skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


This content will become publicly available on April 1, 2026

Title: The need to implement FAIR principles in biomolecular simulations
In the Big Data era, a change of paradigm in the use of molecular dynamics is required. Trajectories should be stored under FAIR (findable, accessible, interoperable and reusable) requirements to favor its reuse by the community under an open science paradigm.  more » « less
Award ID(s):
2154999 2019745
PAR ID:
10583290
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more » ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; « less
Publisher / Repository:
Nature
Date Published:
Journal Name:
Nature Methods
Volume:
22
Issue:
4
ISSN:
1548-7091
Page Range / eLocation ID:
641 to 645
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. The mechanical behavior of unsaturated porous media under non-isothermal conditions plays a vital role in geo-hazards and geo-energy engineering (e.g., landslides triggered by fire and geothermal energy harvest and foundations). Temperature increase can trigger localized failure and cracking in unsaturated porous media. This article investigates the shear banding and cracking in unsaturated porous media under non-isothermal conditions through a thermo–hydro–mechanical (THM) periporomechanics (PPM) paradigm. PPM is a nonlocal formulation of classical poromechanics using integral equations, which is robust in simulating continuous and discontinuous deformation in porous media. As a new contribution, we formulate a nonlocal THM constitutive model for unsaturated porous media in the PPM paradigm in this study. The THM meshfree paradigm is implemented through an explicit Lagrangian meshfree algorithm. The return mapping algorithm is used to implement the nonlocal THM constitutive model numerically. Numerical examples are presented to assess the capability of the proposed THM mesh-free paradigm for modeling shear banding and cracking in unsaturated porous media under non-isothermal conditions. The numerical results are examined to study the effect of temperature variations on the formation of shear banding and cracking in unsaturated porous media. 
    more » « less
  2. Abstract Dynamic crack branching in unsaturated porous media holds significant relevance in various fields, including geotechnical engineering, geosciences, and petroleum engineering. This article presents a numerical investigation into dynamic crack branching in unsaturated porous media using a recently developed coupled micro‐periporomechanics (PPM) paradigm. This paradigm extends the PPM model by incorporating the micro‐rotation of the solid skeleton. Within this framework, each material point is equipped with three degrees of freedom: displacement, micro‐rotation, and fluid pressure. Consistent with the Cosserat continuum theory, a length scale associated with the micro‐rotation of material points is inherently integrated into the model. This study encompasses several key aspects: (1) Validation of the coupled micro‐PPM paradigm for effectively modeling crack branching in deformable porous media, (2) Examination of the transition from a single branch to multiple branches in porous media under drained conditions, (3) Simulation of single crack branching in unsaturated porous media under dynamic loading conditions, and (4) Investigation of multiple crack branching in unsaturated porous media under dynamic loading conditions. The numerical results obtained in this study are systematically analyzed to elucidate the factors that influence crack branching in porous media subjected to dynamic loading. Furthermore, the comprehensive numerical findings underscore the efficacy and robustness of the coupled micro‐PPM paradigm in accurately modeling dynamic crack branching in variably saturated porous media. 
    more » « less
  3. Future generation wireless technologies are expected to serve an increasingly dense and dynamic population of users that generate short bundles of information to be transferred over the shared spectrum. This calls for new distributed and low-overhead Multiple-Access-Control (MAC) strategies to serve such dynamic demands with spectral efficiency characteristics. In this work, we address this need by identifying and developing two fundamentally different MAC paradigms: (i) congestion-based paradigm that estimates the congestion level in the system and adapts to it; and (ii) age-based paradigm that prioritizes demands based on their ages. Despite their apparent differences, we develop policies under each paradigm in a generic multi-channel access scenario that are provably throughput-optimal when they employ any asymptotically-efficient channel encoding/decoding mechanism. We also characterize the stability regions of the two designs, and investigate the conditions under which one design outperforms the other. We perform extensive simulations to validate the theoretical claims and investigate the non-asymptotic performances of our designs. 
    more » « less
  4. null (Ed.)
    While progress has been made on the visual question answering leaderboards, models often utilize spurious correlations and priors in datasets under the i.i.d. setting. As such, evaluation on out-of-distribution (OOD) test samples has emerged as a proxy for generalization. In this paper, we present \textit{MUTANT}, a training paradigm that exposes the model to perceptually similar, yet semantically distinct \textit{mutations} of the input, to improve OOD generalization, such as the VQA-CP challenge. Under this paradigm, models utilize a consistency-constrained training objective to understand the effect of semantic changes in input (question-image pair) on the output (answer). Unlike existing methods on VQA-CP, \textit{MUTANT} does not rely on the knowledge about the nature of train and test answer distributions. \textit{MUTANT} establishes a new state-of-the-art accuracy on VQA-CP with a 10.57{\%} improvement. Our work opens up avenues for the use of semantic input mutations for OOD generalization in question answering. 
    more » « less
  5. We explore task tolerances, i.e., allowable position or rotation inaccuracy, as an important resource to facilitate smooth and effective telemanipulation. Task tolerances provide a robot flexibility to generate smooth and feasible motions; however, in teleoperation, this flexibility may make the user’s control less direct. In this work, we implemented a telema- nipulation system that allows a robot to autonomously adjust its configuration within task tolerances. We conducted a user study comparing a telemanipulation paradigm that exploits task tolerances (functional mimicry) to a paradigm that requires the robot to exactly mimic its human operator (exact mimicry), and assess how the choice in paradigm shapes user experience and task performance. Our results show that autonomous adjustments within task tolerances can lead to performance improvements without sacrificing perceived control of the robot. Additionally, we find that users perceive the robot to be more under control, predictable, fluent, and trustworthy in functional mimicry than in exact mimicry. 
    more » « less