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Damian Gregory Allis, Ph.D. (Online CV)

First appearance: August 16th, 2006. Page subject to updates.

Research Assistant Professor, Department of Chemistry, Syracuse University
Research Fellow, Forensic and National Security Sciences Institute, Syracuse University

work: Syracuse University, 1-014 CST, Syracuse, NY, USA 13244

home: 313 East Willow Street Apt. 501, Syracuse, NY, USA 13203

web: www.somewhereville.com (or www.damianallis.com)

email: damian@somewhereville.com (1st), dgallis@syr.edu (2nd), somewhereville@gmail.com (3rd)

aim/facebook/flickr/gtalk/linkedin/researchgate/myspace/skype/twitter/google+: somewhereville

home: (315) 559-4737

work: (315) 443-2067

fax: (315) 443-4070

RESEARCH DESCRIPTION

Computational quantum chemistry; molecular nanotechnology; the design and simulation of molecules and nanostructures, molecular-based materials for molecular electronics and nonlinear optical materials applications, nanostructures from molecular building blocks and biomimetic principles; mechanosynthetic approaches in advanced molecular manufacturing; the property prediction of solid-state materials from density functional theoretical approaches; inelastic neutron scattering vibrational theory and calculation; computational drug design and modeling interaction pathways; molecular modeling, vibrational properties, and predictive modeling tools for crystal polymorphism; the simulation of internal/external vibrations and conformational changes observed by terahertz (THz) spectroscopy; electronic structure theory of inorganic clusters and organometallic coordination complexes; molecular dynamics simulations and reduced model development of DNA-based nanostructures; computational design principles, property prediction and evaluation in bioconjugate chemistry; molecular mechanics/dynamics force field development; extensive background in computer hardware and software, including systems design, administration, security, cluster assembly, parallel computing platforms, national computing facility utilization (NCSA) and distributed computing, maintenance, graphics design, and web development.

EDUCATION

Syracuse University (Aug 1998 – Oct 2004), Syracuse, New York, USA
Graduate Fellow, Doctor of Philosophy, Physical Inorganic/Computational Quantum Chemistry
Thesis : Computational Quantum Chemistry In Initial Designs And Final Analyses
Thesis Defense : October 15, 2004, 30 GPA credits, summa cum laude

Advisor : Bruce S. Hudson, Ph.D. (2001 – 2004)
The comparison of theory and experiment in the inelastic neutron scattering vibrational structure of molecules and molecular solids, focusing on hydrogen-bonded networks and organic crystal engineering; the application of periodic density functional theory to the study of molecular solids, including polymorphism and crystal structure prediction.

Advisor : James T. Spencer, Ph.D. (1998 – 2004)
Molecular building block and biomimetic approaches to nanostructure design and fabrication; electronic structure theory of main group clusters, emphasizing their interactions with organic species for molecular electronics and nonlinear optical materials applications.

Departmental Research : Jon Zubieta, Ph.D. and Karin Ruhlandt, Ph.D. (2002 – 2004)
Theory and modeling of isomerization/rearrangement pathways of solid-state materials formed via the hydrothermal synthesis of inorganic oxides, with specific focus on the octamolybdate class of isomers (Zubieta); computational molecular biology and transition metal radiopharmaceutical drug design via molecular dynamics simulations (Zubieta, Molecular Insight Pharmaceuticals, Inc.); quantum chemical studies of structure and stability among the heavy alkali organometallic complexes with emphasis on the elucidation of crystal morphology from quantum chemical approaches (Ruhlandt).

Syracuse University (Aug 1994 – May 1998), Syracuse, New York, USA
Bachelor of Science with Honors, Chemistry, May 1998, magna cum laude, 156/120 credits

SELECTED HONORS AND ORGANIZATIONS

Invited Essays, Interviews, Slidecasts, Free Press, Talks

Focal Point: Allis D.G. Stu’s Last Lesson. Sky & Telescope Magazine, December, 2014

Feature Article (Cover): Allis D.G. The 16-inch f/4.5 Collapsible-Truss Dobsonian From New Moon Telescopes: New Design Approaches and Old-Fashioned Craftsmanship. Astronomy Technology Today, May-June 2013 (Vol. 7, Issue 3).

Invited Lecture: Allis D.G. There’s Plenty Marooned At The Bottom – The Possibilities And Politics Of Molecular Manufacturing. SRC, Inc. Syracuse, NY January 25, 2013.

Public Lecture: Allis D.G. A Most Unlikely Obvious Molecule – DNA And Its Consequences. Central New York Skeptics, DeWitt, NY, November 7, 2012.

Public Lecture: Allis D.G. Controversy In Science. Central New York Skeptics, DeWitt, NY, January 18, 2012.

Invited Lecture: Allis D.G. When Mechanical Engineering and Quantum Mechanics Meet – Using Computational Chemistry to Predict a Future for Molecular Manufacturing. A*STAR – Institute of Materials Research and Engineering (IMRE) Workshop on Atom Technology and its Applications, Singapore, June 10, 2010.

Syracuse University Project Advance Spring Meeting, Syracuse, NY, April 27, 2010 and Lubin House, New York City, NY, May 13, 2010.

Invited Lecture: Allis D.G. Vitamin B12 As A Tool For Drug Delivery; Building Atom-By-Atom – Computational Studies In Mechanosynthesis. Syracuse University Project Advance Spring Meeting, Syracuse, NY, April 27, 2010 and Lubin House, New York City, NY, May 13, 2010.

Interview: Syracuse University Partners With Serum Institute Of India To Develop Vaccines For Children. Syracuse University Arts and Sciences Press Release, 2008.

Slidecast: Single-Atom Manipulation and the Chemistry of Mechanosynthesis. NanoScienceWorks, Taylor & Francis (www.nanoscienceworks.org/slidecast), December, 2007.

Guest Essay: Exploring the Productive Nanosystems Roadmap, Center for Responsible Nanotechnology Newsletter (www.crnano.org), October, 2007.

Interview: Solid-State Modeling of the Terahertz Spectrum of the Explosive HMX, Accelrys case study (www.accelrys.com), August, 2006.

Interview: Olson S. An Interview with Damian Gregory Allis. for Nanotech.biz (www.nanotech.biz), November, 2005.

Interview: Caponi K.A. Towards Computing Crystal Forms. Access Magazine, National Center for Supercomputing Applications, Vo. 17, No. 1, Spring 2004.

Invited Lecture: Allis D.G. Single Atom Manipulation and the Chemistry of Mechanosynthesis. Productive Nanosystems: Launching the Technology Roadmap, Arlington, VA USA October 9-10, 2007.

Invited Lecture: Allis D.G. Chemical Origins of Solid-State Terahertz Spectra. DIA/NGA Community Academic Summit, Williamsburg VA June 11-13, 2007.

Lecture: Allis D.G. Novel Imaging and Spectroscopy Technologies – Terahertz Detector Device Deployment and Theory for Terahertz Biomolecular And Molecular Threat Agent Spectroscopy, IC Postdoctoral Research Fellowship Colloquium, Chantilly, VA, April 30 – May 3, 2007.

Invited Lecture: Allis D.G. Nanosystem Simulation and Design for Molecular Manufacturing. Department of Mechanical and Aeronautical Engineering, Clarkson University, Potsdam, NY, February 27, 2007.

Keynote Lecture: Allis D.G. Nanotechnology and Molecular Manufacturing. Ibero-American Conference for University and College Presidents: Global Workforce Trends and Emerging Technologies, Advanced Technology Center ATC, Alamo Community College District, San Antonio, Texas September 18-20, 2006.

Invited Lecture: Allis D.G. Computational Chemistry for the Next 6 Months and 50 (or so) Years: Quantum Theory Applications in Homeland Security and Molecular Manufacturing. Syracuse University Project Advance Spring Meeting, Syracuse, NY, March 22, 2006 and Lubin House, New York City, NY, May 27, 2006.

Lecture: Allis D.G. The Design of Carbon Nanotube-Based Dative Structures from Supramolecular Principles. Foresight Institute Tenth Conference on Nanotechnology, Bethesda, MD, October 10-12, 2002.

Invited Lecture: Allis D.G. An Introduction to Computer Aided Chemistry and Nanomechanical Design Using CAChe. Syracuse University Project Advance Spring Meeting, Lubin House, New York City, NY, May 18-19, 2000.

Selected Honors

NASA Solar System Ambassador (2014-), Director of Central Intelligence Postdoctoral Research Fellow (2005-2007), Marquis Who’s Who in the World, in Science and Engineering, and in America, Foresight Distinguished Student Award in Nanotechnology (2004), Syracuse University All-University Graduate Fellowship (1998-2001, three year appointment), Who’s Who Among Students in America’s Colleges and Universities (1998), Phi Beta Kappa (1998), Syracuse University Merck Index Award (1998), Golden Key National Honors Society (1996), Phi Eta Sigma (1995), Syracuse University Honors Program (1994-8), Syracuse University Dean’s Scholar (1994-8, all semesters), John Philip Sousa Award (Jamesville-DeWitt School District, 1994)

Affiliations, Organizations, and Professional Activities

Ying Tri Region Science & Engineering Fair (Judge, 2013, 2014), CNY Observers & Observing (Executive Director, Lecturer 2013-), Preservation Association of Central New York (Member 2013-), Astronomy Section: Rochester Academy of Sciences (Member, 2013-), Syracuse Innovators Guild (Member 2013-), Union of Concerned Scientists (Member 2013-), Hacks/Hackers Syracuse (Member 2012-), Kopernik Astronomical Society (Member, 2011-), Chinese Optics Letters (Reviewer 2011-), Journal of Molecular Structure (Reviewer 2010-), Materials Chemistry and Physics (Reviewer 2009-), Neutron Scattering Society Of America (Member 2009-), Lifeboat Foundation (Nanotechnology and Chemistry Advisory Board Member 2007-), International Society of Nanoscale Science, Computation, and Engineering (Member 2007-), Technology Alliance of Central New York (TACNY, Organizational Affiliate, Member 2007-), Chemical Physics Letters (Reviewer 2007-), Technology Roadmap for Productive Nanosystems (Contributing Editor and Working Group Member 2005-2007), Inorganic Chemistry Communications (Reviewer 2005-), Molecular Engineering Research Institute (Member 2004-2008), Syracuse Astronomical Society (Board of Directors 2003-2012 and President 2007-2012), American Association for the Advancement of Science (Member 1997-), The Foresight Institute (Member 1997-), The Planetary Society (Member 1996-), American Chemical Society (Member 1995-).

Molecular Graphics In-Print (Excluding Web-Only Content)

Journal of Physical Organic Chemistry (Cover, March 2014), ChemMedChem (Back Cover, April 2013), Future Medicinal Chemistry (Content, Vol. 5 No. 17, 2013), MedChemComm (Cover, September 2012), Journal Of Physical Chemistry A (Cover, November 2010), Molecular Biosystems (Inside Cover, August 2010), Journal of Organic Chemistry (Cover, May 2010), Clinical Chemistry (Cover, April 2010), ChemMedChem (Cover, March 2009), ChemMedChem (Cover, December 2007), Technology Roadmap for Productive Nanosystems (Content, 2008), The Future for Nanoscience and Nanotechnology, RSC and IOP (Content, 2008), Productive Nanosystems: Launching the Technology Roadmap (Cover, 2007), “Erlebnis Wissenschaft” Wiley-VCH Book Series (Content, 2007), Nanotechnologien fur die Optische Industrie, www.hessen-nanotech.de (Content, 2007), Großes Netzwerk für Kleine Teilchen Aerosolforschungin der GSF (Content, 2007), Accelrys Chemical Case Study (Content, 2006), Tennessee’s Business (Cover and Content, Vol. 15, 2006), Revista Latitude (Content, 2006), Nanoaventura, Museu Exploratorio de Ciencias de Campinas, Instituo Sangari, (Content, 2005).

CURRENT RESEARCH AND PROFESSIONAL POSITION

Forensic And National Security Sciences Institute, Syracuse, New York, USA (2012 – )
Research Fellow, Biological and Threat Agent Modeling and Simulation

Syracuse University, Syracuse, New York, USA (2007-)
Research Assistant Professor, Department of Chemistry, Departmental and External Collaborative Computational Chemistry Research

AptaMatrix, Inc. (formerly Orthosystems, Inc.), Syracuse, New York, USA (2010 – )
Bioinformatics, Computational Modeling and Web Development

Nanofactory Collaboration, www.molecularassembler.com/Nanofactory/ (2006 – )
Independent Research, Multiple Ongoing Academic and Industrial Research Projects

SELECTED PAST RESEARCH AND PROFESSIONAL EXPERIENCE

Nanorex, Inc., www.nanorex.com, Bloomfield Hills, Michigan, USA (2004 – 2008)
Senior Scientist and former Scientific Advisory Board Member
– Molecular CAD-based structural DNA nanotechnology software design and force field development
– Quantum/classical nanostructure modeling and software design tools for molecular manufacturing
– nanoEngineer-1 v1.0.0, 2008 winner, Products Category, Nanotech Briefs “Nano50”

Nanohive@HOME, www.nanohive-1.org (February – May, 2007, defunct 2008)
Project Developer, Scientific Advisor, and Content Provider
– BOINC-based distributed computing system (developed by Brian Helfrich) for nanostructure simulations
– General quantum/classical simulation tool for conformational and structural rearrangement searches
– Tooltip Failure Mode Search Project peaked at an unadvertised 3 teraFLOPS (see paper Ref. 42)

Molecular Insight Pharmaceuticals, Inc., Cambridge, Massachusetts, USA (2003 – 2007)
Consultation Position in Computational Radiopharmaceutical Design, www.molecularinsight.com
– Biomolecular modeling and molecular dynamics simulations of novel synthetic radiopharma targets
– Involved in new target planning sessions and responsible for AMBER/GROMOS force field development
– First design study (biotin-based analogues for ReCO3 complexation) is publication Ref. 14 (Bioconj. Chem.)

ICPDRFP/CIA, Washington, D.C. (September 2005 – September 2007, 2 Year Appointment)
Director of Central Intelligence Postdoctoral Research Fellow with Timothy Korter, Ph.D.
– Theory and modeling of molecular phenomena observed in solid-state terahertz (THz) spectroscopy
– Several papers and presentations of results relevant to threat agent/drug identification and polymorphism
– First publication (Publication Ref. 12) highlighted in Science and Chemical and Engineering News

Nanoworks, Inc., Fayetteville, New York, USA (1999 – 2002)
Senior Theoretician, Nanosystems Design and Simulation, Photonic and Thin Film Materials
– Principle Investigator for BMDO 2000 Phase I SBIR: Optical Computing & Optical Signal Processing
– Theory and design of novel molecular nonlinear optical materials for use in optical-based technologies
– Molecular modeling studies served as the basis for experimental work described in Patents (see below) and several publications and presentations

Department of Chemistry, Syracuse University, Syracuse, New York, USA (1996 – 1998)
Undergraduate Researcher, Research Experience for Undergraduates (REU)
– Photolytic studies of borane clusters and aromatic systems by experimental and theoretical methods
– Theoretical studies of the photoisomerization chemistry of rhodium- and manganese-containing boranes

Syracuse Research Corporation/VA Hospital, Syracuse, New York, USA (1995 – 1997)
Biological Sciences Student Trainee, Laboratory Technician for Brad C. Motter, Ph.D.
– Responsible for the design and fabrication of multi-channel tetrode hyperdrives, used chronically in the recording of activity in the mammalian cerebellum V1, V2, and V4 regions
– Surgical assistant, computer interface and protocols developer for device data collection

Northeast Parallel Architectures Center, Syracuse, New York, USA (1994 – 1997)
Internet and Database Development for www.csir.org (website defunct, 2001)
– Responsible for processing and cataloging of software submissions for Chemistry Software and Information Resources (www.csir.org), an online chemistry software information database
– Developed new GUI and HTML protocols to work with the new site requirements, including the restructuring of the existing databases for IEEE compliance

PUBLICATIONS (Peer-Reviewed Only)

49. Bonnard G., Barrès A.-L., Danten, Y., Allis D. G., Mentré O., Tomerini D., Gatti C., Izgorodina E. I., Poizot P., and Frayret C. “Experimental and theoretical studies of tetramethoxy-p-benzoquinone: infrared spectra, structural and lithium insertion properties.” RSC Advances, DOI: 10.1039/c3ra41974f.

48. Lashua A., Smith T., Hu H., Wei L., Allis D.G., Sponsler M., and Hudson B. “Commensurate Urea Inclusion Crystals with the Guest (E,E)-1,4-Diiodo-1,3-Butadiene.” Crystal Growth & Design, DOI: 10.1021/cg400980b.

47. Bonnard G., Barrès A-L., Mentré O., Allis D.G., Gatti C., Poizot P., and Frayret C. “The low-/room-temperature forms of the lithiated salt of 3,6-dihydroxy-2,5-dimethoxy-p-benzoquinone: a combined experimental and dispersion-corrected density functional study.” CrystEngComm, 15 (2013), 15, 2809-2821, DOI:10.1039/C2CE26523; Cover Image: Issue 15, 2013.

46. Hudson B.S. and Allis D.G. “Bond alternation in infinite periodic polyacetylene: Dynamical treatment of the anharmonic potential.” Journal of Molecular Structure, 1032 (2013) 78-82, DOI:10.1016/j.molstruc.2012.07.051.

45. Hudson, B. S. and Allis, D. G. “The Structure of [18]-annulene: Computed Raman Spectra, Zero-Point Level and Proton NMR Chemical Shifts.” Journal of Molecular Structure – Jaan Laane Honour Issue, 1023 (2012) 212–215, DOI:10.1016/j.molstruc.2012.05.016.

44. Clardy-James S., Allis D.G., Fairchild T.J., and Doyle R.P. “Examining the effects of vitamin B12 conjugation on the biological activity of insulin: A molecular dynamic and in vivo oral uptake investigation.” MedChemComm, 3 (2012), 1054-1058, DOI:10.1039/C2MD20040F.

43. Clardy S., Allis D.G., Fairchild T.J., and Doyle R. “Vitamin B12 in Drug Delivery: Breaking Through the Barriers to a B12 Bioconjugate Pharmaceutical.” Expert Opinion on Drug Delivery, 8, 1 (2011) 127-140, DOI:10.1517/17425247.2011.539200.

42. Allis D.G., Helfrich B., Freitas Jr., R. A., and Merkle R. C. “Analysis of Diamondoid Mechanosynthesis Tooltip Pathologies Generated via a Distributed Computing Approach.” Journal of Computational and Theoretical Nanoscience, 8 (2011) 1139-1161, DOI:10.1166/jctn.2011.1792.

41. Allis D.G., Fairchild T.J., and Doyle R. “The Binding of Vitamin B12 to Transcobalamin(II); Structural Considerations for Bioconjugate Design – a Molecular Dynamics Study.” Molecular Biosystems, 6 (2010) 1611-1618. DOI:10.1039/c003476b.

40. Buchanan W.D., Allis D.G., and Ruhlandt-Senge S. “Synthesis and Stabilization – Advances in Organoalkaline Earth Metal Chemistry.” Chemical Communications, 46 (2010) 4449-4465. DOI:10.1039/C002600J.

39. Hudson M.R., Allis D.G., and Hudson B.S. “The Vibrational Spectrum of Parabanic Acid by Inelastic Neutron Scattering Spectroscopy and Simulation by Solid-State DFT.” Journal of Physical Chemistry A, 114(10) (2010) 3630-3641. DOI:10.1021/jp9114095.

38. Hakey P.M., Allis D.G., Hudson M.R., Ouellette W., and Korter T.M. “Terahertz Spectroscopic Investigation of S-(+)-Ketamine Hydrochloride and Vibrational Assignment by Density Functional Theory.” Journal of Physical Chemistry A, 114(12) (2010) 4364-4374. DOI:10.1021/jp910861m.

37. Hakey P.M., Hudson M.R., Allis D.G., Ouellette W., and Korter T.M. “Examination of Phencyclidine Hydrochloride via Cryogenic Terahertz Spectroscopy, Solid-State Density Functional Theory, and X-Ray Diffraction.” Journal of Physical Chemistry A, 113(46) (2009) 13013-13022. DOI:10.1021/jp907083u.

36. Hudson M.R., Allis D.G., Ouellette W., and Hudson B.S. “Low-Temperature X-ray Structure Determination and Inelastic Neutron Scattering Spectroscopic Investigation of L-Alanine Alaninium Nitrate, a Homologue of a Ferroelectric Material.” Physical Chemistry Chemical Physics, 11(41) (2009) 9474-9483. DOI:10.1039/B905070A.

35. Motley T.L., Allis D.G., and Korter T.M. “Investigation of Crystalline 2-Pyridone Using Terahertz Spectroscopy and Solid-State Density Functional Theory.” Chemical Physics Letters 478(4-6) (2009) 166-171. DOI:10.1016/j.cplett.2009.07.078.

34. Hudson M.R., Allis D.G., Ouellette W., Hakey P.M., and Hudson B.S. “The Low-Temperature X-ray Structure, Raman and Inelastic Neutron Scattering Vibrational Spectroscopic Investigation of the Non-centrosymmetric Amino Acid Salt Glycine Lithium Sulfate.” Journal of Molecular Structure, 934(1-3) (2009) 138-144. DOI:10.1016/j.molstruc.2009.06.033.

33. Hakey P.M., Allis D.G., Hudson M.R., Ouellette W., and Korter T.M. “An Investigation of (1R,2S)-(-)-Ephedrine Using Solid-State Density Functional Theory and Cryogenic Terahertz Spectroscopy.” ChemPhysChem 10(14) (2009) 2434-2444. DOI:10.1002/cphc.200900293.

32. Hudson M.R., Allis D.G., and Hudson B.S. “The Inelastic Neutron Scattering Spectrum Of Nicotinic Acid And Its Assignment By Solid-State Density Functional Theory.” Chemical Physics Letters, 473 (1-3) (2009) 81-87. DOI:10.1016/j.cplett.2009.03.052.

31. Hakey P.M., Allis D.G., Ouellette W., and Korter T.M. “The Cryogenic Terahertz Spectrum Of (+)-Methamphetamine Hydrochloride And Assignment Using Solid-State Density Functional Theory.” Journal of Physical Chemistry A, 113(17) (2009) 5119–5127. DOI:10.1021/jp810255e.

30. Hakey P.M., Allis D.G., Hudson M.R., and Korter T.M. “Density Functional Dependence In The Theoretical Analysis Of The Terahertz Spectrum Of The Illicit Drug MDMA (Ecstasy).” IEEE Sensors Journal, accepted.

29. Petrus A.K., Allis D.G., Smith R.P., Fairchild T.J., and Doyle R.P. “Exploring The Implications Of Vitamin B12 Conjugation To Insulin On Insulin Receptor Binding And Cellular Update.” ChemMedChem, 4(3) (2009) 421-426. DOI:10.1002/cmdc.200800346.

28. Rivera S., Allis D.G., and Hudson B.S. “Importance Of Vibrational Zero-Point Energy Contribution To The Relative Polymorph Energies Of Hydrogen-Bonded Species.” Crystal Growth and Design, 8(11) (2008) 3905–3907. DOI:10.1021/cg800524d.

27. Fedor A.M., Allis D.G., and Korter T.M. “The Terahertz Spectrum And Quantum Chemical Assignment Of 2,2’-Bithiophene In Cyclohexane.” Vibrational Spectroscopy, 49(2) (2009) 124-132. DOI:10.1016/j.vibspec.2008.06.001.

26. Allis D.G., Hakey P.M., and Korter T.M. “The Solid-State Terahertz Spectrum of MDMA (Ecstasy) – A Unique Test for Molecular Modeling Assignments.” Chemical Physics Letters, 463 (2008) 353-356. DOI:10.1016/j.cplett.2008.08.024.

25. O’Leary D.J., Allis D.G., Hudson B.S., James S., Morgera K.B., and Baldwin J.E. “Vicinal Deuterium Perturbations on Hydrogen NMR Chemical Shifts in Cyclohexanes.” Journal of the American Chemical Society, 130(41) (2008) 13659-13663. DOI:10.1021/ja802903a.

24. Allis D.G., Zeitler J.A., Taday P.F., and Korter T.M. “Theoretical Analysis of the Solid-State Terahertz Spectrum of the High Explosive RDX.” Chemical Physics Letters, 463 (2008) 84-89. DOI:10.1016/j.cplett.2008.08.014.

23. Armatas N.G., Allis D.G., Prosvirin A., Carnutu G., O’Connor C.J., Dunbar K., and Zubieta J. “Molybdophosphonate Clusters As Building Blocks In The Oxomolybdate-Organodiphosphonate/Cobalt(II)-Organoimine System: Structural Influences Of Secondary Metal Coordination Preferences And Diphosphonate Tether Lengths.” Inorganic Chemistry, 47 (2008) 3, 832 -854. DOI:10.1021/ic701573r.

22. Alexander J.S., Allis D.G., Teng W., and Ruhlandt-Senge K. “Alkali Metal Diphenylmethanides: Synthetic, Calculational and Structural Studies.” Chemistry – A European Journal, 13 (2007) 35, 9899-9911. DOI:10.1002/chem.200700763.

21. Allis D.G., Fedor A.M., Korter T.M., Bjarnason J.E., and Brown E.R. “Assignment Of The Lowest-Lying THz Absorption Signatures In Biotin And Lactose Monohydrate By Solid-State Density Functional Theory.” Chemical Physics Letters, 440 (2007) 203-209. DOI:10.1016/j.cplett.2007.04.032. Reprint in Journal of Intelligence Community Research and Development, 2007.

20. Freitas Jr. R.A., Allis D.G., and Merkle R. “Horizontal Ge-Substituted Polymantane-Based C2 Dimer Placement Tooltip Motifs for Diamond Mechanosynthesis.” Journal of Computational and Theoretical Nanoscience, 4 (2007) 433-442. DOI:10.1166/jctn.2007.004.

19. Allis D.G. and Korter T.M. “Development Of Computational Methodologies for the Prediction And Analysis of Solid-State Terahertz Spectra.” International Journal of High Speed Electronics and Systems, 17(2) (2007) 193-212. DOI:10.1142/S0129156407004436. Reprint in Journal of Intelligence Community Research and Development, 2007.

18. Teng W., Allis D.G., and Ruhlandt-Senge K. “Synthetic, structural and theoretical investigations of alkali metal germanium hydrides – contact molecules and separated ions.” Chemistry – A European Journal, 13(4) (2006) 1309-1319. DOI:10.1002/chem.200601073.

17. Allis D.G. “Understanding the Chemical Origins of Terahertz Spectra.” Journal of Intelligence Community Research and Development. Includes reprints of Pubs. 15 and 18.

16. Allis D.G. and Korter T.M. “Theoretical Analysis of the Terahertz Spectrum of the High Explosive PETN.” Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry, 7(11) (2006) 2398-408. DOI:10.1002/cphc.200600456.

15. Allis D.G., Prokhorova D.A., Fedor A.M., and Korter T.M. “First Principles Analysis of the Terahertz Spectrum of PETN.” Proceedings of SPIE-The International Society for Optical Engineering, 6212 (2006) (Terahertz for Military and Security Applications IV) 62120F/1-62120F/11. DOI:10.1117/12.665787.

14. James S., Maresca K.P., Allis D.G., Valliant J.F., Eckelman W., Babich J.W., and Zubieta J. “Extension Of The Single Amino Acid Chelate Concept (SAAC) To Bifunctional Biotin Analogues For Complexation Of The M(CO)3+1 Core (M = Tc And Re): Syntheses, Characterization, Biotinidase Stability And Avidin Binding.” Bioconjugate Chemistry, 17 (2006) 579-589. DOI:10.1021/bc050297w.

13. Allis D.G. and Hudson B.S. “The Inelastic Neutron Scattering Spectrum of Cs2[B12H12]: Reproduction of its Solid-State Vibrational Spectrum by Periodic DFT.” Journal of Physical Chemistry A, 110 (2006) 3744-3749. DOI:10.1021/jp055285m.

12. Allis D.G., Prokhorova D.A., and Korter T.M. “Solid-State Modeling of the Terahertz Spectrum of the High Explosive HMX.” Journal of Physical Chemistry A, 110 (2006) 1951-1959. DOI:10.1021/jp0554285.

11. Hudson B. S., Allis. D. G., Parker S. F., Ramirez-Cuesta, A. J., Hermanc, H., and Prinzbach, H. “Infrared, Raman and inelastic neutron scattering spectra of dodecahedrane: An Ih molecule in Th site symmetry.” Journal of Physical Chemistry A, 109 (2005) 3418 -3424. DOI:10.1021/jp0503213.

10. Allis D. G. and Drexler K. E. “Design and Analysis of a Molecular Tool for Carbon Transfer in Mechanosynthesis.” Journal of Computational and Theoretical Nanoscience, 2 (2005) 45-55. DOI:10.1166/jctn.2005.003.

9. Hudson B. S., Braden D. A., Allis D. G., Jenkins T., Baronov S., Middleton C., Withnall R., and Brown C. M. “The Crystalline Enol of 1,3-Cyclohexanedione and its Complex with Benzene: Vibrational Spectra, Simulation of Structure and Dynamics and Evidence for Cooperative Hydrogen Bonding.” Journal of Physical Chemistry A, 108 (2004) 7356-7363. DOI:10.1021/jp048613b.

8. Allis D.G., Kosmowski M.E., and Hudson B.S. “The Inelastic Neutron Scattering spectrum of H3B:NH3 and the Reproduction of Its Solid-State Features by Periodic DFT.” Journal of the American Chemical Society, 126(25) (2004) 7756-7757. DOI:10.1021/ja048215m.

7. Allis D.G., Burkholder E., and Zubieta J. “A New Octamolybdate: Observation of the theta-Isomer in [Fe(tpyprz)2]2[Mo8O26]3.7H2O. (tpyprz = tetra-2-pyridylpyrazine).” Polyhedron, 23(7) (2004) 1145-1152. DOI:10.1016/j.poly.2004.01.011.

6. Allis D.G., Prinzbach H., and Hudson B.S. “Inelastic Neutron Scattering Spectra of Pagodane: Experiment and DFT Calculations.” Chemical Physics Letters, 386 (2004) 356-363. DOI:10.1016/j.cplett.2004.01.076.

5. Allis D.G. and Hudson B.S. “Inelastic Neutron Scattering Spectra of NaBH4 and KBH4: Reproduction of Anion Mode Shifts via Periodic DFT.” Chemical Physics Letters, 385 (2004) 166-172 DOI:10.1016/j.cplett.2003.12.046.

4. Allis D.G., Rarig R.S., Burkholder E., and Zubieta J. “A Three-Dimensional Bimetallic Oxide Constructed from Octamolybdate Clusters and Copper-Ligand Cation Polymer Subunits. A Comment on the Stability of the Octamolybdate Isomers.” Journal of Molecular Structure, 688 (2004) 11-31. DOI:10.1016/j.molstruc.2003.08.027.

3. Alexander J.S., Allis D.G., Hudson B.S., and Ruhlandt-Senge K. “An Examination of Metal-Ligand Binding Modes in Rubidium Diphenylmethanide.” Journal of the American Chemical Society, 125(49) (2003) 15002-15003. DOI:10.1021/ja037201y.

2. Allis D.G. and Spencer J.T. “Polyhedral-Based Nonlinear Optical Materials. Part 2. Theoretical Investigation of Some New High Nonlinear Optical Response Compounds Involving Polyhedral Bridges with Charged Aromatic Donors and Acceptors.” Inorganic Chemistry, 40 (2001) 3373-3380. DOI:10.1021/ic0007761.

1. Allis D.G. and Spencer J.T. “Polyhedral-Based Nonlinear Optical Materials. Part 1. Theoretical Investigation of Some New High Nonlinear Optical Response Compounds Involving Carboranes and Charged Aromatic Donors and Acceptors.” Journal of Organometallic Chemistry, 614-615 (2000) 309-313. DOI:10.1016/S0022-328X(00)00589-1.

BOOKS AND CHAPTERS

6. Chapter: Allis D.G. and Korter T.M. “Development Of Computational Methodologies For The Prediction And Analysis Of Solid-State Terahertz Spectra.” Selected Topics in Electronics and Systems – Vol. 46: Terahertz Science and Technology For Military and Security Applications, Woolard D.L., Jensen J.O., Hwu R.J., and Shur M.S. (Editors); World Scientific, 2007.

5. Roadmap: Productive Nanosystems: A Technology Roadmap. Drexler K.E., Randall J., Corchnoy S., Kawczak A., Steve M.L. (Editors), Soreff J., Allis D.G., Von Ehr J. (Contributing Editors), Battelle Memorial Institute and Foresight Nanotech Institute, 2007.  Contributions include: Synthetic Chemistry, Mechanosynthesis, and Design and Modeling.

4. Chapter: Allis D.G. and Spencer J.T. “Nanostructural Architectures From Molecular Building Blocks.” CRC Handbook of Nanoscience, Engineering, and Technology, 2nd Edition, Goddard III W.A., Lyshevski S.E., Brenner D.W., and Iarfrate G.J. (Editors); Francis and Taylor Publishers, 2007.

3. Book: Allis D.G. Computational Quantum Chemistry In Initial Designs And Final Analyses. Syracuse University, Syracuse, NY, USA, UMI No. DA3160378 (2004) 509 pp. Dissertation Abstracts Int., B 2005, 66(1), 293.

2. Chapter: Allis D.G. and Spencer J.T. “Nanostructural Architectures From Molecular Building Blocks.” CRC Handbook of Nanoscience, Engineering, and Technology, Goddard III W.A., Lyshevski S.E., Brenner D.W., and Iarfrate G.J. (Editors); CRC Press, 2002.

1. Chapter: Littger R., Taylor J., Rudd G., Newlon A., Allis D.G., Kotiah S., and Spencer J.T. “Thermal, Photochemical, And Redox Reactions Of Borane And Metallaborane Clusters With Applications To Molecular Electronics.” Contemporary Boron Chemistry, Davidson M.G., Hughes A.K., Marder T.B., and Wade K. (Editors); Royal Society of Chemistry: Cambridge, 2000, 253, 67.

POSTER PRESENTATIONS (* = Lead Author And/Or Presenter)

35. Xiao Y., Mehrotra K.G., Allis D.G., and Borer P.N. “A fast sorting algorithm for aptamer identification using deep sequencing.” Advances in Social Networks Analysis and Mining (ASONAM), 2014 IEEE/ACM International Conference, August 17-20, 2014. DOI:10.1109/ASONAM.2014.6921671.

34. Lavin C.M., Allis D.G., and Ruhlandt-Senge, K. “Role of Weak Interactions in the Coordination Chemistry of Heavy Alkaline Earth MOCVD Precursors: A Theoretical Study.” Abstracts, 38th Northeast Regional Meeting of the American Chemical Society, Rochester, NY, USA, Sept. 30-Oct. 3, 2012.

33. Lashua A.F., Dinca S.A., Smith T.M., Allis D.G., Hudson B.S., and Sponsler M.B. “Isolated polyacetylene in an inclusion complex: Synthesis, methodology, and theory.” Abstracts of Papers, 246th ACS National Meeting & Exposition, Indianapolis, IN, USA, September 8-12, 2013.

32. Hudson B.S. and Allis D.G. “[18]-Annulene: Zero point level average structure and NMR spectrum.” Abstracts of Papers, 244th ACS National Meeting & Exposition, Philadelphia, PA, USA, August 19-23, 2012.

31. Lashua A.F., Allis D., Crill J., Dinca S., Sponsler M., and Hudson B.S. “Isolated polyacetylene in an inclusion complex: Exploration of synthetic methods.” Abstracts of Papers, 244th ACS National Meeting & Exposition, Philadelphia, PA, USA, August 19-23, 2012.

30. Hudson B.S., Rivera S.A., Hudson M.R., and Allis D.G. “Free energy simulation of molecular crystal thermodynamics.” Pacifichem 2010, International Chemical Congress of Pacific Basin Societies, Honolulu, HI, USA, December 15-20, 2010.

29. Hudson B.S., Allis D.G., Hudson M.R., and Rivera S.A. “Periodic lattice DFT calculations of inelastic neutron spectra – applications in structure and energetics in molecular crystals.” Pacifichem 2010, International Chemical Congress of Pacific Basin Societies, Honolulu, HI, USA, December 15-20, 2010.

28. Hudson M.R., Allis D.G., and Hudson B.S. “INS vibrational spectroscopy of parabanic and picolinic acid: Hydrogen-bonding in the solid-state.“ Abstracts of Papers, 239th ACS National Meeting, San Francisco, CA, USA, March 21-25, 2010.

27. Rivera S.A., Allis D.G., and Hudson B.S. “Lattice contraction stabilizes a neutral-to-ionic change in 4- methylpyridine:pentachlorophenol.” Abstracts of Papers, 239th ACS National Meeting, San Francisco, CA, USA, March 21-25, 2010.

26. Hudson B.S. and Allis D.G. “Peierls’ instability of polyacetylene: Calculations on inadequacy as a mechanism of dimerization.” Abstracts of Papers, 239th ACS National Meeting, San Francisco, CA, USA, March 21-25, 2010.

25. Hakey P.M., Allis D.G., Hudson M.R., Ouellette, W., and Korter T.M. “Investigation of biologically active compounds via terahertz spectroscopy.” Abstracts of Papers, 238th ACS National Meeting, Washington, DC, USA, August 16-20, 2009.

24. Hudson M.R., Allis D.G., Ouellette W., and Hudson B.S. “X-ray structure determination and vibrational spectroscopic investigation of L-alanine alaninium nitrate and ferroelectric triglycine sulfate.” Abstracts of Papers, 238th ACS National Meeting, Washington, DC, USA, August 16-20, 2009.

23. Hudson B., Allis D.G., Baldwin J., James S., Morgera K., and O’Leary D. “Computation of Deuterium Isotope Effects on Proton Chemical Shift for Hydrocarbons.” Abstracts, 35th Northeast Regional Meeting of the American Chemical Society, Burlington, VT, USA, June 29-July 2, 2008.

22. Hakey P.M., Allis D.G., Hudson M.R., and Korter T.M. “Cryogenic terahertz spectroscopy and solid-state modeling of illicit drugs.” Abstracts of Papers, 236th ACS National Meeting, Philadelphia, PA, USA, August 17-21, 2008.

21. Rivera S.A., Allis D.G., and Hudson B.S. “Importance of vibrational zero-point energy to relative polymorph energies for hydrogen bonded species.” Abstracts of Papers, 236th ACS National Meeting, Philadelphia, PA, United States, August 17-21, 2008; Abstracts, 35th Northeast Regional Meeting of the American Chemical Society, Burlington, VT, USA, June 29-July 2.

*20. Sims M., Smith B., Helfrich B., Sathaye N., Messick E., Moore T., Fish R., Rajagopalan M., Rotkiewicz P., Hendricks D., Drexler K.E., and Allis D.G. “NanoEngineer-1 – A CAD-Based Molecular Modeling Program For Structural DNA Nanotechnology.” Foundations of Nanoscience 2008 (FNANO08), Snowbird, UT, USA, April 22-25, 2008.

*19. Allis D.G. and Korter T.M. “Understanding the Chemical Origins of Terahertz Spectra.” Intelligence Community Postdoctoral Research Fellowship Colloquium, Washington, DC, USA, April 17-19, 2006.

18. Teng W., Allis D.G., and Ruhlandt-Senge K. “Syntheses and Structures of the First Heavy Alkali Metal Tris(trimethylsilyl)germanides and Heavy Alkali Metal Germyls – contact molecules and separated ions.” Abstracts, 34th Northeast Regional Meeting of the American Chemical Society, Binghamton, NY, USA, October 5-7, 2006.

*17. Allis D.G. and Drexler K.E. “Molecular Tool Designs and Theoretical Analyses for Single Atom Mechanosynthesis.” Foresight Institute 13th Conference on Molecular Nanotechnology, San Francisco, CA, USA, October 23-27, 2005.

*16. Allis D.G. and Hudson B.S. “The Inelastic Neutron Scattering Spectra of Cs2[B12H12] and K2[B12H12].” American Chemical Society Meeting and Exposition, Washington, D.C., USA, August 28 – Sept. 1, 2005.

15. Hudson B.S., Braden D., Allis D.G., Verdal N., Hu H., and Jenkins T.A. “Short, strong, symmetric hydrogen bonds: Vibrational inelastic neutron scattering studies.” Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, USA, March 13-17, 2005.

14. Hudson B.S., Allis D.G., Parker S.F., Ramirez-Cuesta, A.J., Herman H., and Prinzbach, H. “The infrared, Raman and inelastic neutron scattering spectra of dodecahedrane: An Ih molecule in Th site symmetry.” Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, USA, March 13-17, 2005.

*13. Allis D.G., Braden D., Jenkins T.A., Baronov S., Middleton C., Withnall R., Brown C.M., Lan Y., and Hudson B.S. “Crystalline 1,3-cyclohexanedione and its complex with benzene: Vibrational spectra, simulation of structure and dynamics and evidence for cooperative hydrogen bonding.” Abstracts of Papers, 228th ACS National Meeting, Philadelphia, PA, USA, August 22-26, 2004.

12. Hudson B.S., Jenkins T.A., Hu H., Allis D.G., and Verdal N. “Vibrational inelastic neutron scattering studies of short, strong, symmetric hydrogen bonds.” Abstracts of Papers, 228th ACS National Meeting, Philadelphia, PA, USA, August 22-26, 2004.

11. Ruhlandt-Senge K., Alexander J.S., Allis D., and Hudson B.S. “Alkali metal diphenylmethanides: A synthetic, structural, and computational study.” Abstracts of Papers, 227th ACS National Meeting, Anaheim, CA, USA, March 28-April 1, 2004.

10. Baker E., Ruhlandt-Senge K., Alexander J.S., Hope H., Allis D.G., Braden D., Green D., Englich U., and Hudson B.S. “Examinations into alkaline earth metal acetylides.” Abstracts of Papers, 227th ACS National Meeting, Anaheim, CA, United States, March 28-April 1, 2004; Abstracts, 32nd Northeast Regional Meeting of the American Chemical Society, Rochester, NY, USA, October 31-November 3.

9. Ciezak J.A., Hudson B.S., Jenkins T.A., and Allis D. “Inelastic neutron spectroscopy of organic hydrocarbons.” Abstracts of Papers, 225th ACS National Meeting, New Orleans, LA, USA, March 23-27, 2003.

*8. Allis D., Newlon A., Taylor J., and Spencer J.T. “New Classes of Cluster-Based High-Nonlinear Optical Response Compounds.” Abstracts of Papers, 224th ACS National Meeting, Boston, MA, USA, August 18-22, 2002.

*7. Allis D.G., Middleton C., Braden D., Parker S.F., and Hudson B.S. “Solid State DFT Methods and the Property Prediction of High-Symmetry Molecular Crystals.” Gordon Research Conference, Vibrational Spectroscopy, Salve Regina University, Providence, RI, USA, July 28-August 2, 2002.

*6. Allis D.G. and Spencer J.T. “The Use of Polyhedral Materials in Molecular Electronics and Nanostructural Applications.” Foresight Institute Eighth Conference on Nanotechnology, Bethesda, MD, USA, November 3- 5, 2000.

*5. Allis D.G. and Spencer J.T. “New Classes of Large Nonlinear Optical Response Compounds Based Upon Polyhedral Structural Units.” BUSA VII, University of Pittsburgh, Pittsburgh, PA, USA, June 7-10, 2000.

*4. Allis D.G. and Spencer J.T. “The Use of Polyhedral Materials in Molecular Electronics and Nanostructural Applications.” BUSA VII, University of Pittsburgh, Pittsburgh, PA, USA, June 7-10, 2000.

*3. Allis D.G., Taylor J., Rudd G., and Spencer J.T. “Semiempirical and Molecular Mechanics Calculations of Polyhedral Materials in Nanostructures.” Foresight Institute Seventh Conference on Nanotechnology, Santa Clara, CA, USA, October 15-17, 1999.

*2. Allis D.G., Taylor J., Rudd G., and Spencer J.T. “The Use of Polyhedral Materials in Molecular Electronic and Nanostructural Applications.” IMEBORON X, Durham University, Grey’s College, Durham, UK, July 11-15, 1999.

*1. Allis D.G., Goodisman J.S., and Spencer J.T. “Hartree-Fock and Density Functional Theoretical Considerations of the Thermal and Photochemical Pathways in Metallanonaborane Cluster Complexes.” BUSA VI, The University of Georgia, Athens, GA, USA, May 14-16, 1998.

An additional, incomplete list of all presentations (including those as an associated author but non-presenter that I am aware of being on) can be found at www.somewhereville.com.

PATENTS

– Pat. 2001027028 A1 20010419. Application: WO 2000-US27732 20001006. Priority: US 99-159301 19991014; US 2000-679929 20001005. Design and Fabrication of Molecular Nanostructures From Polyhedral-Based Molecular Synthetic Subunits.

– Pat. 2001000631 A1 20010104. Application: WO 2000-US17461 20000623. Priority: US 99-141346 19990628; US 2000-602424 20000623. New Classes of High Linear and Nonlinear Response Compounds.

SOFTWARE

Publications with, currently using, or otherwise familiar with: Gaussian98/03/09, GAMESS-US and PC-GAMESS, NWChem, Crystal06/0914, DMol3, CASTEP, Abinit, MPQC, MOPAC, GROMACS, NAMD, AMBER, NanoEngineer-1, associated MPI versions and numerous QC/MD GUIs (ChemOffice, CAChe, VMD, Materials Studio (Accelrys)).  Unperturbed by new software (they’re all just keywords and text files).

SUPPLEMENTAL INFORMATION

A more extensive CV and research description, including the ever-popular nanotechnology gallery, can be found at www.somewhereville.com.

Obligatory

  • CNYO

  • Sol. Sys. Amb.

  • Ubuntu 4 Nano

  • NMT Review

  • N-Fact. Collab.

  • Pres. Asn. CNY

  • T R P Nanosys

  • Nano Gallery

  • nano gallery
  • Aerial Photos

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    Syracuse Scenes

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