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Articles 1 - 30 of 33
Full-Text Articles in Entire DC Network
Structural Analysis And Activity Correlation Of Amphiphilic Cyclic Antimicrobial Peptides Derived From The [W4R4] Scaffold, Shaima Ahmed El-Mowafi, Anastasia G. Konshina, Eman H. M. Mohammed, Nikolay A. Krylov, Roman G. Efremov, Keykavous Parang
Structural Analysis And Activity Correlation Of Amphiphilic Cyclic Antimicrobial Peptides Derived From The [W4R4] Scaffold, Shaima Ahmed El-Mowafi, Anastasia G. Konshina, Eman H. M. Mohammed, Nikolay A. Krylov, Roman G. Efremov, Keykavous Parang
Pharmacy Faculty Articles and Research
In our ongoing quest to design effective antimicrobial peptides (AMPs), this study aimed to elucidate the mechanisms governing cyclic amphiphilic AMPs and their interactions with membranes. The objective was to discern the nature of these interactions and understand how peptide sequence and structure influence antimicrobial activity. We introduced modifications into the established cyclic AMP peptide, [W4R4], incorporating an extra aromatic hydrophobic residue (W), a positively charged residue (R), or the unique 2,5-diketopiperazine (DKP). This study systematically explored the structure–activity relationships (SARs) of a series of cyclic peptides derived from the [W4R4] scaffold, …
Atomistic And Mesoscale Modeling Of Microstructure Development During Solid-State Sintering, Omar Hussein
Atomistic And Mesoscale Modeling Of Microstructure Development During Solid-State Sintering, Omar Hussein
All Dissertations
Interfaces are ubiquitous in materials systems, and they influence the processing and properties of nearly all engineering and functional materials. Examples include grain boundaries (GBs) in polycrystalline materials, free surfaces in nanoparticles, and phase boundaries in multiphase materials. Therefore, understanding and controlling interfacial processes is a key aspect of materials design and discovery efforts.
Recent developments in advanced manufacturing and synthesis techniques have enabled the fabrication of materials architectures with intricate nanoscale features. Of particular interest is solid-state sintering, known for creating complex and high-precision geometries with controlled microstructures. While sintering science has been the subject of active research, very …
Atomistic And Mesoscale Modeling Of Microstructure Development During Solid-State Sintering, Omar Marwan Isa Hussein
Atomistic And Mesoscale Modeling Of Microstructure Development During Solid-State Sintering, Omar Marwan Isa Hussein
All Dissertations
Interfaces are ubiquitous in materials systems, and they influence the processing and properties of nearly all engineering and functional materials. Examples include grain boundaries (GBs) in polycrystalline materials, free surfaces in nanoparticles, and phase boundaries in multiphase materials. Therefore, understanding and controlling interfacial processes is a key aspect of materials design and discovery efforts. Recent developments in advanced manufacturing and synthesis techniques have enabled the fabrication of materials architectures with intricate nanoscale features. Of particular interest is solid-state sintering, known for creating complex and high-precision geometries with controlled microstructures. While sintering science has been the subject of active research, very …
Combining Simulation And The Mspa Nanopore To Study P53 Dynamics And Interactions, Samantha A. Schultz
Combining Simulation And The Mspa Nanopore To Study P53 Dynamics And Interactions, Samantha A. Schultz
Masters Theses
p53 is a transcription factor and an important tumor suppressor protein that becomes activated due to DNA damage. Because of its role as a tumor suppressor, mutations in the gene that encodes it are found in over 50% of human cancers. The N-terminal transactivation domain (NTAD) of p53 is intrinsically disordered and modulates the function and interactions of p53 in the cell. Its disordered structure allows it to be controlled closely by post-translation modifications that regulate p53’s ability to bind DNA and interact with regulatory binding partners. p53 is an attractive target for developing cancer therapeutics, but its intrinsically disordered …
Thermal Conductivity And Mechanical Properties Of Interlayer-Bonded Graphene Bilayers, Afnan Mostafa
Thermal Conductivity And Mechanical Properties Of Interlayer-Bonded Graphene Bilayers, Afnan Mostafa
Masters Theses
Graphene, an allotrope of carbon, has demonstrated exceptional mechanical, thermal, electronic, and optical properties. Complementary to such innate properties, structural modification through chemical functionalization or defect engineering can significantly enhance the properties and functionality of graphene and its derivatives. Hence, understanding structure-property relationships in graphene-based metamaterials has garnered much attention in recent years. In this thesis, we present molecular dynamics studies aimed at elucidating structure-property relationships that govern the thermomechanical response of interlayer-bonded graphene bilayers.
First, we present a systematic and thorough analysis of thermal transport in interlayer-bonded twisted bilayer graphene (IB-TBG). We find that the introduction of interlayer C-C …
Compatibility Investigation Of Waste Plastics In Bitumen Via A Molecular Dynamics Method, Hui Yao, Xin Li, Hancheng Dan, Qingli Dai, Zhanping You
Compatibility Investigation Of Waste Plastics In Bitumen Via A Molecular Dynamics Method, Hui Yao, Xin Li, Hancheng Dan, Qingli Dai, Zhanping You
Michigan Tech Publications, Part 2
The compatibility between waste plastic polymers and bitumen is the most challenging issue hindering the improvement of modified bitumen performance. The current practice of recycled waste plastics includes the use of polyvinyl chloride (PVC), polypropylene (PP), polyethylene (PE), etc. This study was designed to investigate the compatibility of different waste plastic polymers with bitumen binders by conducting molecular dynamics (MD) simulations at different temperatures. The molecular models of these materials were constructed in this study for the compatibility analysis, and they include the base bitumen, polymers (PVC, PP, and PE), polymer- bitumen blending systems. Using the output and related calculations …
Ionic Partitioning Of Kcl In Aot Reverse Micelles From Molecular Dynamics Simulations, Max Crowder, Isabel Lizarraga, Joshua D. Patterson, Arun K. Sharma
Ionic Partitioning Of Kcl In Aot Reverse Micelles From Molecular Dynamics Simulations, Max Crowder, Isabel Lizarraga, Joshua D. Patterson, Arun K. Sharma
Biology and Chemistry Faculty Publications and Presentations
Reverse micelles are an important class of nanoreactors providing an array of applications. The structure and dynamics of aqueous reverse micelles have been intensely investigated, yet there are many subtleties involved in characterizing the arrangement of water and ionic species within these aggregates. The interfacial arrangement of water and dopants added to bis(2-ethylhexyl) sulfosuccinate sodium salt (AOT) reverse micelles were investigated by fully atomistic molecular dynamics simulations. Reverse micelles of increasing water to surfactant ratio were doped with concentrations of KCl from 0.0 to 1.0 M to analyze the partitioning of ions and water. Detailed analysis of pair density functions …
Molecular Dynamics Study Of Characterization In Metal-Free Friction Materials, Yizhan Zhang
Molecular Dynamics Study Of Characterization In Metal-Free Friction Materials, Yizhan Zhang
Electronic Theses and Dissertations
Metallic friction materials currently used in industry may adversely impact the environment. Substitutions for metals in friction materials, on the other hand, can introduce operational safety issues and other unforeseeable issues such as thermal-mechanical instabilities and insufficient strength. In view of it, this dissertation focuses on developing different kinds of materials from simple structure to complex structure and evaluating the material properties with the assistance of molecular dynamics (MD) tools at the nano scale.
First, the concept of the contacted surfaces in friction at the atomic scale was introduced in order to get accurate understanding of the friction process compared …
Universal Aspects Of Barrier Crossing Under Bias, Sudeep Adhikari, Kevin S. D. Beach
Universal Aspects Of Barrier Crossing Under Bias, Sudeep Adhikari, Kevin S. D. Beach
Faculty and Student Publications
The thermal activation process by which a system passes from one local energy minimum to another is a recurring motif in physics, chemistry, and biology. For instance, biopolymer chains are typically modeled in terms of energy landscapes, with folded and unfolded conformations represented by two distinct wells separated by a barrier. The rate of transfer between wells depends primarily on the height of the barrier, but it also depends on the details of the shape of the landscape along the trajectory. We consider the case of bias due to an external force, analogous to the pulling force applied in optical …
On The Origins Of Life — Modelling The Initial Stages Of Complex Coacervate Droplet Formation, Yixuan Wu
On The Origins Of Life — Modelling The Initial Stages Of Complex Coacervate Droplet Formation, Yixuan Wu
Western Libraries Undergraduate Research Awards (WLURAs)
Coacervate droplets are considered a plausible model for protocells due to their spontaneous formation and ability to compartmentalize macromolecules such as nucleic acid and peptides. Although experimental studies have observed and synthesized coacervates under different laboratory conditions, little is known about their structure. Here we present atomistic molecular dynamic simulations of the interactions between water and oppositely charged proteins that cluster together in a salt-dependent process. Observing such liquid-liquid phase separation on an atomic level would serve as a model for the initial stages of complex coacervate formation. Molecular Dynamics was used to compute diagnostics of the structure at different …
Comparative Analysis Of Conformational Dynamics And Systematic Characterization Of Cryptic Pockets In The Sars-Cov-2 Omicron Ba.2, Ba.2.75 And Xbb.1 Spike Complexes With The Ace2 Host Receptor: Confluence Of Binding And Structural Plasticity In Mediating Networks Of Conserved Allosteric Sites, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker
Comparative Analysis Of Conformational Dynamics And Systematic Characterization Of Cryptic Pockets In The Sars-Cov-2 Omicron Ba.2, Ba.2.75 And Xbb.1 Spike Complexes With The Ace2 Host Receptor: Confluence Of Binding And Structural Plasticity In Mediating Networks Of Conserved Allosteric Sites, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker
Mathematics, Physics, and Computer Science Faculty Articles and Research
In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterization of allosteric binding sites in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 spike full-length trimer complexes with the host receptor ACE2. Microsecond simulations, Markov state models and mutational scanning of binding energies of the SARS-CoV-2 BA.2 and BA.2.75 receptor binding domain complexes revealed the increased thermodynamic stabilization of the BA.2.75 variant and significant dynamic differences between these Omicron variants. Molecular simulations of the SARS-CoV-2 Omicron spike full-length trimer complexes …
Exploring Conformational Landscapes And Cryptic Binding Pockets In Distinct Functional States Of The Sars-Cov-2 Omicron Ba.1 And Ba.2 Trimers: Mutation-Induced Modulation Of Protein Dynamics And Network-Guided Prediction Of Variant-Specific Allosteric Binding Sites, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta
Exploring Conformational Landscapes And Cryptic Binding Pockets In Distinct Functional States Of The Sars-Cov-2 Omicron Ba.1 And Ba.2 Trimers: Mutation-Induced Modulation Of Protein Dynamics And Network-Guided Prediction Of Variant-Specific Allosteric Binding Sites, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta
Mathematics, Physics, and Computer Science Faculty Articles and Research
A significant body of experimental structures of SARS-CoV-2 spike trimers for the BA.1 and BA.2 variants revealed a considerable plasticity of the spike protein and the emergence of druggable binding pockets. Understanding the interplay of conformational dynamics changes induced by the Omicron variants and the identification of cryptic dynamic binding pockets in the S protein is of paramount importance as exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In the current study, we explore conformational landscapes and characterize the universe of binding pockets in multiple open and closed functional spike states of the BA.1 and BA.2 Omicron …
Equilibrium And Active Self-Assembly And Collective Properties Of Network-Based Biomaterials, Lauren Melcher
Equilibrium And Active Self-Assembly And Collective Properties Of Network-Based Biomaterials, Lauren Melcher
Theses
Biological systems have the unique ability to self-organize, respond to environmental stimuli, and generate autonomous motion and work. The fields of biomaterials and synthetic biology seek to recapitulate these remarkable properties of biological systems in in-vitro reconstitutions of biological systems, and in abiotic or biotic-abiotic hybrid materials to better understand the underlying rules of life and to predict the design principles of biomimetic smart materials. Motivated by this, we create bottom-up mathematical models, rooted in experiments, of network-based synthetic and biological materials. These encompass two-dimensional colloidal networks connected by rhythmic crosslinkers, and three-dimensional biopolymer networks assembled via depletion interactions, physical …
Establishing Physical And Chemical Mechanisms Of Polymerization And Pyrolysis Of Phenolic Resins For Carbon-Carbon Composites, Ivan Gallegos, Josh Kemppainen, Jacob R. Gissinger, Malgorzata Kowalik, Adri Van Duin, Kristopher E. Wise, S. Gowtham, Gregory Odegard
Establishing Physical And Chemical Mechanisms Of Polymerization And Pyrolysis Of Phenolic Resins For Carbon-Carbon Composites, Ivan Gallegos, Josh Kemppainen, Jacob R. Gissinger, Malgorzata Kowalik, Adri Van Duin, Kristopher E. Wise, S. Gowtham, Gregory Odegard
Michigan Tech Publications, Part 2
The complex structural and chemical changes that occur during polymerization and pyrolysis critically affect material properties but are difficult to characterize in situ. This work presents a novel, experimentally validated methodology for modeling the complete polymerization and pyrolysis processes for phenolic resin using reactive molecular dynamics. The polymerization simulations produced polymerized structures with mass densities of 1.24 ± 0.01 g/cm3 and Young's moduli of 3.50 ± 0.64 GPa, which are in good agreement with experimental values. The structural properties of the subsequently pyrolyzed structures were also found to be in good agreement with experimental X-ray data for the phenolic-derived carbon …
Evolution Of Overlapping Reading Frames In Virus Genomes, Laura Muñoz Baena
Evolution Of Overlapping Reading Frames In Virus Genomes, Laura Muñoz Baena
Electronic Thesis and Dissertation Repository
Viruses are formidable pathogens that represent the majority of biological entities in our planet, and their genomes are a source of interesting enigmas. One feature in which virus genomes are usually rich, is the presence of overlapping reading frames (OvRFs) — portions of the genome where the same nucleotide sequence encodes more than one protein. OvRFs are hypothesized to be used by viruses to encode proteins more compactly and to regulate transcription. In addition, OvRFs might be a source of gene novelty, facilitating the creation of new open reading frames (ORF) within the transcriptional context of existing ones.
To characterize …
A Polarizable Molecular Dynamics Potential For Molten Salt Property Prediction, Jared Thurgood
A Polarizable Molecular Dynamics Potential For Molten Salt Property Prediction, Jared Thurgood
Theses and Dissertations
The present study attempts to find an alternate computational tool to model the complex physical interactions within the molten salt FLiNaK in a way that is both efficient and accurate. Additionally, this study seeks to describe the effects of several different types of impurities on the FLiNaK salt system. This study selects two different polarizable force fields, the AMOEBA polarizable approach and the polarizable ion model, to determine the density and the structure of the impure FLiNaK salt mixtures at typical operating temperatures in molten salt reactors (between 500-900 °C). This study conducts ab initio molecular dynamics (AIMD) simulations and …
Atomistic Simulations Of Twin Facets Associated With Three-Dimensional { []011 } Twins In Magnesium, Qiyu Zeng, Mingyu Gong, Houyu Ma, Yao Shen, Jian-Feng Nie, Jian Wang, Yue Liu
Atomistic Simulations Of Twin Facets Associated With Three-Dimensional { []011 } Twins In Magnesium, Qiyu Zeng, Mingyu Gong, Houyu Ma, Yao Shen, Jian-Feng Nie, Jian Wang, Yue Liu
Department of Mechanical and Materials Engineering: Faculty Publications
Twinning is a deformation mechanism that creates three-dimensional (3D) twin domains through the migration of twin facets. This occurs via the nucleation and glide of twinning disconnections (TDs), which can pile up to create twin facets. A comprehensive under- standing of twin facets associated with 3D twins, including their atomic structures and energies, is crucial for understanding deformation twinning. In this study, we propose a molecular statics/dynamics (MS/MD) approach to determine characteristic twin facets enclosing 3D non-equilibrium/equilibrium { [] 011 } twin domains, which has been much less studied than the counterpart { [] 012 } twin domains. The stability …
Mechanical Properties And Deformation Mechanisms Of Nanocrystalline U-10mo Alloys By Molecular Dynamics Simulation, Xuelian Ou, Yanxin Shen, Yue Yang, Zhenjiang You, Peng Wang, Yexin Yang, Xiaofeng Tian
Mechanical Properties And Deformation Mechanisms Of Nanocrystalline U-10mo Alloys By Molecular Dynamics Simulation, Xuelian Ou, Yanxin Shen, Yue Yang, Zhenjiang You, Peng Wang, Yexin Yang, Xiaofeng Tian
Research outputs 2022 to 2026
U-Mo alloys were considered to be the most promising candidates for high-density nuclear fuel. The uniaxial tensile behavior of nanocrystalline U-10Mo alloys with average grain sizes of 8–23 nm was systematically studied by molecular dynamics (MD) simulation, mainly focusing on the influence of average grain size on the mechanical properties and deformation mechanisms. The results show that Young’s modulus, yield strength and ultimate tensile strength follow as average grain size increases. During the deformation process, localized phase transitions were observed in samples. Grain boundary sliding and grain rotation, as well as twinning, dominated the deformation in the smaller and larger …
Balancing Functional Tradeoffs Between Protein Stability And Ace2 Binding In The Sars-Cov-2 Omicron Ba.2, Ba.2.75 And Xbb Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic And Energetic Changes, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta
Balancing Functional Tradeoffs Between Protein Stability And Ace2 Binding In The Sars-Cov-2 Omicron Ba.2, Ba.2.75 And Xbb Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic And Energetic Changes, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta
Mathematics, Physics, and Computer Science Faculty Articles and Research
Evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and allosteric modulation. In this study, we systematically characterize conformational dynamics, structural stability and binding affinities of the SARS-CoV-2 Spike Omicron complexes with the host receptor ACE2 for BA.2, BA.2.75, XBB.1 and XBB.1.5 variants. We combined multiscale molecular simulations and dynamic analysis of allosteric interactions together with the ensemble-based mutational scanning of the protein residues and network modeling of epistatic interactions. This multifaceted computational study characterized molecular mechanisms and …
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 …
From Deep Mutational Mapping Of Allosteric Protein Landscapes To Deep Learning Of Allostery And Hidden Allosteric Sites: Zooming In On “Allosteric Intersection” Of Biochemical And Big Data Approaches, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
From Deep Mutational Mapping Of Allosteric Protein Landscapes To Deep Learning Of Allostery And Hidden Allosteric Sites: Zooming In On “Allosteric Intersection” Of Biochemical And Big Data Approaches, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
Mathematics, Physics, and Computer Science Faculty Articles and Research
The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approaches have been developed and actively deployed to facilitate computational and experimental studies of protein dynamics and allosteric mechanisms. In this review, we discuss in detail new developments along two major directions of allosteric research through the lens of data-intensive biochemical approaches and AI-based computational methods. Despite considerable progress in applications of AI methods for protein structure and dynamics studies, the intersection between allosteric …
Coarse-Grained Molecular Simulations And Ensemble-Based Mutational Profiling Of Protein Stability In The Different Functional Forms Of The Sars-Cov-2 Spike Trimers: Balancing Stability And Adaptability In Ba.1, Ba.2 And Ba.2.75 Variants, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta
Coarse-Grained Molecular Simulations And Ensemble-Based Mutational Profiling Of Protein Stability In The Different Functional Forms Of The Sars-Cov-2 Spike Trimers: Balancing Stability And Adaptability In Ba.1, Ba.2 And Ba.2.75 Variants, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta
Mathematics, Physics, and Computer Science Faculty Articles and Research
Evolutionary and functional studies have suggested that the emergence of Omicron variants can be determined by multiple fitness tradeoffs including immune escape, binding affinity, conformational plasticity, protein stability, and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability, and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined the conformational dynamics of the spike trimers that agree with the recent functional studies, suggesting that BA.2.75 trimers are the most stable …
Boron Nitride Nanotubes: Force Field Parameterization, Epoxy Interactions, And Comparison With Carbon Nanotubes For High-Performance Composite Materials, Swapnil S. Bamane, Michael B. Jakubinek, Krishan Kanhaiya, Behnam Ashrafi, Hendrik Heinz, Gregory Odegard
Boron Nitride Nanotubes: Force Field Parameterization, Epoxy Interactions, And Comparison With Carbon Nanotubes For High-Performance Composite Materials, Swapnil S. Bamane, Michael B. Jakubinek, Krishan Kanhaiya, Behnam Ashrafi, Hendrik Heinz, Gregory Odegard
Michigan Tech Publications
Boron nitride nanotubes (BNNTs) are a very promising reinforcement for future high-performance composites because of their excellent thermo-mechanical properties. To take full advantage of BNNTs in composite materials, it is necessary to have a comprehensive understanding of the wetting characteristics of various high-performance resins. Molecular dynamics (MD) simulations provide an accurate and efficient approach to establish the contact angle values of engineering polymers on reinforcement surfaces, which offers a measure for the interaction between the polymer and reinforcement. In this research, MD simulations and experiments are used to determine the wettability of various epoxy systems on BNNT surfaces. The reactive …
Development Of The Tlvmie Force Field And A Standardized Methodology For Improved Pure-Component And Mixture Liquid Viscosity Predictions, Daniel J. Carlson
Development Of The Tlvmie Force Field And A Standardized Methodology For Improved Pure-Component And Mixture Liquid Viscosity Predictions, Daniel J. Carlson
Theses and Dissertations
Existing viscosity prediction methods and relevant literature are reviewed. An exhaustive review of group contribution, corresponding states, and interpolative prediction methods finds that even the best of these models produces large prediction errors and often require significant experimental data. Molecular dynamics simulation techniques for viscosity prediction are evaluated and compared to one another to determine the best choice for this work. A thorough investigation finds that Equilibrium Molecular Dynamics (EMD) simulations are the best option for reproducible and reliable liquid viscosity predictions. The many tuning parameters available in molecular dynamics simulations are investigated for their effects on prediction uncertainty and …
Molecular Dynamic Studies Of Dye–Dye And Dye–Dna Interactions Governing Excitonic Coupling In Squaraine Aggregates Templated By Dna Holliday Junctions, German Barcenas, Austin Biaggne, Olga A. Mass, William B. Knowlton, Bernard Yurke, Lan Li
Molecular Dynamic Studies Of Dye–Dye And Dye–Dna Interactions Governing Excitonic Coupling In Squaraine Aggregates Templated By Dna Holliday Junctions, German Barcenas, Austin Biaggne, Olga A. Mass, William B. Knowlton, Bernard Yurke, Lan Li
Materials Science and Engineering Faculty Publications and Presentations
Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye–DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was …
Probing Dna Structural Heterogeneity By Identifying Conformational Subensembles Of A Bicovalently Bound Cyanine Dye, Matthew S. Barclay, Azhad U. Chowdhury, Austin Biaggne, Jonathan S. Huff, Nicholas D. Wright, Paul H. Davis, Lan Li, William B. Knowlton, Bernard Yurke, Ryan D. Pensack, Daniel B. Turner
Probing Dna Structural Heterogeneity By Identifying Conformational Subensembles Of A Bicovalently Bound Cyanine Dye, Matthew S. Barclay, Azhad U. Chowdhury, Austin Biaggne, Jonathan S. Huff, Nicholas D. Wright, Paul H. Davis, Lan Li, William B. Knowlton, Bernard Yurke, Ryan D. Pensack, Daniel B. Turner
Materials Science and Engineering Faculty Publications and Presentations
DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA–Cy5), double-stranded DNA (dsDNA–Cy5), and Holliday junction DNA (HJ–DNA–Cy5). A line shape analysis of the 2D spectra reveals a strong excitation–emission correlation present in only the dsDNA–Cy5 complex, which is …
Study Of Nanocomposite Materials Using Molecular Dynamics, Prashik Sunil Gaikwad
Study Of Nanocomposite Materials Using Molecular Dynamics, Prashik Sunil Gaikwad
Dissertations, Master's Theses and Master's Reports
There is an increase in demand for new lightweight structural materials in the aerospace industry for more efficient and affordable human space travel. Polymer matrix composites (PMCs) with reinforcement material as carbon nanotubes (CNTs) have shown exceptional increase in the mechanical properties. Flattened carbon nanotubes (flCNTs) are a primary component of many carbon nanotube (CNT) yarn and sheet materials, which are promising reinforcements for the next generation of ultra-strong composites for aerospace applications. These flCNT/polymer materials are subjected to extreme pressure and temperature during curing process. Therefore there is a need to investigate the evolution of properties during the curing …
Development Of Interatomic Potential Of High Entropy Diborides With Artificial Intelligence Approach To Simulate The Thermo-Mechanical Properties, Nur Aziz Octoviawan
Development Of Interatomic Potential Of High Entropy Diborides With Artificial Intelligence Approach To Simulate The Thermo-Mechanical Properties, Nur Aziz Octoviawan
MSU Graduate Theses
The interatomic potentials designed for binary/high entropy diborides and ultra-high temperature composites (UHTC) have been developed through the implementation of deep neural network (DNN) algorithms. These algorithms employed two different approaches and corresponding codes; 1) strictly local & invariant scalar-based descriptors as implemented in the DEEPMD code and 2) equivariant tensor-based descriptors as included in the ALLEGRO code. The samples for training and validation sets of the forces, energy, and virial data were obtained from the ab-initio molecular dynamics (AIMD) simulations and Density Functional Theory (DFT) calculations, including the simulation data from the ultra-high temperature region (> 2000K). The study …
Renewable Fuels: Molecular Dynamics Investigations Into Pyrolysis Of Methyl Linoleate, Elson Osakpolor Eguaosa
Renewable Fuels: Molecular Dynamics Investigations Into Pyrolysis Of Methyl Linoleate, Elson Osakpolor Eguaosa
MSU Graduate Theses
With the rapid depletion of the world’s supply of fossil fuels, especially petroleum products, petroleum prices have risen by approximately 800% between the 1970s and now and are projected to continue rising. It is also expected that the world’s consumption of energy will increase commensurate with its growing population. Although biodiesel is a good renewable alternative, it has its limitations including high production costs and poor low-temperature performance. We seek to improve conventional biodiesel with pyrolysis to produce low molecular-weight compounds with high energy densities. Understanding the pyrolysis path on the atomic scale is key as it will allow us …
Sars-Cov-2 Main Protease Targeting Potent Fluorescent Inhibitors: Repurposing Thioxanthones, Gönül Saadet Batibay, Eyüp Meti̇n
Sars-Cov-2 Main Protease Targeting Potent Fluorescent Inhibitors: Repurposing Thioxanthones, Gönül Saadet Batibay, Eyüp Meti̇n
Turkish Journal of Chemistry
The coronavirus disease, COVID-19, is the major focus of the whole world due to insufficient treatment options. It has spread all around the world and is responsible for the death of numerous human beings. The future consequences for the disease survivors are still unknown. Hence, all contributions to understand the disease and effectively inhibit the effects of the disease have great importance. In this study, different thioxanthone based molecules, which are known to be fluorescent compounds, were selectively chosen to study if they can inhibit the main protease of SARS-CoV-2 using various computational tools. All candidate ligands were optimized, molecular …