{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/72941"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/72941","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Computational study of graphene nanopore sensor for DNA sensing","abstract":"Inexpensive and fast methods to sequence the genome of individuals using nanopore technology can lead to tremendous advancement in the eld of modern medicine. The thickness of the membranes employed in nanopore-based sensors presents a fundamental limitation to the physical dimension, of the translocating DNA molecule, that can be resolved. Typical solid-state membranes are too thick and usually fail to recognize single nucleotides on a DNA strand. Graphene is a sub-nanometer membrane, comprising of carbon atoms arranged in a honeycomb lattice, with remarkable electronic and mechanical properties. The thickness of a graphene membrane (3 A) is comparable to the vertical stacking distance between base pairs in the DNA (3.5 A) making graphene an ideal candidate for DNA sequencing. Resolving at the atomic level electric eld-driven DNA translocation through graphene nanopores is crucial to guide the design of graphene-based sequencing devices. Molecular dynamics (MD) simulations, in principle, can achieve such resolution and are employed to investigate the e ects of applied voltage, DNA conformation and sequence as well as pore charge on the translocation characteristics of DNA. In addition, graphene is electrically active and transverse electronic currents along the graphene membrane can complement ionic current measurements, and potentially extend the molecular sensing capability of graphene-based nanopores. We have combined the self-consistent Poisson-Boltzmann formal- ism with Non-Equilibrium Green's Function (NEGF) technique along with charge densities of DNA arising from MD simulations to show detection of rotational and positional conformation of a double-stranded DNA (dsDNA), inside the nanopore, via sheet currents in graphene nanoribbons. Furthermore, we show the ability of such transverse electronic currents to detect conformational transition, arising due to forced extension, of the dsDNA molecule from helical to zipper form, and also detect ssDNA translocation at single base pair resolution.","abstract_html":"Inexpensive and fast methods to sequence the genome of individuals using nanopore technology can lead to tremendous advancement in the eld of modern medicine. The thickness of the membranes employed in nanopore-based sensors presents a fundamental limitation to the physical dimension, of the translocating DNA molecule, that can be resolved. Typical solid-state membranes are too thick and usually fail to recognize single nucleotides on a DNA strand. Graphene is a sub-nanometer membrane, comprising of carbon atoms arranged in a honeycomb lattice, with remarkable electronic and mechanical properties. The thickness of a graphene membrane (3 A) is comparable to the vertical stacking distance between base pairs in the DNA (3.5 A) making graphene an ideal candidate for DNA sequencing. Resolving at the atomic level electric eld-driven DNA translocation through graphene nanopores is crucial to guide the design of graphene-based sequencing devices. Molecular dynamics (MD) simulations, in principle, can achieve such resolution and are employed to investigate the e ects of applied voltage, DNA conformation and sequence as well as pore charge on the translocation characteristics of DNA. In addition, graphene is electrically active and transverse electronic currents along the graphene membrane can complement ionic current measurements, and potentially extend the molecular sensing capability of graphene-based nanopores. We have combined the self-consistent Poisson-Boltzmann formal- ism with Non-Equilibrium Green's Function (NEGF) technique along with charge densities of DNA arising from MD simulations to show detection of rotational and positional conformation of a double-stranded DNA (dsDNA), inside the nanopore, via sheet currents in graphene nanoribbons. Furthermore, we show the ability of such transverse electronic currents to detect conformational transition, arising due to forced extension, of the dsDNA molecule from helical to zipper form, and also detect ssDNA translocation at single base pair resolution.","abstract_has_math":false,"creators":["Sathe, Chaitanya"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Electrical & Computer Engr","degree_department":null,"school":null,"contributors":["Leburton, Jean-Pierre","Schulten, Klaus J.","Lyding, Joseph W.","Bashir, Rashid"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2015,"date_issued":"2015-01-21T19:49:41Z","date_published":"2015-01-21T19:49:41Z","updated_at":"2026-07-22T22:26:07Z","subjects":["Nanopore","DNA Sequencing","Molecular Dynamics","Graphene","Electron Transport"],"languages":["en"],"rights":["Copyright 2014 Chaitanya Sathe"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/72941","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Leburton, Jean-Pierre","Schulten, Klaus J.","Lyding, Joseph W.","Bashir, Rashid"]},{"key":"dc:creator","label":"Author","values":["Sathe, Chaitanya"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2015-01-21T19:49:41Z","2014-12","2015-01-21"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Electrical & Computer Engr"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Nanopore","DNA Sequencing","Molecular Dynamics","Graphene","Electron Transport"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2014 Chaitanya Sathe"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/72941"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Inexpensive and fast methods to sequence the genome of individuals using nanopore technology can lead to tremendous advancement in the eld of modern medicine. The thickness of the membranes employed in nanopore-based sensors presents a fundamental limitation to the physical dimension, of the translocating DNA molecule, that can be resolved. Typical solid-state membranes are too thick and usually fail to recognize single nucleotides on a DNA strand. Graphene is a sub-nanometer membrane, comprising of carbon atoms arranged in a honeycomb lattice, with remarkable electronic and mechanical properties. The thickness of a graphene membrane (3 A) is comparable to the vertical stacking distance between base pairs in the DNA (3.5 A) making graphene an ideal candidate for DNA sequencing. Resolving at the atomic level electric eld-driven DNA translocation through graphene nanopores is crucial to guide the design of graphene-based sequencing devices. Molecular dynamics (MD) simulations, in principle, can achieve such resolution and are employed to investigate the e ects of applied voltage, DNA conformation and sequence as well as pore charge on the translocation characteristics of DNA. In addition, graphene is electrically active and transverse electronic currents along the graphene membrane can complement ionic current measurements, and potentially extend the molecular sensing capability of graphene-based nanopores. We have combined the self-consistent Poisson-Boltzmann formal- ism with Non-Equilibrium Green's Function (NEGF) technique along with charge densities of DNA arising from MD simulations to show detection of rotational and positional conformation of a double-stranded DNA (dsDNA), inside the nanopore, via sheet currents in graphene nanoribbons. Furthermore, we show the ability of such transverse electronic currents to detect conformational transition, arising due to forced extension, of the dsDNA molecule from helical to zipper form, and also detect ssDNA translocation at single base pair resolution.","Item withdrawn by Laura Spradlin (lspradl2@illinois.edu) on 2014-08-07T20:59:38Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 sathe_chaitanya.pdf: 11831431 bytes, checksum: c9cbdc9fd2266809d61815d7eed7c0ef (MD5)","Made available in DSpace on 2015-01-21T19:49:41Z (GMT). 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Graphene is a sub-nanometer membrane, comprising of carbon atoms arranged in a honeycomb lattice, with remarkable electronic and mechanical properties. The thickness of a graphene membrane (3 A) is comparable to the vertical stacking distance between base pairs in the DNA (3.5 A) making graphene an ideal candidate for DNA sequencing. Resolving at the atomic level electric eld-driven DNA translocation through graphene nanopores is crucial to guide the design of graphene-based sequencing devices. Molecular dynamics (MD) simulations, in principle, can achieve such resolution and are employed to investigate the e ects of applied voltage, DNA conformation and sequence as well as pore charge on the translocation characteristics of DNA. In addition, graphene is electrically active and transverse electronic currents along the graphene membrane can complement ionic current measurements, and potentially extend the molecular sensing capability of graphene-based nanopores. We have combined the self-consistent Poisson-Boltzmann formal- ism with Non-Equilibrium Green's Function (NEGF) technique along with charge densities of DNA arising from MD simulations to show detection of rotational and positional conformation of a double-stranded DNA (dsDNA), inside the nanopore, via sheet currents in graphene nanoribbons. Furthermore, we show the ability of such transverse electronic currents to detect conformational transition, arising due to forced extension, of the dsDNA molecule from helical to zipper form, and also detect ssDNA translocation at single base pair resolution.","Item withdrawn by Laura Spradlin (lspradl2@illinois.edu) on 2014-08-07T20:59:38Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 sathe_chaitanya.pdf: 11831431 bytes, checksum: c9cbdc9fd2266809d61815d7eed7c0ef (MD5)","Made available in DSpace on 2015-01-21T19:49:41Z (GMT). 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