Publications

In this work we analyze the complex scaling method applied to the problem of time-harmonic scalar wave propagation in junctions between `leaky,' or open dielectric waveguides. In [arXiv:2302.04353, arXiv:2310.05816, arXiv:2401.04674, arXiv:2411.11204], it was shown that under suitable assumptions the problem can be reduced to a system of Fredholm second-kind integral equations on an infinite interface, transverse to the waveguides. Here, we show that the kernels appearing in the integral equation admit a rapidly decaying analytic continuation on certain natural totally real submanifolds of $\mathbb{C}^2.$ We then show that for suitable, physically-meaningful, boundary data the resulting solutions to the integral equations themselves admit analytic continuation and satisfy related asymptotic estimates. By deforming the integral equation to a suitable contour, the decay in the kernels, density, and data enable straightforward discretization and truncation, with an error that decays exponentially in the truncation length. We illustrate our results with several representative numerical examples.

Understanding protein conformation is key to understanding their function. Importantly, most proteins adopt multiple conformations with nontrivial ensemble distributions that change depending on their environment to perform functions like catalysis, signaling, and transport. Recently, machine learning techniques, especially deep generative models, have been employed to develop protein conformation generators. These models, known as unified protein ensemble samplers, are trained on the Protein Data Bank (PDB) dataset and can generate diverse protein conformation ensembles given a protein sequence. However, their reliance solely on structural data from the PDB, which primarily captures folded protein states, restricts the diversity of the generated ensembles and can result in physically unrealistic conformations. In this paper, we overcome these challenges by introducing ExEnDiff, an experiment-guided diffusion model for protein conformation generation. ExEnDiff integrates experimental measurements as a physical prior, enabling the generation of protein conformations with desired properties. Our experiments on a variety of fast-folding and intrinsically disordered proteins demonstrate that ExEnDiff significantly advances the capabilities of current unified protein ensemble samplers. With little computational cost, ExEnDiff can capture important proteins' configuration properties and the underlying Boltzmann distribution, paving the way for a next-generation molecular dynamics engine. We further demonstrate the effectiveness of ExEnDiff to capture conformational changes in the presence of mutations and as an efficient tool for determining a reasonable collective variable space for protein ensembles. With these results, ExEnDiff is well poised to push the study of protein ensembles into a data-rich regime currently available to few problems in biology.

This paper presents a novel approach to learning free terminal time closed-loop control for robotic manipulation tasks, enabling dynamic adjustment of task duration and control inputs to enhance performance. We extend the supervised learning approach, namely solving selected optimal open-loop problems and utilizing them as training data for a policy network, to the free terminal time scenario. Three main challenges are addressed in this extension. First, we introduce a marching scheme that enhances the solution quality and increases the success rate of the open-loop solver by gradually refining time discretization. Second, we extend the QRnet in [1] to the free terminal time setting to address discontinuity and improve stability at the terminal state. Third, we present a more automated version of the initial value problem (IVP) enhanced sampling method from previous work [2] to adaptively update the training dataset, significantly improving its quality. By integrating these techniques, we develop a closed-loop policy that operates effectively over a broad domain with varying optimal time durations, achieving near globally optimal total costs. The appendix and videos are available at https://deepoptimalcontrol.github.io/FreeTimeManipulator.

Characterizing the conformational ensemble of biomolecular systems is key to understand their functions. Cryoelectron microscopy (cryo-EM) captures two-dimensional snapshots of biomolecular ensembles, giving in principle access to thermodynamics. However, these images are very noisy and show projections of the molecule in unknown orientations, making it very difficult to identify the biomolecule’s conformation in each individual image. Here, we introduce cryo-EM simulation-based inference (cryoSBI) to infer the conformations of biomolecules and the uncertainties associated with the inference from individual cryo-EM images. CryoSBI builds on simulation-based inference, a merger of physics-based simulations and probabilistic deep learning, allowing us to use Bayesian inference even when likelihoods are too expensive to calculate. We begin with an ensemble of conformations, templates from experiments, and molecular modeling, serving as structural hypotheses. We train a neural network approximating the Bayesian posterior using simulated images from these templates and then use it to accurately infer the conformation of the biomolecule from each experimental image. Training is only done once on simulations, and after that, it takes just a few milliseconds to make inference on an image, making cryoSBI suitable for arbitrarily large datasets and direct analysis on micrographs. CryoSBI eliminates the need to estimate particle pose and imaging parameters, significantly enhancing the computational speed compared to explicit likelihood methods. Importantly, we obtain interpretable machine learning models by integrating physics-based approaches with deep neural networks, ensuring that our results are transparent and reliable. We illustrate and benchmark cryoSBI on synthetic data and showcase its promise on experimental single-particle cryo-EM data.

The remarkable cohesion and coordination observed in moving animal groups and their collective responsiveness to threats are thought to be mediated by scale-free correlations, where changes in the behavior of one animal influence others in the group, regardless of the distance between them. But are these features independent of group size? Here, we investigate group cohesiveness and collective responsiveness in computational models of massive schools of fish of up to 50,000 individuals. We show that as the number of swimmers increases, flow interactions destabilize the school, creating clusters that constantly fragment, disperse, and regroup, similar to their biological counterparts. We calculate the spatial correlation and speed of information propagation in these dynamic clusters. Spatial correlations in cohesive and polarized clusters are indeed scale free, much like in natural animal groups, but fragmentation events are preceded by a decrease in correlation length, thus diminishing the group's collective responsiveness, leaving it more vulnerable to predation events. Importantly, in groups undergoing collective turns, the information about the change in direction propagates linearly in time among group members, thanks to the non-reciprocal nature of the visual interactions between individuals. Merging speeds up the transfer of information within each cluster by several fold, while fragmentation slows it down. Our findings suggest that flow interactions may have played an important role in group size regulation, behavioral adaptations, and dispersion in living animal groups.

Dielectrically confined Coulomb systems are widely employed in molecular dynamics (MD) simulations. Despite extensive efforts in developing efficient and accurate algorithms for these systems, rigorous and accurate error estimates, which are crucial for optimal parameter selection for simulations, are still lacking. In this work, we present a rigorous error analysis in Ewald summation for electrostatic interactions in systems with two dielectric planar interfaces, where the polarization contribution is modeled by an infinitely reflected image charge series. An accurate error estimate is provided for the truncation error of image charge series, as well as decay rates of energy and force correction terms, as functions of system parameters such as vacuum layer thickness, dielectric permittivity, and image truncation levels. Extensive numerical tests conducted across several prototypical parameter settings validate our theoretical predictions. Additionally, our analysis elucidates the nonmonotonic error convergence behavior observed in previous numerical studies. Finally, we provide an optimal parameter selection strategy derived from our theoretical insights, offering practical guidance for efficient and accurate MD simulations of dielectric-confined systems.

This article shows that it is, in principle, possible to make a dielectric rod completely invisible to an incident electromagnetic plane wave of a given frequency. Students can derive the conditions that make the rod invisible if they understand the concept of plane waves, the boundary conditions for electric and magnetic fields, and the complex representation of electromagnetic fields. With access to appropriate software, students can determine the bandwidth of the invisibility and investigate whether it is possible to make an invisible rod out of real-world materials. A more advanced project proposed is to use electromagnetic software to find perfectly conducting hollow structures that are invisible to an incident plane wave.

This paper provides an error estimate for the u-series method of the Coulomb interaction in molecular dynamics simulations. We show that the number of truncated Gaussians M in the u-series and the base of interpolation nodes b in the bilateral serial approximation are two key parameters for the algorithm accuracy, and that the errors converge as O(b−M) for the energy and O(b−3M) for the force. Error bounds due to numerical quadrature and cutoff in both the electrostatic energy and forces are obtained. Closed-form formulae are also provided, which are useful in the parameter setup for simulations under a given accuracy. The results are verified by analyzing the errors of two practical systems.

The optical conductivity provides a comprehensive view of the electronic response of materials to electromagnetic fields, offering insights into transport phenomena, optoelectronic properties, and other fundamental aspects of condensed matter physics. We present an automatic, high-order accurate, and adaptive Brillouin zone integration algorithm for the calculation of the optical conductivity using the Kubo formula, with a nonzero but small broadening factor 𝜂, focusing on the case in which a Hamiltonian in a downfolded model can be evaluated efficiently using Wannier interpolation. The algorithm uses iterated adaptive integration to exploit the localization of the transport distribution near energy and energy-difference isosurfaces, yielding polylogarithmic computational complexity with respect to 𝜂, rather than the algebraic complexity of uniform integration rules. To demonstrate the method, we compute the AC optical conductivity of a three-band tight-binding model, and are able to resolve the Drude and interband peaks with broadening in the sub-meV regime to several digits of accuracy. Our algorithm automates convergence testing to a user-specified error tolerance, providing an important tool in black-box first-principles calculations of electrical transport phenomena and other response functions.

Neural networks have recently emerged as powerful tools for accelerated solving of partial differential equations (PDEs) in both academic and industrial settings. However, their use as standalone surrogate models raises concerns about reliability, as solution accuracy heavily depends on data quality, volume, and training algorithms. This concern is particularly pronounced in tasks that prioritize computational precision and deterministic outcomes. In response, this study introduces “super-fidelity”, a method that employs neural networks for initial warm-starts, significantly speeding up the solution of steady-state PDEs without compromising on accuracy. Drawing from super-resolution in computer vision, super-fidelity maps solutions from low-fidelity computational models to high-fidelity ones using a vector-cloud neural network with equivariance (VCNN-e)—a neural operator that preserves physical symmetries and adapts to different spatial discretizations. We evaluated the proposed method across scenarios with varying degrees of nonlinearity, including (1) two-dimensional laminar flows around elliptical cylinders at low Reynolds numbers, exhibiting monotonic convergence, (2) two-dimensional turbulent flows over airfoils at high Reynolds numbers, characterized by oscillatory convergence, and (3) practical three-dimensional turbulent flows over a wing. The results demonstrate that our neural operator-based initialization can accelerate convergence by at least a factor of two while maintaining the same level of accuracy, outperforming traditional initialization methods using uniform fields or potential flows. The approach's robustness and scalability are confirmed across different linear equation solvers and multi-process computing configurations. Additional investigations highlight its reduced dependence on high quality of training data, and real time savings across multiple simulations, even when including the neural-network model preparation time. Our study presents a promising strategy for accelerated solving of steady-state PDEs using neural operators, ensuring high accuracy in applications where precision is of utmost importance.