Free energy landscapes of prototropic tautomerism in pyridoxal 5′‐phosphate schiff bases at the active site of an enzyme in aqueous medium
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25338
Abstract: We have performed hybrid quantum‐classical metadynamics simulations and quantum chemical calculations to investigate the free energy landscapes of intramolecular proton transfer and associated tautomeric equilibrium in pyridoxal 5 ′ ‐phosphate (PLP) Schiff Bases, namely the… read more here.
Keywords: energy landscapes; plp; active site; free energy ... See more keywords
Energy landscapes and urban trajectories towards sustainability
Sign Up to like & getrecommendations! Published in 2017 at "Energy Policy"
DOI: 10.1016/j.enpol.2017.01.009
Abstract: An urban energy transition is needed to address the two global environmental challenges of urbanisation and increasing carbon emissions. Urban energy landscapes represent the spatial patterns of urban energy systems which are visible in the… read more here.
Keywords: energy landscapes; energy; trajectories towards; towards sustainability ... See more keywords
Analysing single-molecule trajectories to reconstruct free-energy landscapes of cyclic motor proteins.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of theoretical biology"
DOI: 10.1016/j.jtbi.2018.11.015
Abstract: Stochastic trajectories measured in single-molecule experiments have provided key insights into the microscopic behaviour of cyclic motor proteins. However, the fundamental free-energy landscapes of motor proteins are currently only able to be determined by computationally… read more here.
Keywords: cyclic motor; energy landscapes; single molecule; motor proteins ... See more keywords
Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.7b00351
Abstract: In spite of the abundance of glycoproteins in biological processes, relatively little three-dimensional structural data is available for glycan structures. Here, we study the structure and flexibility of the vast majority of mammalian oligosaccharides appearing… read more here.
Keywords: energy landscapes; oligosaccharides within; modeling oligosaccharides; within glycoproteins ... See more keywords
Combined Force-Frequency Sampling for Simulation of Systems Having Rugged Free Energy Landscapes.
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.9b00883
Abstract: An adaptive, machine-learning based sampling method is presented for simulation of systems having rugged, multi-dimensional free energy landscapes. The method's main strength resides in its ability to learn both from the frequency of visits to… read more here.
Keywords: simulation systems; energy landscapes; systems rugged; energy ... See more keywords
Identifying Free Energy Landscapes of Proton-Transfer Processes between Brønsted Acid Sites and Water Clusters Inside the Zeolite Pores
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Physical Chemistry C"
DOI: 10.1021/acs.jpcc.0c07033
Abstract: In the aqueous-phase zeolite-catalyzed reactions, water molecules profoundly alter the reaction activity and reaction mechanisms. This can be ascribed to the changing nature of the Bronsted acid si... read more here.
Keywords: energy landscapes; water; identifying free; landscapes proton ... See more keywords
Energy Landscapes for the Aggregation of Aβ17-42.
Sign Up to like & getrecommendations! Published in 2018 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.7b12896
Abstract: The aggregation of the Aβ peptide (Aβ1-42) to form fibrils is a key feature of Alzheimer's disease. The mechanism is thought to be a nucleation stage followed by an elongation process. The elongation stage involves… read more here.
Keywords: aggregation; energy landscapes; energy; process ... See more keywords
Cellular absorption of small molecules: free energy landscapes of melatonin binding at phospholipid membranes
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-65753-z
Abstract: Free energy calculations are essential to unveil mechanisms at the atomic scale such as binding of small solutes and their translocation across cell membranes, eventually producing cellular absorption. Melatonin regulates biological rhythms and is directly… read more here.
Keywords: cellular absorption; energy landscapes; energy; melatonin binding ... See more keywords
Characterizing the free-energy landscapes of DNA origamis.
Sign Up to like & getrecommendations! Published in 2022 at "Nanoscale"
DOI: 10.1039/d1nr05716b
Abstract: We show how coarse-grained modelling combined with umbrella sampling using distance-based order parameters can be applied to compute the free-energy landscapes associated with mechanical deformations of large DNA nanostructures. We illustrate this approach for the… read more here.
Keywords: energy landscapes; landscapes dna; energy; free energy ... See more keywords
Energy landscapes on polymerized liquid crystal interfaces.
Sign Up to like & getrecommendations! Published in 2023 at "Soft matter"
DOI: 10.1039/d3sm00356f
Abstract: We measure and model monolayers of concentrated diffusing colloidal probes interacting with polymerized liquid crystal (PLC) planar surfaces. At topological defects in local nematic director profiles at PLC surfaces, we observe time-averaged two-dimensional particle density… read more here.
Keywords: van der; liquid crystal; energy; der waals ... See more keywords
Exploring canyons in glassy energy landscapes using metadynamics
Sign Up to like & getrecommendations! Published in 2022 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2210535119
Abstract: Significance The inability of glasses to find their lowest-energy configurations is often attributed to their potential energy landscapes: rugged, barrier-filled surfaces in high-dimensional space that seem incredibly difficult to navigate. We report that for three… read more here.
Keywords: energy; glassy energy; landscapes using; exploring canyons ... See more keywords