2,877 research outputs found
Molecular Modeling in Enzyme Design, Toward In Silico Guided Directed Evolution
Directed evolution (DE) creates diversity in subsequent rounds of mutagenesis in the quest of increased protein stability, substrate binding, and catalysis. Although this technique does not require any structural/mechanistic knowledge of the system, the frequency of improved mutations is usually low. For this reason, computational tools are increasingly used to focus the search in sequence space, enhancing the efficiency of laboratory evolution. In particular, molecular modeling methods provide a unique tool to grasp the sequence/structure/function relationship of the protein to evolve, with the only condition that a structural model is provided. With this book chapter, we tried to guide the reader through the state of the art of molecular modeling, discussing their strengths, limitations, and directions. In addition, we suggest a possible future template for in silico directed evolution where we underline two main points: a hierarchical computational protocol combining several different techniques and a synergic effort between simulations and experimental validation.Peer ReviewedPostprint (author's final draft
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Combining artificial intelligence and robotic system in chemical product/process design
Product design for formulations is an active and challenging area of research. The new challenges of a fast-paced market, products of increasing complexity, and practical translation of sustainability paradigms require re-examination the existing theoretical frameworks to include the advantages from business and research digitalization. This thesis is based on the hypotheses that (i) new products with desired properties can be discovered by using a robotic platform combined with an intelligent optimization algorithm, and (ii) we can the connect data-driven optimisation with physico-chemical knowledge generation, which will result in a suitable model for translation of product discovery to production, thus impacting on the process development steps towards industrial applications. This thesis focuses on two complex physicochemical systems as case studies, namely the oil-in-water shampoo system and sunscreen products.
Firstly, I report the coupling of a machine-learning classification algorithm with the Thompson-Sampling Efficient Multi-Optimization (TSEMO) for the simultaneous optimization of continuous and discrete outputs. The methodology was successfully applied to the design of a formulated liquid product of commercial interest for which no physical models are available. Experiments were carried out in a semi-automated fashion using robotic platforms triggered by the machine-learning algorithms. The proposed closed-loop optimization framework allowed to find suitable recipes meeting the customer-defined criteria within 15 working days, outperforming human intuition in the target performance of the formulations. The framework was then extended to co-optimization of both formulation and process conditions and ingredients selection.
Secondly, I report the methods for the identification of new physical knowledge in a complex system where a prior knowledge is insufficient. The application of feature engineering methods in sun cream protection prediction was discussed. It was found that the concentration of UVA and UVB filters are key features, together with product viscosity, which match with the experts’ domain knowledge in sun cream product design. It was also found that through the combination of feature engineering and machine learning, high-fidelity model could be constructed. Furthermore, a modified mixed-integer nonlinear programming (MINLP) formulation for symbolic regression method was proposed for identification of physical models from noisy experimental data. The globally optimal search was extended to identify physical models and to cope with noise in the experimental data predictor variables.The methodology was proven to be successful in identifying the correct physical models describing the relationship between shear stress and shear rate for both Newtonian and non-Newtonian fluids, and simple kinetic laws of chemical reactions.
The work of this thesis shows that machine learning methods, together with automated experimental system, can speed-up the R&D process of formulated product design as well as gain new physical knowledge of the complex systems
Vision 2040: A Roadmap for Integrated, Multiscale Modeling and Simulation of Materials and Systems
Over the last few decades, advances in high-performance computing, new materials characterization methods, and, more recently, an emphasis on integrated computational materials engineering (ICME) and additive manufacturing have been a catalyst for multiscale modeling and simulation-based design of materials and structures in the aerospace industry. While these advances have driven significant progress in the development of aerospace components and systems, that progress has been limited by persistent technology and infrastructure challenges that must be overcome to realize the full potential of integrated materials and systems design and simulation modeling throughout the supply chain. As a result, NASA's Transformational Tools and Technology (TTT) Project sponsored a study (performed by a diverse team led by Pratt & Whitney) to define the potential 25-year future state required for integrated multiscale modeling of materials and systems (e.g., load-bearing structures) to accelerate the pace and reduce the expense of innovation in future aerospace and aeronautical systems. This report describes the findings of this 2040 Vision study (e.g., the 2040 vision state; the required interdependent core technical work areas, Key Element (KE); identified gaps and actions to close those gaps; and major recommendations) which constitutes a community consensus document as it is a result of over 450 professionals input obtain via: 1) four society workshops (AIAA, NAFEMS, and two TMS), 2) community-wide survey, and 3) the establishment of 9 expert panels (one per KE) consisting on average of 10 non-team members from academia, government and industry to review, update content, and prioritize gaps and actions. The study envisions the development of a cyber-physical-social ecosystem comprised of experimentally verified and validated computational models, tools, and techniques, along with the associated digital tapestry, that impacts the entire supply chain to enable cost-effective, rapid, and revolutionary design of fit-for-purpose materials, components, and systems. Although the vision focused on aeronautics and space applications, it is believed that other engineering communities (e.g., automotive, biomedical, etc.) can benefit as well from the proposed framework with only minor modifications. Finally, it is TTT's hope and desire that this vision provides the strategic guidance to both public and private research and development decision makers to make the proposed 2040 vision state a reality and thereby provide a significant advancement in the United States global competitiveness
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