Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation
We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbor calculations. Within this model, the finiteness of stacking enthalpies is shown to be responsible for the sharpness of calculated melting cur...
Gespeichert in:
| Veröffentlicht in: | Physical review. E, Statistical, nonlinear, and soft matter physics Statistical, nonlinear, and soft matter physics, 2005-11, Vol.72 (5 Pt 1), p.051902-051902, Article 051902 |
|---|---|
| Hauptverfasser: | , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 051902 |
|---|---|
| container_issue | 5 Pt 1 |
| container_start_page | 051902 |
| container_title | Physical review. E, Statistical, nonlinear, and soft matter physics |
| container_volume | 72 |
| creator | Joyeux, Marc Buyukdagli, Sahin |
| description | We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbor calculations. Within this model, the finiteness of stacking enthalpies is shown to be responsible for the sharpness of calculated melting curves. Transfer-integral and molecular dynamics calculations are performed to demonstrate that the proposed model leads to a good agreement with known experimental results for both homogeneous and inhomogeneous DNA. |
| doi_str_mv | 10.1103/PhysRevE.72.051902 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_hal_p</sourceid><recordid>TN_cdi_hal_primary_oai_HAL_hal_00008215v2</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>69048341</sourcerecordid><originalsourceid>FETCH-LOGICAL-c379t-92bbff2362694ab0c99dcd92975f9c5ff4831485d910064a4c2bf86a4d518233</originalsourceid><addsrcrecordid>eNpNUctOwzAQtBAISuEHOCCfkDik-JnEx6otD6kChHq3HD-oIbFLnCL170lpeexlV6OZ2V0NABcYjTBG9OZ5uUkv9nM2KsgIcSwQOQADzDnKCC3yw-1MRUYLzk_AaUpvCFFCS3YMTnBOS5ozNABhugmq8VrVsInG1rBSyRoYA3Q--M7C1Cn97sMrtKFbqnrlbYIutnAZm_hqg43rBFUw0If_yPRxDLulbZve19igunWrOh_DGThyqk72fN-HYHE7W0zus_nT3cNkPM80LUSXCVJVzhGak1wwVSEthNFGEFFwJzR3jpUUs5IbgRHKmWKaVK7MFTMcl4TSIbje2fYXy1XrG9VuZFRe3o_ncouhvkqC-SfpuVc77qqNH2ubOtn4pG1dq-9XZC5Qv43hnkh2RN3GlFrrfp0xkttA5E8gsiByF0gvuty7r6vGmj_JPgH6BXLbiRQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>69048341</pqid></control><display><type>article</type><title>Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation</title><source>MEDLINE</source><source>American Physical Society Journals</source><creator>Joyeux, Marc ; Buyukdagli, Sahin</creator><creatorcontrib>Joyeux, Marc ; Buyukdagli, Sahin</creatorcontrib><description>We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbor calculations. Within this model, the finiteness of stacking enthalpies is shown to be responsible for the sharpness of calculated melting curves. Transfer-integral and molecular dynamics calculations are performed to demonstrate that the proposed model leads to a good agreement with known experimental results for both homogeneous and inhomogeneous DNA.</description><identifier>ISSN: 1539-3755</identifier><identifier>EISSN: 1550-2376</identifier><identifier>DOI: 10.1103/PhysRevE.72.051902</identifier><identifier>PMID: 16383640</identifier><language>eng</language><publisher>United States: American Physical Society</publisher><subject>Anisotropy ; Base Sequence ; Biological Physics ; Computer Simulation ; DNA - chemistry ; Entropy ; Models, Chemical ; Models, Molecular ; Models, Statistical ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleic Acid Denaturation ; Physics ; Sequence Analysis, DNA - methods ; Structure-Activity Relationship ; Temperature ; Thermodynamics</subject><ispartof>Physical review. E, Statistical, nonlinear, and soft matter physics, 2005-11, Vol.72 (5 Pt 1), p.051902-051902, Article 051902</ispartof><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c379t-92bbff2362694ab0c99dcd92975f9c5ff4831485d910064a4c2bf86a4d518233</citedby><cites>FETCH-LOGICAL-c379t-92bbff2362694ab0c99dcd92975f9c5ff4831485d910064a4c2bf86a4d518233</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,2876,2877,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16383640$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-00008215$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Joyeux, Marc</creatorcontrib><creatorcontrib>Buyukdagli, Sahin</creatorcontrib><title>Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation</title><title>Physical review. E, Statistical, nonlinear, and soft matter physics</title><addtitle>Phys Rev E Stat Nonlin Soft Matter Phys</addtitle><description>We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbor calculations. Within this model, the finiteness of stacking enthalpies is shown to be responsible for the sharpness of calculated melting curves. Transfer-integral and molecular dynamics calculations are performed to demonstrate that the proposed model leads to a good agreement with known experimental results for both homogeneous and inhomogeneous DNA.</description><subject>Anisotropy</subject><subject>Base Sequence</subject><subject>Biological Physics</subject><subject>Computer Simulation</subject><subject>DNA - chemistry</subject><subject>Entropy</subject><subject>Models, Chemical</subject><subject>Models, Molecular</subject><subject>Models, Statistical</subject><subject>Molecular Sequence Data</subject><subject>Nucleic Acid Conformation</subject><subject>Nucleic Acid Denaturation</subject><subject>Physics</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Structure-Activity Relationship</subject><subject>Temperature</subject><subject>Thermodynamics</subject><issn>1539-3755</issn><issn>1550-2376</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpNUctOwzAQtBAISuEHOCCfkDik-JnEx6otD6kChHq3HD-oIbFLnCL170lpeexlV6OZ2V0NABcYjTBG9OZ5uUkv9nM2KsgIcSwQOQADzDnKCC3yw-1MRUYLzk_AaUpvCFFCS3YMTnBOS5ozNABhugmq8VrVsInG1rBSyRoYA3Q--M7C1Cn97sMrtKFbqnrlbYIutnAZm_hqg43rBFUw0If_yPRxDLulbZve19igunWrOh_DGThyqk72fN-HYHE7W0zus_nT3cNkPM80LUSXCVJVzhGak1wwVSEthNFGEFFwJzR3jpUUs5IbgRHKmWKaVK7MFTMcl4TSIbje2fYXy1XrG9VuZFRe3o_ncouhvkqC-SfpuVc77qqNH2ubOtn4pG1dq-9XZC5Qv43hnkh2RN3GlFrrfp0xkttA5E8gsiByF0gvuty7r6vGmj_JPgH6BXLbiRQ</recordid><startdate>20051101</startdate><enddate>20051101</enddate><creator>Joyeux, Marc</creator><creator>Buyukdagli, Sahin</creator><general>American Physical Society</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>1XC</scope><scope>VOOES</scope></search><sort><creationdate>20051101</creationdate><title>Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation</title><author>Joyeux, Marc ; Buyukdagli, Sahin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c379t-92bbff2362694ab0c99dcd92975f9c5ff4831485d910064a4c2bf86a4d518233</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Anisotropy</topic><topic>Base Sequence</topic><topic>Biological Physics</topic><topic>Computer Simulation</topic><topic>DNA - chemistry</topic><topic>Entropy</topic><topic>Models, Chemical</topic><topic>Models, Molecular</topic><topic>Models, Statistical</topic><topic>Molecular Sequence Data</topic><topic>Nucleic Acid Conformation</topic><topic>Nucleic Acid Denaturation</topic><topic>Physics</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Structure-Activity Relationship</topic><topic>Temperature</topic><topic>Thermodynamics</topic><toplevel>online_resources</toplevel><creatorcontrib>Joyeux, Marc</creatorcontrib><creatorcontrib>Buyukdagli, Sahin</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><jtitle>Physical review. E, Statistical, nonlinear, and soft matter physics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Joyeux, Marc</au><au>Buyukdagli, Sahin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation</atitle><jtitle>Physical review. E, Statistical, nonlinear, and soft matter physics</jtitle><addtitle>Phys Rev E Stat Nonlin Soft Matter Phys</addtitle><date>2005-11-01</date><risdate>2005</risdate><volume>72</volume><issue>5 Pt 1</issue><spage>051902</spage><epage>051902</epage><pages>051902-051902</pages><artnum>051902</artnum><issn>1539-3755</issn><eissn>1550-2376</eissn><abstract>We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbor calculations. Within this model, the finiteness of stacking enthalpies is shown to be responsible for the sharpness of calculated melting curves. Transfer-integral and molecular dynamics calculations are performed to demonstrate that the proposed model leads to a good agreement with known experimental results for both homogeneous and inhomogeneous DNA.</abstract><cop>United States</cop><pub>American Physical Society</pub><pmid>16383640</pmid><doi>10.1103/PhysRevE.72.051902</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1539-3755 |
| ispartof | Physical review. E, Statistical, nonlinear, and soft matter physics, 2005-11, Vol.72 (5 Pt 1), p.051902-051902, Article 051902 |
| issn | 1539-3755 1550-2376 |
| language | eng |
| recordid | cdi_hal_primary_oai_HAL_hal_00008215v2 |
| source | MEDLINE; American Physical Society Journals |
| subjects | Anisotropy Base Sequence Biological Physics Computer Simulation DNA - chemistry Entropy Models, Chemical Models, Molecular Models, Statistical Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation Physics Sequence Analysis, DNA - methods Structure-Activity Relationship Temperature Thermodynamics |
| title | Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-07T00%3A01%3A54IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_hal_p&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Dynamical%20model%20based%20on%20finite%20stacking%20enthalpies%20for%20homogeneous%20and%20inhomogeneous%20DNA%20thermal%20denaturation&rft.jtitle=Physical%20review.%20E,%20Statistical,%20nonlinear,%20and%20soft%20matter%20physics&rft.au=Joyeux,%20Marc&rft.date=2005-11-01&rft.volume=72&rft.issue=5%20Pt%201&rft.spage=051902&rft.epage=051902&rft.pages=051902-051902&rft.artnum=051902&rft.issn=1539-3755&rft.eissn=1550-2376&rft_id=info:doi/10.1103/PhysRevE.72.051902&rft_dat=%3Cproquest_hal_p%3E69048341%3C/proquest_hal_p%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=69048341&rft_id=info:pmid/16383640&rfr_iscdi=true |