John M. Stubbs

Dr. Stubbs is primarily interested in using computers to investigate and explain chemical phenomena.  His current research focuses on two distinct areas: DNA hybridization on a surface, an important problem for DNA sensor arrays; and supercritical fluids as separation media, which can greatly improve purification efficiency.  He is also interested in the hardware and software aspects of computers in chemistry, primarily using the GNU/Linux operating system and FORTRAN programming language.


Ph.D., Chemistry

University of Minnesota


B.A., Chemistry and German

University of Minnesota, Morris



Physical chemistry; thermophysical properties; Monte Carlo molecular simulation; phase behavior


Current Research

Application of a coarse-grained DNA model to denaturation and hybridization transitions in solution and with surface-bound DNA strands.

Research Interests

Dr. Stubbs' research interests are focused in two areas: DNA melting and hybridization transitions and tunable solvents for separations.  The primary research method for both areas is Monte Carlo molecular simulation, which uses computers to look at model systems and applies statistical mechanics to determine properties of interest.

The first area is focused on DNA sensor microarray technology, which is composed of single-stranded DNA oligomers bound to a surface. The development of this technology relies on knowledge of DNA denaturation or "melting" and hybridization transitions, and their sensitivity to many variables has left several questions unanswered, such as the mechanism by which changes in physical environment between solution and bound DNA act to influence hybridization, or competitive adsorption of nearly identical sequences.

The second area attempts to improve upon separation technology using fairly innocuous materials such as supercritical carbon dioxide and polyethylene glycol to achieve what traditional processes do with more detrimental materials.  Molecular simulations allow the modeling of such systems with the goal of optimizing solvation conditions and is done by carrying out calculations with varying thermodynamic (e.g. temperature and/or pressure) conditions and compositions.

Selected Publications


Cooper, S.J.; Stubbs, J.M. `The effect of unequal strand length on short DNA duplex hybridization in a model microarray system: A Monte Carlo simulation study,' Chem. Phys. Lett., 634, 230-235 (2015)



Stubbs, J.M. `Solute extraction via supercritical ethane from poly(ethylene glycol): A Monte Carlo simulation study,' Fluid Phase Equilib., 360, 351-356 (2013).



Huber, M.T.; Stubbs, J.M. `The influence of carbon dioxide cosolvent on solubility in poly(ethylene glycol)', Theor. Chem. Acc. 131, 1276(1-6) (2012).



Bayron, J.A.; Deveau, A.M.; Stubbs, J.M. `Conformational analysis of 6α- and 6β-naltrexol and derivatives and relationship to opioid receptor affinity', J. Chem. Inf. Model. 52, 391-395 (2012).



Allen, J.H.; Schoch, E.T.; Stubbs, J.M. `Effect of surface binding on heterogeneous DNA melting equilibria: A Monte Carlo simulation study', J. Phys. Chem. B 115, 1720-1726 (2011).


Funded Grants

UNE chemistry researcher John Stubbs receives NSF grant to study DNA interactions

August 27, 2013

BIDDEFORD, Maine John Stubbs, Ph.D., University of New England associate professor of chemistry, was recently awarded a $150,000 grant from the National Science Foundation to continue his research on DNA modeling.  

Stubbs' research project, entitled "RUI: Molecular Simulation of DNA Interactions in Oligonucleotide Microarrays," has extensive biomedical, forensic and environmental applications because it easily enables mutation detection, genetic sequencing (both having impacts on genetic disorder disease screening), species identification, and RNA expression to be carried out.

The three-year award includes support for six UNE undergraduate students to participate in the research, including the presentation of results at American Chemical Society national meetings.

Stubbs' research looks at DNA sensor microarrays, which consist of a single strand of DNA bound to a surface that ideally will only form a double helix with its complement.  This allows one to rapidly test for the presence of a given sequence of DNA in a sample for analysis.  Stubbs explains, "Our research will model these microarrays with computer simulations, which is an extremely useful approach because it provides molecular-level insight into experimental results that are otherwise difficult to interpret in a lab environment."

The results will describe how DNA interactions change when DNA is bound to a surface; this information can then be used to develop more robust DNA sensor microarrays in the future. This could improve both the sensitivity and specificity of applications and speed development of new applications in mutation detection, genetic sequencing, species identification, and RNA expression.

UNE students will be actively engaged in Stubbs' research, including analyzing the data and presenting it at national conferences and local symposia. Stubbs says, "This NSF funding enables me to build on my previous research successes while also providing important opportunities for UNE students.  From performing calculations to interpreting data and presenting results at national meetings, they will experience first-hand how innovative research is conducted, and how it can be used to benefit science and society."

Research Topics

John S

John M. Stubbs




Associate Professor, Chemistry

Morgane Hall

(207) 602-2152