1. Winning the cellular lottery: how proteins reach and recognize targets in DNA Redding, Sy Eugene 2015 Theses Promoters (Genetics)DNA-protein interactionsDNA-binding proteinsBiophysicsBiochemistryBiology
2. Watching the Replisome: Single-molecule Studies of Eukaryotic DNA Replication Duzdevich, Daniel 2017 Theses DNA replicationMolecular biologyCytologyEukaryotic cells--GeneticsBiologyBiophysics
3. Visualizing the One-Dimensional Diffusion of DNA Mismatch Repair Proteins at the Single-Molecule Level Gorman, Jason 2011 Theses BiologyBiochemistryBiophysicsDNA repairEukaryotic cells--Genetics
4. Visualizing cell surface interactions using cryogenic electron microscopy Rapp, Micah 2021 Theses BiophysicsBiochemistryElectron microscopyCOVID-19 (Disease)Low temperature engineeringCell membranesCell receptorsImmunoglobulins
5. Viscous Nonlinear Dynamics of Twist and Writhe Goldstein, Raymond E.; Powers, Thomas R.; Wiggins, Chris H. 1998 Articles Biophysics
6. Using structure to explore the sequence alignment space of remote homologs Kuziemko, Andrew Stephen 2011 Theses BiophysicsHomology (Biology)Sequence alignment (Bioinformatics)
7. Using single molecule magnetic tweezers to dissect titin energy release during muscle contraction Eckels, Edward Charles 2019 Theses BiophysicsBiochemistryPhysiologyMagnetic tweezersMuscle contractionProtein folding
8. Understanding complex biomolecular systems through the synergy of molecular dynamics simulations, NMR spectroscopy and X-Ray crystallography Zeiske, Tim 2016 Theses Molecular dynamics--Simulation methodsMolecular dynamics--Computer simulationNuclear magnetic resonance spectroscopyBiomolecules--Computer simulationX-ray crystallographyMacromolecules--StructureMolecular dynamicsBiophysicsBiochemistry
9. Trapping and Wiggling: Elastohydrodynamics of Driven Microfilaments Wiggins, Chris H.; Riveline, D.; Ott, A.; Goldstein, Raymond E. 1998 Articles Biophysics
10. Transient Dynamics in Neural Networks Schaffer, Evan Shuman 2011 Theses NeurosciencesMathematicsBiophysicsNeural networks (Neurobiology)Transients (Dynamics)Neural circuitry
11. Towards the integration of structural and systems biology: structure-based studies of protein-protein interactions on a genome-wide scale Zhang, Qiangfeng Cliff 2012 Theses BioinformaticsBiophysicsSystems biologyProtein-protein interactionsGenomes
12. Towards more robust and efficient methods for the calculation of Protein-Ligand binding affinities Wang, Lingle 2012 Theses ChemistryBiophysicsDrugs
13. Tools and Methods to Engineer the Industrial Microorganism Acidithiobacillus ferrooxidans Kernan, Timothy Michael 2017 Theses BiophysicsIndustrial microorganismsBioengineering
14. The Synaptic Weight Matrix: Dynamics, Symmetry Breaking, and Disorder Fumarola, Francesco 2018 Theses NeurosciencesBiophysicsNeural circuitryDynamics
15. The signaling lipid sphingosine 1-phosphate regulates mechanical pain Hill, Rose Z.; Hoffman, Benjamin U.; Morita, Takeshi; Campos, Stephanie M.; Lumpkin, Ellen A.; Brem, Rachel B.; Bautista, Diana M. 2018 Articles NeurosciencesPainBiophysicsNociceptive pain
16. The sensitivity of the cochlear amplifier to changes in operating conditions Wang, Yi 2019 Theses Biomedical engineeringBiophysicsCochleaFrequency response (Dynamics)Animal models in researchAudiology
17. The Saccharomyces cerevisiae Srs2 Helicase Regulates Homologous Recombination through the Disassembly of Recombination Intermediates Kaniecki, Kyle Stephen 2018 Theses GeneticsBiophysicsBiochemistrySaccharomyces cerevisiaeGenetic recombination
18. The Role of Ribosome and tRNA Dynamics in the Regulation of Translation Elongation Ning, Wei 2014 Theses RibosomesGenetic translationTransfer RNABiophysics
19. The Role of Initiation Factor Dynamics in Translation Initiation Elvekrog, Margaret Mary 2011 Theses ChemistryBiophysicsBiochemistry
20. The Role of Eukaryotic Recombinase Loop L1 During Homologous Recombination Steinfeld, Justin Benjamin 2018 Theses BiophysicsBiochemistryGeneticsGenetic recombinationEukaryotic cells
21. The relationship between intracellular forces and cellular stiffness investigated by atomic force microscopy Mandriota, Nicola 2016 Theses Cells--Mechanical propertiesCellsBiomechanicsNanotechnologyBiophysics
22. The Regulation and Function of RGK Proteins on Voltage-Gated Calcium Channel Physiology Chang, Donald Dao-Yuan 2015 Theses GTPase-activating proteinProteins--AnalysisCalcium channelsPhysiologyBiophysics
23. The Physical State of Water in Dormant Bacteria DeLay, Michael 2018 Theses BiophysicsBacteriaBacterial sporesWaterBiology
24. The pH-sensing mechanism of antibody recycling by the neonatal Fc receptor revealed using free energy perturbation calculations Sampson, Jared Matthew 2021 Theses BiophysicsImmune system--PhysiologyImmunoglobulinsChemical bondsMutation (Biology)
25. The Molecular Mechanism of the Escherichia Coli vitamin B12 Transporter BtuCD-F: Real-time Observation of the Transporter in Motion Kim, Jinrang 2012 Theses ATP-binding cassette transportersBiological transportEscherichia coliBiophysics
26. The Functional Mechanism of the Bacterial Ribosome, an Archetypal Biomolecular Machine Ray, Korak Kumar 2023 Theses BiophysicsChemistry, Physical and theoreticalRibosomesBiomoleculesMolecular biology--Statistical methodsBayesian statistical decision theoryMarkov processes
27. The Endoplasmic Spreading Mechanism of Fibroblasts: Showcasing the Integrated Cytoskeleton Lynch, Christopher D. 2012 Theses CytologyBiophysicsMolecular biology
28. The Critical Assessment of Protein Dynamics using Molecular Dynamics (MD) Simulations and Nuclear Magnetic Resonance (NMR) Spectroscopy Experimentation Hsu, Andrew 2020 Theses BiophysicsBiochemistryNuclear magnetic resonance spectroscopyMolecular dynamics--Computer simulation
29. The Catalytic Efficiency and Conformational Dynamics of Escherichia coli DNA Repair Enzyme AlkB Ergel, Burce 2012 Theses BiochemistryBiophysicsOxidoreductasesCatalysisProteins
30. The A and B conformations of DNA and RNA subunits. Potential energy calculations for dGpdC Broyde, Suse B.; Stellman, Steven D.; Wartell, Roger M. 1975 Articles BiochemistryBiophysicsGenetics
31. Temporal Processing by Caenorhabditis elegans Sensory Neurons Kato, Saul Sen 2013 Theses NeurosciencesBiologyBiophysics
32. Systematically Mapping the Epigenetic Context Dependence of Transcription Factor Binding Kribelbauer, Judith Franziska 2018 Theses BiochemistryBioinformaticsBiophysicsTranscription factorsGene regulatory networksEpigenetics
33. Synaptic State Matching: A Dynamical Architecture for Predictive Internal Representation and Feature Detection Tavazoie, Saeed 2013 Articles Neural networks (Neurobiology)SynapsesPerceptual-motor processesMolecular biologyBiophysicsNeurosciences
34. Synaptic Elasticity Yang, Ju 2018 Theses BiophysicsNeurosciencesNanotechnologySynapsesNeuroplasticityElasticity
35. Surface Acoustic Waves Enhance Neutrophil Killing of Bacteria Loike, John D.; Plitt, Anna; Kothari, Komal; Zumeris, Jona; Budhu, Sadna; Kavalus, Kaitlyn; Ray, Yonatan; Jacob, Harold 2013 Articles MicrobiologyBiophysics
36. Studies on Eukaryotic Pre-mRNA 3'-End Processing: Insights into PAS Recognition and the U7 snRNP activity Gutierrez Tamayo, Pedro A. 2023 Theses BiologyBiochemical geneticsBiophysicsEukaryotic cells--GeneticsMessenger RNAVertebratesMammals--Molecular genetics
37. Studies of the Unusually Extended DNA Inside the Pf1 Bacteriophage by Solid-State NMR and Computational Methods Sergeyev, Ivan 2012 Theses ChemistryBiophysicsChemistry, Physical and theoretical
38. Studies of the structure of potassium channel KcsA in the open conformation and the effect of anionic lipids on channel inactivation Zhang, Dongyu 2019 Theses ChemistryBiophysicsPotassium channelsMembrane proteinsMembrane lipids
39. Studies of Allostery in the Potassium Channel Kcsa by Solid-state NMR Xu, Yunyao 2018 Theses BiophysicsChemistryPotassium channelsAllosteric regulation
40. Structure of guanylyl-3′,5′-cytidine monophosphate. II. Description of the molecular and crystal structure of the calcium derivative in space group P2₁ Hingerty, B.; Subramanian, E.; Stellman, Steven D.; Broyde, Suse B.; Sato, T.; Langridge, R. 1975 Articles BiochemistryBiophysicsGenetics
41. Structure Characterization of the 70S-BipA Complex Using Novel Methods of Single-Particle Cryo-Electron Microscopy Ho, Danny Nam 2014 Theses Bacterial proteinsElectron microscopyAntibacterial agentsCryoelectronicsBiologyBiophysics
42. Structure-based analysis of CysZ-mediated cellular uptake of sulfate Assur, Zahra; Liu, Qun; Clarke, Oliver B.; Belcher Dufrisne, Meagan Leigh; Wiriyasermkul, Pattama; Giesem, M. Hunter; Leal-Pinto, Edgar; Kloss, Brian; Tabuso, Shantelle; Love, James; Punta, Marco; Banerjee, Surajit; Rajashankar, Kanagalaghatta R.; Rost, Burkhard; Logothetis, Diomedes; Quick, Matthias; Hendrickson, Wayne A.; Mancia, Filippo 2018 Articles CytologySulfatesExtracellular matrixCell physiologyBiophysics
43. Structure and Function of Glutamate Receptor-Like Channels (GLRs) Green, Marriah Noel 2023 Theses NutritionBiochemistryBiophysicsGlutamic acidLigand binding (Biochemistry)Arabidopsis thalianaCell receptors
44. Structure and Function of a Transposon-Encoded CRISPR-Cas System Halpin-Healy, Tyler Sheehan 2021 Theses BiochemistryBiophysicsMolecular biologyVibrio choleraeRNADNA
45. Structural studies on bestrophin anion channels by cryogenic electron microscopy Owji, Aaron Paul 2022 Theses BiophysicsBiochemistryEye--PhysiologyChloride channelsKlebsiella pneumoniaeMammalsMutagenesis
46. Structural Studies of E. coli FtsZ Filaments McCoy, Kelsey 2021 Theses BiophysicsMicrobiologyCytoskeletal proteinsEscherichia coliStaphylococcus aureus
47. Structural Determinants of Ionotropic Glutamate Receptor Function Revealed by Cryo- electron Microscopy Twomey, Edward Charles 2018 Theses BiophysicsGlutamic acid--ReceptorsElectron microscopyNeural transmissionCentral nervous system
48. Structural Determinants of DNA-binding Specificity for Hox Proteins Liu, Peng 2012 Theses BiophysicsBioinformatics
49. Structural basis of suppression of host translation termination by Moloney Murine Leukemia Virus Tang, Xuhua; Zhu, Yiping; Baker, Stacey L.; Bowler, Matthew W.; Chen, Benjamin Jieming; Chen, Chen; Hogg, J. Robert; Goff, Stephen P.; Song, Haiwei 2016 Articles Mouse leukemia virusesReverse transcriptaseMolecular biologyVirologyBiophysicsGenetic translation
50. Structural and Functional Studies of TRPML1 and TRPP2 Benvin, Nicole Marie 2017 Theses BiologyBiochemistryBiophysicsTRP channelsProteins--Structure
51. Structural and Functional Studies of CNG channels Hu, Zhengshan 2023 Theses BiologyBiochemistryBiophysicsCyclic nucleotides--AnalysisIon channelsCryoelectronicsElectron microscopy
52. Structural and Functional Studies of Biotin-Dependent Carboxylases Huang, Christine S. 2013 Theses BiochemistryBiophysics
53. Structural and biophysical studies of the Drosophila melanogaster Dpr and DIP families Cosmanescu, Filip 2018 Theses BiochemistryNeurosciencesBiophysicsDrosophila melanogasterNeurons
54. Structural and Biophysical Studies of Hair Cell Mechanotransduction Proteins Dionne, Gilman 2020 Theses BiochemistryBiophysicsProteinsCellular signal transduction--Research
55. Structural and biophysical characterization of protocadherin extracellular regions Wolcott, Holly Noelle 2014 Theses BiochemistryBiophysics
56. Structural and Biochemical Studies of the Human pre-mRNA 3’-end Processing Complex Hamilton, Keith 2021 Theses BiochemistryBiophysicsMessenger RNA--AnalysisMutagenesis
57. Spectroscopic Studies of Abiotic and Biological Nanomaterials: Silver Nanoparticles, Rhodamine 6G Adsorbed on Graphene, and c-Type Cytochromes and Type IV Pili in Geobacter sulfurreducens Thrall, Elizabeth Simmons 2012 Theses Chemistry, Physical and theoreticalNanoscienceBiophysics
58. Spatial Organization and Segregation of Cells in Breast Cancer Devanny, Alexander 2021 Theses BiophysicsBreast--CancerCytologyCancer cellsBreast--Tumors
59. Solving Challenging Structures using Single-Particle Cryogenic Electron Microscopy Tan, Yong Zi 2019 Theses BiochemistryBiophysicsElectron microscopyMacromolecules--StructureRibosomesMembrane proteinsCytology--Technique
60. Solid State NMR Relaxation Studies of Triosephosphate Isomerase Quinn, Caitlin 2013 Theses ChemistryBiophysics
61. Solid-State NMR Lineshape Broadening at Cryogenic Temperatures Yi, Xu 2023 Theses BiophysicsLow temperature researchTetrahydrofolate dehydrogenaseEscherichia coli
62. Single-molecule studies of nucleic acid dynamics using carbon nanotube-based field-effect transistors Daly, Nathan Scott 2017 Theses Nucleic acidsNucleic acid hybridizationPhysical organic chemistryCarbon nanotubesChemistry, Physical and theoreticalBiophysicsElectrical engineering
63. Single-molecule observations of hRPA, RAD51, and RAD52 on single-stranded DNA Ma, Chu Jian 2017 Theses BiochemistryBiophysicsDNA replicationGenetic recombinationMolecular biology
64. Single-Molecule Imaging of Conformational Dynamics in a Neurotransmitter Transporter Homolog Kolster, Rachel Ann 2016 Theses BiophysicsNeurosciencesBiological transportNeurotransmitters
65. Single-Molecule Analysis of Ribosome and Initiation Factor Dynamics during the Late Stages of Translation Initiation MacDougall, Daniel David 2012 Theses Genetic translationBiochemistryRibosomesBiophysics
66. Routine single particle CryoEM sample and grid characterization by tomography Noble, Alex J.; Dandey, Venkata P.; Wei, Hui; Brasch, Julia; Chase, Jillian; Acharya, Priyamvada; Tan, Yong Zi; Zhang, Zhening; Kim, Laura Y.; Scapin, Giovanna; Rapp, Micah Allen; Eng, Edward T.; Rice, William J.; Cheng, Anchi; Negro, Carl J.; Shapiro, Lawrence S.; Kwong, Peter D.; Jeruzalmi, David; des Georges, Amedee; Potter, Clinton; Carragher, Bridget 2018 Articles TomographyBiochemistryParticlesBiophysicsElectron microscopy
67. RNA force field with accuracy comparable to state-of-the-art protein force fields Tan, Dazhi; Piana, Stefano; Dirks, Robert M.; Shaw, David Elliot 2018 Articles BiochemistryBiophysicsRNA-protein interactionsMolecular dynamicsNucleic acids
68. Relaxation Dynamics of Semiflexible Polymers Bohbot-Raviv, Y.; Zhao, W. Z.; Feingold, M.; Wiggins, Chris H.; Granek, R. 2004 Articles Biophysics
69. Regulation of Release Factor 2 in Non-canonical Translation Pathways Huang, Bridget Yih Jiin 2017 Theses Bacterial proteinsRibosomesBiochemistryProteins--SynthesisBiophysics
70. Regulation of Mitochondrial Complex I Biogenesis in Drosophila Flight Muscles Garcia, Christian Joel; Khajeh, Jahan; Coulanges, Emmanuel; Chen, Emily I-ju; Owusu-Ansah, Edward 2017 Articles Mitochondria--FormationDrosophilaCytologyBiophysics
71. Reduced natriuretic response to acute sodium loading in COMT Gene deleted mice Odlind, Cecilia; Reenilä, Ilkka; Männistö, Pekka; Juvonen, Risto; Uhlén, Staffan; Gogos, Joseph A.; Karayiorgou, Maria; Hansell, Peter 2002 Articles MethyltransferasesSodium in the bodyDopamine--MetabolismPhysiologyBiophysicsCytology
72. Real-time observation of vitamin B12 transport by BtuCD-F at the single-molecule level Zhu, Lingwei 2022 Theses BiophysicsHydrolysisVitamin B12ATP-binding cassette transporters
73. Quantification of gait parameters in freely walking wild type and sensory deprived Drosophila melanogaster Mendes, Cesar; Bartos, Imre; Akay, Turgay; Marka, Szabolcs; Mann, Richard S. 2013 Articles BiochemistryBiophysicsNeurosciences
74. Quantification of Cell Edge Velocities and Traction Forces Reveals Distinct Motility Modules during Cell Spreading Dubin-Thaler, Benjamin J.; Hofman, Jake M.; Cai, Yunfei; Xenias, Harry; Spielman, Ingrid; Shneidman, Anna V.; David, Lawrence A.; Dobereiner, Hans-Gunther; Wiggins, Chris H.; Sheetz, Michael P. 2008 Articles BiophysicsCytology
75. Protein Structure Dynamics and Function at Micelle and Particle Interfaces Chin, Michael 2015 Theses ChemistryBiochemistryBiophysics
76. Proteins at Interfaces: Conformational Behavior and Wear Dumont, Emmanuel Louis Pierre 2014 Theses BiophysicsBiomedical engineering
77. Probing static disorder in protein unfolding and chemical reactions by single-molecule force spectroscopy Kuo, Tzu-Ling 2011 Theses Biophysics
78. Prediction of enzyme function based on 3D templates of evolutionarily important amino acids Kristensen, David; Ward, R Matthew; Lisewski, Andreas; Erdin, Serkan; Chen, Brian Y; Fofanov, Viacheslav; Kimmel, Marek; Kavraki, Lydia; Lichtarge, Olivier 2008 Articles GenomicsProteins--StructureBiophysicsMolecular biology
79. Potassium Channelopathies in Pulmonary Arterial Hypertension Bohnen, Michael S. 2017 Theses BiophysicsMedicinePulmonary hypertensionPotassium channelsIon channels
80. Potassium Channel KcsA and Its Lipid Environment Howarth, Gary Stanley 2019 Theses BiophysicsChemistry, Physical and theoreticalMembrane proteinsPotassium channelsNuclear magnetic resonance spectroscopy
81. Pinpointing beta adrenergic receptor in ageing pathophysiology: victim or executioner? Evidence from crime scenes Santulli, Gaetano; Iaccarino, Guido 2013 Articles BiophysicsCytology
82. Oxidative Folding in Bacteria: Studies Using Single Molecule Force Spectroscopy Kahn, Thomas 2016 Theses Protein foldingOxidoreductasesEscherichia coli--PhysiologyOxidationBiophysicsBiochemistry
83. Origin of Exocytotic Fusion Pore Dynamics Stratton, Benjamin Somerall 2015 Theses VirusesCellular control mechanismsFusionCell membranesCytologyBiophysics
84. Orientations and Proximities of the Extracellular Ends of Transmembrane Helices S0 and S4 in Open and Closed BK Potassium Channels Niu, Xiaowei; Liu, Guoxia; Wu, Roland; Chudasama, Neelesh; Zakharov, Sergey; Karlin, Arthur; Marx, Steven O. 2013 Articles BiochemistryMolecular biologyBiophysicsMedicine
85. Orientation of DNA Minicircles Balances Density and Topological Complexity in Kinetoplast DNA Diao, Yuanan; Rodriguez, Victor Alfonso; Klingbeil, Michele; Arsuaga, Javier 2015 Articles TopologyKinetoplastidaDNA replicationBiophysicsDNA-binding proteinsTrypanosomatidaeGenetics
86. Optimization and characterization of noise for ion channel and carbon nanotube biosensing platforms Ong, Peijie 2020 Theses Electrical engineeringBiophysicsNanotechnologyCarbon nanotubes
87. Nucleosome Curtains and their application to the study of DNA condensation by condensin Moevus, Corentin Jean 2019 Theses BiochemistryBiophysicsDNACondensed matter
89. Nonmuscle Myosin IIA-Dependent Force Inhibits Cell Spreading and Drives F-Actin Flow Cai, Yunfei; Biais, Nicolas; Giannone, Gregory; Tanase, Monica; Jiang, Guoying; Hoffman, Jake M.; Wiggins, Chris H.; Silberzan, Pascal; Buguin, Alex; Ladoux, Benoit; Sheetz, Michael P. 2006 Articles BiophysicsCytology
90. Nonlinear optical microscopy for the invisible: vibrational imaging of small molecules in live cells and electronic imaging of fluorophores into the ultra deep Wei, Lu 2015 Theses ChemistryChemistry, Physical and theoreticalBiophysics
91. Noise Optimization for High-Bandwidth Ion Channel Recordings Rosenstein, Jacob 2013 Theses Electrical engineeringBiophysicsBiomedical engineering
92. NMR Studies of the GCN4 Transcription Factor and Hox DNA Consensus Sequences Crawley, Timothy 2023 Theses BiophysicsMolecular biologyDNABootstrap (Statistics)Nuclear magnetic resonance spectroscopyDNA-binding proteins
93. Neurons in Cat Primary Visual Cortex cluster by degree of tuning but not by absolute spatial phase or temporal response phase Ziskind, Avi 2013 Theses NeurosciencesBiophysicsVisual cortexCatsTetrodes
94. Neuronal MHC-I display in T-cell mediated neurodegeneration Cebrian, Carolina; Zucca, Fabio; Zecca, Luigi; Loike, John D.; Sulzer, David L. 2013 Articles Parkinson's diseaseT cellsNervous system--DegenerationMajor histocompatibility complexNeurologyBiophysicsMedical sciences
95. Network Structures Arising from Spike-Timing Dependent Plasticity Babadi, Baktash 2011 Theses NanoscienceBiophysics
96. Nanoscale Electrical and Coarse-grained Molecular Dynamics Studies of Influenza Hemagglutinin-mediated Membrane Fusion Pores Alcott, Brett Eugene 2017 Theses BiophysicsBiochemistryVirologyMolecular dynamicsMembrane fusion
97. Multiple events on single molecules: unbiased estimation in single-molecule biophysics. Koster, Daniel A.; Wiggins, Chris H.; Dekker, Nynke H. 2006 Articles BiophysicsMathematics
98. Molecular pain, a new era of pain research and medicine Yoshimura, Megumu; Gu, Jianguo; Zhuo, Min; Caterina, Michael; MacDermott, Amy B.; Malmberg, Annika; Neugebauer, Volker 2005 Articles Neurobiology--ResearchPain--Physiological aspectsPain--ResearchBiophysicsMedical sciencesMolecular biology
99. Minimum energy conformations of DNA dimeric subunits: Potential energy calculations for dGpdC, dApdA, dCpdC, dGpdG, and dTpdT Broyde, Suse B.; Wartell, Roger M.; Stellman, Steven D.; Hingerty, B. 1978 Articles BiochemistryBiophysicsGenetics
100. MicroRNAs and the cellular response to rapamycin: Potential role in diagnosis and therapy Totary-Jain, Hana; Marks, Andrew R. 2013 Articles CytologyBiophysicsMedicine