix of non-MPs and MPs, respectively, while CCMpred and MetaPSICOV can do so for only 56 and 77 MPs, respectively. Our contact-assisted folding also greatly outperforms homology modeling.

Sheng Wang, Siqi Sun, Zhen Li et al.

Recently exciting progress has been made on protein contact prediction, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual networks. This deep neural network allows us to model very complex sequence-contact relationship as well as long-range inter-contact correlation. Our method greatly outperforms existing contact prediction methods and leads to much more accurate contact-assisted protein folding. Tested on three datasets of 579 proteins, the average top L long-range prediction accuracy obtained our method, the representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints can yield correct folds (i.e., TMscore>0.6) for 203 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 proteins, respectively. Further, our contact-assisted models have much better quality than template-based models. Using our predicted contacts as restraints, we can (ab initio) fold 208 of the 398 membrane proteins with TMscore>0.5. By contrast, when the training proteins of our method are used as templates, homology modeling can only do so for 10 of them. One interesting finding is that even if we do not train our prediction models with any membrane proteins, our method works very well on membrane protein prediction. Finally, in recent blind CAMEO benchmark our method successfully folded 5 test proteins with a novel fold.