Matching Items (8)
Filtering by
- All Subjects: Molecular Dynamics
- Creators: Beckstein, Oliver
- Creators: Solanki, Kiran
- Status: Published
Description
Recently, the use of zinc oxide (ZnO) nanowires as an interphase in composite materials has been demonstrated to increase the interfacial shear strength between carbon fiber and an epoxy matrix. In this research work, the strong adhesion between ZnO and carbon fiber is investigated to elucidate the interactions at the interface that result in high interfacial strength. First, molecular dynamics (MD) simulations are performed to calculate the adhesive energy between bare carbon and ZnO. Since the carbon fiber surface has oxygen functional groups, these were modeled and MD simulations showed the preference of ketones to strongly interact with ZnO, however, this was not observed in the case of hydroxyls and carboxylic acid. It was also found that the ketone molecules ability to change orientation facilitated the interactions with the ZnO surface. Experimentally, the atomic force microscope (AFM) was used to measure the adhesive energy between ZnO and carbon through a liftoff test by employing highly oriented pyrolytic graphite (HOPG) substrate and a ZnO covered AFM tip. Oxygen functionalization of the HOPG surface shows the increase of adhesive energy. Additionally, the surface of ZnO was modified to hold a negative charge, which demonstrated an increase in the adhesive energy. This increase in adhesion resulted from increased induction forces given the relatively high polarizability of HOPG and the preservation of the charge on ZnO surface. It was found that the additional negative charge can be preserved on the ZnO surface because there is an energy barrier since carbon and ZnO form a Schottky contact. Other materials with the same ionic properties of ZnO but with higher polarizability also demonstrated good adhesion to carbon. This result substantiates that their induced interaction can be facilitated not only by the polarizability of carbon but by any of the materials at the interface. The versatility to modify the magnitude of the induced interaction between carbon and an ionic material provides a new route to create interfaces with controlled interfacial strength.
ContributorsGalan Vera, Magdian Ulises (Author) / Sodano, Henry A (Thesis advisor) / Jiang, Hanqing (Committee member) / Solanki, Kiran (Committee member) / Oswald, Jay (Committee member) / Speyer, Gil (Committee member) / Arizona State University (Publisher)
Created2013
Description
Hydrogen embrittlement (HE) is a phenomenon that affects both the physical and chemical properties of several intrinsically ductile metals. Consequently, understanding the mechanisms behind HE has been of particular interest in both experimental and modeling research. Discrepancies between experimental observations and modeling results have led to various proposals for HE mechanisms. Therefore, to gain insights into HE mechanisms in iron, this dissertation aims to investigate several key issues involving HE such as: a) the incipient crack tip events; b) the cohesive strength of grain boundaries (GBs); c) the dislocation-GB interactions and d) the dislocation mobility.
The crack tip, which presents a preferential trap site for hydrogen segregation, was examined using atomistic methods and the continuum based Rice-Thompson criterion as sufficient concentration of hydrogen can alter the crack tip deformation mechanism. Results suggest that there is a plausible co-existence of the adsorption induced dislocation emission and hydrogen enhanced decohesion mechanisms. In the case of GB-hydrogen interaction, we observed that the segregation of hydrogen along the interface leads to a reduction in cohesive strength resulting in intergranular failure. A methodology was further developed to quantify the role of the GB structure on this behavior.
GBs play a fundamental role in determining the strengthening mechanisms acting as an impediment to the dislocation motion; however, the presence of an unsurmountable barrier for a dislocation can generate slip localization that could further lead to intergranular crack initiation. It was found that the presence of hydrogen increases the strain energy stored within the GB which could lead to a transition in failure mode. Finally, in the case of body centered cubic metals, understanding the complex screw dislocation motion is critical to the development of an accurate continuum description of the plastic behavior. Further, the presence of hydrogen has been shown to drastically alter the plastic deformation, but the precise role of hydrogen is still unclear. Thus, the role of hydrogen on the dislocation mobility was examined using density functional theory and atomistic simulations. Overall, this dissertation provides a novel atomic-scale understanding of the HE mechanism and development of multiscale tools for future endeavors.
The crack tip, which presents a preferential trap site for hydrogen segregation, was examined using atomistic methods and the continuum based Rice-Thompson criterion as sufficient concentration of hydrogen can alter the crack tip deformation mechanism. Results suggest that there is a plausible co-existence of the adsorption induced dislocation emission and hydrogen enhanced decohesion mechanisms. In the case of GB-hydrogen interaction, we observed that the segregation of hydrogen along the interface leads to a reduction in cohesive strength resulting in intergranular failure. A methodology was further developed to quantify the role of the GB structure on this behavior.
GBs play a fundamental role in determining the strengthening mechanisms acting as an impediment to the dislocation motion; however, the presence of an unsurmountable barrier for a dislocation can generate slip localization that could further lead to intergranular crack initiation. It was found that the presence of hydrogen increases the strain energy stored within the GB which could lead to a transition in failure mode. Finally, in the case of body centered cubic metals, understanding the complex screw dislocation motion is critical to the development of an accurate continuum description of the plastic behavior. Further, the presence of hydrogen has been shown to drastically alter the plastic deformation, but the precise role of hydrogen is still unclear. Thus, the role of hydrogen on the dislocation mobility was examined using density functional theory and atomistic simulations. Overall, this dissertation provides a novel atomic-scale understanding of the HE mechanism and development of multiscale tools for future endeavors.
ContributorsAdlakha, Ilaksh (Author) / Solanki, Kiran (Thesis advisor) / Mignolet, Marc (Committee member) / Chawla, Nikhilesh (Committee member) / Jiang, Hanqing (Committee member) / Liu, Yongming (Committee member) / Arizona State University (Publisher)
Created2015
Description
In a typical living cell, millions to billions of proteins—nanomachines that fluctuate and cycle among many conformational states—convert available free energy into mechanochemical work. A fundamental goal of biophysics is to ascertain how 3D protein structures encode specific functions, such as catalyzing chemical reactions or transporting nutrients into a cell. Protein dynamics span femtosecond timescales (i.e., covalent bond oscillations) to large conformational transition timescales in, and beyond, the millisecond regime (e.g., glucose transport across a phospholipid bilayer). Actual transition events are fast but rare, occurring orders of magnitude faster than typical metastable equilibrium waiting times. Equilibrium molecular dynamics (EqMD) can capture atomistic detail and solute-solvent interactions, but even microseconds of sampling attainable nowadays still falls orders of magnitude short of transition timescales, especially for large systems, rendering observations of such "rare events" difficult or effectively impossible.
Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)—an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project—developing a hybrid atomistic-continuum method—is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.
Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)—an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project—developing a hybrid atomistic-continuum method—is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.
ContributorsSeyler, Sean L (Author) / Beckstein, Oliver (Thesis advisor) / Chamberlin, Ralph (Committee member) / Matyushov, Dmitry (Committee member) / Thorpe, Michael F (Committee member) / Vaiana, Sara (Committee member) / Arizona State University (Publisher)
Created2017
Description
Improved knowledge connecting the chemistry, structure, and properties of polymers is necessary to develop advanced materials in a materials-by-design approach. Molecular dynamics (MD) simulations can provide tremendous insight into how the fine details of chemistry, molecular architecture, and microstructure affect many physical properties; however, they face well-known restrictions in their applicable temporal and spatial scales. These limitations have motivated the development of computationally-efficient, coarse-grained methods to investigate how microstructural details affect thermophysical properties. In this dissertation, I summarize my research work in structure-based coarse-graining methods to establish the link between molecular-scale structure and macroscopic properties of two different polymers. Systematically coarse-grained models were developed to study the viscoelastic stress response of polyurea, a copolymer that segregates into rigid and viscous phases, at time scales characteristic of blast and impact loading. With the application of appropriate scaling parameters, the coarse-grained models can predict viscoelastic properties with a speed up of 5-6 orders of magnitude relative to the atomistic MD models. Coarse-grained models of polyethylene were also created to investigate the thermomechanical material response under shock loading. As structure-based coarse-grained methods are generally not transferable to states different from which they were calibrated at, their applicability for modeling non-equilibrium processes such as shock and impact is highly limited. To address this problem, a new model is developed that incorporates many-body interactions and is calibrated across a range of different thermodynamic states using a least square minimization scheme. The new model is validated by comparing shock Hugoniot properties with atomistic and experimental data for polyethylene. Lastly, a high fidelity coarse-grained model of polyethylene was constructed that reproduces the joint-probability distributions of structural variables such as the distributions of bond lengths and bond angles between sequential coarse-grained sites along polymer chains. This new model accurately represents the structure of both the amorphous and crystal phases of polyethylene and enabling investigation of how polymer processing such as cold-drawing and bulk crystallization affect material structure at significantly larger time and length scales than traditional molecular simulations.
ContributorsAgrawal, Vipin (Author) / Oswald, Jay (Thesis advisor) / Peralta, Pedro (Committee member) / Chamberlin, Ralph (Committee member) / Solanki, Kiran (Committee member) / Jiao, Yang (Committee member) / Arizona State University (Publisher)
Created2016
Description
Na+/H+ antiporters are vital membrane proteins for cell homeostasis, transporting Na+ ions in exchange for H+ across the lipid bilayer. In humans, dysfunction of these transporters are implicated in hypertension, heart failure, epilepsy, and autism, making them well-established drug targets. Although experimental structures for bacterial homologs of the human Na+/H+ have been obtained, the detailed mechanism for ion transport is still not well-understood. The most well-studied of these transporters, Escherichia coli NhaA, known to transport 2 H+ for every Na+ extruded, was recently shown to bind H+ and Na+ at the same binding site, for which the two ion species compete. Using molecular dynamics simulations, the work presented in this dissertation shows that Na+ binding disrupts a previously-unidentified salt bridge between two conserved residues, suggesting that one of these residues, Lys300, may participate directly in transport of H+. This work also demonstrates that the conformational change required for ion translocation in a homolog of NhaA, Thermus thermophilus NapA, thought by some to involve only small helical movements at the ion binding site, is a large-scale, rigid-body movement of the core domain relative to the dimerization domain. This elevator-like transport mechanism translates a bound Na+ up to 10 Å across the membrane. These findings constitute a major shift in the prevailing thought on the mechanism of these transporters, and serve as an exciting launchpad for new developments toward understanding that mechanism in detail.
ContributorsDotson, David L (Author) / Beckstein, Oliver (Thesis advisor) / Ozkan, Sefika B (Committee member) / Ros, Robert (Committee member) / Van Horn, Wade (Committee member) / Arizona State University (Publisher)
Created2016
Description
In real world applications, materials undergo a simultaneous combination of tension, compression, and torsion as a result of high velocity impact. The split Hopkinson pressure bar (SHPB) is an effective tool for analyzing stress-strain response of materials at high strain rates but currently little can be done to produce a synchronized combination of these varying impacts. This research focuses on fabricating a flange which will be mounted on the incident bar of a SHPB and struck perpendicularly by a pneumatically driven striker thus allowing for torsion without interfering with the simultaneous compression or tension. Analytical calculations are done to determine size specifications of the flange to protect against yielding or failure. Based on these results and other design considerations, the flange and a complementary incident bar are created. Timing can then be established such that the waves impact the specimen at the same time causing simultaneous loading of a specimen. This thesis allows research at Arizona State University to individually incorporate all uniaxial deformation modes (tension, compression, and torsion) at high strain rates as well as combining either of the first two modes with torsion. Introduction of torsion will expand the testing capabilities of the SHPB at ASU and allow for more in depth analysis of the mechanical behavior of materials under impact loading. Combining torsion with tension or compression will promote analysis of a material's adherence to the Von Mises failure criterion. This greater understanding of material behavior can be implemented into models and simulations thereby improving the accuracy with which engineers can design new structures.
ContributorsVotroubek, Edward Daniel (Author) / Solanki, Kiran (Thesis director) / Oswald, Jay (Committee member) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Natures hardworking machines, proteins, are dynamic beings. Comprehending the role of dynamics in mediating allosteric effects is paramount to unraveling the intricate mechanisms underlying protein function and devising effective protein design strategies. Thus, the essential objective of this thesis is to elucidate ways to use protein dynamics based tools integrated with evolution and docking techniques to investigate the effect of distal allosteric mutations on protein function and further rationally design proteins. To this end, I first employed molecular dynamics (MD) simulations, Dynamic Flexibility Index (DFI) and Dynamic Coupling Index (DCI) on PICK1 PDZ, Butyrylcholinesterase (BChE), and Dihydrofolate reductase (DHFR) to uncover how these proteins utilize allostery to tune activity. Moreover, a new classification technique (“Controller”/“Controlled”) based on asymmetry in dynamic coupling is developed and applied to DHFR to elucidate the effect of allosteric mutations on enzyme activity. Subsequently, an MD driven dynamics design approach is applied on TEM-1 β-lactamase to tailor its activity against β-lactam antibiotics. New variants were created, and using a novel analytical approach called "dynamic distance analysis" (DDA) the degree of dynamic similarity between these variants were quantified. The experimentally confirmed results of these studies showed that the implementation of MD driven dynamics design holds significant potential for generating variants that can effectively modulate activity and stability. Finally, I introduced an evolutionary guided molecular dynamics driven protein design approach, integrated co-evolution and dynamic coupling (ICDC), to identify distal residues that modulate binding site dynamics through allosteric mechanisms. After validating the accuracy of ICDC with a complete mutational data set of β-lactamase, I applied it to Cyanovirin-N (CV-N) to identify allosteric positions and mutations that can modulate binding affinity. To further investigate the impact of mutations on the identified allosteric sites, I subjected putative mutants to binding analysis using Adaptive BP-Dock. Experimental validation of the computational predictions demonstrated the efficacy of integrating MD, DFI, DCI, and evolution to guide protein design. Ultimately, the research presented in this thesis demonstrates the effectiveness of using evolutionary guided molecular dynamics driven design alongside protein dynamics based tools to examine the significance of allosteric interactions and their influence on protein function.
ContributorsKazan, Ismail Can (Author) / Ozkan, Sefika Banu (Thesis advisor) / Ghirlanda, Giovanna (Thesis advisor) / Mills, Jeremy (Committee member) / Beckstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2023
Description
Transition metal ions such as Zn2+, Mn2+, Co2+, and Fe2+ play crucial roles in organisms from all kingdoms of life. The homeostasis of these ions is mainly regulated by a group of secondary transporters from the cation diffusion facilitator (CDF) family. The mammalian zinc transporters (ZnTs), a subfamily of CDF, have been an important target for study as they are associated with several diseases, such as diabetes, delayed growth and osteopenia, Alzheimer’s disease, and Parkinsonism. The bacterial homolog of ZnTs, YiiP, is the first CDF transporter with a determined structure and is used as a model for studying the structural and mechanistic properties of CDF transporters. On the other hand, Molecular dynamics simulation has emerged as a valuable computational tool for exploring the physical basis of biological macromolecules' structure and function with atomic precision at femtosecond resolution. This work aims to elucidate the roles of the three Zn$2+ binding sites found on each YiiP protomer and the role of protons in the transport process of CDFs, which remain under debate despite previous thermodynamic and structural studies on YiiP. Cryo-EM, microscale thermophoresis (MST) and molecular dynamics (MD) simulations were used to address these questions. With a Zn2+ model that accurately reproduces experimental structures of the binding clusters, the dynamical influence of zinc binding on the transporter was accessed through MD simulations, which was consistent with the new cryo-EM structures. Zinc binding affinities obtained through MST were used to infer the stoichiometry of Zn2+/H+ antiport in combination with a microscopic thermodynamic model and constant pH simulations. The most likely microstates of H$^+$ and Zn2+ binding indicated a transport stoichiometry of 1 Zn2+ to 2-3 H+ depending on the external pH. A model describing the entire transport cycle of YiiP was finally built on these findings, providing insight into the structural and mechanistic properties of CDF transporters.
ContributorsFan, Shujie (Author) / Beckstein, Oliver (Thesis advisor) / Ozkan, Banu (Committee member) / Heyden, Matthias (Committee member) / Van Horn, Wade (Committee member) / Arizona State University (Publisher)
Created2023