arXiv subjects

Adam P. Generale

Publications and source records attributed to Adam P. Generale.

3 recordsLinked to original sources

arXiv2025

Refining Coarse-Grained Molecular Topologies: A Bayesian Optimization Approach

Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated with All-Atom (AA) MD simulations have led to the development of Coarse-Grained Molecular Dynamics (CGMD), providing a lower-dimensional compression of the AA structure into representative CG beads, offering reduced computational expense at the cost of predictive accuracy. Existing CGMD methods, such as CG-Martini (calibrated against experimental data), aim to generate an embedding of a topology that sufficiently generalizes across a range of structures. Detrimentally, in attempting to specify parameterization with applicability across molecular classes, it is unable to specialize to domain-specific applications, where sufficient accuracy and computational speed are critical. This work presents a novel approach to optimize derived results from CGMD simulations by refining the general-purpose Martini3 topologies specifically the bonded interaction parameters within a given coarse-grained mapping - for domain-specific applications using Bayesian Optimization methodologies. We have developed and validated a CG potential applicable to any degree of polymerization, representing a significant advancement in the field. Our optimized CG potential, based on the Martini3 framework, aims to achieve accuracy comparable to AAMD while maintaining the computational efficiency of CGMD. This approach bridges the gap between efficiency and accuracy in multiscale molecular simulations, potentially enabling more rapid and cost-effective molecular discovery across various scientific and technological domains.

physics.chem-ph↗

arXiv2024

Modeling Stochastic Conditional Dynamics from Sparse Observations via Kernel-Stabilized Flow Matching

Learning to transform conditional probability densities over time is a fundamental challenge spanning probabilistic modeling and the natural sciences. This task is paramount when forecasting the evolution of stochastic nonlinear dynamical systems in biological and physical domains. While flow-based models can predict the temporal evolution of probability distributions, existing approaches often assume discrete conditioning with samples that are paired across time, limiting their scientific applicability where frequently only sparse data with unpaired continuous conditioning is available. We propose Conditional Variable Flow Matching (CVFM), a framework for learning flows transforming conditional distributions with amortization across the continuous space of conditional densities. CVFM addresses the high-variance instability of prior methods by jointly sampling flows over state and conditioning variables, utilizing a conditioning mismatch kernel alongside a conditional Wasserstein distance to reweight the conditional optimal transport objective. Collectively, these advances allow for learning dynamics from sparse unpaired measurements of state-condition across time. We evaluate CVFM on conditional mapping benchmarks and a case study modeling the temporal evolution of materials internal structure during manufacturing processes, observing improved performance and convergence characteristics over existing conditional variants. Code is available at https://github.com/agenerale/conditional-variable-flow-matching.

cs.LG↗

arXiv2023

Sequential Designs for Filling Output Spaces

Space-filling designs are commonly used in computer experiments to fill the space of inputs so that the input-output relationship can be accurately estimated. However, in certain applications such as inverse design or feature-based modeling, the aim is to fill the response or feature space. In this article, we propose a new experimental design framework that aims to fill the space of the outputs (responses or features). The design is adaptive and model-free, and therefore is expected to be robust to different kinds of modeling choices and input-output relationships. Several examples are given to show the advantages of the proposed method over the traditional input space-filling designs.

stat.ME↗