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Articles 1 - 12 of 12
Full-Text Articles in Physics
Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel
Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel
Honors Scholar Theses
Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …
The Role Of Conformational Changes In Viral And Bacterial Protein Functions, Md Lokman Hossen
The Role Of Conformational Changes In Viral And Bacterial Protein Functions, Md Lokman Hossen
FIU Electronic Theses and Dissertations
Proteins do versatile work in cells. They require a cascade of structural changes to perform different tasks like binding to the other neighboring biomolecules, transporting small chemicals, activating a chemical reaction, etc. The structural conformations of proteins can be critical in changing their working ability. In this dissertation, I investigated the role of conformational changes of viral protein, e.g., spike and envelope protein of SARS-CoV-2, and bacterial protein, e.g., multidrug transporter and toxic extrusion protein- PfMATE from Pyrococcus furiosus. Also, I performed molecular docking-based drug screening targeting the E protein to suggest a set of drugs that can be repurposed …
Monitoring Stem Cell Differentiation Using Raman Microspectroscopy: Chondrogenic Differentiation, Towards Cartilage Formation, Francesca Ravera, Esen Efeoglu, Hugh Byrne
Monitoring Stem Cell Differentiation Using Raman Microspectroscopy: Chondrogenic Differentiation, Towards Cartilage Formation, Francesca Ravera, Esen Efeoglu, Hugh Byrne
Articles
Mesenchymal Stem Cells (MSCs) have the ability to differentiate into chondrocytes, the only cellular components of cartilage and are therefore ideal candidates for cartilage and tissue repair technologies. Chondrocytes are surrounded by cartilage-like extracellular matrix (ECM), a complex network rich in glycosaminoglycans, proteoglycans, and collagen, which, together with a multitude of intracellular signalling molecules, trigger the chondrogenesis and allow the chondroprogenitor to acquire the spherical morphology of the chondrocytes. However, although the mechanisms of the differentiation of MSCs have been extensively explored, it has been difficult to provide a holistic picture of the process, in situ. Raman Micro Spectroscopy (RMS) …
Experimental Evidence Supportive Of The Quantum Dna Model, F. Matthew Mihelic
Experimental Evidence Supportive Of The Quantum Dna Model, F. Matthew Mihelic
Faculty Publications
The DNA molecule can be modeled as a quantum logic processor in which electron spin qubits are held coherently in each nucleotide in a logically and thermodynamically reversible enantiomeric symmetry, and can be coherently conducted along the pi-stacking interactions of aromatic nucleotide bases, while simultaneously being spin-filtered via the helicity of the DNA molecule. Entangled electron pairs can be separated by that spin-filtering, held coherently at biological temperatures in the topologically insulated nucleotide quantum gates, and incorporated into separate DNA strands during DNA replication. Two separate DNA strands that share quantum entangled electrons can be mitotically divided into individual cells, …
Industrial Grade 2d Molybdenum Disulphide (Mos2): An In-Vitro Exploration Of The Impact On Cellular Uptake, Cytotoxicity, And Inflammation, Caroline Moore, Hugh Byrne, Jonathan N. Coleman, Yuri Volkov, Jennifer Mcintyre
Industrial Grade 2d Molybdenum Disulphide (Mos2): An In-Vitro Exploration Of The Impact On Cellular Uptake, Cytotoxicity, And Inflammation, Caroline Moore, Hugh Byrne, Jonathan N. Coleman, Yuri Volkov, Jennifer Mcintyre
Articles
The recent surge in graphene research, since its liquid phase monolayer isolation and characterization in 2004, has led to advancements which are accelerating the exploration of alternative 2D materials such as molybdenum disulphide (MoS2), whose unique physico-chemical properties can be exploited in applications ranging from cutting edge electronic devices to nanomedicine. However, to assess any potential impact on human health and the environment, the need to understand the bio-interaction of MoS2 at a cellular and sub-cellular level is critical. Notably, it is important to assess such potential impacts of materials which are produced by large scale production techniques, rather than …
In Vitro Monitoring Of Time And Dose Dependent Cytotoxicity Of Aminated Nanoparticles Using Raman Spectroscopy, Esen Efeoglu, Alan Casey, Hugh Byrne
In Vitro Monitoring Of Time And Dose Dependent Cytotoxicity Of Aminated Nanoparticles Using Raman Spectroscopy, Esen Efeoglu, Alan Casey, Hugh Byrne
Articles
No abstract provided.
Spectroscopic Studies Of Anthracyclines: Structural Characterization And In Vitro Tracking, Zeineb Farhane, Hugh Byrne, Malgorzata Baranska
Spectroscopic Studies Of Anthracyclines: Structural Characterization And In Vitro Tracking, Zeineb Farhane, Hugh Byrne, Malgorzata Baranska
Articles
A broad spectroscopic characterization, using ultraviolet-visible (UV-vis) and Fourier transform infrared absorption as well as Raman scattering, of two commonly used anthracyclines antibiotics (DOX) daunorubicin (DNR), their epimers (EDOX, EDNR) and ten selected analogs is presented. The paper serves as a comprehensive spectral library of UV-vis, IR and Raman spectra of anthracyclines in the solid state and in solution. The particular advantage of Raman spectroscopy for the measurement and analysis of individual antibiotics is demonstrated. Raman spectroscopy can be used to monitor the in vitro uptake and distribution of the drug in cells, using both 488 nm and 785 nm …
A Comparison Of Catabolic Pathways Induced In Primary Macrophages By Pristine Single Walled Carbon Nanotubes And Pristine Graphene, Caroline More, Jennifer Mcintyre, Luke O'Neill, Hugh Byrne
A Comparison Of Catabolic Pathways Induced In Primary Macrophages By Pristine Single Walled Carbon Nanotubes And Pristine Graphene, Caroline More, Jennifer Mcintyre, Luke O'Neill, Hugh Byrne
Articles
Understanding the correlation between the physico-chemical properties of carbonaceous nanomaterials and how these properties impact on cells and subcelluar mechanisms is critical to their risk assessment and safe translation into newly engineered devices. Here the toxicity, uptake and catabolic response of primary human macrophages to pristine graphene (PG) and pristine single walled carbon nanotubes (pSWCNT) are explored, compared and contrasted. The nanomaterial toxicity was assessed using three complementary techniques (live-dead assay, real time impedance technique and confocal microscopic analysis), all of which indicated no signs of acute cytotoxicity in response to PG or pSWCNT. Transmission electron microscopy (TEM) demonstrated that …
Implications Of The Landauer Limit For Quantum Logic, F. Matthew Mihelic
Implications Of The Landauer Limit For Quantum Logic, F. Matthew Mihelic
Faculty Publications
The design of any system of quantum logic must take into account the implications of the Landauer limit for logical bits. Useful computation implies a deterministic outcome, and so any system of quantum computation must produce a final deterministic outcome, which in a quantum computer requires a quantum decision that produces a deterministic qubit. All information is physical, and any bit of information can be considered to exist in a physicality represented as a decision between the two wells of a double well potential in which the energy barrier between the two wells must be greater than kT·ln2. Any proposed …
Szilard Engine Reversibility As Quantum Gate Function, F. Matthew Mihelic
Szilard Engine Reversibility As Quantum Gate Function, F. Matthew Mihelic
Faculty Publications
A quantum gate is a logically and thermodynamically reversible situation that effects a unitary transformation of qubits of superimposed information, and essentially constitutes a situation for a reversible quantum decision. A quantum decision is a symmetry break, and the effect of the function of a Szilard engine is a symmetry break. A quantum gate is a situation in which a reversible quantum decision can be made, and so if a logically and thermodynamically reversible Szilard engine can be theoretically constructed then it would function as a quantum gate. While the traditionally theorized Szilard engine is not thermodynamically reversible, if one …
Growth And Transport Properties Of Complementary Germanium Nanowire Field Effect Transistors, Andrew B. Greytak, Lincoln J. Lauhon, Mark S. Gudiksen, Charles M. Lieber
Growth And Transport Properties Of Complementary Germanium Nanowire Field Effect Transistors, Andrew B. Greytak, Lincoln J. Lauhon, Mark S. Gudiksen, Charles M. Lieber
Faculty Publications
n- and p-type Ge nanowires were synthesized by a multistep process in which axial elongation, via vapor–liquid–solid (VLS) growth, and doping were accomplished in separate chemical vapor deposition steps. Intrinsic, single-crystal, Ge nanowires prepared by Au nanocluster-mediated VLS growth were surface-doped in situ using diborane or phosphine, and then radial growth of an epitaxial Ge shell was used to cap the dopant layer. Field-effect transistors prepared from these Ge nanowires exhibited on currents and transconductances up to 850 µA/µm and 4.9 µA/V, respectively, with device yields of >85%.
Shape Imprinting Due To Variable Disulfide Bonds In Polyacrylamide Gels, Andrew B. Greytak, Alexander Y. Grosberg, Toyoichi Tanaka
Shape Imprinting Due To Variable Disulfide Bonds In Polyacrylamide Gels, Andrew B. Greytak, Alexander Y. Grosberg, Toyoichi Tanaka
Faculty Publications
Through the use of variable disulfide crosslinkers, we have created polyacrylamide gels whose shape can be altered after polymerization. N,N'-bisacryloylcystamine is incorporated as a crosslinker, along with a smaller amount of a permanent crosslinker. After polymerization, the disulfide bonds are cleaved into thiols through reduction. By reoxidizing the thiols with the gel held in a new macroscopic shape, a new set of disulfide bonds is formed, and the gel is forced to adopt the new shape. Retension of the new shape improves with greater distortion from the original shape, as well as with increased concentration of variable …