Related papers: Piece-wise Multipole-expansion Implicit Solvation …
Mass-conservative reaction-diffusion systems have recently been proposed as a general framework to describe intracellular pattern formation. These systems have been used to model the conformational switching of proteins as they cycle from…
Evaluation in scientific reconstruction is dominated by pointwise metrics - RMSE, MAE, per-event resolution - under the implicit assumption that lower error means better reconstruction. We show that this assumption fails structurally for…
In this paper we present a high-order kernel method for numerically solving diffusion and reaction-diffusion partial differential equations (PDEs) on smooth, closed surfaces embedded in $\mathbb{R}^d$. For two-dimensional surfaces embedded…
Finding accurate solutions to partial differential equations (PDEs) is a crucial task in all scientific and engineering disciplines. It has recently been shown that machine learning methods can improve the solution accuracy by correcting…
Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…
We present a many-body expansion (MBE) formulation and implementation for efficient computation of analytical energy gradients from OSV-MP2 theory based on our earlier work (Zhou et al. J. Chem. Theory Comput. 2020, 16, 196-210). The…
Large thermal fluctuations of the liquid phase obscure the weak macroscopic electric field that drives electrochemical reactions, rendering the extraction of reliable interfacial charge distributions from ab initio molecular dynamics…
We develop a diffuse-interface continuum model for membrane electroporation that couples a phase field for pore geometry to a quasi-static electrolyte potential and a spatially varying leaky-dielectric model for the transmembrane voltage.…
We present an implicit-explicit (IMEX) scheme for semilinear wave equations with strong damping. By treating the nonlinear, nonstiff term explicitly and the linear, stiff part implicitly, we obtain a method which is not only unconditionally…
Membrane-metasurfaces, formed by periodic arrangements of holes in a dielectric layer, are gaining attention for their easier manufacturing via subtractive techniques, unnecessity of substrates, and access to resonant near-fields. Despite…
We introduce a guided stochastic sampling method that augments sampling from diffusion models with physics-based guidance derived from partial differential equation (PDE) residuals and observational constraints, ensuring generated samples…
Achieving large-scale kinetic modelling is a crucial task for the development and optimization of modern plasma devices. With the trend of decreasing pressure in applications such as plasma etching, kinetic simulations are necessary to…
Inelastic losses are crucial to a quantitative analysis of x-ray absorption spectra. However, current treatments are semi-phenomenological in nature. Here a first-principles, many-pole generalization of the plasmon-pole model is developed…
We propose a novel type of nonlinear solver acceleration for systems of nonlinear partial differential equations (PDEs) that is based on online/adaptive learning. It is applied in the context of multiphase flow in porous media. The proposed…
Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting…
We develop a computational method for modeling electrostatic interactions of arbitrarily-shaped, polarizable objects on colloidal length scales, including colloids/nanoparticles, polymers, and surfactants, dispersed in explicit ion…
Diffusion behaviors of heterogeneous materials are of paramount importance in many engineering problems. Numerical models that take into account the internal structure of such materials are robust but computationally very expensive. This…
We present a multiparticle collision dynamics (MPC) implementation of layered immiscible fluids $A$ and $B$ of different shear viscosities separated by planar interfaces. The simulated flow profile for imposed steady shear motion and the…
Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary…
We study semi-linear elliptic PDEs with polynomial non-linearity and provide a probabilistic representation of their solution using branching diffusion processes. When the non-linearity involves the unknown function but not its derivatives,…