Jutta Rogal

Bio: Jutta Rogal is an academic researcher from New York University. The author has contributed to research in topics: Degrees of freedom & Multiscale modeling. The author has co-authored 2 publications. Previous affiliations of Jutta Rogal include Free University of Berlin.

Reaction coordinates in complex systems-a perspective

Abstract: In molecular simulations, the identification of suitable reaction coordinates is central to both the analysis and sampling of transitions between metastable states in complex systems. If sufficient simulation data are available, a number of methods have been developed to reduce the vast amount of high-dimensional data to a small number of essential degrees of freedom representing the reaction coordinate. Likewise, if the reaction coordinate is known, a variety of approaches have been proposed to enhance the sampling along the important degrees of freedom. Often, however, neither one nor the other is available. One of the key questions is therefore, how to construct reaction coordinates and evaluate their validity. Another challenges arises from the physical interpretation of reaction coordinates, which is often addressed by correlating physically meaningful parameters with conceptually well-defined but abstract reaction coordinates. Furthermore, machine learning based methods are becoming more and more applicable also to the reaction coordinate problem. This perspective highlights central aspects in the identification and evaluation of reaction coordinates and discusses recent ideas regarding automated computational frameworks to combine the optimization of reaction coordinates and enhanced sampling.

Atomic-scale modeling of superalloys

Abstract: Atomistic theory holds the promise for the ab initio development of superalloys based on the fundamental principles of quantum mechanics. The last years showed a rapid progress in the field. Results from atomistic modeling enter larger-scale simulations of alloy performance and often may be compared directly to experimental characterization. In this chapter we give an overview of atomistic modeling and simulation for Ni-base superalloys. We cover descriptions of the interatomic interaction from quantum-mechanical simulations with a small number of atoms to multi-million-atom simulations with classical interatomic potentials. Methods to determine structural stability for different chemical compositions, thermodynamic and kinetic properties of typical defects in superalloys, and relations to mechanical deformation are discussed. Connections to other modeling techniques are outlined.

Machine intelligence for chemical reaction space

Abstract: Discovering new reactions, optimizing their performance, and extending the synthetically accessible chemical space are critical drivers for major technological advances and more sustainable processes. The current wave of machine intelligence is revolutionizing all data‐rich disciplines. Machine intelligence has emerged as a potential game‐changer for chemical reaction space exploration and the synthesis of novel molecules and materials. Herein, we will address the recent development of data‐driven technologies for chemical reaction tasks, including forward reaction prediction, retrosynthesis, reaction optimization, catalysts design, inference of experimental procedures, and reaction classification. Accurate predictions of chemical reactivity are changing the R&D processes and, at the same time, promoting an accelerated discovery scheme both in academia and across chemical and pharmaceutical industries. This work will help to clarify the key contributions in the fields and the open challenges that remain to be addressed.

Discover, Sample, and Refine: Exploring Chemistry with Enhanced Sampling Techniques.

Abstract: Over the last few decades, enhanced sampling methods have been continuously improved. Here, we exploit this progress and propose a modular workflow for blind reaction discovery and determination of reaction paths. In a three-step strategy, at first we use a collective variable derived from spectral graph theory in conjunction with the explore variant of the on-the-fly probability enhanced sampling method to drive reaction discovery runs. Once different chemical products are determined, we construct an ad-hoc neural network-based collective variable to improve sampling, and finally we refine the results using the free energy perturbation theory and a more accurate Hamiltonian. We apply this strategy to both intramolecular and intermolecular reactions. Our workflow requires minimal user input and extends the power of ab initio molecular dynamics to explore and characterize the reaction space.

Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI).

Abstract: A method for obtaining appropriate reaction coordinates is required to identify transition states distinguishing the product and reactant in complex molecular systems. Recently, abundant research has been devoted to obtaining reaction coordinates using artificial neural networks from deep learning literature, where many collective variables are typically utilized in the input layer. However, it is difficult to explain the details of which collective variables contribute to the predicted reaction coordinates owing to the complexity of the nonlinear functions in deep neural networks. To overcome this limitation, we used Explainable Artificial Intelligence (XAI) methods of the Local Interpretable Model-agnostic Explanation (LIME) and the game theory-based framework known as Shapley Additive exPlanations (SHAP). We demonstrated that XAI enables us to obtain the degree of contribution of each collective variable to reaction coordinates that is determined by nonlinear regressions with deep learning for the committor of the alanine dipeptide isomerization in vacuum. In particular, both LIME and SHAP provide important features to the predicted reaction coordinates, which are characterized by appropriate dihedral angles consistent with those previously reported from the committor test analysis. The present study offers an AI-aided framework to explain the appropriate reaction coordinates, which acquires considerable significance when the number of degrees of freedom increases.