Dr. Maria E. Gracheva Assistant Professormgrachev/resumes/gracheva_resume.pdfTeraGrid-2012, Award for Supercomputing time at Texas and Purdue U. (Steele and Ranger), TG-PHY110023 extension,

Curriculum Vitae: Dr. Maria Gracheva, Clarkson University. July 21, 2014

Dr. Maria E. Gracheva

Assistant ProfessorDepartment of PhysicsSchool of Arts and SciencesClarkson UniversityPhone office: (315) 268-77-57; Fax: (315) 268-7754E-mail: [email protected]://www.clarkson.edu/∼ gracheva

EDUCATION

Institution Degree Years Field of study

University of Illinois,Beckman Institute for AdvancedScience and Technology,Urbana, IL, USA

Postdoctoral 2004-2008 Bio-Nanotechnology

University of Minnesota,Department of Mathematics,Minneapolis, MN, USA

Postdoctoral 2001-2003 Bio-mathematics

Lehigh University,Department of Physics,Bethlehem, PA, USA

Postdoctoral 1999-2001 Physics

Moscow State Engineering PhysicsInstitute (MEPhI),Moscow, Russia

PhD Dec. 1998 Solid State Physics

Moscow State Engineering PhysicsInstitute (MEPhI),Moscow, Russia

MS Feb. 1995 Solid State Physics

PROFESSIONAL EXPERIENCE

2008-present Assistant Professor of Physics, Department of PhysicsClarkson University, Potsdam, NY

2004-2008 Postdoctoral Associate, University of Illinois at Urbana-ChampaignBeckman Institute for Advanced Science and Technology &Department of Electronics and Computer Science, Urbana, ILwith Prof. Jean-Pierre Leburton

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2001-2003 Postdoctoral Associate, Department of MathematicsUniversity of Minnesota at Minneapolis, Minneapolis, MNwith Prof. Hans Othmer

2001-2003 ”Pre-Calculus” Lecturer, Department of MathematicsUniversity of Minnesota at Minneapolis, Minneapolis, MN

1999-2001 Postdoctoral Associate, Department of PhysicsLehigh University, Bethlehem, PAwith Prof. James D. Gunton

1999-2001 Teaching Assistant and Laboratory Instructor for ”Physics for Life Sciences”Department of Physics, Lehigh University, Bethlehem, PA

1995-1998 Research and Teaching Assistant, Moscow State Engineering PhysicsInstitute, Department of Physics and Technical Applicationsof Superconductivity, Moscow, Russia

AWARDS/SCHOLARSHIPS/HONORS

• NSF-CAREER 2014, Project title ”CAREER: Coupling nanoscale device modelingwith coarse-grained biomolecular simulations”.

• XSEDE-2013, Award for Supercomputing time (on Kraken and Stampede), GrantTG-PHY130028, ”Controlling DNA translocation through a semiconductor membrane”,May 14, 2013 - May 13, 2014.

• NSF-REU 2012, Project title ”REU Supplement: EAGER: Layered semiconductormembranes for tunable separation and filtering of ions and biomolecules”.

• TeraGrid-2012, Award for Supercomputing time at Texas and Purdue U. (Steeleand Ranger), TG-PHY110023 extension, ”Controlling DNA translocation through asemiconductor membrane”, January 21, 2012 - April 7, 2013.

• NSF-EAGER 2011, Project title ”EAGER: Layered semiconductor membranes fortunable separation and filtering of ions and biomolecules”.

• TeraGrid-2011, Award for Supercomputing time, Texas and Purdue, TG-PHY110023,”Controlling DNA translocation through a semiconductor membrane”, April 7, 2011 -April 7, 2012.

• NCSA-2008, Award for Supercomputing time at National Center for Supercomput-ing Applications (NCSA, UIUC), TG-PHY070026N extension, ”Application of layeredsemiconductor nanostructures for ion/bio-molecule filtering and characterization”, Au-gust 1, 2008.

• Who’s Who in Science and Engineering, 10th Anniversary Edition, 2008-2009.

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• Best Paper Finalists IEEE-NANO-2008, ”Simulation of electrically tunable semi-conductor nanopores for DNA sequencing”, with Jean-Pierre Leburton.

• NCSA-2007, Award for Supercomputing time at NCSA (UIUC), TG-PHY070026N,”Application of layered semiconductor nanostructures for ion/bio-molecule filteringand characterization”, August 1 (2007).

• Research Fellowship Samsung Electronics Corporation, ”Genius Student Program”,1997-1998.

AWARDS/HONORS WITH STUDENTS

• Craig C. Wells, McNair Summer Scholarship at Clarkson University, June - August2014.

• Craig C. Wells, Best Poster Award at SURE conference at Clarkson University, April2014.

• I-ning Amy Jou, Award for computational time on XSEDE network at Cornell Uni-versity, 2013.

• I-ning Amy Jou, Teaching Assistant Excellence Award, Department of Physics, Clark-son University, 2012.

MAIN RESEARCH INTERESTSBio-Nanotechnology, Biophysics and Solid State Physics with an emphasis on large scale andmulti-scale computations:

• Bio-Nanotechnology: biomolecular sensing, solid state electronics for biomolecularsensing, ion and protein separation, DNA sensors, protein filtering with solid statemembranes, biomolecule characterization, chemically decorated membranes, nanoporegating, nanochannels and nanostructures, nanoparticle filtering and separation.

• Biophysics: cell motility, cell signaling, signaling cascades and networks, signaling intissues, topology of cell connectivity in tissues.

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MENTORING ACTIVITIES AT CLARKSON - RESEARCH

PhD and MS Thesis Completed at Clarkson:

• Tetiana Timchenko, MS 2014 - currently entering a graduate school in Ukraine.Thesis title: Single-stranded DNA capture and translocation through solid-state nanopore.

• George T. Nelson, MS 2011 - went to a Medical School, currently a PhD candidate atRIT.Project title: DNA translocation through a double layered membrane.

• Alexey Nikolaev, MS 2011 - currently a PhD candidate at Hunter College (NYC) inComputer Sciences.Thesis title: Poisson-Nernst-Planck model for simulation ionic current through thenanopore in a semiconductor membrane.

Senior Undergraduate Thesis Completed at Clarkson:

• Chris McKinney, BS 2013 - currently with PeaceCorps in Kenia, Africa.Honors Thesis title: Computational model of a polymer decorated nanopore.

PhD students at present:

• I-ning Amy Jou, expected PhD 2015,Research topic: Electrostatic control over biomolecules in a nanopore

• Zachery K. Hullings, expected PhD 2016,Research topic: DNA in a nanochannel

Post-doctoral Associate:

• Dr. Irina Dokukina, (2008-2009)Research topic: Cell motility of substrates with different rigidities

Visiting Fellows Hosted:

• Prof. Vyacheslav N. Gorshkov, Ukraine Polytechnical University, Ukraine (June 2012).

• Dr. Sergey Makarov, Moscow Lomonosov State University, Russia (June-August 2010)

• Dr. Sergey Makarov, Moscow Lomonosov State University, Russia (June-August 2009)

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Clarkson Undergraduate Student Research Funded through the PI:

• Craig C. Wells, Spring 2014, REU supplement NSF funded research, Chemically dec-orated nanopore; McNair Scholarship supported research over June-August 2014.

• Craig C. Wells, Fall 2013, REU supplement NSF funded research, Chemically decoratednanopore.

• Chris McKinney, Fall 2012 - Spring 2013, REU supplement NSF funded research dur-ing, Computational model of a polymer decorated nanopore.

• Chris McKinney, June-August 2012, NSF funded research, Computational model of apolymer decorated nanopore.

• Padraic Cashin, June-August 2010, REU supplement NSF funded, Brownian Dynamicsmodel of a DNA in an electrostatic trap.

• Padraic Cashin, Fall 2010, NSF funded, Brownian Dynamics model of a DNA in anelectrostatic trap.

• Padraic Cashin, June-August 2011, start-up funded, Brownian Dynamics model of aDNA in an electrostatic trap.

Clarkson Undergraduate Research - Credit:

• Vicky Nguen, Fall 2012, DNA - pore interaction.

• Padraic Cashin, Spring 2010, Brownian dynamics model of DNA in a nanoslit.

• Padraic Cashin, Fall 2009, Brownian dynamics model of DNA in a nanoslit.

• Jeremiah M. Dederick, Fall 2009, Electrostatic potential distribution in a nanoslit.

• Suzanne Van Arsdale, Spring 2009, Enzymatic chemical reactions.

International Students performing Research at Clarkson:

• Anna Nadtochiy, June-August 2013, Protein filtering through a nanopore.

• Anna Nadtochiy, June-August 2012, Nanoparticle and protein filtering through ananopore.

• Dmitry Bikulov, June-August 2011, Brownian dynamics model of DNA in a nanosli.

• Dmitry Bikulov, June-August 2010, Cell biomechanics model.

• Andrey Borunov, June-August 2009, Solid-state ion filter.

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TEACHING ACTIVITIES

Teaching interestsSolid-State Physics, Biophysics, Computational Physics and Simulations, Modern Physics.

Teaching accomplishments

• Developed a course and new in-lecture demonstrations for Physics for Life SciencesPH141/PH142: the refraction of light rays with lenses, the total internal reflection,the chain of wires of different conductivity, and many more.

• Developed a new course Computer Modeling in Physics PH479/PH474/PH625. Thiscourse covers the professional experience requirement which is necessary for graduationof all physics majors. Thus teaching this course constitutes a significant service to thedepartment.

• Developed a new course Solid State Physics PH341/PH541. Newly developed demon-strations and games on crystal lattices were very well received by the students in thiscourse. This course also provides an introduction of physical concepts governing thebehavior of the solid-state materials, and thus is very useful for engineering studentspursuing carriers in electrical engineering, chemical engineering, etc. Usually a half ofthis class comes from engineering.

• Developed a new course Introduction to Biophysics PH426/PH526. This course is de-signed for students interested in pursuing either medical/biomedical track in biomolec-ular sciences or biophysical track in physics.

Undergraduate Courses Taught at Clarkson

• PH141, Physics for Life Sciences (Lecture)

• PH142, Physics for Life Sciences (Lecture)

• PH231, Fundamentals of Modern Physics (Lecture)

• PH341, Solid State Physics (Lecture)

• PH380, Electromagnetic Theory I (Lecture)

• PH381, Electromagnetic Theory II (Directed Study)

• PH426, Introduction to Biophysics (Lecture)

• PH474, Directed Study Theoretical (Lab)

• PH479, Directed Study Theoretical (Lab)

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Graduate Courses Taught at Clarkson

• PH526, Introduction to Biophysics (Lecture)

• PH541, Solid State Physics (Lecture)

• PH581, Electromagnetic Theory II (Directed Study)

• PH625, Computer Modeling in Physics (Lab)

• PH681, Selected Topics in Physics (Directed Study)

Summary of Courses Taught at Clarkson

Semester Course Enrollment Semester Course Enrollment

Fall 2008 PH426(526) 5 Spring 2009 PH341(541) 4

Fall 2009PH380PH474PH625

1011

Spring 2010PH341(541)PH479PH625

611

Fall 2010 PH625 3 Spring 2011

PH341(541)PH381(581)PH574PH625

14311

Fall 2011 PH231 16 Spring 2012 PH341 12


1971

Spring 2013PH341(541)PH480PH681

1123


7952

Spring 2014PH142PH480

721


5412

Spring 2015 PH142

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DEPARTMENTAL AND UNIVERSITY SERVICE

Service to Clarkson University

• Faculty Senate, Member (September 2012 - present)

• Judge at Clarkson University SURE conference (April 2014)

• Faculty Adviser to Sci-Fi Club at Clarkson University (August 2012 - present)

• Committee on Grants administration lifecycle process review (October 2011-July 2012)

• Clarkson University Open House, annually every Fall and Spring semester (2008 -present)

• Funded 6 undergraduate/BS graduates for summer research from grants and REUsupplements

• Student recruitment: recruited five graduate students internationally and nationallyto pursue advanced degrees at Clarkson: Alexey Nikolaev, Irina Dokukina, I-ning AmyJou, George Nelson, Tetiana Timchenko

Service to Department of Physics

• Academic adviser to undergraduate students, totaling 20 (2008 - present)

• Research adviser to 6 undergraduate students (2008 - present)

• Academic and Research adviser to graduate students, 5 total (2008 - present)

• Graduate student review and hiring Committee (2008 - present)

• Search Committee for an administrative assistant (2011, 2013)

• Member and chair in multiple PhD&MS (8), Graduate Comprehensive Examination(10) and Honors Thesis Committees (1) - listed below:

Member and Chair in PhD and MS Advisory Committees (8)

• Chair, I-ning Amy Jou (2014)

• Chair, Tetiana Timchenko (2014)

• Member, Simon Rock (2014)

• Member, Daniel Crain (2012)

• Member, John Garland (2011)

• Chair, George Nelson (2011)

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• Chair, Alexey Nikolaev (2011)

• Member, Jianping Zheng (2010)

• Member, Christopher Sulyma (2010)

Member and Chair of Comprehensive, PhD Thesis Proposals and QualifyingExams (10)


• Member, David Simpson (2014)

• Chair, Zachery K. Hulings (2014)

• Member, Daegon Gonyer (2014)

• Member, Michael Turk (2013)

• Member, Xingzhao Shi (2012)

• Member, Daniel Crane (2011)

• Member, Simon Rock (2011)


• Member, Paul Perez (2011)

• Member, Jianping Zheng (2010)

• Chair, Alexei Nikolaev (2010)

Hohor thesis - adviser (1)

• Chair, Christopher McKinney (2013)

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PROFESSIONAL ACTIVITIES AND SERVICE

Editorial Activities:

• Book: Editor, ”Nanopore-based technology: Single molecule characterization andDNA sequencing”, Publisher: Humana Press, Springer (2012), ISBN 978-1-61779-772-9. Chapters from this book were downloaded 4923 in 2012 and 2013, Sprigner.comweb-stite (official data).

Reviewer Activities:Reviewer for funding agencies: National Science Foundation (NSF), Department ofEnergy (DOE)

• NSF DMR-DMREF write-in reviewer (June 2014).

• NSF CBET Panel (March 2014).

• DOE write-in reviewer (June-July 2013).

• NSF DMR write-in reviewer (February 2013).

• NSF DMR write-in reviewer (May 2012).

• NSF CBET Panel (November 2011).

• NSF CBET Panel (October 2010).

Reviewer of manuscripts for journals:ACS NanoChemical ReviewsElectrophoresisIEEE Transactions on Electronic DevicesIEEE Transactions on NanotechnologyLangmuirNano LettersNanotechnologyPhysical BiologyScientific ReportsThe Journal of Chemical PhysicsThe Journal of Computational ElectronicsThe Journal of Theoretical Biology

Membership in Professional Societies:American Physical Society (APS)Biophysical Society (BPS)

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Member in Research Centers:Center for Advanced Material Processing (CAMP)Nanoengineering and Biotechnology Laboratories Center (NABLAB)

Other Recognitions, Research Highlights:

• In total 4923 chapter downloads for my Nanopore Book on Springer web-site (2074downloads for 2012, 2849 downloads for 2013).

• Research articles in total cited 414 times (without self-citations). In total 328 articlescited our works (without self-citations).

• Invited article, Journal of Computational Electronics, ”Poisson-Nernst-Planck modelfor an ionic transistor based on a semiconductor membrane” (June 2014).

• Brownian dynamics paper receives an editorial highlight in the Nanotechnology Journal(August 2012).

• ”Daily Courier Observer” article, ”Clarkson University Professor contributes to bookabout Nanopores”, (July 19, 2012).

• Nanopore Book publicity: http://www.clarkson.edu/news/2012/news-release 2012-07-17-1.html

• ”Semiconductor membrane mimics biological behavior of ion channels”,http://www.nsf.gov/news, http://www.physorg.com,Physicsdaily.com, Institute of Physics (IOP), Beckman Institute, NCSA, Electrical andComputer Engineering Department of UIUC and other sites internationally.

• ”Scientists tap NCSA resources to design a tunable semiconductor membrane thatcould be used for protein filtering or DNA sequencing”, ACCESS journal, NCSA, vol.20(3), Fall 2007.

• Featured in ”DNA Sequencing Using Nanopores - Toward the Genomic Analysis ofCancer ”, American Chemical Society, Chemistry Magazine, Autumn 2007.

• Nanotechnology Journal Cover article, volume 17(13), 2006.

• The Most Accessed paper (10% all publications under Institute of Physics publishinghouse), Nanotechnology 17(3), 2006.

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SCIENTIFIC WORKS(32 peer-reviewed research publications, 3 book chapters, 1 book edited, 1 patent, 53 confer-ence presentations and invited lectures, including invited talks at international conferences):

Patent:

1. ”Solid State Device: Molecular detection device”, with Jean-Pierre Leburton, GregoryTimp and Julien Vidal, filed in May (2007), US Patent application #20090084688.Granted in January 2012, issued on June 5, 2012, patent number 8,192,600.

Book:

1. ”Nanopore-based technology: Single molecule characterization and DNA sequencing”,Editor: Maria Gracheva, Publisher: Humana Press, Springer (2012), ISBN 978-1-61779-772-9.

Book chapters:

1. (Clarkson University publicity) ”Polymer Translocation Through an ElectricallyTunable Nanopore in a Multilayered Semiconductor Membrane, D.V. Melnikov, A.Nikolaev, J.-P. Leburton, M.E. Gracheva, Book Chapter in ”Nanopore-based technol-ogy: single molecule characterization and DNA sequencing”, edited by M.E. Gracheva,p. 187-210, Humana Press (2012), ISBN 978-1-61779-772-9, DOI 10.1007/978-1-61779-773-6. (Methods Mol Biol; 2012;870:187-207)

2. ”Simulation of electronic sensing of biomolecules in translocation through a nanoporein a semiconductor membrane”, M.E. Gracheva, A. Leroux, J. Destine, J.-P. Leburton,Book Chapter in ”Nanopores: sensing and fundamental biological interactions”, editedby S.M. Iqbal and R. Bashir, Springer (2010).

3. ”The role of noise in some physical and biological systems”, J.D. Gunton, R. Toral,C. Mirasso and M.E. Gracheva, chapter in book ”Recent Research Developments inApplied Physics”, eds. M. Kawasaki, N. Ashgriz, R. Anthony (2003).

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Peer-reviewed publications (indicated (*) undergraduate and (**) graduate authors):

1. (Invited Paper) ”Poisson-Nernst-Planck model for an ionic transistor based on asemiconductor membrane”, A. Nikolaev**, M. Gracheva, Journal of ComputationalElectronics (Special Issue) (2014). (accepted)

2. ”Charged particle separation by electrically tunable nanoporous membrane”, Ining A.Jou**, D. Melnikov, A. Nadtochiy*, M.E. Gracheva, Nanotechnology 25(14), 14521(1-9) (2014). doi: 10.1088/0957-4484/25/14/145201

3. ”Filtering of nanoparticles with tunable semiconductor membranes, A. Nadtochiy*, D.Melnikov, M.E. Gracheva, ACS Nano 7, 7053-7061 (2013). DOI: 10.1021/nn4023697

4. ”Mathematical modeling of group of neurons and astrocytes in ischemic stroke”, S.Makarov**, Yu. Dzhebrailova, M. Gracheva, E. Grachev, A. Kochetov, L. Gubskiy,Journal of Neurology and Psychiatry 8 59-62 (2012).

5. ”DNA translocation through a nanopore in a single layered doped semiconductor mem-brane”, Ining A. Jou**, D. Melnikov, Christopher R. McKinney*, M.E. Gracheva,Phys. Rev E 86 061906 (2012). DOI: 10.1103/PhysRevE.86.061906

6. (Editorial in Nanotechnology Journal on this article) ”Slowing down and stretch-ing out DNA with an electrically tunable nanopore in a p-n semiconductor mem-brane”, D. Melnikov, J.-P. Leburton, M.E. Gracheva, Nanotechnology 23 25501 (2012).doi:10.1088/0957-4484/23/25/255501.

7. ”Simulation of ionic current through the nanopore in a double-layered semiconductormembrane”, A. Nikolaev*, M. Gracheva, Nanotechnology 22(16), p. 165202 (2011).

8. ”SPICE-circuit simulation of the electrical response of semiconductor membrane to asingle-stranded DNA translocating through a nanopore”, A. Leroux, J. Destine, B.Vanderheyden, M.E. Gracheva, J.-P. Leburton, IEEE Transactions on Nanotechnology9(3), p. 322-329 (2010).

9. ”A model of fibroblast motility on substrates with different rigidities”, I. Dokukina,M. Gracheva, Biophysical Journal 98(12), p. 2794-2803 (2010).

10. ”Multilayered semiconductor membranes for nanopore ionic conductance modulation”,M.E. Gracheva, D.V. Melnikov and J.-P. Leburton, ACS Nano 2(11), p. 2349-2355(2008).

11. ”Simulation of electrically tunable semiconductor nanopores for ion current/single bio-molecule manipulation”, M.E. Gracheva, J.-P. Leburton, J. Comput. Electronics 7(1),p. 6-9 (2008).

12. ”Role of network connectivity in intercellular calcium signaling”, I.V. Dokukina*, M.E.Gracheva, E.A. Grachev and J.D. Gunton, Physica D 237, p. 745-754 (2008).

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13. ”The influence of the tissue structure on intercellular calcium signaling”, I.V. Dokuk-ina*, A.A. Tsukanov, M.E. Gracheva and E.A. Grachev, Biophyzika 53(2), p. 305-314(2008) (in Russian).

14. ”p − n semiconductor membrane for electrically tunable ion current rectification andfiltering”, M.E. Gracheva, J. Vidal and J.-P. Leburton, NanoLetters 7(6), p. 1717-1722 (2007). (This article was featured by: NSF.gov, Physicsdaily.com, IOP,Beckman Institute, NCSA, Electrical and computer engineering Depart-ment of UIUC and other sites internationally.)

15. ”Electrolytic charge inversion at the liquid-solid interface in a nanopore in a dopedsemiconductor membrane”, M.E. Gracheva and J.-P. Leburton, Nanotechnology 18, p.145704-145710 (2007).

16. ”Electrically tunable solid-state silicon nanopore ion filter”, J. Vidal, M.E. Grachevaand J.-P. Leburton, Nanoscale Research Letters 2, p. 61-68 (2007).

17. ”Modulation of mitochondrial calcium dynamics by cytosolic buffer proteins and cellu-lar plasma membrane fluxes”, I.V. Dokukina, M.E. Gracheva, E.A. Grachev, MoscowState University Physics Bulletin (Vestnik Moskovskogo Universiteta, Fizika) 2, p.23-26 (2007).

18. (Journal Cover article) ”Electrical Signatures of Single-Stranded DNA with SingleBase Mutations in a Nanopore Capacitor”, M.E. Gracheva, A. Aksimentiev and J.-P.Leburton, Nanotechnology 17(13), p. 3160-3165 (2006).

19. (The Most Accessed paper - top 10% of Institute of Physics (IOP) Publish-ing) ”Simulation of the electric response of DNA translocation through a semiconduc-tor nanopore-capacitor”, M.E. Gracheva, A. Xiong, A. Aksimentiev, K. Schulten, G.Timp and J.-P. Leburton, Nanotechnology 17(3), p. 622-633 (2006).

20. ”A finite-size scaling study of a model of globular proteins”, D.L. Pagan, M.E. Grachevaand J.D. Gunton, J. of Chem. Physics 120(17), p. 8292-8298 (2004).

21. ”A continuum model of motility in amoeboid cells”, M.E. Gracheva and H.G. Othmer,Bulletin of Math. Biology 66(1), p. 167-193 (2004).

22. ”Intercellular communication via intracellular calcium oscillations”, M.E. Grachevaand J.D. Gunton, J. of Theor. Biology 221(4), p. 513-518 (2003).

23. ”Stochastic simulation of intercellular calcium spiking in hepatocytes”, M.E. Gracheva,R. Toral and J.D. Gunton, J. Theor. Biology 212, p. 111-125 (2001).

24. ”Coarse-grained Ginzburg-Landau free energy for Lennard-Jones systems”, M.E. Gracheva,J.M. Rickman and J.D. Gunton, J. Chem. Phys. 113(9), p. 3525-3529 (2000).

25. ”Phase transitions in a two-dimensional vortex system with defects: Monte Carlo sim-ulation”, V.A. Kashurnikov, I.A. Rudnev, M.E. Gracheva and O.A. Nikitenko, J. ofExp. and Theor. Physics 117, p. 196 (2000).

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26. ”Phase transitions in a two-dimensional vortex lattice with defects: Monte Carlo simu-lation”, I.A. Rudnev, V.A. Kashurnikov, M.E. Gracheva and O.A. Nikitenko, PhysicaC 332, p. 383 (2000).

27. ”Vortex lattice melting in layered HTSC in the field of defects”, M.E. Gracheva, V.A.Kashurnikov, I.A. Rudnev and O.A. Nikitenko, Low Temperature Physics 25(10, p.765(1999).

28. ”Dynamics of vortex lattice in the current state in high-temperature superconductors:Monte Carlo method”, M.E. Gracheva, V.A. Kashurnikov, I.A. Rudnev, Low Temper-ature Physics 25(2), p.105 (1999).

29. ”Phase diagram of layered HTSC: simulation by means of Monte Carlo method”,M.E. Gracheva, V.A. Kashurnikov, I.A. Rudnev, Physics of low-dimensional struc-tures 9/10, p. 202-208 (1998).

30. ”Monte Carlo simulation of phase transitions in the vortex system of high-temperaturesuperconductors”, M.E. Gracheva, M.V. Katargin, V.A. Kashurnikov and I.A. Rudnev,Low Temperature Physics 23(11), p.863 (1997).

31. ”Features of the melting dynamics of a vortex lattice in a high-Tc superconductor inthe presence of pinning centers”, M.E. Gracheva, V.A. Kashurnikov and I.A. Rudnev,J. of Exp. and Theor. Physics Letters 66, p.269-274, (1997).

32. ”Monte-Carlo simulation of the two-dimensional vortex lattice melting in high-temperaturesuperconductors with defects”, M.E. Gracheva, V.A. Kashurnikov and I.A. Rudnev,Physics of low-dimensional structures 8/9, p. 125-134 (1997).

PresentationsInvited Presentations and Seminars:

1. (Invited) Oxford Nanopore Ltd. (Cambridge, MA), ”Tunable solid state devices forDNA sensing”, June 11 (2014).

2. (Invited) ”DNA sequencing and detection with nanoprobes”, CECAM, Pisa Italy, June9 - June 13 (2012).

3. (Invited) Slowing down and stretching DNA translocating thorough a semiconductormembrane with a nanopore, Department of Chemical Engineering, Clarkson University,February 7th (2012).

4. (Invited) ”Electrically tunable DNA translocation through a nanopore in a multilayeredsemiconductor membrane”, Nanoelectronic Devices for Defense & Security Conference(NANO-DDS), Polytechnic Institute of New York University, New York, NY, Sept. 28- Aug. 1 (2011).

5. (Invited) ”Controlling DNA translocation through a semiconductor membrane”, CE-CAM workshop on “Molecular simulation in external electric and electromagneticfields”, University College Dublin, Ireland, May 19th - May 21st (2011).

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6. (Invited) ”Biosensing with nanopores: DNA characterization with solid-state pore”,SUNY Potsdam, April 15th, 2011.

7. (Invited seminar) “DNA sensing and characterization with a semiconductor nanopore,SUNY Binghamton University, October 18th (2010).

8. (Invited) ”The effect of the nanopore geometry on ionic currents in double layeredsemiconductor membranes”, Summer School “Biosensing with channels”, Berder Is-land, France, August 21th -August 27th (2010).

9. (Invited) ”A model of fibroblast rigidity sensing”, the American Mathematical SocietyMeeting, Macalester College College, St. Paul MN, April 10th - April 11th (2010).

10. (Invited) ”SPICE-circuit simulation of the electrical response of a semiconductor mem-brane to a DNA molecule translocating through a nanopore”, Nanoelectronic Devicesfor Defense & Security Conference (NANO-DDS), Fort Lauderdale FL, September 28th- October 2nd (2009).

11. (Invited) 4th Special Workshop on Electronic Recognition of Bio-molecules, Universityof Liege, Belgium, September 10-12 (2008).

12. (Invited) 15th International Conference on Superlattices, Nanostructures and Nanode-vices (ICSNN 2008), Natal, Brazil, August 3-8 (2008).

13. (Invited) ”A model of fibroblast motility on substrates with different rigidities”, theAmerican Mathematical Society Meeting, Indiana University, Bloomington Indiana,April 5-6 (2008).

14. (Invited) ”Protein and ion filtering with a semiconductor nanopore membranes”, Nanohour,University of Illinois at Urbana-Champaign, February 13 (2008).

15. (Invited) ”Protein and ion filtering with a semiconductor nanopore”, NanoBio Seminarat the University of Illinois at Urbana-Champaign, December 6 (2007).

16. (Invited) ”Simulation of electrically tunable semiconductor nanopores for ion cur-rent/protein manipulation and DNA sequencing”, Clarkson University, November 30(2007).

17. (Invited, Best Paper Finalist) ”Simulation of electrically tunable semiconductor nanoporesfor DNA sequencing”, with Jean-Pierre Leburton, IEEE-NANO, Hong Kong, August(2007).UIUC ECE news hightlight: http://www.ece.uiuc.edu/news/.

18. (Invited) ”Nanopore in a silicon membrane for ion current manipulation”, NanoBioSeminar at the University of Illinois at Urbana-Champaign, April 12 (2007).

19. (Invited) ”DNA detection and sequencing with a semiconductor nanopore”, Pennsyl-vania State University, September 18-20 (2006).

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20. (Invited) ”Multi-grid method for DNA translocation through a semiconductor nanopore”,with Jean-Pierre Leburton, ERBM-3, Belgium, September 6-8 (2006).

21. (Invited) ”Self-consistent simulation of DNA translocation through an artificial nanopore”,2nd Conference on nanoscale devices and system integration, Houston, Texas, April4-6 (2005).

22. (Invited) ”Simulation of DNA translocation through a nanopore”, with Jean-PierreLeburton, ERBM-2, Beckman Institute, Urbana-Champaign, Illinois, September 7-9(2005).

Other Conference and Workshop Presentations

1. (Talk) ”Computational model of controlled translocation of DNA molecule througha nanopore membrane with tunable electrostatic potential”, the American PhysicalSociety Meeting, Pittsburgh PA, March 16th - March 20th (2009).

2. (Talk) ’Fibroblast motility on substrates with different rigidities: modeling approach”,M. Gracheva and I. Dokukina, the American Physical Society Meeting, Pittsburgh PA,March 16th - March 20th (2009).

3. (Talk) ’Simulation of electrically tunable semiconductor nanopores for ion current/singlebio-molecule manipulation”, with Jean-Pierre Leburton, IWCE-12, University of Mas-sachusetts, Amherst, October 8-10 (2007).

4. (Talk) ”Semiconductor membranes for ion current rectification and filtering”, withJean-Pierre Leburton, the University of Illinois at Urbana-Champaign, Nanoscale Work-shop Meeting, July 30-31 (2007).

5. (Talk) ”Topology of cellular networks in calcium signaling”, with I. Dokukina andE.A. Grachev, p. 111 in Abstract Book, 9th European symposium on calcium-bindingproteins in normal and transformed cells (9th European Calcium Society meeting),Strasbourg, France, 19-22 July 2006.

6. (Talk) ”Decoding complex electrical signals produced by the DNA translocating througha solid state nanopore”, 6th Understanding Complex Systems Symposium, dedicatedto Paul C. Lauterbur, Nobel Prize in Physiology or Medicine, University of Illinois atUrbana-Champaign, May 15-18 (2006).

7. (Talk) ”Electrical Signatures of Single-Stranded DNA in a Nanopore Capacitor: Sin-gle Base Mutations”, with Jean-Pierre Leburton and A. Aksimentiev, MNTL/CNSTNanotechnology Workshop, Urbana-Champaign, Illinois, May 5-6 (2006).

8. (Talk) ”Electrical response of DNA translocation through nanopore MOS-capacitor”,with Jean-Pierre Leburton, A. Aksimentiev and G. Timp, MNTL/CNST Nanotech-nology Workshop, Urbana-Champaign, Illinois, May 5-6 (2005).

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9. (Talk) ”A Monte Carlo study of a model of globular protein nanoparticles”, with D.L.Pagan and J.D. Gunton, NSTI Nanotechnology conference and trade show Nanotech2004, Boston, Massachusetts, March 7-11 (2004).

10. (Talk) ”Phase diagram for a model of globular proteins”, D. Pagan, J.D. Gunton, M.E.Gracheva, the American Physical Society Meeting, Austin, Texas (2003).

11. (Talk) ”Modeling cell motility”, M. E. Gracheva, H. G. Othmer, Gordon ResearchConference in Theoretical Biology and Biomathematics, Tilton School, New Hampshire(2002).

12. (Talk) ”Stochastic simulation of cell-cell signaling in hepatocytes”, M. E. Gracheva, R.Toral, J. D. Gunton, First International Conference on Computational Nanoscience -ICCN 2001, Hilton Head Island, South Carolina (2001).

13. (Talk) ”Intercellular calcium signaling via calcium receptor”, M. E. Gracheva and J.D. Gunton, Symposium on Computational Cell Biology 2001: Lenox, Massachusetts(2001).

14. (Talk) ”Numerical study of liquid-solid phase coexistence”, M.E. Gracheva, J.M. Rick-man, J.D. Gunton, the American Physical Society (APS) Meeting, Minneapolis, Min-nesota (2000).

15. (Talk) ”Coarse-Grained Free Energy Functional for Lennard-Jones Systems”, M.E.Gracheva, J.M. Rickman, J.D. Gunton, D.C. Coffey, the Material Research Society(MRS) Symposium, Boston, Massachusetts (1999).

16. (Talk) ”Self-organizing and disintegration of two-dimensional quasi-particles system ina trap”, I.V. Voronin, M.E. Gracheva, E.Yu. Ul’ianov, in Proceedings of the Interna-tional Conference of Graduate and Postgraduate Students “Lomonosov-98”, MoscowState University, Moscow (1998).

17. (Talk) ”Simulation of current-voltage characteristics of high-temperature superconduc-tors with various types of defect structures”, M.E. Gracheva, V.A. Kashurnikov, I.A.Rudnev, 5-th International Workshop on high-temperature superconductors and novelinorganic materials engineering; MSU-HTSC V (Moscow State University), abstractS-54 (1998).

18. (Talk) ”Dynamics of vortex lattice with current in high temperature superconductors”,M.E. Gracheva, V.A. Kashurnikov, I.A. Rudnev, Third Meeting on Low-TemperatureSuperconductivity, Moscow State University, Russia (1998).

19. (Talk) ”Vortex lattice melting of HTSC in defect field”, M.E. Gracheva, V.A. Kashurnikov,O.A. Nikitenko, I.A. Rudnev, Third Meeting on Low-Temperature Superconductivity,the Moscow State University, Russia (1998).

20. (Talk) ”Monte-Carlo simulation of vortex lattice in high-temperature superconduc-tors”, M.E. Gracheva, V.A. Kashurnikov, I.A. Rudnev, in Proceedings of the First

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Open Scientific Conference, the Joint Institute for Nuclear Research, Dubna, Russia(1997).

21. (Talk) ”Effect of defects configuration on vortex lattice in high-temperature supercon-ductors”, M.E. Gracheva, in Proceedings of the International Conference of Gradu-ate and Postgraduate Students ”Lomonosov-97”, the Moscow State University, Russia(1997).

Posters:

1. (Poster) ”Separation of nanoparticles by charge with an electrically tunable mem-brane”, Spring CAMP Meeting, Saratoga Spring, NY, May 2014.

2. (Poster) ”DNA dynamics inside a nanochannel: Solution of Poisson equation in theDebye approximation for a wedge-like geometry”, Spring CAMP Meeting, SaratogaSpring, NY, May 2014.

3. (Poster) (Best Poster Award in Chemistry/Physics category) ”Tethered DNA enter-ing and escaping a nanopore in a solid-state membrane with switching electrolyte bias”,presented by Craig C. Wells*, with I-ning Amy Jou**, Dmitriy Melnikov and MariaGracheva, SURE conference, Clarkson University, Potsdam, NY, April 12 (2014).

4. (Poster) ”Separation of nanoparticles by charge and size with a tunable semiconductormembrane”, Biophysical Society Meeting, San Francisco, CA, 2014

5. (Poster) ”Statistical analysis of the single-stranded DNA capture and translocationthrough a semiconductor nanopore ”, Clarkson University Graduate Student Sympo-sium, Potsdam, NY, December, 2013.

6. (Poster) ”Brownian Dynamics Simulations of DNA Interaction with a NanoporousSolid State Membrane”, Biophysical Society Meeting, Philadelphia, PA, 2013.

7. (Poster) ”Electrically tunable DNA translocation through a nanopore in a multilayeredsemiconductor membrane”, the Biophysical Society Meeting, San Diego CA, February29th (2012).

8. (Poster) ”Electrostatic trapping of polymers during translocation through a semicon-ductor nanopore”, the Biophysical Society Meeting, Baltimore, MD, March 5th - March7th (2011).

9. (Poster) ”Simulation of ionic current through the nanopore in a double layered semi-conductor membrane”, the Biophysical Society Meeting, Baltimore, MD, March 5th -March 7th (2011).

10. (Poster) ”Regulation of the ionic current flowing through a nanopore in a semiconduc-tor membrane”, the Biophysical Society Meeting, San Francisco CA, February 20th -February 28th (2010).

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11. (Poster) ”Computational model of controlled translocation of DNA molecule througha nanopore membrane with tunable electrostatic potential”, the Biophysical SocietyMeeting, Boston MA, February 28th - March 4th (2009).

On-Campus and Local Presentations:

1. (Invited Seminar) Slowing down and stretching DNA translocating thorough a semi-conductor membrane with a nanopore, Department of Chemical Engineering, ClarksonUniversity, February 7th (2012).

2. (Freshman Seminar) Single molecule sensing with a semiconductor nanopore, ClarksonUniversity, November (2011).

3. (Freshman Seminar) Single molecule sensing with a semiconductor nanopore, ClarksonUniversity, September (2010).

4. (Poster) Kick off campaign, undergraduate presentation by Padraic Cashin* on “Lay-ered semiconductor membranes for DNA characterization”, Clarkson University, Oc-tober (2011).

5. (Talk) SURE conference, a talk presented by an undergraduate student Padraic Cashin*on “DNA translocation through a nanopore in a single layered semiconductor mem-brane”, Clarkson University, July (2011).

6. (Poster) SURE conference, undergraduate presentation by Padraic Cashin* on “Aworm-like chain model of a single-stranded DNA”, Clarkson University, May (2010).

7. (Freshman Seminar) DNA detection and sequencing with a semiconductor nanopore,Department of Physics, Clarkson University, October 2 (2009).

8. (Freshman Seminar) DNA detection and sequencing with a semiconductor nanopore,Department of Physics, Clarkson University, October 20 (2008).

Participation in Teaching Effectiveness Conferences:

• Annual teaching effectiveness conference sponsored by Associated Colleges: ”Teachingdigital natives”, Clarkson, Potsdam, November, 2013.

• Annual teaching effectiveness conference sponsored by Associated Colleges: ”Effectiveengagement techniques”, Clarkson, Potsdam, November 3, 2012.

• Annual teaching effectiveness conference sponsored by Associated Colleges: ”Effectiveteaching: developing critical thinking”, SUNY, Potsdam, November 12, 2011.

• Annual teaching effectiveness conference sponsored by Associated Colleges: ”Movingaway from Teacher centered paradigms”, St. Lawrence University, Canton, November,2010.

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• Annual teaching effectiveness conference sponsored by Associated Colleges: ”Teachingdigital natives”, Clarkson University, November 7, 2009.

• Annual teaching effectiveness conference sponsored by Associated Colleges: ”GlobalLearning: Remapping the Curriculum”, SUNY Canton, November 1, 2008.

RESEARCH FUNDING

Total funding received (excluding start-up): $702,981.00Gracheva’s share: $586,654.00 (value calculated according to percentages given when mul-tiple PIs are on the contract)

1. NSF-CAREER: ”CAREER: Coupling nanoscale device modeling with coarse-grainedbiomolecular simulations”Agency: NSF-DMR Agency Identification No.: DMR-1352218Time Period: 06/15/2014-05/31/2019 Award Amount: $400,000.00Investigator:Maria Gracheva (PI)

2. NSF: “REU Supplement: EAGER: Layered Semiconductor membranes for tunableseparation and filtering of ions and biomolecules”Agency: NSF-CBET Agency Identification No.: CBET-1119446Time Period: 05/15/2011-04/30/2013 Award Amount: $6,000.00Investigator:Maria Gracheva (PI)

3. NSF: “EAGER: Layered Semiconductor membranes for tunable separation and filteringof ions and biomolecules”Agency: NSF-CBET Agency Identification No.: CBET-1119446Time Period: 05/15/2011-04/30/2013 Award Amount: $122,490.00Investigator:Maria Gracheva (PI)

4. USAR: “Smart Responsive Nanocomposites for Soldier Protection”Agency: US-Army Agency Identification No.: W911NF-05-1-0339Time Period: 06/12/2009-09/30/2012 Award Amount: $174,491.00Investigators:Dan Goia (PI)Vladimir Privman (co-PI)Maria Gracheva (co-PI) (33% share)

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Documents

Dr. Maria E. Gracheva Assistant Professormgrachev/resumes/gracheva_resume.pdfTeraGrid-2012, Award for Supercomputing time at Texas and Purdue U. (Steele and Ranger), TG-PHY110023 extension,