Related papers: FP-AbDiff: Improving Score-based Antibody Design b…
We investigate whether the discrepancy between observed galactic rotation curves and those predicted from baryonic matter can be interpreted as the manifestation of an emergent entropic force. Starting from a minimal statistical framework,…
The classical Fokker-Planck equation (FPE) is a key tool in physics for describing systems influenced by drag forces and Gaussian noise, with applications spanning multiple fields. We consider the fractional Fokker-Planck equation (FFPE),…
In this work, we develop novel structure-preserving numerical schemes for a class of nonlinear Fokker--Planck equations with nonlocal interactions. Such equations can cover many cases of importance, such as porous medium equations with…
We introduce IgDiff, an antibody variable domain diffusion model based on a general protein backbone diffusion framework which was extended to handle multiple chains. Assessing the designability and novelty of the structures generated with…
The Fokker-Planck (FP) equation governing the evolution of the probability density function (PDF) is applicable to many disciplines but it requires specification of the coefficients for each case, which can be functions of space-time and…
Fourier phase retrieval (FPR) is an inverse problem that recovers the signal from its Fourier magnitude measurement, it's ill-posed especially when the sampling rates are low. In this paper, an untrained generative prior is introduced to…
Structure-based drug design (SBDD), which aims to generate 3D ligand molecules binding to target proteins, is a fundamental task in drug discovery. Existing SBDD methods typically treat protein as rigid and neglect protein structural change…
In this paper, we propose efficient quantum algorithms for solving nonlinear stochastic differential equations (SDE) via the associated Fokker-Planck equation (FPE). We discretize the FPE in space and time using two well-known numerical…
Recent advances in structure-based protein design have accelerated de novo binder generation, yet interfaces on large domains or spanning multiple domains remain challenging due to high computational cost and declining success with…
Understanding the quasi-static fracture formation and evolution is essential for assessing the mechanical properties and structural load-bearing capacity of materials. Peridynamics (PD) provides an effective computational method to depict…
To make useful connections with experimental measurements, correlated electronic structure theories must accurately predict chemical properties in addition to energies. We present a finite-difference based algorithm to compute first-order…
Score-based diffusion models have emerged as one of the most promising frameworks for deep generative modelling, due to their state-of-the art performance in many generation tasks while relying on mathematical foundations such as stochastic…
We introduce an innovative approach for solving high-dimensional Fokker-Planck-L\'evy (FPL) equations in modeling non-Brownian processes across disciplines such as physics, finance, and ecology. We utilize a fractional score function and…
Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding…
Inverse design coupled with adjoint optimization is a powerful method to design on-chip nanophotonic devices with multi-wavelength and multi-mode optical functionalities. Although only two simulations are required in each iteration of this…
This paper investigates a Stochastic Partial Differential Equation (SPDE) derived from the Fokker-Planck equation associated with Score-based Generative Models. We modify the standard Fokker-Planck equation to better represent practical…
We present model-assisted density fitting (MADF) basis set generator, an algorithm for generating primitive atomic Gaussian density fitting (DF) basis sets (DFBSs) from a contracted Gaussian orbital basis set (OBS). The MADF algorithm…
AI-assisted protein design has emerged as a critical tool for advancing biotechnology, as deep generative models have demonstrated their reliability in this domain. However, most existing models primarily utilize protein sequence or…
Antimicrobial resistance threatens healthcare sustainability and motivates low-cost computational discovery of antimicrobial peptides (AMPs). De novo peptide generation must optimize antimicrobial activity and safety through low predicted…
In this study, we propose a new method that is useful for estimating unknown parameter values of stochastic differential equation (SDE) models, based on probability density function (PDF) data measured from random dynamical systems. As our…