ORCID Profile
0000-0002-5976-2224
Current Organisation
University of California, San Diego
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: American Chemical Society (ACS)
Date: 18-10-2013
DOI: 10.1021/AM402828K
Abstract: Using first principles calculations we investigate the binding and diffusion of Li on silicene and evaluate the prospects for application to Li-ion batteries. We find that the defect formation energy for silicene is half that of graphene, showing that silicene is more likely to contain defects. The overall lithium adsorption energy on silicene with defects is greater than the bulk cohesive energy of lithium giving stability for use in storage. Our results predict high mobility for lithium atoms on the surface of silicene with energy barriers in the range of 0.28-0.30 eV. Further, we find that the diffusion barrier through silicene is significantly lower than the diffusion barrier through graphene, with a value of 0.05 eV for the double vacancy and 0.88 eV for the single vacancy. The low diffusion barriers, both on the surface and through the hollow site, suggest a suitable material for use in Li-ion batteries.
Publisher: American Chemical Society (ACS)
Date: 05-10-2017
Abstract: Glutamate transport through the excitatory amino acid transporters is coupled to the cotransport of three Na
Publisher: Springer Science and Business Media LLC
Date: 10-2022
DOI: 10.1007/S10822-022-00462-5
Abstract: The SAMPL series of challenges aim to focus the community on specific modeling challenges, while testing and hopefully driving progress of computational methods to help guide pharmaceutical drug discovery. In this study, we report on the results of the SAMPL8 host–guest blind challenge for predicting absolute binding affinities. SAMPL8 focused on two host–guest datasets, one involving the cucurbituril CB8 (with a series of common drugs of abuse) and another involving two different Gibb deep-cavity cavitands. The latter dataset involved a previously featured deep cavity cavitand (TEMOA) as well as a new variant (TEETOA), both binding to a series of relatively rigid fragment-like guests. Challenge participants employed a reasonably wide variety of methods, though many of these were based on molecular simulations, and predictive accuracy was mixed. As in some previous SAMPL iterations (SAMPL6 and SAMPL7), we found that one approach to achieve greater accuracy was to apply empirical corrections to the binding free energy predictions, taking advantage of prior data on binding to these hosts. Another approach which performed well was a hybrid MD-based approach with reweighting to a force matched QM potential. In the cavitand challenge, an alchemical method using the AMOEBA-polarizable force field achieved the best success with RMSE less than 1 kcal/mol, while another alchemical approach ( ATM/GAFF2-AM1BCC/TIP3P/HREM ) had RMSE less than 1.75 kcal/mol. The work discussed here also highlights several important lessons for ex le, retrospective studies of reference calculations demonstrate the sensitivity of predicted binding free energies to ethyl group s ling and/or guest starting pose, providing guidance to help improve future studies on these systems.
Publisher: Elsevier BV
Date: 2019
Publisher: AIP Publishing
Date: 11-02-2019
DOI: 10.1063/1.5082975
Abstract: Solvation free energies of ions are difficult to determine from molecular dynamics simulations due to the long-range Coulomb interactions. Various approximations and corrections are introduced to enable their calculation in small systems, which, however, raises issues of robustness. We show that solvation free energies of ions can be calculated using the spherical boundary conditions without introducing any corrections at the boundary via a buffer zone. The results are shown to converge for a droplet size of 21 Å and are independent of the parameters used for confining water or restraining the ion. The proposed method thus resolves the robustness issues in solvation free energy calculations of ions and can be used with confidence to determine force field parameters from such calculations. We apply the method to calculate the solvation free energies of the side chain analogs of charged amino acids. Tests using periodic boundary conditions show that similar results are also obtained in that case.
Publisher: MDPI AG
Date: 11-11-2015
DOI: 10.3390/BIOM5043067
Publisher: American Chemical Society (ACS)
Date: 13-12-2012
DOI: 10.1021/JP2099834
Publisher: American Thoracic Society
Date: 07-2022
Publisher: Zenodo
Date: 2020
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D3SC01975F
Publisher: Elsevier BV
Date: 08-2019
Publisher: MDPI AG
Date: 18-03-2016
Location: United States of America
No related grants have been discovered for Jeffry Setiadi.