Energy Landscape Analysis of the Epithelial-Mesenchymal Transition Network.
Sign Up to like & getrecommendations! Published in 2022 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-2277-3_11
Abstract: The epithelial-mesenchymal transition (EMT) is a key developmental program that is often activated during the cancer invasion, metastasis, and drug resistance. However, it remains a critical question to elucidate the mechanisms of EMT. For example,… read more here.
Keywords: mesenchymal transition; analysis; landscape; energy landscape ... See more keywords
Energy Landscape of a Bridge between Protein Folds
Sign Up to like & getrecommendations! Published in 2017 at "Biophysical Journal"
DOI: 10.1016/j.bpj.2016.11.1071
Abstract: The entire structure space of the protein universe, so called fold-space, is estimated to contain thousands of different folds. Most proteins displaying high sequence identity are homologous and thus share the same fold, however, remarkable… read more here.
Keywords: protein; landscape bridge; bridge; energy landscape ... See more keywords
Sampling stable amorphous tantalum states from energy landscape
Sign Up to like & getrecommendations! Published in 2021 at "Scripta Materialia"
DOI: 10.1016/j.scriptamat.2021.114018
Abstract: Abstract Amorphous pure metals are important for technological applications and provide a simple system for the study of fundamental science. Through detailed analysis of the microscopic structure of vapor-deposited Ta film, we reveal the presence… read more here.
Keywords: sampling stable; stable amorphous; energy landscape; energy ... See more keywords
Mapping Topological Dipole Textures, Chirality, and the Potential Energy Landscape of Polar Skyrmions Using 4D-STEM
Sign Up to like & getrecommendations! Published in 2020 at "Microscopy and Microanalysis"
DOI: 10.1017/s1431927620016529
Abstract: polar skyrmions in (PbTiO3)n/(SrTiO3)n superlattices suggests a perfect system for exploring interesting physical responses, including emergent toroidal order and local negative capacitance [1, 2]. Here, we explore the topologically non-trivial dipole textures of polar skyrmions,… read more here.
Keywords: energy landscape; dipole textures; polar skyrmions; potential energy ... See more keywords
Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.0c00879
Abstract: Proteins are allosteric machines that couple motions at distinct, often distant, sites to control biological function. Low-frequency structural vibrations are a mechanism of this long-distance connection and are often used computationally to predict correlations, but… read more here.
Keywords: frequency; energy landscape; normal mode;
Energy Landscape of State-Specific Electronic Structure Theory
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.1c01089
Abstract: State-specific approximations can provide a more accurate representation of challenging electronic excitations by enabling relaxation of the electron density. While state-specific wave functions are known to be local minima or saddle points of the approximate… read more here.
Keywords: state specific; energy landscape; energy; exact energy ... See more keywords
Exploring the Quantum Chemical Energy Landscape with GNN-Guided Artificial Force
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c01061
Abstract: Artificial force has been proven useful to get over energy barriers and quickly search a large portion of the energy landscape. This work proposes a method based on graph neural networks to optimize the choice… read more here.
Keywords: artificial force; energy landscape; energy; chemical ... See more keywords
Chasing the Full Free Energy Landscape of Neuroreceptor/Ligand Unbinding by Metadynamics Simulations.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.9b00118
Abstract: Predicting the complete free energy landscape associated with protein-ligand unbinding may greatly help designing drugs with highly optimized pharmacokinetics. Here we investigate the unbinding of the iperoxo agonist to its target human neuroreceptor M2, embedded… read more here.
Keywords: energy landscape; landscape; ligand unbinding; full free ... See more keywords
An explicit characterization of the free energy landscape of a protein in the space of all its Cα carbons.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.9b00800
Abstract: By using an approach that allows computing the free energy in high-dimensional spaces together with a clustering technique capable of identifying kinetic attractors stabilized by entropy, we analyze a molecular dynamics trajectory of the Villin… read more here.
Keywords: free energy; energy landscape; space carbons; energy ... See more keywords
Tuning the potential energy landscape to suppress Ostwald Ripening in surface-supported catalyst systems.
Sign Up to like & getrecommendations! Published in 2019 at "Nano letters"
DOI: 10.1021/acs.nanolett.9b02237
Abstract: Rational control of nanoparticle (NP) size distribution during operation is crucial to improve catalytic performance and noble metal sustainability. Herein, we explore the Ostwald ripening (OR) of metal atoms on zeolite surfaces by a coupled… read more here.
Keywords: ostwald ripening; potential energy; energy landscape; surface ... See more keywords
Probing the Protein Folding Energy Landscape: Dissociation of Amyloid-β Fibrils by Laser-Induced Plasmonic Heating.
Sign Up to like & getrecommendations! Published in 2023 at "ACS nano"
DOI: 10.1021/acsnano.3c01489
Abstract: Insoluble amyloid fibrils made from proteins and peptides are difficult to be degraded in both living and artificial systems. The importance of studying their physical stability lies primarily with their association with human neurodegenerative diseases,… read more here.
Keywords: protein folding; energy landscape; energy; amyloid fibrils ... See more keywords