Dynamical models of molecular chains and efficient integration algorithms
Chains of point masses and chains of rigid bodies are used to model biological polymers. To investigate their dynamics we propose a method which allows an efficient realization of the constraints jointly with a simple and accurate integration of the free rigid body motion. The method is quite effect...
Uložené v:
| Vydané v: | Communications in nonlinear science & numerical simulation Ročník 14; číslo 2; s. 593 - 612 |
|---|---|
| Hlavní autori: | , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
Elsevier B.V
01.02.2009
|
| Predmet: | |
| ISSN: | 1007-5704, 1878-7274 |
| On-line prístup: | Získať plný text |
| Tagy: |
Pridať tag
Žiadne tagy, Buďte prvý, kto otaguje tento záznam!
|
| Abstract | Chains of point masses and chains of rigid bodies are used to model biological polymers. To investigate their dynamics we propose a method which allows an efficient realization of the constraints jointly with a simple and accurate integration of the free rigid body motion. The method is quite effective to evolute the geodesic flow of a rigid body chain and the global performance depends on the computational complexity of the algorithms used to compute the interaction forces. Our approach is suitable to describe a chain of rigid bodies immersed in a thermal bath. In the method we propose, the constraints are realized by hard springs whose elastic constant is set to maximize the energy dissipation rate of a Runge–Kutta integrator scheme. Moreover the use of local Lagrangian coordinates is introduced using the possibility of a continuous change of chart, such that the distance from the coordinate singularities is the highest possible. For a chain of point masses the numerical results are checked with another method where the constraints are exactly realized by means of Lagrangian coordinates. When the chain is subject to regular interactions potentials plus a thermal bath the exact and approximate constraints realization provide comparable results. |
|---|---|
| AbstractList | Chains of point masses and chains of rigid bodies are used to model biological polymers. To investigate their dynamics we propose a method which allows an efficient realization of the constraints jointly with a simple and accurate integration of the free rigid body motion. The method is quite effective to evolute the geodesic flow of a rigid body chain and the global performance depends on the computational complexity of the algorithms used to compute the interaction forces. Our approach is suitable to describe a chain of rigid bodies immersed in a thermal bath. In the method we propose, the constraints are realized by hard springs whose elastic constant is set to maximize the energy dissipation rate of a Runge-Kutta integrator scheme. Moreover the use of local Lagrangian coordinates is introduced using the possibility of a continuous change of chart, such that the distance from the coordinate singularities is the highest possible. For a chain of point masses the numerical results are checked with another method where the constraints are exactly realized by means of Lagrangian coordinates. When the chain is subject to regular interactions potentials plus a thermal bath the exact and approximate constraints realization provide comparable results. |
| Author | Rambaldi, Sandro Turchetti, Giorgio Bazzani, Armando Benedetti, Carlo Rossi, Luca |
| Author_xml | – sequence: 1 givenname: Armando surname: Bazzani fullname: Bazzani, Armando organization: Centro Interdipartimentale Galvani, Università di Bologna, Italy – sequence: 2 givenname: Carlo surname: Benedetti fullname: Benedetti, Carlo email: benedetti@bo.infn.it organization: Dipartimento di Fisica, Università di Bologna, Via Irnerio 46, 40126, Bologna, Italy – sequence: 3 givenname: Sandro surname: Rambaldi fullname: Rambaldi, Sandro organization: Centro Interdipartimentale Galvani, Università di Bologna, Italy – sequence: 4 givenname: Luca surname: Rossi fullname: Rossi, Luca organization: Dipartimento di Fisica, Università di Bologna, Via Irnerio 46, 40126, Bologna, Italy – sequence: 5 givenname: Giorgio surname: Turchetti fullname: Turchetti, Giorgio organization: Centro Interdipartimentale Galvani, Università di Bologna, Italy |
| BookMark | eNp9kbtOAzEQRS0UJELgC2i2ApoNfuz6UVCg8IoUiQZqy_HOJo527WBvkPL3OIQ61VzNnDsazb1EIx88IHRD8JRgwh82U-uTT1OKscidKcbsDI2JFLIUVFSjrPOkrAWuLtBlShucXaquxmj-vPemd9Z0RR8a6FIR2qw6sLvOxMKujfOpML4poG2ddeCHwvkBVtEMLvjCdKsQ3bDu0xU6b02X4Pq_TtDX68vn7L1cfLzNZ0-L0rJKDaUyjW2VBNpWzZIyYZXidYuXtpYUlFgSyykWilvTMCOl4VDLZU1Fvp_XjFg2QXfHvdsYvneQBt27ZKHrjIewS1oqTpkiQmXy9iTJKiGoVDKD9ydBwgWhgitFMsqOqI0hpQit3kbXm7jXBOtDFnqj_7LQhywOzZxFdj0eXfnB8OMg6nR4pYXGRbCDboI76f8F_vOVHQ |
| Cites_doi | 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T 10.1103/PhysRevE.48.1469 10.1126/science.282.5389.740 10.1146/annurev.physchem.48.1.545 10.1103/RevModPhys.75.23 10.1016/j.plrev.2004.03.001 10.1073/pnas.87.9.3526 10.1039/b605744f 10.1007/s10569-006-9037-6 10.1103/RevModPhys.72.259 |
| ContentType | Journal Article |
| Copyright | 2007 Elsevier B.V. |
| Copyright_xml | – notice: 2007 Elsevier B.V. |
| DBID | AAYXX CITATION 7SC 7TB 8FD FR3 JQ2 KR7 L7M L~C L~D |
| DOI | 10.1016/j.cnsns.2007.10.003 |
| DatabaseName | CrossRef Computer and Information Systems Abstracts Mechanical & Transportation Engineering Abstracts Technology Research Database Engineering Research Database ProQuest Computer Science Collection Civil Engineering Abstracts Advanced Technologies Database with Aerospace Computer and Information Systems Abstracts Academic Computer and Information Systems Abstracts Professional |
| DatabaseTitle | CrossRef Civil Engineering Abstracts Technology Research Database Computer and Information Systems Abstracts – Academic Mechanical & Transportation Engineering Abstracts ProQuest Computer Science Collection Computer and Information Systems Abstracts Engineering Research Database Advanced Technologies Database with Aerospace Computer and Information Systems Abstracts Professional |
| DatabaseTitleList | Civil Engineering Abstracts Civil Engineering Abstracts Civil Engineering Abstracts |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Applied Sciences |
| EISSN | 1878-7274 |
| EndPage | 612 |
| ExternalDocumentID | 10_1016_j_cnsns_2007_10_003 S1007570407002791 |
| GroupedDBID | --K --M -01 -0A -0I -0Y -SA -S~ .~1 0R~ 1B1 1RT 1~. 1~5 29F 4.4 457 4G. 5GY 5VR 5VS 7-5 71M 8P~ 92M 9D9 9DA AACTN AAEDT AAEDW AAIAV AAIKJ AAKOC AALRI AAOAW AAQFI AAQXK AAXUO ABAOU ABFNM ABJNI ABMAC ABNEU ABXDB ABYKQ ACAZW ACDAQ ACFVG ACGFS ACNNM ACRLP ADBBV ADEZE ADGUI ADMUD ADTZH AEBSH AECPX AEKER AENEX AFKWA AFTJW AFUIB AGHFR AGUBO AGYEJ AHJVU AIEXJ AIGVJ AIKHN AITUG AIVDX AJBFU AJOXV ALMA_UNASSIGNED_HOLDINGS AMFUW AMRAJ ARUGR ASPBG AVWKF AXJTR AZFZN BJAXD BKOJK BLXMC CAJEA CAJUS CCEZO CCVFK CHBEP CS3 CUBFJ DU5 EBS EFJIC EFLBG EJD EO8 EO9 EP2 EP3 FA0 FDB FEDTE FGOYB FIRID FNPLU FYGXN G-Q GBLVA HVGLF HZ~ IHE J1W JJJVA JUIAU KOM M41 MHUIS MO0 N9A O-L O9- OAUVE OGIMB OZT P-8 P-9 P2P PC. Q-- Q-0 Q38 R-A R-I R2- RIG ROL RPZ RT1 RT9 S.. SDF SDG SES SEW SPC SPCBC SPD SSQ SST SSW SSZ T5K T8Q T8Y U1F U1G U5A U5I U5K UHS ~G- ~LA 9DU AATTM AAXKI AAYWO AAYXX ABWVN ACLOT ACRPL ACVFH ADCNI ADNMO AEIPS AEUPX AFJKZ AFPUW AGQPQ AIGII AIIUN AKBMS AKRWK AKYEP ANKPU APXCP CITATION EFKBS ~HD 7SC 7TB 8FD FR3 JQ2 KR7 L7M L~C L~D |
| ID | FETCH-LOGICAL-c349t-9adcf98e2f4db237c9965f0bc582e97b1c620796cad3a88a6e58b5270076531c3 |
| ISICitedReferencesCount | 0 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000260204500023&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1007-5704 |
| IngestDate | Sun Sep 28 03:55:03 EDT 2025 Sat Sep 27 20:23:49 EDT 2025 Thu Oct 02 09:54:01 EDT 2025 Sat Nov 29 03:22:35 EST 2025 Fri Feb 23 02:29:59 EST 2024 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 2 |
| Keywords | Runge–Kutta 45.40.−f Rigidity constraints Flipping rule 07.05.Tp Hard springs 02.60.Lj 36.20.Fz Molecular chains |
| Language | English |
| License | https://www.elsevier.com/tdm/userlicense/1.0 |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-c349t-9adcf98e2f4db237c9965f0bc582e97b1c620796cad3a88a6e58b5270076531c3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Article-2 ObjectType-Feature-1 |
| PQID | 1671276991 |
| PQPubID | 23500 |
| PageCount | 20 |
| ParticipantIDs | proquest_miscellaneous_896239179 proquest_miscellaneous_34772898 proquest_miscellaneous_1671276991 crossref_primary_10_1016_j_cnsns_2007_10_003 elsevier_sciencedirect_doi_10_1016_j_cnsns_2007_10_003 |
| PublicationCentury | 2000 |
| PublicationDate | 2009-02-01 |
| PublicationDateYYYYMMDD | 2009-02-01 |
| PublicationDate_xml | – month: 02 year: 2009 text: 2009-02-01 day: 01 |
| PublicationDecade | 2000 |
| PublicationTitle | Communications in nonlinear science & numerical simulation |
| PublicationYear | 2009 |
| Publisher | Elsevier B.V |
| Publisher_xml | – name: Elsevier B.V |
| References | Pande, Grosberg, Tanaka (bib4) 2000; 72 Arribas, Elipe, Palacios (bib11) 2006; 96 Stillinger, Head-Gordon, Hirshfeld (bib1) 1993; 48 Brucale, Zuccheri, Rossi, Bazzani, Castellani, Samorí (bib12) 2006; 4 Banavar, Maritan (bib6) 2003; 75 Onuchic, Luthey-Schulten, Wolynes (bib5) 1997; 48 Hess, Bekker, Berendsen, Fraaije (bib8) 1997; 18 Duan, Kollman (bib10) 1998; 282 Forester, Smith (bib9) 1997; 19 Sneppen, Zocchi (bib2) 2005 Finkelstein, Galzitskaya (bib3) 2004; 1 Honeycutt, Thirumalai (bib7) 1990; 87 Pande (10.1016/j.cnsns.2007.10.003_bib4) 2000; 72 Banavar (10.1016/j.cnsns.2007.10.003_bib6) 2003; 75 Sneppen (10.1016/j.cnsns.2007.10.003_bib2) 2005 Onuchic (10.1016/j.cnsns.2007.10.003_bib5) 1997; 48 Hess (10.1016/j.cnsns.2007.10.003_bib8) 1997; 18 Brucale (10.1016/j.cnsns.2007.10.003_bib12) 2006; 4 Honeycutt (10.1016/j.cnsns.2007.10.003_bib7) 1990; 87 Duan (10.1016/j.cnsns.2007.10.003_bib10) 1998; 282 Arribas (10.1016/j.cnsns.2007.10.003_bib11) 2006; 96 Stillinger (10.1016/j.cnsns.2007.10.003_bib1) 1993; 48 Finkelstein (10.1016/j.cnsns.2007.10.003_bib3) 2004; 1 Forester (10.1016/j.cnsns.2007.10.003_bib9) 1997; 19 |
| References_xml | – volume: 19 start-page: 102 year: 1997 ident: bib9 publication-title: J Comp Chem – volume: 72 start-page: 259 year: 2000 ident: bib4 publication-title: Rev Mod Phys – volume: 87 start-page: 3526 year: 1990 ident: bib7 publication-title: Proc Natl Acad Sci – volume: 96 start-page: 239 year: 2006 ident: bib11 publication-title: Celest Mech Dyn Astr – volume: 282 start-page: 740 year: 1998 ident: bib10 publication-title: Science – volume: 4 start-page: 3427 year: 2006 ident: bib12 publication-title: Org Biomol Chem – volume: 1 start-page: 23 year: 2004 ident: bib3 publication-title: Phys Life Rev – volume: 48 start-page: 1469 year: 1993 ident: bib1 publication-title: Phys Rev E – volume: 48 start-page: 545 year: 1997 ident: bib5 publication-title: Annu Rev Phys Chem – volume: 18 start-page: 1463 year: 1997 ident: bib8 publication-title: J Comp Chem – year: 2005 ident: bib2 article-title: Physics in molecular biology – volume: 75 start-page: 23 year: 2003 ident: bib6 publication-title: Rev Mod Phys – volume: 18 start-page: 1463 year: 1997 ident: 10.1016/j.cnsns.2007.10.003_bib8 publication-title: J Comp Chem doi: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H – volume: 19 start-page: 102 year: 1997 ident: 10.1016/j.cnsns.2007.10.003_bib9 publication-title: J Comp Chem doi: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T – volume: 48 start-page: 1469 year: 1993 ident: 10.1016/j.cnsns.2007.10.003_bib1 publication-title: Phys Rev E doi: 10.1103/PhysRevE.48.1469 – volume: 282 start-page: 740 year: 1998 ident: 10.1016/j.cnsns.2007.10.003_bib10 publication-title: Science doi: 10.1126/science.282.5389.740 – year: 2005 ident: 10.1016/j.cnsns.2007.10.003_bib2 – volume: 48 start-page: 545 year: 1997 ident: 10.1016/j.cnsns.2007.10.003_bib5 publication-title: Annu Rev Phys Chem doi: 10.1146/annurev.physchem.48.1.545 – volume: 75 start-page: 23 year: 2003 ident: 10.1016/j.cnsns.2007.10.003_bib6 publication-title: Rev Mod Phys doi: 10.1103/RevModPhys.75.23 – volume: 1 start-page: 23 year: 2004 ident: 10.1016/j.cnsns.2007.10.003_bib3 publication-title: Phys Life Rev doi: 10.1016/j.plrev.2004.03.001 – volume: 87 start-page: 3526 year: 1990 ident: 10.1016/j.cnsns.2007.10.003_bib7 publication-title: Proc Natl Acad Sci doi: 10.1073/pnas.87.9.3526 – volume: 4 start-page: 3427 year: 2006 ident: 10.1016/j.cnsns.2007.10.003_bib12 publication-title: Org Biomol Chem doi: 10.1039/b605744f – volume: 96 start-page: 239 year: 2006 ident: 10.1016/j.cnsns.2007.10.003_bib11 publication-title: Celest Mech Dyn Astr doi: 10.1007/s10569-006-9037-6 – volume: 72 start-page: 259 year: 2000 ident: 10.1016/j.cnsns.2007.10.003_bib4 publication-title: Rev Mod Phys doi: 10.1103/RevModPhys.72.259 |
| SSID | ssj0016954 |
| Score | 1.8355345 |
| Snippet | Chains of point masses and chains of rigid bodies are used to model biological polymers. To investigate their dynamics we propose a method which allows an... |
| SourceID | proquest crossref elsevier |
| SourceType | Aggregation Database Index Database Publisher |
| StartPage | 593 |
| SubjectTerms | Algorithms Biological Computer simulation Flipping rule Hard springs Mathematical models Molecular chains Nonlinear dynamics Rigid-body dynamics Rigidity constraints Runge-Kutta method Runge–Kutta Thermal baths |
| Title | Dynamical models of molecular chains and efficient integration algorithms |
| URI | https://dx.doi.org/10.1016/j.cnsns.2007.10.003 https://www.proquest.com/docview/1671276991 https://www.proquest.com/docview/34772898 https://www.proquest.com/docview/896239179 |
| Volume | 14 |
| WOSCitedRecordID | wos000260204500023&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVESC databaseName: Elsevier SD Freedom Collection Journals 2021 customDbUrl: eissn: 1878-7274 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0016954 issn: 1007-5704 databaseCode: AIEXJ dateStart: 19960101 isFulltext: true titleUrlDefault: https://www.sciencedirect.com providerName: Elsevier |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV1Lb9NAEF6FlgMX3oi0PBaJnopR_NzdY9QmoigKCKUoN2t3bZdUjhNip6r6S_i5zL6ciCqoHLhYkZ_KzrezOzPfzCD0PmKioBn3vUBQ3cIM5pzIuOdHajcgYUuvs96_j8h4TKdT9rXT-eVyYa5KUlX0-pot_6uo4RwIW6XO_oO425fCCfgNQocjiB2OdxL8qekxr7JCVJcbTdWYuya4KtFXkWKUuzzX1SMUF8DVjNDU5PJisZo1P2wVc1fEYDuPRFNoK1NjA17pMoMUiKq1iQCVx_VsbjuDbZylNzemg9RxX6UqZIv2CijcLG8Ms-CEr8r2yjc-F7zMZsZ5rYorbCJEMJu1V2Ft2UbOd8Ec3blVt8pRGhPTgLjVx9EW7oIt5RqbXop2nU4M_frWEmC8EZcfZVVXtalRqel74WbFc1H-8Zd0eD4apZPBdHIUDpc_PdWNTEXtj8JTg4x7aD8gMQOVv98_G0w_txGqhOkOe-0_cBWtNHfw1rd37Xr-WP_1pmbyGD201gjuGxQ9QZ28eooeWcsEW71fP0NnLaiwARVeFLgFFTagwiAf3IIKb4EKb0D1HJ0PB5OTT55twuHJMGKNx3gmC0bzoIgyEYREgoEcFz0hYxrkjAhfJkGPsETyLOSU8iSPqYgVnYEkoN9l-ALtASLzlwhHKqjLeM7huUiQgvJepmpNSeFzwUTSRR_cIKVLU2sldSTEy1SPqeqaStRJGNMuStxAphbpZhuYAhT-_uA7N-wpKFMVIeNVvljXqZ8QPyAJ2Exd9HbHPWEEBilltIvwjjsoA5uCwUp3cIcPHaIHm5nxCu01q3X-Gt2XV82sXr2xqPsN_KGyYQ |
| linkProvider | Elsevier |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Dynamical+models+of+molecular+chains+and+efficient+integration+algorithms&rft.jtitle=Communications+in+nonlinear+science+%26+numerical+simulation&rft.au=Bazzani%2C+Armando&rft.au=Benedetti%2C+Carlo&rft.au=Rambaldi%2C+Sandro&rft.au=Rossi%2C+Luca&rft.date=2009-02-01&rft.issn=1007-5704&rft.volume=14&rft.issue=2&rft.spage=593&rft.epage=612&rft_id=info:doi/10.1016%2Fj.cnsns.2007.10.003&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1007-5704&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1007-5704&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1007-5704&client=summon |