Exploring canyons in glassy energy landscapes using metadynamics.

Proc Natl Acad Sci U S A

Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19014.

Published: October 2022

The complex physics of glass-forming systems is controlled by the structure of the low-energy portions of their potential energy landscapes. Here we report that a modified metadynamics algorithm efficiently explores and samples low-energy regions of such high-dimensional landscapes. In the energy landscape for a model foam, our algorithm finds and descends meandering canyons in the landscape, which contain dense clusters of energy minima along their floors. Similar canyon structures in the energy landscapes of two model glass formers-hard sphere fluids and the Kob-Andersen glass-allow us to reach high densities and low energies, respectively. In the hard sphere system, fluid configurations are found to form continuous regions that cover the canyon floors up to densities well above the jamming transition. For the Kob-Andersen glass former, our technique samples low-energy states with modest computational effort, with the lowest energies found approaching the predicted Kauzmann limit.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9618120PMC
http://dx.doi.org/10.1073/pnas.2210535119DOI Listing

Publication Analysis

Top Keywords

energy landscapes
12
samples low-energy
8
energy
5
exploring canyons
4
canyons glassy
4
glassy energy
4
landscapes
4
landscapes metadynamics
4
metadynamics complex
4
complex physics
4

Similar Publications

In the current cybersecurity landscape, Distributed Denial of Service (DDoS) attacks have become a prevalent form of cybercrime. These attacks are relatively easy to execute but can cause significant disruption and damage to targeted systems and networks. Generally, attackers perform it to make reprisal but sometimes this issue can be authentic also.

View Article and Find Full Text PDF

Transforming Medicine: Cutting-Edge Applications of Nanoscale Materials in Drug Delivery.

ACS Nano

January 2025

CAS, a division of the American Chemical Society, Columbus, Ohio 43210, United States.

Since their inception in the early 1960s, the development and use of nanoscale materials have progressed tremendously, and their roles in diverse fields ranging from human health to energy and electronics are undeniable. The application of nanotechnology inventions has revolutionized many aspects of everyday life including various medical applications and specifically drug delivery systems, maximizing the therapeutic efficacy of the contained drugs by means of bioavailability enhancement or minimization of adverse effects. In this review, we utilize the CAS Content Collection, a vast repository of scientific information extracted from journal and patent publications, to analyze trends in nanoscience research relevant to drug delivery in an effort to provide a comprehensive and detailed picture of the use of nanotechnology in this field.

View Article and Find Full Text PDF

Large-scale and long-term wildlife research and monitoring using camera traps: a continental synthesis.

Biol Rev Camb Philos Soc

January 2025

Wildlife Observatory of Australia (WildObs), Queensland Cyber Infrastructure Foundation (QCIF), Brisbane, Queensland, 4072, Australia.

Camera traps are widely used in wildlife research and monitoring, so it is imperative to understand their strengths, limitations, and potential for increasing impact. We investigated a decade of use of wildlife cameras (2012-2022) with a case study on Australian terrestrial vertebrates using a multifaceted approach. We (i) synthesised information from a literature review; (ii) conducted an online questionnaire of 132 professionals; (iii) hosted an in-person workshop of 28 leading experts representing academia, non-governmental organisations (NGOs), and government; and (iv) mapped camera trap usage based on all sources.

View Article and Find Full Text PDF

Cyclin-dependent kinases (CDKs), play essential roles in cell cycle progression. CDK activity is controlled through phosphorylation and inhibition by CDK inhibitors, such as p16. Mutations in p16 can lead to diseases such as cancer.

View Article and Find Full Text PDF

Amyloid fibrils are highly stable misfolded protein assemblies that play an important role in several neurodegenerative and systemic diseases. Although structural information of the amyloid state is now abundant, mechanistic details about the misfolding process remain elusive. Inspired by the Φ-value analysis of protein folding, we combined experiments and molecular simulations to resolve amino-acid contacts and determine the structure of the transition-state ensemble-the rate-limiting step-for fibril elongation of PI3K-SH3 amyloid fibrils.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!