Notes on the thermodynamics of superentropic AdS black holes

Wu, Di; Wu, Puxun; Yu, Hongwei; Wu, Shuang-Qing

doi:10.1103/physrevd.101.024057

Cited by 43 publications

(47 citation statements)

References 33 publications

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“…Kofke and collaborators have developed other descriptors of phase space overlap between two states A and B. [97][98][99][100][101][102][103] We shall focus on two metrics that Wu and Kofke have devised. 101,102 The first is based on the overlap of total energy distributions:…”

Section: Analysis Of Phase Space Overlap Of δU(λ) Distributions From End-state Simulations As a Function Of Reference Potentialmentioning

confidence: 99%

Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods

Giese

York

2019

J. Chem. Theory Comput.

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We use the PBE0/6-31G* density functional method to perform ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations under periodic boundary conditions with rigorous electrostatics using the ambient potential composite Ewald method in order to test the convergence of MM→QM/MM free energy corrections for the prediction of 17 small-molecule solvation free energies and 8 ligand binding free energies to T4 lysozyme. The “indirect” thermodynamic cycle for calculating free energies is used to explore whether a series of reference potentials improve the statistical quality of the predictions. Specifically, we construct a series of reference potentials that optimizes a molecular mechanical (MM) force field’s parameters to reproduce the ab initio QM/MM forces from a QM/MM simulation. The optimizations form a systematic progression of successively expanded parameters that include bond, angle, dihedral and charge parameters. For each reference potential, we calculate benchmark quality reference values for the MM→QM/MM correction by performing the mixed MM and QM/MM Hamiltonians at 11 intermediate states, each for 200 ps. We then compare forward and reverse application of Zwanzig’s relation, thermodynamic integration, and Bennett’s acceptance ratio (BAR) methods as a function of reference potential, simulation time, and the number of simulated intermediate states. We find that Zwanzig’s equation is inadequate unless a large number of intermediate states are explicitly simulated. The TI and BAR mean signed errors are very small even when only the end-state simulations are considered, and the standard deviation of the TI and BAR errors are decreased by choosing a reference potential that optimizes the bond and angle parameters. We find a robust approach for the data sets of fairly rigid molecules considered here is to use bond+angle reference potential together with the end-state-only BAR analysis. This requires a QM/MM simulations to be performed in order to generate reference data to parameterize the bond+angle reference potential, and then this same simulation serves a dual purpose as the full QM/MM end-state. The convergence of the results with respect to time suggests that computational resources may be used more efficiently by running multiple simulations for no more than 50 ps, rather than running one long simulation.

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Section: Analysis Of Phase Space Overlap Of δU(λ) Distributions From End-state Simulations As a Function Of Reference Potentialmentioning

confidence: 99%

Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods

Giese

York

2019

J. Chem. Theory Comput.

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“…Biotechnology is taking advantage of biological nanopores for low-cost DNA and RNA sequencing, 1,2 detection of small molecules, 3 polymers, 4 polypeptides, 5 and protein folding. 6 Among many channels, α-hemolysin is widely used for this purpose.…”

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confidence: 99%

Quiet Outer Membrane Protein G (OmpG) Nanopore for Biosensing

et al. 2019

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Interest in nanopore technology has been growing due to nanopores' unique capabilities in small molecule sensing, measurement of protein folding, and low-cost DNA and RNA sequencing. The E. coli β-barrel outer membrane protein OmpG is an excellent alternative to other protein nanopores because of its single polypeptide chain. However, the flexibility of its extracellular loops ultimately limits applications in traditional biosensing. We deleted several residues in and near loop 6 of OmpG. The dynamic structure of the new construct determined by NMR shows that loops 1, 2, 6, and 7 have reduced flexibilities compared to those of wild-type. Electrophysiological measurements show that the new design virtually eliminates flickering between open and closed states across a wide pH range. Modification of the pore lumen with a copper chelating moiety facilitates detection of small molecules. As proof of concept, we demonstrate concurrent singlemolecule biosensing of glutamate and adenosine triphosphate.

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“…22 Nonetheless, Onivyde® is currently being tested in variety of solid tumor types, including lung and breast cancer. 23,24 We have recently demonstrated the utility of a first-generation mesoporous silica nanoparticle (MSNP) drug carrier for irinotecan delivery in an orthotopic PDAC model, with improved efficacy and reduced toxicity compared to an in-house liposome. 14 MSNPs are excellent carriers due to high biocompatibility, large surface area, tunable particle/pore sizes and tunable surface functionalization.…”

mentioning

confidence: 99%