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Articles 1 - 11 of 11
Full-Text Articles in Physics
Quantifying Anticancer Drug Doxorubicin Binding To Dna Using Optical Tweezers, Zachary Ells
Quantifying Anticancer Drug Doxorubicin Binding To Dna Using Optical Tweezers, Zachary Ells
Honors Program Theses and Projects
Doxorubicin is a successful anticancer drug approved for use in the 1970s and is considered to be one of the most effective cancer treatment methods today. Although Doxorubicin has positive survival statistics it has very negative side effects in many cases. Bleeding from the soles of the palms and feet, along with excruciating pain is often exhibited through the administration of this drug. Based on the preliminary findings utilizing optical tweezers we anticipate that this study will provide critical information about the drug binding mechanism. Single molecule biophysics techniques have provided useful insight into the DNA-binding mechanisms of small molecules. …
Single‐Molecule 3d Orientation Imaging Reveals Nanoscale Compositional Heterogeneity In Lipid Membranes, Jin Lu, Hesam Mazidi, Tianben Ding, Oumeng Zhang, Matthew D. Lew
Single‐Molecule 3d Orientation Imaging Reveals Nanoscale Compositional Heterogeneity In Lipid Membranes, Jin Lu, Hesam Mazidi, Tianben Ding, Oumeng Zhang, Matthew D. Lew
Electrical & Systems Engineering Publications and Presentations
In soft matter, thermal energy causes molecules to continuously translate and rotate, even in crowded environments, thereby impacting the spatial organization and function of most molecular assemblies, such as lipid membranes. Directly measuring the orientation and spatial organization of large collections (>3000 molecules μm−2) of single molecules with nanoscale resolution remains elusive. In this paper, we utilize SMOLM, single‐molecule orientation localization microscopy, to directly measure the orientation spectra (3D orientation plus “wobble”) of lipophilic probes transiently bound to lipid membranes, revealing that Nile red's (NR) orientation spectra are extremely sensitive to membrane chemical composition. SMOLM images resolve …
Evolutionary Algorithms Converge Towards Evolved Biological Photonic Structures, Mamadou Aliou Barry, Vincent Berthier, Bobo D. Wilts, Marie-Claire Cambourieux, Pauline Bennet, Rémi Pollès, Olivier Teytaud, Emmanuel Centeno, Nicolas Biais, Antoine Moreau
Evolutionary Algorithms Converge Towards Evolved Biological Photonic Structures, Mamadou Aliou Barry, Vincent Berthier, Bobo D. Wilts, Marie-Claire Cambourieux, Pauline Bennet, Rémi Pollès, Olivier Teytaud, Emmanuel Centeno, Nicolas Biais, Antoine Moreau
Publications and Research
Nature features a plethora of extraordinary photonic architectures that have been optimized through natural evolution in order to more efciently refect, absorb or scatter light. While numerical optimization is increasingly and successfully used in photonics, it has yet to replicate any of these complex naturally occurring structures. Using evolutionary algorithms inspired by natural evolution and performing particular optimizations (maximize refection for a given wavelength, for a broad range of wavelength or maximize the scattering of light), we have retrieved the most stereotypical natural photonic structures. Whether those structures are Bragg mirrors, chirped dielectric mirrors or the gratings on top of …
Circuits With Broken Fibration Symmetries Perform Core Logic Computations In Biological Networks, Ian Leifer, Flaviano Morone, Saulo D. S. Reis, José S. Andrade Jr., Mariano Sigman, Hernán A. Makse
Circuits With Broken Fibration Symmetries Perform Core Logic Computations In Biological Networks, Ian Leifer, Flaviano Morone, Saulo D. S. Reis, José S. Andrade Jr., Mariano Sigman, Hernán A. Makse
Publications and Research
We show that logic computational circuits in gene regulatory networks arise from a fibration symmetry breaking in the network structure. From this idea we implement a constructive procedure that reveals a hierarchy of genetic circuits, ubiquitous across species, that are surprising analogues to the emblematic circuits of solid-state electronics: starting from the transistor and progressing to ring oscillators, current-mirror circuits to toggle switches and flip-flops. These canonical variants serve fundamental operations of synchronization and clocks (in their symmetric states) and memory storage (in their broken symmetry states). These conclusions introduce a theoretically principled strategy to search for computational building blocks …
Kinetic Exclusion Assay Of Biomolecules By Aptamer Capture, Mark H. Smith, Daniel Fologea
Kinetic Exclusion Assay Of Biomolecules By Aptamer Capture, Mark H. Smith, Daniel Fologea
Physics Faculty Publications and Presentations
DNA aptamers are short nucleotide oligomers selected to bind a target ligand with affinity and specificity rivaling that of antibodies. These remarkable features recommend aptamers as candidates for analytical and therapeutic applications that traditionally use antibodies as biorecognition elements. Numerous traditional and emerging analytical techniques have been proposed and successfully implemented to utilize aptamers for sensing purposes. In this work, we exploited the analytical capabilities offered by the kinetic exclusion assay technology to measure the affinity of fluorescent aptamers for their thrombin target and quantify the concentration of analyte in solution. Standard binding curves constructed by using equilibrated mixtures of …
Additive Modulation Of Dna-Dna Interactions By Interstitial Ions, Wei Meng, Raju Timsina, Abby Bull, Kurt Andresen, Xiangyun Qiu
Additive Modulation Of Dna-Dna Interactions By Interstitial Ions, Wei Meng, Raju Timsina, Abby Bull, Kurt Andresen, Xiangyun Qiu
Physics and Astronomy Faculty Publications
Quantitative understanding of biomolecular electrostatics, particularly involving multivalent ions and highly charged surfaces, remains lacking. Ion-modulated interactions between nucleic acids provide a model system in which electrostatics plays a dominant role. Using ordered DNA arrays neutralized by spherical cobalt3+ hexammine and Mg2+ ions, we investigate how the interstitial ions modulate DNA-DNA interactions. Using methods of ion counting, osmotic stress, and x-ray diffraction, we systematically determine thermodynamic quantities, including ion chemical potentials, ion partition, DNA osmotic pressure and force, and DNA-DNA spacing. Analyses of the multidimensional data provide quantitative insights into their interdependencies. The key finding of this study is that …
Temporary Membrane Permeabilization Via The Pore-Forming Toxin Lysenin, Nisha Shrestha, Christopher A. Thomas, Devon Richtsmeier, Andrew Bogard, Rebecca Hermann, Malyk Walker, Gamid Abatchev, Raquel J. Brown, Daniel Fologea
Temporary Membrane Permeabilization Via The Pore-Forming Toxin Lysenin, Nisha Shrestha, Christopher A. Thomas, Devon Richtsmeier, Andrew Bogard, Rebecca Hermann, Malyk Walker, Gamid Abatchev, Raquel J. Brown, Daniel Fologea
Physics Faculty Publications and Presentations
Pore-forming toxins are alluring tools for delivering biologically-active, impermeable cargoes to intracellular environments by introducing large conductance pathways into cell membranes. However, the lack of regulation often leads to the dissipation of electrical and chemical gradients, which might significantly affect the viability of cells under scrutiny. To mitigate these problems, we explored the use of lysenin channels to reversibly control the barrier function of natural and artificial lipid membrane systems by controlling the lysenin’s transport properties. We employed artificial membranes and electrophysiology measurements in order to identify the influence of labels and media on the lysenin channel’s conductance. Two cell …
Got Science? Club, Nora Husein, Randa Ismail
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.
Fibration Symmetries Uncover The Building Blocks Of Biological Networks, Flaviano Morone, Ian Leifer, Hernán A. Makse
Fibration Symmetries Uncover The Building Blocks Of Biological Networks, Flaviano Morone, Ian Leifer, Hernán A. Makse
Publications and Research
A major ambition of systems science is to uncover the building blocks of any biological network to decipher how cellular function emerges from their interactions. Here, we introduce a graph representation of the information flow in these networks as a set of input trees, one for each node, which contains all pathways along which information can be transmitted in the network. In this representation, we find remarkable symmetries in the input trees that deconstruct the network into functional building blocks called fibers. Nodes in a fiber have isomorphic input trees and thus process equivalent dynamics and synchronize their activity. Each …
Consciousness As A Factor In Evolution, Kenneth A. Augustyn
Consciousness As A Factor In Evolution, Kenneth A. Augustyn
Michigan Tech Publications
What I call the mind began as a non-conscious robotic biochemical process control system in the very earliest forms of life. As life evolved, problems in control became more difficult and exceeded the computational capabilities of the organisms. Nature discovered a means of transcending computable physical processes resulting in non-computational subjective mental capabilities that, while still not conscious, had a degree of genuine autonomy from the physical world. These autonomous subjective wants and goals now affected the course of (but not the mechanism of) evolution. The integrated amalgam of robotic and transrobotic unconscious capabilities eventually gave rise to consciousness, which …
Special Issue On The Third Workshop On Biological Mentality, Kenneth A. Augustyn
Special Issue On The Third Workshop On Biological Mentality, Kenneth A. Augustyn
Michigan Tech Publications
The Third Workshop on Biological Mentality was held from September 23, 2019 to March 2, 2020 as a series of twenty-one Monday online conferencing sessions, each consisting of a talk followed by a Q&A discussion. Like the two previous workshops [1, 2], the objective of this workshop was to seek a deeper level of understanding the physical foundations of biological mentality (whether conscious or nonconscious).