subject:(Coarse grained models)

Rice University

1. Yrazu, Fernando Miguel. Cracking the spectrins' riddle.

Degree: PhD, Chemical Engineering, 2017, Rice University

URL: http://hdl.handle.net/1911/105473

► The contrasting folding characteristics of three protein segments, each belonging to the same three-helix bundle family, have been the subject of experimental studies for more… (more)

Subjects/Keywords: coarse grained models; spectrins; structure based models

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APA (6^th Edition):

Yrazu, F. M. (2017). Cracking the spectrins' riddle. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/105473

Chicago Manual of Style (16^th Edition):

Yrazu, Fernando Miguel. “Cracking the spectrins' riddle.” 2017. Doctoral Dissertation, Rice University. Accessed January 16, 2021. http://hdl.handle.net/1911/105473.

MLA Handbook (7^th Edition):

Yrazu, Fernando Miguel. “Cracking the spectrins' riddle.” 2017. Web. 16 Jan 2021.

Vancouver:

Yrazu FM. Cracking the spectrins' riddle. [Internet] [Doctoral dissertation]. Rice University; 2017. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1911/105473.

Council of Science Editors:

Yrazu FM. Cracking the spectrins' riddle. [Doctoral Dissertation]. Rice University; 2017. Available from: http://hdl.handle.net/1911/105473

Rice University

2. Yrazu, Fernando Miguel. Cracking the spectrins' riddle.

Degree: PhD, Engineering, 2017, Rice University

URL: http://hdl.handle.net/1911/105472

► The contrasting folding characteristics of three protein segments, each belonging to the same three-helix bundle family, have been the subject of experimental studies for more… (more)

Subjects/Keywords: coarse grained models; spectrins; structure based models

Record Details Similar Records Cite « Share

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Yrazu, F. M. (2017). Cracking the spectrins' riddle. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/105472

Chicago Manual of Style (16^th Edition):

Yrazu, Fernando Miguel. “Cracking the spectrins' riddle.” 2017. Doctoral Dissertation, Rice University. Accessed January 16, 2021. http://hdl.handle.net/1911/105472.

MLA Handbook (7^th Edition):

Yrazu, Fernando Miguel. “Cracking the spectrins' riddle.” 2017. Web. 16 Jan 2021.

Vancouver:

Yrazu FM. Cracking the spectrins' riddle. [Internet] [Doctoral dissertation]. Rice University; 2017. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1911/105472.

Council of Science Editors:

Yrazu FM. Cracking the spectrins' riddle. [Doctoral Dissertation]. Rice University; 2017. Available from: http://hdl.handle.net/1911/105472

Arizona State University

3. Agrawal, Vipin. Predicting Structure-Property Relationships in Polymers through the Development of Thermodynamically Consistent Coarse-Grained Molecular Models.

Degree: Mechanical Engineering, 2016, Arizona State University

URL: http://repository.asu.edu/items/40183

► Improved knowledge connecting the chemistry, structure, and properties of polymers is necessary to develop advanced materials in a materials-by-design approach. Molecular dynamics (MD) simulations can… (more)

▼ Improved knowledge connecting the chemistry, structure, and properties of polymers is necessary to develop advanced materials in a materials-by-design approach. Molecular dynamics (MD) simulations can provide tremendous insight into how the fine details of chemistry, molecular architecture, and microstructure affect many physical properties; however, they face well-known restrictions in their applicable temporal and spatial scales. These limitations have motivated the development of computationally-efficient, coarse-grained methods to investigate how microstructural details affect thermophysical properties. In this dissertation, I summarize my research work in structure-based coarse-graining methods to establish the link between molecular-scale structure and macroscopic properties of two different polymers. Systematically coarse-grained models were developed to study the viscoelastic stress response of polyurea, a copolymer that segregates into rigid and viscous phases, at time scales characteristic of blast and impact loading. With the application of appropriate scaling parameters, the coarse-grained models can predict viscoelastic properties with a speed up of 5-6 orders of magnitude relative to the atomistic MD models. Coarse-grained models of polyethylene were also created to investigate the thermomechanical material response under shock loading. As structure-based coarse-grained methods are generally not transferable to states different from which they were calibrated at, their applicability for modeling non-equilibrium processes such as shock and impact is highly limited. To address this problem, a new model is developed that incorporates many-body interactions and is calibrated across a range of different thermodynamic states using a least square minimization scheme. The new model is validated by comparing shock Hugoniot properties with atomistic and experimental data for polyethylene. Lastly, a high fidelity coarse-grained model of polyethylene was constructed that reproduces the joint-probability distributions of structural variables such as the distributions of bond lengths and bond angles between sequential coarse-grained sites along polymer chains. This new model accurately represents the structure of both the amorphous and crystal phases of polyethylene and enabling investigation of how polymer processing such as cold-drawing and bulk crystallization affect material structure at significantly larger time and length scales than traditional molecular simulations.

Subjects/Keywords: Engineering; Mechanical engineering; Coarse-Grained models; Polyethylene; Polymers; Polyurea

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APA (6^th Edition):

Agrawal, V. (2016). Predicting Structure-Property Relationships in Polymers through the Development of Thermodynamically Consistent Coarse-Grained Molecular Models. (Doctoral Dissertation). Arizona State University. Retrieved from http://repository.asu.edu/items/40183

Chicago Manual of Style (16^th Edition):

Agrawal, Vipin. “Predicting Structure-Property Relationships in Polymers through the Development of Thermodynamically Consistent Coarse-Grained Molecular Models.” 2016. Doctoral Dissertation, Arizona State University. Accessed January 16, 2021. http://repository.asu.edu/items/40183.

MLA Handbook (7^th Edition):

Agrawal, Vipin. “Predicting Structure-Property Relationships in Polymers through the Development of Thermodynamically Consistent Coarse-Grained Molecular Models.” 2016. Web. 16 Jan 2021.

Vancouver:

Agrawal V. Predicting Structure-Property Relationships in Polymers through the Development of Thermodynamically Consistent Coarse-Grained Molecular Models. [Internet] [Doctoral dissertation]. Arizona State University; 2016. [cited 2021 Jan 16]. Available from: http://repository.asu.edu/items/40183.

Council of Science Editors:

Agrawal V. Predicting Structure-Property Relationships in Polymers through the Development of Thermodynamically Consistent Coarse-Grained Molecular Models. [Doctoral Dissertation]. Arizona State University; 2016. Available from: http://repository.asu.edu/items/40183

Duke University

4. Altan, Irem. Understanding the Structure and Formation of Protein Crystals Using Computer Simulation and Theory .

Degree: 2019, Duke University

URL: http://hdl.handle.net/10161/20129

► The complexity of protein-protein interactions enables proteins to self-assemble into a rich array of structures, such as virus capsids, amyloid fibers, amorphous aggregates, and… (more)

▼ The complexity of protein-protein interactions enables proteins to self-assemble into a rich array of structures, such as virus capsids, amyloid fibers, amorphous aggregates, and protein crystals. While some of these assemblies form under biological conditions, protein crystals, which are crucial for obtaining protein structures from diffraction methods, do not typically form readily. Crystallizing proteins thus requires significant trial and error, limiting the number of structures that can be obtained and studied. Understanding how proteins interact with one another and with their environment would allow us to elucidate the physicochemical processes that lead to crystal formation and provide insight into other self-assembly phenomena. This thesis explores this problem from a soft matter theory and simulation perspective. We first attempt to reconstruct the water structure inside a protein crystal using all-atom molecular dynamics simulations with the dual goal of benchmarking empirical water models and increasing the information extracted from X-ray diffraction data. We find that although water models recapitulate the radial distribution of water around protein atoms, they fall short of reproducing its orientational distribution. Nevertheless, high-intensity peaks in water density are sufficiently well captured to detect the protonation states of certain solvent-exposed residues. We next study a human gamma D-crystallin mutant, the crystals of which have inverted solubility. We parameterize a patchy particle and show that the temperature-dependence of the patch that contains the solubility inverting mutation reproduces the experimental phase diagram. We also consider the hypothesis that the solubility is inverted because of increased surface hydrophobicity, and show that even though this scenario is thermodynamically plausible, microscopic evidence for it is lacking, partly because our understanding of water as a biomolecular solvent is limited. Finally, we develop computational methods to understand the self-assembly of a two-dimensional protein crystal and show that specialized Monte Carlo moves are necessary for proper sampling. Advisors/Committee Members: Charbonneau, Patrick (advisor).

Subjects/Keywords: Computational chemistry; Biophysics; Statistical physics; biomolecular solvation; coarse-grained models; protein crystallization; self-assembly

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APA (6^th Edition):

Altan, I. (2019). Understanding the Structure and Formation of Protein Crystals Using Computer Simulation and Theory . (Thesis). Duke University. Retrieved from http://hdl.handle.net/10161/20129

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Altan, Irem. “Understanding the Structure and Formation of Protein Crystals Using Computer Simulation and Theory .” 2019. Thesis, Duke University. Accessed January 16, 2021. http://hdl.handle.net/10161/20129.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Altan, Irem. “Understanding the Structure and Formation of Protein Crystals Using Computer Simulation and Theory .” 2019. Web. 16 Jan 2021.

Vancouver:

Altan I. Understanding the Structure and Formation of Protein Crystals Using Computer Simulation and Theory . [Internet] [Thesis]. Duke University; 2019. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10161/20129.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Altan I. Understanding the Structure and Formation of Protein Crystals Using Computer Simulation and Theory . [Thesis]. Duke University; 2019. Available from: http://hdl.handle.net/10161/20129

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Edinburgh

5. Gkeka, Paraskevi. Molecular dynamics studies of peptide-membrane interactions : insights from coarse-grained models.

Degree: PhD, 2010, University of Edinburgh

URL: http://hdl.handle.net/1842/4652

► Peptide-membrane interactions play an important role in a number of biological processes, such as antimicrobial defence mechanisms, viral translocation, membrane fusion and functions ofmembrane proteins.… (more)

▼ Peptide-membrane interactions play an important role in a number of biological processes, such as antimicrobial defence mechanisms, viral translocation, membrane fusion and functions ofmembrane proteins. In particular, amphipathic α-helical peptides comprise a large family of membrane-active peptides that could exhibit a broad range of biological activities. A membrane, interacting with an amphipathic α-helical peptide, may experience a number of possible structural transitions, including stretching, reorganization of lipid molecules, formation of defects, transient and stable pores, formation of vesicles, endo- and pinocytosis and other phenomena. Naturally, theoretical and experimental studies of these interactions have been an intense on-going area of research. However, complete understanding of the relationship between the structure of the peptide and themechanismof interaction it induces, as well asmolecular details of this process, still remain elusive. Lack of this knowledge is a key challenge in our efforts to elucidate some of the biological functions of membrane active peptides or to design peptides with tailored functionalities that can be exploited in drug delivery or antimicrobial strategies. In principle,molecular dynamics is a powerful research tool to study peptide-membrane interactions, which can provide a detailed description of these processes on molecular level. However, a model operating on the appropriate time and length scale is imperative in this description. In this study, we adopt a coarse-grained approach where the accessible simulation time and length scales reach microseconds and tens of nanometers, respectively. Thus, the two key objectives of this study are to validate the applicability of the adopted coarse-grained approach to the study of peptide-membrane interactions and to provide a systematic description of these interactions as a function of peptide structure and surface chemistry. We applied the adopted strategy to a range of peptide systems, whose behaviour has been well established in either experiments or detailed atomistic simulations and outlined the scope and applicability of the coarse-grained model. We generated some useful insights on the relationship between the structure of the peptides and themechanism of peptide-membrane interactions. Particularly interesting results have been obtained for LS3, a membrane spanning peptide, with a propensity to self-assembly into ion-conducting channels. Firstly, we captured, for the first time, the complete process of self-assembly of LS3 into a hexameric ion-conducting channel and explored its properties. The channel has structure of a barrel-stave pore with peptides aligned along the lipid tails. However, we discovered that a shorter version of the peptide leads to a more disordered, less stable structure often classified as a toroidal pore. This link between two types of pores has been established for the first time and opens interesting opportunities in tuning peptide structures for a particular pore-inducing mechanism. We also…

Subjects/Keywords: 572; molecular dynamics; simulation; coarse-grained models

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APA (6^th Edition):

Gkeka, P. (2010). Molecular dynamics studies of peptide-membrane interactions : insights from coarse-grained models. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/4652

Chicago Manual of Style (16^th Edition):

Gkeka, Paraskevi. “Molecular dynamics studies of peptide-membrane interactions : insights from coarse-grained models.” 2010. Doctoral Dissertation, University of Edinburgh. Accessed January 16, 2021. http://hdl.handle.net/1842/4652.

MLA Handbook (7^th Edition):

Gkeka, Paraskevi. “Molecular dynamics studies of peptide-membrane interactions : insights from coarse-grained models.” 2010. Web. 16 Jan 2021.

Vancouver:

Gkeka P. Molecular dynamics studies of peptide-membrane interactions : insights from coarse-grained models. [Internet] [Doctoral dissertation]. University of Edinburgh; 2010. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1842/4652.

Council of Science Editors:

Gkeka P. Molecular dynamics studies of peptide-membrane interactions : insights from coarse-grained models. [Doctoral Dissertation]. University of Edinburgh; 2010. Available from: http://hdl.handle.net/1842/4652

Rice University

6. Truong, Ha Huynh. Exploring the Folding Energy Landscape: Designed, Simplified, and α-helical Membrane Proteins.

Degree: PhD, Natural Sciences, 2016, Rice University

URL: http://hdl.handle.net/1911/96518

► This thesis discusses our efforts in using the energy landscape theory and coarse-grained molecular dynamics protein folding models to explore the folding energy landscape of… (more)

Subjects/Keywords: Protein folding; Protein structure prediction; Binding interface prediction; Coarse-grained models; Molecular dynamics; Energy Landscape Theory

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APA (6^th Edition):

Truong, H. H. (2016). Exploring the Folding Energy Landscape: Designed, Simplified, and α-helical Membrane Proteins. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/96518

Chicago Manual of Style (16^th Edition):

Truong, Ha Huynh. “Exploring the Folding Energy Landscape: Designed, Simplified, and α-helical Membrane Proteins.” 2016. Doctoral Dissertation, Rice University. Accessed January 16, 2021. http://hdl.handle.net/1911/96518.

MLA Handbook (7^th Edition):

Truong, Ha Huynh. “Exploring the Folding Energy Landscape: Designed, Simplified, and α-helical Membrane Proteins.” 2016. Web. 16 Jan 2021.

Vancouver:

Truong HH. Exploring the Folding Energy Landscape: Designed, Simplified, and α-helical Membrane Proteins. [Internet] [Doctoral dissertation]. Rice University; 2016. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1911/96518.

Council of Science Editors:

Truong HH. Exploring the Folding Energy Landscape: Designed, Simplified, and α-helical Membrane Proteins. [Doctoral Dissertation]. Rice University; 2016. Available from: http://hdl.handle.net/1911/96518

University of Iowa

7. Li, Shuxiang. Computer simulations exploring conformational preferences of short peptides and developing a bacterial chromosome model.

Degree: PhD, Biochemistry, 2017, University of Iowa

URL: https://ir.uiowa.edu/etd/5960

► Computer simulations provide a potentially powerful complement to conventional experimental techniques in elucidating the structures, dynamics and interactions of macromolecules. In this thesis, I… (more)

▼ Computer simulations provide a potentially powerful complement to conventional experimental techniques in elucidating the structures, dynamics and interactions of macromolecules. In this thesis, I present three applications of computer simulations to investigate important biomolecules with sizes ranging from two-residue peptides, to proteins, and to whole chromosome structures. First, I describe the results of 441 independent explicit-solvent molecular dynamics (MD) simulations of all possible two-residue peptides that contain the 20 standard amino acids with neutral and protonated histidine. 3JHNHα coupling constants and δHα chemical shifts calculated from the MD simulations correlated quite well with recently published experimental measurements for a corresponding set of two-residue peptides. Neighboring residue effects (NREs) on the average 3JHNHα and δHα values of adjacent residues were also reasonably well reproduced. The intrinsic conformational preferences of each residue, and their NREs on the conformational preferences of adjacent residues, were analyzed. Finally, these NREs were compared with corresponding effects observed in a coil library and the average β-turn preferences of all residue types were determined. Second, I compare the abilities of three derivatives of the Amber ff99SB force field to reproduce a recent report of 3JHNHα scalar coupling constants for hundreds of two-residue peptides. All-atom MD simulations of 256 two-residue peptides were performed and the results showed that a recently-developed force field (RSFF2) produced a dramatic improvement in the agreement with experimental 3JHNHα coupling constants. I further show that RSFF2 also improved modestly agreement with experimental 3JHNHα coupling constants of five model proteins. However, an analysis of NREs on the 3JHNHα coupling constants of the two-residue peptides indicated little difference between the force fields’ abilities to reproduce experimental NREs. I speculate that this might indicate limitations in the force fields’ descriptions of nonbonded interactions between adjacent side chains or with terminal capping groups. Finally, coarse-grained (CG) models and multi-scale modeling methods are used to develop structural models of entire E. coli chromosomes confined within the experimentally-determined volume of the nucleoid. The final resolution of the chromosome structures built here was one-nucleotide-per-bead (1 NTB), which represents a significant increase in resolution relative to previously published CG chromosome models, in which one bead corresponds to hundreds or even thousands of basepairs. Based on the high-resolution final 1 NTB structures, important physical properties such as major and minor groove widths, distributions of local DNA bending angles, and topological parameters (Linking Number (Lk), Twist (Tw) and Writhe (Wr)) were accurately computed and compared with experimental measurements or predictions from a worm-like chain (WLC) model. All these analyses indicated that the chromosome… Advisors/Committee Members: Elcock, Adrian H. (supervisor).

Subjects/Keywords: Chromosome model; Coarse-grained models; DNA supercoiling; Intrinsic conformational preference; Molecular dynamics simulation; Neighboring residue effects; Biochemistry

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APA (6^th Edition):

Li, S. (2017). Computer simulations exploring conformational preferences of short peptides and developing a bacterial chromosome model. (Doctoral Dissertation). University of Iowa. Retrieved from https://ir.uiowa.edu/etd/5960

Chicago Manual of Style (16^th Edition):

Li, Shuxiang. “Computer simulations exploring conformational preferences of short peptides and developing a bacterial chromosome model.” 2017. Doctoral Dissertation, University of Iowa. Accessed January 16, 2021. https://ir.uiowa.edu/etd/5960.

MLA Handbook (7^th Edition):

Li, Shuxiang. “Computer simulations exploring conformational preferences of short peptides and developing a bacterial chromosome model.” 2017. Web. 16 Jan 2021.

Vancouver:

Li S. Computer simulations exploring conformational preferences of short peptides and developing a bacterial chromosome model. [Internet] [Doctoral dissertation]. University of Iowa; 2017. [cited 2021 Jan 16]. Available from: https://ir.uiowa.edu/etd/5960.

Council of Science Editors:

Li S. Computer simulations exploring conformational preferences of short peptides and developing a bacterial chromosome model. [Doctoral Dissertation]. University of Iowa; 2017. Available from: https://ir.uiowa.edu/etd/5960

8. Goldtzvik, Yonathan Yitshak. UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS.

Degree: Biophysics (BIPH), 2017, University of Maryland

URL: http://hdl.handle.net/1903/20356

► Molecular motors are indispensable machines that are in charge of transporting cargoes within living cells. Despite recent advances in the study of these molecules, there… (more)

▼ Molecular motors are indispensable machines that are in charge of transporting cargoes within living cells. Despite recent advances in the study of these molecules, there is much that we still do not understand regarding the underlying mechanisms that allow them to efficiently move cargoes along polar cellular filaments. In this thesis, I report my investigation on two motor proteins superfamilies, dyneins and kinesins. Using theoretical modeling, we provide fundamental insight into their function. Dynein is a large motor that transports cargo along microtubules towards their negative pole. Unlike other motors, such as conventional kinesin, the motility of dynein is highly stochastic. We developed a novel theoretical approach, which reproduces a wide variety of its properties, including the unique step size distribution observed in experiments. Furthermore, our model enables us to derive several simple expressions that can be fitted to experiment, thus providing a physical interpretation. A less understood aspect of dynein is the complex set of allosteric transitions in response to ATP binding and hydrolysis, and microtubule binding. The resulting conformational transitions propel the motor forward to the minus end of the microtubule. Furthermore, its activity is regulated by external strain. Using coarse grained Brownian dynamics simulations, we show that a couple of insert loops in the AAA2, a sub domain in the AAA+ ring in the motor domain, play an important role in several of the alllosteric pathways. Kinesins are highly processive motor proteins that transport cargo along microtubules toward their positive poles. Experiments show that the kinesin motor domains propel the motor forward by passing each other in a hand-over-hand motion. However, there is a debate as to whether the motor domains do so in a symmetrical manner or an asymmetrical motion. Using coarse grained Brownian dynamics simulations of the kinesin dimer, we show that the kinesin stepping mechanism is influenced by the size of its cargo. Furthermore, we find that stepping occurs by a combinations of both the symmetric and asymmetric mechanisms. The results I present in this thesis are a testimony that theoretical approaches are invaluable to the study of molecular motors. Advisors/Committee Members: Thirumalai, Devarajan (advisor).

Subjects/Keywords: Biophysics; Biology; Molecular physics; Brownian Dynamics Simulations; Coarse Grained Models; Dynein; Kinesin; Molecular Motors; Motor Proteins

10 more images…

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APA (6^th Edition):

Goldtzvik, Y. Y. (2017). UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS. (Thesis). University of Maryland. Retrieved from http://hdl.handle.net/1903/20356

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Goldtzvik, Yonathan Yitshak. “UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS.” 2017. Thesis, University of Maryland. Accessed January 16, 2021. http://hdl.handle.net/1903/20356.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Goldtzvik, Yonathan Yitshak. “UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS.” 2017. Web. 16 Jan 2021.

Vancouver:

Goldtzvik YY. UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS. [Internet] [Thesis]. University of Maryland; 2017. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1903/20356.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Goldtzvik YY. UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS. [Thesis]. University of Maryland; 2017. Available from: http://hdl.handle.net/1903/20356

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Lund

9. Kurut Sabanoglu, Anil. Anisotropic Protein Interactions in Salt Solutions and at Interfaces: Coarse Grained Modeling.

Degree: 2014, University of Lund

URL: https://lup.lub.lu.se/record/4610736 ; https://portal.research.lu.se/ws/files/5797055/4610765.pdf

► Anisotropic protein interactions have a strong orientation dependence resulting from an uneven distribution of charged and hydrophobic residues on the protein surface. They play an… (more)

Subjects/Keywords: Theoretical Chemistry; Anisotropic interactions; protein electrostatics; phase association; surface adsorption; coarse grained models; Monte Carlo simulations

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APA (6^th Edition):

Kurut Sabanoglu, A. (2014). Anisotropic Protein Interactions in Salt Solutions and at Interfaces: Coarse Grained Modeling. (Doctoral Dissertation). University of Lund. Retrieved from https://lup.lub.lu.se/record/4610736 ; https://portal.research.lu.se/ws/files/5797055/4610765.pdf

Chicago Manual of Style (16^th Edition):

Kurut Sabanoglu, Anil. “Anisotropic Protein Interactions in Salt Solutions and at Interfaces: Coarse Grained Modeling.” 2014. Doctoral Dissertation, University of Lund. Accessed January 16, 2021. https://lup.lub.lu.se/record/4610736 ; https://portal.research.lu.se/ws/files/5797055/4610765.pdf.

MLA Handbook (7^th Edition):

Kurut Sabanoglu, Anil. “Anisotropic Protein Interactions in Salt Solutions and at Interfaces: Coarse Grained Modeling.” 2014. Web. 16 Jan 2021.

Vancouver:

Kurut Sabanoglu A. Anisotropic Protein Interactions in Salt Solutions and at Interfaces: Coarse Grained Modeling. [Internet] [Doctoral dissertation]. University of Lund; 2014. [cited 2021 Jan 16]. Available from: https://lup.lub.lu.se/record/4610736 ; https://portal.research.lu.se/ws/files/5797055/4610765.pdf.

Council of Science Editors:

Kurut Sabanoglu A. Anisotropic Protein Interactions in Salt Solutions and at Interfaces: Coarse Grained Modeling. [Doctoral Dissertation]. University of Lund; 2014. Available from: https://lup.lub.lu.se/record/4610736 ; https://portal.research.lu.se/ws/files/5797055/4610765.pdf

University of Lund

10. Henriques, Joao. Modeling and simulation of intrinsically disordered proteins.

Degree: 2016, University of Lund

URL: https://lup.lub.lu.se/record/9284f1ea-e14d-43fd-95d9-362a30aea721 ; https://portal.research.lu.se/ws/files/16773089/thesis_no_papers.pdf

► This work is primarily about the development, validation and application of computer simulation models for intrinsically disordered proteins, both in solution and in the presence… (more)

▼ This work is primarily about the development, validation and application of computer simulation models for intrinsically disordered proteins, both in solution and in the presence of uniformly charged, ideal surfaces. The models in question are either coarse-grained or atomistic in nature, and their applications are dependent on the specific purpose of each study. Both, Metropolis Monte Carlo and molecular dynamics simulations were employed to execute them.In regard to the coarse-grained models, it was found that a simple physical model can be used to mimic the properties of flexible proteins, helping to understand how and why these proteins adsorb to surfaces under certain conditions. The same model later shown that two disordered proteins from different sources (saliva and milk) possess similar structural and thermodynamic properties in solution and when adsorbed to surfaces, thus being hypothesized that it may be possible to use one of them as a substitute for the other under a pharmaceutical context.After a first indication that the atomistic models used until recently for the simulation of well-folded proteins may not be applicable to their disordered counterparts, it was then confirmed - by evaluating several such models against experimental evidence - that these models do indeed produce overly collapsed IDP conformational ensembles. New models, favoring protein–water over protein–protein interactions, were then shown to effectively produce more extended conformations, which are in much better agreement with each other and with experimental evidence. One of the new atomistic models was then used to perform the structural characterization of a disordered peptide conjugated to a small molecule, which has been shown to possess promising therapeutical applications. The value of computer simulations is well illustrated in this study, as the insight obtainable from experiment was limited and it was only through the analysis of the simulations that a possible link between the average conjugate structure and its increased antifungal activity is established.

Subjects/Keywords: Theoretical Chemistry; Intrinsically disordered proteins; Coarse-grained models; Atomistic models; Metropolis Monte Carlo simulations; Molecular dynamics simulations; Sampling; Conformational analysis; Charge regulation; Surface adsorption

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APA (6^th Edition):

Henriques, J. (2016). Modeling and simulation of intrinsically disordered proteins. (Doctoral Dissertation). University of Lund. Retrieved from https://lup.lub.lu.se/record/9284f1ea-e14d-43fd-95d9-362a30aea721 ; https://portal.research.lu.se/ws/files/16773089/thesis_no_papers.pdf

Chicago Manual of Style (16^th Edition):

Henriques, Joao. “Modeling and simulation of intrinsically disordered proteins.” 2016. Doctoral Dissertation, University of Lund. Accessed January 16, 2021. https://lup.lub.lu.se/record/9284f1ea-e14d-43fd-95d9-362a30aea721 ; https://portal.research.lu.se/ws/files/16773089/thesis_no_papers.pdf.

MLA Handbook (7^th Edition):

Henriques, Joao. “Modeling and simulation of intrinsically disordered proteins.” 2016. Web. 16 Jan 2021.

Vancouver:

Henriques J. Modeling and simulation of intrinsically disordered proteins. [Internet] [Doctoral dissertation]. University of Lund; 2016. [cited 2021 Jan 16]. Available from: https://lup.lub.lu.se/record/9284f1ea-e14d-43fd-95d9-362a30aea721 ; https://portal.research.lu.se/ws/files/16773089/thesis_no_papers.pdf.

Council of Science Editors:

Henriques J. Modeling and simulation of intrinsically disordered proteins. [Doctoral Dissertation]. University of Lund; 2016. Available from: https://lup.lub.lu.se/record/9284f1ea-e14d-43fd-95d9-362a30aea721 ; https://portal.research.lu.se/ws/files/16773089/thesis_no_papers.pdf

University of Michigan

11. Gagnon, Jessica K. Flexible Receptor Docking Method Development and Molecular Dynamics Studies Towards Targeting Dynamic Protein Surfaces.

Degree: PhD, Chemistry, 2015, University of Michigan

URL: http://hdl.handle.net/2027.42/116710

► Protein-protein interactions are integral for cellular function, playing a huge role in processes such as cell signaling and transcription regulation. Targeting these essential interactions with… (more)

▼ Protein-protein interactions are integral for cellular function, playing a huge role in processes such as cell signaling and transcription regulation. Targeting these essential interactions with small molecule inhibitors is important from a biochemical and pharmaceutical perspective. This dissertation contains chapters on multidisciplinary, collaborative approaches to investigate transcription regulation as well as MHC Class I assembly, which is involved in the immune response. During these projects I applied a variety of computational tools and developed a new docking methodology in CHARMM (CDOCKER). This new version of CDOCKER incorporates receptor flexibility through maintaining selected side-chains in an all-atom representation, while the rest of the receptor is represented as a grid. This version of CDOCKER includes a newly implemented sampling protocol that leads to docking accuracy that is competitive with and even exceeds that of other commonly used docking software in redocking trials. This docking methodology was applied to identify a putative ATP binding on calreticulin (CRT), a chaperone key to MHC Class I assembly and the immune response. This work was a collaborative effort with the Raghavan research group at the University of Michigan and was the first demonstration that CRT both binds and catalyzes ATP. We added further automated functionality to the CDOCKER method to investigate small- molecules covalently bound to receptors in collaboration with the Mapp research group at the University of Michigan. The tethering method was able to stabilize the dynamic surface of GACKIX for crystallization and modeled small-molecules that were identified experimentally but were unable to be crystalized. Finally, we employed Gō-like models to investigate the allosteric signaling between the two binding sites on GACKIX. These studies demonstrated the positive allostery arises from the first peptide paying the entropic cost of binding for the second peptide. The developments in docking methodology within CHARMM allow for targeting of fluid receptors such as GACKIX. A multidisciplinary approach to investigate complex cellular processes such as transcription regulation or the immune response takes advantage of the strengths of the different approaches and leads to advancements in understanding of the process at different size scales, atomistic to in vitro and even in vivo. Advisors/Committee Members: Brooks III, Charles L (committee member), Carlson, Heather A (committee member), Kubarych, Kevin J (committee member), Mapp, Anna K (committee member).

Subjects/Keywords: flexible receptor docking development; CHARMM simulation package; computational biophysics; protein-ligand interactions; KIX domain of CREB binding protein; coarse-grained go-like models; Chemistry; Science

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gagnon, J. K. (2015). Flexible Receptor Docking Method Development and Molecular Dynamics Studies Towards Targeting Dynamic Protein Surfaces. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/116710

Chicago Manual of Style (16^th Edition):

Gagnon, Jessica K. “Flexible Receptor Docking Method Development and Molecular Dynamics Studies Towards Targeting Dynamic Protein Surfaces.” 2015. Doctoral Dissertation, University of Michigan. Accessed January 16, 2021. http://hdl.handle.net/2027.42/116710.

MLA Handbook (7^th Edition):

Gagnon, Jessica K. “Flexible Receptor Docking Method Development and Molecular Dynamics Studies Towards Targeting Dynamic Protein Surfaces.” 2015. Web. 16 Jan 2021.

Vancouver:

Gagnon JK. Flexible Receptor Docking Method Development and Molecular Dynamics Studies Towards Targeting Dynamic Protein Surfaces. [Internet] [Doctoral dissertation]. University of Michigan; 2015. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/2027.42/116710.

Council of Science Editors:

Gagnon JK. Flexible Receptor Docking Method Development and Molecular Dynamics Studies Towards Targeting Dynamic Protein Surfaces. [Doctoral Dissertation]. University of Michigan; 2015. Available from: http://hdl.handle.net/2027.42/116710

University of Lund

12. Thuresson, Axel. Swelling and Microstructure of Nanoplatelet Systems.

Degree: 2017, University of Lund

URL: https://lup.lub.lu.se/record/ba0361c9-7492-41cc-9287-5d8534490f5d ; https://portal.research.lu.se/ws/files/25069090/Axel_Thuresson_spikfil.pdf

► Many clay minerals consist of charged nanoplatelets that swell in an aqueous solution. The swelling and the microstructure depend on the type of clay mineral… (more)

▼ Many clay minerals consist of charged nanoplatelets that swell in an aqueous solution. The swelling and the microstructure depend on the type of clay mineral but are also dependent on, for example, the ionic composition and the temperature of the solution. The synthetic clay mineral Laponite and the natural clay mineral montmorillonite have been studied experimentally and theoretically. The swelling has been studied by swelling pressure measurements in a test cell and the microstructure has been studied by small angle X-ray scattering (SAXS), and cryogenic transmission electron microscopy (cryo-TEM). Theoretically, Metropolis Monte Carlo (MC) simulations and molecular dynamics (MD) simulations were used to study the electrostatic interactions between the platelets and an adsorbing polymer was also included. Coarse-grained models have been used to represent the platelets, the ions, and the polymers. This thesis can be divided into three parts:In the first part, the tactoid formation (platelets aggregating face-to-face with an equidistant separation) and the microstructure of negatively charged platelets were investigated by simulations. Tactoid formation was promoted by increasing the platelet surface charge density, the platelet size, the ion valency, and the salt concentration. With enough added salt, an isodesmic model was suggested that gives a monotonically decaying distribution of aggregation numbers.In the second part, the tactoid formation and the microstructure were investigated with respect to the platelet size for flocculated Laponite and montmorillonite at elevated salt concentrations, with and without the addition of the polymer polyethylene glycol (PEG). The smaller Laponite platelets give rise to a more disordered microstructure compared to the larger montmorillonite platelets. The number of platelets per tactoid increased with the addition of PEG. The simulations suggested that the role of the salt is to screen the repulsive interactions between the platelets, and the role of the polymer is to bridge between the platelets.In the third part, the temperature response of Na/Ca montmorillonite was investigated. It was found that the swelling pressure increased with increased temperature if sodium is the dominating counterion whereas the opposite was found if calcium is the dominating counterion. The simulations predicted this behavior and it was shown that the results could be explained by a single equation.

Subjects/Keywords: Theoretical Chemistry; Nanoplatelets; Model clay system; Coarse grained models; Statistical mechanics; MC simulations; MD simulations; SAXS; Cryo-TEM; Laponite; Montmorillonite; Swelling; Tactoid

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APA (6^th Edition):

Thuresson, A. (2017). Swelling and Microstructure of Nanoplatelet Systems. (Doctoral Dissertation). University of Lund. Retrieved from https://lup.lub.lu.se/record/ba0361c9-7492-41cc-9287-5d8534490f5d ; https://portal.research.lu.se/ws/files/25069090/Axel_Thuresson_spikfil.pdf

Chicago Manual of Style (16^th Edition):

Thuresson, Axel. “Swelling and Microstructure of Nanoplatelet Systems.” 2017. Doctoral Dissertation, University of Lund. Accessed January 16, 2021. https://lup.lub.lu.se/record/ba0361c9-7492-41cc-9287-5d8534490f5d ; https://portal.research.lu.se/ws/files/25069090/Axel_Thuresson_spikfil.pdf.

MLA Handbook (7^th Edition):

Thuresson, Axel. “Swelling and Microstructure of Nanoplatelet Systems.” 2017. Web. 16 Jan 2021.

Vancouver:

Thuresson A. Swelling and Microstructure of Nanoplatelet Systems. [Internet] [Doctoral dissertation]. University of Lund; 2017. [cited 2021 Jan 16]. Available from: https://lup.lub.lu.se/record/ba0361c9-7492-41cc-9287-5d8534490f5d ; https://portal.research.lu.se/ws/files/25069090/Axel_Thuresson_spikfil.pdf.

Council of Science Editors:

Thuresson A. Swelling and Microstructure of Nanoplatelet Systems. [Doctoral Dissertation]. University of Lund; 2017. Available from: https://lup.lub.lu.se/record/ba0361c9-7492-41cc-9287-5d8534490f5d ; https://portal.research.lu.se/ws/files/25069090/Axel_Thuresson_spikfil.pdf

Penn State University

13. Yuan, Hongyan. A SOLVENT-FREE COARSE-GRAINED MODEL FOR BIOLOGICAL AND BIOMIMETIC FLUID MEMBRANES.

Degree: 2010, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/11093

► Mechanics of biological membranes is involved in numerous intriguing biophysical and biological cellular phenomena of different length scales. On the length scale much larger than… (more)

▼ Mechanics of biological membranes is involved in numerous intriguing biophysical and biological cellular phenomena of different length scales. On the length scale much larger than the membrane thickness, fluid bilayer membranes or biomimetic membranes, from the mechanics viewpoint, can be simplified as “thin fluid shells” with their mechanical behaviors dictated by only a few effective mechanical properties such as bilayer membrane bending rigidity, area compression modulus, in-plane viscosity, line tension between two different components, and spontaneous curvature. Solving mechanics problems of the fluid membranes with complicated shapes or multi-components in static or dynamic conditions largely resorts to computer simulations. There are two approaches to establish a simulation model for fluid membranes at the large length scale. One is the numerical implementations of the continuum membrane models. The other is the highly coarse-grained inter-particle interaction-based membrane simulation models. One of the drawbacks of the former class of models is that extra or dedicated computational effort is needed to take into account the in-plane fluidity and topological changes. Conversely, the latter class of models can naturally capture the in-plane fluidity and viscosity, and simulate topological changes. On the other hand, the disadvantage of the inter-particle interaction-based models is that they suffer length scale limitations due to the small intrinsic particle size, which is not the case for the former class of models. In this study, we established a one-particle-thick fluid membrane model, where each particle represents a cluster of lipid molecules. The model features an inter-particle pair potential with the interaction strength weighed by the relative particle orientations. The model is solvent-free, and the orientation dependence of the inter-particle pair potential substitutes for the hydrophobic effect. Particles can robustly self-assemble into fluid membranes with experimentally relevant membrane properties such as bending rigidity. Three potential parameters separately and effectively control diffusivity, bending rigidity, and spontaneous curvature of the model membrane. The high level of coarse-graining and the efficiency of the model enable the studies of large-scale membrane problems that are typically not accessible by previous coarse-grained models. This model is well suited to study the mechanics of both homogeneous and heterogeneous fluid vesicles, such as morphology and shape changes in static or dynamic situations. In order for this solvent-free membrane model to be biologically or experimentally relevant in the fluid vesicle case where the vesicle volume is controlled by the osmotic pressure, the membrane model is extended to the fluid vesicle case by incorporating a volume-control algorithm based on an external potential associated with vesicle volume. The instantaneous volume of the vesicles is calculated via an efficient, accurate and robust local triangulation algorithm. The… Advisors/Committee Members: Sulin Zhang, Dissertation Advisor/Co-Advisor, Sulin Zhang, Committee Chair/Co-Chair, Peter J Butler, Committee Member, Long Qing Chen, Committee Member, Bruce Gluckman, Committee Member, Bernhard R Tittmann, Committee Member.

Subjects/Keywords: lipid bilayer; fluid membranes; bending rigidity; coarse-grained; solvent-free; membrane models; molecular dynamics simulations; anisotropic interparticle interaction; liquid crystal

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APA (6^th Edition):

Yuan, H. (2010). A SOLVENT-FREE COARSE-GRAINED MODEL FOR BIOLOGICAL AND BIOMIMETIC FLUID MEMBRANES. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/11093

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Yuan, Hongyan. “A SOLVENT-FREE COARSE-GRAINED MODEL FOR BIOLOGICAL AND BIOMIMETIC FLUID MEMBRANES.” 2010. Thesis, Penn State University. Accessed January 16, 2021. https://submit-etda.libraries.psu.edu/catalog/11093.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Yuan, Hongyan. “A SOLVENT-FREE COARSE-GRAINED MODEL FOR BIOLOGICAL AND BIOMIMETIC FLUID MEMBRANES.” 2010. Web. 16 Jan 2021.

Vancouver:

Yuan H. A SOLVENT-FREE COARSE-GRAINED MODEL FOR BIOLOGICAL AND BIOMIMETIC FLUID MEMBRANES. [Internet] [Thesis]. Penn State University; 2010. [cited 2021 Jan 16]. Available from: https://submit-etda.libraries.psu.edu/catalog/11093.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Yuan H. A SOLVENT-FREE COARSE-GRAINED MODEL FOR BIOLOGICAL AND BIOMIMETIC FLUID MEMBRANES. [Thesis]. Penn State University; 2010. Available from: https://submit-etda.libraries.psu.edu/catalog/11093

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

14. Schafer, Nicholas Peter. Folding, Binding, Misfolding and Aggregation with AWSEM.

Degree: PhD, Natural Sciences, 2014, Rice University

URL: http://hdl.handle.net/1911/77518

► This thesis discusses our recent results using the Associative-memory, Water-mediated, Structure and Energy Model (AWSEM), an optimized, coarse-grained molecular dynamics protein folding model, to fold,… (more)

Subjects/Keywords: Protein folding; Coarse-grained models; Optimization; Misfolding; Aggregation; Binding interface prediction; Protein structure prediction

…particularly those interested in using coarse-grained molecular dynamics models that are optimized… …Accurate coarse-grained structure prediction models can be used to investigate a wide range of… …review [39, 40, 41, 42]. In the case of coarse-grained models, the Hamiltonian… …correlation between optimized parameters in a x coarse-grained Hamiltonian and experimental… …review of the results of the AMH/AMC/AMW/AWSEM family of coarse-grained molecular dynamics…

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Schafer, N. P. (2014). Folding, Binding, Misfolding and Aggregation with AWSEM. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/77518

Chicago Manual of Style (16^th Edition):

Schafer, Nicholas Peter. “Folding, Binding, Misfolding and Aggregation with AWSEM.” 2014. Doctoral Dissertation, Rice University. Accessed January 16, 2021. http://hdl.handle.net/1911/77518.

MLA Handbook (7^th Edition):

Schafer, Nicholas Peter. “Folding, Binding, Misfolding and Aggregation with AWSEM.” 2014. Web. 16 Jan 2021.

Vancouver:

Schafer NP. Folding, Binding, Misfolding and Aggregation with AWSEM. [Internet] [Doctoral dissertation]. Rice University; 2014. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1911/77518.

Council of Science Editors:

Schafer NP. Folding, Binding, Misfolding and Aggregation with AWSEM. [Doctoral Dissertation]. Rice University; 2014. Available from: http://hdl.handle.net/1911/77518

15. Boz, Mustafa Burak. Modeling and simulations of single stranded rna viruses.

Degree: PhD, Chemistry and Biochemistry, 2012, Georgia Tech

URL: http://hdl.handle.net/1853/44815

► The presented work is the application of recent methodologies on modeling and simulation of single stranded RNA viruses. We first present the methods of modeling… (more)

▼ The presented work is the application of recent methodologies on modeling and simulation of single stranded RNA viruses. We first present the methods of modeling RNA molecules using the coarse-grained modeling package, YUP. Coarse-grained models simplify complex structures such as viruses and let us study general behavior of the complex biological systems that otherwise cannot be studied with all-atom details. Second, we modeled the first all-atom T=3, icosahedral, single stranded RNA virus, Pariacoto virus (PaV). The x-ray structure of PaV shows only 35% of the total RNA genome and 88% of the capsid. We modeled both missing portions of RNA and protein. The final model of the PaV demonstrated that the positively charged protein N- terminus was located deep inside the RNA. We propose that the positively charged N- terminal tails make contact with the RNA genome and neutralize the negative charges in RNA and subsequently collapse the RNA/protein complex into an icosahedral virus. Third, we simulated T=1 empty capsids using a coarse-grained model of three capsid proteins as a wedge-shaped triangular capsid unit. We varied the edge angle and the potentials of the capsid units to perform empty capsid assembly simulations. The final model and the potential are further improved for the whole virus assembly simulations. Finally, we performed stability and assembly simulations of the whole virus using coarse-grained models. We tested various strengths of RNA-protein tail and capsid protein-capsid protein attractions in our stability simulations and narrowed our search for optimal potentials for assembly. The assembly simulations were carried out with two different protocols: co-transcriptional and post-transcriptional. The co-transcriptional assembly protocol mimics the assembly occurring during the replication of the new RNA. Proteins bind the partly transcribed RNA in this protocol. The post-transcriptional assembly protocol assumes that the RNA is completely transcribed in the absence of proteins. Proteins later bind to the fully transcribed RNA. We found that both protocols can assemble viruses, when the RNA structure is compact enough to yield a successful virus particle. The post-transcriptional protocol depends more on the compactness of the RNA structure compared to the co-transcriptional assembly protocol. Viruses can exploit both assembly protocols based on the location of RNA replication and the compactness of the final structure of the RNA. Advisors/Committee Members: Stephen C. Harvey (Committee Chair), Adegboyega Oyelere (Committee Member), Loren Williams (Committee Member), Rigoberto Hernandez (Committee Member), Roger Wartell (Committee Member).

Subjects/Keywords: Virus assembly; Coarse-grained models; RNA virus; RNA viruses; RNA; Nucleic acids

…modeling RNA molecules using the coarse-grained modeling package, YUP. Coarse-grained models… …stability and assembly simulations of the whole virus using coarse-grained models. We tested… …proteins from RNA viruses are used to encapsidate a charged cargo using coarse-grained models… …tractability. In these cases, investigators often resort to lower-resolution coarse-grained models… …possible. Therefore, it is necessary to use coarse-grained models. This is not a serious…

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Boz, M. B. (2012). Modeling and simulations of single stranded rna viruses. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/44815

Chicago Manual of Style (16^th Edition):

Boz, Mustafa Burak. “Modeling and simulations of single stranded rna viruses.” 2012. Doctoral Dissertation, Georgia Tech. Accessed January 16, 2021. http://hdl.handle.net/1853/44815.

MLA Handbook (7^th Edition):

Boz, Mustafa Burak. “Modeling and simulations of single stranded rna viruses.” 2012. Web. 16 Jan 2021.

Vancouver:

Boz MB. Modeling and simulations of single stranded rna viruses. [Internet] [Doctoral dissertation]. Georgia Tech; 2012. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1853/44815.

Council of Science Editors:

Boz MB. Modeling and simulations of single stranded rna viruses. [Doctoral Dissertation]. Georgia Tech; 2012. Available from: http://hdl.handle.net/1853/44815

16. Cabeza de Vaca López, Israel. Mapping biophysics through enhanced Monte Carlo techniques.

Degree: Departament de Física, 2015, Universitat Politècnica de Catalunya

URL: http://hdl.handle.net/10803/334172

► Aquesta tesi es centra en l'estudi de les interaccions moleculars amb detall atomic i es divideix en un capítol d'introducció i quatre capítols que fan… (more)

▼ Aquesta tesi es centra en l'estudi de les interaccions moleculars amb detall atomic i es divideix en un capítol d'introducció i quatre capítols que fan referència a diferents problemes i enfocaments metodològics. Tots ells se centren en el desenvolupament i millora dels algoritmes computacionals de Monte Carlo per estudiar, de manera eficient, el comportament d'aquests sistemes a un nivell mecànica molecular clàssica. Els quatre problemes biofísics estudiats en aquesta tesi són: acoblament induït entre la proteïna-lligand i entre DNA-lligant per comprendre el mecanisme d'unió, resposta de les proteïnes a l'estirament, i la generació/puntuació d'acoblament entre poses proteïna-proteïna. La tesi s'organitza de la següent manera: El primer capítol correspon a l'estat de l'art en mètodes computacionals per estudiar les interaccions biofísiques, que és el punt de partida d'aquesta tesi. El nostre PELE algoritme i els principals mètodes estàndard com ara la dinàmica molecular s'explicaran en detall. El capítol dos es centra en les principals modificacions PELE per afegir noves característiques, com ara l'addició d'un nou camp de força, solvent implícit i modes normals per aquests estudis de simulació d'ADN. Es fa un estudi, comparació i validació de les conformacions generades per sis fragments d'ADN representatius amb PELE utilitzant dinàmica molecular com a referència. El tercer capítol està dedicat a l'aplicació dels nous mètodes implementats i provats en PELE per estudiar les interaccions proteïna-lligand i la interacció lligand-DNA utilitzant quatre sistemes. En primer lloc, se estudia la unió a proteïnes GUN4 combinant PELE i simulacions de dinàmica molecular. A més, es proposa un acoblament que ha sigut corroborat per una nova estructura cristal·lina publicada durant el procés de revisió de l'estudi mostrant l'exactitud de les nostres prediccions. En el segon projecte, hem utilitzat la nostra versió millorada de PELE per generar el primer model estructural d'una glucosa alfa substrat 1,6-bisfosfat unit a la fosfomanomutasa humana 2, que demostra que aquest lligant pot adoptar dues orientacions de baiza energia. El tercer projecte és l'estudi de les interaccions d'ADN lligant per tres medicaments cisplatí on se avalua l'energia lliure d'unió utilitzant Markov States Models. Es mostren excel·lents resultats respecte d'altres mètodes d'energia lliure estudiats amb dinàmica molecular. L'últim projecte és l'estudi de l'intercalador d'ADN anomenat daunomicina on es simula i estudia el procés d'unió amb PELE. El capítol 4 es centra en l'estudi computacional dels perfils d'extensió de la força durant el desplegament de la proteïna. Hem afegit una restricció harmònica dinàmica seguint un procediment similar al aplicat en dinàmica molecular en el nostre algoritme Monte Carlo per fixar o moure alguns àtoms seleccionats obligant a desplegar la proteïna en una direcció definida. Aquesta tècnica s'ha implementat i comparat amb dinàmica molecular per les proteïnes ubiquitina i azurin. D'altra banda, hem afegit aquesta modificació… Advisors/Committee Members: [email protected] (authoremail), false (authoremailshow), Guallar i Tasies, Víctor (director), true (authorsendemail).

Subjects/Keywords: Monte Carlo; Molecular dynamics; PELE; Induced fit docking; Markov states models; Coarse grained; Protein/DNA-ligand interactions; Intercalators; 53; 577

…induced fit docking, Markov States Models, Coarse grained, Protein/DNA-ligand interactions… …Molecular dynamics MC Monte Carlo CG Coarse grained MSM Markov State Models NA Nucleic… …dynamic level. The range of the coarse-grained models is quite diverse, going from few atoms… …1.3.2 Coarse grained models In molecular simulations, coarse grained (CG) methods… …multiscale approach based on a coarse-grained model and all-atom refinement to generate and score…

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cabeza de Vaca López, I. (2015). Mapping biophysics through enhanced Monte Carlo techniques. (Thesis). Universitat Politècnica de Catalunya. Retrieved from http://hdl.handle.net/10803/334172

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Cabeza de Vaca López, Israel. “Mapping biophysics through enhanced Monte Carlo techniques.” 2015. Thesis, Universitat Politècnica de Catalunya. Accessed January 16, 2021. http://hdl.handle.net/10803/334172.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Cabeza de Vaca López, Israel. “Mapping biophysics through enhanced Monte Carlo techniques.” 2015. Web. 16 Jan 2021.

Vancouver:

Cabeza de Vaca López I. Mapping biophysics through enhanced Monte Carlo techniques. [Internet] [Thesis]. Universitat Politècnica de Catalunya; 2015. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10803/334172.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Cabeza de Vaca López I. Mapping biophysics through enhanced Monte Carlo techniques. [Thesis]. Universitat Politècnica de Catalunya; 2015. Available from: http://hdl.handle.net/10803/334172

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

17. Delort, Bartholomé. Études par dynamique moléculaire de l’interaction de Récepteurs Couplés aux Protéines-G avec leurs partenaires extra et intra-cellulaires : Molecular dynamics studies of the interaction between G-Protein-Coupled Receptors and their extra and intra-cellular partners.

Degree: Docteur es, Ingénierie Biomoléculaire, 2018, Montpellier

URL: http://www.theses.fr/2018MONTS113

►

Les Récepteurs Couplés aux Protéines-G forment la plus importante famille de protéines membranaires chez l’homme et sont impliqués dans de nombreux processus de signalisation cellulaire.… (more)

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Les Récepteurs Couplés aux Protéines-G forment la plus importante famille de protéines membranaires chez l’homme et sont impliqués dans de nombreux processus de signalisation cellulaire. Aussi, ils forment un vivier très important de cibles thérapeutiques, déjà identifiées ou potentielles. L’activation d’un RCPG est amorcée par la liaison d’un ligand dans sa partie extra-cellulaire, modifiant ainsi ses propriétés dynamiques intrinsèques. Ces changements structuraux vont alors se répercuter le long des domaines trans-membranaires et promouvoir la dissociation de la Protéine-G hétéro-trimérique, de l’autre côté de la membrane, propageant ainsi le signal au compartiment intra-cellulaire. Ce processus peut être modulé par la liaison de nombreux autres partenaires des RCPGs. Malgré de nombreuses données structurales existantes, ces mécanismes restent encore mal connus à l’échelle moléculaire. Ainsi, la dynamique moléculaire s’est révélée être un outil formidable pour mieux comprendre ces mécanismes. Toutefois, les échelles de taille et de temps requises pour discuter de la dynamique de ces systèmes membranaires limitent ces études aux laboratoires ayant accès à une très grande puissance de calcul. L’objectif des travaux présentés dans ce manuscrit a été de prédire et de mieux comprendre la dynamique d’interaction de différents récepteurs de cette famille avec leurs partenaires, en développant un protocole de dynamique moléculaire, peu coûteux en ressources de calcul, combinant le champ de forces gros-grains MARTINI à un protocole de dynamique moléculaire « Replica-Exchange ».Dans un premier temps, nous présentons la validation de notre protocole pour la prédiction de la liaison de peptides à leur récepteur avec l’étude des peptides Neurotensine, agoniste du Récepteur de la Neurotensine-1, et CVX15, antagoniste du Récepteur Chemokine C-X-C de type-4. Nous montrons également que notre protocole est capable de prédire la sélectivité de plusieurs peptides dérivés de la Neurotensine envers plusieurs récepteurs sauvages et mutés, ne présentant qu’un résidu de différence.Dans un second temps, nous nous sommes intéressés à la dynamique de formation d’un hétéro-dimère de RCPGs impliquant le Récepteur de la Ghréline et le récepteur de la Dopamine D2, couplés aux protéines Gq et Gi respectivement. Ce modèle validé au laboratoire par des mesures LRET montre une interface impliquant une forte complémentarité entre les protéines-G. En se basant sur notre modèle, nous avons conçu et synthétisé des peptides inhibiteurs de la formation de cet hétéro-dimère de protéines-G.Enfin, nous présentons d’autres exemples d’applications de notre protocole et comment il peut être utilisé de concert avec l’expérience avec : la prédiction de la liaison de toxines de serpents aux Récepteurs de la Vasopressine-1a et V2 ; la prédiction de la liaison des peptides Ghréline et Leap2 au Récepteur GHSR-1a et la prédiction de la sélectivité de couplage de différents récepteurs aux peptides C-terminaux de la sous-unité α des protéines-G.

G-Protein Coupled…

Advisors/Committee Members: Floquet, Nicolas (thesis director).

Subjects/Keywords: Récepteurs Couplés aux Protéines-G (RCPGs); Dynamique Moléculaire « Replica-Exchange » (REMD); Modèles Gros-Grains (CG); Champ de forces MARTINI ElNeDyn; Liaison et sélectivité de différents peptides; Dimérisation; G-Proteins Coupled Receptors (GPCRs); Replica-Exchange Molecular Dynamics (REMD); Coarse-Grained models (CG); MARTINI ElNeDyn force field; Binding and selectivity of peptides; Dimerization

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Delort, B. (2018). Études par dynamique moléculaire de l’interaction de Récepteurs Couplés aux Protéines-G avec leurs partenaires extra et intra-cellulaires : Molecular dynamics studies of the interaction between G-Protein-Coupled Receptors and their extra and intra-cellular partners. (Doctoral Dissertation). Montpellier. Retrieved from http://www.theses.fr/2018MONTS113

Chicago Manual of Style (16^th Edition):

Delort, Bartholomé. “Études par dynamique moléculaire de l’interaction de Récepteurs Couplés aux Protéines-G avec leurs partenaires extra et intra-cellulaires : Molecular dynamics studies of the interaction between G-Protein-Coupled Receptors and their extra and intra-cellular partners.” 2018. Doctoral Dissertation, Montpellier. Accessed January 16, 2021. http://www.theses.fr/2018MONTS113.

MLA Handbook (7^th Edition):

Delort, Bartholomé. “Études par dynamique moléculaire de l’interaction de Récepteurs Couplés aux Protéines-G avec leurs partenaires extra et intra-cellulaires : Molecular dynamics studies of the interaction between G-Protein-Coupled Receptors and their extra and intra-cellular partners.” 2018. Web. 16 Jan 2021.

Vancouver:

Delort B. Études par dynamique moléculaire de l’interaction de Récepteurs Couplés aux Protéines-G avec leurs partenaires extra et intra-cellulaires : Molecular dynamics studies of the interaction between G-Protein-Coupled Receptors and their extra and intra-cellular partners. [Internet] [Doctoral dissertation]. Montpellier; 2018. [cited 2021 Jan 16]. Available from: http://www.theses.fr/2018MONTS113.

Council of Science Editors:

Delort B. Études par dynamique moléculaire de l’interaction de Récepteurs Couplés aux Protéines-G avec leurs partenaires extra et intra-cellulaires : Molecular dynamics studies of the interaction between G-Protein-Coupled Receptors and their extra and intra-cellular partners. [Doctoral Dissertation]. Montpellier; 2018. Available from: http://www.theses.fr/2018MONTS113

18. Καραΐσκος, Εμμανουήλ. Μοριακές προσομοιώσεις αγκυρωμένων πολυμερικών αλυσίδων.

Degree: 2005, University of Patras; Πανεπιστήμιο Πατρών

URL: http://hdl.handle.net/10442/hedi/26620

Subjects/Keywords: Αγκυρωμένες πολυμερικές αλυσίδες; Διακλαδισμένες αλυσίδες; Δυδιάσπαρτες αλυσίδες; Υπολογιστική μοντελοποίηση; Μοριακές προσομοιώσεις; Στατιστική θερμοδυναμική; Αδροποιημένα μοντέλα; End - anchored polymers; Branched chains; Bimodal chains; Computer modeling; Configurational bias; Monte carlo simulation; Statistical thermodynamics; Coarse - grained models

Record Details Similar Records Cite « Share

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Καραΐσκος, . �. (2005). Μοριακές προσομοιώσεις αγκυρωμένων πολυμερικών αλυσίδων. (Thesis). University of Patras; Πανεπιστήμιο Πατρών. Retrieved from http://hdl.handle.net/10442/hedi/26620

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Καραΐσκος, Εμμανουήλ. “Μοριακές προσομοιώσεις αγκυρωμένων πολυμερικών αλυσίδων.” 2005. Thesis, University of Patras; Πανεπιστήμιο Πατρών. Accessed January 16, 2021. http://hdl.handle.net/10442/hedi/26620.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Καραΐσκος, Εμμανουήλ. “Μοριακές προσομοιώσεις αγκυρωμένων πολυμερικών αλυσίδων.” 2005. Web. 16 Jan 2021.

Vancouver:

Καραΐσκος �. Μοριακές προσομοιώσεις αγκυρωμένων πολυμερικών αλυσίδων. [Internet] [Thesis]. University of Patras; Πανεπιστήμιο Πατρών; 2005. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10442/hedi/26620.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Καραΐσκος �. Μοριακές προσομοιώσεις αγκυρωμένων πολυμερικών αλυσίδων. [Thesis]. University of Patras; Πανεπιστήμιο Πατρών; 2005. Available from: http://hdl.handle.net/10442/hedi/26620

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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