arXiv subjects

Christian Holm

Publications and source records attributed to Christian Holm.

At least 37 records · Page 2Linked to original sources

arXiv2024

Robustness of quantum algorithms against coherent control errors

Coherent control errors, for which ideal Hamiltonians are perturbed by unknown multiplicative noise terms, are a major obstacle for reliable quantum computing. In this paper, we present a framework for analyzing the robustness of quantum algorithms against coherent control errors using Lipschitz bounds. We derive worst-case fidelity bounds which show that the resilience against coherent control errors is mainly influenced by the norms of the Hamiltonians generating the individual gates. These bounds are explicitly computable even for large circuits, and they can be used to guarantee fault-tolerance via threshold theorems. Moreover, we apply our theoretical framework to derive a novel guideline for robust quantum algorithm design and transpilation, which amounts to reducing the norms of the Hamiltonians. Using the $3$-qubit Quantum Fourier Transform as an example application, we demonstrate that this guideline targets robustness more effectively than existing ones based on circuit depth or gate count. Furthermore, we apply our framework to study the effect of parameter regularization in variational quantum algorithms. The practicality of the theoretical results is demonstrated via implementations in simulation and on a quantum computer.

quant-ph↗

arXiv2024

CO2-induced Drastic Decharging of Dielectric Surfaces in Aqueous Suspensions

We study the influence of airborne CO2 on the charge state of carboxylate stabilized polymer latex particles suspended in aqueous electrolytes. We combine conductometric experiments interpreted in terms of Hessinger's conductivity model with Poisson-Boltzmann cell (PBC) model calculations with charge regulation boundary conditions. Without CO2, a minority of the weakly acidic surface groups are dissociated and only a fraction of the total number of counter-ions actually contribute to conductivity. The remaining counter-ions exchange freely with added other ions like Na+, K+ or Cs+. From the PBC-calculations we infer a corresponding pKa of 4.26 as well as a renormalized charge in reasonably good agreement with the number of freely mobile counter-ions. Equilibration of salt- and CO2-free suspensions against ambient air leads to a drastic de-charging, which exceeds by far the expected effects of to dissolved CO2 and its dissociation products. Further, no counter-ion-exchange is observed. To reproduce the experimental findings, we have to assume an effective pKa of 6.48. This direct influence of CO2 on the state of surface group dissociation explains our recent finding of a CO2-induced decrease of the ζ-potential and supports the suggestion of an additional charge regulation caused by molecular CO2. Given the importance of charged surfaces in contact with aqueous electrolytes, we anticipate that our observations bear substantial theoretical challenges and important implications for applications ranging from desalination to bio-membranes.

cond-mat.soft↗

arXiv2024

Peptide Classification from Statistical Analysis of Nanopore Translocation Experiments

Protein characterization using nanopore-based devices promises to be a breakthrough method in basic research, diagnostics, and analytics. Current research includes the use of machine learning to achieve this task. In this work, a comprehensive statistical analysis of nanopore current signals is performed and demonstrated to be sufficient for classifying up to 42 peptides with over 70 % accuracy. Two sets of features, the statistical moments and the catch22 set, are compared both in their representations and after training small classifier neural networks. We demonstrate that complex features of the events, captured in both the catch22 set and the central moments, are key in classifying peptides with otherwise similar mean currents. These results highlight the efficacy of purely statistical analysis of nanopore data and suggest a path forward for more sophisticated classification techniques.

physics.bio-ph↗

arXiv2024

Collective variables of neural networks: empirical time evolution and scaling laws

This work presents a novel means for understanding learning dynamics and scaling relations in neural networks. We show that certain measures on the spectrum of the empirical neural tangent kernel, specifically entropy and trace, yield insight into the representations learned by a neural network and how these can be improved through architecture scaling. These results are demonstrated first on test cases before being shown on more complex networks, including transformers, auto-encoders, graph neural networks, and reinforcement learning studies. In testing on a wide range of architectures, we highlight the universal nature of training dynamics and further discuss how it can be used to understand the mechanisms behind learning in neural networks. We identify two such dominant mechanisms present throughout machine learning training. The first, information compression, is seen through a reduction in the entropy of the NTK spectrum during training, and occurs predominantly in small neural networks. The second, coined structure formation, is seen through an increasing entropy and thus, the creation of structure in the neural network representations beyond the prior established by the network at initialization. Due to the ubiquity of the latter in deep neural network architectures and its flexibility in the creation of feature-rich representations, we argue that this form of evolution of the network's entropy be considered the onset of a deep learning regime.

cs.LG↗

arXiv2024

SwarmRL: Building the Future of Smart Active Systems

This work introduces SwarmRL, a Python package designed to study intelligent active particles. SwarmRL provides an easy-to-use interface for developing models to control microscopic colloids using classical control and deep reinforcement learning approaches. These models may be deployed in simulations or real-world environments under a common framework. We explain the structure of the software and its key features and demonstrate how it can be used to accelerate research. With SwarmRL, we aim to streamline research into micro-robotic control while bridging the gap between experimental and simulation-driven sciences. SwarmRL is available open-source on GitHub at https://github.com/SwarmRL/SwarmRL.

cs.RO↗

arXiv2024

Emergence of Chemotactic Strategies with Multi-Agent Reinforcement Learning

Reinforcement learning (RL) is a flexible and efficient method for programming micro-robots in complex environments. Here we investigate whether reinforcement learning can provide insights into biological systems when trained to perform chemotaxis. Namely, whether we can learn about how intelligent agents process given information in order to swim towards a target. We run simulations covering a range of agent shapes, sizes, and swim speeds to determine if the physical constraints on biological swimmers, namely Brownian motion, lead to regions where reinforcement learners' training fails. We find that the RL agents can perform chemotaxis as soon as it is physically possible and, in some cases, even before the active swimming overpowers the stochastic environment. We study the efficiency of the emergent policy and identify convergence in agent size and swim speeds. Finally, we study the strategy adopted by the reinforcement learning algorithm to explain how the agents perform their tasks. To this end, we identify three emerging dominant strategies and several rare approaches taken. These strategies, whilst producing almost identical trajectories in simulation, are distinct and give insight into the possible mechanisms behind which biological agents explore their environment and respond to changing conditions.

physics.bio-ph↗

arXiv2024

Emergence of Accurate Atomic Energies from Machine Learned Noble Gas Potentials

The quantum theory of atoms in molecules (QTAIM) gives access to well-defined local atomic energies. Due to their locality, these energies are potentially interesting in fitting atomistic machine learning models as they inform about physically relevant properties. However, computationally, quantum-mechanically accurate local energies are notoriously difficult to obtain for large systems. Here, we show that by employing semi-empirical correlations between different components of the total energy, we can obtain well-defined local energies at a moderate cost. We employ this methodology to investigate energetics in noble liquids or argon, krypton, and their mixture. Instead of using these local energies to fit atomistic models, we show how well these local energies are reproduced by machine-learned models trained on the total energies. The results of our investigation suggest that smaller neural networks, trained only on the total energy of an atomistic system, are more likely to reproduce the underlying local energy partitioning faithfully than larger networks. Furthermore, we demonstrate that networks more capable of this energy decomposition are, in turn, capable of transferring to previously unseen systems. Our results are a step towards understanding how much physics can be learned by neural networks and where this can be applied, particularly how a better understanding of physics aids in the transferability of these neural networks.

cond-mat.soft↗

arXiv2024

Zero Shot Molecular Generation via Similarity Kernels

Generative modelling aims to accelerate the discovery of novel chemicals by directly proposing structures with desirable properties. Recently, score-based, or diffusion, generative models have significantly outperformed previous approaches. Key to their success is the close relationship between the score and physical force, allowing the use of powerful equivariant neural networks. However, the behaviour of the learnt score is not yet well understood. Here, we analyse the score by training an energy-based diffusion model for molecular generation. We find that during the generation the score resembles a restorative potential initially and a quantum-mechanical force at the end. In between the two endpoints, it exhibits special properties that enable the building of large molecules. Using insights from the trained model, we present Similarity-based Molecular Generation (SiMGen), a new method for zero shot molecular generation. SiMGen combines a time-dependent similarity kernel with descriptors from a pretrained machine learning force field to generate molecules without any further training. Our approach allows full control over the molecular shape through point cloud priors and supports conditional generation. We also release an interactive web tool that allows users to generate structures with SiMGen online (https://zndraw.icp.uni-stuttgart.de).

physics.chem-ph↗

arXiv2024

ZnTrack -- Data as Code

The past decade has seen tremendous breakthroughs in computation and there is no indication that this will slow any time soon. Machine learning, large-scale computing resources, and increased industry focus have resulted in rising investments in computer-driven solutions for data management, simulations, and model generation. However, with this growth in computation has come an even larger expansion of data and with it, complexity in data storage, sharing, and tracking. In this work, we introduce ZnTrack, a Python-driven data versioning tool. ZnTrack builds upon established version control systems to provide a user-friendly and easy-to-use interface for tracking parameters in experiments, designing workflows, and storing and sharing data. From this ability to reduce large datasets to a simple Python script emerges the concept of Data as Code, a core component of the work presented here and an undoubtedly important concept as the age of computation continues to evolve. ZnTrack offers an open-source, FAIR data compatible Python package to enable users to harness these concepts of the future.

cs.SE↗

arXiv2023

Optimal motility strategies for self-propelled agents to explore porous media

Micro-robots for, e.g., biomedical applications, need to be equipped with motility strategies that enable them to navigate through complex environments. Inspired by biological microorganisms we recreate motility patterns such as run-and-reverse, run-and-tumble or run-reverse-flick applied to active rod-like particles in silico. We investigate their capability to efficiently explore disordered porous environments with various porosities and mean pore sizes ranging down to the scale of the active particle. By calculating the effective diffusivity for the different patterns, we can predict the optimal one for each porous sample geometry. We find that providing the agent with very basic sensing and decision making capabilities yields a motility pattern outperforming the biologically inspired patterns for all investigated porous samples.

cond-mat.soft↗

arXiv2023

Environmental effects on emergent strategy in micro-scale multi-agent reinforcement learning

Multi-Agent Reinforcement Learning (MARL) is a promising candidate for realizing efficient control of microscopic particles, of which micro-robots are a subset. However, the microscopic particles' environment presents unique challenges, such as Brownian motion at sufficiently small length-scales. In this work, we explore the role of temperature in the emergence and efficacy of strategies in MARL systems using particle-based Langevin molecular dynamics simulations as a realistic representation of micro-scale environments. To this end, we perform experiments on two different multi-agent tasks in microscopic environments at different temperatures, detecting the source of a concentration gradient and rotation of a rod. We find that at higher temperatures, the RL agents identify new strategies for achieving these tasks, highlighting the importance of understanding this regime and providing insight into optimal training strategies for bridging the generalization gap between simulation and reality. We also introduce a novel Python package for studying microscopic agents using reinforcement learning (RL) to accompany our results.

physics.bio-ph↗

arXiv2023

Generating Minimal Training Sets for Machine Learned Potentials

This letter presents a novel approach for identifying uncorrelated atomic configurations from extensive data sets with a non-standard neural network workflow known as random network distillation (RND) for training machine-learned inter-atomic potentials (MLPs). This method is coupled with a DFT workflow wherein initial data is generated with cheaper classical methods before only the minimal subset is passed to a more computationally expensive ab initio calculation. This benefits training not only by reducing the number of expensive DFT calculations required but also by providing a pathway to the use of more accurate quantum mechanical calculations for training. The method's efficacy is demonstrated by constructing machine-learned inter-atomic potentials for the molten salts KCl and NaCl. Our RND method allows accurate models to be fit on minimal data sets, as small as 32 configurations, reducing the required structures by at least one order of magnitude compared to alternative methods.

physics.comp-ph↗

arXiv2023

Explaining Giant Apparent $\mathrm{p}K_\mathrm{A}$ Shifts in Weak Polyelectrolyte Brushes

Recent experiments on weak polyelectrolyte brushes found marked shifts in the effective p$K_\mathrm{A}$ that are linear in the logarithm of the salt concentration. Comparing explicit-particle simulations with mean-field calculations we show that for high grafting densities the salt concentration effect can be explained using the ideal Donnan theory, but for low grafting densities the full shift is due to a combination of the Donnan effect and the polyelectrolyte effect. The latter originates from electrostatic correlations which are neglected in the Donnan picture and which are only approximately included in the mean-field theory. Moreover, we demonstrate that the magnitude of the polyelectrolyte effect is almost invariant with respect to salt concentration but depends on the grafting density of the brush. This invariance is due to a complex cancellation of multiple effects. Based on our results, we show how the experimentally determined p$K_\mathrm{A}$ shifts may be used to infer the grafting density of brushes, a parameter that is difficult to measure directly.

cond-mat.soft↗

arXiv2023

A Generalized Grand-Reaction Method for Modelling the Exchange of Weak (Polyprotic) Acids between a Solution and a Weak Polyelectrolyte Phase

We introduce a Monte-Carlo method that allows for the simulation of a polymeric phase containing a weak polyelectrolyte, which is coupled to a reservoir at a fixed pH, salt concentration and total concentration of a weak polyprotic acid. The method generalizes the established Grand-Reaction Method by Landsgesell et al. [Macromolecules 53, 3007-3020 (2020)] and thus allows for the simulation of polyelectrolyte systems coupled to reservoirs with a more complex chemical composition. In order to set the required input parameters that correspond to a desired reservoir composition, we propose a generalization of the recently published chemical potential tuning algorithm of Miles et al. [Phys. Rev. E 105, 045311 (2022)]. To test the proposed tuning procedure, we perform extensive numerical tests for both ideal and interacting systems. Finally, as a showcase, we apply the method to a simple test system which consists of a weak polybase solution that is coupled to a reservoir containing a small diprotic acid. The complex interplay of the ionization various species, the electrostatic interactions and the partitioning of small ions leads to a non-monotonous, stepwise swelling behaviour of the weak polybase chains.

cond-mat.soft↗

arXiv2023

Towards a Phenomenological Understanding of Neural Networks: Data

A theory of neural networks (NNs) built upon collective variables would provide scientists with the tools to better understand the learning process at every stage. In this work, we introduce two such variables, the entropy and the trace of the empirical neural tangent kernel (NTK) built on the training data passed to the model. We empirically analyze the NN performance in the context of these variables and find that there exists correlation between the starting entropy, the trace of the NTK, and the generalization of the model computed after training is complete. This framework is then applied to the problem of optimal data selection for the training of NNs. To this end, random network distillation (RND) is used as a means of selecting training data which is then compared with random selection of data. It is shown that not only does RND select data-sets capable of outperforming random selection, but that the collective variables associated with the RND data-sets are larger than those of the randomly selected sets. The results of this investigation provide a stable ground from which the selection of data for NN training can be driven by this phenomenological framework.

cs.LG↗

arXiv2023

Ratcheting charged polymers through symmetric nanopores using pulsed fields: Designing a low pass filter for concentrating DNA

We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation and pulsed fields. Using Langevin Dynamics simulations, we show that it is possible to design pulsed field sequences to ratchet captured semiflexible molecules in such a way that only short chains successfully translocate, effectively transforming the nanopore process into a low pass molecular filter. We also show that asymmetric pulses can significantly enhance the device efficiency. The process itself can be performed with many pores in parallel, and it should be possible to integrate it directly into nanopore sequencing devices, increasing its potential utility.

cond-mat.soft↗

arXiv2022

Order and Information in the Patterns of Spinning Magnetic Micro-disks at the Air-water Interface

The application of the Shannon entropy to study the relationship between information and structures has yielded insights into molecular and material systems. However, the difficulty in directly observing and manipulating atoms and molecules hampers the ability of these systems to serve as model systems for further exploring the links between information and structures. Here, we use, as a model experimental system, hundreds of spinning magnetic micro-disks self-organizing at the air-water interface to generate various spatiotemporal patterns with varying degrees of orders. Using the neighbor distance as the information-bearing variable, we demonstrate the links among information, structure, and interactions. Most importantly, we establish a direct link between information and structure without using explicit knowledge of interactions. Finally, we show that the Shannon entropy by neighbor distances is a powerful observable in characterizing structural changes. Our findings are relevant for analyzing natural self-organizing systems and for designing collective robots.

cond-mat.soft↗

arXiv2021

Efficient Data Selection Methods for the Development of Machine Learned Potentials

We present an investigation into data selection methods for the efficient sampling of configuration space as applied to the development of inter-atomic potentials for scale bridging in molecular dynamics (MD) simulations. This investigation suggests that the most efficient sampling techniques are those that incorporate information on an atomic level such as forces or atomic energies. Finally, we generate an inter-atomic potential for the a sodium chloride system using each data selection technique and find that the global selection methods result in non-physical simulations.

physics.comp-ph↗