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[39] Rivard, B.R.; Cooper, S.J.; Pelletier, L.D.; Stubbs, J.M. `Impact of DNA strand length on duplex stability in solution and in a microarray environment via molecular simulation', College of Arts & Sciences Spring Research Symposium, Biddeford, ME (5/2017)

[38] Mei, K.J.; Stubbs, J.M. `Determining the feasibility of supercritical carbon dioxide + water for extracting organic compounds in extraterrestrial environments: A Monte Carlo simulation study', College of Arts & Sciences Spring Research Symposium, Biddeford, ME (5/2017)

[37] Rivard, B.R.; Cooper, S.J.; Pelletier, L.D.; Stubbs, J.M. `Impact of DNA strand length on duplex stability in solution and in a microarray environment via molecular simulation', 253rd American Chemical Society National Meeting, San Francisco, CA (4/2017)

[36] Mei, K.J.; Stubbs, J.M. `Determining the feasibility of supercritical carbon dioxide + water for extracting organic compounds in extraterrestrial environments: A Monte Carlo simulation study', 253rd American Chemical Society National Meeting, San Francisco, CA (4/2017)

[35] Mei, K.J.; Stubbs, J.M. `Optimization of supercritical carbon dioxide/water extraction of organic compounds towards planetary exploration using Monte Carlo simulations', Summer Undergraduate Research Experience (SURE) Symposium, Biddeford, ME (10/2016)

[34] Lucy, C.J.; Stubbs, J.M. `The impact of single base deletions on DNA microarray hybridization', Summer Undergraduate Research Experience (SURE) Symposium, Biddeford, ME (10/2016)

[33] Rivard, B.R.; Stubbs, J.M. `Impact of DNA single strand length on duplex stability in solution and in a microarray environment', Summer Undergraduate Research Experience (SURE) Symposium, Biddeford, ME (10/2016)

[32] Pham, M.; Stubbs, J.M. `Effects of single base deletions on DNA hybridization on model microarrays', Seventeenth Annual UNE CAS Arts & Sciences Symposium, Biddeford, ME (5/2016)

[31] Rivard, B.R.; Stubbs, J.M. `Structure and stability of DNA duplexes with dangling ends and a central mutation in a model microarray system', 251st American Chemical Society National Meeting, San Diego, CA (3/2016)

[30] Rivard, B.R.; Stubbs, J.M. `Structure and stability of DNA duplexes with a central mutation in a model microarray system', Summer Undergraduate Research Experience (SURE) Symposium, Biddeford, ME (9/2015)

[29] Cooper, S.J.; Stubbs, J.M. `Molecular simulation of changes in the structure of DNA double helicies due to unequal strand lengths and to surface binding', Sixteenth Annual UNE CAS Arts & Sciences Symposium, Biddeford, ME (5/2015)

[28] Scamman, W.C.; Stubbs, J.M. `Modified coarse-grained DNA model and its application to surface density effects on decamer hybridization', 249th American Chemical Society National Meeting, Denver, CO (3/2015)

[27] Cooper, S.J.; Stubbs, J.M. `Effect of unequal strand length on DNA hybridization in a model microarray system via Monte Carlo simulation', 249th American Chemical Society National Meeting, Denver, CO (3/2015)

[26] Scamman, W.C.; Stubbs, J.M. `A modified coarse-grained DNA model and its application to surface density effects on hybridization', Summer Undergraduate Research Experience (SURE) Symposium, Biddeford, ME (10/2014)

[25] Cooper, S.J.; Stubbs, J.M. `The impact of unequal strand length on DNA hybridization in a model microarray system via molecular simulation', Summer Undergraduate Research Experience (SURE) Symposium, Biddeford, ME (10/2014)

[24] Cooper, S.J.; Stubbs, J.M. `The effect of shortened target strands on DNA hybridization in a model microarray system', Fourteenth Annual UNE CAS Arts & Sciences Symposium, Biddeford, ME (5/2013)

[23] van den Berg, M.; Stubbs, J.M. `DNA hybridization in microarrays: The effects of probe density and other variables', Honors' Thesis, Fourteenth Annual UNE CAS Arts & Sciences Symposium, Biddeford, ME (5/2013)

[22] van den Berg, M.; Stubbs, J.M. `Effect of probe density on DNA hybridization in microarrays: A Monte Carlo simulation study', 245th American Chemical Society National Meeting, New Orleans, LA (4/2013)

[21] Huber, M.T.; Stubbs, J.M. `The effect of temperature and pressure on the solubility of selected solutes in supercritical carbon dioxide', Summer Undergraduate Research Experience (SURE) Symposium, Biddeford, ME (9/2012)

[20] van den Berg, M.; Stubbs, J.M. `DNA hybridization in microarrays: The effects of probe density and other variables', Summer Undergraduate Research Experience (SURE) Symposium, Biddeford, ME (9/2012)

[19] Huber, M.T.; Stubbs, J.M. `The effect of solute polarity on solubility in polyethylene glycol with varying concentrations of supercritical carbon dioxide', Thirteenth Annual UNE CAS Arts & Sciences Symposium, Biddeford, ME (5/2012)

[18] van den Berg, M.; Stubbs, J.M. `The effects of probe density on DNA hybridization in microarrays', Thirteenth Annual UNE CAS Arts & Sciences Symposium, Biddeford, ME (5/2012)

[17] Chan, W.-P.; Deveau, A.M.; Stubbs, J.M. `Computational investigation and nuclear magnetic resonance spectroscopy analysis of 6β-naltrexol derivatives', Thirteenth Annual UNE CAS Arts & Sciences Symposium, Biddeford, ME (5/2012)

[16] Huber, M.T.; Stubbs, J.M. `The effects of supercritical carbon dioxide on the solubility of small solutes in polyethylene glycol: A Monte Carlo study', Fourth Annual Northeast Undergraduate Research and Development Symposium, Biddeford, ME (3/2012)

[15] Chan, W.-P.; Deveau, A.M.; Stubbs, J.M. `Computational investigation and nuclear magnetic resonance spectroscopy analysis of derivatives of 6-beta naltrexol', Third Annual CAS Undergraduate Summer Research Symposium, Biddeford, ME (8/2011)

[14] Huber, M.T.; Stubbs, J.M. `The effects of supercritical carbon dioxide on the solubility of ethyl benzene and 1-octene within a polyethylene glycol solution', Third Annual CAS Undergraduate Summer Research Symposium, Biddeford, ME (8/2011)

[13] Chan, W.-P.; Stubbs, J.M. `Computational investigation of transition states for deprotonation and lithium-halogen exchange during the attempted formation of 6- desoxynaltrexone', Twelfth Annual UNE CAS Arts & Sciences Symposium, Biddeford, ME (5/2011)

[12] Chan, W.-P.; Stubbs, J.M. `Computational investigation of unexpected results during the attempted formation of 6-desoxynaltrexone', Third Annual Northeast Undergraduate Research and Development Symposium, Biddeford, ME (3/2011)

[11] Chan, W.-P.; Stubbs, J.M. `Computational investigation of unexpected results during the attempted formation of 6-desoxynaltrexone', Second Annual College of Arts and Sciences Undergraduate Summer Research Symposium, UNE (8/2010)

[10] St. John, M.; Stubbs, J.M. `Predicting the strength of the hybridization between the nucleotide probe and target DNA by comparison of complimentary pairing versus sequence specific disorder', Second Annual College of Arts and Sciences Undergraduate Summer Research Symposium, UNE (8/2010)

[9] Allen, J.H. `Heterogeneous DNA duplex stability', Eleventh Annual UNE CAS Arts & Sciences Symposium, UNE (5/2010)

[8] Bayron, J.A. `In silico conformational analysis of 6-alpha- and 6-beta-naltrexol and derivatives', Eleventh Annual UNE CAS Arts & Sciences Symposium, UNE (5/2010)

[7] Bayron, J.A.; Deveau, A.M.; Stubbs, J.M. `In silico conformational analysis of 6-alpha- and 6-beta-naltrexol and derivatives', Second Annual Northeast Undergraduate Research and Development Symposium, Biddeford, ME (4/2010)

[6] Schoch, E.T.; Stubbs, J.M. `Monte Carlo coarse grain model exploration of DNA probes for use in microarrays', First Annual College of Arts and Sciences Undergraduate Summer Research Symposium, UNE (8/2009)

[5] Schoch, E.T. `Influence of nucleotide loop length on model DNA hairpin loop stability', Tenth Annual UNE CAS Arts & Sciences Symposium, UNE (4/2009)

[4] Schoch, E.T.; Stubbs, J.M. `Monte Carlo exploration of conformational changes of hairpin loops at varying nucleotide lengths and temperatures', First Annual Northeast Undergraduate Research and Development Symposium, Biddeford, ME (3/2009)

[3] Tito, N.B.; Stubbs, J.M. `Validation of a new molecular model of DNA, and its applications to the simulation of homo- and heterogeneous melting equilibria of decamers', Ninth Annual UNE CAS Arts & Sciences Symposium, UNE (4/2008)

[2] Peters, J.F.; Stubbs, J.M. `Optimizing extraction of ethyl benzene from poly(ethylene glycol) using supercritical carbon dioxide: A Monte Carlo study', Fifth Midwest Undergraduate Computational Chemistry Consortium Conference, Minneapolis, MN (7/2005)

[1] Pedersen, R.D.; Stubbs, J.M. `Molecular simulations of DNA hybridization and melting using a coarse-grained model', Fifth Midwest Undergraduate Computational Chemistry Consortium Conference, Minneapolis, MN (7/2005)

Presentations

[26] Rivard, B.R.; Stubbs, J.M. `DNA mutation and fluorescent label effects in surface-bound 25mer microarrays: Molecular simulation of bright mismatches', Poster, 253rd American Chemical Society National Meeting, San Francisco, CA (4/2017)

[25] Mei, K.J.; Lucy, C.J.; Pham, M.; Stubbs, J.M. `Impact of sequence homology on DNA microarray hybridization interactions: A Monte Carlo molecular simulation study', Poster, 253rd American Chemical Society National Meeting, San Francisco, CA (4/2017)

[24] Stubbs, J.M. `Modeling supercritical fluids with molecular simulation', Joint EMLG/JMLG Annual Meeting 2016, Platanias-Chania, Crete, Greece (9/2016)

[23] Stubbs, J.M.; Cooper, S.J.; Rivard, B.R.; Pelletier, L.D. `DNA strand length differences and their impact on hybridization in model DNA microarrays: A Monte Carlo molecular simulation study', 251st American Chemical Society National Meeting, San Diego, CA (3/2016)

[22] Stubbs, J.M.; Cooper, S.J.; Scamman, W.C.; van den Berg, M.P. `Molecular simulation of surface density effects on heterogeneous DNA hybridization', 249th American Chemical Society National Meeting, Denver, CO (3/2015)

[21] Stubbs, J.M. `DNA hybridization on a surface: Insights from molecular simulation', Colby College Chemistry Seminar, Waterville, ME (4/2014)

[20] van den Berg, M.P.; Stubbs, J.M. `Monte Carlo molecular simulation of surface binding density effects on DNA hybridization of two undecamer sequences', Poster, 247th American Chemical Society National Meeting, Dallas, TX (3/2014)

[19] Huber, M.T.; Stubbs, J.M. `The influence of carbon dioxide on the solubility of polar and non-polar solutes in poly(ethylene glycol): A Monte Carlo simulation study', Poster, Foundations of Molecular Modeling and Simulation 2012, Mt. Hood, OR (7/2012)

[18] Stubbs, J.M. `Monte Carlo molecular simulation of ethyl benzene partitioning between supercritical ethane and poly(ethylene glycol)', Poster, 243rd ACS National Meeting, San Diego, CA (3/2012)

[17] Bayron, J.A.; Deveau, A.M.; Stubbs, J.M. `Relationships between opioid receptor affinity and calculated properties of 6α- and 6β-naltrexol and derivatives', Poster, 243rd ACS National Meeting, San Diego, CA (3/2012)

[16] Stubbs, J.M. `Extraction of ethylbenzene from poly(ethylene glycol) with supercritical carbon dioxide: A Monte Carlo study', Poster, 241st ACS National Meeting, Anaheim, CA (3/2011)

[15] Allen, J.H.; Schoch, E.T.; Stubbs, J.M. `Effect of binding orientation on heterogeneous DNA melting transitions via Monte Carlo molecular simulation', 241st ACS National Meeting, Anaheim, CA (3/2011)

[14] Stubbs, J.M.; Tito, N.B.; Buchanan, M.; Pedersen, R.D. `Predicting melting equilibria for DNA using a coarse-grained model: A Monte Carlo study', Poster, 238th ACS National Meeting, Washington, D.C. (8/2009)

[13] Stubbs, J.M.; Tito, N.B. `Modeling heterogeneous melting equilibria of surface-immobilized DNA using Monte Carlo molecular simulation', 2009 Midwest Thermodynamics & Statistical Mechanics Conference, Detroit, MI (5/2009)

[12] Stubbs, J.M.; Siepmann, J.I. `Interfacial properties of aqueous surfactant mixtures: A Monte Carlo study', 231st ACS National Meeting, Atlanta, GA (3/2006)

[11] Stubbs, J.M.; Siepmann, J.I. `Monte Carlo simulation of water/1-butanol/2-ethoxyethan-1-ol mixtures at vapor/liquid interfaces', Poster, 229th ACS National Meeting, San Diego, CA (3/2005)

[10] Stubbs, J.M.; Siepmann, J.I. `Vibrational spectra of 1-hexanol in n-hexane using a multiscale modeling approach', 2004 Midwest Thermodynamics & Statistical Mechanics Conference, Buffalo, NY (6/2004)

[9] Stubbs, J.M.; Siepmann, J.I. `Aggregation of hexanol isomers and of 2-alkoxyethanols in n-hexane: Aggregation, steric hindrance, inter- and intramolecular hydrogen bonding and vibrational spectroscopy', Poster, Tenth International Conference on Properties and Phase Equilibria for Product and Process Design, Snowbird, UT (5/2004)

[8] Stubbs, J.M.; Siepmann, J.I.; Wick, C.D.; Zhang, L.; Potoff, J. `Extension of the TraPPE force field to nitrogen functionalities', 2003 AIChE Annual Meeting, Session on `Development and validation of intermolecular potential functions I', San Francisco, CA (11/2003)

[7] Stubbs, J.M.; Siepmann, J.I. `Vibrational spectra of 1-hexanol in n-hexane via ab initio molecular dynamics', 226th ACS National Meeting, New York, NY (9/2003)

[6] Stubbs, J.M.; Siepmann, J.I. `Aggregation of hexanol isomers and of 2-ethoxyethanol in n-hexane', 226th ACS National Meeting, New York, NY (9/2003)

[5] Stubbs, J.M.; Siepmann, J.I. `Aggregation of hexanol isomers in n-hexane', 2003 Midwest Thermodynamics & Statistical Mechanics Conference, Columbus, OH (5/2003)

[4] Stubbs, J.M.; Siepmann, J.I.; Wick, C.D.; Zhuravlev, N.D. `Predicting phase equilibria using configurational-bias Monte Carlo simulations in the Gibbs ensemble', 2002 AIChE Annual Meeting, Session on `Obtaining physical and chemical properties for process design by computational chemistry', Indianapolis, IN (11/2002)

[3] Stubbs, J.M. `Monte Carlo simulations of 1-hexanol in n-hexane: The formation of hydrogen-bonded clusters in n-hexane rich solution', Theoretisch-Chemisches Seminar, Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum, Germany (10/2001)

[2] Stubbs, J.M.; Siepmann, J.I. `Monte Carlo calculations for the aggregation of alkanols in nonpolar solvents', 2001 Midwest Thermodynamics & Statistical Mechanics Conference, East Lansing, MI (5/2001)

[1] Stubbs, J.M.; Siepmann, J.I. `Monte Carlo simulations of 1-hexanol in n-hexane: The formation of hydrogen-bonded clusters in n-hexane rich solution', 33rd Midwest Theoretical Chemistry Conference, Iowa City, IA (5/2000)