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The plant component develops a biophysical model incorporating a spreading force, analyzing shape approximations, energy minimization, and a modified Helfrich energy while exploring polysaccharide deposition and required synthesis rates. The viral component conducts simulations of SARS-CoV-2 variants, estimating binding free energy and hydrogen-bonding behavior, assessing antibody escape and ACE2 weakening, studying furin cleavage domains, and evaluating a decoy therapeutic concept using truncated human ACE2.",{"@graph":63,"@context":118},[64,80,101],{"@type":65,"itemListElement":66},"BreadcrumbList",[67,71,74,77],{"item":68,"name":69,"@type":70,"position":9},"https://docshare.wps.com","Home","ListItem",{"item":72,"name":10,"@type":70,"position":73},"https://docshare.wps.com/template/",2,{"item":75,"name":11,"@type":70,"position":76},"https://docshare.wps.com/template/presentations/",3,{"item":78,"name":59,"@type":70,"position":79},"https://docshare.wps.com/template/studies-in-computational-biophysics-sars-cov-2-and-plant-cell-plate-maturation-dissertation/564047/",4,{"url":78,"name":59,"@type":81,"image":82,"author":87,"headline":59,"publisher":90,"fileFormat":93,"inLanguage":57,"description":61,"dateModified":94,"datePublished":95,"encodingFormat":93,"isAccessibleForFree":96,"interactionStatistic":97},"DigitalDocument",{"url":83,"@type":84,"width":85,"height":86},"https://docshare.wps.com/thumbnails/studies-in-computational-biophysics-sars-cov-2-and-plant-cell-plate-maturation-dissertation/564047.png","ImageObject",442,249,{"name":88,"@type":89},"dhado","Person",{"url":68,"name":91,"@type":92},"DocShare","Organization","application/pdf","2026-10-19","2026-10-12",true,{"@type":98,"interactionType":99,"userInteractionCount":9},"InteractionCounter",{"@type":100},"ViewAction",{"@type":102,"mainEntity":103},"FAQPage",[104,110,114],{"name":105,"@type":106,"acceptedAnswer":107},"What model is proposed for plant cell plate maturation in this dissertation?","Question",{"text":108,"@type":109},"A biophysical model incorporates a spreading force, including shape approximations, energy minimization, and a modified Helfrich energy, alongside analysis of polysaccharide deposition.","Answer",{"name":111,"@type":106,"acceptedAnswer":112},"Which computational methods are used for the SARS-CoV-2 in silico studies?",{"text":113,"@type":109},"The work includes classical molecular dynamics and endpoint free energy analysis, including MM/GBSA and hydrogen-bond counting, with ColabFold/AlphaFold used for specific binding-domain predictions.",{"name":115,"@type":106,"acceptedAnswer":116},"What do the SARS-CoV-2 simulations conclude about Omicron-related behavior?",{"text":117,"@type":109},"The simulations address broad antibody escape, weakened ACE2 binding, and modest Furin cleavage, supported by binding strength metrics such as hydrogen bonds and binding free energy.","https://schema.org",{"og:url":78,"og:type":120,"og:title":59,"og:site_name":91,"og:description":61},"article",{"robots":122,"canonical":78},"index,follow",{"doc_id":124,"site_id":56},564047,1792382265,{"code":4,"msg":5,"data":127},{"doc_id":124,"user_id":128,"nickname":88,"user_avatar":129,"doc_module":9,"category_id":8,"category_name":11,"doc_title":59,"doc_description":61,"doc_content":130,"file_id":131,"file_url":132,"file_type":133,"file_size":134,"view_count":9,"is_deleted":4,"is_public":9,"is_downloadable":9,"audit_status":9,"page_count":135,"language":136,"language_code":57,"site_id":56,"html_lang":57,"table_of_contents":137,"faqs":138,"seo_title":139,"seo_description":61,"update_tm":140,"read_time":141},5909893218464,"https://ap-avatar.wpscdn.com/davatar_085a072bc5b1113ac321206ff7593b45","Studies in Computational Biophysics: SARS-CoV-2 and Plant Cell Plate Maturation  \nBy  \nMuhammad Zaki Jawaid  \nDissertation  \nSubmitted in partial satisfaction of the requirements for the degree of  \nDoctor of Philosophy  \nin  \nPhysics  \nin the  \nOffice of Graduate Studies  \nof the  \nUniversity of California  \nDavis  \nApproved:  \n\n| Daniel L. Cox, Chair |\n| --- |\n| Georgia Drakakaki |\n\nRajiv R. P. Singh Committee in Charge  \n2022  \nCopyright © 2022 by Muhammad Zaki Jawaid  \nAll rights reserved.  \nFor Ammi, Abbu, Adeel, Mony, and Sidra.  \nContents  \nList [of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vi](of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vi)  \nList of Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxiv  \nAbstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxv  \nAcknowledgments .................................. xxvii  \n1 Introduction to Part 1: Physical Models of Biological Membranes 1  \n1.1 Background and Motivation ......................... 1  \n1.2 Understanding membrane biophysics using analytical and computational tools ...................................... 4  \n1.3 Objectives of Part 1 ............................. 5  \n2 A Biophysical Model for Plant Cell Plate Maturation Based on the Contribution of a Spreading Force 8  \n2. 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8  \n2.2 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11  \n2.2.1 Shape Approximation ........................ 11  \n2.2.2 Naming convention of different approximated conformations ... 12  \n2.2.3 Energy minimization . . . . . . . . . . . . . . . . . . . . . . . . . 12  \n2.2.4 Modified Helfrich energy ....................... 14  \n2.2.5 Model parameter ranges and the need of a spreading force .... 15  \n2.2.6 A spreading force is required for cell plate maturation while its absence energetically favors the accumulation of tubular and vesicular networks ................................ 16  \n2.2.7 Exploring polysaccharide deposition as a contributing factor to cell plate maturation and model prediction ............... 19  \n2.2.8 Estimating the required polysaccharide synthesis rates for a stabilizing/spreading force ........................ 22  \n2.3 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23  \n2.4 Supplemental Information . . . . . . . . . . . . . . . . . . . . . . . . . . 26  \n2.4. 1 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . 26  \n2.4.2 Supplemental Results ........................ 31  \n3 Introduction to Part 2: In Silico Studies of SARS-CoV-2 43  \n3.1 Background and Motivation ......................... 43  \n3.2 Methods: Studying molecular interactions using in silico approaches ... 44  \n3.2.1 Classical Molecular Dynamics .................... 44  \n3.2.2 Estimating binding free energy using MM/GBSA ......... 47  \n3.2.3 Hbond Count . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48  \n3.3 Objectives of Part 2 ............................. 49  \n4 SARS-CoV-2 Omicron simulations: broad antibody escape, weakened ACE2 binding, modest Furin cleavage 50  \n4. 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50  \n4.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51  \n4.2. 1 Molecular Models . . . . . . . . . . . . . . . . . . . . . . . . . . . 51  \n4.2.2 Molecular Dynamics ......................... 52  \n4.2.3 Endpoint Free Energy Analysis ................... 53  \n4.2.4 Use of ColabFold/AlphaFold for Furin binding domain ...... 54  \n4.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54  \n4.3.1 Binding Strengths: HBond and Binding Free Energy ....... 54  \n4.3.2 Mutations leading to Ab Escape and weaker ACE2 binding ... 54  \n4.3.3 Mutations in the FCD . . . . . . . . . . . . . . . . . ","cbCaifeKncKnX77B","https://ap.wps.com/l/cbCaifeKncKnX77B","pdf",13674395,130,"English","# Introduction to Part 1: Physical Models of Biological Membranes\n## Background and Motivation\n## Understanding membrane biophysics using analytical and computational tools\n## Objectives of Part 1\n# A Biophysical Model for Plant Cell Plate Maturation Based on the Contribution of a Spreading Force\n## Introduction\n## Results\n## Discussion\n# Introduction to Part 2: In Silico Studies of SARS-CoV-2\n## Background and Motivation\n## Methods: Studying molecular interactions using in silico approaches\n## Objectives of Part 2\n# SARS-CoV-2 Omicron simulations: broad antibody escape, weakened ACE2 binding, modest Furin cleavage\n## Introduction\n## Materials and Methods\n## Results\n## Discussion\n# Computational study of the furin cleavage domain of SARS-CoV-2: delta binds strongest of extant variants\n## Introduction\n## Results\n## Discussion\n# Computational design of a novel decoy therapeutic agent for SARSCoV-2 using truncated human angiotensin converting enzyme 2\n## Introduction\n## Results\n## Discussion\n# Conclusion","[{\"question\":\"What model is proposed for plant cell plate maturation in this dissertation?\",\"answer\":\"A biophysical model incorporates a spreading force, including shape approximations, energy minimization, and a modified Helfrich energy, alongside analysis of polysaccharide deposition.\"},{\"question\":\"Which computational methods are used for the SARS-CoV-2 in silico studies?\",\"answer\":\"The work includes classical molecular dynamics and endpoint free energy analysis, including MM/GBSA and hydrogen-bond counting, with ColabFold/AlphaFold used for specific binding-domain predictions.\"},{\"question\":\"What do the SARS-CoV-2 simulations conclude about Omicron-related behavior?\",\"answer\":\"The simulations address broad antibody escape, weakened ACE2 binding, and modest Furin cleavage, supported by binding strength metrics such as hydrogen bonds and binding free energy.\"}]","Studies in Computational Biophysics: SARS-CoV-2 and Plant Cell Plate Maturation - Dissertation | PDF",1791840001,46]