Biochemistry, Biophysics, and Structural Biology Commons^™

Synthesis And Study Of High-Spin Stable Organic Radicals For Electrical Conductors And Mannosamine Nitroxide For Mri Contrast Agents, Shuyang Zhang

Department of Chemistry: Dissertations, Theses, and Student Research

In the first project, we describe the synthesis of an ambient stable high spin organic diradical 4 based on the Blatter moiety. The high-spin (S = 1) organic diradical 4, which consists of two Blatter radical moieties in a conjugated structure, exhibits a nearly exclusive population (88%) on triplet ground state at room temperature as a consequence of a large single-triplet energy gap (ΔEST = 0.5 kcal/mol). The target diradical molecule is synthesized over five steps with structural confirmation by single-crystal X-ray diffraction. The thermogravimetric analysis (TGA) shows the onset of decomposition at ~264 oC, indicating the diradical molecule has …

A Pipeline To Generate Deep Learning Surrogates Of Genome-Scale Metabolic Models, Achilles Rasquinha

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Genome-Scale Metabolic Models (GEMMs) are powerful reconstructions of biological systems that help metabolic engineers understand and predict growth conditions subjected to various environmental factors around the cellular metabolism of an organism in observation, purely in silico. Applications of metabolic engineering range from perturbation analysis and drug-target discovery to predicting growth rates of biotechnologically important metabolites and reaction objectives within dierent single-cell and multi-cellular organism types. GEMMs use mathematical frameworks for quantitative estimations of flux distributions within metabolic networks. The reasons behind why an organism activates, stuns, or fluctuates between alternative pathways for growth and survival, however, remain relatively unknown. GEMMs …

Got Science? Club, Nora Husein, Randa Ismail

Honors Expanded Learning Clubs

Got Science? Club allows students to learn about the science that can be found in our daily lives using everyday items such as food and school supplies. Students will learn about these sciences through hands-on experiments, allowing them to truly experience the science around them.

Periodic Table Club, Makayla Gill, Kailynn Jensen

Honors Expanded Learning Clubs

This club is dedicated to teaching the generation of future scientists the periodic table. This is designed to be a unique take on a STEM club that uses the periodic table as a backbone for a solid foundation in chemistry.

"Flagella Base Model" And "Flagellin Monomer", Brandon Lasalle, Rebecca Roston

3-D Printed Model Structural Files

"Flagella Base Model" and "Flagellin monomer"

Description: This is a teaching model of the proteins that make a bacterial flagella. All models are depicted in space-fill. The Flagellin monomer and the Flagella base can slot together to show protein quaternary structure and filamentous protein assembly.

Printable models are already uploaded to Shapeways.com in the MacroMolecules shop under the names "Flagella Base Model" and "Flagellin monomer".

This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Model designer: Brandon Lasalle Authors: Brandon Lasalle and Rebecca Roston …

Amino Acid Pop-Set: Model File Name: Amino-Acid-Wgrp-Pop_Sc3.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model for protein primary structure. It consists of four amino acids (tryptophan, proline, arginine, and glycine) depicted in stick and space-fill representations, five peptide bonds depicted in space-fill, and an N-terminus and a C-terminus depicted in space-fill. It is designed so that students can make various peptides to explore the amount of space of the electron clouds of the amino acids and bonds, and explore the psi and phi angles for the peptides. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Amino acid pop-set”. This model has …

Lipoprotein Signal Peptidase Ii: Model File Name: 5dir-Lipoii-Reps_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of lipoprotein signal peptidase II (PDB: 5DIR). It is designed with different regions of the protein depicted in space-filling, ribbon, stick, and backbone-only representations to explore protein secondary structure and illustrate how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lipoprotein signal peptidase II” and is intended to accompany the “Crambin”, “Cytochrome c” and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in …

3 Water Molecules: Model File Name: 3hoh-Final.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of 3 water molecules depicted in space-fill. It is designed to the same scale as the “Lipoprotein signal peptidase II”, “Crambin”, and “Cytochrome c” models to illustrate the amount of space taken up by proteins. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “3 water molecules” and is intended to accompany the “Lipoprotein signal peptidase II”, “Crambin”, and “Cytochrome c” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering …

Crambin: Model File Name: 2fd7-Crambin-Stick_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of cytochrome c (PDB: 2FD7). It is designed in a stick representation to explore protein secondary structure and how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Crambin” and is intended to accompany the “Lipoprotein signal peptidase II”, “Cytochrome c”, and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Cytochrome C: Model File Name: 1b7v-Cytc-Stick_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of cytochrome c (PDB: 1B7V). It is designed in a stick representation to explore protein secondary structure and how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Cytochrome c” and is intended to accompany the “Lipoprotein signal peptidase II”, “Crambin”, and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Human Hexokinase I - Allosteric Regulation: Model File Name: 1dgk-Editb22-Allostery_Sc06.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of human Hexokinase I in a surface representation with small molecules ADP and G6P included (PDB: 1DGK). It is designed to be hollow with a lever to mimic allosteric regulation. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Human Hexokinase I - Allosteric regulation model”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Model File Name: 1ehz-Trna(Thick).Stl, Michelle Howell, Karin Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1ehz-tRNA(thick).stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of Phe-tRNA in a thick stick-representation (PDB: 1ehz), designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com under the name “tRNA-Phe small”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following materials: Strong & Flexible Plastic and Elasto Plastic.

Model File Name: 1lmb-Dbd-Tfmono.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-DBD-TFmono.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of the DNA binding domain of a Lambda repressor transcription factor monomer that accompanies the full color DNA helix (PDB: 1lmb). It is in a cartoon ribbon representation with key amino acid residues in stick representation to highlight interactions with the DNA. This model is designed to accompany a teaching module illustrating transcription factor-DNA binding. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lambda TF DBD”. This model has been printed …

Model File Name: 1ehz-Trna(Thin-Big).X3d, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1ehz-tRNA(thin-big).x3d

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of Phe-tRNA in a large, but thin stick-representation (PDB: 1ehz), designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Full color Phe-tRNA (1ehz)”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Strong & Flexible Plastic.

Model File Name: 1lmb-Dnalong_Fordimer-Test6b.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-DNAlong_fordimer-test6b.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of the 19-bp segment of DNA to which Lambda repressor transcription factor interacts (PDB: 1lmb). It is in a stick representation and has been designed with sites to add magnets to illustrate binding interactions with the transcription factor. Sphere magnets with a 1/8” diameter can be purchased separately from K&J Magnets. The model can interact with the dimer form of the transcription factor. This model is designed to accompany a teaching module illustrating transcription factor-DNA binding. The printable model …

Model File Name: 1lmb-Tfdimer-Mags-Joints-Jnd-Sc1-8-Parts-V4b.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-TFdimer-mags-joints-jnd-sc1-8-parts-v4b.stl

Additional files: 1lmb-Lys-Ser-extras-v4b.stl and 1lmb-TFdimer-Leu-v4b.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a ribbon and stick representation of the transcription factor lambda repressor (PDB: 1lmb). Key amino acid residues are in stick representation to illustrate the interactions between the repressor and the DNA to which it binds. Some of these residues have been designed with sites to add magnets to illustrate these interactions. Sphere magnets with a 1/8” diameter can be purchased separately from K&J Magnets. Some of the residues can be interchanged with other …

Model File Name: Dna-294bp-Magnet-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Kalika Mahato, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-294bp-magnet-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (294 bp). The DNA model has small sites on the ends where the user can glue magnets to mimic circular DNA, and to aid in manipulating the model. Disc magnets with a diameter of 1/8” or 1/10” and thickness of 1/16” can be purchased online from K&J Magnetics and glued into the magnet sites. The model is designed to go with a teaching module on DNA supercoiling. The model can …

Model File Name: Dna-294bp-Handle-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-294bp-handle-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (294 bp). The DNA model has small handles on the ends to aid in holding and manipulating the model. The model is designed to go with a teaching module on DNA supercoiling. The model can be accompanied by Nucleosome and H1 histone models to demonstrate DNA packaging in the cell. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “294bp DNA (handles)”. …

Model File Name: Dna-420bp-Handle-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Kalika Mahato, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-420bp-handle-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (420 bp). The DNA model has small handles on the ends to aid in holding and manipulating the model. The model is designed to go with a teaching module on DNA supercoiling. The model can be accompanied by Nucleosome and H1 histone models to demonstrate DNA packaging in the cell. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “420bp DNA (handles)”. …

Model File Name: Dnalong-3pc-Lego.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNAlong-3pc-Lego.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a stick representation of the DNA to which the transcription factor lambda repressor binds (PDB: 1lmb). This model can be adapted to accompany a teaching module illustrating transcription factor-DNA binding. The model has been designed in 3 parts that can be joined together by Lego®-style junctions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lego DNA with GCbp”. This model has been printed successfully using these parameters on Shapeways’ laser …

Model File Name: Dna-420bp-Magnet-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Kalika Mahato, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-420bp-magnet-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (420 bp). The DNA model has small sites on the ends where the user can glue magnets to mimic circular DNA, and to aid in manipulating the model. Disc magnets with a diameter of 1/8” or 1/10” and thickness of 1/16” can be purchased online from K&J Magnetics and glued into the magnet sites. The model is designed to go with a teaching module on DNA supercoiling. The model can …

Model File Name: H1-Protein.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: H1-protein.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a crude representation of an H1-protein intended to accompany the nucleosome and a long, thin double stranded DNA helix model in order to illustrate DNA packaging and supercoiling. This model is designed to go with a teaching module on DNA supercoiling. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Histone H1 protein”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following materials: Strong …

Model File Name: Dna-Short-Helix.X3d, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-short-helix.x3d

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a DNA helix in which the atoms are colored by heteroatom (PDB: 1lmb). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions, and with one that studies transcription factor-DNA binding. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “DNA helix - polynucleotide molecule”. This model has been printed successfully using these parameters on Shapeways’ binder jetting printer in the Coated Full …

Model File Name: Ssdna.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: ssDNA.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a single stranded piece of DNA in stick representation (PDB: 1ehz). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “ssDNA”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Elasto Plastic material.

Model File Name: Nucleosome.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: Nucleosome.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a crude representation of a nucleosome intended to accompany the H1 histone protein and a long, thin double stranded DNA helix model in order to illustrate DNA packaging and supercoiling. This model is designed to go with a teaching module on DNA supercoiling. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Nucleosome”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Strong & Flexible …

Model File Name: Tf-Monomer-Stick.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: TF-monomer-stick.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a ribbon and stick representation of a Lambda repressor transcription factor monomer that accompanies the full color DNA helix (PDB: 1lmb). This model is designed to go with a teaching module illustrating transcription factor-DNA binding. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lambda TF monomer”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Strong & Flexible Plastic material.

Model File Name: Rna-Short-Helix.X3d, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: RNA-short-helix.x3d

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a DNA helix in which the atoms are colored by heteroatom (PDB: 1lmb). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “RNA helix - polynucleotide molecule”. This model has been printed successfully using these parameters on Shapeways’ binder jetting printer in the Coated Full Color Sandstone material.

Video Guide To Design Flexible Dna.Mp4, Michelle Howell, Karin V. Van Dijk, Christine S. Booth, Tomáš Helikar, Brian Couch, Rebecca Roston

3-D Printed Model Structural Files

Model file name: Video guide to design flexible DNA.mp4

Authors: Michelle E Howell, Karin van Dijk, Christine S Booth, Tomas Helikar, Brian A Couch, Rebecca L Roston

This 30-minute video includes step-by-step instructions to design and 3-D print a long flexible DNA model that mimics the structure and function of DNA. The instructions are applicable for designing the model using open-source 3-D computer graphics software Blender 2.79 which is available for download at https://www.blender.org/download/.

.mp4 file download (70 MB) below.

Model File Name: Ssrna.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: ssRNA.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a single stranded piece of RNA in stick representation (PDB: 1ehz). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “ssRNA”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Elasto Plastic material.

Model File Name: Helix_H2o_Sphere2.Dae, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

Model file name: Helix_H2O_sphere2.dae

Authors: Michelle E Howell, Rebecca L Roston

This is a teaching model of a space fill representation of a protein α-helix (PDB: 3vjo). A space fill water molecule is also represented to illustrate the lack of space down the axis of an α-helix. This model can accompany a corresponding stick representation, a kinked α-helix, and a β-sheet. This model is designed to accompany a teaching module illustrating protein secondary structure and function. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Helix and Water (Space-fill) …