Ligand strain energy, the energy difference between the bound and unbound conformations of a ligand, is an important component of structure-based small molecule drug design. A large majority of observed ligands in protein-small molecule co-crystal structures bind in low-strain conformations, making strain energy a useful filter for structure-based drug design. In this work we present a tool for calculating ligand strain with a high accuracy. StrainRelief uses a MACE Neural Network Potential (NNP), trained on a large database of Density Functional Theory (DFT) calculations to estimate ligand strain of neutral molecules with quantum accuracy. We show that this tool estimates strain energy differences relative to DFT to within 1.4 kcal/mol, more accurately than alternative NNPs. These results highlight the utility of NNPs in drug discovery, and provide a useful tool for drug discovery teams.

Accurate constitutive models of soft materials are crucial for understanding their mechanical behavior and ensuring reliable predictions in the design process. To this end, scientific machine learning research has produced flexible and general material model architectures that can capture the behavior of a wide range of materials, reducing the need for expert-constructed closed-form models. The focus has gradually shifted towards embedding physical constraints in the network architecture to regularize these over-parameterized models. Two popular approaches are input convex neural networks (ICNN) and neural ordinary differential equations (NODE). A related alternative has been the generalization of closed-form models, such as sparse regression from a large library. Remarkably, all prior work using ICNN or NODE uses the invariants of the Cauchy-Green tensor and none uses the principal stretches. In this work, we construct general polyconvex functions of the principal stretches in a physics-aware deep-learning framework and offer insights and comparisons to invariant-based formulations. The framework is based on recent developments to characterize polyconvex functions in terms of convex functions of the right stretch tensor $\mathbf{U}$, its cofactor $\text{cof}\mathbf{U}$, and its determinant $J$. Any convex function of a symmetric second-order tensor can be described with a convex and symmetric function of its eigenvalues. Thus, we first describe convex functions of $\mathbf{U}$ and $\text{cof}\mathbf{U}$ in terms of their respective eigenvalues using deep Holder sets composed with ICNN functions. A third ICNN takes as input $J$ and the two convex functions of $\mathbf{U}$ and $\text{cof}\mathbf{U}$, and returns the strain energy as output. The ability of the model to capture arbitrary materials is demonstrated using synthetic and experimental data.

Free-form structural forms are widely used to design spatial structures for their irregular spatial morphology. Current free-form form-finding methods cannot adequately meet the material properties, structural requirements or construction conditions, which brings the deviation between the initial 3D geometric design model and the constructed free-form structure. Thus, the main focus of this paper is to improve the rationality of free-form morphology considering multiple objectives in line with the characteristics and constraints of material. In this paper, glued laminated timber is selected as a case. Firstly, machine learning is adopted based on the predictive capability. By selecting a free-form timber grid structure and following the principles of NURBS, the free-form structure is simplified into free-form curves. The transformer is selected to train and predict the curvatures of the curves considering the material characteristics. After predicting the curvatures, the curves are transformed into vectors consisting of control points, weights, and knot vectors. To ensure the constructability and robustness of the structure, minimising the mass of the structure, stress and strain energy are the optimisation objectives. Two parameters (weight and the z-coordinate of the control points) of the free-from morphology are extracted as the variables of the free-form morphology to conduct the optimisation. The evaluation algorithm was selected as the optimal tool due to its capability to optimise multiple parameters. While optimising the two variables, the mechanical performance evaluation indexes such as the maximum displacement in the z-direction are demonstrated in the 60th step. The optimisation results for structure mass, stress and strain energy after 60 steps show the tendency of oscillation convergence, which indicates the efficiency of the proposal multi-objective optimisation.

While there has been discussion about noise levels in molecular docking datasets such as PDBBind, a thorough analysis of their physical/chemical and bioactivity noise characteristics is still lacking. PoseCheck addresses this issue by examining molecular strain energy, molecular-protein clashes, and interactions, but it is primarily created for $de$ $novo$ drug design. Another important metric in molecular docking, Binding Affinity Energy, is better assessed by the new empirical score function, AA-Score, which has demonstrated improved performance over existing methods. To tackle these challenges, we propose the COMPASS method, which integrates the PoseCheck and AA-Score modules. This approach evaluates dataset noise levels and the physical/chemical and bioactivity feasibility of docked molecules. Our analysis of the PDBBind dataset using COMPASS reveals significant noise in the ground truth data. Additionally, we incorporate COMPASS with the state-of-the-art molecular docking method, DiffDock, in inference mode to achieve efficient and accurate assessments of docked ligands. Finally, we propose a new paradigm to enhance model performance for molecular docking through fine-tuning and discuss the potential benefits of this approach. The source code is available publicly at https://github.com/BIMSBbioinfo/Compass.

In this work, we introduce AutoFragDiff, a fragment-based autoregressive diffusion model for generating 3D molecular structures conditioned on target protein structures. We employ geometric vector perceptrons to predict atom types and spatial coordinates of new molecular fragments conditioned on molecular scaffolds and protein pockets. Our approach improves the local geometry of the resulting 3D molecules while maintaining high predicted binding affinity to protein targets. The model can also perform scaffold extension from user-provided starting molecular scaffold.

Abstract-- Soft robotic grasping has rapidly spread through the academic robotics community in recent years and pushed into industrial applications. At the same time, multimaterial 3D printing has become widely available, enabling the monolithic manufacture of devices containing rigid and elastic sections. We propose a novel design technique that leverages both technologies and can automatically design bespoke soft robotic grippers for fruit-picking and similar applications. We demonstrate the novel topology optimisation formulation that generates multi-material soft grippers, can solve internal and external pressure boundaries, and investigate methods to produce air-tight designs. Compared to existing methods, it vastly expands the searchable design space while increasing simulation accuracy.

There has been a massive increase in research interest towards applying data driven methods to problems in mechanics. While traditional machine learning (ML) methods have enabled many breakthroughs, they rely on the assumption that the training (observed) data and testing (unseen) data are independent and identically distributed (i.i.d). Thus, traditional ML approaches often break down when applied to real world mechanics problems with unknown test environments and data distribution shifts. In contrast, out-of-distribution (OOD) generalization assumes that the test data may shift (i.e., violate the i.i.d. assumption). To date, multiple methods have been proposed to improve the OOD generalization of ML methods. However, because of the lack of benchmark datasets for OOD regression problems, the efficiency of these OOD methods on regression problems, which dominate the mechanics field, remains unknown. To address this, we investigate the performance of OOD generalization methods for regression problems in mechanics. Specifically, we identify three OOD problems: covariate shift, mechanism shift, and sampling bias. For each problem, we create two benchmark examples that extend the Mechanical MNIST dataset collection, and we investigate the performance of popular OOD generalization methods on these mechanics-specific regression problems. Our numerical experiments show that in most cases, while the OOD generalization algorithms perform better compared to traditional ML methods on these OOD problems, there is a compelling need to develop more robust OOD generalization methods that are effective across multiple OOD scenarios. Overall, we expect that this study, as well as the associated open access benchmark datasets, will enable further development of OOD generalization methods for mechanics specific regression problems.

Data-driven methods are becoming an essential part of computational mechanics due to their unique advantages over traditional material modeling. Deep neural networks are able to learn complex material response without the constraints of closed-form approximations. However, imposing the physics-based mathematical requirements that any material model must comply with is not straightforward for data-driven approaches. In this study, we use a novel class of neural networks, known as neural ordinary differential equations (N-ODEs), to develop data-driven material models that automatically satisfy polyconvexity of the strain energy function with respect to the deformation gradient, a condition needed for the existence of minimizers for boundary value problems in elasticity. We take advantage of the properties of ordinary differential equations to create monotonic functions that approximate the derivatives of the strain energy function with respect to the invariants of the right Cauchy-Green deformation tensor. The monotonicity of the derivatives guarantees the convexity of the energy. The N-ODE material model is able to capture synthetic data generated from closed-form material models, and it outperforms conventional models when tested against experimental data on skin, a highly nonlinear and anisotropic material. We also showcase the use of the N-ODE material model in finite element simulations. The framework is general and can be used to model a large class of materials. Here we focus on hyperelasticity, but polyconvex strain energies are a core building block for other problems in elasticity such as viscous and plastic deformations. We therefore expect our methodology to further enable data-driven methods in computational mechanics

Partial Differential Equations (PDE) are fundamental to model different phenomena in science and engineering mathematically. Solving them is a crucial step towards a precise knowledge of the behaviour of natural and engineered systems. In general, in order to solve PDEs that represent real systems to an acceptable degree, analytical methods are usually not enough. One has to resort to discretization methods. For engineering problems, probably the best known option is the finite element method (FEM). However, powerful alternatives such as mesh-free methods and Isogeometric Analysis (IGA) are also available. The fundamental idea is to approximate the solution of the PDE by means of functions specifically built to have some desirable properties. In this contribution, we explore Deep Neural Networks (DNNs) as an option for approximation. They have shown impressive results in areas such as visual recognition. DNNs are regarded here as function approximation machines. There is great flexibility to define their structure and important advances in the architecture and the efficiency of the algorithms to implement them make DNNs a very interesting alternative to approximate the solution of a PDE. We concentrate in applications that have an interest for Computational Mechanics. Most contributions that have decided to explore this possibility have adopted a collocation strategy. In this contribution, we concentrate in mechanical problems and analyze the energetic format of the PDE. The energy of a mechanical system seems to be the natural loss function for a machine learning method to approach a mechanical problem. As proofs of concept, we deal with several problems and explore the capabilities of the method for applications in engineering.