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Thomas A. Knotts, Ph.D. - Publications

Affiliations: 
2006 University of Wisconsin, Madison, Madison, WI 
Area:
polymer
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30 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Smith AK, Soltani M, Wilkerson JW, Timmerman BD, Zhao EL, Bundy BC, Knotts TA. Coarse-grained simulation of PEGylated and tethered protein devices at all experimentally accessible surface residues on β-lactamase for stability analysis and comparison. The Journal of Chemical Physics. 154: 075102. PMID 33607875 DOI: 10.1063/5.0032019  0.341
2020 Wilkerson JW, Smith AK, Wilding KM, Bundy BC, Knotts TA. The Effects of -Azidophenylalanine Incorporation on Protein Structure and Stability. Journal of Chemical Information and Modeling. PMID 32966074 DOI: 10.1021/acs.jcim.0c00725  0.322
2020 Smith AK, Wilkerson JW, Knotts TA. Parameterization of Unnatural Amino Acids with Azido and Alkynyl R-Groups for Use in Molecular Simulations. The Journal of Physical Chemistry. A. PMID 32614187 DOI: 10.1021/Acs.Jpca.0C04605  0.394
2018 Bush DB, Knotts TA. The effects of antigen size, binding site valency, and flexibility on fab-antigen binding near solid surfaces. The Journal of Chemical Physics. 149: 165102. PMID 30384722 DOI: 10.1063/1.5045356  0.349
2018 Wilding KM, Smith AK, Wilkerson JW, Bush DB, Knotts TA, Bundy BC. The Locational Impact of Site-Specific PEGylation: Streamlined Screening with Cell-Free Protein Expression and Coarse-Grain Simulation. Acs Synthetic Biology. PMID 29295615 DOI: 10.1021/Acssynbio.7B00316  0.405
2017 Grawe RW, Knotts TA. The effects of tether placement on antibody stability on surfaces. The Journal of Chemical Physics. 146: 215102. PMID 28576081 DOI: 10.1063/1.4983705  0.431
2017 Messerly RA, Knotts TA, Wilding WV. Uncertainty quantification and propagation of errors of the Lennard-Jones 12-6 parameters for n-alkanes. The Journal of Chemical Physics. 146: 194110. PMID 28527455 DOI: 10.1063/1.4983406  0.365
2017 Bush DB, Knotts TA. Probing the effects of surface hydrophobicity and tether orientation on antibody-antigen binding. The Journal of Chemical Physics. 146: 155103. PMID 28433015 DOI: 10.1063/1.4980083  0.415
2016 Messerly RA, Knotts TA, Rowley RL, Wilding WV. Improved Estimates of the Critical Point Constants for Large n-Alkanes Using Gibbs Ensemble Monte Carlo Simulations Journal of Chemical & Engineering Data. 61: 3640-3649. DOI: 10.1021/Acs.Jced.6B00574  0.377
2016 Messerly RA, Knotts TA, Rowley RL, Wilding WV. An improved approach for predicting the critical constants of large molecules with Gibbs Ensemble Monte Carlo simulation Fluid Phase Equilibria. 425: 432-442. DOI: 10.1016/J.Fluid.2016.06.041  0.326
2015 Messerly RA, Rowley RL, Knotts TA, Wilding WV. An improved statistical analysis for predicting the critical temperature and critical density with Gibbs ensemble Monte Carlo simulation. The Journal of Chemical Physics. 143: 104101. PMID 26374012 DOI: 10.1063/1.4928865  0.343
2015 Bush DB, Knotts TA. Communication: Antibody stability and behavior on surfaces. The Journal of Chemical Physics. 143: 061101. PMID 26277119 DOI: 10.1063/1.4928455  0.336
2015 Welling RC, Knotts TA. The effects of multiple probes on the hybridization of target DNA on surfaces. The Journal of Chemical Physics. 142: 015102. PMID 25573584 DOI: 10.1063/1.4904929  0.378
2014 Loong BK, Knotts TA. Communication: Using multiple tethers to stabilize proteins on surfaces. The Journal of Chemical Physics. 141: 051104. PMID 25106561 DOI: 10.1063/1.4891971  0.481
2013 Wei S, Knotts TA. A coarse grain model for protein-surface interactions. The Journal of Chemical Physics. 139: 095102. PMID 24028132 DOI: 10.1063/1.4819131  0.491
2013 Schmitt TJ, Rogers JB, Knotts TA. Exploring the mechanisms of DNA hybridization on a surface. The Journal of Chemical Physics. 138: 035102. PMID 23343305 DOI: 10.1063/1.4775480  0.413
2013 Loong B, Schinn SM, Bush DB, Knotts TA. Strategies to stabilize proteins on surfaces from improved modeling of protein-surface interactions Engineering Sciences and Fundamentals 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 2: 615.  0.351
2012 Lewis JI, Moss DJ, Knotts TA. Multiple molecule effects on the cooperativity of protein folding transitions in simulations. The Journal of Chemical Physics. 136: 245101. PMID 22755602 DOI: 10.1063/1.4729604  0.458
2011 Schmitt TJ, Knotts TA. Thermodynamics of DNA hybridization on surfaces. The Journal of Chemical Physics. 134: 205105. PMID 21639485 DOI: 10.1063/1.3592557  0.415
2011 Wei S, Knotts TA. Effects of tethering a multistate folding protein to a surface. The Journal of Chemical Physics. 134: 185101. PMID 21568530 DOI: 10.1063/1.3589863  0.51
2010 Wei S, Knotts TA. Predicting stability of alpha-helical, orthogonal-bundle proteins on surfaces. The Journal of Chemical Physics. 133: 115102. PMID 20866158 DOI: 10.1063/1.3479039  0.497
2009 Schmitt TJ, Clark JE, Knotts TA. Thermal and mechanical multistate folding of ribonuclease H. The Journal of Chemical Physics. 131: 235101. PMID 20025349 DOI: 10.1063/1.3270167  0.391
2008 Knotts TA, Rathore N, de Pablo JJ. An entropic perspective of protein stability on surfaces. Biophysical Journal. 94: 4473-83. PMID 18326646 DOI: 10.1529/Biophysj.107.123158  0.674
2007 Knotts TA, Rathore N, Schwartz DC, de Pablo JJ. A coarse grain model for DNA. The Journal of Chemical Physics. 126: 084901. PMID 17343470 DOI: 10.1063/1.2431804  0.601
2006 Rathore N, Knotts TA, de Pablo JJ. Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations. Biophysical Journal. 90: 1767-73. PMID 16361344 DOI: 10.1529/biophysj.105.071076  0.664
2005 Knotts TA, Rathore N, de Pablo JJ. Structure and stability of a model three-helix-bundle protein on tailored surfaces. Proteins. 61: 385-97. PMID 16106409 DOI: 10.1002/Prot.20581  0.673
2005 Knotts TA, Rathore N, De Pablo JJ. A new model for simulation of long DNA Aiche Annual Meeting, Conference Proceedings. 10468.  0.558
2005 Knotts TA, Rathore N, De Pablo JJ. Proteins in inhomogeneous environments: Answers from advanced Monte Carlo simulations Aiche Annual Meeting, Conference Proceedings. 167.  0.621
2003 Rathore N, Knotts TA, de Pablo JJ. Configurational temperature density of states simulations of proteins. Biophysical Journal. 85: 3963-8. PMID 14645085 DOI: 10.1016/S0006-3495(03)74810-3  0.65
2003 Rathore N, Knotts TA, de Pablo JJ. Erratum: “Density of states simulations of proteins” [J. Chem. Phys. 118, 4285 (2003)] The Journal of Chemical Physics. 118: 9460-9461. DOI: 10.1063/1.1570399  0.563
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