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You searched for subject:(CHARMM). Showing records 1 – 19 of 19 total matches.

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George Mason University

1. Chang, Wenling Eileen. Computational Modeling of Anti-aggregation Effect of Non-steroidal Anti-inflammatory Drugs in Alzheimer’s Amyloidogenesis .

Degree: 2011, George Mason University

 Alzheimer’s disease (AD) represents a growing biomedical, social, and economical problem. Millions of people have suffered from the disease globally. Studies have shown that aggregated… (more)

Subjects/Keywords: Amyloid Beta; Naproxen; anti-aggregation; REMD; CHARMM; NSAID

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APA (6th Edition):

Chang, W. E. (2011). Computational Modeling of Anti-aggregation Effect of Non-steroidal Anti-inflammatory Drugs in Alzheimer’s Amyloidogenesis . (Thesis). George Mason University. Retrieved from http://hdl.handle.net/1920/6265

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

Chicago Manual of Style (16th Edition):

Chang, Wenling Eileen. “Computational Modeling of Anti-aggregation Effect of Non-steroidal Anti-inflammatory Drugs in Alzheimer’s Amyloidogenesis .” 2011. Thesis, George Mason University. Accessed May 08, 2021. http://hdl.handle.net/1920/6265.

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

MLA Handbook (7th Edition):

Chang, Wenling Eileen. “Computational Modeling of Anti-aggregation Effect of Non-steroidal Anti-inflammatory Drugs in Alzheimer’s Amyloidogenesis .” 2011. Web. 08 May 2021.

Vancouver:

Chang WE. Computational Modeling of Anti-aggregation Effect of Non-steroidal Anti-inflammatory Drugs in Alzheimer’s Amyloidogenesis . [Internet] [Thesis]. George Mason University; 2011. [cited 2021 May 08]. Available from: http://hdl.handle.net/1920/6265.

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

Council of Science Editors:

Chang WE. Computational Modeling of Anti-aggregation Effect of Non-steroidal Anti-inflammatory Drugs in Alzheimer’s Amyloidogenesis . [Thesis]. George Mason University; 2011. Available from: http://hdl.handle.net/1920/6265

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


University of Maryland

2. Pandit, Kunal. Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain.

Degree: Chemical Engineering, 2012, University of Maryland

 Most molecular dynamics (MD) simulations of bacterial membranes simplify the membrane by composing it of only 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) or in some cases with1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) as… (more)

Subjects/Keywords: Biophysics; Chemical engineering; CHARMM; cyclic lipid; E. coli; membrane; molecular dynamics

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APA (6th Edition):

Pandit, K. (2012). Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain. (Thesis). University of Maryland. Retrieved from http://hdl.handle.net/1903/16057

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

Chicago Manual of Style (16th Edition):

Pandit, Kunal. “Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain.” 2012. Thesis, University of Maryland. Accessed May 08, 2021. http://hdl.handle.net/1903/16057.

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

MLA Handbook (7th Edition):

Pandit, Kunal. “Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain.” 2012. Web. 08 May 2021.

Vancouver:

Pandit K. Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain. [Internet] [Thesis]. University of Maryland; 2012. [cited 2021 May 08]. Available from: http://hdl.handle.net/1903/16057.

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

Council of Science Editors:

Pandit K. Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain. [Thesis]. University of Maryland; 2012. Available from: http://hdl.handle.net/1903/16057

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


Universidade de Brasília

3. Cristiano Guimarães do Amaral Pinheiro. Interações Moleculares de peptídeos com membranas fosfolipídicas.

Degree: 2009, Universidade de Brasília

Peptide insertion through the plasmatic membrane is a major paradigm for the cellular-environment communications. At the level of atomic interactions, the structural and energetic knowledge… (more)

Subjects/Keywords: Campo de Força; peptídeos; GROMOS; CHARMM; BIOQUIMICA; peptide insertion; CHARMM; lipid bilayer membranres; GROMOS; Force Field; peptides; Molecular Dynamics; Dinâmica Molecular; inserção de peptídeos; bicamadas lipídicas

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APA (6th Edition):

Pinheiro, C. G. d. A. (2009). Interações Moleculares de peptídeos com membranas fosfolipídicas. (Thesis). Universidade de Brasília. Retrieved from http://bdtd.bce.unb.br/tedesimplificado/tde_busca/arquivo.php?codArquivo=4726 ; http://bdtd.bce.unb.br/tedesimplificado/tde_busca/arquivo.php?codArquivo=4725

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

Chicago Manual of Style (16th Edition):

Pinheiro, Cristiano Guimarães do Amaral. “Interações Moleculares de peptídeos com membranas fosfolipídicas.” 2009. Thesis, Universidade de Brasília. Accessed May 08, 2021. http://bdtd.bce.unb.br/tedesimplificado/tde_busca/arquivo.php?codArquivo=4726 ; http://bdtd.bce.unb.br/tedesimplificado/tde_busca/arquivo.php?codArquivo=4725.

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

MLA Handbook (7th Edition):

Pinheiro, Cristiano Guimarães do Amaral. “Interações Moleculares de peptídeos com membranas fosfolipídicas.” 2009. Web. 08 May 2021.

Vancouver:

Pinheiro CGdA. Interações Moleculares de peptídeos com membranas fosfolipídicas. [Internet] [Thesis]. Universidade de Brasília; 2009. [cited 2021 May 08]. Available from: http://bdtd.bce.unb.br/tedesimplificado/tde_busca/arquivo.php?codArquivo=4726 ; http://bdtd.bce.unb.br/tedesimplificado/tde_busca/arquivo.php?codArquivo=4725.

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

Council of Science Editors:

Pinheiro CGdA. Interações Moleculares de peptídeos com membranas fosfolipídicas. [Thesis]. Universidade de Brasília; 2009. Available from: http://bdtd.bce.unb.br/tedesimplificado/tde_busca/arquivo.php?codArquivo=4726 ; http://bdtd.bce.unb.br/tedesimplificado/tde_busca/arquivo.php?codArquivo=4725

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


Université de Grenoble

4. Cisse, Cheickna. Etude structurale des aptamères peptidiques anti-Fur et de leur interaction avec leur cible : Structural study of anti-Fur peptide aptamers and their interactions with their target.

Degree: Docteur es, Chimie, 2012, Université de Grenoble

Fur (Ferric Uptake Regulator) est un régulateur transcriptionnel spécifique des bactéries qui intervient dans le contrôle de l'homéostasie du fer, ce qui en fait une… (more)

Subjects/Keywords: Fur; Aptamères peptidiques; Amarrage moléculaire; Est d'activité de liaison à l'ADN; AUTODOCK4; CHARMM; Fur; Peptide aptamers; Molecular docking; DNA binding assays; AUTODOCK4; CHARMM

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APA (6th Edition):

Cisse, C. (2012). Etude structurale des aptamères peptidiques anti-Fur et de leur interaction avec leur cible : Structural study of anti-Fur peptide aptamers and their interactions with their target. (Doctoral Dissertation). Université de Grenoble. Retrieved from http://www.theses.fr/2012GRENV012

Chicago Manual of Style (16th Edition):

Cisse, Cheickna. “Etude structurale des aptamères peptidiques anti-Fur et de leur interaction avec leur cible : Structural study of anti-Fur peptide aptamers and their interactions with their target.” 2012. Doctoral Dissertation, Université de Grenoble. Accessed May 08, 2021. http://www.theses.fr/2012GRENV012.

MLA Handbook (7th Edition):

Cisse, Cheickna. “Etude structurale des aptamères peptidiques anti-Fur et de leur interaction avec leur cible : Structural study of anti-Fur peptide aptamers and their interactions with their target.” 2012. Web. 08 May 2021.

Vancouver:

Cisse C. Etude structurale des aptamères peptidiques anti-Fur et de leur interaction avec leur cible : Structural study of anti-Fur peptide aptamers and their interactions with their target. [Internet] [Doctoral dissertation]. Université de Grenoble; 2012. [cited 2021 May 08]. Available from: http://www.theses.fr/2012GRENV012.

Council of Science Editors:

Cisse C. Etude structurale des aptamères peptidiques anti-Fur et de leur interaction avec leur cible : Structural study of anti-Fur peptide aptamers and their interactions with their target. [Doctoral Dissertation]. Université de Grenoble; 2012. Available from: http://www.theses.fr/2012GRENV012


Penn State University

5. Nangia, Shivangi. Molecular Dynamics Simulations of MATRIX ASSISTED LASER DESORPTION (MALD).

Degree: 2012, Penn State University

 This thesis analyzes the desolvation process of analyte molecules from the matrix clusters in Matrix Assisted Laser Desorption (MALD). The key idea of this research… (more)

Subjects/Keywords: Matrix Assisted Laser Desorption Ionization (MALDI); Chemistry at HARvard Molecular Mechanics (CHARMM)

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APA (6th Edition):

Nangia, S. (2012). Molecular Dynamics Simulations of MATRIX ASSISTED LASER DESORPTION (MALD). (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/12682

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

Chicago Manual of Style (16th Edition):

Nangia, Shivangi. “Molecular Dynamics Simulations of MATRIX ASSISTED LASER DESORPTION (MALD).” 2012. Thesis, Penn State University. Accessed May 08, 2021. https://submit-etda.libraries.psu.edu/catalog/12682.

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

MLA Handbook (7th Edition):

Nangia, Shivangi. “Molecular Dynamics Simulations of MATRIX ASSISTED LASER DESORPTION (MALD).” 2012. Web. 08 May 2021.

Vancouver:

Nangia S. Molecular Dynamics Simulations of MATRIX ASSISTED LASER DESORPTION (MALD). [Internet] [Thesis]. Penn State University; 2012. [cited 2021 May 08]. Available from: https://submit-etda.libraries.psu.edu/catalog/12682.

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

Council of Science Editors:

Nangia S. Molecular Dynamics Simulations of MATRIX ASSISTED LASER DESORPTION (MALD). [Thesis]. Penn State University; 2012. Available from: https://submit-etda.libraries.psu.edu/catalog/12682

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


Clemson University

6. Brice, Allyn. A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION.

Degree: PhD, Physical Chemistry, 2011, Clemson University

  Glycosylase enzymes initiate the process of base excision repair (BER) in order to prevent the irreversible modification of the genome. In the BER process… (more)

Subjects/Keywords: Base Flipping; CHARMM; Generalized Born; Glycosylase; MM/PBSA; Umbrella Sampling; Physical Chemistry

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APA (6th Edition):

Brice, A. (2011). A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION. (Doctoral Dissertation). Clemson University. Retrieved from https://tigerprints.clemson.edu/all_dissertations/845

Chicago Manual of Style (16th Edition):

Brice, Allyn. “A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION.” 2011. Doctoral Dissertation, Clemson University. Accessed May 08, 2021. https://tigerprints.clemson.edu/all_dissertations/845.

MLA Handbook (7th Edition):

Brice, Allyn. “A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION.” 2011. Web. 08 May 2021.

Vancouver:

Brice A. A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION. [Internet] [Doctoral dissertation]. Clemson University; 2011. [cited 2021 May 08]. Available from: https://tigerprints.clemson.edu/all_dissertations/845.

Council of Science Editors:

Brice A. A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION. [Doctoral Dissertation]. Clemson University; 2011. Available from: https://tigerprints.clemson.edu/all_dissertations/845


Brigham Young University

7. Smith, Addison Kyle. Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models.

Degree: PhD, 2021, Brigham Young University

 Proteins that have been modified by attaching them to a surface or to a polyethylene glycol (PEG) molecule can see many uses in therapeutics and… (more)

Subjects/Keywords: Protein device; CHARMM; unnatural amino acid; protein; simulation; molecular dynamics; parameterization; azide; alkyne; Engineering

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APA (6th Edition):

Smith, A. K. (2021). Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models. (Doctoral Dissertation). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=9792&context=etd

Chicago Manual of Style (16th Edition):

Smith, Addison Kyle. “Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models.” 2021. Doctoral Dissertation, Brigham Young University. Accessed May 08, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=9792&context=etd.

MLA Handbook (7th Edition):

Smith, Addison Kyle. “Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models.” 2021. Web. 08 May 2021.

Vancouver:

Smith AK. Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models. [Internet] [Doctoral dissertation]. Brigham Young University; 2021. [cited 2021 May 08]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=9792&context=etd.

Council of Science Editors:

Smith AK. Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models. [Doctoral Dissertation]. Brigham Young University; 2021. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=9792&context=etd


Iowa State University

8. Ravindrudu, Rahul. An integrated software environment for protein structure refinement.

Degree: 2008, Iowa State University

 The development of an integrated software environment for protein structure refinement is reported. Energy minimization is combined with geometric embedding in the refinement program. The… (more)

Subjects/Keywords: CHARMM; energy minimization; protein; refinement; Computer Sciences

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APA (6th Edition):

Ravindrudu, R. (2008). An integrated software environment for protein structure refinement. (Thesis). Iowa State University. Retrieved from https://lib.dr.iastate.edu/etd/11855

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

Chicago Manual of Style (16th Edition):

Ravindrudu, Rahul. “An integrated software environment for protein structure refinement.” 2008. Thesis, Iowa State University. Accessed May 08, 2021. https://lib.dr.iastate.edu/etd/11855.

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

MLA Handbook (7th Edition):

Ravindrudu, Rahul. “An integrated software environment for protein structure refinement.” 2008. Web. 08 May 2021.

Vancouver:

Ravindrudu R. An integrated software environment for protein structure refinement. [Internet] [Thesis]. Iowa State University; 2008. [cited 2021 May 08]. Available from: https://lib.dr.iastate.edu/etd/11855.

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

Council of Science Editors:

Ravindrudu R. An integrated software environment for protein structure refinement. [Thesis]. Iowa State University; 2008. Available from: https://lib.dr.iastate.edu/etd/11855

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

9. Georgoulia, Panagiota. Δομικές και υπολογιστικές μελέτες πεπτιδίων.

Degree: 2012, Democritus University of Thrace (DUTH); Δημοκρίτειο Πανεπιστήμιο Θράκης (ΔΠΘ)

A computational solution to the protein folding problem has evolved to the Holy Grail of modern Biochemistry and Structural Biology. Peptides have been an attractive… (more)

Subjects/Keywords: Προσομοιώσεις μοριακής δυναμικής; Τετραπεπτίδια; Πενταπεπτίδια; Αναδιπλωσιμότητα; Αναδίπλωση πεπτιδίων; Συναρτήσεις εκτίμησης αναδιπλωσιμότητας; Force fields; Amber; CHARMM; OPLS

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APA (6th Edition):

Georgoulia, P. (2012). Δομικές και υπολογιστικές μελέτες πεπτιδίων. (Thesis). Democritus University of Thrace (DUTH); Δημοκρίτειο Πανεπιστήμιο Θράκης (ΔΠΘ). Retrieved from http://hdl.handle.net/10442/hedi/28423

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

Chicago Manual of Style (16th Edition):

Georgoulia, Panagiota. “Δομικές και υπολογιστικές μελέτες πεπτιδίων.” 2012. Thesis, Democritus University of Thrace (DUTH); Δημοκρίτειο Πανεπιστήμιο Θράκης (ΔΠΘ). Accessed May 08, 2021. http://hdl.handle.net/10442/hedi/28423.

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

MLA Handbook (7th Edition):

Georgoulia, Panagiota. “Δομικές και υπολογιστικές μελέτες πεπτιδίων.” 2012. Web. 08 May 2021.

Vancouver:

Georgoulia P. Δομικές και υπολογιστικές μελέτες πεπτιδίων. [Internet] [Thesis]. Democritus University of Thrace (DUTH); Δημοκρίτειο Πανεπιστήμιο Θράκης (ΔΠΘ); 2012. [cited 2021 May 08]. Available from: http://hdl.handle.net/10442/hedi/28423.

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

Council of Science Editors:

Georgoulia P. Δομικές και υπολογιστικές μελέτες πεπτιδίων. [Thesis]. Democritus University of Thrace (DUTH); Δημοκρίτειο Πανεπιστήμιο Θράκης (ΔΠΘ); 2012. Available from: http://hdl.handle.net/10442/hedi/28423

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


University of Vienna

10. Maurer, Sonja. Start configurations for simulation of ionic liquids.

Degree: 2010, University of Vienna

Diese Arbeit hat zwei Schwerpunkte. Einerseits soll eine Methode gefunden werden, um schnell und einfach ein Startsystem für eine Simulation zu generieren. Andererseits soll das… (more)

Subjects/Keywords: 30.99 Naturwissenschaften allgemein: Sonstiges; 35.21 Lösungen, Flüssigkeiten; 35.99 Chemie: Sonstiges; 35.06 Computeranwendungen; ionische Flüssigkeit / Simulation / Equilibrierung / Start Konfiguration / packmol / charmm / Korrelationsfunktion / Kollektivität; ionic liquid / simulation / equilibration / start configuration / packmol / charmm / correlation function / collectivity

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APA (6th Edition):

Maurer, S. (2010). Start configurations for simulation of ionic liquids. (Thesis). University of Vienna. Retrieved from http://othes.univie.ac.at/8955/

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

Chicago Manual of Style (16th Edition):

Maurer, Sonja. “Start configurations for simulation of ionic liquids.” 2010. Thesis, University of Vienna. Accessed May 08, 2021. http://othes.univie.ac.at/8955/.

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

MLA Handbook (7th Edition):

Maurer, Sonja. “Start configurations for simulation of ionic liquids.” 2010. Web. 08 May 2021.

Vancouver:

Maurer S. Start configurations for simulation of ionic liquids. [Internet] [Thesis]. University of Vienna; 2010. [cited 2021 May 08]. Available from: http://othes.univie.ac.at/8955/.

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

Council of Science Editors:

Maurer S. Start configurations for simulation of ionic liquids. [Thesis]. University of Vienna; 2010. Available from: http://othes.univie.ac.at/8955/

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


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

 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)

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 (6th 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 (16th 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 May 08, 2021. http://hdl.handle.net/2027.42/116710.

MLA Handbook (7th Edition):

Gagnon, Jessica K. “Flexible Receptor Docking Method Development and Molecular Dynamics Studies Towards Targeting Dynamic Protein Surfaces.” 2015. Web. 08 May 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 May 08]. 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


Seton Hall University

12. Dwyer, Patrick J. From Dye Sensitized Solar Cells to Organic Field Effect Transistors: A Computational Investigation into the Structural and Electronic Properties of Novel Phthalocyanines.

Degree: PhD, Chemistry and Biochemistry, 2015, Seton Hall University

  Phthalocyanines (Pc) have gained intense research attention in many diverse application areas due to their highly tunable electronic and structural properties through modification of… (more)

Subjects/Keywords: Phthalocyanine; Density Functional Theory; Molecular Dynamics; Dye Densitized Solar Cell; Charge Transport; Electronic Structure; DFT; MD; CHARMM; Forcefield; Materials Chemistry; Physical Chemistry

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APA (6th Edition):

Dwyer, P. J. (2015). From Dye Sensitized Solar Cells to Organic Field Effect Transistors: A Computational Investigation into the Structural and Electronic Properties of Novel Phthalocyanines. (Doctoral Dissertation). Seton Hall University. Retrieved from https://scholarship.shu.edu/dissertations/2122

Chicago Manual of Style (16th Edition):

Dwyer, Patrick J. “From Dye Sensitized Solar Cells to Organic Field Effect Transistors: A Computational Investigation into the Structural and Electronic Properties of Novel Phthalocyanines.” 2015. Doctoral Dissertation, Seton Hall University. Accessed May 08, 2021. https://scholarship.shu.edu/dissertations/2122.

MLA Handbook (7th Edition):

Dwyer, Patrick J. “From Dye Sensitized Solar Cells to Organic Field Effect Transistors: A Computational Investigation into the Structural and Electronic Properties of Novel Phthalocyanines.” 2015. Web. 08 May 2021.

Vancouver:

Dwyer PJ. From Dye Sensitized Solar Cells to Organic Field Effect Transistors: A Computational Investigation into the Structural and Electronic Properties of Novel Phthalocyanines. [Internet] [Doctoral dissertation]. Seton Hall University; 2015. [cited 2021 May 08]. Available from: https://scholarship.shu.edu/dissertations/2122.

Council of Science Editors:

Dwyer PJ. From Dye Sensitized Solar Cells to Organic Field Effect Transistors: A Computational Investigation into the Structural and Electronic Properties of Novel Phthalocyanines. [Doctoral Dissertation]. Seton Hall University; 2015. Available from: https://scholarship.shu.edu/dissertations/2122

13. Painter, Gallia Marie. Multiscale Modeling of Polymer Bond Scission.

Degree: MSs (Engineering), Chemical Engineering, 2009, Case Western Reserve University School of Graduate Studies

 Polymers under stress, such as during flow or stretching, exhibit deformations that can greatly affect the properties of the material. Bonds within these large molecules… (more)

Subjects/Keywords: Chemical Engineering; CHARMM; POLYMER; SCISSION; elongation; BOND; chains; Chain scission

…while accurately modeling a shorter chain explicitly in the quantum domain. CHARMM (… …equilibrium configuration, one of the chains was stretched using the AFM module in CHARMM. This… …x28;namely proteins) at the atomic level. CHARMM was also used to attempt to study the… …chemistry packages for our simulations: CHARMM and Gaussian 03W. CHARMM is primarily used as a… …properties of these molecules. 13 Methods I. CHARMM Input files in CHARMM were generated from… 

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

APA (6th Edition):

Painter, G. M. (2009). Multiscale Modeling of Polymer Bond Scission. (Masters Thesis). Case Western Reserve University School of Graduate Studies. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=case1247171422

Chicago Manual of Style (16th Edition):

Painter, Gallia Marie. “Multiscale Modeling of Polymer Bond Scission.” 2009. Masters Thesis, Case Western Reserve University School of Graduate Studies. Accessed May 08, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=case1247171422.

MLA Handbook (7th Edition):

Painter, Gallia Marie. “Multiscale Modeling of Polymer Bond Scission.” 2009. Web. 08 May 2021.

Vancouver:

Painter GM. Multiscale Modeling of Polymer Bond Scission. [Internet] [Masters thesis]. Case Western Reserve University School of Graduate Studies; 2009. [cited 2021 May 08]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=case1247171422.

Council of Science Editors:

Painter GM. Multiscale Modeling of Polymer Bond Scission. [Masters Thesis]. Case Western Reserve University School of Graduate Studies; 2009. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=case1247171422

14. Åkesson, Patrik. Molecular Dynamics of the Adsorption of Organic Molecules on Organic Substrates.

Degree: The Institute of Technology, 2013, Linköping UniversityLinköping University

A great interest has been shown for self-assembled organic nano-structures that can be used in a variety of optoelectronic applications, from element detection to… (more)

Subjects/Keywords: Molecular Dynamics; Empirical Force Field; Computational Physics; Material Science; Simulated Annealing; Organic Molecules; Sexiphenyl; Sexithiophene; LAMMPS; CHARMM; Molekyldynamik; Empiriska kraftfält; Beräkningsfysik; Materialvetenskap; Organiska molekyler; Sexifenyl; Sexitiofen; LAMMPS; CHARMM

…Force Fields . . . . . . . . . . . 2.2.2 CHARMM FF . . . . . . . . . . 2.3 Molecular Dynamics… …Bibliography 82 vi Glossary 6P Sexiphenyl 6T Sexithiophene AFM Atomic Force Microscopy CHARMM… …Chemistry at HARvard Macromolecular Mechanics CGenFF CHARMM General Force Field CMAP Correction… …Chemistry at HARvard Macromolecular Mechanics (CHARMM). They are both powerful tools… …2.2.2 CHARMM FF CHARMM [13] is a molecular simulation and modelling program. It is… 

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

APA (6th Edition):

Åkesson, P. (2013). Molecular Dynamics of the Adsorption of Organic Molecules on Organic Substrates. (Thesis). Linköping UniversityLinköping University. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-103688

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

Chicago Manual of Style (16th Edition):

Åkesson, Patrik. “Molecular Dynamics of the Adsorption of Organic Molecules on Organic Substrates.” 2013. Thesis, Linköping UniversityLinköping University. Accessed May 08, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-103688.

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

MLA Handbook (7th Edition):

Åkesson, Patrik. “Molecular Dynamics of the Adsorption of Organic Molecules on Organic Substrates.” 2013. Web. 08 May 2021.

Vancouver:

Åkesson P. Molecular Dynamics of the Adsorption of Organic Molecules on Organic Substrates. [Internet] [Thesis]. Linköping UniversityLinköping University; 2013. [cited 2021 May 08]. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-103688.

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

Council of Science Editors:

Åkesson P. Molecular Dynamics of the Adsorption of Organic Molecules on Organic Substrates. [Thesis]. Linköping UniversityLinköping University; 2013. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-103688

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


Duquesne University

15. Harrison, Melinda Ann. Transfer of Cu(I) between Metal Binding Sites and the Development of Cu(I) Force Field Parameters Using Charmm.

Degree: PhD, Chemistry and Biochemistry, 2007, Duquesne University

 Binding and transfer of Cu(I) between three key proteins in the bacterium Enterococcus hirae has been studied. CopA, an ATPase protein, was truncated, and its… (more)

Subjects/Keywords: Enterococcus hirae; E. hirae; Cu(I) ATPase; Cu(I) Parameters; Cu(I) proteins; metalloproteins; CHARMM Cu(I) parameters

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APA (6th Edition):

Harrison, M. A. (2007). Transfer of Cu(I) between Metal Binding Sites and the Development of Cu(I) Force Field Parameters Using Charmm. (Doctoral Dissertation). Duquesne University. Retrieved from https://dsc.duq.edu/etd/1723

Chicago Manual of Style (16th Edition):

Harrison, Melinda Ann. “Transfer of Cu(I) between Metal Binding Sites and the Development of Cu(I) Force Field Parameters Using Charmm.” 2007. Doctoral Dissertation, Duquesne University. Accessed May 08, 2021. https://dsc.duq.edu/etd/1723.

MLA Handbook (7th Edition):

Harrison, Melinda Ann. “Transfer of Cu(I) between Metal Binding Sites and the Development of Cu(I) Force Field Parameters Using Charmm.” 2007. Web. 08 May 2021.

Vancouver:

Harrison MA. Transfer of Cu(I) between Metal Binding Sites and the Development of Cu(I) Force Field Parameters Using Charmm. [Internet] [Doctoral dissertation]. Duquesne University; 2007. [cited 2021 May 08]. Available from: https://dsc.duq.edu/etd/1723.

Council of Science Editors:

Harrison MA. Transfer of Cu(I) between Metal Binding Sites and the Development of Cu(I) Force Field Parameters Using Charmm. [Doctoral Dissertation]. Duquesne University; 2007. Available from: https://dsc.duq.edu/etd/1723

16. Smith, Addison Kyle. Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models.

Degree: PhD, 2021, Brigham Young University

 Proteins that have been modified by attaching them to a surface or to a polyethylene glycol (PEG) molecule can see many uses in therapeutics and… (more)

Subjects/Keywords: Protein device; CHARMM; unnatural amino acid; protein; simulation; molecular dynamics; parameterization; azide; alkyne; Engineering

…use in the CHARMM force field. Chapter 8 explores the challenges as3 sociated with… …CHARMM FF. This FF was specifically created for use in protein and macromolecule systems [… …63, 64]. The CHARMM set of parameters and equations is the predominant force field… …differences between CHARMM and AMBER stem from how parameters are derived [65, 66]. The… …atoms beyond the initial published set. The CHARMM general force field (CGenFF)… 

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APA (6th Edition):

Smith, A. K. (2021). Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models. (Doctoral Dissertation). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=9796&context=etd

Chicago Manual of Style (16th Edition):

Smith, Addison Kyle. “Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models.” 2021. Doctoral Dissertation, Brigham Young University. Accessed May 08, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=9796&context=etd.

MLA Handbook (7th Edition):

Smith, Addison Kyle. “Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models.” 2021. Web. 08 May 2021.

Vancouver:

Smith AK. Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models. [Internet] [Doctoral dissertation]. Brigham Young University; 2021. [cited 2021 May 08]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=9796&context=etd.

Council of Science Editors:

Smith AK. Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models. [Doctoral Dissertation]. Brigham Young University; 2021. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=9796&context=etd

17. Sawert, David; Holmes, Oskar Anderhagen. Analys av Organiska Molekyler i Mikroskopiska Vattendroppar.

Degree: Molecular and Condensed Matter Physics, 2020, Uppsala University

  The aim of the study was to analyse where different organic molecules situated themselves in relation to the water surface of a water microdroplet… (more)

Subjects/Keywords: Simulering; Kraftfält; CGENFF; OPLS-AA; GAFF; CHARMM; AMBER; Biochemistry and Molecular Biology; Biokemi och molekylärbiologi

…molekyler på ytor, inte nödvändigtvis i vätskor. 3.3.4 CGenFF CGenFF, eller CHARMM General… …Forcefield, är en vidareutveckling av CHARMM. Innan utökningen så hade CHARMM stöd för proteiner… 

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

APA (6th Edition):

Sawert, David; Holmes, O. A. (2020). Analys av Organiska Molekyler i Mikroskopiska Vattendroppar. (Thesis). Uppsala University. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-415316

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

Chicago Manual of Style (16th Edition):

Sawert, David; Holmes, Oskar Anderhagen. “Analys av Organiska Molekyler i Mikroskopiska Vattendroppar.” 2020. Thesis, Uppsala University. Accessed May 08, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-415316.

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

MLA Handbook (7th Edition):

Sawert, David; Holmes, Oskar Anderhagen. “Analys av Organiska Molekyler i Mikroskopiska Vattendroppar.” 2020. Web. 08 May 2021.

Vancouver:

Sawert, David; Holmes OA. Analys av Organiska Molekyler i Mikroskopiska Vattendroppar. [Internet] [Thesis]. Uppsala University; 2020. [cited 2021 May 08]. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-415316.

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

Council of Science Editors:

Sawert, David; Holmes OA. Analys av Organiska Molekyler i Mikroskopiska Vattendroppar. [Thesis]. Uppsala University; 2020. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-415316

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

18. Smith, Joshua Dee. Verifying Molecular Dynamics Using Dielectric Spectroscopy.

Degree: MS, 2014, Brigham Young University

  The electrical properties of proteins in solution are important for their structure and function. Computational biophysics studies of proteins need accurate parameters to ensure… (more)

Subjects/Keywords: alanine; amino acid; CHARMM; dielectric; dielectric increment; dielectric probe; dielectric response; dielectric spectroscopy; dipole; dipole moment; Dipole Moment Watcher; displacement current; GROMOS; l-alanine; Laplace; material properties; molecular dynamics; OPLS; partial charges; permittivity; permittivity spectra; relative permittivity; simulation; spectroscopy; system dipole moment; TIP3P; Visual Molecular Dynamics; Electrical and Computer Engineering

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

APA (6th Edition):

Smith, J. D. (2014). Verifying Molecular Dynamics Using Dielectric Spectroscopy. (Masters Thesis). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=5220&context=etd

Chicago Manual of Style (16th Edition):

Smith, Joshua Dee. “Verifying Molecular Dynamics Using Dielectric Spectroscopy.” 2014. Masters Thesis, Brigham Young University. Accessed May 08, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=5220&context=etd.

MLA Handbook (7th Edition):

Smith, Joshua Dee. “Verifying Molecular Dynamics Using Dielectric Spectroscopy.” 2014. Web. 08 May 2021.

Vancouver:

Smith JD. Verifying Molecular Dynamics Using Dielectric Spectroscopy. [Internet] [Masters thesis]. Brigham Young University; 2014. [cited 2021 May 08]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=5220&context=etd.

Council of Science Editors:

Smith JD. Verifying Molecular Dynamics Using Dielectric Spectroscopy. [Masters Thesis]. Brigham Young University; 2014. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=5220&context=etd

19. Thomson, Karen J. A Computational Study of the Mechanism for F1-ATPase Inhibition by the Epsilon Subunit.

Degree: 2013, IUPUI

Indiana University-Purdue University Indianapolis (IUPUI)

The multi-protein complex of F0F1 ATP synthase has been of great interest in the fields of microbiology and biochemistry, due… (more)

Subjects/Keywords: ATP synthase; molecular dynamics; computer simulation; CHARMM; Molecular dynamics  – Research  – Analysis  – Evaluation; Adenosine triphosphatase  – Regulation; Adenosine triphosphatase  – Computer simulation; Computational biology; Escherichia coli  – Research; Proteins  – Structure; Molecular biology  – Mathematical models; Chemistry  – Data processing; Proteins  – Conformation; Crystallography  – Technique; Molecular dynamics; Bioenergetics; Computer simulation

…derivational basis for the numerical methods used in CHARMM, as CHARMm is the software primarily used… …potential. The full potential (as used by CHARMm [16]) is comprised of a sum… …used if specified in the dynamics input of CHARMm. [16] 18 2.2 Molecular… …investigation of molecular transition pathways, there are several methods available using CHARMm… …was selected. 23 The program CHARMm [15,16] versions c36a1 and c35b3 were used… 

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

APA (6th Edition):

Thomson, K. J. (2013). A Computational Study of the Mechanism for F1-ATPase Inhibition by the Epsilon Subunit. (Thesis). IUPUI. Retrieved from http://hdl.handle.net/1805/5024

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

Chicago Manual of Style (16th Edition):

Thomson, Karen J. “A Computational Study of the Mechanism for F1-ATPase Inhibition by the Epsilon Subunit.” 2013. Thesis, IUPUI. Accessed May 08, 2021. http://hdl.handle.net/1805/5024.

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

MLA Handbook (7th Edition):

Thomson, Karen J. “A Computational Study of the Mechanism for F1-ATPase Inhibition by the Epsilon Subunit.” 2013. Web. 08 May 2021.

Vancouver:

Thomson KJ. A Computational Study of the Mechanism for F1-ATPase Inhibition by the Epsilon Subunit. [Internet] [Thesis]. IUPUI; 2013. [cited 2021 May 08]. Available from: http://hdl.handle.net/1805/5024.

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

Council of Science Editors:

Thomson KJ. A Computational Study of the Mechanism for F1-ATPase Inhibition by the Epsilon Subunit. [Thesis]. IUPUI; 2013. Available from: http://hdl.handle.net/1805/5024

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

.