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Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids
The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG mod...
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Published in: | The Journal of chemical physics 2015-12, Vol.143 (24), p.243148-243148 |
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description | The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed "pressure-matching" variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model. |
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Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model.</description><identifier>ISSN: 0021-9606</identifier><identifier>EISSN: 1089-7690</identifier><identifier>DOI: 10.1063/1.4937383</identifier><identifier>PMID: 26723633</identifier><language>eng</language><publisher>United States: American Institute of Physics</publisher><subject>ATOMIC MODELS ; ATOMS ; COMPARATIVE EVALUATIONS ; COMPRESSIBILITY ; COMPUTERIZED SIMULATION ; CORRELATIONS ; DENSITY ; Dependence ; ENERGY DENSITY ; EQUILIBRIUM ; FLUCTUATIONS ; Flux density ; Granulation ; HEPTANE ; Heptanes ; Heptanes - chemistry ; INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY ; LIQUIDS ; MANY-BODY PROBLEM ; Molecular Dynamics Simulation ; Molecular Structure ; Multiscale analysis ; Optimization ; POTENTIALS ; Pressure ; SPACE DEPENDENCE ; THERMODYNAMIC PROPERTIES ; Thermodynamics ; TOLUENE ; Toluene - chemistry ; Variation ; VARIATIONAL METHODS</subject><ispartof>The Journal of chemical physics, 2015-12, Vol.143 (24), p.243148-243148</ispartof><rights>2015 AIP Publishing LLC.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c341t-c750a15c323eb82ca6abb195e9634f9e451ae48edd54249f43ea8a555a3ed3ea3</citedby><cites>FETCH-LOGICAL-c341t-c750a15c323eb82ca6abb195e9634f9e451ae48edd54249f43ea8a555a3ed3ea3</cites><orcidid>0000-0001-9675-8489</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,782,784,885,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26723633$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/22493386$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Dunn, Nicholas J H</creatorcontrib><creatorcontrib>Noid, W G</creatorcontrib><title>Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids</title><title>The Journal of chemical physics</title><addtitle>J Chem Phys</addtitle><description>The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed "pressure-matching" variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model.</description><subject>ATOMIC MODELS</subject><subject>ATOMS</subject><subject>COMPARATIVE EVALUATIONS</subject><subject>COMPRESSIBILITY</subject><subject>COMPUTERIZED SIMULATION</subject><subject>CORRELATIONS</subject><subject>DENSITY</subject><subject>Dependence</subject><subject>ENERGY DENSITY</subject><subject>EQUILIBRIUM</subject><subject>FLUCTUATIONS</subject><subject>Flux density</subject><subject>Granulation</subject><subject>HEPTANE</subject><subject>Heptanes</subject><subject>Heptanes - chemistry</subject><subject>INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY</subject><subject>LIQUIDS</subject><subject>MANY-BODY PROBLEM</subject><subject>Molecular Dynamics Simulation</subject><subject>Molecular Structure</subject><subject>Multiscale analysis</subject><subject>Optimization</subject><subject>POTENTIALS</subject><subject>Pressure</subject><subject>SPACE DEPENDENCE</subject><subject>THERMODYNAMIC PROPERTIES</subject><subject>Thermodynamics</subject><subject>TOLUENE</subject><subject>Toluene - chemistry</subject><subject>Variation</subject><subject>VARIATIONAL METHODS</subject><issn>0021-9606</issn><issn>1089-7690</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><recordid>eNpFkU1v1DAQhi0EokvhwB9AlriARIrtsZ3kWCq-pEpc4Gw59oS6cuKtPw7LryftLuU0o5lnHmn0EvKaswvONHzkF3KEHgZ4QnacDWPX65E9JTvGBO9GzfQZeVHKLWOM90I-J2dC9wI0wI78-ZRqTUvX9tQlmwt2v7MNK3q6JI-x0HpjK7XOtWwrxgP1WFwOE24LpKXm5mrL-IHuM5by0NnVb67lYRCmEEM90DRvvoiuRZtpDHct-PKSPJttLPjqVM_Jry-ff159665_fP1-dXndOZC8dq5XzHLlQABOg3BW22nio8JRg5xHlIpblAN6r6SQ4ywB7WCVUhbQbz2ck7dHbyo1mOJCRXfj0rqiq0ZsJwCD3qh3R2qf013DUs0SisMY7YqpFcN7BYxzofh_4SN6m1petx-M4AJ63fP-nnp_pFxOpWSczT6HxeaD4czcx2a4OcW2sW9OxjYt6B_JfznBX9IOkuo</recordid><startdate>20151228</startdate><enddate>20151228</enddate><creator>Dunn, Nicholas J H</creator><creator>Noid, W G</creator><general>American Institute of Physics</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>8FD</scope><scope>H8D</scope><scope>L7M</scope><scope>7X8</scope><scope>OTOTI</scope><orcidid>https://orcid.org/0000-0001-9675-8489</orcidid></search><sort><creationdate>20151228</creationdate><title>Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids</title><author>Dunn, Nicholas J H ; Noid, W G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c341t-c750a15c323eb82ca6abb195e9634f9e451ae48edd54249f43ea8a555a3ed3ea3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>ATOMIC MODELS</topic><topic>ATOMS</topic><topic>COMPARATIVE EVALUATIONS</topic><topic>COMPRESSIBILITY</topic><topic>COMPUTERIZED SIMULATION</topic><topic>CORRELATIONS</topic><topic>DENSITY</topic><topic>Dependence</topic><topic>ENERGY DENSITY</topic><topic>EQUILIBRIUM</topic><topic>FLUCTUATIONS</topic><topic>Flux density</topic><topic>Granulation</topic><topic>HEPTANE</topic><topic>Heptanes</topic><topic>Heptanes - chemistry</topic><topic>INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY</topic><topic>LIQUIDS</topic><topic>MANY-BODY PROBLEM</topic><topic>Molecular Dynamics Simulation</topic><topic>Molecular Structure</topic><topic>Multiscale analysis</topic><topic>Optimization</topic><topic>POTENTIALS</topic><topic>Pressure</topic><topic>SPACE DEPENDENCE</topic><topic>THERMODYNAMIC PROPERTIES</topic><topic>Thermodynamics</topic><topic>TOLUENE</topic><topic>Toluene - chemistry</topic><topic>Variation</topic><topic>VARIATIONAL METHODS</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dunn, Nicholas J H</creatorcontrib><creatorcontrib>Noid, W G</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><jtitle>The Journal of chemical physics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dunn, Nicholas J H</au><au>Noid, W G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids</atitle><jtitle>The Journal of chemical physics</jtitle><addtitle>J Chem Phys</addtitle><date>2015-12-28</date><risdate>2015</risdate><volume>143</volume><issue>24</issue><spage>243148</spage><epage>243148</epage><pages>243148-243148</pages><issn>0021-9606</issn><eissn>1089-7690</eissn><abstract>The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed "pressure-matching" variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model.</abstract><cop>United States</cop><pub>American Institute of Physics</pub><pmid>26723633</pmid><doi>10.1063/1.4937383</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0001-9675-8489</orcidid></addata></record> |
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subjects | ATOMIC MODELS ATOMS COMPARATIVE EVALUATIONS COMPRESSIBILITY COMPUTERIZED SIMULATION CORRELATIONS DENSITY Dependence ENERGY DENSITY EQUILIBRIUM FLUCTUATIONS Flux density Granulation HEPTANE Heptanes Heptanes - chemistry INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY LIQUIDS MANY-BODY PROBLEM Molecular Dynamics Simulation Molecular Structure Multiscale analysis Optimization POTENTIALS Pressure SPACE DEPENDENCE THERMODYNAMIC PROPERTIES Thermodynamics TOLUENE Toluene - chemistry Variation VARIATIONAL METHODS |
title | Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids |
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