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1. Learning to Accelerate Partial Differential Equations via Latent Global Evolution

   Wu, Tailin; Maruyama, Takashi; Leskovec, Jure (January 2022, Advances in neural information processing systems)

   Simulating the time evolution of Partial Differential Equations (PDEs) of large-scale systems is crucial in many scientific and engineering domains such as fluid dynamics, weather forecasting and their inverse optimization problems. However, both classical solvers and recent deep learning-based surrogate models are typically extremely computationally intensive, because of their local evolution: they need to update the state of each discretized cell at each time step during inference. Here we develop Latent Evolution of PDEs (LE-PDE), a simple, fast and scalable method to accelerate the simulation and inverse optimization of PDEs. LE-PDE learns a compact, global representation of the system and efficiently evolves it fully in the latent space with learned latent evolution models. LE-PDE achieves speedup by having a much smaller latent dimension to update during long rollout as compared to updating in the input space. We introduce new learning objectives to effectively learn such latent dynamics to ensure long-term stability. We further introduce techniques for speeding-up inverse optimization of boundary conditions for PDEs via backpropagation through time in latent space, and an annealing technique to address the non-differentiability and sparse interaction of boundary conditions. We test our method in a 1D benchmark of nonlinear PDEs, 2D Navier-Stokes flows into turbulent phase and an inverse optimization of boundary conditions in 2D Navier-Stokes flow. Compared to state-of-the-art deep learning-based surrogate models and other strong baselines, we demonstrate up to 128x reduction in the dimensions to update, and up to 15x improvement in speed, while achieving competitive accuracy. 

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2. The Local Topological Free Energy of the SARS-CoV-2 Spike Protein

   https://doi.org/10.3390/polym14153014  

   Baldwin, Quenisha; Sumpter, Bobby; Panagiotou, Eleni (August 2022, Polymers)

   The novel coronavirus SARS-CoV-2 infects human cells using a mechanism that involves binding and structural rearrangement of its Spike protein. Understanding protein rearrangement and identifying specific amino acids where mutations affect protein rearrangement has attracted much attention for drug development. In this manuscript, we use a mathematical method to characterize the local topology/geometry of the SARS-CoV-2 Spike protein backbone. Our results show that local conformational changes in the FP, HR1, and CH domains are associated with global conformational changes in the RBD domain. The SARS-CoV-2 variants analyzed in this manuscript (alpha, beta, gamma, delta Mink, G614, N501) show differences in the local conformations of the FP, HR1, and CH domains as well. Finally, most mutations of concern are either in or in the vicinity of high local topological free energy conformations, suggesting that high local topological free energy conformations could be targets for mutations with significant impact of protein function. Namely, the residues 484, 570, 614, 796, and 969, which are present in variants of concern and are targeted as important in protein function, are predicted as such from our model. 

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3. Long-wavelength equations of motion for thin double vorticity layers

   https://doi.org/10.1017/jfm.2022.342  

   Baker, Gregory; Chang, Ching; Llewellyn Smith, Stefan G.; Pullin, D.I. (July 2022, Journal of Fluid Mechanics)

   We consider the time evolution in two spatial dimensions of a double vorticity layer consisting of two contiguous, infinite material fluid strips, each with uniform but generally differing vorticity, embedded in an otherwise infinite, irrotational, inviscid incompressible fluid. The potential application is to the wake dynamics formed by two boundary layers separating from a splitter plate. A thin-layer approximation is constructed where each layer thickness, measured normal to the common centre curve, is small in comparison with the local radius of curvature of the centre curve. The three-curve equations of contour dynamics that fully describe the double-layer dynamics are expanded in the small thickness parameter. At leading order, closed nonlinear initial-value evolution equations are obtained that describe the motion of the centre curve together with the time and spatial variation of each layer thickness. In the special case where the layer vorticities are equal, these equations reduce to the single-layer equation of Moore ( Stud. Appl. Math. , vol. 58, 1978, pp. 119–140). Analysis of the linear stability of the first-order equations to small-amplitude perturbations shows Kelvin–Helmholtz instability when the far-field fluid velocities on either side of the double layer are unequal. Equal velocities define a circulation-free double vorticity layer, for which solution of the initial-value problem using the Laplace transform reveals a double pole in transform space leading to linear algebraic growth in general, but there is a class of interesting initial conditions with no linear growth. This is shown to agree with the long-wavelength limit of the full linearized, three-curve stability equations. 

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4. On the dynamics of a free surface of an ideal fluid in a bounded domain in the presence of surface tension

   https://doi.org/10.1017/jfm.2018.885  

   Dyachenko, Sergey A. (February 2019, Journal of Fluid Mechanics)

   We derive a set of equations in conformal variables that describe a potential flow of an ideal two-dimensional inviscid fluid with free surface in a bounded domain. This formulation is free of numerical instabilities present in the equations for the surface elevation and potential derived in Dyachenko et al.  ( Plasma Phys. Rep. vol. 22 (10), 1996, pp. 829–840) with some restrictions on analyticity relieved, which allows to treat a finite volume of fluid enclosed by a free-moving boundary. We illustrate with a comparison of numerical simulations of the Dirichlet ellipse, an exact solution for a zero surface tension fluid. We demonstrate how the oscillations of the free surface of a unit disc droplet may lead to breaking of one droplet into two when surface tension is present. 

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5. Notes on solutions of KZ equations modulo $p^s$ and $$p$$-adic limit $$s\to\infty$$

   Alexander Varchenko (January 2022, Contemporary mathematics)

   We consider the KZ equations over C in the case, when the hypergeometric solutions are hyperelliptic integrals of genus g. Then the space of solutions is a 2g-dimensional complex vector space. We also consider the same equations modulo ps, where p is an odd prime and s is a positive integer, and over the field Q_p of p-adic numbers. We construct polynomial solutions of the KZ equations modulo ps and study the space Mps of all constructed solutions. We show that the p-adic limit of Mps as s→∞ gives us a g-dimensional vector space of solutions of the KZ equations over Qp. The solutions over Qp are power series at a certain asymptotic zone of the KZ equations. In the appendix written jointly with Steven Sperber we consider all asymptotic zones of the KZ equations in the case g=1 of elliptic integrals. The p-adic limit of Mps as s→∞ gives us a one-dimensional space of solutions over Qp at every asymptotic zone. We apply Dwork's theory and show that our germs of solutions over Qp defined at different asymptotic zones analytically continue into a single global invariant line subbundle of the associated KZ connection. Notice that the corresponding KZ connection over C does not have proper nontrivial invariant subbundles, and therefore our invariant line subbundle is a new feature of the KZ equations over Qp. We describe the Frobenius transformations of solutions of the KZ equations for g=1 and then recover the unit roots of the zeta functions of the elliptic curves defined by the equations y2=βx(x−1)(x−α) over the finite field Fp. Here α,β∈F×p,α≠1 

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