Self-healing umbrella sampling: convergence and efficiency
Sign Up to like & getrecommendations! Published in 2017 at "Statistics and Computing"
DOI: 10.1007/s11222-015-9613-2
Abstract: The Self-Healing Umbrella Sampling (SHUS) algorithm is an adaptive biasing algorithm which has been proposed in Marsili et al. (J Phys Chem B 110(29):14011–14013, 2006) in order to efficiently sample a multimodal probability measure. We show… read more here.
Keywords: algorithm; healing umbrella; umbrella sampling; self healing ... See more keywords
Free Energy Calculation of Membrane Permeation - Simulation Results Suggest Relaxation of Headgroup-Solute Interactions is the Slowest Degree of Freedom
Sign Up to like & getrecommendations! Published in 2017 at "Biophysical Journal"
DOI: 10.1016/j.bpj.2016.11.1258
Abstract: Molecular Dynamics (MD) simulations have been extensively used to investigate membrane-solute interactions. Understanding the interactions associated with solute translocation across lipid bilayers facilitates prediction of passive permeation rates of cell membranes, which is a very… read more here.
Keywords: energy; permeation; solute interactions; umbrella sampling ... See more keywords
Vitamin E does not Preferentially Bind to Polyunsaturated Lipids as Revealed by Umbrella Sampling MD Simulations
Sign Up to like & getrecommendations! Published in 2017 at "Biophysical Journal"
DOI: 10.1016/j.bpj.2016.11.445
Abstract: Alpha-tocopherol (αtoc) is the active form of vitamin E that is retained in the human body. It is a lipid-soluble antioxidant, which protects polyunsaturated fatty acids (PUFA) by terminating a chain of chemical reactions that… read more here.
Keywords: vitamin preferentially; toc; preferentially bind; bind polyunsaturated ... See more keywords
Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00508
Abstract: The cardiac troponin (cTn) complex is an important regulatory protein in heart contraction. Upon binding of Ca2+, cTn undergoes a conformational shift that allows the troponin I switch peptide (cTnISP) to be released from the… read more here.
Keywords: hydrophobic patch; umbrella sampling; switch peptide; troponin ... See more keywords
Determination of Equilibrium Adsorbed Morphologies of Surfactants at Metal-Water Interfaces Using a Modified Umbrella Sampling-Based Methodology.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00078
Abstract: Surfactants adsorb to metal-water interfaces in various morphologies, including self-assembled monolayers (SAMs), cylindrical and spherical micelles, or hemimicelles. Current molecular simulation methods are unable to efficiently sample the formation of these morphologies because of the… read more here.
Keywords: modified umbrella; methodology; umbrella sampling; water ... See more keywords
Finite temperature string method with umbrella sampling using path collective variables: application to secondary structure change in a protein.
Sign Up to like & getrecommendations! Published in 2022 at "Soft matter"
DOI: 10.1039/d2sm00888b
Abstract: The transition of an α-helix to a β-sheet in proteins is among the most complex conformational changes seen in biomolecular systems. Due to long time scales involved in the transition, it is challenging to study… read more here.
Keywords: umbrella sampling; finite temperature; temperature string; collective variables ... See more keywords
Umbrella sampling: A powerful method to sample tails of distributions
Sign Up to like & getrecommendations! Published in 2017 at "Monthly Notices of the Royal Astronomical Society"
DOI: 10.1093/mnras/sty2140
Abstract: We present the umbrella sampling (US) technique and show that it can be used to sample extremely low probability areas of the posterior distribution that may be required in statistical analyses of data. In this… read more here.
Keywords: sample; sampling powerful; powerful method; umbrella windows ... See more keywords
A Curvilinear-Path Umbrella Sampling Approach to Characterizing the Interactions Between Rapamycin and Three FKBP12 Variants
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.879000
Abstract: Rapamycin is an immunosuppressant macrolide that exhibits anti-proliferative properties through inhibiting the mTOR kinase. In fact, the drug first associates with the FKBP12 enzyme before interacting with the FRB domain of its target. Despite the… read more here.
Keywords: curvilinear path; path umbrella; approach characterizing; umbrella sampling ... See more keywords
Umbrella Sampling Simulations of Carbon Nanoparticles Crossing Immiscible Solvents
Sign Up to like & getrecommendations! Published in 2022 at "Molecules"
DOI: 10.3390/molecules27030956
Abstract: We use molecular dynamics to compute the free energy of carbon nanoparticles crossing a hydrophobic–hydrophilic interface. The simulations are performed on a biphasic system consisting of immiscible solvents (i.e., cyclohexane and water). We solvate a… read more here.
Keywords: carbon; umbrella sampling; immiscible solvents; carbon nanoparticles ... See more keywords