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Self-Assembly Of Black Cumin Oil-Based Nanoemulsion On Various Surfactants: A Molecular Dynamics Study, Aulia Fikri Hidayat, Taufik Muhammad Fakih
Self-Assembly Of Black Cumin Oil-Based Nanoemulsion On Various Surfactants: A Molecular Dynamics Study, Aulia Fikri Hidayat, Taufik Muhammad Fakih
Makara Journal of Science
Black cumin is commonly used as traditional medicine due to its wide range of pharmacological potential. Black cumin oil (BCO) was often prepared as nanoemulsion to improve its solubility, stability, and bioavailability. This study was conducted to investigate the molecular behavior as well as structural evolution of BCO-surfactant systems during self-assembly micellization using molecular dynamics (MD) simulations. Several BCO constituents and variations of surfactants were employed to model BCO-surfactant systems. 50 ns of MD simulations were performed to elucidate their evolution of structures and physicochemical properties during formation. Results showed that BCO-tween20 and BCO-lecithin were able to form spherical-shaped micelles …
Computational Analysis Of Type 3 Iodothyronine Deiodinase: Potential Inhibitors, Substrate Binding, And Dimer Structure, Eric Scott Marsan
Computational Analysis Of Type 3 Iodothyronine Deiodinase: Potential Inhibitors, Substrate Binding, And Dimer Structure, Eric Scott Marsan
Chemistry & Biochemistry Theses & Dissertations
Thyroid hormones (THs) in mammalian tissues are crucial for development and maintaining metabolic homeostasis. Iodothyronine deiodinases (Dios) remove iodines from THs by a selenocysteine (Sec) residue, which either activates or inactivates them. Halogen bonding (XB) has been proposed to describe the interaction between the Se and I atoms of the T4-Dio complex. Disruption of TH homeostasis by xenobiotics, such as polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) can cause deleterious effects on the endocrine system. Experimental studies have indicated that PBDEs and PCBs could disrupt TH homeostasis by inhibiting Dio through XB formation. However, no current quantitative study exists …
Coevolution, Dynamics And Allostery Conspire In Shaping Cooperative Binding And Signal Transmission Of The Sars-Cov-2 Spike Protein With Human Angiotensin-Converting Enzyme 2, Gennady M. Verkhivker
Coevolution, Dynamics And Allostery Conspire In Shaping Cooperative Binding And Signal Transmission Of The Sars-Cov-2 Spike Protein With Human Angiotensin-Converting Enzyme 2, Gennady M. Verkhivker
Mathematics, Physics, and Computer Science Faculty Articles and Research
Binding to the host receptor is a critical initial step for the coronavirus SARS-CoV-2 spike protein to enter into target cells and trigger virus transmission. A detailed dynamic and energetic view of the binding mechanisms underlying virus entry is not fully understood and the consensus around the molecular origins behind binding preferences of SARS-CoV-2 for binding with the angiotensin-converting enzyme 2 (ACE2) host receptor is yet to be established. In this work, we performed a comprehensive computational investigation in which sequence analysis and modeling of coevolutionary networks are combined with atomistic molecular simulations and comparative binding free energy analysis of …
A Physics-Based Intermolecular Potential For Biomolecular Simulation, Joshua Andrew Rackers
A Physics-Based Intermolecular Potential For Biomolecular Simulation, Joshua Andrew Rackers
Arts & Sciences Electronic Theses and Dissertations
The grand challenge of biophysics is to use the fundamental laws of physics to predict how biological molecules will move and interact. The atomistic HIPPO (Hydrogen-like Intermolecular Polarizable Potential) force field is meant to address this challenge. It does so by breaking down the intermolecular potential energy function of biomolecular interactions into physically meaningful components (electrostatics, polarization, dispersion, and exchangerepulsion) and using this function to drive molecular dynamics simulations. This force field is able to achieve accuracy within 1 kcal/mol for each component when compared with ab initio Symmetry Adapted Perturbation Theory calculations. HIPPO is capable of this accuracy because …
Fast-Forward Protein Folding And Design: Development, Analysis, And Applications Of The Fast Sampling Algorithm, Maxwell Isaac Zimmerman
Fast-Forward Protein Folding And Design: Development, Analysis, And Applications Of The Fast Sampling Algorithm, Maxwell Isaac Zimmerman
Arts & Sciences Electronic Theses and Dissertations
Molecular dynamics simulations are a powerful tool to explore conformational landscapes, though limitations in computational hardware commonly thwart observation of biologically relevant events. Since highly specialized or massively parallelized distributed supercomputers are not available to most scientists, there is a strong need for methods that can access long timescale phenomena using commodity hardware. In this thesis, I present the goal-oriented sampling method, Fluctuation Amplification of Specific Traits (FAST), that takes advantage of Markov state models (MSMs) to adaptively explore conformational space using equilibrium-based simulations. This method follows gradients in conformational space to quickly explore relevant conformational transitions with orders of …
Ab Initio Methyl Linoleate Bond Dissociation Energies: First Principles Fishing For Wise Crack Products, Zachary Ryan Wilson
Ab Initio Methyl Linoleate Bond Dissociation Energies: First Principles Fishing For Wise Crack Products, Zachary Ryan Wilson
MSU Graduate Theses
With the prices of petroleum reflecting demand for this finite resource, attention has been turned to alternative sources of energy. Biodiesel, defined as fatty acid methyl esters (FAMEs), exhibits many of the same properties as conventional diesel but is derived from biological sources. FAMEs are subsequently thermally cracked to form more light-weight petrochemical products. I aim to further understand the thermal cracking procedure, at an atomic-level, in hopes that this may aid in future engineering of viable fuels. I studied the effective computational modeling of bond disassociations in the FAME methyl linoleate. Bond dissociation in a 44-reaction database with known …
Computational Optimization And Characterization Of Molecularly Imprinted Polymers, Jacob Jordan Terracina
Computational Optimization And Characterization Of Molecularly Imprinted Polymers, Jacob Jordan Terracina
Legacy Theses & Dissertations (2009 - 2024)
Molecularly imprinted polymers (MIPs) are a class of materials containing sites capable of selectively binding to the imprinted target molecule. Computational chemistry techniques were used to study the effect of different fabrication parameters (the monomer-to-target ratios, pre-polymerization solvent, temperature, and pH) on the formation of the MIP binding sites. Imprinted binding sites were built in silico for the purposes of better characterizing the receptor – ligand interactions. Chiefly, the sites were characterized with respect to their selectivities and the heterogeneity between sites.
Theoretical Investigation Of Interaction Between The Set Of Ligands And Α7 Nicotinic Acetylcholine Receptor, O. E. Glukhova, Tatiana Prytkova, D. S. Shmygin
Theoretical Investigation Of Interaction Between The Set Of Ligands And Α7 Nicotinic Acetylcholine Receptor, O. E. Glukhova, Tatiana Prytkova, D. S. Shmygin
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Nicotinic acetylcholine receptors (nAChRs) are neuron receptor proteins that provide a transmission of nerve impulse through the synapses. They are composed of a pentametric assembly of five homologous subunits (5 α7 subunits for α7nAChR, for example), oriented around the central pore. These receptors might be found in the chemical synapses of central and peripheral nervous system, and also in the neuromuscular synapses. Transmembrane domain of the one of such receptors constitutes ion channel. The conductive properties of ion channel strongly depend on the receptor conformation changes in the response of binding with some molecule, f.e. acetylcholine. Investigation of interaction between …
Use Of Quantum Mechanical Calculations To Investigate Small Silicon Carbide Clusters, Jean W. Henry
Use Of Quantum Mechanical Calculations To Investigate Small Silicon Carbide Clusters, Jean W. Henry
Theses and Dissertations
Density Functional Theory (DFT) method was employed to model silicon carbide small clusters. Comparing the DFT calculation results with experimental results that observed by using photoelectron spectroscopy (PES), DFT predicts the same structures that experiment observed. For electron affinity, DFT results are in good agreement with experimental results, the root mean square negative offset 0.1 eV found using medium size of basis set (cc-pVDZ+) calculation. DFT results for vibrational frequencies are in good agreement with experiment results; the root mean square error is 72.5 cm-1 wave number. 16 ground state structures of SimCn (m ≤ 4, …