Steven J Stuart
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Explore the profile of Steven J Stuart including associated specialties, affiliations and a list of published articles.
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Articles
27
Citations
169
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Recent Articles
1.
Karabin M, Stuart S
J Chem Phys
. 2020 Sep;
153(11):114103.
PMID: 32962382
As one of the most robust global optimization methods, simulated annealing has received considerable attention with many variations that attempt to improve the cooling schedule. This paper introduces a variant...
2.
Abramyan T, Hyde-Volpe D, Stuart S, Latour R
Biointerphases
. 2017 May;
12(2):02D409.
PMID: 28514864
The use of standard molecular dynamics simulation methods to predict the interactions of a protein with a material surface have the inherent limitations of lacking the ability to determine the...
3.
Kucukkal M, Stuart S
J Mol Model
. 2017 Apr;
23(4):148.
PMID: 28365822
Single-walled carbon nanotubes show promise as nanoscale transistors for nanocomputing applications. This use will require appropriate methods for creating electrical connections between distinct nanotubes, analogous to welding of metallic wires...
4.
Abramyan T, Snyder J, Thyparambil A, Stuart S, Latour R
J Comput Chem
. 2016 Jun;
37(21):1973-82.
PMID: 27292100
Clustering methods have been widely used to group together similar conformational states from molecular simulations of biomolecules in solution. For applications such as the interaction of a protein with a...
5.
Li X, Snyder J, Stuart S, Latour R
J Chem Phys
. 2015 Oct;
143(14):144105.
PMID: 26472361
The recently developed "temperature intervals with global exchange of replicas" (TIGER2) accelerated sampling method is found to have inaccuracies when applied to systems with explicit solvation. This inaccuracy is due...
6.
Abramyan T, Snyder J, Yancey J, Thyparambil A, Wei Y, Stuart S, et al.
Biointerphases
. 2015 Mar;
10(2):021002.
PMID: 25818122
Interfacial force field (IFF) parameters for use with the CHARMM force field have been developed for interactions between peptides and high-density polyethylene (HDPE). Parameterization of the IFF was performed to...
7.
Snyder J, Abramyan T, Yancey J, Thyparambil A, Wei Y, Stuart S, et al.
Biointerphases
. 2012 Sep;
7(1-4):56.
PMID: 22941539
Adsorption free energies for eight host-guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass]...
8.
Hur J, Stuart S
J Chem Phys
. 2012 Aug;
137(5):054102.
PMID: 22894327
An improvement to the AIREBO potential for hydrocarbons is presented in which contributions to the bond order are determined by the local bonding environment around the bond, rather than the...
9.
Kucukkal T, Stuart S
J Phys Chem B
. 2012 Jul;
116(30):8733-40.
PMID: 22747103
Molecular dynamics simulations were carried out for concentrated aqueous solutions of three dipeptides: Gly-Ala, Gly-Pro, and Ala-Pro. The simulations were performed using both polarizable and nonpolarizable force fields, as a...
10.
Collier G, Vellore N, Yancey J, Stuart S, Latour R
Biointerphases
. 2012 May;
7(1-4):24.
PMID: 22589067
All-atom empirical molecular mechanics protein force fields, which have been developed to represent the energetics of peptide folding behavior in aqueous solution, have not been parameterized for protein interactions with...