Browsing by Subject "Molecular dynamics"

Now showing 1 - 20 of 26

Open Access
Ab initio temperature dependent studies of the homoepitaxial growth on Si(0 0 1) surface
(2001) Dağ, S.; Çıracı, Salim; Kılıç, Ç.; Fong, C. Y.
We performed ab initio zero temperature and finite temperature molecular dynamics calculations to investigate the homoepitaxial growth on the Si(0 0 1) surface. How do the deposited atoms (adatoms) form addimers and how do the addimers reach their favorable positions at the nucleation site of the growth process are presented. Once two epitaxial addimers, one over the dimer row and oriented perpendicular to the surface dimer bonds and the other over the adjacent trough, are aligned at high temperature, the nucleation site of the growth process is formed. The concerted bond exchange between these addimers and the reconstructed surface dimers is found to be the atomistic mechanism that leads to the homoepitaxial growth. © 2001 Elsevier Science B.V.
Open Access
Atomic strings of group IV, III-V, and II-VI elements
(American Institute of Physics, 2004) Tongay, S.; Durgun, Engin; Çıracı, Salim
A systematic first-principles study of atomic strings made by group IV, III-V, and II-VI elements has revealed interesting mechanical, electronic, and transport properties. The double bond structure underlies their unusual properties. We found that linear chain of C, Si, Ge, SiGe, GaAs, InSb, and CdTe are stable and good conductor, although their parent diamond (zincblende) crystals are covalent (polar) semiconductors but, compounds SiC, BN, AlP, and ZnSe are semiconductors. First row elements do not form zigzag structures.
Open Access
The BioPAX community standard for pathway data sharing
(Nature Publishing Group, 2010-09) Demir, Emek; Cary, M. P.; Paley, S.; Fukuda, K.; Lemer, C.; Vastrik, I.; Wu, G.; D'Eustachio, P.; Schaefer, C.; Luciano, J.; Schacherer, F.; Martinez-Flores, I.; Hu, Z.; Jimenez-Jacinto, V.; Joshi-Tope, G.; Kandasamy, K.; Lopez-Fuentes, A. C.; Mi, H.; Pichler, E.; Rodchenkov, I.; Splendiani, A.; Tkachev, S.; Zucker, J.; Gopinath, G.; Rajasimha, H.; Ramakrishnan, R.; Shah, I.; Syed, M.; Anwar, N.; Babur, Özgün; Blinov, M.; Brauner, E.; Corwin, D.; Donaldson, S.; Gibbons, F.; Goldberg, R.; Hornbeck, P.; Luna, A.; Murray-Rust, P.; Neumann, E.; Reubenacker, O.; Samwald, M.; Iersel, Martijn van; Wimalaratne, S.; Allen, K.; Braun, B.; Whirl-Carrillo, M.; Cheung, Kei-Hoi; Dahlquist, K.; Finney, A.; Gillespie, M.; Glass, E.; Gong, L.; Haw, R.; Honig, M.; Hubaut, O.; Kane, D.; Krupa, S.; Kutmon, M.; Leonard, J.; Marks, D.; Merberg, D.; Petri, V.; Pico, A.; Ravenscroft, D.; Ren, L.; Shah, N.; Sunshine, M.; Tang R.; Whaley, R.; Letovksy, S.; Buetow, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Doğrusöz, Uğur; McWeeney, S.; Aladjem, M.; Birney, E.; Collado-Vides, J.; Goto, S.; Hucka, M.; Novère, Nicolas Le; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G. D.
Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. © 2010 Nature America, Inc. All rights reserved.
Open Access
Chiral ceramic nanoparticles and peptide catalysis
(American Chemical Society, 2017) Jiang S.; Chekini, M.; Qu, Z.-B.; Wang Y.; Yeltik A.; Liu, Y.; Kotlyar, A.; Zhang, T.; Li, B.; Demir, Hilmi Volkan; Kotov, N. A.
The chirality of nanoparticles (NPs) and their assemblies has been investigated predominantly for noble metals and II-VI semiconductors. However, ceramic NPs represent the majority of nanoscale materials in nature. The robustness and other innate properties of ceramics offer technological opportunities in catalysis, biomedical sciences, and optics. Here we report the preparation of chiral ceramic NPs, as represented by tungsten oxide hydrate, WO3-x·H2O, dispersed in ethanol. The chirality of the metal oxide core, with an average size of ca. 1.6 nm, is imparted by proline (Pro) and aspartic acid (Asp) ligands via bio-to-nano chirality transfer. The amino acids are attached to the NP surface through C-O-W linkages formed from dissociated carboxyl groups and through amino groups weakly coordinated to the NP surface. Surprisingly, the dominant circular dichroism bands for NPs coated by Pro and Asp are different despite the similarity in the geometry of the NPs; they are positioned at 400-700 nm and 500-1100 nm for Pro- and Asp-modified NPs, respectively. The differences in the spectral positions of the main chiroptical band for the two types of NPs are associated with the molecular binding of the two amino acids to the NP surface; Asp has one additional C-O-W linkage compared to Pro, resulting in stronger distortion of the inorganic crystal lattice and greater intensity of CD bands associated with the chirality of the inorganic core. The chirality of WO3-x·H2O atomic structure is confirmed by atomistic molecular dynamics simulations. The proximity of the amino acids to the mineral surface is associated with the catalytic abilities of WO3-x·H2O NPs. We found that NPs facilitate formation of peptide bonds, leading to Asp-Asp and Asp-Pro dipeptides. The chiroptical activity, chemical reactivity, and biocompatibility of tungsten oxide create a unique combination of properties relevant to chiral optics, chemical technologies, and biomedicine.
Open Access
Development of force fields for novel 2D materials for temperature dependent vibrational properties
(2019-09) Mobaraki, Arash
A new era of nanodevice engineering has been started after fabricating graphene. This motivated vast number of researches for predicting, fabricating and utilizing 2D materials. Temperature dependent properties are essential for device applications. Although rigorous density functional theory based approaches are able to predict electronic and mechanical properties accurately, but they are mostly limited to zero temperature and ab initio based molecular dynamics are computationally very demanding. Classical molecular dynamics is a very powerful alternative, however its accuracy is basically depend on the interatomic potential used for describing the considered system and therefore constructing accurate force fields is always an open problem, especially for the emerging 2D materials with extra ordinary properties. Single-layer transition metal dichalcogenides (TMDs) are new class of 2D materials which are shown to be good candidates for thermoelectric applications, flexible electronic and optoelectronic devices. In order to investigate thermal properties of TMDs, Stillinger-Weber type potentials are developed using particle swarm optimization method. These potentials are validated by comparing the resulted phonon dispersion curves and thermal conductivities with available first principle and experimental results. In addition, for understanding the anharmonic effects imposed by the generated force fields the trends of the shifts of the optical phonon frequencies at 􀀀 point with variation in the temperature are compared with available experimental data. In all cases, optimized potentials generate results which are in agreement with the target data. In the second step, spectral energy density method together with phonon mode decomposition is used for obtaining temperature dependent phonon frequencies and lifetimes in entire Brillouin zone. The contribution of each phonon branch in thermal conductivity is predicted utilizing the obtained phonon lifetimes and group velocities within the framework of relaxation time approximation. Eventually, with the aim of constructing transferable potentials for describing 2D and bulk structures, a very fast and reliable optimization method is presented. Combining local and global optimization methods and utilizing the energy curves obtained from first principle method, novel Stillinger-Weber type potentials for graphene, silicene and group III nitrides are developed. The proposed approach provides a solid framework for parameter selection and investigating the role of each parameter in the resulted phonon dispersion curves.
Open Access
Dynamic correlation effects on the plasmon dispersion in a two-dimensional electron gas
(The American Physical Society, 2003) Yurtsever, A.; Moldoveanu, V.; Tanatar, Bilal
The charge-density oscillations (plasmons) of a low-density two-dimensional uniform electron gas are studied within the framework of finite temperature and frequency dependent (dynamic) version of Singwi, Tosi, Land, and Sjölander theory and compared with the recent experimental results. The use of the Hartree-Fock approximation for the static structure factor leads to a finite temperature dynamical counterpart of the static Hubbard approximation. We observe important differences between dynamic and static local-field factors as well as between the corresponding plasmon dispersion laws. Our calculated plasmon energies that include dynamic correlations are in very-good agreement with the recent experimental results.
Open Access
Dynamic correlations in double-layer electron systems
(The American Physical Society, 2001) Tanatar, Bilal; Davoudi, B.
We study the effects of dynamic correlations on the ground-state properties of a double-layer two-dimensional electron gas within the quantum Singwi-Tosi-Land-Sjölander theory (STLS). The intralayer and interlayer static structure factors, the pair-correlation functions, and the wave vector and frequency-dependent local-field factors have been calculated for a range of electron densities and layer separations. We find that the local-field factors have an oscillatory frequency dependence and the magnitude of interlayer local-field factors is about an order of magnitude smaller than that of the intralayer. Our results are compared with the random-phase approximation and the static STLS approximation to assess the importance of dynamical correlations. We also calculate the dispersion relations for the optical and acoustic plasmons and the damping of these modes to compare them with other mean-field theories, and we comment on the relevance of our results to the recent experiments.
Open Access
Effects of temperature, pH and counterions on the stability of peptide amphiphile nanofiber structures
(Royal Society of Chemistry, 2016) Ozkan A.D.; Tekinay, A. B.; Güler, Mustafa O.; Tekin, E. D.
Peptide amphiphiles are a class of self-assembling molecules that are widely used to form bioactive nanostructures for various applications in bionanomedicine. However, peptide molecules can exhibit distinct behaviors under different conditions, suggesting that environmental variables such as temperature, pH, electrolytes and the presence of biological factors may greatly affect the self-assembly process. In this work, we used united-atom molecular dynamics simulations to understand the effects of three counterions (Na+, Ca2+ at pH 7 and Cl- at pH 2) and temperature change on the stability of the lauryl-VVAGERGD peptide amphiphile self-assembly. This molecule contains a bioactive RGD peptide sequence and has been shown to support cellular adhesion and proliferation in vitro. A 19-layered peptide nanostructure, containing 12 peptide amphiphile molecules per layer, was previously shown to exhibit optimal stability and it was used as the model nanofiber system. Peptide backbone stability was studied under increasing temperatures (300-358 K) using the number of hydrogen bonds and root-mean-square deviations of nanofiber size. At higher temperatures, fiber disintegration was observed to be dependent on the type of counter-ion used for nanofiber formation. Interestingly, rapid heating to higher temperatures could sometimes reestablish the integrity of the nanofiber backbone, possibly by allowing the system to bypass an energy barrier and assuming a more thermodynamically stable configuration. As counterion identity was observed to exhibit remarkable effects on the thermal stability of peptide nanofibers, we suggest that these behaviors should be considered while developing new materials for potential applications.
Open Access
Fast multipole methods in service of various scientific disciplines
(IEEE, 2014) Gürel, Levent
For more than two decades, several forms of fast multipole methods have been extremely successful in various scientific disciplines. Reduced complexity solutions are obtained for solving different forms of equations that are derived from Maxwell's equations, such as Helmholtz's equation for electrodynamics and Laplace's equation for electrostatics. Fast multipole solvers are developed for and applied to the integral equations derived from Helmholtz's and Laplace's equations. Fast multipole solvers are kernel-dependent techniques, i.e., they rely on certain analytical properties of the integral-equation kernels, such as diagonalizability. Electromagnetics is not the only discipline benefiting from the fast multipole methods; a plethora of computations in various disciplines, such as the solution of Schroedinger's equation in quantum mechanics and the calculation of gravitational force in astrophysics, to name a few, exploit the reduced-complexity nature of the fast multipole methods. Acoustics, molecular dynamics, structural mechanics, and fluid dynamics can be mentioned as other disciplines served by the fast multipole methods. © 2014 IEEE.
Open Access
Finite temperature studies of Te adsorption on Si(0 0 1)
(Elsevier, 2002) Sen, P.; Çıracı, Salim; Batra, I. P.; Grein, C. H.; Sivananthan, S.
We perform first principles density functional calculations to investigate the adsorption of Te on the Si(0 0 1) surface from low coverage up to a monolayer coverage. At low coverage, a Te atom is adsorbed on top of the Si surface dimer bond. At higher coverages, Te atoms adsorption causes the Si-Si dimer bond to break, lifting the (2 × 1) reconstruction. We find no evidence of the Te-Te dimer bond formation as a possible source of the (2 × 1) reconstruction at a monolayer coverage. Finite temperature ab initio molecular dynamics calculations show that Te covered Si(0 0 1) surfaces do not have any definitive reconstruction. Vibrations of the bridged Te atoms in the strongly anharmonic potentials prevent the reconstruction structure from attaining any permanent, two-dimensional periodic geometry. This explains why experiments attempting to find a definite model for the reconstruction reached conflicting conclusions. © 2002 Elsevier Science B.V. All rights reserved.
Open Access
Hierarchical self-assembly of histidine-functionalized peptide amphiphiles into supramolecular chiral nanostructures
(American Chemical Society, 2017) Koc, M. H.; Ciftci, G. C.; Baday, S.; Castelletto, V.; Hamley, I. W.; Güler, Mustafa O.
Controlling the hierarchical organization of self-assembling peptide amphiphiles into supramolecular nanostructures opens up the possibility of developing biocompatible functional supramolecular materials for various applications. In this study, we show that the hierarchical self-assembly of histidine- (His-) functionalized PAs containing d- or l-amino acids can be controlled by both solution pH and molecular chirality of the building blocks. An increase in solution pH resulted in the structural transition of the His-functionalized chiral PA assemblies from nanosheets to completely closed nanotubes through an enhanced hydrogen-bonding capacity and π-π stacking of imidazole ring. The effects of the stereochemistry and amino acid sequence of the PA backbone on the supramolecular organization were also analyzed by CD, TEM, SAXS, and molecular dynamics simulations. In addition, an investigation of chiral mixtures revealed the differences between the hydrogen-bonding capacities and noncovalent interactions of PAs with d- and l-amino acids.
Open Access
A highly sensitive atomic force microscope for linear measurements of molecular forces in liquids
(American Institute of Physics, 2005) Patil, S.; Matei, G.; Dong, H.; Hoffmann, P. M.; Karaköse, M.; Oral, A.
We describe a highly improved atomic force microscope for quantitative nanomechanical measurements in liquids. The main feature of this microscope is a modified fiber interferometer mounted on a five axis inertial slider which provides a deflection sensitivity that is significantly better than conventional laser deflection based systems. The measured low noise floor of 572.0 fmHz provides excellent cantilever amplitude resolution. This allows us to operate the instrument far below resonance at extremely small cantilever amplitudes of less than 1 Å. Thus linear measurements of nanomechanical properties of liquid systems can be performed. In particular, we present measurements of solvation forces in confined octamethylcyclotetrasiloxane and water with amplitudes smaller than the size of the respective molecules. In general, the development of the instrument is important in the context of quantitative nanomechanical measurements in liquid environments.
Open Access
Hydrogen storage capacity of titanium met-cars
(IOP Publishing Ltd., 2006) Akman, N.; Durgun, Engin; Yildirim, T.; Çıracı, Salim
The adsorption of hydrogen molecules on the titanium metallocarbohedryne (met-car) cluster has been investigated by using the first-principles plane wave method. We have found that, while a single Ti atom at the corner can bind up to three hydrogen molecules, a single Ti atom on the surface of the cluster can bind only one hydrogen molecule. Accordingly, a Ti8C12 met-car can bind up to 16H2 molecules and hence can be considered as a high-capacity hydrogen storage medium. Strong interaction between two met-car clusters leading to the dimer formation can affect H2 storage capacity slightly. Increasing the storage capacity by directly inserting H 2 into the met-car or by functionalizing it with an Na atom have been explored. It is found that the insertion of neither an H2 molecule nor an Na atom could further promote the H2 storage capacity of a Ti8C12 cluster. We have also tested the stability of the H2-adsorbed Ti8C12 met-car with ab initio molecular dynamics calculations which have been carried out at room temperature.
Open Access
Insight on tricalcium silicate hydration and dissolution mechanism from molecular simulations
(American Chemical Society, 2015) Manzano, H.; Durgun, Engin; Arbeloa, I. L.; Grossman, J. C.
Hydration of mineral surfaces, a critical process for many technological applications, encompasses multiple coupled chemical reactions and topological changes, challenging both experimental characterization and computational modeling. In this work, we used reactive force field simulations to understand the surface properties, hydration, and dissolution of a model mineral, tricalcium silicate. We show that the computed static quantities, i.e., surface energies and water adsorption energies, do not provide useful insight into predict mineral hydration because they do not account for major structural changes at the interface when dynamic effects are included. Upon hydration, hydrogen atoms from dissociated water molecules penetrate into the crystal, forming a disordered calcium silicate hydrate layer that is similar for most of the surfaces despite wide-ranging static properties. Furthermore, the dynamic picture of hydration reveals the hidden role of surface topology, which can lead to unexpected water tessellation that stabilizes the surface against dissolution.
Open Access
Interactions between densely grafted molten polymer brushes: scaling theories versus molecular simulations
(Scientific and Technical Research Council of Turkey - TUBITAK,Turkiye Bilimsel ve Teknik Arastirma Kurumu, 2021-02-27) Erbaş, Aykut
Using molecular dynamics simulations and scaling arguments, we analyzed the interactions between two identical molten polymer brushes intermediately and strongly compressed towards each other at melt conditions. The width of the overlap region, in which monomers of the linear chains composing the two brushes interact, increases as the polymer-grafted surfaces are brought closer. If two-brush coated surfaces are as close as the characteristics size of the grafted chains, the overlap region is directly controlled by intersurface distance. At intermediate compression, the width of the overlap region scales with the end-to-end size of chain sections within the overlap region. This result is consistent with the scaling regimes in the literature. As the intersurface distance is decreased, the number fraction of chains (chains with their free ends in the overlap region) decreases with a power law. Our results could be useful for studies on tribological behavior of polymer-grafted surfaces as well as for the self-assembly of polymer coated colloids.
Open Access
Manipulation of atoms across a surface at room temperature
(Nature Publishing Group, 2000) Fishlock, T. W.; Oral, A.; Egdell, R. G.; Pethica, J. B.
Since the realization that the tips of scanning probe microscopes can interact with atoms at surfaces, there has been much interest in the possibility of building or modifying nanostructures or molecules directly from single atoms. Individual large molecules can be positioned on surfaces, and atoms can be transferred controllably between the sample and probe tip. The most complex structures are produced at cryogenic temperatures by sliding atoms across a surface to chosen sites. But there are problems in manipulating atoms laterally at higher temperatures - atoms that are sufficiently well bound to a surface to be stable at higher temperatures require a stronger tip interaction to be moved. This situation differs significantly from the idealized weakly interacting tips of scanning tunnelling or atomic force microscopes. Here we demonstrate that precise positioning of atoms on a copper surface is possible at room temperature. The triggering mechanism for the atomic motion unexpectedly depends on the tunnelling current density, rather than the electric field or proximity of tip and surface.
Open Access
Molecular dynamics simulations study of [5]rotaxane in bulk and at interfaces
(2022-06) Özkan, Ata Utku
Rotaxanes are a class mechanically interlocked molecular architectures that exhibit quasi-mechanical movement in response to specific stimuli. [5]Rotaxane is a complex rotaxane structure that is reported to show extraordinary cyctotoxic properties with light stimuli. By using all-atom classical molecular dynamics simulations, we study equilibrium and kinetics properties of various charge states of [5]Rotaxane in salt-free water as well as [5]Rotaxane network derivatives at the interface of water and chloroform. By analyzing molecular configurations, hydrogen bonding and size, energy based metrics of individual molecules both in bulk and water-chloroform interfaces, we demonstrate that charge-state of [5]Rotaxane directly influences the molecular conformation and solvation properties. While charge-neutral and negatively charges molecules often tend to collapse in a way that they expose their porphyrin core, positively charged moieties tend to take more extended molecular configuration screening the core. Further, sudden changes in the charge states emulating the pH alterations in solution conditions leads to gradual, 1000-ps level, changes in molecular conformation of [5]Rotaxane via shuttling motion of CB6 rings along [5]Rotaxane axles. Finally, simulations with 2D networks of [5]Rotaxane confirm the possibility of molecular film formation at hydrophobic-hydrophilic interfaces. Overall, our results suggest that [5]Rotaxane can exhibit a rich spectrum of molecular configurations and assembly properties depending on the ionic strengths of the solution or external stimuli.
Embargo
Molecular rheology of unentangled polymer melts in nanochannels
(2024-08) Yıldırım, Ahmet Burak
We investigate the rheological properties of non-Newtonian melts of short polymer chains at the molecular level, with a focus on nanoscale confinement. Using a combination of all-atom molecular dynamics (MD) and coarse-grained simulations, we examine the behavior of oligomer melts with various topologies under non-equilibrium conditions. Our findings reveal significant deviations in the microscopic stress tensor under steady-state shear compared to predictions from continuum models, highlighting the limitations of the Oldroyd-B and generalized Phan-Thien–Tanner (gPTT) models in capturing nanoscale phenomena. We demonstrate that these deviations result in excess viscoelastic stress, which diminishes with decreasing confinement and vanishes in bulk systems. This excess stress is linked to the spatial orientation of carbon-carbon bonds near surfaces, where adsorbed chains form effective polymer brush-like layers. Additionally, we explore the effects of chain rigidity, surface-oligomer attraction, and molecular variables on rheological responses, providing a comprehensive understanding of the interplay between molecular-scale phenomena and macroscopic behavior in confined polymeric systems.
Open Access
Optimized stillinger-weber potentials for 1H, 1T and 1T′ phases of WS2 for molecular dynamics studies: thermal transport as an example
(2024-01) Waheed, Alim Mohamed
The advent of graphene has poured numerous amount of research effort into the study 2D materials and utilizing it for device fabrication. Monolayer Transition Metal Dichalcogenides are one such class of polymorphic material with high prospect in versatile device applications due to its unique properties exhibited across the various phases. Classical Molecular Dynamics is a powerful tool that can be utilized to study the thermal and mechanical properties of these phases. Considering this, we optimise Stillinger-Weber type Potential for the seperate 1H, 1T and 1T′ phases of WS2 using Particle Swarm Optimization. These potentials are validated by comparison of phonon dispersion curves, Density Functional Theory (DFT) based target characteristic data and through an accuracy assessment conducted using Non-Equilibrium Molecular Dynamic (NEMD) simulations to evaluate thermal conductivity of the polymorphic structures. Thermal conductivity results obtained for 1H and 1T′ are in good agreement with first principle predictions calculated using Boltzmann Transport Equation. NEMD simulation of 1T phase prove to be challenging due to its dynamic instability with incoherent buckle structure formation along the symmetric directions.
Open Access
Phase boundary of the boson Mott insulator in a rotating optical lattice
(The American Physical Society, 2007) Umucalilar, R. O.; Oktel, M. Ö.
We consider the Bose-Hubbard model in a two-dimensional rotating optical lattice and investigate the consequences of the effective magnetic field created by rotation. Using a Gutzwiller-type variational wave function, we find an analytical expression for the Mott insulator (MI)-superfluid (SF) transition boundary in terms of the maximum eigenvalue of the Hofstadter butterfly. The dependence of phase boundary on the effective magnetic field is complex, reflecting the self-similar properties of the single particle energy spectrum. Finally, we argue that fractional quantum Hall phases exist close to the MI-SF transition boundaries, including MI states with particle densities greater than one.