arXiv subjects

Patrick Reiser

Publications and source records attributed to Patrick Reiser.

17 recordsLinked to original sources

arXiv2025

Learning Potential Energy Surfaces of Hydrogen Atom Transfer Reactions in Peptides

Hydrogen atom transfer (HAT) reactions are essential in many biological processes, such as radical migration in damaged proteins, but their mechanistic pathways remain incompletely understood. Simulating HAT is challenging due to the need for quantum chemical accuracy at biologically relevant scales; thus, neither classical force fields nor DFT-based molecular dynamics are applicable. Machine-learned potentials offer an alternative, able to learn potential energy surfaces (PESs) with near-quantum accuracy. However, training these models to generalize across diverse HAT configurations, especially at radical positions in proteins, requires tailored data generation and careful model selection. Here, we systematically generate HAT configurations in peptides to build large datasets using semiempirical methods and DFT. We benchmark three graph neural network architectures (SchNet, Allegro, and MACE) on their ability to learn HAT PESs and indirectly predict reaction barriers from energy predictions. MACE consistently outperforms the others in energy, force, and barrier prediction, achieving a mean absolute error of 1.13 kcal/mol on out-of-distribution DFT barrier predictions. Using molecular dynamics, we show our MACE potential is stable, reactive, and generalizes beyond training data to model HAT barriers in collagen I. This accuracy enables integration of ML potentials into large-scale collagen simulations to compute reaction rates from predicted barriers, advancing mechanistic understanding of HAT and radical migration in peptides. We analyze scaling laws, model transferability, and cost-performance trade-offs, and outline strategies for improvement by combining ML potentials with transition state search algorithms and active learning. Our approach is generalizable to other biomolecular systems, enabling quantum-accurate simulations of chemical reactivity in complex environments.

cs.LG↗

arXiv2024

Discovering one molecule out of a million: inverse design of molecular hole transporting semiconductors tailored for perovskite solar cells

The inverse design of tailored organic molecules for specific optoelectronic devices of high complexity holds an enormous potential, but has not yet been realized1,2. The complexity and literally infinite diversity of conjugated molecular structures present both, an unprecedented opportunity for technological breakthroughs as well as an unseen optimization challenge. Current models rely on big data which do not exist for specialized research films. However, a hybrid computational and high throughput experimental screening workflow allowed us to train predictive models with as little as 149 molecules. We demonstrate a unique closed-loop workflow combining high throughput synthesis and Bayesian optimization that discovers new hole transporting materials with tailored properties for solar cell applications. A series of high-performance molecules were identified from minimal suggestions, achieving up to 26.23% (certified 25.88%) power conversion efficiency in perovskite solar cells. Our work paves the way for rapid, informed discovery in vast molecular libraries, revolutionizing material selection for complex devices. We believe that our approach can be generalized to other emerging fields and indeed accelerate the development of optoelectronic semiconductor devices in general.

cond-mat.mtrl-sci↗

arXiv2024

Identifying the Origin of Thermal Modulation of Exchange Bias in MnPS3/Fe3GeTe2 van der Waals Heterostructures

The exchange bias phenomenon, inherent in exchange-coupled ferromagnetic and antiferromagnetic systems, has intrigued researchers for decades. Van der Waals materials, with their layered structure, provide an optimal platform for probing such physical phenomena. However, achieving a facile and effective means to manipulate exchange bias in van der Waals heterostructures remains challenging. In this study, we investigate the origin of exchange bias in MnPS3/Fe3GeTe2 van der Waals heterostructures. Our work demonstrates a method to modulate unidirectional exchange anisotropy, achieving an unprecedented nearly 1000% variation through simple thermal cycling. Despite the compensated interfacial spin configuration of MnPS3, magneto-transport measurements reveal a huge 170 mT exchange bias at 5 K, one of the largest observed in van der Waals antiferromagnet-ferromagnet interfaces. This substantial magnitude of the exchange bias is linked to an anomalous weak ferromagnetic ordering in MnPS3 below 40 K. On the other hand, the tunability of exchange bias during thermal cycling is ascribed to the modified arrangement of interfacial atoms and changes in the vdW gap during field cooling. Our findings highlight a robust and easily adjustable exchange bias in van der Waals antiferromagnetic/ferromagnetic heterostructures, presenting a straightforward approach to enhance other interface-related spintronic phenomena for practical applications. A detailed study of the interface reveals migration of atoms between the layers, leading to the formation of amorphous region on either side of the van der Waals gap, underscoring the importance of precise characterization of interfaces in van der Waals heterostructures, which are often presumed to have pristine interfaces.

cond-mat.mtrl-sci↗

arXiv2023

Nanoscale magnetism and magnetic phase transitions in atomically thin CrSBr

Since their first observation in 2017, atomically thin van der Waals (vdW) magnets have attracted significant fundamental, and application-driven attention. However, their low ordering temperatures, $T_c$, sensitivity to atmospheric conditions and difficulties in preparing clean large-area samples still present major limitations to further progress. The remarkably stable high-$T_c$ vdW magnet CrSBr has the potential to overcome these key shortcomings, but its nanoscale properties and rich magnetic phase diagram remain poorly understood. Here we use single spin magnetometry to quantitatively characterise saturation magnetization, magnetic anisotropy constants, and magnetic phase transitions in few-layer CrSBr by direct magnetic imaging. We show pristine magnetic phases, devoid of defects on micron length-scales, and demonstrate remarkable air-stability down the monolayer limit. We address the spin-flip transition in bilayer CrSBr by direct imaging of the emerging antiferromagnetic (AFM) to ferromagnetic (FM) phase wall and elucidate the magnetic properties of CrSBr around its ordering temperature. Our work will enable the engineering of exotic electronic and magnetic phases in CrSBr and the realisation of novel nanomagnetic devices based on this highly promising vdW magnet.

cond-mat.mes-hall↗

arXiv2023

Shallow Silicon Vacancy Centers with lifetime-limited optical linewidths in Diamond Nanostructures

The negatively charged silicon vacancy center (SiV$^-$) in diamond is a promising, yet underexplored candidate for single-spin quantum sensing at sub-kelvin temperatures and tesla-range magnetic fields. A key ingredient for such applications is the ability to perform all-optical, coherent addressing of the electronic spin of near-surface SiV$^-$ centers. We present a robust and scalable approach for creating individual, $\sim$50nm deep SiV$^-$ with lifetime-limited optical linewidths in diamond nanopillars through an easy-to-realize and persistent optical charge-stabilization scheme. The latter is based on single, prolonged 445nm laser illumination that enables continuous photoluminescence excitation spectroscopy, without the need for any further charge stabilization or repumping. Our results constitute a key step towards the use of near-surface, optically coherent SiV$^-$ for sensing under extreme conditions, and offer a powerful approach for stabilizing the charge-environment of diamond color centers for quantum technology applications.

quant-ph↗

arXiv2023

JARVIS-Leaderboard: A Large Scale Benchmark of Materials Design Methods

Lack of rigorous reproducibility and validation are major hurdles for scientific development across many fields. Materials science in particular encompasses a variety of experimental and theoretical approaches that require careful benchmarking. Leaderboard efforts have been developed previously to mitigate these issues. However, a comprehensive comparison and benchmarking on an integrated platform with multiple data modalities with both perfect and defect materials data is still lacking. This work introduces JARVIS-Leaderboard, an open-source and community-driven platform that facilitates benchmarking and enhances reproducibility. The platform allows users to set up benchmarks with custom tasks and enables contributions in the form of dataset, code, and meta-data submissions. We cover the following materials design categories: Artificial Intelligence (AI), Electronic Structure (ES), Force-fields (FF), Quantum Computation (QC) and Experiments (EXP). For AI, we cover several types of input data, including atomic structures, atomistic images, spectra, and text. For ES, we consider multiple ES approaches, software packages, pseudopotentials, materials, and properties, comparing results to experiment. For FF, we compare multiple approaches for material property predictions. For QC, we benchmark Hamiltonian simulations using various quantum algorithms and circuits. Finally, for experiments, we use the inter-laboratory approach to establish benchmarks. There are 1281 contributions to 274 benchmarks using 152 methods with more than 8 million data-points, and the leaderboard is continuously expanding. The JARVIS-Leaderboard is available at the website: https://pages.nist.gov/jarvis_leaderboard

cond-mat.mtrl-sci↗

arXiv2023

An integrated system built for small-molecule semiconductors via high-throughput approaches

High-throughput synthesis of solution-processable structurally variable small-molecule semiconductors is both an opportunity and a challenge. A large number of diverse molecules provide a possibility for quick material discovery and machine learning based on experimental data. However, the diversity of molecular structure leads to the complexity of molecular properties, such as solubility, polarity, and crystallinity, which poses great challenges to solution processing and purification. Here, we first report an integrated system for the high-throughput synthesis, purification, and characterization of molecules with a large variety. Based on the principle of Like dissolves like, we combine theoretical calculations and a robotic platform to accelerate the purification of those molecules. With this platform, a material library containing 125 molecules and their optical-electric properties was built within a timeframe of weeks. More importantly, the high repeatability of recrystallization we design is a reliable approach to further upgrading and industrial production.

physics.app-ph↗

arXiv2023

Neural networks trained on synthetically generated crystals can extract structural information from ICSD powder X-ray diffractograms

Machine learning techniques have successfully been used to extract structural information such as the crystal space group from powder X-ray diffractograms. However, training directly on simulated diffractograms from databases such as the ICSD is challenging due to its limited size, class-inhomogeneity, and bias toward certain structure types. We propose an alternative approach of generating synthetic crystals with random coordinates by using the symmetry operations of each space group. Based on this approach, we demonstrate online training of deep ResNet-like models on up to a few million unique on-the-fly generated synthetic diffractograms per hour. For our chosen task of space group classification, we achieved a test accuracy of 79.9% on unseen ICSD structure types from most space groups. This surpasses the 56.1% accuracy of the current state-of-the-art approach of training on ICSD crystals directly. Our results demonstrate that synthetically generated crystals can be used to extract structural information from ICSD powder diffractograms, which makes it possible to apply very large state-of-the-art machine learning models in the area of powder X-ray diffraction. We further show first steps toward applying our methodology to experimental data, where automated XRD data analysis is crucial, especially in high-throughput settings. While we focused on the prediction of the space group, our approach has the potential to be extended to related tasks in the future.

cond-mat.mtrl-sci↗

arXiv2023

Accurate GW frontier orbital energies of 134 kilo molecules

The QM9 dataset [Scientific Data, Vol. 1, 140022 (2014)] became a standard dataset to benchmark machine learning methods, especially on molecular graphs. It contains geometries as well as multiple computed molecular properties of 133,885 compounds at B3LYP/6-31G(2df,p) level of theory, including frontier orbitals (HOMO and LUMO) energies. However, the accuracy of HOMO/LUMO predictions from density functional theory, including hybrid methods such as B3LYP, is limited for many applications. In contrast, the GW method significantly improves HOMO/LUMO prediction accuracy, with mean unsigned errors in the GW100 benchmark dataset of 100 meV. In this work, we present a new dataset of HOMO/LUMO energies for the QM9 compounds, computed using the GW method. This database may serve as a benchmark of HOMO/LUMO prediction, delta-learning, and transfer learning, particularly for larger molecules where GW is the most accurate but still numerically feasible method. We expect this dataset to enable the development of more accurate machine learning models for predicting molecular properties

physics.chem-ph↗

arXiv2023

Connectivity Optimized Nested Graph Networks for Crystal Structures

Graph neural networks (GNNs) have been applied to a large variety of applications in materials science and chemistry. Here, we recapitulate the graph construction for crystalline (periodic) materials and investigate its impact on the GNNs model performance. We suggest the asymmetric unit cell as a representation to reduce the number of atoms by using all symmetries of the system. This substantially reduced the computational cost and thus time needed to train large graph neural networks without any loss in accuracy. Furthermore, with a simple but systematically built GNN architecture based on message passing and line graph templates, we introduce a general architecture (Nested Graph Network, NGN) that is applicable to a wide range of tasks. We show that our suggested models systematically improve state-of-the-art results across all tasks within the MatBench benchmark. Further analysis shows that optimized connectivity and deeper message functions are responsible for the improvement. Asymmetric unit cells and connectivity optimization can be generally applied to (crystal) graph networks, while our suggested nested graph framework will open new ways of systematic comparison of GNN architectures.

cs.LG↗

arXiv2023

Temperature Dependent Photophysics of Single NV Centers in Diamond

We present a comprehensive study of the temperature and magnetic-field dependent photoluminescence (PL) of individual NV centers in diamond, spanning the temperature-range from cryogenic to ambient conditions. We directly observe the emergence of the NV's room-temperature effective excited state structure and provide a clear explanation for a previously poorly understood broad quenching of NV PL at intermediate temperatures around 50 K. We develop a model that quantitatively explains all of our findings, including the strong impact that strain has on the temperaturedependence of the NV's PL. These results complete our understanding of orbital averaging in the NV excited state and have significant implications for the fundamental understanding of the NV center and its applications in quantum sensing.

cond-mat.mes-hall↗

arXiv2022

MEGAN: Multi-Explanation Graph Attention Network

We propose a multi-explanation graph attention network (MEGAN). Unlike existing graph explainability methods, our network can produce node and edge attributional explanations along multiple channels, the number of which is independent of task specifications. This proves crucial to improve the interpretability of graph regression predictions, as explanations can be split into positive and negative evidence w.r.t to a reference value. Additionally, our attention-based network is fully differentiable and explanations can actively be trained in an explanation-supervised manner. We first validate our model on a synthetic graph regression dataset with known ground-truth explanations. Our network outperforms existing baseline explainability methods for the single- as well as the multi-explanation case, achieving near-perfect explanation accuracy during explanation supervision. Finally, we demonstrate our model's capabilities on multiple real-world datasets. We find that our model produces sparse high-fidelity explanations consistent with human intuition about those tasks.

cs.LG↗

arXiv2022

Graph neural networks for materials science and chemistry

Machine learning plays an increasingly important role in many areas of chemistry and materials science, e.g. to predict materials properties, to accelerate simulations, to design new materials, and to predict synthesis routes of new materials. Graph neural networks (GNNs) are one of the fastest growing classes of machine learning models. They are of particular relevance for chemistry and materials science, as they directly work on a graph or structural representation of molecules and materials and therefore have full access to all relevant information required to characterize materials. In this review article, we provide an overview of the basic principles of GNNs, widely used datasets, and state-of-the-art architectures, followed by a discussion of a wide range of recent applications of GNNs in chemistry and materials science, and concluding with a road-map for the further development and application of GNNs.

physics.chem-ph↗

arXiv2022

Charge Transfer Simulations using Hamiltonian Elements and Forces from Neural Networks

The trajectory surface hopping method has been widely used in the simulation of charge transport in organic semiconductors. In the present study, we employ the machine learning (ML) based Hamiltonian to simulate the charge transport in anthracene and pentacene. The neural network (NN) based models are able to predict not just site energies and couplings but also the gradients of the site energy as well as off-diagonal gradients necessary for forces. We train the models on DFTB-quality data for both anthracene and pentacene. By using the obtained models in propagation simulations, we evaluate their performance in reproducing hole mobilities in these materials in terms of both quality and computational cost. The results show that the charge mobilities obtained using the NN-based Hamiltonian are in very good agreements with the charge mobilities computed using the DFTB-based Hamiltonian.

physics.chem-ph↗

arXiv2021

Low temperature photo-physics of single NV centers in diamond

We investigate the magnetic field dependent photo-physics of individual Nitrogen-Vacancy (NV) color centers in diamond under cryogenic conditions. At distinct magnetic fields, we observe significant reductions in the NV photoluminescence rate, which indicate a marked decrease in the optical readout efficiency of the NV's ground state spin. We assign these dips to excited state level anti-crossings, which occur at magnetic fields that strongly depend on the effective, local strain environment of the NV center. Our results offer new insights into the structure of the NVs' excited states and a new tool for their effective characterization. Using this tool, we observe strong indications for strain-dependent variations of the NV's orbital g-factor, obtain new insights into NV charge state dynamics, and draw important conclusions regarding the applicability of NV centers for low-temperature quantum sensing.

cond-mat.mes-hall↗

arXiv2021

Implementing graph neural networks with TensorFlow-Keras

Graph neural networks are a versatile machine learning architecture that received a lot of attention recently. In this technical report, we present an implementation of convolution and pooling layers for TensorFlow-Keras models, which allows a seamless and flexible integration into standard Keras layers to set up graph models in a functional way. This implies the usage of mini-batches as the first tensor dimension, which can be realized via the new RaggedTensor class of TensorFlow best suited for graphs. We developed the Keras Graph Convolutional Neural Network Python package kgcnn based on TensorFlow-Keras that provides a set of Keras layers for graph networks which focus on a transparent tensor structure passed between layers and an ease-of-use mindset.

cs.LG↗

arXiv2021

Analyzing dynamical disorder for charge transport in organic semiconductors via machine learning

Organic semiconductors are indispensable for today's display technologies in form of organic light emitting diodes (OLEDs) and further optoelectronic applications. However, organic materials do not reach the same charge carrier mobility as inorganic semiconductors, limiting the efficiency of devices. To find or even design new organic semiconductors with higher charge carrier mobility, computational approaches, in particular multiscale models, are becoming increasingly important. However, such models are computationally very costly, especially when large systems and long time scales are required, which is the case to compute static and dynamic energy disorder, i.e. dominant factor to determine charge transport. Here we overcome this drawback by integrating machine learning models into multiscale simulations. This allows us to obtain unprecedented insight into relevant microscopic materials properties, in particular static and dynamic disorder contributions for a series of application-relevant molecules. We find that static disorder and thus the distribution of shallow traps is highly asymmetrical for many materials, impacting widely considered Gaussian disorder models. We furthermore analyse characteristic energy level fluctuation times and compare them to typical hopping rates to evaluate the importance of dynamic disorder for charge transport. We hope that our findings will significantly improve the accuracy of computational methods used to predict application relevant materials properties of organic semiconductors, and thus make these methods applicable for virtual materials design.

cond-mat.soft↗