Molecular dynamics simulations of amphiphilic graft copolymer molecules at a water/air interface.

PubMed

Anderson, Philip M; Wilson, Mark R

2004-11-01

Fully atomistic molecular dynamics simulations of amphiphilic graft copolymer molecules have been performed at a range of surface concentrations at a water/air interface. These simulations are compared to experimental results from a corresponding system over a similar range of surface concentrations. Neutron reflectivity data calculated from the simulation trajectories agrees well with experimentally acquired profiles. In particular, excellent agreement in neutron reflectivity is found for lower surface concentration simulations. A simulation of a poly(ethylene oxide) (PEO) chain in aqueous solution has also been performed. This simulation allows the conformational behavior of the free PEO chain and those tethered to the interface in the previous simulations to be compared. (c) 2004 American Institute of Physics.

Molecular Mechanisms of ZnO Nanoparticle Dispersion in Solution: Modeling of Surfactant Association, Electrostatic Shielding and Counter Ion Dynamics.

PubMed

Duchstein, Patrick; Milek, Theodor; Zahn, Dirk

2015-01-01

Molecular models of 5 nm sized ZnO/Zn(OH)2 core-shell nanoparticles in ethanolic solution were derived as scale-up models (based on an earlier model created from ion-by-ion aggregation and self-organization) and subjected to mechanistic analyses of surface stabilization by block-copolymers. The latter comprise a poly-methacrylate chain accounting for strong surfactant association to the nanoparticle by hydrogen bonding and salt-bridges. While dangling poly-ethylene oxide chains provide only a limited degree of sterical hindering to nanoparticle agglomeration, the key mechanism of surface stabilization is electrostatic shielding arising from the acrylates and a halo of Na+ counter ions associated to the nanoparticle. Molecular dynamics simulations reveal different solvent shells and distance-dependent mobility of ions and solvent molecules. From this, we provide a molecular rationale of effective particle size, net charge and polarizability of the nanoparticles in solution.

Molecular Mechanisms of ZnO Nanoparticle Dispersion in Solution: Modeling of Surfactant Association, Electrostatic Shielding and Counter Ion Dynamics

PubMed Central

Duchstein, Patrick; Milek, Theodor; Zahn, Dirk

2015-01-01

Molecular models of 5 nm sized ZnO/Zn(OH)2 core-shell nanoparticles in ethanolic solution were derived as scale-up models (based on an earlier model created from ion-by-ion aggregation and self-organization) and subjected to mechanistic analyses of surface stabilization by block-copolymers. The latter comprise a poly-methacrylate chain accounting for strong surfactant association to the nanoparticle by hydrogen bonding and salt-bridges. While dangling poly-ethylene oxide chains provide only a limited degree of sterical hindering to nanoparticle agglomeration, the key mechanism of surface stabilization is electrostatic shielding arising from the acrylates and a halo of Na+ counter ions associated to the nanoparticle. Molecular dynamics simulations reveal different solvent shells and distance-dependent mobility of ions and solvent molecules. From this, we provide a molecular rationale of effective particle size, net charge and polarizability of the nanoparticles in solution. PMID:25962096

Fiber lubrication: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Liu, Hongyi

Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence of water increases the attractive interaction energy of the diblock copolymer on the cellulose surface, compared with that on the PP surface. Water decreases the interaction energy of the triblock copolymer on the cellulose surface, compared with that on the PP surface. MesoDyn was adopted to investigate the self-assembled morphology of the triblock copolymer, in aqueous solution, confined and sheared at solid-liquid interfaces. In a bulk aqueous solution, when the polymer concentration reached 10% v/v, micelles were observed with PPO blocks in the core and PEO blocks in the shell of the micelles. At the concentrations of 25% and 50%, worm-like micelles and irregular cylinders were observed in solutions, respectively. The micelles were formed faster in aqueous solutions confined by cellulose surfaces than that in the bulk. The formed micelles were broken under shearing, which led to a depletion of polymers at the interfaces. During the shearing on the PP surfaces, the polymers were adsorbed on the surfaces protecting the PP surfaces. This simulation study in the fiber lubrication was in good agreement with the experimental results and so provided an approach to visualize the polymer configuration at the liquid-solid interface, predict the lubricant-surface systems, and theoretically guide the experiments of designing new/efficient lubricants for fibers.

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules

NASA Astrophysics Data System (ADS)

Hamelberg, Donald; Mongan, John; McCammon, J. Andrew

2004-06-01

Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution.

Molecular Design of High Performance Molecular Devices Based on Direct Ab-initio Molecular Dynamics Method: Diffusion of Lithium Ion on Fluorinated Amorphous Carbon

NASA Astrophysics Data System (ADS)

Kawabata, Hiroshi; Iyama, Tetsuji; Tachikawa, Hiroto

2008-01-01

Hybrid density functional theory (DFT) calculations have been carried out for the lithium adsorbed on a fluorinated graphene surface (F-graphene, C96F24) to elucidate the effect of fluorination of amorphous carbon on the diffusion mechanism of lithium ion. Also, direct molecular orbital-molecular dynamics (MO-MD) calculation [H. Tachikawa and A. Shimizu: J. Phys. Chem. B 109 (2005) 13255] was applied to diffusion processes of the Li+ ion on F-graphene. The B3LYP/LANL2MB calculation showed that the Li+ ion is most stabilized around central position of F-graphene, and the energy was gradually instabilized for the edge region. The direct MO-MD calculations showed that the Li+ ion diffuses on the bulk surface region of F-graphite at 300 K. The nature of the interaction between Li+ and F-graphene was discussed on the basis of theoretical results.

Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.

PubMed

Koromyslova, Anna D; Chugunov, Anton O; Efremov, Roman G

2014-04-28

Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them--protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.

Correlating structural dynamics and catalytic activity of AgAu nanoparticles with ultrafast spectroscopy and all-atom molecular dynamics simulations.

PubMed

Ferbonink, G F; Rodrigues, T S; Dos Santos, D P; Camargo, P H C; Albuquerque, R Q; Nome, R A

2018-05-29

In this study, we investigated hollow AgAu nanoparticles with the goal of improving our understanding of the composition-dependent catalytic activity of these nanoparticles. AgAu nanoparticles were synthesized via the galvanic replacement method with controlled size and nanoparticle compositions. We studied extinction spectra with UV-Vis spectroscopy and simulations based on Mie theory and the boundary element method, and ultrafast spectroscopy measurements to characterize decay constants and the overall energy transfer dynamics as a function of AgAu composition. Electron-phonon coupling times for each composition were obtained from pump-power dependent pump-probe transients. These spectroscopic studies showed how nanoscale surface segregation, hollow interiors and porosity affect the surface plasmon resonance wavelength and fundamental electron-phonon coupling times. Analysis of the spectroscopic data was used to correlate electron-phonon coupling times to AgAu composition, and thus to surface segregation and catalytic activity. We have performed all-atom molecular dynamics simulations of model hollow AgAu core-shell nanoparticles to characterize nanoparticle stability and equilibrium structures, besides providing atomic level views of nanoparticle surface segregation. Overall, the basic atomistic and electron-lattice dynamics of core-shell AgAu nanoparticles characterized here thus aid the mechanistic understanding and performance optimization of AgAu nanoparticle catalysts.

Competing Thermodynamic and Dynamic Factors Select Molecular Assemblies on a Gold Surface

NASA Astrophysics Data System (ADS)

Haxton, Thomas K.; Zhou, Hui; Tamblyn, Isaac; Eom, Daejin; Hu, Zonghai; Neaton, Jeffrey B.; Heinz, Tony F.; Whitelam, Stephen

2013-12-01

Controlling the self-assembly of surface-adsorbed molecules into nanostructures requires understanding physical mechanisms that act across multiple length and time scales. By combining scanning tunneling microscopy with hierarchical ab initio and statistical mechanical modeling of 1,4-substituted benzenediamine (BDA) molecules adsorbed on a gold (111) surface, we demonstrate that apparently simple nanostructures are selected by a subtle competition of thermodynamics and dynamics. Of the collection of possible BDA nanostructures mechanically stabilized by hydrogen bonding, the interplay of intermolecular forces, surface modulation, and assembly dynamics select at low temperature a particular subset: low free energy oriented linear chains of monomers and high free energy branched chains.

Surface free energy and some other properties of a crystal-vapor interface: Molecular dynamics simulation of a Lennard-Jones system

NASA Astrophysics Data System (ADS)

Baidakov, V. G.; Tipeev, A. O.; Protsenko, K. R.

2017-07-01

The surface tension γ and surface energy u bar have been calculated in molecular dynamics simulation of an FCC crystal-vapor equilibrium in systems containing from 54000 to 108000 Lennard-Jones (LJ) particles with a cutoff radius of the potential rc = 6.78 d . The surface entropy s bar and the surface free energy σ along the sublimation line have been determined by the method of thermodynamic integration from the zero of temperature, where the classical entropy has been obtained from the dynamical theory of crystal lattice by data on γ (T) and u bar (T) . Calculations were made on the planes (1 0 0), (1 1 0) and (1 1 1) of an LJ crystal. The anisotropy of surface properties is considerable at low temperatures and smooths over at the approach of the triple point. At a temperature 1/3 lower than the melting temperature of the bulk phase changes are observed in the character of temperature dependences of the properties of a crystal-vapor interface, which are connected with surface premelting. The temperature of the beginning of surface premelting correlates with that at which the metastable extension of the melting line meets the spinodal of a stretched liquid.

Searching for protein binding sites from Molecular Dynamics simulations and paramagnetic fragment-based NMR studies.

PubMed

Bernini, Andrea; Henrici De Angelis, Lucia; Morandi, Edoardo; Spiga, Ottavia; Santucci, Annalisa; Assfalg, Michael; Molinari, Henriette; Pillozzi, Serena; Arcangeli, Annarosa; Niccolai, Neri

2014-03-01

Hotspot delineation on protein surfaces represents a fundamental step for targeting protein-protein interfaces. Disruptors of protein-protein interactions can be designed provided that the sterical features of binding pockets, including the transient ones, can be defined. Molecular Dynamics, MD, simulations have been used as a reliable framework for identifying transient pocket openings on the protein surface. Accessible surface area and intramolecular H-bond involvement of protein backbone amides are proposed as descriptors for characterizing binding pocket occurrence and evolution along MD trajectories. TEMPOL induced paramagnetic perturbations on (1)H-(15)N HSQC signals of protein backbone amides have been analyzed as a fragment-based search for surface hotspots, in order to validate MD predicted pockets. This procedure has been applied to CXCL12, a small chemokine responsible for tumor progression and proliferation. From combined analysis of MD data and paramagnetic profiles, two CXCL12 sites suitable for the binding of small molecules were identified. One of these sites is the already well characterized CXCL12 region involved in the binding to CXCR4 receptor. The other one is a transient pocket predicted by Molecular Dynamics simulations, which could not be observed from static analysis of CXCL12 PDB structures. The present results indicate how TEMPOL, instrumental in identifying this transient pocket, can be a powerful tool to delineate minor conformations which can be highly relevant in dynamic discovery of antitumoral drugs. Copyright © 2013 Elsevier B.V. All rights reserved.

Influence of surface oxidation on ion dynamics and capacitance in porous and nonporous carbon electrodes

DOE PAGES

Dyatkin, Boris; Zhang, Yu; Mamontov, Eugene; ...

2016-04-07

Here, we investigate the influence of surface chemistry and ion confinement on capacitance and electrosorption dynamics of room-temperature ionic liquids (RTILs) in supercapacitors. Using air oxidation and vacuum annealing, we produced defunctionalized and oxygen-rich surfaces of carbide-derived carbons (CDCs) and graphene nanoplatelets (GNPs). While oxidized surfaces of porous CDCs improve capacitance and rate handling abilities of ions, defunctionalized nonporous GNPs improve charge storage densities on planar electrodes. Quasi-elastic neutron scattering (QENS) and inelastic neutron scattering (INS) probed the structure, dynamics, and orientation of RTIL ions confined in divergently functionalized pores. Oxidized, ionophilic surfaces draw ions closer to pore surfaces andmore » enhance potential-driven ion transport during electrosorption. Molecular dynamics (MD) simulations corroborated experimental data and demonstrated the significance of surface functional groups on ion orientations, accumulation densities, and capacitance.« less

Nonadiabatic excited-state molecular dynamics modeling of photoinduced dynamics in conjugated molecules.

PubMed

Nelson, Tammie; Fernandez-Alberti, Sebastian; Chernyak, Vladimir; Roitberg, Adrian E; Tretiak, Sergei

2011-05-12

Nonadiabatic dynamics generally defines the entire evolution of electronic excitations in optically active molecular materials. It is commonly associated with a number of fundamental and complex processes such as intraband relaxation, energy transfer, and light harvesting influenced by the spatial evolution of excitations and transformation of photoexcitation energy into electrical energy via charge separation (e.g., charge injection at interfaces). To treat ultrafast excited-state dynamics and exciton/charge transport we have developed a nonadiabatic excited-state molecular dynamics (NA-ESMD) framework incorporating quantum transitions. Our calculations rely on the use of the Collective Electronic Oscillator (CEO) package accounting for many-body effects and actual potential energy surfaces of the excited states combined with Tully's fewest switches algorithm for surface hopping for probing nonadiabatic processes. This method is applied to model the photoinduced dynamics of distyrylbenzene (a small oligomer of polyphenylene vinylene, PPV). Our analysis shows intricate details of photoinduced vibronic relaxation and identifies specific slow and fast nuclear motions that are strongly coupled to the electronic degrees of freedom, namely, torsion and bond length alternation, respectively. Nonadiabatic relaxation of the highly excited mA(g) state is predicted to occur on a femtosecond time scale at room temperature and on a picosecond time scale at low temperature.

Ice formation on kaolinite: Insights from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sosso, Gabriele C.; Tribello, Gareth A.; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

2016-12-01

The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral.

Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation

NASA Technical Reports Server (NTRS)

Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.

2007-01-01

The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics

NASA Astrophysics Data System (ADS)

Mansbach, Rachael A.; Ferguson, Andrew L.

2015-03-01

The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics.

PubMed

Mansbach, Rachael A; Ferguson, Andrew L

2015-03-14

The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.

Atomistic modelling of evaporation and explosive boiling of thin film liquid argon over internally recessed nanostructured surface

NASA Astrophysics Data System (ADS)

Hasan, Mohammad Nasim; Shavik, Sheikh Mohammad; Rabbi, Kazi Fazle; Haque, Mominul

2016-07-01

Molecular dynamics (MD) simulations have been carried out to investigate evaporation and explosive boiling phenomena of thin film liquid argon on nanostructured solid surface with emphasis on the effect of solid-liquid interfacial wettability. The nanostructured surface considered herein consists of trapezoidal internal recesses of the solid platinum wall. The wetting conditions of the solid surface were assumed such that it covers both the hydrophilic and hydrophobic conditions and hence effect of interfacial wettability on resulting evaporation and boiling phenomena was the main focus of this study. The initial configuration of the simulation domain comprised of a three phase system (solid platinum, liquid argon and vapor argon) on which equilibrium molecular dynamics (EMD) was performed to reach equilibrium state at 90 K. After equilibrium of the three-phase system was established, the wall was set to different temperatures (130 K and 250 K for the case of evaporation and explosive boiling respectively) to perform non-equilibrium molecular dynamics (NEMD). The variation of temperature and density as well as the variation of system pressure with respect to time were closely monitored for each case. The heat flux normal to the solid surface was also calculated to illustrate the effectiveness of heat transfer for hydrophilic and hydrophobic surfaces in cases of both nanostructured surface and flat surface. The results obtained show that both the wetting condition of the surface and the presence of internal recesses have significant effect on normal evaporation and explosive boiling of the thin liquid film. The heat transfer from solid to liquid in cases of surface with recesses are higher compared to flat surface without recesses. Also the surface with higher wettability (hydrophilic) provides more favorable conditions for boiling than the low-wetting surface (hydrophobic) and therefore, liquid argon responds quickly and shifts from liquid to vapor phase faster in case of hydrophilic surface. The heat transfer rate is also much higher in case of hydrophilic surface.

Atomistic modelling of evaporation and explosive boiling of thin film liquid argon over internally recessed nanostructured surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasan, Mohammad Nasim, E-mail: nasim@me.buet.ac.bd.com; Shavik, Sheikh Mohammad, E-mail: shavik@me.buet.ac.bd.com; Rabbi, Kazi Fazle, E-mail: rabbi35.me10@gmail.com

2016-07-12

Molecular dynamics (MD) simulations have been carried out to investigate evaporation and explosive boiling phenomena of thin film liquid argon on nanostructured solid surface with emphasis on the effect of solid-liquid interfacial wettability. The nanostructured surface considered herein consists of trapezoidal internal recesses of the solid platinum wall. The wetting conditions of the solid surface were assumed such that it covers both the hydrophilic and hydrophobic conditions and hence effect of interfacial wettability on resulting evaporation and boiling phenomena was the main focus of this study. The initial configuration of the simulation domain comprised of a three phase system (solidmore » platinum, liquid argon and vapor argon) on which equilibrium molecular dynamics (EMD) was performed to reach equilibrium state at 90 K. After equilibrium of the three-phase system was established, the wall was set to different temperatures (130 K and 250 K for the case of evaporation and explosive boiling respectively) to perform non-equilibrium molecular dynamics (NEMD). The variation of temperature and density as well as the variation of system pressure with respect to time were closely monitored for each case. The heat flux normal to the solid surface was also calculated to illustrate the effectiveness of heat transfer for hydrophilic and hydrophobic surfaces in cases of both nanostructured surface and flat surface. The results obtained show that both the wetting condition of the surface and the presence of internal recesses have significant effect on normal evaporation and explosive boiling of the thin liquid film. The heat transfer from solid to liquid in cases of surface with recesses are higher compared to flat surface without recesses. Also the surface with higher wettability (hydrophilic) provides more favorable conditions for boiling than the low-wetting surface (hydrophobic) and therefore, liquid argon responds quickly and shifts from liquid to vapor phase faster in case of hydrophilic surface. The heat transfer rate is also much higher in case of hydrophilic surface.« less

Molecular dynamics and dynamic Monte-Carlo simulation of irradiation damage with focused ion beams

NASA Astrophysics Data System (ADS)

Ohya, Kaoru

2017-03-01

The focused ion beam (FIB) has become an important tool for micro- and nanostructuring of samples such as milling, deposition and imaging. However, this leads to damage of the surface on the nanometer scale from implanted projectile ions and recoiled material atoms. It is therefore important to investigate each kind of damage quantitatively. We present a dynamic Monte-Carlo (MC) simulation code to simulate the morphological and compositional changes of a multilayered sample under ion irradiation and a molecular dynamics (MD) simulation code to simulate dose-dependent changes in the backscattering-ion (BSI)/secondary-electron (SE) yields of a crystalline sample. Recent progress in the codes for research to simulate the surface morphology and Mo/Si layers intermixing in an EUV lithography mask irradiated with FIBs, and the crystalline orientation effect on BSI and SE yields relating to the channeling contrast in scanning ion microscopes, is also presented.

The classical and quantum dynamics of molecular spins on graphene.

PubMed

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2016-02-01

Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain's threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.

The classical and quantum dynamics of molecular spins on graphene

NASA Astrophysics Data System (ADS)

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2016-02-01

Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.

Semiclassical modelling of finite-pulse effects on non-adiabatic photodynamics via initial condition filtering: The predissociation of NaI as a test case

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martínez-Mesa, Aliezer; Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam-Golm; Saalfrank, Peter

2015-05-21

Femtosecond-laser pulse driven non-adiabatic spectroscopy and dynamics in molecular and condensed phase systems continue to be a challenge for theoretical modelling. One of the main obstacles is the “curse of dimensionality” encountered in non-adiabatic, exact wavepacket propagation. A possible route towards treating complex molecular systems is via semiclassical surface-hopping schemes, in particular if they account not only for non-adiabatic post-excitation dynamics but also for the initial optical excitation. One such approach, based on initial condition filtering, will be put forward in what follows. As a simple test case which can be compared with exact wavepacket dynamics, we investigate the influencemore » of the different parameters determining the shape of a laser pulse (e.g., its finite width and a possible chirp) on the predissociation dynamics of a NaI molecule, upon photoexcitation of the A(0{sup +}) state. The finite-pulse effects are mapped into the initial conditions for semiclassical surface-hopping simulations. The simulated surface-hopping diabatic populations are in qualitative agreement with the quantum mechanical results, especially concerning the subpicosend photoinduced dynamics, the main deviations being the relative delay of the non-adiabatic transitions in the semiclassical picture. Likewise, these differences in the time-dependent electronic populations calculated via the semiclassical and the quantum methods are found to have a mild influence on the overall probability density distribution. As a result, the branching ratios between the bound and the dissociative reaction channels and the time-evolution of the molecular wavepacket predicted by the semiclassical method agree with those computed using quantum wavepacket propagation. Implications for more challenging molecular systems are given.« less

Inclusion Complexes Behavior at the Air-Water Interface. Molecular Dynamic Simulation Study.

NASA Astrophysics Data System (ADS)

Gargallo, L.; Vargas, D.; Sandoval, C.; Saavedra, M.; Becerra, N.; Leiva, A.; Radić, D.

2008-08-01

The interfacial properties of the inclusion complexes (ICs), obtained from the threading of α-cyclodextrin (α-CD) onto poly(ethylene-oxide)(PEO), poly(ɛ-caprolactone)(PEC) and poly(tetrahydrofuran)(PTHF) and their precursor homopolymers (PHPoly), were studied at the air-water interface. The free surface energy was determined by wettability measurements. The experimental behavior of these systems was described by an atomistic molecular dynamics simulation (MDS).

Surface Modification Engineered Assembly of Novel Quantum Dot Architectures for Advanced Applications

DTIC Science & Technology

2008-02-09

Campbell, S. Ogata, and F. Shimojo, “ Multimillion atom simulations of nanosystems on parallel computers,” in Proceedings of the International...nanomesas: multimillion -atom molecular dynamics simulations on parallel computers,” J. Appl. Phys. 94, 6762 (2003). 21. P. Vashishta, R. K. Kalia...and A. Nakano, “ Multimillion atom molecular dynamics simulations of nanoparticles on parallel computers,” Journal of Nanoparticle Research 5, 119-135

The determination of temperature stability of silver nanotubes by the molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Filatov, O.; Soldatenko, S.; Soldatenko, O.

2018-04-01

Molecular dynamics simulation using the embedded-atom method is applied to study thermal stability of silver nanotubes and its coefficient of linear thermal expansion. The correspondence of face centered cubic structure potential for this task is tested. Three types of nanotubes are modelled: scrolled from graphene-like plane, scrolled from plane with cubic structure and cut from cylinder. It is established that only the last two of them are stable. The last one describes in details. There is critical temperature when free ends of the nanotube close but the interior surface retains. At higher temperatures, the interior surface collapses and the nanotube is unstable.

Computer Simulation of the Forces Acting on the Polystyrene Probe Submerged into the Succinonitrile Near Phase Transition

NASA Technical Reports Server (NTRS)

Bune, Andris V.; Kaukler, William F.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Modeling approach to simulate both mesoscale and microscopic forces acting in a typical AFM experiment is presented. At mesoscale level interaction between the cantilever tip and the sample surface is primarily described by the balance of attractive Van der Waals and repulsive forces. The model of cantilever oscillations is applicable to both non-contact and "tapping" AFM. This model can be farther enhanced to describe nanoparticle manipulation by cantilever. At microscopic level tip contamination and details of tip-surface interaction can be simulated using molecular dynamics approach. Integration of mesoscale model with molecular dynamic model is discussed.

A Wsbnd Ne interatomic potential for simulation of neon implantation in tungsten

NASA Astrophysics Data System (ADS)

Backman, Marie; Juslin, Niklas; Huang, Guiyang; Wirth, Brian D.

2016-08-01

An interatomic pair potential for Wsbnd Ne is developed for atomistic molecular dynamics simulations of neon implantation in tungsten. The new potential predicts point defect energies and binding energies of small clusters that are in good agreement with electronic structure calculations. Molecular dynamics simulations of small neon clusters in tungsten show that trap mutation, in which an interstitial neon cluster displaces a tungsten atom from its lattice site, occurs for clusters of three or more neon atoms. However, near a free surface, trap mutation can occur at smaller sizes, including even a single neon interstitial in close proximity to a (100) or (110) surface.

Melting of Cu nanoclusters by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Wang, Li; Zhang, Yanning; Bian, Xiufang; Chen, Ying

2003-04-01

We present a detailed molecular dynamics study of the melting of copper nanoclusters with up to 8628 atoms within the framework of the embedded-atom method. The finding indicates that there exists an intermediate nanocrystal regime above 456 atoms. The linear relation between the cluster size and its thermodynamics properties is obeyed in this regime. Melting first occurs at the surface of the clusters, leading to Tm, N= Tm,Bulk- αN-1/3, dropping from Tm,Bulk=1360 K to Tm,456=990 K. In addition, the size, surface energy as well as the root mean square displacement (RMSD) of the clusters in the intermediate regime have been investigated.

Reflection mass spectrometry technique for monitoring and controlling composition during molecular beam epitaxy

DOEpatents

Brennan, T.M.; Hammons, B.E.; Tsao, J.Y.

1992-12-15

A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a substrate by accurately measuring the molecular fluxes reflected from the substrate. The reflected flux is extremely sensitive to the state of the growing surface and the measurements obtained enable control of newly forming surfaces that are dynamically changing as a result of growth. 3 figs.

Reflection mass spectrometry technique for monitoring and controlling composition during molecular beam epitaxy

DOEpatents

Brennan, Thomas M.; Hammons, B. Eugene; Tsao, Jeffrey Y.

1992-01-01

A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a substrate by accurately measuring the molecular fluxes reflected from the substrate. The reflected flux is extremely sensitive to the state of the growing surface and the measurements obtained enable control of newly forming surfaces that are dynamically changing as a result of growth.

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

PubMed

Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

2015-06-09

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Making molecular balloons in laser-induced explosive boiling of polymer solutions.

PubMed

Leveugle, Elodie; Sellinger, Aaron; Fitz-Gerald, James M; Zhigilei, Leonid V

2007-05-25

The effect of the dynamic molecular rearrangements leading to compositional segregation is revealed in coarse-grained molecular dynamics simulations of short pulse laser interaction with a polymer solution in a volatile matrix. An internal release of matrix vapor at the onset of the explosive boiling of the overheated liquid is capable of pushing polymer molecules to the outskirts of a transient bubble, forming a polymer-rich surface layer enclosing the volatile matrix material. The results explain unexpected "deflated balloon" structures observed in films deposited by the matrix-assisted pulsed laser evaporation technique.

Ionic liquid structure, dynamics, and electrosorption in carbon electrodes with bimodal pores and heterogeneous surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dyatkin, Boris; Osti, Naresh C.; Zhang, Yu

In this paper, we investigate the aggregation, diffusion, and resulting electrochemical behavior of ionic liquids inside carbon electrodes with complex pore architectures and surface chemistries. Carbide-derived carbons (CDCs) with bimodal porosities and defunctionalized or oxidized electrode surfaces served as model electrode materials. Our goal was to obtain a fundamental understanding of room-temperature ionic liquid ion orientation, mobility, and electrosorption behavior. Neat 1-octyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide confined in CDCs was studied using an integrated experimental and modeling approach, consisting of quasielastic neutron scattering, small-angle neutron scattering, X-ray pair distribution function analysis, and electrochemical measurements, which were combined with molecular dynamics simulations. Our analysismore » shows that surface oxygen groups increase the diffusion of confined electrolytes. Consequently, the ions become more than twice as mobile in oxygen-rich pores. Although greater self-diffusion of ions translates into higher electrochemical mobilities in oxidized pores, bulk-like behavior of ions dominates in the larger mesopores and increases the overall capacitance in defunctionalized pores. Experimental results highlight strong confinement and surface effects of carbon electrodes on electrolyte behavior, and molecular dynamics simulations yield insight into diffusion and capacitance differences in specific pore regions. Finally, we demonstrate the significance of surface defects on electrosorption dynamics of complex electrolytes in hierarchical pore architectures of supercapacitor electrodes.« less

Ionic liquid structure, dynamics, and electrosorption in carbon electrodes with bimodal pores and heterogeneous surfaces

DOE PAGES

Dyatkin, Boris; Osti, Naresh C.; Zhang, Yu; ...

2017-12-05

In this paper, we investigate the aggregation, diffusion, and resulting electrochemical behavior of ionic liquids inside carbon electrodes with complex pore architectures and surface chemistries. Carbide-derived carbons (CDCs) with bimodal porosities and defunctionalized or oxidized electrode surfaces served as model electrode materials. Our goal was to obtain a fundamental understanding of room-temperature ionic liquid ion orientation, mobility, and electrosorption behavior. Neat 1-octyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide confined in CDCs was studied using an integrated experimental and modeling approach, consisting of quasielastic neutron scattering, small-angle neutron scattering, X-ray pair distribution function analysis, and electrochemical measurements, which were combined with molecular dynamics simulations. Our analysismore » shows that surface oxygen groups increase the diffusion of confined electrolytes. Consequently, the ions become more than twice as mobile in oxygen-rich pores. Although greater self-diffusion of ions translates into higher electrochemical mobilities in oxidized pores, bulk-like behavior of ions dominates in the larger mesopores and increases the overall capacitance in defunctionalized pores. Experimental results highlight strong confinement and surface effects of carbon electrodes on electrolyte behavior, and molecular dynamics simulations yield insight into diffusion and capacitance differences in specific pore regions. Finally, we demonstrate the significance of surface defects on electrosorption dynamics of complex electrolytes in hierarchical pore architectures of supercapacitor electrodes.« less

Molecular dynamics simulation of the folding of single alkane chains with different lengths on single-walled carbon nanotubes and graphene.

PubMed

Liu, Yan Fang; Yang, Hua; Zhang, Hui

2018-05-31

Chain folding is an important step during polymer crystallization. In order to study the effects of the surface on chain folding, molecular dynamics simulations of the folding of different alkane chains on three kinds of single-walled carbon nanotubes (SWCNTs) and graphene were performed. The folding behaviors of the single alkane chains on these surfaces were found to be different from their folding behaviors in vacuum. The end-to-end distances of the chains were calculated to explore the chain folding. An increasing tendency to fold into two or more stems with increasing alkane chain length was observed. This result indicates that the occurrence and the stability of chain folding are related to the surface curvature, the diameter of the SWCNT, and surface texture. In addition, the angle between the direction of the alkane chain segment and the direction of the surface texture was measured on different surfaces.

Nonadiabatic ab initio molecular dynamics with PME-ONIOM scheme of photoisomerization reaction between 1,3-cyclohexadiene and 1,3,5-cis-hexatriene in solution phase

NASA Astrophysics Data System (ADS)

Ohta, Ayumi; Kobayashi, Osamu; Danielache, Sebastian O.; Nanbu, Shinkoh

2017-03-01

The ultra-fast photoisomerization reactions between 1,3-cyclohexadiene (CHD) and 1,3,5-cis-hexatriene (HT) in both hexane and ethanol solvents were revealed by nonadiabatic ab initio molecular dynamics (AI-MD) with a particle-mesh Ewald summation method and our Own N-layered Integrated molecular Orbital and molecular Mechanics model (PME-ONIOM) scheme. Zhu-Nakamura version trajectory surface hopping method (ZN-TSH) was employed to treat the ultra-fast nonadiabatic decaying process. The results for hexane and ethanol simulations reasonably agree with experimental data. The high nonpolar-nonpolar affinity between CHD and the solvent was observed in hexane solvent, which definitely affected the excited state lifetimes, the product branching ratio of CHD:HT, and solute (CHD) dynamics. In ethanol solvent, however, the CHD solute was isomerized in the solvent cage caused by the first solvation shell. The photochemical dynamics in ethanol solvent results in the similar property to the process appeared in vacuo (isolated CHD dynamics).

Computational Evaluation of Mg–Salen Compounds as Subsurface Fluid Tracers: Molecular Dynamics Simulations in Toluene–Water Mixtures and Clay Mineral Nanopores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greathouse, Jeffery A.; Boyle, Timothy J.; Kemp, Richard A.

Molecular tracers that can be selectively placed underground and uniquely identified at the surface using simple on-site spectroscopic methods would significantly enhance subsurface fluid monitoring capabilities. To ensure their widespread utility, the solubility of these tracers must be easily tuned to oil- or water-wet conditions as well as reducing or eliminating their propensity to adsorb onto subsurface rock and/or mineral phases. In this work, molecular dynamics simulations were used to investigate the relative solubilities and mineral surface adsorption properties of three candidate tracer compounds comprising Mg–salen derivatives of varying degrees of hydrophilic character. Simulations in water–toluene liquid mixtures indicate thatmore » the partitioning of each Mg–salen compound relative to the interface is strongly influenced by the degree of hydrophobicity of the compound. Simulations of these complexes in fluid-filled mineral nanopores containing neutral (kaolinite) and negatively charged (montmorillonite) mineral surfaces reveal that adsorption tendencies depend upon a variety of parameters, including tracer chemical properties, mineral surface type, and solvent type (water or toluene). Simulation snapshots and averaged density profiles reveal insight into the solvation and adsorption mechanisms that control the partitioning of these complexes in mixed liquid phases and nanopore environments. As a result, this work demonstrates the utility of molecular simulation in the design and screening of molecular tracers for use in subsurface applications.« less

Computational Evaluation of Mg–Salen Compounds as Subsurface Fluid Tracers: Molecular Dynamics Simulations in Toluene–Water Mixtures and Clay Mineral Nanopores

DOE PAGES

Greathouse, Jeffery A.; Boyle, Timothy J.; Kemp, Richard A.

2018-04-11

Molecular tracers that can be selectively placed underground and uniquely identified at the surface using simple on-site spectroscopic methods would significantly enhance subsurface fluid monitoring capabilities. To ensure their widespread utility, the solubility of these tracers must be easily tuned to oil- or water-wet conditions as well as reducing or eliminating their propensity to adsorb onto subsurface rock and/or mineral phases. In this work, molecular dynamics simulations were used to investigate the relative solubilities and mineral surface adsorption properties of three candidate tracer compounds comprising Mg–salen derivatives of varying degrees of hydrophilic character. Simulations in water–toluene liquid mixtures indicate thatmore » the partitioning of each Mg–salen compound relative to the interface is strongly influenced by the degree of hydrophobicity of the compound. Simulations of these complexes in fluid-filled mineral nanopores containing neutral (kaolinite) and negatively charged (montmorillonite) mineral surfaces reveal that adsorption tendencies depend upon a variety of parameters, including tracer chemical properties, mineral surface type, and solvent type (water or toluene). Simulation snapshots and averaged density profiles reveal insight into the solvation and adsorption mechanisms that control the partitioning of these complexes in mixed liquid phases and nanopore environments. As a result, this work demonstrates the utility of molecular simulation in the design and screening of molecular tracers for use in subsurface applications.« less

Dynamic structural disorder in supported nanoscale catalysts

NASA Astrophysics Data System (ADS)

Rehr, J. J.; Vila, F. D.

2014-04-01

We investigate the origin and physical effects of "dynamic structural disorder" (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale.

Ultrafast inter- and intramolecular vibrational energy transfer between molecules at interfaces studied by time- and polarization-resolved SFG spectroscopy.

PubMed

Yamamoto, Susumu; Ghosh, Avishek; Nienhuys, Han-Kwang; Bonn, Mischa

2010-10-28

We present experimental results on femtosecond time-resolved surface vibrational spectroscopy aimed at elucidating the sub-picosecond reorientational dynamics of surface molecules. The approach, which relies on polarization- and time-resolved surface sum frequency generation (SFG), provides a general means to monitor interfacial reorientational dynamics through vibrations inherent in surface molecules in their electronic ground state. The technique requires an anisotropic vibrational excitation of surface molecules using orthogonally polarized infrared excitation light. The decay of the resulting anisotropy is followed in real-time. We employ the technique to reveal the reorientational dynamics of vibrational transition dipoles of long-chain primary alcohols on the water surface, and of water molecules at the water-air interface. The results demonstrate that, in addition to reorientational motion of specific molecules or molecular groups at the interface, inter- and intramolecular energy transfer processes can serve to scramble the initial anisotropy very efficiently. In the two exemplary cases demonstrated here, energy transfer occurs much faster than reorientational motion of interfacial molecules. This has important implications for the interpretation of static SFG spectra. Finally, we suggest experimental schemes and strategies to decouple effects resulting from energy transfer from those associated with surface molecular motion.

Molecular dynamics and quasidynamics simulations of the annealing of bulk and near-surface interstitials formed in molecular-beam epitaxial Si due to low-energy particle bombardment during deposition

NASA Technical Reports Server (NTRS)

Kitabatake, M.; Fons, P.; Greene, J. E.

1991-01-01

The relaxation, diffusion, and annihilation of split and hexagonal interstitials resulting from 10 eV Si irradiation of (2x1)-terminated Si(100) are investigated. Molecular dynamics and quasidynamics simulations, utilizing the Tersoff many-body potential are used in the investigation. The interstitials are created in layers two through six, and stable atomic configurations and total potential energies are derived as a function of site symmetry and layer depth. The interstitial Si atoms are allowed to diffuse, and the total potential energy changes are calculated. Lattice configurations along each path, as well as the starting configurations, are relaxed, and minimum energy diffusion paths are derived. The results show that the minimum energy paths are toward the surface and generally involved tetrahedral sites. The calculated interstitial migration activation energies are always less than 1.4 eV and are much lower in the near-surface region than in the bulk.

Computer Simulation of the Forces Acting on a Submerged Polystyrene Probe as it Approaches the Succinonitrile Melt-Solid Interface

NASA Technical Reports Server (NTRS)

Bune, Andris V.; Kaukler, William; Whitaker, Ann (Technical Monitor)

2001-01-01

A Modeling approach to simulate both mesoscale and microscopic forces acting in a typical AFM experiment is presented. A mesoscale level interaction between the cantilever tip and the sample surface is primarily described by the balance of attractive Van der Waals and repulsive forces. Ultimately, the goal is to measure the forces between a particle and the crystal-melt interface. Two modes of AFM operation are considered in this paper - a stationary and a "tapping" one. The continuous mechanics approach to model tip-surface interaction is presented. At microscopic levels, tip contamination and details of tip-surface interaction are modeled using a molecular dynamics approach for the case of polystyrene - succinonitrile contact. Integration of the mesoscale model with a molecular dynamic model is discussed.

Adsorption of Aqueous Crude Oil Components on the Basal Surfaces of Clay Minerals: Molecular Simulations Including Salinity and Temperature Effects

DOE PAGES

Greathouse, J. A.; Cygan, R. T.; Fredrich, J. T.; ...

2017-09-28

Molecular simulations of the adsorption of representative organic molecules onto the basal surfaces of various clay minerals were used to assess the mechanisms of enhanced oil recovery associated with salinity changes and water flooding. Simulations at the density functional theory (DFT) and classical levels provide insights into the molecular structure, binding energy, and interfacial behavior of saturate, aromatic, and resin molecules near clay mineral surfaces. Periodic DFT calculations reveal binding geometries and ion pairing mechanisms at mineral surfaces while also providing a basis for validating the classical force field approach. Through classical molecular dynamics simulations, the influence of aqueous cationsmore » at the interface and the role of water solvation are examined to better evaluate the dynamical nature of cation-organic complexes and their co-adsorption onto the clay surfaces. The extent of adsorption is controlled by the hydrophilic nature and layer charge of the clay mineral. All organic species studied showed preferential adsorption on hydrophobic mineral surfaces. However, the anionic form of the resin (decahydro-2-naphthoic acid)—expected to be prevalent at near-neutral pH conditions in petroleum reservoirs—readily adsorbs to the hydrophilic kaolinite surface through a combination of cation pairing and hydrogen bonding with surface hydroxyl groups. Analysis of cation-organic pairing in both the adsorbed and desorbed states reveals a strong preference for organic anions to coordinate with divalent calcium ions rather than monovalent sodium ions, lending support to current theories regarding low-salinity water flooding.« less

Adsorption of Aqueous Crude Oil Components on the Basal Surfaces of Clay Minerals: Molecular Simulations Including Salinity and Temperature Effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greathouse, J. A.; Cygan, R. T.; Fredrich, J. T.

Molecular simulations of the adsorption of representative organic molecules onto the basal surfaces of various clay minerals were used to assess the mechanisms of enhanced oil recovery associated with salinity changes and water flooding. Simulations at the density functional theory (DFT) and classical levels provide insights into the molecular structure, binding energy, and interfacial behavior of saturate, aromatic, and resin molecules near clay mineral surfaces. Periodic DFT calculations reveal binding geometries and ion pairing mechanisms at mineral surfaces while also providing a basis for validating the classical force field approach. Through classical molecular dynamics simulations, the influence of aqueous cationsmore » at the interface and the role of water solvation are examined to better evaluate the dynamical nature of cation-organic complexes and their co-adsorption onto the clay surfaces. The extent of adsorption is controlled by the hydrophilic nature and layer charge of the clay mineral. All organic species studied showed preferential adsorption on hydrophobic mineral surfaces. However, the anionic form of the resin (decahydro-2-naphthoic acid)—expected to be prevalent at near-neutral pH conditions in petroleum reservoirs—readily adsorbs to the hydrophilic kaolinite surface through a combination of cation pairing and hydrogen bonding with surface hydroxyl groups. Analysis of cation-organic pairing in both the adsorbed and desorbed states reveals a strong preference for organic anions to coordinate with divalent calcium ions rather than monovalent sodium ions, lending support to current theories regarding low-salinity water flooding.« less

Quantum State-Resolved Collision Dynamics of Nitric Oxide at Ionic Liquid and Molten Metal Surfaces

NASA Astrophysics Data System (ADS)

Zutz, Amelia Marie

Detailed molecular scale interactions at the gas-liquid interface are explored with quantum state-to-state resolved scattering of a jet-cooled beam of NO(2pi1/2; N = 0) from ionic liquid and molten metal surfaces. The scattered distributions are probed via laser-induced fluorescence methods, which yield rotational and spin-orbit state populations that elucidate the dynamics of energy transfer at the gas-liquid interface. These collision dynamics are explored as a function of incident collision energy, surface temperature, scattering angle, and liquid identity, all of which are found to substantially affect the degree of rotational, electronic and vibrational excitation of NO via collisions at the liquid surface. Rotational distributions observed reveal two distinct scattering pathways, (i) molecules that trap, thermalize and eventually desorb from the surface (trapping-desorption, TD), and (ii) those that undergo prompt recoil (impulsive scattering, IS) prior to complete equilibration with the liquid surface. Thermally desorbing NO molecules are found to have rotational temperatures close to, but slightly cooler than the surface temperature, indicative of rotational dependent sticking probabilities on liquid surfaces. Nitric oxide is a radical with multiple low-lying electronic states that serves as an ideal candidate for exploring nonadiabatic state-changing collision dynamics at the gas-liquid interface, which induce significant excitation from ground (2pi1/2) to excited (2pi 3/2) spin-orbit states. Molecular beam scattering of supersonically cooled NO from hot molten metals (Ga and Au, Ts = 300 - 1400 K) is also explored, which provide preliminary evidence for vibrational excitation of NO mediated by thermally populated electron-hole pairs in the hot, conducting liquid metals. The results highlight the presence of electronically nonadiabatic effects and build toward a more complete characterization of energy transfer dynamics at gas-liquid interfaces.

Molecular dynamics simulation of shock induced ejection on fused silica surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Rui; Xiang, Meizhen; Jiang, Shengli

2014-05-21

Shock response and surface ejection behaviors of fused silica are studied by using non-equilibrium molecular dynamics combining with the Tersoff potential. First, bulk structure and Hugoniot curves of fused silica are calculated and compared with experimental results. Then, the dynamical process of surface ejection behavior is simulated under different loading velocities ranging from 3.5 to 5.0 km∕s, corresponding to shock wave velocities from 7.1 to 8.8 km∕s. The local atomistic shear strain parameter is used to describe the local plastic deformation under conditions of shock compression or releasing. Our result shows that the shear strain is localized in the bottom area ofmore » groove under the shock compression. Surface ejection is observed when the loading velocity exceeds 4.0 km∕s. Meanwhile, the temperature of the micro-jet is ∼5574.7 K, which is close to experiment measurement. Several kinds of structural defects including non-bridging oxygen are found in the bulk area of the sample after ejection.« less

Femtosecond-laser induced dynamics of CO on Ru(0001): Deep insights from a hot-electron friction model including surface motion

NASA Astrophysics Data System (ADS)

Scholz, Robert; Floß, Gereon; Saalfrank, Peter; Füchsel, Gernot; Lončarić, Ivor; Juaristi, J. I.

2016-10-01

A Langevin model accounting for all six molecular degrees of freedom is applied to femtosecond-laser induced, hot-electron driven dynamics of Ru(0001)(2 ×2 ):CO. In our molecular dynamics with electronic friction approach, a recently developed potential energy surface based on gradient-corrected density functional theory accounting for van der Waals interactions is adopted. Electronic friction due to the coupling of molecular degrees of freedom to electron-hole pairs in the metal are included via a local density friction approximation, and surface phonons by a generalized Langevin oscillator model. The action of ultrashort laser pulses enters through a substrate-mediated, hot-electron mechanism via a time-dependent electronic temperature (derived from a two-temperature model), causing random forces acting on the molecule. The model is applied to laser induced lateral diffusion of CO on the surface, "hot adsorbate" formation, and laser induced desorption. Reaction probabilities are strongly enhanced compared to purely thermal processes, both for diffusion and desorption. Reaction yields depend in a characteristic (nonlinear) fashion on the applied laser fluence, as well as branching ratios for various reaction channels. Computed two-pulse correlation traces for desorption and other indicators suggest that aside from electron-hole pairs, phonons play a non-negligible role for laser induced dynamics in this system, acting on a surprisingly short time scale. Our simulations on precomputed potentials allow for good statistics and the treatment of long-time dynamics (300 ps), giving insight into this system which hitherto has not been reached. We find generally good agreement with experimental data where available and make predictions in addition. A recently proposed laser induced population of physisorbed precursor states could not be observed with the present low-coverage model.

Driving and controlling molecular surface rotors with a terahertz electric field.

PubMed

Neumann, Jan; Gottschalk, Kay E; Astumian, R Dean

2012-06-26

Great progress has been made in the design and synthesis of molecular motors and rotors. Loosely inspired by biomolecular machines such as kinesin and the FoF1 ATPsynthase, these molecules are hoped to provide elements for construction of more elaborate structures that can carry out tasks at the nanoscale corresponding to the tasks accomplished by elementary machines in the macroscopic world. Most of the molecular motors synthesized to date suffer from the drawback that they operate relatively slowly (less than kHz). Here we show by molecular dynamics studies of a diethyl sulfide rotor on a gold(111) surface that a high-frequency oscillating electric field normal to the surface can drive directed rotation at GHz frequencies. The maximum directed rotation rate is 10(10) rotations per second, significantly faster than the rotation of previously reported directional molecular rotors. Understanding the fundamental basis of directed motion of surface rotors is essential for the further development of efficient externally driven artificial rotors. Our results represent a step toward the design of a surface-bound molecular rotary motor with a tunable rotation frequency and direction.

Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations

DOE PAGES

Chen, Ying; Bylaska, Eric J.; Weare, John H.

2017-03-31

Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite (α-Fe(OOH). Ab-initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Here, several exchange correlation functionals were employed (PBE96, PBE96+Grimme, and PBE0) in the simulations of a (3 x 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a=30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick).

Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Ying; Bylaska, Eric J.; Weare, John H.

Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite (α-Fe(OOH). Ab-initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Here, several exchange correlation functionals were employed (PBE96, PBE96+Grimme, and PBE0) in the simulations of a (3 x 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a=30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick).

How the Dynamics of a Supramolecular Polymer Determines Its Dynamic Adaptivity and Stimuli-Responsiveness: Structure-Dynamics-Property Relationships From Coarse-Grained Simulations.

PubMed

Torchi, Andrea; Bochicchio, Davide; Pavan, Giovanni M

2018-04-12

The rational design of supramolecular polymers that can adapt or respond in time to specific stimuli in a controlled way is interesting for many applications, but this requires understanding the molecular factors that make the material faster or slower in responding to the stimulus. To this end, it is necessary to study the dynamic adaptive properties at submolecular resolution, which is difficult at an experimental level. Here we show coarse-grained molecular dynamics simulations (<5 Å resolution) demonstrating how the dynamic adaptivity and stimuli responsiveness of a supramolecular polymer is controlled by the intrinsic dynamics of the assembly, which is in turn determined by the structure of the monomers. As a representative case, we focus on a water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer incorporating (charged) receptor monomers, experimentally seen to undergo dynamic clustering following the superselective binding to a multivalent recruiter. Our simulations show that the dynamic reorganization of the supramolecular structure proceeds via monomer diffusion on the dynamic fiber surface (exchange within the fiber). Rationally changing the structure of the monomers to make the fiber surface more or less dynamic allows tuning the rate of response to the stimulus and of supramolecular reconfiguration. Simple in silico experiments draw a structure-dynamics-property relationship revealing the key factors underpinning the dynamic adaptivity and stimuli-responsiveness of these supramolecular polymers. We come out with clear evidence that to master the bioinspired properties of these fibers, it is necessary to control their intrinsic dynamics, while the high-resolution of our molecular models permits us to show how.

Phonons on fcc (100), (110), and (111) surfaces using Lennard-Jones potentials. II. Temperature dependence of surface phonons studied with molecular dynamics

NASA Astrophysics Data System (ADS)

Koleske, D. D.; Sibener, S. J.

In this paper we present temperature dependent studies of the surface phonon dispersion relations for fcc (100), (110), and (111) faces using molecular dynamics (MD) simulations and Lennard-Jones potentials. This study was conducted in order to investigate how anharmonic potential terms influence the dynamical properties of the surface. This was accomplished by examining the temperature dependence of the Q-resolved phonon spectral density function. All phonon frequencies were found to decrease linearly in T as the temperature was increased, while at low temperatures the phonon linewidths increased linearly with T. At higher temperatures, some of the phonon linewidths changed from having a linear to a quadratic dependence on T. The temperature at which this T to T2 change occurs is surface dependent and occurs at the lowest temperature on the (110) surface. The T2 dependence arises from the increasing importance of higher-order phonon-phonon scattering terms. The phonons which exhibit T2 dependence tend to be modes which propagate perpendicularly or nearly perpendicularly to the direction of maximum root-mean-squared displacement (RMSD). This is especially true for the linewidth of the S 1 mode at overlineX on the (110) surface where, at T ≈ 15-23% of the melting temperature, the RMSD perpendicular to the atomic rows become larger than the RMSD normal to the surface. Our results indicate that the dynamics on the (110) surface may be significantly influenced by anharmonic potential terms at temperatures as low as 15% of the melting temperature.

Molecular dynamics simulations of the surface tension and structure of salt solutions and clusters.

PubMed

Sun, Lu; Li, Xin; Hede, Thomas; Tu, Yaoquan; Leck, Caroline; Ågren, Hans

2012-03-15

Sodium halides, which are abundant in sea salt aerosols, affect the optical properties of aerosols and are active in heterogeneous reactions that cause ozone depletion and acid rain problems. Interfacial properties, including surface tension and halide anion distributions, are crucial issues in the study of the aerosols. We present results from molecular dynamics simulations of water solutions and clusters containing sodium halides with the interatomic interactions described by a conventional force field. The simulations reproduce experimental observations that sodium halides increase the surface tension with respect to pure water and that iodide anions reach the outermost layer of water clusters or solutions. It is found that the van der Waals interactions have an impact on the distribution of the halide anions and that a conventional force field with optimized parameters can model the surface tension of the salt solutions with reasonable accuracy. © 2012 American Chemical Society

The Role of Electronic Excitations on Chemical Reaction Dynamics at Metal, Semiconductor and Nanoparticle Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tully, John C.

Chemical reactions are often facilitated and steered when carried out on solid surfaces, essential for applications such as heterogeneous catalysis, solar energy conversion, corrosion, materials processing, and many others. A critical factor that can determine the rates and pathways of chemical reactions at surfaces is the efficiency and specificity of energy transfer; how fast does energy move around and where does it go? For reactions on insulator surfaces energy transfer generally moves in and out of vibrations of the adsorbed molecule and the underlying substrate. By contrast, on metal surfaces, metallic nanoparticles and semiconductors, another pathway for energy flow opensmore » up, excitation and de-excitation of electrons. This so-called “nonadiabatic” mechanism often dominates the transfer of energy and can directly impact the course of a chemical reaction. Conventional computational methods such as molecular dynamics simulation do not account for this nonadiabatic behavior. The current DOE-BES funded project has focused on developing the underlying theoretical foundation and the computational methodology for the prediction of nonadiabatic chemical reaction dynamics at surfaces. The research has successfully opened up new methodology and new applications for molecular simulation. In particular, over the last three years, the “Electronic Friction” theory, pioneered by the PI, has now been developed into a stable and accurate computational method that is sufficiently practical to allow first principles “on-the-fly” simulation of chemical reaction dynamics at metal surfaces.« less

Molecular-level characterization of the structure and the surface chemistry of periodic mesoporous organosilicates using DNP-surface enhanced NMR spectroscopy.

PubMed

Grüning, Wolfram R; Rossini, Aaron J; Zagdoun, Alexandre; Gajan, David; Lesage, Anne; Emsley, Lyndon; Copéret, Christophe

2013-08-28

We present the molecular level characterization of a phenylpyridine-based periodic mesoporous organosilicate and its post-functionalized organometallic derivatives through the fast acquisition of high quality natural isotopic abundance 1D (13)C, (15)N, and (29)Si and 2D (1)H-(13)C and (1)H-(29)Si solid-state NMR spectra enhanced with dynamic nuclear polarization.

Surface Structure of Liquid Li and Na: An ab initio Molecular Dynamics Study

NASA Astrophysics Data System (ADS)

González, D. J.; González, L. E.; Stott, M. J.

2004-02-01

Molecular dynamics simulations of the liquid-vapor interfaces of liquid metals have been performed using first principles methods. Results are presented for liquid lithium and sodium near their respective triple points, for samples of 2000 particles in a slab geometry. The atomic density profiles show a pronounced stratification extending several atomic diameters into the bulk, which is similar to that already experimentally observed in liquid K, Ga, In, and Hg.

Constitutional Dynamics of Metal-Organic Motifs on a Au(111) Surface.

PubMed

Kong, Huihui; Zhang, Chi; Xie, Lei; Wang, Likun; Xu, Wei

2016-06-13

Constitutional dynamic chemistry (CDC), including both dynamic covalent chemistry and dynamic noncovalent chemistry, relies on reversible formation and breakage of bonds to achieve continuous changes in constitution by reorganization of components. In this regard, CDC is considered to be an efficient and appealing strategy for selective fabrication of surface nanostructures by virtue of dynamic diversity. Although constitutional dynamics of monolayered structures has been recently demonstrated at liquid/solid interfaces, most of molecular reorganization/reaction processes were thought to be irreversible under ultrahigh vacuum (UHV) conditions where CDC is therefore a challenge to be achieved. Here, we have successfully constructed a system that presents constitutional dynamics on a solid surface based on dynamic coordination chemistry, in which selective formation of metal-organic motifs is achieved under UHV conditions. The key to making this reversible switching successful is the molecule-substrate interaction as revealed by DFT calculations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR.

PubMed

Westermaier, Yvonne; Ruiz-Carmona, Sergio; Theret, Isabelle; Perron-Sierra, Françoise; Poissonnet, Guillaume; Dacquet, Catherine; Boutin, Jean A; Ducrot, Pierre; Barril, Xavier

2017-08-01

The knowledge of the free energy of binding of small molecules to a macromolecular target is crucial in drug design as is the ability to predict the functional consequences of binding. We highlight how a molecular dynamics (MD)-based approach can be used to predict the free energy of small molecules, and to provide priorities for the synthesis and the validation via in vitro tests. Here, we study the dynamics and energetics of the nuclear receptor REV-ERBα with its co-repressor NCoR and 35 novel agonists. Our in silico approach combines molecular docking, molecular dynamics (MD), solvent-accessible surface area (SASA) and molecular mechanics poisson boltzmann surface area (MMPBSA) calculations. While docking yielded initial hints on the binding modes, their stability was assessed by MD. The SASA calculations revealed that the presence of the ligand led to a higher exposure of hydrophobic REV-ERB residues for NCoR recruitment. MMPBSA was very successful in ranking ligands by potency in a retrospective and prospective manner. Particularly, the prospective MMPBSA ranking-based validations for four compounds, three predicted to be active and one weakly active, were confirmed experimentally.

Factors determining electrostatic fields in molecular dynamics simulations of the Ras/effector interface.

PubMed

Ensign, Daniel L; Webb, Lauren J

2011-12-01

Using molecular dynamics simulations, we explore geometric and physical factors contributing to calculated electrostatic fields at the binding surface of the GTPase Ras with a spectroscopically labeled variant of a downstream effector, the Ras-binding domain of Ral guanine nucleotide dissociation stimulator (RalGDS). A related system (differing by mutation of one amino acid) has been studied in our group using vibrational Stark effect spectroscopy, a technique sensitive to electrostatic fields. Electrostatic fields were computed using the AMBER 2003 force field and averaged over snapshots from molecular dynamics simulation. We investigate geometric factors by exploring how the orientation of the spectroscopic probe changes on Ras-effector binding. In addition, we explore the physical origin of electrostatic fields at our spectroscopic probe by comparing contributions to the field from discrete components of the system, such as explicit solvent, residues on the Ras surface, and residues on the RalGDS surface. These models support our experimental hypothesis that vibrational Stark shifts are caused by Ras binding to its effector and not the structural rearrangements of the effector surface or probe reorientation on Ras-effector binding, for at least some of our experimental probes. These calculations provide physical insight into the origin, magnitude, and importance of electrostatic fields in protein-protein interactions and suggest new experiments to probe the field's role in protein docking. Copyright © 2011 Wiley-Liss, Inc.

Dynamic Response in Nanoelectrowetting on a Dielectric.

PubMed

Choudhuri, Jyoti Roy; Vanzo, Davide; Madden, Paul Anthony; Salanne, Mathieu; Bratko, Dusan; Luzar, Alenka

2016-09-27

Droplet spreading at an applied voltage underlies the function of tunable optical devices including adjustable lenses and matrix display elements. Faster response and the enhanced resolution motivate research toward miniaturization of these devices to nanoscale dimensions. The response of an aqueous nanodroplet to an applied field can differ significantly from macroscopic predictions. Understanding these differences requires characterization at the molecular level. We describe the equilibrium and nonequilibrium molecular dynamics simulations of nanosized aqueous droplets on a hydrophobic surface with the embedded concentric electrodes. Constant electrode potential is enforced by a rigorous account of the metal polarization. We demonstrate that the reduction of the equilibrium contact angle is commensurate to, and adjusts reversibly with, the voltage change. For a droplet with O(10) nm diameter, a typical response time to the imposition of the field is of O(10(2)) ps. Drop relaxation is about twice as fast when the field is switched off. The friction coefficient obtained from the rate of the drop relaxation on the nonuniform surface, decreases when the droplet approaches equilibrium from either direction, that is, by spreading or receding. The strong dependence of the friction on the surface hydrophilicity points to the dominance of the liquid-surface friction at the drop's perimeter as described in the molecular kinetic theory. This approach enables correct predictions of trends in dynamic responses associated with varied voltage or substrate material.

The molecular dynamics simulation of ion-induced ripple growth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suele, P.; Heinig, K.-H.

The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength ({lambda}) regime BH theory fails to reproduce the resultsmore » obtained by molecular dynamics. We find that at short wavelengths ({lambda}<35 nm) the adatom yield drops hence no surface diffusion takes place which is sufficient for ripple growth. The MD simulations predict that the growth of ripples with {lambda}>35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in {lambda} long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for {lambda}>35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.« less

A quasi-molecular dynamics simulation study on the effect of particles collisions in pulsed-laser desorption

NASA Astrophysics Data System (ADS)

Xinyu-Tan; Duanming-Zhang; Shengqin-Feng; Li, Zhi-hua; Li, Guan; Li, Li; Dan, Liu

2006-05-01

The dynamics characteristic and effect of atoms and particulates ejected from the surface generated by nanosecond pulsed-laser ablation are very important. In this work, based on the consideration of the inelasticity and non-uniformity of the plasma particles thermally desorbed from a plane surface into vacuum induced by nanosecond laser ablation, the one-dimensional particles flow is studied on the basis of a quasi-molecular dynamics (QMD) simulation. It is assumed that atoms and particulates ejected from the surface of a target have a Maxwell velocity distribution corresponding to the surface temperature. Particles collisions in the ablation plume. The particles mass is continuous and satisfies fractal theory distribution. Meanwhile, the particles are inelastic. Our results show that inelasticity and non-uniformity strongly affect the dynamics behavior of the particles flow. Along with the decrease of restitution coefficient e and increase of fractional dimension D, velocity distributions of plasma particles system all deviate from the initial Gaussian distribution. The increasing of dissipation energy ΔE leads to density distribution clusterized and closed up to the center mass. Predictions of the particles action based on the proposed fractal and inelasticity model are found to be in agreement with the experimental observation. This verifies the validity of the present model for the dynamics behavior of pulsed-laser-induced particles flow.

Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Liang; Cheng, Xiaolin; Glass, Dennis C.

2012-06-05

The effect of surface hydration water on internal protein motion is of fundamental interest in molecular biophysics. Here, by decomposing the picosecond to nanosecond atomic motion in molecular dynamics simulations of lysozyme at different hydration levels into three components localized single-well diffusion, methyl group rotation, and nonmethyl jumps we show that the effect of surface hydration is mainly to increase the volume of the localized single-well diffusion. As a result, these diffusive motions are coupled in such a way that the hydration effect propagates from the protein surface into the dry core.

Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo

DOE PAGES

White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; ...

2015-07-07

Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficientmore » as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.« less

1,3,5-trinitro-1,3,5-triazine decomposition and chemisorption on Al(111) surface: first-principles molecular dynamics study.

PubMed

Umezawa, Naoto; Kalia, Rajiv K; Nakano, Aiichiro; Vashista, Priya; Shimojo, Fuyuki

2007-06-21

We have investigated the decomposition and chemisorption of a 1,3,5-trinitro-1,3,5-triazine (RDX) molecule on Al(111) surface using molecular dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). The real-space DFT calculations are based on higher-order finite difference and norm-conserving pseudopotential methods. Strong attractive forces between oxygen and aluminum atoms break N-O and N-N bonds in the RDX and, subsequently, the dissociated oxygen atoms and NO molecules oxidize the Al surface. In addition to these Al surface-assisted decompositions, ring cleavage of the RDX molecule is also observed. These reactions occur spontaneously without potential barriers and result in the attachment of the rest of the RDX molecule to the surface. This opens up the possibility of coating Al nanoparticles with RDX molecules to avoid the detrimental effect of oxidation in high energy density material applications.

Oxidation of InP nanowires: a first principles molecular dynamics study.

PubMed

Berwanger, Mailing; Schoenhalz, Aline L; Dos Santos, Cláudia L; Piquini, Paulo

2016-11-16

InP nanowires are candidates for optoelectronic applications, and as protective capping layers of III-V core-shell nanowires. Their surfaces are oxidized under ambient conditions which affects the nanowire physical properties. The majority of theoretical studies of InP nanowires, however, do not take into account the oxide layer at their surfaces. In this work we use first principles molecular dynamics electronic structure calculations to study the first steps in the oxidation process of a non-saturated InP nanowire surface as well as the properties of an already oxidized surface of an InP nanowire. Our calculations show that the O 2 molecules dissociate through several mechanisms, resulting in incorporation of O atoms into the surface layers. The results confirm the experimental observation that the oxidized layers become amorphous but the non-oxidized core layers remain crystalline. Oxygen related bonds at the oxidized layers introduce defective levels at the band gap region, with greater contributions from defects involving In-O and P-O bonds.

Molecular dynamics simulation of temperature effects on low energy near-surface cascades and surface damage in Cu

NASA Astrophysics Data System (ADS)

Zhu, Guo; Sun, Jiangping; Guo, Xiongxiong; Zou, Xixi; Zhang, Libin; Gan, Zhiyin

2017-06-01

The temperature effects on near-surface cascades and surface damage in Cu(0 0 1) surface under 500 eV argon ion bombardment were studied using molecular dynamics (MD) method. In present MD model, substrate system was fully relaxed for 1 ns and a read-restart scheme was introduced to save total computation time. The temperature dependence of damage production was calculated. The evolution of near-surface cascades and spatial distribution of adatoms at varying temperature were analyzed and compared. It was found that near-surface vacancies increased with temperature, which was mainly due to the fact that more atoms initially located in top two layers became adatoms with the decrease of surface binding energy. Moreover, with the increase of temperature, displacement cascades altered from channeling-like structure to branching structure, and the length of collision sequence decreased gradually, because a larger portion of energy of primary knock-on atom (PKA) was scattered out of focused chain. Furthermore, increasing temperature reduced the anisotropy of distribution of adatoms, which can be ascribed to that regular registry of surface lattice atoms was changed with the increase of thermal vibration amplitude of surface atoms.

Between soap bubbles and vesicles: The dynamics of freely floating smectic bubbles

NASA Astrophysics Data System (ADS)

Stannarius, Ralf; May, Kathrin; Harth, Kirsten; Trittel, Torsten

2013-03-01

The dynamics of droplets and bubbles, particularly on microscopic scales, are of considerable importance in biological, environmental, and technical contexts. We introduce freely floating bubbles of smectic liquid crystals and report their unique dynamic properties. Smectic bubbles can be used as simple models for dynamic studies of fluid membranes. In equilibrium, they form minimal surfaces like soap films. However, shape transformations of closed smectic membranes that change the surface area involve the formation and motion of molecular layer dislocations. These processes are slow compared to the capillary wave dynamics, therefore the effective surface tension is zero like in vesicles. Freely floating smectic bubbles are prepared from collapsing catenoid films and their dynamics is studied with optical high-speed imaging. Experiments are performed under normal gravity and in microgravity during parabolic flights. Supported by DLR within grant OASIS-Co.

Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study.

PubMed

Dhindsa, Gurpreet K; Bhowmik, Debsindhu; Goswami, Monojoy; O'Neill, Hugh; Mamontov, Eugene; Sumpter, Bobby G; Hong, Liang; Ganesh, Panchapakesan; Chu, Xiang-Qiang

2016-09-14

Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on ND surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. Our new findings may provide new design principles for safer, improved drug delivery platforms.

Investigation for Molecular Attraction Impact Between Contacting Surfaces in Micro-Gears

NASA Astrophysics Data System (ADS)

Yang, Ping; Li, Xialong; Zhao, Yanfang; Yang, Haiying; Wang, Shuting; Yang, Jianming

2013-10-01

The aim of this research work is to provide a systematic method to perform molecular attraction impact between contacting surfaces in micro-gear train. This method is established by integrating involute profile analysis and molecular dynamics simulation. A mathematical computation of micro-gear involute is presented based on geometrical properties, Taylor expression and Hamaker assumption. In the meantime, Morse potential function and the cut-off radius are introduced with a molecular dynamics simulation. So a hybrid computational method for the Van Der Waals force between the contacting faces in micro-gear train is developed. An example is illustrated to show the performance of this method. The results show that the change of Van Der Waals force in micro-gear train has a nonlinear characteristic with parameters change such as the modulus of the gear and the tooth number of gear etc. The procedure implies a potential feasibility that we can control the Van Der Waals force by adjusting the manufacturing parameters for gear train design.

A Method for Molecular Dynamics on Curved Surfaces

PubMed Central

Paquay, Stefan; Kusters, Remy

2016-01-01

Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in the field of diffusive transport have focused on solving the diffusion equation on curved surfaces, for which it is not tractable to incorporate particle interactions even though these play a crucial role in crowded systems. We show here that it is possible to take such interactions into account by combining standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface. Furthermore, unlike Brownian dynamics schemes in local coordinates, our method is based on Cartesian coordinates, allowing for the reuse of many other standard tools without modifications, including parallelization through domain decomposition. We show that by applying the schemes to the Langevin equation for various surfaces, we obtain confined Brownian motion, which has direct applications to many biological and physical problems. Finally we present two practical examples that highlight the applicability of the method: 1) the influence of crowding and shape on the lateral diffusion of proteins in curved membranes; and 2) the self-assembly of a coarse-grained virus capsid protein model. PMID:27028633

A Method for Molecular Dynamics on Curved Surfaces

NASA Astrophysics Data System (ADS)

Paquay, Stefan; Kusters, Remy

2016-03-01

Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in the field of diffusive transport have focussed on solving the diffusion equation on curved surfaces, for which it is not tractable to incorporate particle interactions even though these play a crucial role in crowded systems. We show here that it is possible to combine standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface, in which such interactions can be taken into account. Furthermore, unlike Brownian dynamics schemes in local coordinates, our method is based on Cartesian coordinates allowing for the reuse of many other standard tools without modifications, including parallelisation through domain decomposition. We show that by applying the schemes to the Langevin equation for various surfaces, confined Brownian motion is obtained, which has direct applications to many biological and physical problems. Finally we present two practical examples that highlight the applicability of the method: (i) the influence of crowding and shape on the lateral diffusion of proteins in curved membranes and (ii) the self-assembly of a coarse-grained virus capsid protein model.

DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

NASA Astrophysics Data System (ADS)

Humeniuk, Alexander; Mitrić, Roland

2017-12-01

A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

Structure of water clusters on graphene: A classical molecular dynamics approach

NASA Astrophysics Data System (ADS)

Maekawa, Yuki; Sasaoka, Kenji; Yamamoto, Takahiro

2018-03-01

The microscopic structure of surface water adsorbed on graphene is elucidated theoretically by classical molecular dynamics simulation. At a low temperature (100 K), the main polygon consisting of hydrogen bonds in single-layered water on graphene is tetragonal, whereas the dominant polygons in double-layered water are tetragonal, pentagonal, and hexagonal. On the other hand, at room temperature, the tetragonal, pentagonal, and hexagonal water clusters are the main structures in both single- and double-layered water.

Control of unstable interfaces through ballistic induced alloying: Monte Carlo and molecular dynamics calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gomez, Liliana; Slutzky, Claudia; Ferron, Julio

2005-06-15

The explosive features of highly cohesive materials growing over soft metal substrates can be suppressed, and layer by layer growth achieved, by controlling a slight alloying at the interface. By means of Monte Carlo and molecular dynamic simulations, applied to the Co/Cu(111) system, we have proved the stability reached by Co growing over an alloyed CoCu surface, and the factibility of using hyperthermal ions to tailor this alloying.

Exploiting molecular dynamics in Nested Sampling simulations of small peptides

NASA Astrophysics Data System (ADS)

Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor

2016-04-01

Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.

Atomic structure and dynamics properties of Cu50Zr50 films

NASA Astrophysics Data System (ADS)

Chen, Heng; Qu, Bingyan; Li, Dongdong; Zhou, Rulong; Zhang, Bo

2018-01-01

In this paper, the structural and dynamic properties of Cu50Zr50 films are investigated by molecular dynamics simulations. Our results show that the dynamics of the surface atoms are much faster than those of the bulk. Especially, the diffusion coefficient of the surface atoms is about forty times larger than that of the bulk at 600 K, which qualitatively agrees with the experimental results. Meanwhile, we find that the population of the icosahedral (-like) clusters in the surface region is obviously higher than that of the bulk, which prevents the surface from crystallization. A new method to determine the string-like collective atomic motion is introduced in the paper, and it suggests a possible connection between the glass formation ability and collective atomic motion. By using the method, the effects of surface on collective motion are illustrated. Our results show that the string-like collective atomic motion of surface atoms is weakened while that of the interior atoms is strengthened. The studies clearly explain the effects of surface on the structural and dynamic properties of Cu50Zr50 films from the atomic scale.

Early Stage of Oxidation on Titanium Surface by Reactive Molecular Dynamics Simulation

DOE PAGES

Yang, Liang; Wang, C. Z.; Lin, Shiwei; ...

2018-01-01

Understanding of metal oxidation is very critical to corrosion control, catalysis synthesis, and advanced materials engineering. Metal oxidation is a very complex phenomenon, with many different processes which are coupled and involved from the onset of reaction. In this work, the initial stage of oxidation on titanium surface was investigated in atomic scale by molecular dynamics (MD) simulations using a reactive force field (ReaxFF). We show that oxygen transport is the dominant process during the initial oxidation. Our simulation also demonstrate that a compressive stress was generated in the oxide layer which blocked the oxygen transport perpendicular to the Titaniummore » (0001) surface and further prevented oxidation in the deeper layers. As a result, the mechanism of initial oxidation observed in this work can be also applicable to other self-limiting oxidation.« less

Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

NASA Astrophysics Data System (ADS)

VandeVondele, Joost; Rothlisberger, Ursula

2000-09-01

We present a method for calculating multidimensional free energy surfaces within the limited time scale of a first-principles molecular dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This simple procedure yields a very substantial increase in sampling accuracy while retaining the high quality of the underlying ab initio potential surface and can thus be used for a parameter free calculation of free energy surfaces. The success of the method is demonstrated by the applications to two gas phase molecules, ethane and peroxynitrous acid, as test case systems. A statistical analysis of the results shows that the entire free energy landscape is well converged within a 40 ps simulation at 500 K, even for a system with barriers as high as 15 kcal/mol.

The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein-Protein Interactions.

PubMed

Tan, Yaw Sing; Spring, David R; Abell, Chris; Verma, Chandra S

2015-07-14

A computational ligand-mapping approach to detect protein surface pockets that interact with hydrophobic moieties is presented. In this method, we incorporated benzene molecules into explicit solvent molecular dynamics simulations of various protein targets. The benzene molecules successfully identified the binding locations of hydrophobic hot-spot residues and all-hydrocarbon cross-links from known peptidic ligands. They also unveiled cryptic binding sites that are occluded by side chains and the protein backbone. Our results demonstrate that ligand-mapping molecular dynamics simulations hold immense promise to guide the rational design of peptidic modulators of protein-protein interactions, including that of stapled peptides, which show promise as an exciting new class of cell-penetrating therapeutic molecules.

Molecular Insight into the Slipperiness of Ice.

PubMed

Weber, Bart; Nagata, Yuki; Ketzetzi, Stefania; Tang, Fujie; Smit, Wilbert J; Bakker, Huib J; Backus, Ellen H G; Bonn, Mischa; Bonn, Daniel

2018-05-16

Measurements of the friction coefficient of steel-on-ice over a large temperature range reveal very high friction at low temperatures (-100 °C) and a steep decrease in the friction coefficient with increasing temperature. Very low friction is only found over the limited temperature range typical for ice skating. The strong decrease in the friction coefficient with increasing temperature exhibits Arrhenius behavior with an activation energy of E a ≈ 11.5 kJ mol -1 . Remarkably, molecular dynamics simulations of the ice-air interface reveal a very similar activation energy for the mobility of surface molecules. Weakly hydrogen-bonded surface molecules diffuse over the surface in a rolling motion, their number and mobility increasing with increasing temperature. This correlation between macroscopic friction and microscopic molecular mobility indicates that slippery ice arises from the high mobility of its surface molecules, making the ice surface smooth and the shearing of the weakly bonded surface molecules easy.

Water's Interfacial Hydrogen Bonding Structure Reveals the Effective Strength of Surface-Water Interactions.

PubMed

Shin, Sucheol; Willard, Adam P

2018-06-05

We combine all-atom molecular dynamics simulations with a mean field model of interfacial hydrogen bonding to analyze the effect of surface-water interactions on the structural and energetic properties of the liquid water interface. We show that the molecular structure of water at a weakly interacting ( i.e., hydrophobic) surface is resistant to change unless the strength of surface-water interactions are above a certain threshold. We find that below this threshold water's interfacial structure is homogeneous and insensitive to the details of the disordered surface, however, above this threshold water's interfacial structure is heterogeneous. Despite this heterogeneity, we demonstrate that the equilibrium distribution of molecular orientations can be used to quantify the energetic component of the surface-water interactions that contribute specifically to modifying the interfacial hydrogen bonding network. We identify this specific energetic component as a new measure of hydrophilicity, which we refer to as the intrinsic hydropathy.

Solid surface vs. liquid surface: nanoarchitectonics, molecular machines, and DNA origami.

PubMed

Ariga, Katsuhiko; Mori, Taizo; Nakanishi, Waka; Hill, Jonathan P

2017-09-13

The investigation of molecules and materials at interfaces is critical for the accumulation of new scientific insights and technological advances in the chemical and physical sciences. Immobilization on solid surfaces permits the investigation of different properties of functional molecules or materials with high sensitivity and high spatial resolution. Liquid surfaces also present important media for physicochemical innovation and insight based on their great flexibility and dynamicity, rapid diffusion of molecular components for mixing and rearrangements, as well as drastic spatial variation in the prevailing dielectric environment. Therefore, a comparative discussion of the relative merits of the properties of materials when positioned at solid or liquid surfaces would be informative regarding present-to-future developments of surface-based technologies. In this perspective article, recent research examples of nanoarchitectonics, molecular machines, DNA nanotechnology, and DNA origami are compared with respect to the type of surface used, i.e. solid surfaces vs. liquid surfaces, for future perspectives of interfacial physics and chemistry.

A significant reduction of ice adhesion on nanostructured surfaces that consist of an array of single-walled carbon nanotubes: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Bao, Luyao; Huang, Zhaoyuan; Priezjev, Nikolai V.; Chen, Shaoqiang; Luo, Kai; Hu, Haibao

2018-04-01

It is well recognized that excessive ice accumulation at low-temperature conditions can cause significant damage to civil infrastructure. The passive anti-icing surfaces provide a promising solution to suppress ice nucleation and enhance ice removal. However, despite extensive efforts, it remains a challenge to design anti-icing surfaces with low ice adhesion. Using all-atom molecular dynamics (MD) simulations, we show that surfaces with single-walled carbon nanotube array (CNTA) significantly reduce ice adhesion due to the extremely low solid areal fraction. It was found that the CNTA surface exhibits up to a 45% decrease in the ice adhesion strength in comparison with the atomically smooth graphene surface. The details of the ice detachment from the CNTA surface were examined for different water-carbon interaction energies and temperatures of the ice cube. Remarkably, the results of MD simulations demonstrate that the ice detaching strength depends linearly on the ratio of the ice-surface interaction energy and the ice temperature. These results open the possibility for designing novel robust surfaces with low ice adhesion for passive anti-icing applications.

Direct Quantum Dynamics Using Grid-Based Wave Function Propagation and Machine-Learned Potential Energy Surfaces.

PubMed

Richings, Gareth W; Habershon, Scott

2017-09-12

We describe a method for performing nuclear quantum dynamics calculations using standard, grid-based algorithms, including the multiconfiguration time-dependent Hartree (MCTDH) method, where the potential energy surface (PES) is calculated "on-the-fly". The method of Gaussian process regression (GPR) is used to construct a global representation of the PES using values of the energy at points distributed in molecular configuration space during the course of the wavepacket propagation. We demonstrate this direct dynamics approach for both an analytical PES function describing 3-dimensional proton transfer dynamics in malonaldehyde and for 2- and 6-dimensional quantum dynamics simulations of proton transfer in salicylaldimine. In the case of salicylaldimine we also perform calculations in which the PES is constructed using Hartree-Fock calculations through an interface to an ab initio electronic structure code. In all cases, the results of the quantum dynamics simulations are in excellent agreement with previous simulations of both systems yet do not require prior fitting of a PES at any stage. Our approach (implemented in a development version of the Quantics package) opens a route to performing accurate quantum dynamics simulations via wave function propagation of many-dimensional molecular systems in a direct and efficient manner.

Molecular dynamics study of the structural and dynamic characteristics of the polyextremophilic short-chain dehydrogenase from the Thermococcus sibiricus archaeon and its homologues

NASA Astrophysics Data System (ADS)

Popinako, Anna V.; Antonov, Mikhail Yu.; Bezsudnova, Ekaterina Yu.; Prokopiev, Georgiy A.; Popov, Vladimir O.

2017-11-01

The study of structural adaptations of proteins from polyextremophilic organisms using computational molecular dynamics method is appealing because the obtained knowledge can be applied to construction of synthetic proteins with high activity and stability in polyextreme media which is useful for many industrial applications. To investigate molecular adaptations to high temperature, we have focused on a superthermostable short-chain dehydrogenase TsAdh319 from the Thermococcus sibiricus polyextremophilic archaeon and its closest structural homologues. Molecular dynamics method is widely used for molecular structure refinement, investigation of biological macromolecules motion, and, consequently, for interpreting the results of certain biophysical experiments. We performed molecular dynamics simulations of the proteins at different temperatures. Comparison of root mean square fluctuations (RMSF) of the atoms in thermophilic alcohol dehydrogenases (ADHs) at 300 K and 358 K revealed the existence of stable residues at 358 K. These residues surround the active site and form a "nucleus of rigidity" in thermophilic ADHs. The results of our studies suggest that the existence of the "nucleus of rigidity" is crucial for the stability of TsAdh319. Absence of the "nucleus of rigidity" in non-thermally stable proteins causes fluctuations throughout the protein, especially on the surface, triggering the process of denaturation at high temperatures.

Using Molecular Dynamics Simulation to Reinforce Student Understanding of Intermolecular Forces

ERIC Educational Resources Information Center

Burkholder, Phillip R.; Purser, Gordon H.; Cole, Renee S.

2008-01-01

Intermolecular forces play an important role in many aspects of chemistry ranging from inorganic to biological chemistry. These forces dictate molecular conformation, species aggregation (including self-assembly), trends in solubility and boiling points, adsorption characteristics, viscosity, phase changes, surface tension, capillary action, vapor…

Enhanced conformational sampling via novel variable transformations and very large time-step molecular dynamics

NASA Astrophysics Data System (ADS)

Tuckerman, Mark

2006-03-01

One of the computational grand challenge problems is to develop methodology capable of sampling conformational equilibria in systems with rough energy landscapes. If met, many important problems, most notably protein folding, could be significantly impacted. In this talk, two new approaches for addressing this problem will be presented. First, it will be shown how molecular dynamics can be combined with a novel variable transformation designed to warp configuration space in such a way that barriers are reduced and attractive basins stretched. This method rigorously preserves equilibrium properties while leading to very large enhancements in sampling efficiency. Extensions of this approach to the calculation/exploration of free energy surfaces will be discussed. Next, a new very large time-step molecular dynamics method will be introduced that overcomes the resonances which plague many molecular dynamics algorithms. The performance of the methods is demonstrated on a variety of systems including liquid water, long polymer chains simple protein models, and oligopeptides.

[Preparation and evaluation of novel mesoporous molecular sieve of baicalin surface molecularly imprinted polymers].

PubMed

Gu, Xia-li; He, Hong-liang; Shi, Li-ying; Gao, Yan-kun; Chen, Li-na

2015-05-01

Taking mesoporous molecular sieve MCM-41 as a substrate, baicalin (BA) as template, acrylamide (AM) as the functional monomer, ethylene glycol dimethacrylate (EGDMA) as a cross-linking agent, ethanol as solvent, under thermal polymerization initiator of azobis isobutyronitrilo (AIBN) , a kind of selective recognition of baicalin surface molecularly imprinted polymer was synthesized. The surface morphologies and characteristics of the MIPs were characterized by infrared spectroscopy (IR) and transmission electron microscope (TEM). The adsorption properties of polymer microsphere for the template were tested by the dynamic adsorption equilibrium experiments and static adsorption equilibrium experiments. The experiment showed that the imprinting process was successfully and the well-ordered one-dimensional pore structure of MCM-41 was still preserved. Furthermore, molecularly imprinted polymers had higher selective ability for BA, then provided a new method for the efficient separation and enrichment of baicalin active ingredients from medicinal plants Scutellaria baicalensis.

Molecular structures and intramolecular dynamics of pentahalides

NASA Astrophysics Data System (ADS)

Ischenko, A. A.

2017-03-01

This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

Reactive pathways of hydrogen and carbon removal from organosilicate glass low- κ films by F atoms

NASA Astrophysics Data System (ADS)

Voronina, Ekaterina N.; Mankelevich, Yuri A.; Rakhimova, Tatyana V.

2017-07-01

Direct molecular dynamic simulation on the base of the density functional theory (DFT) method is used to study some critical reactions of F atoms with organosilicate glass (OSG) low-κ films. Here static and dynamic DFT-based approaches are applied for a variety of reactive pathways of hydrogen and carbon removal in the form of volatile products (HF, CF2 and CF3 molecules) from initial SiCH3 surface groups. These reactions constitute an important part of the proposed multi-step mechanism of OSG films damage and etching by thermal F atoms. Two models (POSS and TMCTS macromolecules and their modifications) are used to illustrate the peculiarities and dynamics of the successive reactions of F atoms with the initial SiCH3 and appeared SiCHxFy (x + y ≤ 3) surface groups. Contribution to the Topical Issue "Dynamics of Molecular Systems (MOLEC 2016)", edited by Alberto Garcia-Vela, Luis Banares and Maria Luisa Senent.

The classical and quantum dynamics of molecular spins on graphene

PubMed Central

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2015-01-01

Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic1 and quantum computing2 devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics3,4, and electrical spin-manipulation4-11. However, the influence of the graphene environment on the spin systems has yet to be unraveled12. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets13 on graphene. While the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly-developed model. Coupling to Dirac electrons introduces a dominant quantum-relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully-coherent, resonant spin tunneling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin-manipulation in graphene nanodevices. PMID:26641019

Dynamic information for cardiotoxin protein desorption from a methyl-terminated self-assembled monolayer using steered molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Hung, Shih-Wei; Hsiao, Pai-Yi; Chieng, Ching-Chang

2011-05-01

Dynamic information, such as force, structural change, interaction energy, and potential of mean force (PMF), about the desorption of a single cardiotoxin (CTX) protein from a methyl-terminated self-assembled monolayer (SAM) surface was investigated by means of steered molecular dynamics (SMD) simulations. The simulation results indicated that Loop I is the first loop to depart from the SAM surface, which is in good agreement with the results of the nuclear magnetic resonance spectroscopy experiment. The free energy landscape and the thermodynamic force of the CTX desorption process was represented by the PMF and by the derivative of PMF with respect to distance, respectively. By applying Jarzynski's equality, the PMF can be reconstructed from the SMD simulation. The PMFs, calculated by different estimators based upon Jarzynski's equality, were compared with the conventional umbrella sampling method. The best estimation was obtained by using the fluctuation-dissipation estimator with a pulling velocity of v = 0.25 nm/ns for the present study.

Sum frequency generation vibrational spectroscopy (SFG-VS) for complex molecular surfaces and interfaces: Spectral lineshape measurement and analysis plus some controversial issues

NASA Astrophysics Data System (ADS)

Wang, Hong-Fei

2016-12-01

Sum-frequency generation vibrational spectroscopy (SFG-VS) was first developed in the 1980s and it has been proven a uniquely sensitive and surface/interface selective spectroscopic probe for characterization of the structure, conformation and dynamics of molecular surfaces and interfaces. In recent years, there have been many progresses in the development of methodology and instrumentation in the SFG-VS toolbox that have significantly broadened the application to complex molecular surfaces and interfaces. In this review, after presenting a unified view on the theory and methodology focusing on the SFG-VS spectral lineshape, as well as the new opportunities in SFG-VS applications with such developments, some of the controversial issues that have been puzzling the community are discussed. The aim of this review is to present to the researchers and students interested in molecular surfaces and interfacial sciences up-to-date perspectives complementary to the existing textbooks and reviews on SFG-VS.

Sum frequency generation vibrational spectroscopy (SFG-VS) for complex molecular surfaces and interfaces: Spectral lineshape measurement and analysis plus some controversial issues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hong-Fei

Sum-frequency generation vibrational spectroscopy (SFG-VS) was first developed in the 1980s and it has been proven a uniquely sensitive and surface/interface selective spectroscopic probe for characterization of the structure, conformation and dynamics of molecular surfaces and interfaces. In recent years, there has been significant progress in the development of methodology and instrumentation in the SFG-VS toolbox that has significantly broadened the application to complex molecular surfaces and interfaces. In this review, after presenting a unified view on the theory and methodology focusing on the SFG-VS spectral lineshape, as well as the new opportunities in SFG-VS applications with such developments, somemore » of the controversial issues that have been puzzling the community are to be discussed. The aim of this review is to present to the researchers and students interested in molecular surfaces and interfacial sciences up-to-date perspectives complementary to the existing textbooks and reviews on SFG-VS.« less

Stacking the Deck: Leveraging Surface Interactions to Tune Interfacial Electronic Structure

NASA Astrophysics Data System (ADS)

Maughan, Bret; Eads, Calley; Zahl, Percy; Sutter, Peter; Monti, Oliver

We present results from a series of experiments aimed at understanding and controlling molecular interactions in phthalocyanine (Pc) thin-films on Cu(110) to tailor the interfacial electronic structure. Using low-temperature scanning tunneling microscopy (LT-STM), we identify interactions that drive surface-molecule coupling, molecular self-assembly and thin-film order. We provide evidence that interactions with native Cu adatoms play a pivotal role in self-assembly of Pc systems, along with anisotropic nanoribbon growth dynamics, supported by an agent-based kinetic Monte Carlo (AB-KMC) simulation. We show further that self-assembled nanoribbon length can be controlled using surface diffusion barriers and that ordered 2D thin-film growth is promoted by diminishing surface-molecule interactions that otherwise dominate native Cu(110) interfaces. Altogether, this detailed structural understanding allows us to interpret interfacial electronic structure and dynamics, uncovered through ultraviolet (UPS) and two-photon photoemission (2PPE) spectroscopy experiments, in molecular configuration-specific detail. In all, our understanding of interfacial processes guides strategic modifications to both surface and molecule to harness interfacial interactions and thereby modify the collective electronic structure of the interface. NSF No. CHE-1213243 and No. CHE-1565497, Arizona TRIF, DOE/BNL Cntrct No. DE-SC0012704, and DOE No. DE-SC0016343.

Enantiospecific adsorption of propranolol enantiomers on naturally chiral copper surface: A molecular dynamics simulation investigation

NASA Astrophysics Data System (ADS)

Sedghamiz, Tahereh; Bahrami, Maryam; Ghatee, Mohammad Hadi

2017-04-01

Adsorption of propranolol enantiomers on naturally chiral copper (Cu(3,1,17)S) and achiral copper (Cu(100)) surfaces were studied by molecular dynamics simulation to unravel the features of adsorbate-adsorbent enantioselectivity. Adsorption of S- and R-propranolol on Cu(3,1,17)S terraces (with 100 plane) leads mainly to endo- and exo-conformers, respectively. Simulated pair correlation function (g(r)) and mean square displacement (MSD) were analyzed to identify adsorption sites of enantiomers on Cu(3,1,17)S substrate surface, and their simulated binding energies were used to access the adsorption strength. According to (g(r)), R-propranolol adsorbs via naphtyl group while S-propranolol mainly adsorbs through chain group. R-enantiomer binds more tightly to the chiral substrate surface than S-enantiomer as indicated by a higher simulated binding energy by 2.74 kJ mol-1 per molecule. The difference in binding energies of propranolol enantiomers on naturally chiral Cu(3,1,17)S is almost six times larger than on the achiral Cu(100) surface, which substantiates the appreciably strong specific enantioselective adsorption on the former surface.

Protein–Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, Amity; Reardon, Patrick N.; Chacon, Stephany S.

Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na+-montmorillonite (001), Ca2+-montmorillonite (001), goethite (100), and Na+-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, four-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvatedmore » structure without these mineral surfaces present. Over the Na+-birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation.« less

DFT-derived reactive potentials for the simulation of activated processes: the case of CdTe and CdTe:S.

PubMed

Hu, Xiao Liang; Ciaglia, Riccardo; Pietrucci, Fabio; Gallet, Grégoire A; Andreoni, Wanda

2014-06-19

We introduce a new ab initio derived reactive potential for the simulation of CdTe within density functional theory (DFT) and apply it to calculate both static and dynamical properties of a number of systems (bulk solid, defective structures, liquid, surfaces) at finite temperature. In particular, we also consider cases with low sulfur concentration (CdTe:S). The analysis of DFT and classical molecular dynamics (MD) simulations performed with the same protocol leads to stringent performance tests and to a detailed comparison of the two schemes. Metadynamics techniques are used to empower both Car-Parrinello and classical molecular dynamics for the simulation of activated processes. For the latter, we consider surface reconstruction and sulfur diffusion in the bulk. The same procedures are applied using previously proposed force fields for CdTe and CdTeS materials, thus allowing for a detailed comparison of the various schemes.

Structure and Li+ ion transport in a mixed carbonate/LiPF6 electrolyte near graphite electrode surfaces: a molecular dynamics study.

PubMed

Boyer, Mathew J; Vilčiauskas, Linas; Hwang, Gyeong S

2016-10-12

Electrolyte and electrode materials used in lithium-ion batteries have been studied separately to a great extent, however the structural and dynamical properties of the electrolyte-electrode interface still remain largely unexplored despite its critical role in governing battery performance. Using molecular dynamics simulations, we examine the structural reorganization of solvent molecules (cyclic ethylene carbonate : linear dimethyl carbonate 1 : 1 molar ratio doped with 1 M LiPF 6 ) in the vicinity of graphite electrodes with varying surface charge densities (σ). The interfacial structure is found to be sensitive to the molecular geometry and polarity of each solvent molecule as well as the surface structure and charge distribution of the negative electrode. We also evaluated the potential difference across the electrolyte-electrode interface, which exhibits a nearly linear variation with respect to σ up until the onset of Li + ion accumulation onto the graphite edges from the electrolyte. In addition, well-tempered metadynamics simulations are employed to predict the free-energy barriers to Li + ion transport through the relatively dense interfacial layer, along with analysis of the Li + solvation sheath structure. Quantitative analysis of the molecular arrangements at the electrolyte-electrode interface will help better understand and describe electrolyte decomposition, especially in the early stages of solid-electrolyte-interphase (SEI) formation. Moreover, the computational framework presented in this work offers a means to explore the effects of solvent composition, electrode surface modification, and operating temperature on the interfacial structure and properties, which may further assist in efforts to engineer the electrolyte-electrode interface leading to a SEI layer that optimizes battery performance.

Rational design of novel, fluorescent, tagged glutamic acid dendrimers with different terminal groups and in silico analysis of their properties

PubMed Central

Martinho, Nuno; Silva, Liana C; Florindo, Helena F; Brocchini, Steve; Zloh, Mire; Barata, Teresa S

2017-01-01

Dendrimers are hyperbranched polymers with a multifunctional architecture that can be tailored for the use in various biomedical applications. Peptide dendrimers are particularly relevant for drug delivery applications due to their versatility and safety profile. The overall lack of knowledge of their three-dimensional structure, conformational behavior and structure–activity relationship has slowed down their development. Fluorophores are often conjugated to dendrimers to study their interaction with biomolecules and provide information about their mechanism of action at the molecular level. However, these probes can change dendrimer surface properties and have a direct impact on their interactions with biomolecules and with lipid membranes. In this study, we have used computer-aided molecular design and molecular dynamics simulations to identify optimal topology of a poly(l-glutamic acid) (PG) backbone dendrimer that allows incorporation of fluorophores in the core with minimal availability for undesired interactions. Extensive all-atom molecular dynamic simulations with the CHARMM force field were carried out for different generations of PG dendrimers with the core modified with a fluorophore (nitrobenzoxadiazole and Oregon Green 488) and various surface groups (glutamic acid, lysine and tryptophan). Analysis of structural and topological features of all designed dendrimers provided information about their size, shape, internal distribution and dynamic behavior. We have found that four generations of a PG dendrimer are needed to ensure minimal exposure of a core-conjugated fluorophore to external environment and absence of undesired interactions regardless of the surface terminal groups. Our findings suggest that NBD-PG-G4 can provide a suitable scaffold to be used for biophysical studies of surface-modified dendrimers to provide a deeper understanding of their intermolecular interactions, mechanisms of action and trafficking in a biological system. PMID:29026301

Rational design of novel, fluorescent, tagged glutamic acid dendrimers with different terminal groups and in silico analysis of their properties.

PubMed

Martinho, Nuno; Silva, Liana C; Florindo, Helena F; Brocchini, Steve; Zloh, Mire; Barata, Teresa S

2017-01-01

Dendrimers are hyperbranched polymers with a multifunctional architecture that can be tailored for the use in various biomedical applications. Peptide dendrimers are particularly relevant for drug delivery applications due to their versatility and safety profile. The overall lack of knowledge of their three-dimensional structure, conformational behavior and structure-activity relationship has slowed down their development. Fluorophores are often conjugated to dendrimers to study their interaction with biomolecules and provide information about their mechanism of action at the molecular level. However, these probes can change dendrimer surface properties and have a direct impact on their interactions with biomolecules and with lipid membranes. In this study, we have used computer-aided molecular design and molecular dynamics simulations to identify optimal topology of a poly(l-glutamic acid) (PG) backbone dendrimer that allows incorporation of fluorophores in the core with minimal availability for undesired interactions. Extensive all-atom molecular dynamic simulations with the CHARMM force field were carried out for different generations of PG dendrimers with the core modified with a fluorophore (nitrobenzoxadiazole and Oregon Green 488) and various surface groups (glutamic acid, lysine and tryptophan). Analysis of structural and topological features of all designed dendrimers provided information about their size, shape, internal distribution and dynamic behavior. We have found that four generations of a PG dendrimer are needed to ensure minimal exposure of a core-conjugated fluorophore to external environment and absence of undesired interactions regardless of the surface terminal groups. Our findings suggest that NBD-PG-G4 can provide a suitable scaffold to be used for biophysical studies of surface-modified dendrimers to provide a deeper understanding of their intermolecular interactions, mechanisms of action and trafficking in a biological system.

Molecular dynamics analysis of a equilibrium nanoscale droplet on a solid surface with periodic roughness

NASA Astrophysics Data System (ADS)

Furuta, Yuma; Surblys, Donatas; Yamaguchi, Yastaka

2016-11-01

Molecular dynamics simulations of the equilibrium wetting behavior of hemi-cylindrical argon droplets on solid surfaces with a periodic roughness were carried out. The rough solid surface is located at the bottom of the calculation cell with periodic boundary conditions in surface lateral directions and mirror boundary condition at the top boundary. Similar to on a smooth surface, the change of the cosine of the droplet contact angle was linearly correlated to the potential well depth of the inter-atomic interaction between liquid and solid on a surface with a short roughness period while the correlation was deviated on one with a long roughness period. To further investigate this feature, solid-liquid, solid-vapor interfacial free energies per unit projected area of solid surface were evaluated by using the thermodynamic integration method in independent quasi-one-dimensional simulation systems with a liquid-solid interface or vapor-solid interface on various rough solid surfaces at a constant pressure. The cosine of the apparent contact angles estimated from the density profile of the droplet systems corresponded well with ones calculated from Young's equation using the interfacial energies evaluated in the quasi-one dimensional systems.

Understanding and Controlling Living/Inorganic Interfaces to Enable Reconfigurable Switchable Materials

DTIC Science & Technology

2018-03-01

of environmental conditions and surface treatment on binding affinity. 15. SUBJECT TERMS bacterial adhesion, genetically engineered proteins for...mannose binding both experimentally and in molecular dynamics simulation ............................................................ 6 Fig. 3 COMSOL...Research Laboratory (ARL) strengths (e.g., molecular biology/synthetic biology, biomolecular recognition, materials characterization and polymer science

Molecular dynamics simulation aiming at interfacial characteristics of polymer chains on nanotubes with different layers

NASA Astrophysics Data System (ADS)

Li, Kun; Gu, Boqin; Zhu, Wanfu

2017-03-01

A molecular dynamics (MD) simulations study is performed on multiwalled carbon nanotubes (MWNTs)/acrylonitrile-butadiene rubber (NBR) composites. The physisorption and interfacial characteristics between the various MWNTs and polymer macromolecular chains are identified. The effects of nanotube layers on the nanotubes/polymer interactions are examined. Each of the situation result and surface features is characterized by binding energy (Eb). It is shown that the binding energy (Eb) increase with the number of layers.

Atomistic Simulations of Surface Cross-Slip Nucleation in Face-Centered Cubic Nickel and Copper (Postprint)

DTIC Science & Technology

2013-02-15

molecular dynamics code, LAMMPS [9], developed at Sandia National Laboratory. The simulation cell is a rectangular parallelepiped, with the z-axis...with assigned energies within LAMMPs of greater than 4.42 eV (Ni) or 3.52 eV (Cu) (the energy of atoms in the stacking fault region), the partial...molecular dynamics code LAMMPS , which was developed at Sandia National Laboratory by Dr. Steve Plimpton and co-workers. This work was supported by the

Gordon Research Conference on High Temperature Chemistry (1982), Tilton School, Tilton, New Hampshire, July 26-30, 1982.

DTIC Science & Technology

1982-08-01

Session on Recent Advances in High Temperature Chemistry’ Thursday. July 29 Ab Initio Calculations of Molecular W. Weltner, Discussion Leader Structure...atomic fluorescence 13 R. Schoonmaker, Oberlin College: "Scattering of molecular beams from surfaces, dynamics of gas-surface interactions and the...Air Force Geophys. Lab., Ianscom, AFB ,iA Group V1310, lela Park, Cleveland, OH 44112 01731 Saboungi, Marie-Louise off campus Myers, Clifford and

Molecular dynamics of the water liquid-vapor interface

NASA Technical Reports Server (NTRS)

Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

1987-01-01

The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.

Surface chemistry of copper metal and copper oxide atomic layer deposition from copper(ii) acetylacetonate: a combined first-principles and reactive molecular dynamics study.

PubMed

Hu, Xiao; Schuster, Jörg; Schulz, Stefan E; Gessner, Thomas

2015-10-28

Atomistic mechanisms for the atomic layer deposition using the Cu(acac)2 (acac = acetylacetonate) precursor are studied using first-principles calculations and reactive molecular dynamics simulations. The results show that Cu(acac)2 chemisorbs on the hollow site of the Cu(110) surface and decomposes easily into a Cu atom and the acac-ligands. A sequential dissociation and reduction of the Cu precursor [Cu(acac)2 → Cu(acac) → Cu] are observed. Further decomposition of the acac-ligand is unfavorable on the Cu surface. Thus additional adsorption of the precursors may be blocked by adsorbed ligands. Molecular hydrogen is found to be nonreactive towards Cu(acac)2 on Cu(110), whereas individual H atoms easily lead to bond breaking in the Cu precursor upon impact, and thus release the surface ligands into the gas-phase. On the other hand, water reacts with Cu(acac)2 on a Cu2O substrate through a ligand-exchange reaction, which produces gaseous H(acac) and surface OH species. Combustion reactions with the main by-products CO2 and H2O are observed during the reaction between Cu(acac)2 and ozone on the CuO surface. The reactivity of different co-reactants toward Cu(acac)2 follows the order H > O3 > H2O.

Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Bret, E-mail: jackson@chem.umass.edu; Nattino, Francesco; Kroes, Geert-Jan

The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrationalmore » basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.« less

Kinetics from Replica Exchange Molecular Dynamics Simulations.

PubMed

Stelzl, Lukas S; Hummer, Gerhard

2017-08-08

Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

Adaptively biased molecular dynamics for free energy calculations

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2008-04-01

We present an adaptively biased molecular dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using nonequilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential and is inspired by the metadynamics method. The ABMD method has several useful features, including a small number of control parameters and an O(t ) numerical cost with molecular dynamics time t. The ABMD method naturally allows for extensions based on multiple walkers and replica exchange, where different replicas can have different temperatures and/or collective variables. This is beneficial not only in terms of the speed and accuracy of a calculation, but also in terms of the amount of useful information that may be obtained from a given simulation. The workings of the ABMD method are illustrated via a study of the folding of the Ace-GGPGGG-Nme peptide in a gaseous and solvated environment.

Adsorption and recognition characteristics of surface molecularly imprinted polymethacrylic acid/silica toward genistein.

PubMed

Zhang, Yanyan; Gao, Baojiao; An, Fuqiang; Xu, Zeqing; Zhang, Tingting

2014-09-12

In this paper, on the basis of surface-initiated graft polymerization, a new surface molecular imprinting technique is established by molecular design. And molecularly imprinted polymer MIP-PMAA/SiO2 is successfully prepared with genistein as template. The adsorption and recognition characteristics of MIP-PMAA/SiO2 for genistein are studied in depth by using static method, dynamic method and competitive adsorption experiment. The experimental results show that MIP-PMAA/SiO2 possesses very strong adsorption affinity and specific recognition for genistein. The saturated adsorption capacity could reach to 0.36mmolg(-1). The selectivity coefficients relative to quercetin and rutin are 5.4 and 11.8, respectively. Besides, MIP-PMAA/SiO2 is regenerated easily and exhibits excellent reusability. Copyright © 2014 Elsevier B.V. All rights reserved.

Ab initio molecular dynamics simulations for the role of hydrogen in catalytic reactions of furfural on Pd(111)

NASA Astrophysics Data System (ADS)

Xue, Wenhua; Dang, Hongli; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

2014-03-01

In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of hydrogen has attracted wide attention. We report ab initio molecular dynamics simulations for furfural and hydrogen on the Pd(111) surface at finite temperatures. The simulations demonstrate that the presence of hydrogen is important in promoting furfural conversion. In particular, hydrogen molecules dissociate rapidly on the Pd(111) surface. As a result of such dissociation, atomic hydrogen participates in the reactions with furfural. The simulations also provide detailed information about the possible reactions of hydrogen with furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

Multiscale molecular dynamics simulations of rotary motor proteins.

PubMed

Ekimoto, Toru; Ikeguchi, Mitsunori

2018-04-01

Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.

PubMed

Tavernelli, Ivano

2015-03-17

Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics/molecular mechanics (QM/MM) approach has the advantage of providing an atomistic (even though approximated) description of the solvent molecules, which is crucial for the characterization of all ultrafast relaxation phenomena that depend on the geometrical arrangement at the interface between a molecule and the solvent, for example, the hydrogen bond network. After a short description of the TDDFT-based implementation of Ehrenfest and trajectory surface hopping dynamics, I will present applications in different domains of molecular chemistry and physics: the analysis and the understanding of (time-resolved) X-ray absorption spectra, the interpretation of the ultrafast relaxation dynamics of photoexcited dyes in solution, and the design of specific laser pulses (capable of inducing desired chemical reactions) using local control theory.

The interface of SrTiO3 and H2O from density functional theory molecular dynamics

PubMed Central

Spijker, P.; Foster, A. S.

2016-01-01

We use dispersion-corrected density functional theory molecular dynamics simulations to predict the ionic, electronic and vibrational properties of the SrTiO3/H2O solid–liquid interface. Approximately 50% of surface oxygens on the planar SrO termination are hydroxylated at all studied levels of water coverage, the corresponding number being 15% for the planar TiO2 termination and 5% on the stepped TiO2-terminated surface. The lateral ordering of the hydration structure is largely controlled by covalent-like surface cation to H2O bonding and surface corrugation. We find a featureless electronic density of states in and around the band gap energy region at the solid–liquid interface. The vibrational spectrum indicates redshifting of the O–H stretching band due to surface-to-liquid hydrogen bonding and blueshifting due to high-frequency stretching vibrations of OH fragments within the liquid, as well as strong suppression of the OH stretching band on the stepped surface. We find highly varying rates of proton transfer above different SrTiO3 surfaces, owing to differences in hydrogen bond strength and the degree of dissociation of incident water. Trends in proton dynamics and the mode of H2O adsorption among studied surfaces can be explained by the differential ionicity of the Ti–O and Sr–O bonds in the SrTiO3 crystal. PMID:27713660

Molecular dynamics simulations of the orientation properties of cytochrome c on the surface of single-walled carbon nanotubes.

PubMed

Zhang, Bing; Xu, Jia; Mo, Shu-Fan; Yao, Jian-Xi; Dai, Song-Yuan

2016-12-01

Electron transfer between cytochrome c (Cytc) and electrodes can be influenced greatly by the orientation of protein on the surface of the electrodes. In the present study, different initial orientations of Cytc on the surface of five types of single-walled carbon nanotubes (SWNTs), with different diameters and chirality, were constructed. Properties of the orientations of proteins on the surface of these tubes were first investigated through molecular dynamics simulations. It was shown that variations in SWNT diameter do not significantly affect the orientation; however, the chirality of the SWNTs is crucial to the orientation of the heme embedded in Cytc, and the orientation of the protein can consequently be influenced by the heme orientation. A new electron pathway between Cytc and SWNT, which hopefully benefits electron transfer efficiency, has also been proposed. This study promises to provide theoretical guidance for the rational design of bio-sensors or bio-fuel cells by using Cytc-decorated carbon nanotube electrodes.

Experimental and theoretical evidence for bilayer-by-bilayer surface melting of crystalline ice

PubMed Central

Sánchez, M. Alejandra; Kling, Tanja; Ishiyama, Tatsuya; van Zadel, Marc-Jan; Mezger, Markus; Jochum, Mara N.; Cyran, Jenée D.; Smit, Wilbert J.; Bakker, Huib J.; Shultz, Mary Jane; Morita, Akihiro; Donadio, Davide; Nagata, Yuki; Bonn, Mischa; Backus, Ellen H. G.

2017-01-01

On the surface of water ice, a quasi-liquid layer (QLL) has been extensively reported at temperatures below its bulk melting point at 273 K. Approaching the bulk melting temperature from below, the thickness of the QLL is known to increase. To elucidate the precise temperature variation of the QLL, and its nature, we investigate the surface melting of hexagonal ice by combining noncontact, surface-specific vibrational sum frequency generation (SFG) spectroscopy and spectra calculated from molecular dynamics simulations. Using SFG, we probe the outermost water layers of distinct single crystalline ice faces at different temperatures. For the basal face, a stepwise, sudden weakening of the hydrogen-bonded structure of the outermost water layers occurs at 257 K. The spectral calculations from the molecular dynamics simulations reproduce the experimental findings; this allows us to interpret our experimental findings in terms of a stepwise change from one to two molten bilayers at the transition temperature. PMID:27956637

A Computational Study of the Rheology and Structure of Surfactant Covered Droplets

NASA Astrophysics Data System (ADS)

Maia, Joao; Boromand, Arman; Jamali, Safa

2015-11-01

The use of different types of surface-active agents is ubiquitous practice in different industrial applications ranging from cosmetic and food industries to polymeric nano-composite and blends. This allows stable multiphasic systems like foams and emulsions to be produced. Stability and shelf-life of those products are directly determined by the efficiency of the surfactant molecules. Although the effect of molecular configuration of the surface-active molecules on the planar interfaces has been studied both experimentally and computationally, it remains challenging to track the efficiency and effectiveness of different surfactant molecules on curved interfaces. In this study we address this gap by using Dissipative Particle Dynamics, to study the effectiveness and efficiency of different surfactant molecules (linear vs. branched) on a curved interface in equilibrium and far from equilibrium. In particular, we are interested to relate interfacial properties of the surface covered droplets and its dynamics to the molecular configuration of the surface active molecules under equilibrium and far from equilibrium condition.

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

PubMed Central

Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations.

PubMed

Ahlstrom, Logan S; Vorontsov, Ivan I; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.

What can molecular dynamics simulations reveal about the stability of proteinaceous soil organic matter on mineral surfaces?

NASA Astrophysics Data System (ADS)

Andersen, A.; Reardon, P. N.; Chacon, S. S.; Qafoku, N. P.; Washton, N.; Kleber, M.

2015-12-01

With the increased attention on climate change and the role of increasing atmospheric CO2 levels in global warming, the need for an accurate depiction of the carbon cycling processes involved in the Earth's three major carbon pools, i.e., atmosphere, terrestrial systems, and oceans has never been greater. Within the terrestrial system, soil organic matter (SOM) represents an important carbon sub-pool. Complexation of SOM with mineral interfaces and particles is believed to protect SOM from possible biotic and abiotic transformation and mineralization to carbon dioxide. However, obtaining a molecular scale picture of the interactions of the various types of SOM with a variety of soil minerals is a challenging endeavor, especially for experimental techniques. Molecular scale simulations techniques can be applied to study the atomistic, molecular, and nanoscale aspects of SOM-mineral associations, and, therefore, and aid in filling current knowledge gaps in the potential fate and stability of SOM in soil systems. Here, we will discuss our recent results from large-scale molecular dynamics simulation of protein, GB1, and its interaction with clay and oxide/hydroxide minerals (i.e., kaolinite, Na+-MMT, Ca2+-MMT, goethite, and birnessite) including a comparison of structural changes of the protein by, protein orientation with respect to, degree of protein binding to, and mobility on the mineral surfaces. Our molecular simulations indicate that these mineral surfaces, with the exception of birnessite, potentially preserve the physical properties of the GB1 protein.

Cluster adsorption on amorphous and crystalline surfaces - A molecular dynamics study of model Pt on Cu and model Pd on Pt

NASA Technical Reports Server (NTRS)

Garofalini, S. H.; Halicioglu, T.; Pound, G. M.

1981-01-01

Molecular dynamics was used to study the structure, dispersion and short-time behavior of ten-atom clusters adsorbed onto amorphous and crystalline substrates, in which the cluster atoms differed from the substrate atoms. Two adatom-substrate model systems were chosen; one, in which the interaction energy between adatom pairs was greater than that between substrate pairs, and the other, in which the reverse was true. At relatively low temperature ranges, increased dispersion of cluster atoms occurred: (a) on the amorphous substrate as compared to the FCC(100) surface, (b) with increasing reduced temperature, and (c) with adatom-substrate interaction energy stronger than adatom-adatom interaction. Two-dimensional clusters (rafts) on the FCC(100) surface displayed migration of edge atoms only, indicating a mechanism for the cluster rotation and shape changes found in experimental studies.

Molecular dynamics simulation of self-diffusion processes in titanium in bulk material, on grain junctions and on surface.

PubMed

Sushko, Gennady B; Verkhovtsev, Alexey V; Yakubovich, Alexander V; Schramm, Stefan; Solov'yov, Andrey V

2014-08-21

The process of self-diffusion of titanium atoms in a bulk material, on grain junctions and on surface is explored numerically in a broad temperature range by means of classical molecular dynamics simulation. The analysis is carried out for a nanoscale cylindrical sample consisting of three adjacent sectors and various junctions between nanocrystals. The calculated diffusion coefficient varies by several orders of magnitude for different regions of the sample. The calculated values of the bulk diffusion coefficient correspond reasonably well to the experimental data obtained for solid and molten states of titanium. Investigation of diffusion in the nanocrystalline titanium is of a significant importance because of its numerous technological applications. This paper aims to reduce the lack of data on diffusion in titanium and describe the processes occurring in bulk, at different interfaces and on surface of the crystalline titanium.

An investigation into the melting of silicon nanoclusters using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Fang, Kuan-Chuan; Weng, Cheng-I.

2005-02-01

Using the Stillinger-Weber (SW) potential model, we have performed molecular dynamics (MD) simulations to investigate the melting of silicon nanoclusters comprising a maximum of 9041 atoms. This study investigates the size, surface energy and root mean square displacement (RMSD) characteristics of the silicon nanoclusters as they undergo a heating process. The numerical results reveal that an intermediate nanocrystal regime exists for clusters with more than 357 atoms. Within this regime, a linear relationship exists between the cluster size and its melting temperature. It is found that melting of the silicon nanoclusters commences at the surface and that Tm,N = Tm,Bulk-αN-1/3. Therefore, the extrapolated melting temperature of the bulk with a surface decreases from Tm,Bulk = 1821 K to a value of Tm,357 = 1380 K at the lower limit of the intermediate nanocrystal regime.

Molecular insight into the counteraction of trehalose on urea-induced protein denaturation using molecular dynamics simulation.

PubMed

Zhang, Na; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

2012-06-21

Considerable experimental evidence indicates that trehalose can counteract the denaturing effects of urea on proteins. However, its molecular mechanism remains unknown due to the limitations of current experimental techniques. Herein, molecular dynamics simulations were performed to investigate the counteracting effects of trehalose against urea-induced denaturation of chymotrypsin inhibitor 2. The simulations indicate that the protein unfolds in 8 mol/L urea, but at the same condition the protein retains its native structure in the ternary solution of 8 mol/L urea and 1 mol/L trehalose. It is confirmed that the preferential exclusion of trehalose from the protein surface is the origin of its counteracting effects. It is found that trehalose binds urea via hydrogen bonds, so urea molecules are also expelled from the protein surface along with the preferential exclusion of trehalose. The exclusion of urea from the protein surface leads to the alleviation of the Lennard-Jones interactions between urea and the hydrophobic side chains of the protein in the ternary solution. In contrast, the electrostatic interactions between urea and the protein change little in the presence of trehalose because the decrease in the electrostatic interactions between urea and the protein backbone is canceled by the increase in the electrostatic interactions between urea and the charged side chains of the protein. The results have provided molecular explanations for the counteraction of urea-induced protein denaturation by trehalose.

Origin of 1/f noise in hydration dynamics on lipid membrane surfaces

PubMed Central

Yamamoto, Eiji; Akimoto, Takuma; Yasui, Masato; Yasuoka, Kenji

2015-01-01

Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although water structures and diffusivities near the membrane surfaces have been extensively studied, hydration dynamics on the surfaces has remained an open question. Here we investigate residence time statistics of water molecules on the surface of lipid membranes using all-atom molecular dynamics simulations. We show that hydration dynamics on the lipid membranes exhibits 1/f noise. Constructing a dichotomous process for the hydration dynamics, we find that residence times in each state follow a power-law with exponential cutoff and that the process can be regarded as a correlated renewal process where interoccurrence times are correlated. The results imply that the origin of the 1/f noise in hydration dynamics on the membrane surfaces is a combination of a power-law distribution with cutoff of interoccurrence times of switching events and a long-term correlation between the interoccurrence times. These results suggest that the 1/f noise attributed to the correlated renewal process may contribute to the stability of the hydration layers and lipid membranes. PMID:25743377

The Effect of Water on the Work of Adhesion at Epoxy Interfaces by Molecular Dynamics Simulation

NASA Technical Reports Server (NTRS)

Hinkley, J.A.; Frankland, S.J.V.; Clancy, T.C.

2009-01-01

Molecular dynamics simulation can be used to explore the detailed effects of chemistry on properties of materials. In this paper, two different epoxies found in aerospace resins are modeled using molecular dynamics. The first material, an amine-cured tetrafunctional epoxy, represents a composite matrix resin, while the second represents a 177 C-cured adhesive. Surface energies are derived for both epoxies and the work of adhesion values calculated for the epoxy/epoxy interfaces agree with experiment. Adding water -- to simulate the effect of moisture exposure -- reduced the work of adhesion in one case, and increased it in the other. To explore the difference, the various energy terms that make up the net work of adhesion were compared and the location of the added water was examined.

Discotic columnar liquid crystal studied in the bulk and nanoconfined states by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Busselez, Rémi; Cerclier, Carole V.; Ndao, Makha; Ghoufi, Aziz; Lefort, Ronan; Morineau, Denis

2014-10-01

A prototypical Gay Berne discotic liquid crystal was studied by means of molecular dynamics simulations both in the bulk state and under confinement in a nanoporous channel. The phase behavior of the confined system strongly differs from its bulk counterpart: the bulk isotropic-to-columnar transition is replaced by a continuous ordering from a paranematic to a columnar phase. Moreover, a new transition is observed at a lower temperature in the confined state, which corresponds to a reorganization of the intercolumnar order. It reflects the competing effects of pore surface interaction and genuine hexagonal packing of the columns. The translational molecular dynamics in the different phases has been thoroughly studied and discussed in terms of collective relaxation modes, non-Gaussian behavior, and hopping processes.

Free energy calculations of short peptide chains using Adaptively Biased Molecular Dynamics

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2008-10-01

We performed a computational study of monomer peptides composed of methionine, alanine, leucine, glutamate, lysine (all amino acids with a helix-forming propensities); and proline, glycine tyrosine, serine, arginine (which all have poor helix-forming propensities). The free energy landscapes as a function of the handedness and radius of gyration have been calculated using the recently introduced Adaptively Biased Molecular Dynamics (ABMD) method, combined with replica exchange, multiple walkers, and post-processing Umbrella Correction (UC). Minima that correspond to some of the left- and right-handed 310-, α- and π-helixes were identified by secondary structure assignment methods (DSSP, Stride). The resulting free energy surface (FES) and the subsequent steered molecular dynamics (SMD) simulation results are in agreement with the empirical evidence of preferred secondary structures for the peptide chains considered.

2D-HB-Network at the air-water interface: A structural and dynamical characterization by means of ab initio and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Pezzotti, Simone; Serva, Alessandra; Gaigeot, Marie-Pierre

2018-05-01

Following our previous work where the existence of a special 2-Dimensional H-Bond (2D-HB)-Network was revealed at the air-water interface [S. Pezzotti et al., J. Phys. Chem. Lett. 8, 3133 (2017)], we provide here a full structural and dynamical characterization of this specific arrangement by means of both Density Functional Theory based and Force Field based molecular dynamics simulations. We show in particular that water at the interface with air reconstructs to maximize H-Bonds formed between interfacial molecules, which leads to the formation of an extended and non-interrupted 2-Dimensional H-Bond structure involving on average ˜90% of water molecules at the interface. We also show that the existence of such an extended structure, composed of H-Bonds all oriented parallel to the surface, constrains the reorientional dynamics of water that is hence slower at the interface than in the bulk. The structure and dynamics of the 2D-HB-Network provide new elements to possibly rationalize several specific properties of the air-water interface, such as water surface tension, anisotropic reorientation of interfacial water under an external field, and proton hopping.

Molecular dynamics simulation of siderite-hematite-quartz flotation with sodium oleate

NASA Astrophysics Data System (ADS)

Li, Lixia; Hao, Haiqing; Yuan, Zhitao; Liu, Jiongtian

2017-10-01

Models of sodium oleate adsorption on siderite, hematite and quartz were investigated by molecular dynamic simulation, respectively. Surface energy was calculated to confirm the cleavage plan of hematite and quartz. Both natural cleavage plane of siderite and calculated plane were used to investigate the flotation of the three minerals. Based on the molecular simulation in solution with water as medium, adsorption quantity and interaction capability of oleate ions on the three minerals indicated that siderite could be collected efficiently by sodium oleate at neutral pH. Results of flotation experiments were further demonstrated by analysis of relative concentration of carbon atoms and oxygen atoms.

Structural Origin of Enhanced Dynamics at the Surface of a Glassy Alloy

NASA Astrophysics Data System (ADS)

Sun, Gang; Saw, Shibu; Douglass, Ian; Harrowell, Peter

2017-12-01

The enhancement of mobility at the surface of an amorphous alloy is studied using a combination of molecular dynamic simulations and normal mode analysis of the nonuniform distribution of Debye-Waller factors. The increased mobility at the surface is found to be associated with the appearance of Arrhenius temperature dependence. We show that the transverse Debye-Waller factor exhibits a peak at the surface. Over the accessible temperature range, we find that the bulk and surface diffusion coefficients obey the same empirical relationship with the respective Debye-Waller factors. Extrapolating this relationship to lower T , we argue that the observed decrease in the constraint at the surface is sufficient to account for the experimentally observed surface enhancement of mobility.

Mechanisms of oriented attachment of TiO2 nanocrystals in vacuum and humid environments: reactive molecular dynamics.

PubMed

Raju, Muralikrishna; van Duin, Adri C T; Fichthorn, Kristen A

2014-01-01

Oriented attachment (OA) of nanocrystals is now widely recognized as a key process in the solution-phase growth of hierarchical nanostructures. However, the microscopic origins of OA remain unclear. We perform molecular dynamics simulations using a recently developed ReaxFF reactive force field to study the aggregation of various titanium dioxide (anatase) nanocrystals in vacuum and humid environments. In vacuum, the nanocrystals merge along their direction of approach, resulting in a polycrystalline material. By contrast, in the presence of water vapor the nanocrystals reorient themselves and aggregate via the OA mechanism to form a single or twinned crystal. They accomplish this by creating a dynamic network of hydrogen bonds between surface hydroxyls and surface oxygens of aggregating nanocrystals. We determine that OA is dominant on surfaces that have the greatest propensity to dissociate water. Our results are consistent with experiment, are likely to be general for aqueous oxide systems, and demonstrate the critical role of solvent in nanocrystal aggregation. This work opens up new possibilities for directing nanocrystal growth to fabricate nanomaterials with desired shapes and sizes.

Direct observation of a single nanoparticle-ubiquitin corona formation

NASA Astrophysics Data System (ADS)

Ding, Feng; Radic, Slaven; Chen, Ran; Chen, Pengyu; Geitner, Nicholas K.; Brown, Jared M.; Ke, Pu Chun

2013-09-01

The advancement of nanomedicine and the increasing applications of nanoparticles in consumer products have led to administered biological exposure and unintentional environmental accumulation of nanoparticles, causing concerns over the biocompatibility and sustainability of nanotechnology. Upon entering physiological environments, nanoparticles readily assume the form of a nanoparticle-protein corona that dictates their biological identity. Consequently, understanding the structure and dynamics of a nanoparticle-protein corona is essential for predicting the fate, transport, and toxicity of nanomaterials in living systems and for enabling the vast applications of nanomedicine. Here we combined multiscale molecular dynamics simulations and complementary experiments to characterize the silver nanoparticle-ubiquitin corona formation. Notably, ubiquitins competed with citrates for the nanoparticle surface, governed by specific electrostatic interactions. Under a high protein/nanoparticle stoichiometry, ubiquitins formed a multi-layer corona on the particle surface. The binding exhibited an unusual stretched-exponential behavior, suggesting a rich binding kinetics. Furthermore, the binding destabilized the α-helices while increasing the β-sheet content of the proteins. This study revealed the atomic and molecular details of the structural and dynamic characteristics of nanoparticle-protein corona formation.The advancement of nanomedicine and the increasing applications of nanoparticles in consumer products have led to administered biological exposure and unintentional environmental accumulation of nanoparticles, causing concerns over the biocompatibility and sustainability of nanotechnology. Upon entering physiological environments, nanoparticles readily assume the form of a nanoparticle-protein corona that dictates their biological identity. Consequently, understanding the structure and dynamics of a nanoparticle-protein corona is essential for predicting the fate, transport, and toxicity of nanomaterials in living systems and for enabling the vast applications of nanomedicine. Here we combined multiscale molecular dynamics simulations and complementary experiments to characterize the silver nanoparticle-ubiquitin corona formation. Notably, ubiquitins competed with citrates for the nanoparticle surface, governed by specific electrostatic interactions. Under a high protein/nanoparticle stoichiometry, ubiquitins formed a multi-layer corona on the particle surface. The binding exhibited an unusual stretched-exponential behavior, suggesting a rich binding kinetics. Furthermore, the binding destabilized the α-helices while increasing the β-sheet content of the proteins. This study revealed the atomic and molecular details of the structural and dynamic characteristics of nanoparticle-protein corona formation. Electronic supplementary information (ESI) available: Experimental and computational methods as well as supporting figures. See DOI: 10.1039/c3nr02147e

Photo-responsive surface topology in chiral nematic media

NASA Astrophysics Data System (ADS)

Liu, Danqing; Bastiaansen, Cees W. M.; Toonder, Jaap. M. J.; Broer, Dirk J.

2012-03-01

We report on the design and fabrication of 'smart surfaces' that exhibit dynamic changes in their surface topology in response to exposure to light. The principle is based on anisotropic geometric changes of a liquid crystal network upon a change of the molecular order parameter. The photomechanical property of the coating is induced by incorporating an azobenzene moiety into the liquid crystal network. The responsive surface topology consists of regions with two different types of molecular order: planar chiral-nematic areas and homeotropic. Under flood exposure with 365 nm light the surfaces deform from flat to one with a surface relief. The height of the relief structures is of the order of 1 um corresponding to strain difference of around 20%. Furthermore, we demonstrate surface reliefs can form either convex or concave structures upon exposure to UV light corresponding to the decrease or increase molecular order parameter, respectively, related to the isomeric state of the azobenzene crosslinker. The reversible deformation to the initial flat state occurs rapidly after removing the light source.

Interfacial water on crystalline silica: a comparative molecular dynamics simulation study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, Tuan A.; Argyris, Dimitrios; Papavassiliou, Dimitrios V.

2011-03-03

All-atom molecular dynamics simulations were conducted to study the dynamics of aqueous electrolyte solutions confined in slit-shaped silica nanopores of various degrees of protonation. Five degrees of protonation were prepared by randomly removing surface hydrogen atoms from fully protonated crystalline silica surfaces. Aqueous electrolyte solutions containing NaCl or CsCl salt were simulated at ambient conditions. In all cases, the ionic concentration was 1 M. The results were quantified in terms of atomic density distributions within the pores, and the self-diffusion coefficient along the direction parallel to the pore surface. We found evidence for ion-specific properties that depend on ion surface,more » water ion, and only in some cases ion ion correlations. The degree of protonation strongly affects the structure, distribution, and the dynamic behavior of confined water and electrolytes. Cl ions adsorb on the surface at large degrees of protonation, and their behavior does not depend significantly on the cation type (either Na+ or Cs+ ions are present in the systems considered). The cations show significant ion-specific behavior. Na+ ions occupy different positions within the pore as the degree of protonation changes, while Cs+ ions mainly remain near the pore center at all conditions considered. For a given degree of protonation, the planar self-diffusion coefficient of Cs+ is always greater than that of Na+ ions. The results are useful for better understanding transport under confinement, including brine behavior in the subsurface, with important applications such as environmental remediation.« less

Ab initio study on the dynamics of furfural at the liquid-solid interfaces

NASA Astrophysics Data System (ADS)

Dang, Hongli; Xue, Wenhua; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

2013-03-01

Catalytic biomass conversion sometimes occurs at the liquid-solid interfaces. We report ab initio molecular dynamics simulations at finite temperatures for the catalytic reactions involving furfural at the water-Pd and water-Cu interfaces. We found that, during the dynamic process, the furan ring of furfural prefers to be parallel to the Pd surface and the aldehyde group tends to be away from the Pd surface. On the other hand, at the water-Cu(111) interface, furfural prefers to be tilted to the Cu surface while the aldehyde group is bonded to the surface. In both cases, interaction of liquid water and furfural is identified. The difference of dynamic process of furfural at the two interfaces suggests different catalytic reaction mechanisms for the conversion of furfural, consistent with the experimental investigations. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSED's and NERSC's supercomputers

Strain-induced friction anisotropy between graphene and molecular liquids

NASA Astrophysics Data System (ADS)

Liao, Meng; To, Quy-Dong; Léonard, Céline; Monchiet, Vincent; Vo, Van-Hoang

2017-01-01

In this paper, we study the friction behavior of molecular liquids with anisotropically strained graphene. Due to the changes of lattice and the potential energy surface, the friction is orientation dependent and can be computed by tensorial Green-Kubo formula. Simple quantitative estimations are also proposed for the zero-time response and agree reasonably well with the molecular dynamics results. From simulations, we can obtain the information of structures, dynamics of the system, and study the influence of strain and molecular shapes on the anisotropy degree. It is found that unilateral strain can increase friction in all directions but the strain direction is privileged. Numerical evidences also show that nonspherical molecules are more sensitive to strain and give rise to more pronounced anisotropy effects.

Computational and theoretical approaches for studies of a lipid recognition protein on biological membranes

PubMed Central

Yamamoto, Eiji

2017-01-01

Many cellular functions, including cell signaling and related events, are regulated by the association of peripheral membrane proteins (PMPs) with biological membranes containing anionic lipids, e.g., phosphatidylinositol phosphate (PIP). This association is often mediated by lipid recognition modules present in many PMPs. Here, I summarize computational and theoretical approaches to investigate the molecular details of the interactions and dynamics of a lipid recognition module, the pleckstrin homology (PH) domain, on biological membranes. Multiscale molecular dynamics simulations using combinations of atomistic and coarse-grained models yielded results comparable to those of actual experiments and could be used to elucidate the molecular mechanisms of the formation of protein/lipid complexes on membrane surfaces, which are often difficult to obtain using experimental techniques. Simulations revealed some modes of membrane localization and interactions of PH domains with membranes in addition to the canonical binding mode. In the last part of this review, I address the dynamics of PH domains on the membrane surface. Local PIP clusters formed around the proteins exhibit anomalous fluctuations. This dynamic change in protein-lipid interactions cause temporally fluctuating diffusivity of proteins, i.e., the short-term diffusivity of the bound protein changes substantially with time, and may in turn contribute to the formation/dissolution of protein complexes in membranes. PMID:29159013

Effects of temperature and surface orientation on migration behaviours of helium atoms near tungsten surfaces

NASA Astrophysics Data System (ADS)

Wang, Xiaoshuang; Wu, Zhangwen; Hou, Qing

2015-10-01

Molecular dynamics simulations were performed to study the dependence of migration behaviours of single helium atoms near tungsten surfaces on the surface orientation and temperature. For W{100} and W{110} surfaces, He atoms can quickly escape out near the surface without accumulation even at a temperature of 400 K. The behaviours of helium atoms can be well-described by the theory of continuous diffusion of particles in a semi-infinite medium. For a W{111} surface, the situation is complex. Different types of trap mutations occur within the neighbouring region of the W{111} surface. The trap mutations hinder the escape of He atoms, resulting in their accumulation. The probability of a He atom escaping into vacuum from a trap mutation depends on the type of the trap mutation, and the occurrence probabilities of the different types of trap mutations are dependent on the temperature. This finding suggests that the escape rate of He atoms on the W{111} surface does not show a monotonic dependence on temperature. For instance, the escape rate at T = 1500 K is lower than the rate at T = 1100 K. Our results are useful for understanding the structural evolution and He release on tungsten surfaces and for designing models in other simulation methods beyond molecular dynamics.

Leapfrog Diffusion Mechanism for One-Dimensional Chains on Missing-Row Reconstructed Surfaces

NASA Astrophysics Data System (ADS)

Montalenti, F.; Ferrando, R.

1999-02-01

We analyze the in-channel diffusion of dimers and longer n-adatom chains on Au and Pt (110) \\(1×2\\) surfaces by molecular dynamics simulations. From our calculations it arises that, on the missing-row reconstructed surface, a novel diffusion process, called leapfrog, dominates over concerted jumps, thus becoming the most frequent diffusion mechanism.

Collinear Collision Chemistry: 1. A Simple Model for Inelastic and Reactive Collision Dynamics

ERIC Educational Resources Information Center

Mahan, Bruce H.

1974-01-01

Discusses a model for the collinear collision of an atom with a diatomic molecule on a simple potential surface. Indicates that the model can provide a framework for thinking about molecular collisions and reveal many factors which affect the dynamics of reactive and inelastic collisions. (CC)

Influence of surface morphology on adsorption of potassium stearate molecules on diamond-like carbon substrate: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Guo, Shusen; Cao, Yongzhi; Sun, Tao; Zhang, Junjie; Gu, Le; Zhang, Chuanwei; Xu, Zhiqiang

2018-05-01

Molecular dynamics (MD) simulations were used to provide insights into the influence of nano-scale surface morphology on adsorptive behavior of Potassium stearate molecules on diamond-like carbon (DLC) substrates. Particular focus was given to explain that how the distinctive geometric properties of different surface morphologies affect the equilibrium structures and substrate-molecules interactions of monolayers, which was achieved through adsorptive analysis methods including adsorptive process, density profile, density distribution and surface potential energy. Analysis on surface potential energy demonstrated that the adsorptivity of amorphous smooth substrate is uniformly distributed over the surface, while DLC substrates with different surface morphologies appear to be more potentially corrugated, which improves the adsorptivity significantly. Because of the large distance of molecules from carbon atoms located at the square groove bottom, substrate-molecules interactions vanish significantly, and thus potassium stearate molecules cannot penetrate completely into the square groove. It can be observed that the equilibrium substrate-molecules interactions of triangle groove and semi-circle groove are much more powerful than that of square groove due to geometrically advantageous properties. These findings provided key information of optimally design of solid substrates with controllable adsorptivity.

Investigations into the mechanism of material removal and surface modification at atomic scale on stainless steel using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Ranjan, Prabhat; Balasubramaniam, R.; Jain, V. K.

2018-06-01

A molecular dynamics simulation (MDS) has been carried out to investigate the material removal phenomenon of chemo-mechanical magnetorheological finishing (CMMRF) process. To understand the role of chemical assisted mechanical abrasion in CMMRF process, material removal phenomenon is subdivided into three different stages. In the first stage, new atomic bonds viz. Fe-O-Si is created on the surface of the workpiece (stainless steel). The second stage deals with the rupture of parent bonds like Fe-Fe on the workpiece. In the final stage, removal of material from the surface in the form of dislodged debris (cluster of atoms) takes place. Effects of process parameters like abrasive particles, depth of penetration and initial surface condition on finishing force, potential energy (towards secondary phenomenon such as chemical instability of the finished surface) and material removal at atomic scale have been investigated. It was observed that the type of abrasive particle is one of the important parameters to produce atomically smooth surface. Experiments were also conducted as per the MDS to generate defect-free and sub-nanometre-level finished surface (Ra value better than 0.2 nm). The experimental results reasonably agree well with the simulation results.

Combination of first-principles molecular dynamics and XANES simulations for LiCoO2-electrolyte interfacial reactions in a lithium-ion battery

NASA Astrophysics Data System (ADS)

Tamura, Tomoyuki; Kohyama, Masanori; Ogata, Shuji

2017-07-01

We performed a first-principles molecular dynamics (FPMD) simulation of the interfacial reactions between a LiCoO2 electrode and a liquid ethylene carbonate (EC) electrolyte. For configurations during the FPMD simulation, we also performed first-principles Co K-edge x-ray absorption near-edge structure (XANES) simulations, which can properly reproduce the bulk and surface spectra of LiCoO2. We observed strong absorption of an EC molecule on the LiCoO2 {110} surface, involving ring opening of the molecule, bond formation between oxygen atoms in the molecule and surface Co ions, and emission of one surface Li ion, while all the surface Co ions remain Co3 +. The surface Co ions having the bond with an oxygen atom in the molecule showed remarkable changes in simulated K-edge spectra which are similar to those of the in situ observation under electrolyte soaking [D. Takamatsu et al., Angew. Chem., Int. Ed. 51, 11597 (2012), 10.1002/anie.201203910]. Thus, the local environmental changes of surface Co ions due to the reactions with an EC molecule can explain the experimental spectrum changes.

Molecular Dynamics Simulations of the Interfacial Region between Boehmite and Gibbsite Basal Surfaces and High Ionic Strength Aqueous Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, Zhizhang; Ilton, Eugene S.; Prange, Micah P.

Classical molecular dynamics (MD) simulations were used to study the interactions of up to 2 M NaCl and NaNO3 aqueous solutions with the presumed inert boehmite (010) and gibbsite (001) surfaces. The force field parameters used in these simulations were validated against density functional theory calculations of Na+ and Cl- hydrated complexes adsorbed at the boehmite (010) surface. In all the classical MD simulations and regardless of the ionic strength or the nature of the anion, Na+ ions were found to preferably form inner-sphere complexes over outer-sphere complexes at the aluminum (oxy)hydroxide surfaces, adsorbing closer to the surface than bothmore » water molecules and anions. In contrast, Cl- ions were distributed almost equally between inner- and outer-sphere positions. The resulting asymmetry in adsorption strengths offers molecular-scale evidence for the observed isoelectric point (IEP) shift to higher pH at high ionic strength for aluminum (oxy)hydroxides. As such, the MD simulations also provided clear evidence against the assumption that the basal surfaces of boehmite and gibbsite are inert to background electrolytes. Finally, the MD simulations indicated that, although the adsorption behavior of Na+ in NaNO3 and NaCl solutions was similar, the different affinities of NO3- and Cl- for the aluminum (oxy)hydroxide surfaces might have macroscopic consequences, such as difference in the sensitivity of the IEP to the electrolyte concentration.« less

Energetics and Dynamics of GaAs Epitaxial Growth via Quantum Wave Packet Studies

NASA Technical Reports Server (NTRS)

Dzegilenko, Fedor N.; Saini, Subhash (Technical Monitor)

1998-01-01

The dynamics of As(sub 2) molecule incorporation into the flat Ga-terminated GaAs(100) surface is studied computationally. The time-dependent Schrodinger equation is solved on a two-dimensional potential energy surface obtained using density functional theory calculations. The probabilities of trapping and subsequent dissociation of the molecular As(sub 2) bond are calculated as a function of beam translational energy and vibrational quantum number of As(sub 2).

Non-Born-Oppenheimer molecular dynamics of the spin-forbidden reaction O(3P) + CO(X 1Σ+) → CO2(tilde X{}^1Σ _g^ +)

NASA Astrophysics Data System (ADS)

Jasper, Ahren W.; Dawes, Richard

2013-10-01

The lowest-energy singlet (1 1A') and two lowest-energy triplet (1 3A' and 1 3A″) electronic states of CO2 are characterized using dynamically weighted multireference configuration interaction (dw-MRCI+Q) electronic structure theory calculations extrapolated to the complete basis set (CBS) limit. Global analytic representations of the dw-MRCI+Q/CBS singlet and triplet surfaces and of their CASSCF/aug-cc-pVQZ spin-orbit coupling surfaces are obtained via the interpolated moving least squares (IMLS) semiautomated surface fitting method. The spin-forbidden kinetics of the title reaction is calculated using the coupled IMLS surfaces and coherent switches with decay of mixing non-Born-Oppenheimer molecular dynamics. The calculated spin-forbidden association rate coefficient (corresponding to the high pressure limit of the rate coefficient) is 7-35 times larger at 1000-5000 K than the rate coefficient used in many detailed chemical models of combustion. A dynamical analysis of the multistate trajectories is presented. The trajectory calculations reveal direct (nonstatistical) and indirect (statistical) spin-forbidden reaction mechanisms and may be used to test the suitability of transition-state-theory-like statistical methods for spin-forbidden kinetics. Specifically, we consider the appropriateness of the "double passage" approximation, of assuming statistical distributions of seam crossings, and of applications of the unified statistical model for spin-forbidden reactions.

Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lisal, Martin; Department of Physics, Faculty of Science, J. E. Purkinje University, 400 96 Usti n. Lab.; Izak, Pavel

Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf{sub 2}N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 {mu}mol/m{sup 2} at 300 K. For [bmim][Tf{sub 2}N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are {+-}0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and itsmore » value decreases with increase of the n-hexane surface density. The [bmim][Tf{sub 2}N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.« less

Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface.

PubMed

Lísal, Martin; Izák, Pavel

2013-07-07

Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf2N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 μmol/m(2) at 300 K. For [bmim][Tf2N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are ±0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and its value decreases with increase of the n-hexane surface density. The [bmim][Tf2N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.

Long Distance Modulation of Disorder-to-Order Transitions in Protein Allostery.

PubMed

Wang, Jingheng; Custer, Gregory; Beckett, Dorothy; Matysiak, Silvina

2017-08-29

Elucidation of the molecular details of allosteric communication between distant sites in a protein is key to understanding and manipulating many biological regulatory processes. Although protein disorder is acknowledged to play an important thermodynamic role in allostery, the molecular mechanisms by which this disorder is harnessed for long distance communication are known for a limited number of systems. Transcription repression by the Escherichia coli biotin repressor, BirA, is allosterically activated by binding of the small molecule effector biotinoyl-5'-AMP. The effector acts by promoting BirA dimerization, which is a prerequisite for sequence-specific binding to the biotin biosynthetic operon operator sequence. A 30 Å distance separates the effector binding and dimerization surfaces in BirA, and previous studies indicate that allostery is mediated, in part, by disorder-to-order transitions on the two coupled sites. In this work, combined experimental and computational methods have been applied to investigate the molecular basis of allosteric communication in BirA. Double-mutant cycle analysis coupled with thermodynamic measurements indicates functional coupling between residues in disordered loops on the two distant surfaces. All atom molecular dynamics simulations reveal that this coupling occurs through long distance reciprocal modulation of the structure and dynamics of disorder-to-order transitions on the two surfaces.

Spin-symmetry conversion and internal rotation in high J molecular systems

NASA Astrophysics Data System (ADS)

Mitchell, Justin; Harter, William

2006-05-01

Dynamics and spectra of molecules with internal rotation or rovibrational coupling is approximately modeled by rigid or semi-rigid rotors with attached gyroscopes. Using Rotational Energy (RE)^1 surfaces, high resolution molecular spectra for high angular momentum show two distinct but related phenomena; spin-symmetry conversion and internal rotation. For both cases the high total angular momentum allows for transitions that would otherwise be forbidden. Molecular body-frame J-localization effects associated with tight energy level-clusters dominate the rovibronic spectra of high symmetry molecules, particularly spherical tops at J>10. ^2 The effects include large and widespread spin-symmetry mixing contrary to conventional wisdom^3 about weak nuclear moments. Such effects are discussed showing how RE surface plots may predict them even at low J. Classical dynamics of axially constrained rotors are approximated by intersecting rotational-energy-surfaces (RES) that have (J-S).B.(J-S) forms in the limit of constraints that do no work. Semi-classical eigensolutions are compared to those found by direct diagonalization. ^1 W.G Hater, in Handbook of Atomic, Molecular and Optical Physics, edited by G.W.F Drake (Springer, Germany 2006) ^2 W. G. Harter, Phys. Rev. A24,192-262(1981). ^3 G. Herzberg, Infrared and Raman Spectra (VanNostrand 1945) pp. 458,463.

Adsorption of Kinetic Hydrate Inhibitors on Growing Surfaces: A Molecular Dynamics Study.

PubMed

Yagasaki, Takuma; Matsumoto, Masakazu; Tanaka, Hideki

2018-04-05

We investigate the mechanism of a typical kinetic hydrate inhibitor (KHI), polyvinylcaprolactam (PVCap), which has been applied to prevent hydrate plugs from forming in gas pipe lines, using molecular dynamics simulations of crystal growth of ethylene oxide hydrate. Water-soluble ethylene oxide is chosen as a guest species to avoid problems associated with the presence of the gas phase in the simulation cell such as slow crystal growth. A PVCap dodecamer adsorbs irreversibly on the hydrate surface which grows at supercooling of 3 K when the hydrophobic part of two pendent groups are trapped in open cages at the surface. The amide hydrogen bonds make no contribution to the adsorption. PVCap can adsorb on various crystallographic planes of sI hydrate. This is in contrast to antifreeze proteins, each of which prefers a specific plane of ice. The trapped PVCap gives rise to necessarily the concave surface of the hydrate. The crystal growth rate decreases with increasing surface curvature, indicating that the inhibition by PVCap is explained by the Gibbs-Thomson effect.

Molecular Dynamics Simulations of the Oil-Detachment from the Hydroxylated Silica Surface: Effects of Surfactants, Electrostatic Interactions, and Water Flows on the Water Molecular Channel Formation.

PubMed

Tang, Jian; Qu, Zhou; Luo, Jianhui; He, Lanyan; Wang, Pingmei; Zhang, Ping; Tang, Xianqiong; Pei, Yong; Ding, Bin; Peng, Baoliang; Huang, Yunqing

2018-02-15

The detachment process of an oil molecular layer situated above a horizontal substrate was often described by a three-stage process. In this mechanism, the penetration and diffusion of water molecules between the oil phase and the substrate was proposed to be a crucial step to aid in removal of oil layer/drops from substrate. In this work, the detachment process of a two-dimensional alkane molecule layer from a silica surface in aqueous surfactant solutions is studied by means of molecular dynamics (MD) simulations. By tuning the polarity of model silica surfaces, as well as considering the different types of surfactant molecules and the water flow effects, more details about the formation of water molecular channel and the expansion processes are elucidated. It is found that for both ionic and nonionic type surfactant solutions, the perturbation of surfactant molecules on the two-dimensional oil molecule layer facilitates the injection and diffusion of water molecules between the oil layer and silica substrate. However, the water channel formation and expansion speed is strongly affected by the substrate polarity and properties of surfactant molecules. First, only for the silica surface with relative stronger polarity, the formation of water molecular channel is observed. Second, the expansion speed of the water molecular channel upon the ionic surfactant (dodecyl trimethylammonium bromide, DTAB and sodium dodecyl benzenesulfonate, SDBS) flooding is more rapidly than the nonionic surfactant system (octylphenol polyoxyethylene(10) ether, OP-10). Third, the water flow speed may also affect the injection and diffusion of water molecules. These simulation results indicate that the water molecular channel formation process is affected by multiple factors. The synergistic effects of perturbation of surfactant molecules and the electrostatic interactions between silica substrate and water molecules are two key factors aiding in the injection and diffusion of water molecules and helpful for the oil detachment from silica substrate.

Enhanced dynamics of hydrated tRNA on nanodiamond surfaces: A combined neutron scattering and MD simulation study

DOE PAGES

Dhindsa, Gurpreet K.; Bhowmik, Debsindhu; Goswami, Monojoy; ...

2016-09-01

Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on NDmore » surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. As a result, our new findings may provide new design principles for safer, improved drug delivery platforms.« less

Modulators of heterogeneous protein surface water dynamics

NASA Astrophysics Data System (ADS)

Han, Songi

The hydration water that solvates proteins is a major factor in driving or enabling biological events, including protein-protein and protein-ligand interactions. We investigate the role of the protein surface in modulating the hydration water fluctuations on both the picosecond and nanosecond timescale with an emerging experimental NMR technique known as Overhauser Dynamic Nuclear Polarization (ODNP). We carry out site-specific ODNP measurements of the hydration water fluctuations along the surface of Chemotaxis Y (CheY), and correlate the measured fluctuations to hydropathic and topological properties of the CheY surface as derived from molecular dynamics (MD) simulation. Furthermore, we compare hydration water fluctuations measured on the CheY surface to that of other globular proteins, as well as intrinsically disordered proteins, peptides, and liposome surfaces to systematically test characteristic effects of the biomolecular surface on the hydration water dynamics. Our results suggest that the labile (ps) hydration water fluctuations are modulated by the chemical nature of the surface, while the bound (ns) water fluctuations are present on surfaces that feature a rough topology and chemical heterogeneity such as the surface of a folded and structured protein. In collaboration with: Ryan Barnes, Dept of Chemistry and Biochemistry, University of California Santa Barbara

Biomimetic design of platelet adhesion inhibitors to block integrin α2β1-collagen interactions: I. Construction of an affinity binding model.

PubMed

Zhang, Lin; Sun, Yan

2014-04-29

Platelet adhesion on a collagen surface through integrin α2β1 has been proven to be significant for the formation of arterial thrombus. However, the molecular determinants mediating the integrin-collagen complex remain unclear. In the present study, the dynamics of integrin-collagen binding and molecular interactions were investigated using molecular dynamics (MD) simulations and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) analysis. Hydrophobic interaction is identified as the major driving force for the formation of the integrin-collagen complex. On the basis of the MD simulation and MM-PBSA results, an affinity binding model (ABM) of integrin for collagen is constructed; it is composed of five residues, including Y157, N154, S155, R288, and L220. The ABM has been proven to capture the major binding motif contributing 84.8% of the total binding free energy. On the basis of the ABM, we expect to establish a biomimetic design strategy of platelet adhesion inhibitors, which would be beneficial for the development of potent peptide-based drugs for thrombotic diseases.

Molecular dynamics simulations of energy dissipation and non-thermal diffusion on amorphous solid water.

PubMed

Fredon, A; Cuppen, H M

2018-02-21

Molecules in space are synthesized via a large variety of gas-phase reactions, and reactions on dust-grain surfaces, where the surface acts as a catalyst. Especially, saturated, hydrogen-rich molecules are formed through surface chemistry where the interstellar grains act as a meeting place and absorbing energy. Here we present the results of thousands of molecular dynamics simulations to quantify the outcome of an energy dissipation process. Admolecules on top of an amorphous solid water surface have been given translational energy between 0.5 and 5 eV. Three different surface species are considered, CO 2 , H 2 O and CH 4 , spanning a range in binding energies, number of internal degrees of freedom and molecular weight. The results are compared against a previous study using a crystalline water ice surface. Possible outcomes of a dissipation process are adsorption - possibly after long-range diffusion-, desorption and desorption of a surface molecule. The three admolecules were found to bind at different locations on the surface, particularly in terms of height. Water preferably binds on top of the surface, whereas methane fills the nanopores on the surface. This has direct consequences for desorption, travelled distance, and kick-out probabilities. The admolecules are found to frequently travel several tens of angstroms before stabilizing on a binding site, allowing follow-up reactions en route. We present kick-out probabilities and we have been able to quantify the desorption probability which depends on the binding energy of the species, the translational excitation, and a factor that accounts for difference in binding site height. We provide expressions that can be incorporated in astrochemical models to predict grain surface formation and return into the gas phase of these products.

Molecular-dynamics analysis of mobile helium cluster reactions near surfaces of plasma-exposed tungsten

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Lin; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu; Hammond, Karl D.

We report the results of a systematic atomic-scale analysis of the reactions of small mobile helium clusters (He{sub n}, 4 ≤ n ≤ 7) near low-Miller-index tungsten (W) surfaces, aiming at a fundamental understanding of the near-surface dynamics of helium-carrying species in plasma-exposed tungsten. These small mobile helium clusters are attracted to the surface and migrate to the surface by Fickian diffusion and drift due to the thermodynamic driving force for surface segregation. As the clusters migrate toward the surface, trap mutation (TM) and cluster dissociation reactions are activated at rates higher than in the bulk. TM produces W adatoms and immobile complexes ofmore » helium clusters surrounding W vacancies located within the lattice planes at a short distance from the surface. These reactions are identified and characterized in detail based on the analysis of a large number of molecular-dynamics trajectories for each such mobile cluster near W(100), W(110), and W(111) surfaces. TM is found to be the dominant cluster reaction for all cluster and surface combinations, except for the He{sub 4} and He{sub 5} clusters near W(100) where cluster partial dissociation following TM dominates. We find that there exists a critical cluster size, n = 4 near W(100) and W(111) and n = 5 near W(110), beyond which the formation of multiple W adatoms and vacancies in the TM reactions is observed. The identified cluster reactions are responsible for important structural, morphological, and compositional features in the plasma-exposed tungsten, including surface adatom populations, near-surface immobile helium-vacancy complexes, and retained helium content, which are expected to influence the amount of hydrogen re-cycling and tritium retention in fusion tokamaks.« less

H(D) → D(H) + Cu(111) collision system: Molecular dynamics study of surface temperature effects

PubMed Central

Vurdu, Can D.; Güvenç, Ziya B.

2011-01-01

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London–Eyring–Polanyi–Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures. PMID:21528959

H(D) → D(H) + Cu(111) collision system: molecular dynamics study of surface temperature effects.

PubMed

Vurdu, Can D; Güvenç, Ziya B

2011-04-28

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London-Eyring-Polanyi-Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martinez, Andre P.; Carrillo, Jan-Michael Y.; Dobrynin, Andrey V.

The molecular weight and polydispersity of the chains in a polymer brush are critical parameters determining the brush properties. However, the characterization of polymer brushes is hindered by the vanishingly small mass of polymer present in brush layers. In this study, in order to obtain sufficient quantities of polymer for analysis, polymer brushes were grown from high surface area fibrous nylon membranes by ATRP. We synthesized the brushes with varying surface initiator densities, polymerization times, and amounts of sacrificial initiator, then cleaved from the substrate, and analyzed by GPC and NMR. Characterization showed that the surface-grown polymer chains were moremore » polydisperse and had lower average molecular weight compared to solution-grown polymers synthesized concurrently. Furthermore, the molecular weight distribution of the polymer brushes was observed to be bimodal, with a low molecular weight population of chains representing a significant mass fraction of the polymer chains at high surface initiator densities. Moreover, the origin of this low MW polymer fraction is proposed to be the termination of growing chains by recombination during the early stages of polymerization, a mechanism confirmed by molecular dynamics simulations of brush polymerization.« less

Water Adsorption on Clean and Defective Anatase TiO2 (001) Nanotube Surfaces: A Surface Science Approach.

PubMed

Kenmoe, Stephane; Lisovski, Oleg; Piskunov, Sergei; Bocharov, Dmitry; Zhukovskii, Yuri F; Spohr, Eckhard

2018-05-31

We use ab initio molecular dynamics simulations to study the adsorption of thin water films with 1 and 2 ML coverage on anatase TiO 2 (001) nanotubes. The nanotubes are modeled as 2D slabs, which consist of partially constrained and partially relaxed structural motifs from nanotubes. The effect of anion doping on the adsorption is investigated by substituting O atoms with N and S impurities on the nanotube slab surface. Due to strain-induced curvature effects, water adsorbs molecularly on defect-free surfaces via weak bonds on Ti sites and H bonds to surface oxygens. While the introduction of an S atom weakens the interaction of the surface with water, which adsorbs molecularly, the presence of an N impurity renders the surface more reactive to water, with a proton transfer from the water film and the formation of an NH group at the N site. At 2 ML coverage, a further surface-assisted proton transfer takes place in the water film, resulting in the formation of an OH - group and an NH 2 + cationic site on the surface.

Novel methodology developments in modern molecular simulations

NASA Astrophysics Data System (ADS)

Minary, Peter

The present thesis aims to summarize novel methodological developments and their uses in the rapidly expanding field of molecular simulations. A new formalism designed to treat long range interactions on surfaces/wires, systems which are infinitely replicated in two/one spatial directions but have finite extent in the remaining dimensions, is developed in the first part of this thesis. The method is tested on both model and realistic problems and is found to be accurate, efficient and a marked improvement over existing formulations in speed, accuracy and utility. In the second part of this thesis, a novel ab initio molecular dynamics technique capable of treating metallic systems and highly exothermic chemical reactions is presented. The combination of the aforementioned methods are applied in the next part to study functionalization reactions at the Si(100)-2x1 semiconductor interface. Here, a set of forty finite temperature ab initio molecular dynamics trajectories is employed to investigate the microscopic mechanism of the addition of 1,3-butadiene to the Si(100)-2x1 surface. The detailed study of the trajectories indicate a common non-concerted stepwise mechanism that proceeds via an intermediate carbocation. In the remaining parts of the thesis, a novel set of methods is introduced to significantly enhance conformational sampling in molecular dynamics simulations of biomolecular systems. First, a new set of equations of motion and a reversible, resonance free, integrator are developed which permits step sizes on the order of 100 fs to be used. The new technique provides sufficient sampling to impact studies of the 200--300 residue proteins of greatest interest. Second, it is shown that combining molecular dynamics with novel variable transformations designed to warp configuration space so as to reduce barrier regions and enhance attractive basins lead to substantial gains in conformational sampling efficiency. Here, new transformations designed to overcome barriers induced by intermolecular interactions are introduced. The method is shown to substantially enhance conformational sampling in long alkane chains and in a model protein over standard molecular dynamics as well as parallel tempering.

Atomic scale friction of molecular adsorbates during diffusion.

PubMed

Lechner, B A J; de Wijn, A S; Hedgeland, H; Jardine, A P; Hinch, B J; Allison, W; Ellis, J

2013-05-21

Experimental observations suggest that molecular adsorbates exhibit a larger friction coefficient than atomic species of comparable mass, yet the origin of this increased friction is not well understood. We present a study of the microscopic origins of friction experienced by molecular adsorbates during surface diffusion. Helium spin-echo measurements of a range of five-membered aromatic molecules, cyclopentadienyl, pyrrole, and thiophene, on a copper(111) surface are compared with molecular dynamics simulations of the respective systems. The adsorbates have different chemical interactions with the surface and differ in bonding geometry, yet the measurements show that the friction is greater than 2 ps(-1) for all these molecules. We demonstrate that the internal and external degrees of freedom of these adsorbate species are a key factor in the underlying microscopic processes and identify the rotation modes as the ones contributing most to the total measured friction coefficient.

Mussel adhesion is dictated by time-regulated secretion and molecular conformation of mussel adhesive proteins

NASA Astrophysics Data System (ADS)

Petrone, Luigi; Kumar, Akshita; Sutanto, Clarinda N.; Patil, Navinkumar J.; Kannan, Srinivasaraghavan; Palaniappan, Alagappan; Amini, Shahrouz; Zappone, Bruno; Verma, Chandra; Miserez, Ali

2015-10-01

Interfacial water constitutes a formidable barrier to strong surface bonding, hampering the development of water-resistant synthetic adhesives. Notwithstanding this obstacle, the Asian green mussel Perna viridis attaches firmly to underwater surfaces via a proteinaceous secretion (byssus). Extending beyond the currently known design principles of mussel adhesion, here we elucidate the precise time-regulated secretion of P. viridis mussel adhesive proteins. The vanguard 3,4-dihydroxy-L-phenylalanine (Dopa)-rich protein Pvfp-5 acts as an adhesive primer, overcoming repulsive hydration forces by displacing surface-bound water and generating strong surface adhesion. Using homology modelling and molecular dynamics simulations, we find that all mussel adhesive proteins are largely unordered, with Pvfp-5 adopting a disordered structure and elongated conformation whereby all Dopa residues reside on the protein surface. Time-regulated secretion and structural disorder of mussel adhesive proteins appear essential for optimizing extended nonspecific surface interactions and byssus' assembly. Our findings reveal molecular-scale principles to help the development of wet-resistant adhesives.

Effect of glycosylation on hydration behavior at the ice-binding surface of the Ocean Pout type III antifreeze protein: a molecular dynamics simulation.

PubMed

Halder, Swagata; Mukhopadhyay, Chaitali

2017-12-01

Antifreeze proteins (AFPs), found in certain vertebrates, plants, fungi and bacteria have the ability to permit their survival in subzero environments by thermal hysteresis mechanism. However, the exact mechanism of ice growth inhibition is still not clearly understood. Here, four long explicit molecular dynamics (MD) simulations have been carried out at two different temperatures (277 and 298 K) with and without glycan to study the conformational rigidity of the Ocean pout type III antifreeze protein in aqueous medium and the structural arrangements of water molecules hydrating its ice-binding surface. It is found that irrespective of the temperature the ice-binding surface (IBS) of the protein is relatively more rigid than its non ice-binding surface (NonIBS) in its native and glycosylated form. Hydrophilic residues N14, T18 and Q44 are essential to antifreeze activity. Radial distribution, density distribution function and nearest neighbor orientation plots with respect to individual two surfaces confirm that density of water molecule near these binding surface in native and glycosylated form are relatively more than the nonbinding surface. The glycosylated form shows a strong peak than the native one. From rotational auto correlation function of water molecules around ice-binding sites, it is prominent that with increase in temperature, strong interaction between the water oxygen and the hydrogen bond acceptor group on the protein-binding surface decreases. This provides a possible molecular reason behind the ice-binding activity of ocean pout at the prism plane of ice.

Simulation studies for surfaces and materials strength

NASA Technical Reports Server (NTRS)

Halicioglu, Timur

1992-01-01

Investigations were carried out in two major areas during the last reporting period. Energy- and structure-related properties of small gold clusters deposited on the GaAs(110) surface were investigated using a molecular dynamics procedure. Additionally, a comparative study of the many-body potentials of silicon systems was performed.

Animated molecular dynamics simulations of hydrated caesium-smectite interlayers

PubMed Central

Sutton, Rebecca; Sposito, Garrison

2002-01-01

Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers) provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs+ formed inner sphere complexes with the mineral surface, and could be seen to jump from one attracting location near a layer charge site to the next, while water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. Cs-montmorillonite hydrates featured the largest extent of this sharing interaction, because interlayer ions were able to inhabit positions near surface cavities as well as at their edges, close to oxygen triads. The greater positional freedom of Cs+ within the montmorillonite interlayer, a result of structural hydroxyl orientation and low tetrahedral charge, promoted the optimization of distances between cations and water molecules required for water sharing. Preference of Cs+ for locations near oxygen triads was observed within interlayer beidellite and hectorite. Water molecules also could be seen to interact directly with the mineral surface, entering its surface cavities to approach attracting charge sites and structural hydroxyls. With increasing water content, water molecules exhibited increased frequency and duration of both cavity habitation and water sharing interactions. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output.

Gradual Crossover from Subdiffusion to Normal Diffusion: A Many-Body Effect in Protein Surface Water

NASA Astrophysics Data System (ADS)

Tan, Pan; Liang, Yihao; Xu, Qin; Mamontov, Eugene; Li, Jinglai; Xing, Xiangjun; Hong, Liang

2018-06-01

Dynamics of hydration water is essential for the function of biomacromolecules. Previous studies have demonstrated that water molecules exhibit subdiffusion on the surface of biomacromolecules; yet the microscopic mechanism remains vague. Here, by performing neutron scattering, molecular dynamics simulations, and analytic modeling on hydrated perdeuterated protein powders, we found water molecules jump randomly between trapping sites on protein surfaces, whose waiting times obey a broad distribution, resulting in subdiffusion. Moreover, the subdiffusive exponent gradually increases with observation time towards normal diffusion due to a many-body volume-exclusion effect.

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations.

PubMed

Sinko, William; de Oliveira, César Augusto F; Pierce, Levi C T; McCammon, J Andrew

2012-01-10

Molecular dynamics (MD) is one of the most common tools in computational chemistry. Recently, our group has employed accelerated molecular dynamics (aMD) to improve the conformational sampling over conventional molecular dynamics techniques. In the original aMD implementation, sampling is greatly improved by raising energy wells below a predefined energy level. Recently, our group presented an alternative aMD implementation where simulations are accelerated by lowering energy barriers of the potential energy surface. When coupled with thermodynamic integration simulations, this implementation showed very promising results. However, when applied to large systems, such as proteins, the simulation tends to be biased to high energy regions of the potential landscape. The reason for this behavior lies in the boost equation used since the highest energy barriers are dramatically more affected than the lower ones. To address this issue, in this work, we present a new boost equation that prevents oversampling of unfavorable high energy conformational states. The new boost potential provides not only better recovery of statistics throughout the simulation but also enhanced sampling of statistically relevant regions in explicit solvent MD simulations.

Heterogeneity in homogeneous nucleation from billion-atom molecular dynamics simulation of solidification of pure metal.

PubMed

Shibuta, Yasushi; Sakane, Shinji; Miyoshi, Eisuke; Okita, Shin; Takaki, Tomohiro; Ohno, Munekazu

2017-04-05

Can completely homogeneous nucleation occur? Large scale molecular dynamics simulations performed on a graphics-processing-unit rich supercomputer can shed light on this long-standing issue. Here, a billion-atom molecular dynamics simulation of homogeneous nucleation from an undercooled iron melt reveals that some satellite-like small grains surrounding previously formed large grains exist in the middle of the nucleation process, which are not distributed uniformly. At the same time, grains with a twin boundary are formed by heterogeneous nucleation from the surface of the previously formed grains. The local heterogeneity in the distribution of grains is caused by the local accumulation of the icosahedral structure in the undercooled melt near the previously formed grains. This insight is mainly attributable to the multi-graphics processing unit parallel computation combined with the rapid progress in high-performance computational environments.Nucleation is a fundamental physical process, however it is a long-standing issue whether completely homogeneous nucleation can occur. Here the authors reveal, via a billion-atom molecular dynamics simulation, that local heterogeneity exists during homogeneous nucleation in an undercooled iron melt.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varanasi, S. R., E-mail: s.raovaranasi@uq.edu.au, E-mail: guskova@ipfdd.de; John, A.; Guskova, O. A., E-mail: s.raovaranasi@uq.edu.au, E-mail: guskova@ipfdd.de

Fullerene C{sub 60} sub-colloidal particle with diameter ∼1 nm represents a boundary case between small and large hydrophobic solutes on the length scale of hydrophobic hydration. In the present paper, a molecular dynamics simulation is performed to investigate this complex phenomenon for bare C{sub 60} fullerene and its amphiphilic/charged derivatives, so called shape amphiphiles. Since most of the unique properties of water originate from the pattern of hydrogen bond network and its dynamics, spatial, and orientational aspects of water in solvation shells around the solute surface having hydrophilic and hydrophobic regions are analyzed. Dynamical properties such as translational-rotational mobility, reorientationalmore » correlation and occupation time correlation functions of water molecules, and diffusion coefficients are also calculated. Slower dynamics of solvent molecules—water retardation—in the vicinity of the solutes is observed. Both the topological properties of hydrogen bond pattern and the “dangling” –OH groups that represent surface defects in water network are monitored. The fraction of such defect structures is increased near the hydrophobic cap of fullerenes. Some “dry” regions of C{sub 60} are observed which can be considered as signatures of surface dewetting. In an effort to provide molecular level insight into the thermodynamics of hydration, the free energy of solvation is determined for a family of fullerene particles using thermodynamic integration technique.« less

Design of Supercapacitor Electrodes Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Bo, Zheng; Li, Changwen; Yang, Huachao; Ostrikov, Kostya; Yan, Jianhua; Cen, Kefa

2018-06-01

Electric double-layer capacitors (EDLCs) are advanced electrochemical devices for energy storage and have attracted strong interest due to their outstanding properties. Rational optimization of electrode-electrolyte interactions is of vital importance to enhance device performance for practical applications. Molecular dynamics (MD) simulations could provide theoretical guidelines for the optimal design of electrodes and the improvement of capacitive performances, e.g., energy density and power density. Here we discuss recent MD simulation studies on energy storage performance of electrode materials containing porous to nanostructures. The energy storage properties are related to the electrode structures, including electrode geometry and electrode modifications. Altering electrode geometry, i.e., pore size and surface topography, can influence EDL capacitance. We critically examine different types of electrode modifications, such as altering the arrangement of carbon atoms, doping heteroatoms and defects, which can change the quantum capacitance. The enhancement of power density can be achieved by the intensified ion dynamics and shortened ion pathway. Rational control of the electrode morphology helps improve the ion dynamics by decreasing the ion diffusion pathway. Tuning the surface properties (e.g., the affinity between the electrode and the ions) can affect the ion-packing phenomena. Our critical analysis helps enhance the energy and power densities of EDLCs by modulating the corresponding electrode structures and surface properties.[Figure not available: see fulltext.

Poly-proline-based chiral stationary phases: a molecular dynamics study of triproline, tetraproline, pentaproline and hexaproline interfaces.

PubMed

Ashtari, M; Cann, N M

2012-11-23

Poly-proline chains and derivatives have been recently examined as the basis for new chiral stationary phases in high performance liquid chromatography. The selectivity of poly-proline has been measured for peptides with up to ten proline units. In this article, we employ molecular dynamics simulations to examine the interfacial structure and solvation of surface-bound poly-proline chiral selectors. Specifically, we study the interfacial structure of trimethylacetyl-terminated poly-proline chains with three-to-six prolines. The surface includes silanol groups and end-caps, to better capture the characteristics of the stationary phase, and the solvent is either a polar water/methanol or a relatively apolar n-hexane/2-propanol mixture. We begin with a comprehensive ab initio study of the conformers, their energies, and an assessment of conformer flexibility. Force fields have been developed for each poly-proline selector. Molecular dynamics simulations are employed to study the preferred backbone conformations and solvent hydrogen bonding for different poly-proline/solvent interfaces. For triproline, the effect of two different terminal groups, trimethylacetyl and t-butyl carbamate are compared. Copyright © 2012 Elsevier B.V. All rights reserved.

Molecular dynamic approach to the study of the intense heat and mass transfer processes on the vapor-liquid interface

NASA Astrophysics Data System (ADS)

Levashov, V. Yu; Kamenov, P. K.

2017-10-01

The paper is devoted to research of the heat and mass transfer processes on the vapor-liquid interface. These processes can be realized for example at metal tempering, accidents at nuclear power stations, followed by the release of the corium into the heat carrier, getting hot magma into the water during volcanic eruptions and other. In all these examples the vapor film can arise on the heated body surface. In this paper the vapor film formation process will be considered with help of molecular dynamics simulation methods. The main attention during this process modeling will be focused on the subject of the fluid and vapor interactions with the heater surface. Another direction of this work is to study of the processes inside the droplet that may take place as result of impact of the high-power laser radiation. Such impact can lead to intensive evaporation and explosive destruction of the droplet. At that the duration of heat and mass transfer processes in droplet substance is tens of femtoseconds. Thus, the methods of molecular dynamics simulation can give the possibilities describe the heat and mass transfer processes in the droplet and the vapor phase formation.

Molecular Modeling of Three Phase Contact for Static and Dynamic Contact Angle Phenomena

NASA Astrophysics Data System (ADS)

Malani, Ateeque; Amat, Miguel; Raghavanpillai, Anilkumar; Wysong, Ernest; Rutledge, Gregory

2012-02-01

Interfacial phenomena arise in a number of industrially important situations, such as repellency of liquids on surfaces, condensation, etc. In designing materials for such applications, the key component is their wetting behavior, which is characterized by three-phase static and dynamic contact angle phenomena. Molecular modeling has the potential to provide basic insight into the detailed picture of the three-phase contact line resolved on the sub-nanometer scale which is essential for the success of these materials. We have proposed a computational strategy to study three-phase contact phenomena, where buoyancy of a solid rod or particle is studied in a planar liquid film. The contact angle is readily evaluated by measuring the position of solid and liquid interfaces. As proof of concept, the methodology has been validated extensively using a simple Lennard-Jones (LJ) fluid in contact with an LJ surface. In the dynamic contact angle analysis, the evolution of contact angle as a function of force applied to the rod or particle is characterized by the pinning and slipping of the three phase contact line. Ultimately, complete wetting or de-wetting is observed, allowing molecular level characterization of the contact angle hysteresis.

Exploring the free energy surface using ab initio molecular dynamics

DOE PAGES

Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

2016-04-22

Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO 2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string methodmore » in collective variables to study the melting pathways in the high pressure cotunnite phase of SiO 2 and the hcp to fcc phase transition in Ti.« less

Effects of CO2 adsorption on proton migration on a hydrated ZrO2 surface: an ab initio molecular dynamics study.

PubMed

Sato, Ryuhei; Shibuta, Yasushi; Shimojo, Fuyuki; Yamaguchi, Shu

2017-08-02

Hydration reactions on a carbonate-terminated cubic ZrO 2 (110) surface were analyzed using ab initio molecular dynamics (AIMD) simulations. After hydration reactions, carbonates were still present on the surface at 500 K. However, these carbonates are very weak conjugate bases and only act as steric hindrance in proton hopping processes between acidic chemisorbed H 2 O molecules (Zr-OH 2 ) and monodentate hydroxyl groups (Zr-OH - ). Similar to a carbonate-free hydrated surface, Zr-OH 2 , Zr-OH - , and polydentate hydroxyl groups ([double bond splayed left]OH + ) were observed, while the ratio of acidic Zr-OH 2 was significantly larger than that on the carbonate-free hydrated surface. A thermodynamic discussion and bond property analysis reveal that CO 2 adsorption significantly decreases the basicity of surface oxide ions ([double bond splayed left]O), whereas the acidity of Zr-OH 2 is not affected. As a result, protons released from [double bond splayed left]OH + react with Zr-OH - to form Zr-OH 2 , leading to a deficiency of proton acceptor sites, which decreases the proton conductivity by the hopping mechanism.

Differential Geometry Based Multiscale Models

PubMed Central

Wei, Guo-Wei

2010-01-01

Large chemical and biological systems such as fuel cells, ion channels, molecular motors, and viruses are of great importance to the scientific community and public health. Typically, these complex systems in conjunction with their aquatic environment pose a fabulous challenge to theoretical description, simulation, and prediction. In this work, we propose a differential geometry based multiscale paradigm to model complex macromolecular systems, and to put macroscopic and microscopic descriptions on an equal footing. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum mechanical description of the aquatic environment with the microscopic discrete atom-istic description of the macromolecule. Multiscale free energy functionals, or multiscale action functionals are constructed as a unified framework to derive the governing equations for the dynamics of different scales and different descriptions. Two types of aqueous macromolecular complexes, ones that are near equilibrium and others that are far from equilibrium, are considered in our formulations. We show that generalized Navier–Stokes equations for the fluid dynamics, generalized Poisson equations or generalized Poisson–Boltzmann equations for electrostatic interactions, and Newton's equation for the molecular dynamics can be derived by the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. Comparison is given to classical descriptions of the fluid and electrostatic interactions without geometric flow based micro-macro interfaces. The detailed balance of forces is emphasized in the present work. We further extend the proposed multiscale paradigm to micro-macro analysis of electrohydrodynamics, electrophoresis, fuel cells, and ion channels. We derive generalized Poisson–Nernst–Planck equations that are coupled to generalized Navier–Stokes equations for fluid dynamics, Newton's equation for molecular dynamics, and potential and surface driving geometric flows for the micro-macro interface. For excessively large aqueous macromolecular complexes in chemistry and biology, we further develop differential geometry based multiscale fluid-electro-elastic models to replace the expensive molecular dynamics description with an alternative elasticity formulation. PMID:20169418

Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

NASA Astrophysics Data System (ADS)

Zhang, Junfang; Rivero, Mayela; Choi, S. K.

2007-02-01

We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 Å. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.

Dynamic slip of polydisperse linear polymers using partitioned plate

NASA Astrophysics Data System (ADS)

Ebrahimi, Marzieh; Konaganti, Vinod Kumar; Hatzikiriakos, Savvas G.

2018-03-01

The slip velocity of an industrial grade high molecular weight high-density polyethylene (HDPE) is studied in steady and dynamic shear experiments using a stress/strain controlled rotational rheometer equipped with a parallel partitioned plate geometry. Moreover, fluoroalkyl silane-based coating is used to understand the effect of surface energy on slip in steady and dynamic conditions. The multimode integral Kaye-Bernstein-Kearsley-Zapas constitutive model is applied to predict the transient shear response of the HDPE melt obtained from rotational rheometer. It is found that a dynamic slip model with a slip relaxation time is needed to adequately predict the experimental data at large shear deformations. Comparison of the results before and after coating shows that the slip velocity is largely affected by surface energy. Decreasing surface energy by coating increases slip velocity and decreases the slip relaxation time.

Protein-Ligand Interaction Detection with a Novel Method of Transient Induced Molecular Electronic Spectroscopy (TIMES): Experimental and Theoretical Studies.

PubMed

Zhang, Tiantian; Wei, Tao; Han, Yuanyuan; Ma, Heng; Samieegohar, Mohammadreza; Chen, Ping-Wei; Lian, Ian; Lo, Yu-Hwa

2016-11-23

Protein-ligand interaction detection without disturbances (e.g., surface immobilization, fluorescent labeling, and crystallization) presents a key question in protein chemistry and drug discovery. The emergent technology of transient induced molecular electronic spectroscopy (TIMES), which incorporates a unique design of microfluidic platform and integrated sensing electrodes, is designed to operate in a label-free and immobilization-free manner to provide crucial information for protein-ligand interactions in relevant physiological conditions. Through experiments and theoretical simulations, we demonstrate that the TIMES technique actually detects protein-ligand binding through signals generated by surface electric polarization. The accuracy and sensitivity of experiments were demonstrated by precise measurements of dissociation constant of lysozyme and N -acetyl-d-glucosamine (NAG) ligand and its trimer, NAG 3 . Computational fluid dynamics (CFD) computation is performed to demonstrate that the surface's electric polarization signal originates from the induced image charges during the transition state of surface mass transport, which is governed by the overall effects of protein concentration, hydraulic forces, and surface fouling due to protein adsorption. Hybrid atomistic molecular dynamics (MD) simulations and free energy computation show that ligand binding affects lysozyme structure and stability, producing different adsorption orientation and surface polarization to give the characteristic TIMES signals. Although the current work is focused on protein-ligand interactions, the TIMES method is a general technique that can be applied to study signals from reactions between many kinds of molecules.

Evolutionary screening and adsorption behavior of engineered M13 bacteriophage and derived dodecapeptide for selective decoration of gold interfaces.

PubMed

Causa, F; Della Moglie, R; Iaccino, E; Mimmi, S; Marasco, D; Scognamiglio, P L; Battista, E; Palmieri, C; Cosenza, C; Sanguigno, L; Quinto, I; Scala, G; Netti, P A

2013-01-01

There is a growing interest in identifying biomacromolecules such as proteins and peptides to functionalize metallic surfaces through noncovalent binding. One method for functionalizing materials without fundamentally changing their inherent structure is using biorecognition moieties. Here, we proved a general route to select a biomolecule adhesive motif for surface functionalization by comprehensively screening phage displayed peptides. In particular, we selected a genetically engineered M13 bacteriophage and a linear dodecapeptide derived from its pIII domain for recognizing gold surfaces in a specific and selective manner. In the phage context, we demonstrated the adhesive motif was capable to adsorb on gold in a preferential way with a morphological and viscoelastic signature of the adsorbed layer as evidenced by QCM-D and AFM investigations. Out of the phage context, the linear dodecapeptide is reproducibly found to adhere to the gold surface, and by quantitative SPR measurements, high affinity constants (K(eq)~10(6)M(-1), binding energy ~-8 kcal/mol) were determined. We proved that the interactions occurring at gold interface were mainly hydrophobic as a consequence of high frequency of hydrophobic residues in the peptide sequence. Moreover, by CD, molecular dynamics and steered molecular dynamics, we demonstrated that the molecular flexibility only played a minor role in the peptide adsorption. Such noncovalent but specific modification of inorganic surfaces through high affinity biomolecule adsorption represents a general strategy to modulate the functionality of multipurpose metallic surfaces. Copyright © 2012 Elsevier Inc. All rights reserved.

Exploring the science of thinking independently together: Faraday Discussion Volume 204 - Complex Molecular Surfaces and Interfaces, Sheffield, UK, July 2017.

PubMed

Samperi, M; Hirsch, B E; Diaz Fernandez, Y A

2017-11-23

The 2017 Faraday Discussion on Complex Molecular Surfaces and Interfaces brought together theoreticians and experimentalists from both physical and chemical backgrounds to discuss the relevant applied and fundamental research topics within the broader field of chemical surface analysis and characterization. Main discussion topics from the meeting included the importance of "disordered" two-dimensional (2D) molecular structures and the utility of kinetically trapped states. An emerging need for new experimental tools to address dynamics and kinetic pathways involved in self-assembled systems, as well as the future prospects and current limitations of in silico studies were also discussed. The following article provides a brief overview of the work presented and the challenges discussed during the meeting.

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of small membranes using all atomistic and coarse-grained methods. The molecular interaction between common polymer chains used in biomedical applications and the cell membrane is unknown. This interaction may affect the biocompatibility of the polymer chains. Molecular dynamics simulations offer an emerging tool to characterize the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. We systematically characterize with long-time all-atomistic molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a model phospholipid membrane. We find that the length of polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilize advanced sampling techniques in molecular dynamics to characterize the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. These results can be used to design polymer chain lengths and chemistries to optimize their interaction with cell membranes at the molecular level.

Periodic protein adsorption at the gold/biotin aqueous solution interface: evidence of kinetics with time delay

NASA Astrophysics Data System (ADS)

Neff, H.; Laborde, H. M.; Lima, A. M. N.

2016-11-01

An oscillatory molecular adsorption pattern of the protein neutravidin from aqueous solution onto gold, in presence of a pre-deposited self assembled mono-molecular biotin film, is reported. Real time surface Plasmon resonance sensing was utilized for evaluation of the adsorption kinetics. Two different fractions were identified: in the initial phase, protein molecules attach irreversibly onto the Biotin ligands beneath towards the jamming limit, forming a neutravidin-biotin fraction. Afterwards, the growth rate exhibits distinct, albeit damped adsorption-desorption oscillations over an extended time span, assigned to a quasi reversibly bound fraction. These findings agree with, and firstly confirm a previously published model, proposing macro-molecular adsorption with time delay. The non-linear dynamic model is applicable to and also resembles non-damped oscillatory binding features of the hetero-catalytic oxidation of carbon monoxide molecules on platinum in the gas phase. An associated surface residence time can be linked to the dynamics and time scale required for self-organization.

Computer simulation of surface and film processes

NASA Technical Reports Server (NTRS)

Tiller, W. A.; Halicioglu, M. T.

1984-01-01

All the investigations which were performed employed in one way or another a computer simulation technique based on atomistic level considerations. In general, three types of simulation methods were used for modeling systems with discrete particles that interact via well defined potential functions: molecular dynamics (a general method for solving the classical equations of motion of a model system); Monte Carlo (the use of Markov chain ensemble averaging technique to model equilibrium properties of a system); and molecular statics (provides properties of a system at T = 0 K). The effects of three-body forces on the vibrational frequencies of triatomic cluster were investigated. The multilayer relaxation phenomena for low index planes of an fcc crystal was analyzed also as a function of the three-body interactions. Various surface properties for Si and SiC system were calculated. Results obtained from static simulation calculations for slip formation were presented. The more elaborate molecular dynamics calculations on the propagation of cracks in two-dimensional systems were outlined.

Recent Advances and Perspectives on Nonadiabatic Mixed Quantum-Classical Dynamics.

PubMed

Crespo-Otero, Rachel; Barbatti, Mario

2018-05-16

Nonadiabatic mixed quantum-classical (NA-MQC) dynamics methods form a class of computational theoretical approaches in quantum chemistry tailored to investigate the time evolution of nonadiabatic phenomena in molecules and supramolecular assemblies. NA-MQC is characterized by a partition of the molecular system into two subsystems: one to be treated quantum mechanically (usually but not restricted to electrons) and another to be dealt with classically (nuclei). The two subsystems are connected through nonadiabatic couplings terms to enforce self-consistency. A local approximation underlies the classical subsystem, implying that direct dynamics can be simulated, without needing precomputed potential energy surfaces. The NA-MQC split allows reducing computational costs, enabling the treatment of realistic molecular systems in diverse fields. Starting from the three most well-established methods-mean-field Ehrenfest, trajectory surface hopping, and multiple spawning-this review focuses on the NA-MQC dynamics methods and programs developed in the last 10 years. It stresses the relations between approaches and their domains of application. The electronic structure methods most commonly used together with NA-MQC dynamics are reviewed as well. The accuracy and precision of NA-MQC simulations are critically discussed, and general guidelines to choose an adequate method for each application are delivered.

Nonadiabatic Molecular Dynamics and Orthogonality Constrained Density Functional Theory

NASA Astrophysics Data System (ADS)

Shushkov, Philip Georgiev

The exact quantum dynamics of realistic, multidimensional systems remains a formidable computational challenge. In many chemical processes, however, quantum effects such as tunneling, zero-point energy quantization, and nonadiabatic transitions play an important role. Therefore, approximate approaches that improve on the classical mechanical framework are of special practical interest. We propose a novel ring polymer surface hopping method for the calculation of chemical rate constants. The method blends two approaches, namely ring polymer molecular dynamics that accounts for tunneling and zero-point energy quantization, and surface hopping that incorporates nonadiabatic transitions. We test the method against exact quantum mechanical calculations for a one-dimensional, two-state model system. The method reproduces quite accurately the tunneling contribution to the rate and the distribution of reactants between the electronic states for this model system. Semiclassical instanton theory, an approach related to ring polymer molecular dynamics, accounts for tunneling by the use of periodic classical trajectories on the inverted potential energy surface. We study a model of electron transfer in solution, a chemical process where nonadiabatic events are prominent. By representing the tunneling electron with a ring polymer, we derive Marcus theory of electron transfer from semiclassical instanton theory after a careful analysis of the tunneling mode. We demonstrate that semiclassical instanton theory can recover the limit of Fermi's Golden Rule rate in a low-temperature, deep-tunneling regime. Mixed quantum-classical dynamics treats a few important degrees of freedom quantum mechanically, while classical mechanics describes affordably the rest of the system. But the interface of quantum and classical description is a challenging theoretical problem, especially for low-energy chemical processes. We therefore focus on the semiclassical limit of the coupled nuclear-electronic dynamics. We show that the time-dependent Schrodinger equation for the electrons employed in the widely used fewest switches surface hopping method is applicable only in the limit of nearly identical classical trajectories on the different potential energy surfaces. We propose a short-time decoupling algorithm that restricts the use of the Schrodinger equation only to the interaction regions. We test the short-time approximation on three model systems against exact quantum-mechanical calculations. The approximation improves the performance of the surface hopping approach. Nonadiabatic molecular dynamics simulations require the efficient and accurate computation of ground and excited state potential energy surfaces. Unlike the ground state calculations where standard methods exist, the computation of excited state properties is a challenging task. We employ time-independent density functional theory, in which the excited state energy is represented as a functional of the total density. We suggest an adiabatic-like approximation that simplifies the excited state exchange-correlation functional. We also derive a set of minimal conditions to impose exactly the orthogonality of the excited state Kohn-Sham determinant to the ground state determinant. This leads to an efficient, variational algorithm for the self-consistent optimization of the excited state energy. Finally, we assess the quality of the excitation energies obtained by the new method on a set of 28 organic molecules. The new approach provides results of similar accuracy to time-dependent density functional theory.

Molecular dynamics simulation study of the structure of poly(ethylene oxide) brushes on nonpolar surfaces in aqueous solution.

PubMed

Bedrov, Dmitry; Smith, Grant D

2006-07-04

The structure of poly(ethylene oxide) (PEO, M(w) = 526) brushes of various grafting density (sigma) on nonpolar graphite and hydrophobic (oily) surfaces in aqueous solution has been studied using atomistic molecular dynamics simulations. Additionally, the influence of PEO-surface interactions on the brush structure was investigated by systematically reducing the strength of the (dispersion) attraction between PEO and the surfaces. PEO chains were found to adsorb strongly to the graphite surface due primarily to the relative strength of dispersion interactions between PEO and the atomically dense graphite compared to those between water and graphite. For the oily surface, PEO-surface and water-surface dispersion interactions are much weaker, greatly reducing the energetic driving force for PEO adsorption. This reduction is mediated to some extent by a hydrophobic driving force for PEO adsorption on the oily surface. Reduction in the strength of PEO-surface attraction results in reduced adsorption of PEO for both surfaces, with the effect being much greater for the graphite surface where the strong PEO-surface dispersion interactions dominate. At high grafting density (sigma approximately 1/R(g)(2)), the PEO density profiles exhibited classical brush behavior and were largely independent of the strength of the PEO-surface interaction. With decreasing grafting density (sigma < 1/R(g)(2)), coverage of the surface by PEO requires an increasingly large fraction of PEO segments resulting in a strong dependence of the PEO density profile on the nature of the PEO-surface interaction.

Attachment dynamics of Photosystem I on nano-tailored surfaces for photovoltaic applications

NASA Astrophysics Data System (ADS)

Mukherjee, Dibyendu; Bruce, Barry D.; Khomami, Bamin

2010-03-01

Photosystem I (PSI), a biological photodiode, is a supra-molecular protein complex that charge separates upon exposure to light. Effective use of photo-electrochemical activities of PSI for hybrid photovoltaic (PV) device fabrications requires optimal encapsulation of these proteins onto organic/ inorganic substrates. Our results indicate that various experimental parameters alter the surface attachment dynamics of PSI deposited from colloidal aqueous buffer suspensions onto OH-terminated alkanethiolate/Au SAM substrates, thereby resulting in complex structural arrangements which affect the electron transfer and capture pathway of PSI. We present surface topographical, specific adsorption and polarization fluorescence characterizations of PSI/Au SAM substrates to elucidate the protein-surface interaction kinetics as well as the directional attachment dynamics of PSI. Our final goal is to enable site-specific homogeneous attachment of directionally aligned PSI onto chemically tailored nano-patterned substrates.

Absorption and folding of melittin onto lipid bilayer membranes via unbiased atomic detail microsecond molecular dynamics simulation.

PubMed

Chen, Charles H; Wiedman, Gregory; Khan, Ayesha; Ulmschneider, Martin B

2014-09-01

Unbiased molecular simulation is a powerful tool to study the atomic details driving functional structural changes or folding pathways of highly fluid systems, which present great challenges experimentally. Here we apply unbiased long-timescale molecular dynamics simulation to study the ab initio folding and partitioning of melittin, a template amphiphilic membrane active peptide. The simulations reveal that the peptide binds strongly to the lipid bilayer in an unstructured configuration. Interfacial folding results in a localized bilayer deformation. Akin to purely hydrophobic transmembrane segments the surface bound native helical conformer is highly resistant against thermal denaturation. Circular dichroism spectroscopy experiments confirm the strong binding and thermostability of the peptide. The study highlights the utility of molecular dynamics simulations for studying transient mechanisms in fluid lipid bilayer systems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014. Published by Elsevier B.V.

Defocused Imaging of UV-Driven Surface-Bound Molecular Motors.

PubMed

Krajnik, Bartosz; Chen, Jiawen; Watson, Matthew A; Cockroft, Scott L; Feringa, Ben L; Hofkens, Johan

2017-05-31

Synthetic molecular motors continue to attract great interest due to their ability to transduce energy into nanomechanical motion, the potential to do work and drive systems out-of-equilibrium. Of particular interest are unidirectional rotary molecular motors driven by chemical fuel or light. Probing the mechanistic details of their operation at the single-molecule level is hampered by the diffraction limit, which prevents the collection of dynamic positional information by traditional optical methods. Here, we use defocused wide-field imaging to examine the unidirectional rotation of individual molecular rotary motors on a quartz surface in unprecedented detail. The sequential occupation of nanomechanical states during the UV and heat-induced cycle of rotation are directly imaged in real-time. The approach will undoubtedly prove important in elucidating the mechanistic details and assessing the utility of novel synthetic molecular motors in the future.

Principles that Govern the Performance of Molecular Motors

NASA Astrophysics Data System (ADS)

Eide, Jon; Chakraborty, Arup; Oster, George

2003-03-01

We have created a two dimensional polymeric coarse-grained model to simulate the power stroke from the F0F1 ATP synthase class of molecular motors. There has been much work to understand the structure and dynamics of this type of molecular motor using both constrained molecular dynamics and general Markov models but neither of them have been able to elucidate in a qualitative manner how a constant force is created and transferred in the motor at a nearly 100efficiency. Our model is a modified Rouse system using Brownian and Monte Carlo (with solvent) Dynamics, concentrating only on the catalytic site and protein structures that we think are important for motor motion and energy transfer. While modeling the real system as closely as possible, we have determined the optimum characteristics for maximum efficiency. The efficiency depends on the load against the polymer, the polymer flexibility, polymer and surface matching, and solvent interactions. Insight into the basic principles behind the mechanical motion of this system may have implications for many other molecular motors driven by nucleotide hydrolysis and help design synthetic devices that can carry out biomimetic tasks.

Characterizing water-metal interfaces and machine learning potential energy surfaces

NASA Astrophysics Data System (ADS)

Ryczko, Kevin

In this thesis, we first discuss the fundamentals of ab initio electronic structure theory and density functional theory (DFT). We also discuss statistics related to computing thermodynamic averages of molecular dynamics (MD). We then use this theory to analyze and compare the structural, dynamical, and electronic properties of liquid water next to prototypical metals including platinum, graphite, and graphene. Our results are built on Born-Oppenheimer molecular dynamics (BOMD) generated using density functional theory (DFT) which explicitly include van der Waals (vdW) interactions within a first principles approach. All calculations reported use large simulation cells, allowing for an accurate treatment of the water-electrode interfaces. We have included vdW interactions through the use of the optB86b-vdW exchange correlation functional. Comparisons with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional are also shown. We find an initial peak, due to chemisorption, in the density profile of the liquid water-Pt interface not seen in the liquid water-graphite interface, liquid watergraphene interface, nor interfaces studied previously. To further investigate this chemisorption peak, we also report differences in the electronic structure of single water molecules on both Pt and graphite surfaces. We find that a covalent bond forms between the single water molecule and the platinum surface, but not between the single water molecule and the graphite surface. We also discuss the effects that defects and dopants in the graphite and graphene surfaces have on the structure and dynamics of liquid water. Lastly, we introduce artificial neural networks (ANNs), and demonstrate how they can be used to machine learn electronic structure calculations. As a proof of principle, we show the success of an ANN potential energy surfaces for a dimer molecule with a Lennard-Jones potential.

Quantification of evaporation induced error in atom probe tomography using molecular dynamics simulation.

PubMed

Chen, Shu Jian; Yao, Xupei; Zheng, Changxi; Duan, Wen Hui

2017-11-01

Non-equilibrium molecular dynamics was used to simulate the dynamics of atoms at the atom probe surface and five objective functions were used to quantify errors. The results suggested that before ionization, thermal vibration and collision caused the atoms to displace up to 1Å and 25Å respectively. The average atom displacements were found to vary between 0.2 and 0.5Å. About 9 to 17% of the atoms were affected by collision. Due to the effects of collision and ion-ion repulsion, the back-calculated positions were on average 0.3-0.5Å different from the pre-ionized positions of the atoms when the number of ions generated per pulse was minimal. This difference could increase up to 8-10Å when 1.5ion/nm 2 were evaporated per pulse. On the basis of the results, surface ion density was considered an important factor that needed to be controlled to minimize error in the evaporation process. Copyright © 2017. Published by Elsevier B.V.

A roaming wavepacket in the dynamics of electronically excited 2-hydroxypyridine.

PubMed

Poisson, Lionel; Nandi, Dhananjay; Soep, Benoît; Hochlaf, Majdi; Boggio-Pasqua, Martial; Mestdagh, Jean-Michel

2014-01-14

How much time does it take for a wavepacket to roam on a multidimensional potential energy surface? This combined theoretical and pump-probe femtosecond time experiment on 2-hydroxypyridine proposes an answer. Bypassing the well-established transition state and conical intersection relaxation pathways, this molecular system undergoes relaxation into the S1 excited state: the central ring is destabilized by the electronic excitation, within ~100 fs after absorption of the pump photon, then the H-atom bound to oxygen undergoes a roaming behavior when it couples to other degrees of freedom of the molecule. The timescale of the latter process is measured to be ~1.3 ps. Further evolution of the wavepacket is either an oscillation onto the S1 potential or a conversion into the triplet state for timescale larger than ~110 ps. Our work introduces a new tool for the understanding of time-resolved relaxation dynamics applied to large molecules through the roaming dynamics characterized by its strongly delocalized wavepacket on flat molecular potential energy surfaces.

Investigation of the interfacial properties of polyurethane/carbon nanotube hybrid composites: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Goclon, Jakub; Panczyk, Tomasz; Winkler, Krzysztof

2018-03-01

Considering the varied applications of hybrid polymer/carbon nanotube composites and the constant progress in the synthesis methods of such materials, we report a theoretical study of interfacial layer formation between pristine single-wall carbon nanotubes (SWCNTs) and polyurethane (PU) using molecular dynamic simulations. We vary the SWCNT diameter and the number of PU chains to examine various PU-SWCNT interaction patterns. Our simulations indicate the important role of intra-chain forces in PU. No regular polymeric structures could be identified on the carbon nanotube surface during the simulations. We find that increasing the SWCNT diameter results in stronger polymer binding. However, higher surface loadings of PU lead to stronger interpenetration by the polymeric segments; this effect is more apparent for SWCNTs with small diameters. Our core finding is that the attached PU binds most strongly to the carbon nanotubes with the largest diameters. Polymer dynamics reveal the loose distribution of PU chains in these systems.

The effect of salt on the melting of ice: A molecular dynamics simulation study.

PubMed

Kim, Jun Soo; Yethiraj, Arun

2008-09-28

The effect of added salt (NaCl) on the melting of ice is studied using molecular dynamics simulations. The equilibrium freezing point depression observed in the simulations is in good agreement with experimental data. The kinetic aspects of melting are investigated in terms of the exchange of water molecules between ice and the liquid phase. The ice/liquid equilibrium is a highly dynamic process with frequent exchange of water molecules between ice and the liquid phase. The balance is disturbed when ice melts and the melting proceeds in two stages; the inhibition of the association of water molecules to the ice surface at short times, followed by the increased dissociation of water molecules from the ice surface at longer times. We also find that Cl(-) ions penetrate more deeply into the interfacial region than Na(+) ions during melting. This study provides an understanding of the kinetic aspects of melting that could be useful in other processes such as the inhibition of ice growth by antifreeze proteins.

Wetting properties of molecularly rough surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Svoboda, Martin; Lísal, Martin, E-mail: lisal@icpf.cas.cz; Department of Physics, Institute of Science, J. E. Purkinje University, 400 96 Ústí n. Lab.

2015-09-14

We employ molecular dynamics simulations to study the wettability of nanoscale rough surfaces in systems governed by Lennard-Jones (LJ) interactions. We consider both smooth and molecularly rough planar surfaces. Solid substrates are modeled as a static collection of LJ particles arranged in a face-centered cubic lattice with the (100) surface exposed to the LJ fluid. Molecularly rough solid surfaces are prepared by removing several strips of LJ atoms from the external layers of the substrate, i.e., forming parallel nanogrooves on the surface. We vary the solid-fluid interactions to investigate strongly and weakly wettable surfaces. We determine the wetting properties bymore » measuring the equilibrium droplet profiles that are in turn used to evaluate the contact angles. Macroscopic arguments, such as those leading to Wenzel’s law, suggest that surface roughness always amplifies the wetting properties of a lyophilic surface. However, our results indicate the opposite effect from roughness for microscopically corrugated surfaces, i.e., surface roughness deteriorates the substrate wettability. Adding the roughness to a strongly wettable surface shrinks the surface area wet with the liquid, and it either increases or only marginally affects the contact angle, depending on the degree of liquid adsorption into the nanogrooves. For a weakly wettable surface, the roughness changes the surface character from lyophilic to lyophobic due to a weakening of the solid-fluid interactions by the presence of the nanogrooves and the weaker adsorption of the liquid into the nanogrooves.« less

Exploration of the Energy Landscape of Acetylcholinesterase by Molecular Dynamics Simulation.

NASA Astrophysics Data System (ADS)

McCammon, J. Andrew

2002-03-01

Proteins have rough energy landscapes. Often more states than just the ground state are occupied and have biological functions. It is essential to study these conformational substates and the dynamical transitions among them. Acetylcholinesterase (AChE) is an important enzyme that has biological functions including the termination of synaptic transmission signals. X-ray structures show that it has an active site that is accessible only via a long and narrow channel from its surface. Therefore the fact that acetylcholine and larger ligands can reach the active site is believed to reflect the protein's structural fluctuation. We carried out long molecular dynamics simulations to investigate the dynamics of AChE and its relation to biological function, and compared our results with experiments. The results reveal several "doors" that open intermittantly between the active site and the surface. Instead of having simple exponential decay correlation functions, the time series of these channels reveal complex, fractal gating between conformations. We also compared the AChE dynamics data with those from an AchE-fasciculin complex. (Fasciculin is a small protein that is a natural inhibitor of AChE.) The results show remarkable effects of the protein-protein interaction, including allosteric and dynamical inhibition by fasciculin besides direct steric blocking. More information and images can be found at http://mccammon.ucsd.edu

Facilitated receptor-recognition and enhanced bioactivity of bone morphogenetic protein-2 on magnesium-substituted hydroxyapatite surface

PubMed Central

Huang, Baolin; Yuan, Yuan; Li, Tong; Ding, Sai; Zhang, Wenjing; Gu, Yuantong; Liu, Changsheng

2016-01-01

Biomaterial surface functionalized with bone morphogenetic protein-2 (BMP-2) is a promising approach to fabricating successful orthopedic implants/scaffolds. However, the bioactivity of BMP-2 on material surfaces is still far from satisfactory and the mechanism of related protein-surface interaction remains elusive. Based on the most widely used bone-implants/scaffolds material, hydroxyapatite (HAP), we developed a matrix of magnesium-substituted HAP (Mg-HAP, 2.2 at% substitution) to address these issues. Further, we investigated the adsorption dynamics, BMPRs-recruitment, and bioactivity of recombinant human BMP-2 (rhBMP-2) on the HAP and Mg-HAP surfaces. To elucidate the mechanism, molecular dynamic simulations were performed to calculate the preferred orientations, conformation changes, and cysteine-knot stabilities of adsorbed BMP-2 molecules. The results showed that rhBMP-2 on the Mg-HAP surface exhibited greater bioactivity, evidenced by more facilitated BMPRs-recognition and higher ALP activity than on the HAP surface. Moreover, molecular simulations indicated that BMP-2 favoured distinct side-on orientations on the HAP and Mg-HAP surfaces. Intriguingly, BMP-2 on the Mg-HAP surface largely preserved the active protein structure evidenced by more stable cysteine-knots than on the HAP surface. These findings explicitly clarify the mechanism of BMP-2-HAP/Mg-HAP interactions and highlight the promising application of Mg-HAP/BMP-2 matrixes in bone regeneration implants/scaffolds. PMID:27075233

Facilitated receptor-recognition and enhanced bioactivity of bone morphogenetic protein-2 on magnesium-substituted hydroxyapatite surface

NASA Astrophysics Data System (ADS)

Huang, Baolin; Yuan, Yuan; Li, Tong; Ding, Sai; Zhang, Wenjing; Gu, Yuantong; Liu, Changsheng

2016-04-01

Biomaterial surface functionalized with bone morphogenetic protein-2 (BMP-2) is a promising approach to fabricating successful orthopedic implants/scaffolds. However, the bioactivity of BMP-2 on material surfaces is still far from satisfactory and the mechanism of related protein-surface interaction remains elusive. Based on the most widely used bone-implants/scaffolds material, hydroxyapatite (HAP), we developed a matrix of magnesium-substituted HAP (Mg-HAP, 2.2 at% substitution) to address these issues. Further, we investigated the adsorption dynamics, BMPRs-recruitment, and bioactivity of recombinant human BMP-2 (rhBMP-2) on the HAP and Mg-HAP surfaces. To elucidate the mechanism, molecular dynamic simulations were performed to calculate the preferred orientations, conformation changes, and cysteine-knot stabilities of adsorbed BMP-2 molecules. The results showed that rhBMP-2 on the Mg-HAP surface exhibited greater bioactivity, evidenced by more facilitated BMPRs-recognition and higher ALP activity than on the HAP surface. Moreover, molecular simulations indicated that BMP-2 favoured distinct side-on orientations on the HAP and Mg-HAP surfaces. Intriguingly, BMP-2 on the Mg-HAP surface largely preserved the active protein structure evidenced by more stable cysteine-knots than on the HAP surface. These findings explicitly clarify the mechanism of BMP-2-HAP/Mg-HAP interactions and highlight the promising application of Mg-HAP/BMP-2 matrixes in bone regeneration implants/scaffolds.

Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface

NASA Astrophysics Data System (ADS)

Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

2015-07-01

The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid–vapor interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagayama, Gyoko, E-mail: nagayama@mech.kyutech.ac.jp; Takematsu, Masaki; Mizuguchi, Hirotaka

2015-07-07

The structure and thermodynamic properties of the liquid–vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid–vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain lengthmore » of the molecules affects the condensation/evaporation behavior at the liquid–vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid–vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid–vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.« less

Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface.

PubMed

Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

2015-07-07

The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

Interaction of a sodium ion with the water liquid-vapor interface

NASA Technical Reports Server (NTRS)

Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

1989-01-01

Molecular dynamics results are presented for the density profile of a sodium ion near the water liquid-vapor interface at 320 K. These results are compared with the predictions of a simple dielectric model for the interaction of a monovalent ion with this interface. The interfacial region described by the model profile is too narrow and the profile decreases too abruptly near the solution interface. Thus, the simple model does not provide a satisfactory description of the molecular dynamics results for ion positions within two molecular diameters from the solution interface where appreciable ion concentrations are observed. These results suggest that surfaces associated with dielectric models of ionic processes at aqueous solution interfaces should be located at least two molecular diameters inside the liquid phase. A free energy expense of about 2 kcal/mol is required to move the ion within two molecular layers of the free water liquid-vapor interface.

vmdICE: a plug-in for rapid evaluation of molecular dynamics simulations using VMD.

PubMed

Knapp, Bernhard; Lederer, Nadja; Omasits, Ulrich; Schreiner, Wolfgang

2010-12-01

Molecular dynamics (MD) is a powerful in silico method to investigate the interactions between biomolecules. It solves Newton's equations of motion for atoms over a specified period of time and yields a trajectory file, containing the different spatial arrangements of atoms during the simulation. The movements and energies of each single atom are recorded. For evaluating of these simulation trajectories with regard to biomedical implications, several methods are available. Three well-known ones are the root mean square deviation (RMSD), the root mean square fluctuation (RMSF) and solvent accessible surface area (SASA). Herein, we present a novel plug-in for the software "visual molecular dynamics" (VMD) that allows an interactive 3D representation of RMSD, RMSF, and SASA, directly on the molecule. On the one hand, our plug-in is easy to handle for inexperienced users, and on the other hand, it provides a fast and flexible graphical impression of the spatial dynamics of a system for experts in the field. © 2010 Wiley Periodicals, Inc.

Molecular Dynamics Simulation of the Crystal Nucleation and Growth Behavior of Methane Hydrate in the Presence of the Surface and Nanopores of Porous Sediment.

PubMed

Yan, Ke-Feng; Li, Xiao-Sen; Chen, Zhao-Yang; Xia, Zhi-Ming; Xu, Chun-Gang; Zhang, Zhiqiang

2016-08-09

The behavior of hydrate formation in porous sediment has been widely studied because of its importance in the investigation of reservoirs and in the drilling of natural gas hydrate. However, it is difficult to understand the hydrate nucleation and growth mechanism on the surface and in the nanopores of porous media by experimental and numerical simulation methods. In this work, molecular dynamics simulations of the nucleation and growth of CH4 hydrate in the presence of the surface and nanopores of clay are carried out. The molecular configurations and microstructure properties are analyzed for systems containing one H2O hydrate layer (System A), three H2O hydrate layers (System B), and six H2O hydrate layers (System C) in both clay and the bulk solution. It is found that hydrate formation is more complex in porous media than in the pure bulk solution and that there is cooperativity between hydrate growth and molecular diffusion in clay nanopores. The hydroxylated edge sites of the clay surface could serve as a source of CH4 molecules to facilitate hydrate nucleation. The diffusion velocity of molecules is influenced by the growth of the hydrate that forms a block in the throats of the clay nanopore. Comparing hydrate growth in different clay pore sizes reveals that the pore size plays an important role in hydrate growth and molecular diffusion in clay. This simulation study provides the microscopic mechanism of hydrate nucleation and growth in porous media, which can be favorable for the investigation of the formation of natural gas hydrate in sediments.

SIMULATION STUDIES OF THE WETTING OF CRYSTALLINE FACES OF COTTON CELLULOSE

USDA-ARS?s Scientific Manuscript database

Models of the surfaces of nano-sized cellulose crystals were constructed and a model droplet of water was placed on each. Then, the model atoms were given motion that corresponds to room temperature (a molecular dynamics simulation), and the spreading of the water over the surfaces was studied. Besi...

A New Exploration of the Torsional Energy Surface of N-Pentane Using Molecular Modeling Software

ERIC Educational Resources Information Center

Galembeck, Sergio E.; Caramori, Giovanni F.; Romero, Jose Ricardo

2005-01-01

The torsional potential energy surface of a chemical compounds, the accessible conformations at a specified temperature and the transition states that connect these confirmations establishes many chemical properties such as dynamic behavior, reactivity and biological activity. A conformational search of n-pentane is presented using computational…

Effect of Intercalated Water on Potassium Ion Transport through Kv1.2 Channels Studied via On-the-Fly Free-Energy Parametrization.

PubMed

Paz, S Alexis; Maragliano, Luca; Abrams, Cameron F

2018-05-08

We introduce a two-dimensional version of the method called on-the-fly free energy parametrization (OTFP) to reconstruct free-energy surfaces using Molecular Dynamics simulations, which we name OTFP-2D. We first test the new method by reconstructing the well-known dihedral angles free energy surface of solvated alanine dipeptide. Then, we use it to investigate the process of K + ions translocation inside the Kv1.2 channel. By comparing a series of two-dimensional free energy surfaces for ion movement calculated with different conditions on the intercalated water molecules, we first recapitulate the widely accepted knock-on mechanism for ion translocation and then confirm that permeation occurs with water molecules alternated among the ions, in accordance with the latest experimental findings. From a methodological standpoint, our new OTFP-2D algorithm demonstrates the excellent sampling acceleration of temperature-accelerated molecular dynamics and the ability to efficiently compute 2D free-energy surfaces. It will therefore be useful in large variety complex biomacromolecular simulations.

Crystal Orientation Effect on the Subsurface Deformation of Monocrystalline Germanium in Nanometric Cutting.

PubMed

Lai, Min; Zhang, Xiaodong; Fang, Fengzhou

2017-12-01

Molecular dynamics simulations of nanometric cutting on monocrystalline germanium are conducted to investigate the subsurface deformation during and after nanometric cutting. The continuous random network model of amorphous germanium is established by molecular dynamics simulation, and its characteristic parameters are extracted to compare with those of the machined deformed layer. The coordination number distribution and radial distribution function (RDF) show that the machined surface presents the similar amorphous state. The anisotropic subsurface deformation is studied by nanometric cutting on the (010), (101), and (111) crystal planes of germanium, respectively. The deformed structures are prone to extend along the 110 slip system, which leads to the difference in the shape and thickness of the deformed layer on various directions and crystal planes. On machined surface, the greater thickness of subsurface deformed layer induces the greater surface recovery height. In order to get the critical thickness limit of deformed layer on machined surface of germanium, the optimized cutting direction on each crystal plane is suggested according to the relevance of the nanometric cutting to the nanoindentation.

Molecular dynamic simulations of the high-speed copper nanoparticles collision with the aluminum surface

NASA Astrophysics Data System (ADS)

Pogorelko, V. V.; Mayer, A. E.

2016-11-01

With the use of the molecular dynamic simulations, we investigated the effect of the high-speed (500 m/s, 1000 m/s) copper nanoparticle impact on the mechanical properties of an aluminum surface. Dislocation analysis shows that a large number of dislocations are formed in the impact area; the total length of dislocations is determined not only by the speed and size of the incoming copper nanoparticle (kinetic energy of the nanoparticle), but by a temperature of the system as well. The dislocations occupy the whole area of the aluminum single crystal at high kinetic energy of the nanoparticle. With the decrease of the nanoparticle kinetic energy, the dislocation structures are formed in the near-surface layer; formation of the dislocation loops takes place. Temperature rise of the system (aluminum substrate + nanoparticle) reduces the total dislocation length in the single crystal of aluminum; there is deeper penetration of the copper atoms in the aluminum at high temperatures. Average energy of the nanoparticles and room temperature of the system are optimal for production of high-quality layers of copper on the aluminum surface.

Molecular simulations and experimental studies of zeolites

NASA Astrophysics Data System (ADS)

Moloy, Eric C.

Zeolites are microporous aluminosilicate tetrahedral framework materials that have symmetric cages and channels with open-diameters between 0.2 and 2.0 nm. Zeolites are used extensively in the petrochemical industries for both their microporosity and their catalytic properties. The role of water is paramount to the formation, structure, and stability of these materials. Zeolites frequently have extra-framework cations, and as a result, are important ion-exchange materials. Zeolites also play important roles as molecular sieves and catalysts. For all that is known about zeolites, much remains a mystery. How, for example, can the well established metastability of these structures be explained? What is the role of water with respect to the formation, stabilization, and dynamical properties? This dissertation addresses these questions mainly from a modeling perspective, but also with some experimental work as well. The first discussion addresses a special class of zeolites: pure-silica zeolites. Experimental enthalpy of formation data are combined with molecular modeling to address zeolitic metastability. Molecular modeling is used to calculate internal surface areas, and a linear relationship between formation enthalpy and internal surface areas is clearly established, producing an internal surface energy of approximately 93 mJ/m2. Nitrate bearing sodalite and cancrinite have formed under the caustic chemical conditions of some nuclear waste processing centers in the United States. These phases have fouled expensive process equipment, and are the primary constituents of the resilient heels in the bottom of storage tanks. Molecular modeling, including molecular mechanics, molecular dynamics, and density functional theory, is used to simulate these materials with respect to structure and dynamical properties. Some new, very interesting results are extracted from the simulation of anhydrous Na6[Si6Al 6O24] sodalite---most importantly, the identification of two distinct oxygen sites (rather than one), and formation of a new supercell. New calorimetric measurements of enthalpy are used to examine the energetics of the hydrosodalite family of zeolites---specifically, formation enthalpies and hydration energies. Finally, force-field computational methods begin the examination of water in terms of energetics, structure, and radionuclide containment and diffusion.

Molecular models of alginic acid: Interactions with calcium ions and calcite surfaces

NASA Astrophysics Data System (ADS)

Perry, Thomas D.; Cygan, Randall T.; Mitchell, Ralph

2006-07-01

Cation binding by polysaccharides is observed in many environments and is important for predictive environmental modeling, and numerous industrial and food technology applications. The complexities of these cation-organic interactions are well suited for predictive molecular modeling and the analysis of conformation and configuration of polysaccharides and their influence on cation binding. In this study, alginic acid was chosen as a model polymer system and representative disaccharide and polysaccharide subunits were developed. Molecular dynamics simulation of the torsion angles of the ether linkage between various monomeric subunits identified local and global energy minima for selected disaccharides. The simulations indicate stable disaccharide configurations and a common global energy minimum for all disaccharide models at Φ = 274 ± 7°, Ψ = 227 ± 5°, where Φ and Ψ are the torsion angles about the ether linkage. The ability of disaccharide subunits to bind calcium ions and to associate with the (101¯4) surface of calcite was also investigated. Molecular models of disaccharide interactions with calcite provide binding energy differences for conformations that are related to the proximity and residence densities of the electron-donating moieties with calcium ions on the calcite surface, which are controlled, in part, by the torsion of the ether linkage between monosaccharide units. Dynamically optimized configurations for polymer alginate models with calcium ions were also derived.

Study of lysozyme mobility and binding free energy during adsorption on a graphene surface

NASA Astrophysics Data System (ADS)

Nakano, C. Masato; Ma, Heng; Wei, Tao

2015-04-01

Understanding protein adsorption is a key to the development of biosensors and anti-biofouling materials. Hydration essentially controls the adsorption process on hydrophobic surfaces, but its effect is complicated by various factors. Here, we present an ideal model system to isolate hydration effects—lysozyme adsorption on a flat hydrophobic graphene surface. Our all-atom molecular dynamics and molecular-mechanics/Poisson-Boltzmann surface area computation study reveal that lysozyme on graphene displays much larger diffusivity than in bulk water. Protein's hydration free energy within the first hydration shell is dominated by the protein-water electrostatic interactions and acts as an energy barrier for protein adsorption. On the other hand, the surface tension, especially that from the hydrophobic graphene, can effectively weaken the barrier to promote adsorption.

Determination of Protein Surface Hydration by Systematic Charge Mutations

NASA Astrophysics Data System (ADS)

Yang, Jin; Jia, Menghui; Qin, Yangzhong; Wang, Dihao; Pan, Haifeng; Wang, Lijuan; Xu, Jianhua; Zhong, Dongping; Dongping Zhong Collaboration; Jianhua Xu Collaboration

Protein surface hydration is critical to its structural stability, flexibility, dynamics and function. Recent observations of surface solvation on picosecond time scales have evoked debate on the origin of such relatively slow motions, from hydration water or protein charged sidechains, especially with molecular dynamics simulations. Here, we used a unique nuclease with a single tryptophan as a local probe and systematically mutated neighboring three charged residues to differentiate the contributions from hydration water and charged sidechains. By mutations of alternative one and two and all three charged residues, we observed slight increases in the total tryptophan Stokes shifts with less neighboring charged residue(s) and found insensitivity of charged sidechains to the relaxation patterns. The dynamics is correlated with hydration water relaxation with the slowest time in a dense charged environment and the fastest time at a hydrophobic site. On such picosecond time scales, the protein surface motion is restricted. The total Stokes shifts are dominantly from hydration water relaxation and the slow dynamics is from water-driven relaxation, coupled with local protein fluctuations.

Preferential sites for InAsP/InP quantum wire nucleation using molecular dynamics

NASA Astrophysics Data System (ADS)

Nuñez-Moraleda, Bernardo; Pizarro, Joaquin; Guerrero, Elisa; Guerrero-Lebrero, Maria P.; Yáñez, Andres; Molina, Sergio Ignacio; Galindo, Pedro Luis

2014-11-01

In this paper, stress fields at the surface of the capping layer of self-assembled InAsP quantum wires grown on an InP (001) substrate have been determined from atomistic models using molecular dynamics and Stillinger-Weber potentials. To carry out these calculations, the quantum wire compositional distribution was extracted from previous works, where the As and P distributions were determined by electron energy loss spectroscopy and high-resolution aberration-corrected Z-contrast imaging. Preferential sites for the nucleation of wires on the surface of the capping layer were studied and compared with (i) previous simulations using finite element analysis to solve anisotropic elastic theory equations and (ii) experimentally measured locations of stacked wires. Preferential nucleation sites of stacked wires were determined by the maximum stress location at the MD model surface in good agreement with experimental results and those derived from finite element analysis. This indicates that MD simulations based on empirical potentials provide a suitable and flexible tool to study strain dependent atom processes.

Regimes of Flow over Complex Structures of Endothelial Glycocalyx: A Molecular Dynamics Simulation Study.

PubMed

Jiang, Xi Zhuo; Feng, Muye; Ventikos, Yiannis; Luo, Kai H

2018-04-10

Flow patterns on surfaces grafted with complex structures play a pivotal role in many engineering and biomedical applications. In this research, large-scale molecular dynamics (MD) simulations are conducted to study the flow over complex surface structures of an endothelial glycocalyx layer. A detailed structure of glycocalyx has been adopted and the flow/glycocalyx system comprises about 5,800,000 atoms. Four cases involving varying external forces and modified glycocalyx configurations are constructed to reveal intricate fluid behaviour. Flow profiles including temporal evolutions and spatial distributions of velocity are illustrated. Moreover, streamline length and vorticity distributions under the four scenarios are compared and discussed to elucidate the effects of external forces and glycocalyx configurations on flow patterns. Results show that sugar chain configurations affect streamline length distributions but their impact on vorticity distributions is statistically insignificant, whilst the influence of the external forces on both streamline length and vorticity distributions are trivial. Finally, a regime diagram for flow over complex surface structures is proposed to categorise flow patterns.

Effect of temperature on the adsorption of sulfanilamide onto aluminum oxide and its molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ji, Ying-xue; Wang, Feng-he; Duan, Lun-chao; Zhang, Fan; Gong, Xue-dong

2013-11-01

The effect of temperature on the adsorption of sulfanilamide (SA) onto aluminum oxide was researched through batch adsorption experiments, and was then simulated using the molecular dynamics (MD) method. The results show that SA can be adsorbed effectively by the adsorbent of aluminum oxide due to their interactions between SA molecule and the surface of aluminum oxide crystal, and temperature is a key factor which influences the adsorption efficiency obviously. The removal ratio of SA at 298 K is the highest among the selected temperatures (293 K, 298 K, 303 K). MD simulations revealed the interactions between SA molecules and (0 1 2) surface of aluminum oxide crystal at molecular level. The SA molecule has clung to the (0 1 2) face of aluminum oxide crystal, and its structure is deformed during its combining process with the surface. Both binding energies (Eb) and deformation energies (ΔEdeform) in the SA-aluminum oxide system follow the same order as: SA-Al2O3 (298 K) > SA-Al2O3 (293 K) > SA-Al2O3 (303 K). Their deformation energies are far less than their non-bonding energies. Analysis of radial distribution functions (RDFs) indicates that SA can be adsorbed effectively by aluminum oxide crystal mainly through non-bond interactions. The simulation results agree well with the experimental results, which verify the rationality and reliability of the MD simulation. The further MD simulations provide theoretically optimal temperature (301 K) for the adsorption of SA onto aluminum oxide. The molecular dynamics simulation will be useful for better understanding the adsorption mechanism of antibiotics onto metal oxides, which will also be helpful for optimizing experimental conditions to improve the adsorptive removal efficiency of antibiotics.

Study of Effect of Impacting Direction on Abrasive Nanometric Cutting Process with Molecular Dynamics

NASA Astrophysics Data System (ADS)

Li, Junye; Meng, Wenqing; Dong, Kun; Zhang, Xinming; Zhao, Weihong

2018-01-01

Abrasive flow polishing plays an important part in modern ultra-precision machining. Ultrafine particles suspended in the medium of abrasive flow removes the material in nanoscale. In this paper, three-dimensional molecular dynamics (MD) simulations are performed to investigate the effect of impacting direction on abrasive cutting process during abrasive flow polishing. The molecular dynamics simulation software Lammps was used to simulate the cutting of single crystal copper with SiC abrasive grains at different cutting angles (0o-45o). At a constant friction coefficient, we found a direct relation between cutting angle and cutting force, which ultimately increases the number of dislocation during abrasive flow machining. Our theoretical study reveal that a small cutting angle is beneficial for improving surface quality and reducing internal defects in the workpiece. However, there is no obvious relationship between cutting angle and friction coefficient.

Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

NASA Technical Reports Server (NTRS)

Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

2001-01-01

Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

GPU-enabled molecular dynamics simulations of ankyrin kinase complex

NASA Astrophysics Data System (ADS)

Gautam, Vertika; Chong, Wei Lim; Wisitponchai, Tanchanok; Nimmanpipug, Piyarat; Zain, Sharifuddin M.; Rahman, Noorsaadah Abd.; Tayapiwatana, Chatchai; Lee, Vannajan Sanghiran

2014-10-01

The ankyrin repeat (AR) protein can be used as a versatile scaffold for protein-protein interactions. It has been found that the heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. Using ILK-AR with high affinity for the PINCH1 as our model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. In this study, the long time scale dynamics simulations with GPU accelerated molecular dynamics (MD) simulations in AMBER12 have been performed to locate the hot spots of protein-protein interaction by the analysis of the Molecular Mechanics-Poisson-Boltzmann Surface Area/Generalized Born Solvent Area (MM-PBSA/GBSA) of the MD trajectories. Our calculations suggest good binding affinity of the complex and also the residues critical in the binding.

Study of Effect of Impacting Direction on Abrasive Nanometric Cutting Process with Molecular Dynamics.

PubMed

Li, Junye; Meng, Wenqing; Dong, Kun; Zhang, Xinming; Zhao, Weihong

2018-01-11

Abrasive flow polishing plays an important part in modern ultra-precision machining. Ultrafine particles suspended in the medium of abrasive flow removes the material in nanoscale. In this paper, three-dimensional molecular dynamics (MD) simulations are performed to investigate the effect of impacting direction on abrasive cutting process during abrasive flow polishing. The molecular dynamics simulation software Lammps was used to simulate the cutting of single crystal copper with SiC abrasive grains at different cutting angles (0 o -45 o ). At a constant friction coefficient, we found a direct relation between cutting angle and cutting force, which ultimately increases the number of dislocation during abrasive flow machining. Our theoretical study reveal that a small cutting angle is beneficial for improving surface quality and reducing internal defects in the workpiece. However, there is no obvious relationship between cutting angle and friction coefficient.

Novel surface diffusion characteristics for a robust pentacene derivative on Au(1 1 1) surfaces

NASA Astrophysics Data System (ADS)

Miller, Ryan A.; Larson, Amanda; Pohl, Karsten

2017-06-01

Molecular dynamics simulations have been performed in both the ab initio and classical mechanics frameworks of 5,6,7-trithiapentacene-13-one (TTPO) molecules on flat Au(1 1 1) surfaces. Results show new surface diffusion characteristics including a strong preference for the molecule to align its long axis parallel to the sixfold Au(1 1 1) symmetry directions and subsequently diffuse along these close-packed directions, and a calculated activation energy for diffusion of 0.142 eV, about four times larger than that for pure pentacene on Au. The temperature-dependent diffusion coefficients were calculated to help quantify the molecular mobility during the experimentally observed process of forming self-assembled monolayers on gold electrodes.

The 1-ethyl-3-methylimidazolium bis(trifluoro-methylsulfonyl)-imide ionic liquid nanodroplets on solid surfaces and in electric field: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Dong, Dengpan; Vatamanu, Jenel P.; Wei, Xiaoyu; Bedrov, Dmitry

2018-05-01

Atomistic molecular dynamics simulations were conducted to study the wetting states of 1-ethyl-3-methylimidazolium bis(trifluoro-methylsulfonyl)-imide ionic liquid (IL) nanodroplets on surfaces with different strengths of van der Waals (VDW) interactions and in the presence of an electric field. By adjusting the depth of Lennard-Jones potential, the van der Waals interaction between the solid surface and ionic liquid was systematically varied. The shape of the droplets was analyzed to extract the corresponding contact angle utilized to characterize wetting states of the nanodroplets. The explored range of surface-IL interactions allowed contact angles ranging from complete IL spreading on the surface to poor wettability. The effect of the external electrical field was explored by adding point charges to the surface atoms. Systems with two charge densities (±0.002 e/atom and ±0.004 e/atom) that correspond to 1.36 V/nm and 2.72 V/nm electric fields were investigated. Asymmetrical wetting states were observed for both cases. At 1.36 V/nm electric field, contributions of IL-surface VDW interactions and Coulombic interactions to the wetting state were competitive. At 2.72 V/nm field, electrostatic interactions dominate the interaction between the nanodroplet and surface, leading to enhanced wettability on all surfaces.

How Properties of Solid Surfaces Modulate the Nucleation of Gas Hydrate

PubMed Central

Bai, Dongsheng; Chen, Guangjin; Zhang, Xianren; Sum, Amadeu K.; Wang, Wenchuan

2015-01-01

Molecular dynamics simulations were performed for CO2 dissolved in water near silica surfaces to investigate how the hydrophilicity and crystallinity of solid surfaces modulate the local structure of adjacent molecules and the nucleation of CO2 hydrates. Our simulations reveal that the hydrophilicity of solid surfaces can change the local structure of water molecules and gas distribution near liquid-solid interfaces, and thus alter the mechanism and dynamics of gas hydrate nucleation. Interestingly, we find that hydrate nucleation tends to occur more easily on relatively less hydrophilic surfaces. Different from surface hydrophilicity, surface crystallinity shows a weak effect on the local structure of adjacent water molecules and on gas hydrate nucleation. At the initial stage of gas hydrate growth, however, the structuring of molecules induced by crystalline surfaces are more ordered than that induced by amorphous solid surfaces. PMID:26227239

Wetting and evaporation of salt-water nanodroplets: A molecular dynamics investigation.

PubMed

Zhang, Jun; Borg, Matthew K; Sefiane, Khellil; Reese, Jason M

2015-11-01

We employ molecular dynamics simulations to study the wetting and evaporation of salt-water nanodroplets on platinum surfaces. Our results show that the contact angle of the droplets increases with the salt concentration. To verify this, a second simulation system of a thin salt-water film on a platinum surface is used to calculate the various surface tensions. We find that both the solid-liquid and liquid-vapor surface tensions increase with salt concentration and as a result these cause an increase in the contact angle. However, the evaporation rate of salt-water droplets decreases as the salt concentration increases, due to the hydration of salt ions. When the water molecules have all evaporated from the droplet, two forms of salt crystals are deposited, clump and ringlike, depending on the solid-liquid interaction strength and the evaporation rate. To form salt crystals in a ring, it is crucial that there is a pinned stage in the evaporation process, during which salt ions can move from the center to the rim of the droplets. With a stronger solid-liquid interaction strength, a slower evaporation rate, and a higher salt concentration, a complete salt crystal ring can be deposited on the surface.

A Molecular Dynamics Investigation of the Physical-Chemical Properties of Calicivirus Capsid Protein Adsorption to Fomites

NASA Astrophysics Data System (ADS)

Peeler, David; Matysiak, Silvina

2013-03-01

Any inanimate object with an exposed surface bears the possibility of hosting a virus and may therefore be labeled a fomite. This research hopes to distinguish which chemical-physical differences in fomite surface and virus capsid protein characteristics cause variations in virus adsorption through an alignment of in silico molecular dynamics simulations with in vitro measurements. The impact of surface chemistry on the adsorption of the human norovirus (HNV)-surrogate calicivirus capsid protein 2MS2 has been simulated for monomer and trimer structures and is reported in terms of protein-self assembled monolayer (SAM) binding free energy. The coarse-grained MARTINI forcefield was used to maximize spatial and temporal resolution while minimizing computational load. Future work will investigate the FCVF5 and SMSVS4 calicivirus trimers and will extend beyond hydrophobic and hydrophilic SAM surface chemistry to charged SAM surfaces in varying ionic concentrations. These results will be confirmed by quartz crystal microbalance experiments conducted by Dr. Wigginton at the University of Michigan. This should provide a novel method for predicting the transferability of viruses that cannot be studied in vitro such as dangerous foodborne and nosocomially-acquired viruses like HNV.

Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding

NASA Astrophysics Data System (ADS)

Radic, Slaven; Nedumpully-Govindan, Praveen; Chen, Ran; Salonen, Emppu; Brown, Jared M.; Ke, Pu Chun; Ding, Feng

2014-06-01

Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding.Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding. Electronic supplementary information (ESI) is available: Fluorescence spectra, ITC, CD spectra and other data as described in the text. See DOI: 10.1039/c4nr01544d

Local mass and energy transports in evaporation processes from a vapor-liquid interface in a slit pore based on molecular dynamics

NASA Astrophysics Data System (ADS)

Fujiwara, K.; Shibahara, M.

2018-02-01

Molecular evaporation processes from a vapor-liquid interface formed in a slit-like pore were examined based on the classical molecular dynamics method, in order to elucidate a molecular mechanism of local mass and energy transports in a slit. The calculation system consisted of monatomic molecules and atoms which interact through the 12-6 Lennard-Jones potential. At first, a liquid was situated in a slit with a vapor-liquid interface, and instantaneous amounts of the mass and energy fluxes defined locally in the slit were obtained in two dimensions to reveal local fluctuation properties of the fluid in equilibrium states. Then, imposing a temperature gradient in the calculation system, non-equilibrium evaporation processes in the slit were investigated in details based on the local mass and energy fluxes. In this study, we focused on the fluid which is in the vicinity of the solid surface and in contact with the vapor phase. In the non-equilibrium evaporation processes, the results revealed that the local energy transport mechanism in the vicinity of the solid surface is different from that of the vapor phase, especially in the case of the relatively strong fluid-solid interaction. The results also revealed that the local mass transport in the vicinity of the solid surface can be interpreted based on the mechanism of the local energy transport, and the mechanism provides valuable information about pictures of the evaporation phenomena especially in the vicinity of the hydrophilic surfaces. It suggests that evaluating and changing this mechanism of the local energy transport are necessary to control the local mass flux more precisely in the vicinity of the solid surface.

Terraced spreading of simple liquids on solid surfaces

NASA Technical Reports Server (NTRS)

Yang, Ju-Xing; Koplik, Joel; Banavar, Jayanth R.

1992-01-01

We have studied the spreading of liquid drops on a solid surface by molecular-dynamics simulations of coexisting three-phase Lennard-Jones systems of liquid, vapor, and solid. We consider both spherically symmetric atoms and diatomic molecules, and a range of interaction strengths. As the attraction between liquid and solid increases we observe a smooth transition in spreading regimes, from partial to complete to terraced wetting. In the terraced case, where distinct monomolecular layers spread with different velocities, the layers are ordered but not solid, with substantial molecular diffusion both within and between layers. The quantitative behavior resembles recent experimental findings, but the detailed dynamics differ. In particular, the layers exhibit an unusual spreading law, where their radii vary in time as R-squared approximately equal to log10t, which disagrees with experiments on polymeric liquids as well as recent calculations.

Glass transition of polymers in bulk, confined geometries, and near interfaces

NASA Astrophysics Data System (ADS)

Napolitano, Simone; Glynos, Emmanouil; Tito, Nicholas B.

2017-03-01

When cooled or pressurized, polymer melts exhibit a tremendous reduction in molecular mobility. If the process is performed at a constant rate, the structural relaxation time of the liquid eventually exceeds the time allowed for equilibration. This brings the system out of equilibrium, and the liquid is operationally defined as a glass—a solid lacking long-range order. Despite almost 100 years of research on the (liquid/)glass transition, it is not yet clear which molecular mechanisms are responsible for the unique slow-down in molecular dynamics. In this review, we first introduce the reader to experimental methodologies, theories, and simulations of glassy polymer dynamics and vitrification. We then analyse the impact of connectivity, structure, and chain environment on molecular motion at the length scale of a few monomers, as well as how macromolecular architecture affects the glass transition of non-linear polymers. We then discuss a revised picture of nanoconfinement, going beyond a simple picture based on interfacial interactions and surface/volume ratio. Analysis of a large body of experimental evidence, results from molecular simulations, and predictions from theory supports, instead, a more complex framework where other parameters are relevant. We focus discussion specifically on local order, free volume, irreversible chain adsorption, the Debye-Waller factor of confined and confining media, chain rigidity, and the absolute value of the vitrification temperature. We end by highlighting the molecular origin of distributions in relaxation times and glass transition temperatures which exceed, by far, the size of a chain. Fast relaxation modes, almost universally present at the free surface between polymer and air, are also remarked upon. These modes relax at rates far larger than those characteristic of glassy dynamics in bulk. We speculate on how these may be a signature of unique relaxation processes occurring in confined or heterogeneous polymeric systems.

Membrane surface engineering for protein separations: experiments and simulations.

PubMed

Liu, Zizhao; Du, Hongbo; Wickramasinghe, S Ranil; Qian, Xianghong

2014-09-09

A bisphosphonate derived ligand was successfully synthesized and grafted from the surface of regenerated cellulose membrane using atom transfer radical polymerization (ATRP) for protein separations. This ligand has a remarkable affinity for arginine (Arg) residues on protein surface. Hydrophilic residues N-(2-hydroxypropyl) methacrylamide (HPMA) was copolymerized to enhance the flexibility of the copolymer ligand and further improve specific protein adsorption. The polymerization of bisphosphonate derivatives was successful for the first time using ATRP. Static and dynamic binding capacities were determined for binding and elution of Arg rich lysozyme. The interaction mechanism between the copolymer ligand and lysozyme was elucidated using classical molecular dynamics (MD) simulations.

Scattering of water from the glycerol liquid-vacuum interface

NASA Technical Reports Server (NTRS)

Benjamin, I.; Wilson, M. A.; Pohorille, A.; Nathanson, G. M.

1995-01-01

Molecular dynamics calculations of the scattering of D2O from the glycerol surface at different collision energies are reported. The results for the trapping probabilities and energy transfer are in good agreement with experiments. The calculations demonstrate that the strong attractive forces between these two strongly hydrogen bonding molecules have only a minor effect on the initial collision dynamics. The trapping probability is influenced to a significant extent by the repulsive hard sphere-like initial encounter with the corrugated surface and, only at a later stage, by the efficiency of energy flow in the multiple interactions between the water and the surface molecules.

Theoretical study of the potential energy surfaces and dynamics of CaNC/CaCN

NASA Astrophysics Data System (ADS)

Nanbu, Shinkoh; Minamino, Satoshi; Aoyagi, Mutsumi

1997-05-01

Potential energy surfaces for the ground and two low-lying electronically excited states of CaNC/CaCN, are calculated using the ab initio molecular orbital (MO) configuration interaction (CI) method. The absorption and emission spectra of the system are computed by performing time-dependent quantum dynamical calculations on these surfaces. The most stable geometries for the two lowest lying 12Σ+ and 12Π electronic states correspond to the calcium isocyanide (CaNC) structure. These two states are characterized by ionic bonding and the potential energy curves along the bending coordinate are relatively isotropic. The result of our wave packet dynamics shows that the characteristics of the experimental spectra observed by the laser-induced fluorescence spectroscopy can be explained by the Renner-Teller splitting.

Structural features of the adsorption layer of pentacene on the graphite surface and the PMMA/graphite hybrid surface

NASA Astrophysics Data System (ADS)

Fadeeva, A. I.; Gorbunov, V. A.; Litunenko, T. A.

2017-08-01

Using the molecular dynamics and the Monte Carlo methods, we have studied the structural features and growth mechanism of the pentacene film on graphite and polymethylmethacrylate /graphite surfaces. Monolayer capacity and molecular area, optimal angles between the pentacene molecules and graphite and PMMA/graphite surfaces as well as the characteristic angles between the neighboring pentacene molecules in the adsorption layer were estimated. It is shown that the orientation of the pentacene molecules in the film is determined by a number of factors, including the surface concentration of the molecules, relief of the surface, presence or absence of the polymer layer and its thickness. The pentacene molecules adsorbed on the graphite surface keep a horizontal position relative to the long axis at any surface coverage/thickness of the film. In the presence of the PMMA layer on the graphite, the increase of the number of pentacene molecules as well as the thickness of the PMMA layer induce the change of molecular orientation from predominantly horizontal to vertical one. The reason for such behavior is supposed to be the roughness of the PMMA surface.

Distribution of Chains in Polymer Brushes Produced by a “Grafting From” Mechanism

DOE PAGES

Martinez, Andre P.; Carrillo, Jan-Michael Y.; Dobrynin, Andrey V.; ...

2016-01-11

The molecular weight and polydispersity of the chains in a polymer brush are critical parameters determining the brush properties. However, the characterization of polymer brushes is hindered by the vanishingly small mass of polymer present in brush layers. In this study, in order to obtain sufficient quantities of polymer for analysis, polymer brushes were grown from high surface area fibrous nylon membranes by ATRP. We synthesized the brushes with varying surface initiator densities, polymerization times, and amounts of sacrificial initiator, then cleaved from the substrate, and analyzed by GPC and NMR. Characterization showed that the surface-grown polymer chains were moremore » polydisperse and had lower average molecular weight compared to solution-grown polymers synthesized concurrently. Furthermore, the molecular weight distribution of the polymer brushes was observed to be bimodal, with a low molecular weight population of chains representing a significant mass fraction of the polymer chains at high surface initiator densities. Moreover, the origin of this low MW polymer fraction is proposed to be the termination of growing chains by recombination during the early stages of polymerization, a mechanism confirmed by molecular dynamics simulations of brush polymerization.« less

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations.

PubMed

Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

2012-04-14

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

NASA Astrophysics Data System (ADS)

Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

2012-04-01

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ17-42 protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ17-42 protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ17-42 are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ17-42 protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

Self-assembly of Spherical Macroions in Solution: A Coarse-grained Molecular Dynamics Study

NASA Astrophysics Data System (ADS)

Liu, Zhuonan; Liu, Tianbo; Tsige, Mesfin

2015-03-01

Macroions (such as polyoxometalates) in solution can form a stable hollow spherical super-molecular structure called blackberry when they have moderate surface charge density and size (1-10 nm). Depending on the surface charge density of macroions, the size of the blackberry can be from 20 to more than 100 nm. Other macroions such as dendrimers can also self-assemble into similar super-molecular structure in solution. Existing theories such as Debye-Hückel and DLVO theories cannot explain this phenomenon and we are not aware of any other theory that can explain this. Previous studies using all-atom Molecular Dynamics simulations have shown identical macroions forming oligomers mediated by counterions. Due to the limitations in all-atom simulation and available computational capabilities, these studies handled only small systems with simple macroions, leading to less conclusive but still relevant results on the self-assembly behavior. To overcome these limitations, in this work large-scale coarse-grained modeling of macroions in solution is used. In order to understand the origin of the attractive force that is responsible for the self-assembly of macroions, different types of macroions in different solution conditions are studied. This work was supported by NSF Grant DMR0847580.

Molecular Diagnostics of Fusion and Laboratory Plasmas

NASA Astrophysics Data System (ADS)

Fantz, U.

2005-05-01

The presence of molecules in the cold scrape-off layer of fusion experiments and industrial plasmas requires an understanding of the molecular dynamics in these low temperature plasmas. Suitable diagnostic methods can provide an insight in molecular processes in the plasma volume as well as for plasma surface interactions. A very simple but powerful technique is the molecular emission spectroscopy. Spectra are obtained easily, whereas interpretation might be very complex and relies on the availability of atomic and molecular data. Examples are given for hydrogen plasmas and plasmas with hydrocarbons which both are of importance in industrial applications as well as in fusion experiments.

Interdigitation between Triglycerides and Lipids Modulates Surface Properties of Lipid Droplets.

PubMed

Bacle, Amélie; Gautier, Romain; Jackson, Catherine L; Fuchs, Patrick F J; Vanni, Stefano

2017-04-11

Intracellular lipid droplets (LDs) are the main cellular site of metabolic energy storage. Their structure is unique inside the cell, with a core of esterified fatty acids and sterols, mainly triglycerides and sterol esters, surrounded by a single monolayer of phospholipids. Numerous peripheral proteins, including several that were previously associated with intracellular compartments surrounded by a lipid bilayer, have been recently shown to target the surface of LDs, but how they are able to selectively target this organelle remains largely unknown. Here, we use atomistic and coarse-grained molecular dynamics simulations to investigate the molecular properties of the LD surface and to characterize how it differs from that of a lipid bilayer. Our data suggest that although several surface properties are remarkably similar between the two structures, key differences originate from the interdigitation between surface phospholipids and core neutral lipids that occurs in LDs. This property is extremely sensitive to membrane undulations, unlike in lipid bilayers, and it strongly affects both lipid-packing defects and the lateral pressure profile. We observed a marked change in overall surface properties for surface tensions >10 mN/m, indicative of a bimodal behavior. Our simulations provide a comprehensive molecular characterization of the unique surface properties of LDs and suggest how the molecular properties of the surface lipid monolayer can be modulated by the underlying neutral lipids. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A Surface Science Perspective on TiO2 Photocatalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henderson, Michael A.

2011-06-15

The field of surface science provides a unique approach to understanding bulk, surface and interfacial phenomena occurring during TiO2 photochemistry and photocatalysis. This review highlights, from a surface science perspective, recent literature providing molecular-level insights into phonon-initiated events on TiO2 surfaces obtained in seven key scientific issues: (1) photon absorption, (2) charge transport and trapping, (3) electron transfer dynamics, (4) the adsorbed state, (5) mechanisms, (6) poisons and promoters, and (7) phase and form.

Rapid and Clean Covalent Attachment of Methylsiloxane Polymers and Oligomers to Silica Using B(C6F5)3 Catalysis.

PubMed

Flagg, Daniel H; McCarthy, Thomas J

2017-08-22

The rapid, room-temperature covalent attachment of alkylhydridosilanes (R 3 Si-H) to silicon oxide surfaces to form monolayers using tris(pentafluorophenyl)borane (B(C 6 F 5 ) 3 , BCF) catalysis has recently been described. This method, unlike alternative routes to monolayers, produces only unreactive H 2 gas as a byproduct and reaches completion within minutes. We report the use of this selective reaction between surface silanols and hydridosilanes to prepare surface-grafted poly(dimethylsiloxane)s (PDMSs) with various graft architectures that are controlled by the placement of hydridosilane functionality at one end, both ends, or along the chain of PDMS samples of controlled molecular weight. We also report studies of model methylsiloxane monolayers prepared from pentamethyldisiloxane, heptamethyltrisiloxane (two isomers), heptamethylcyclotetrasiloxane, and tris(trimethylsiloxy)silane. These modified silica surfaces with structurally defined methylsiloxane groups are not accessible by conventional silane surface chemistry and proved to be useful in exploring the steric limitations of the reaction. Linear monohydride- and dihydride-terminated PDMS-grafted surfaces exhibit increasing thickness and decreasing contact angle hysteresis with increasing molecular weight up to a particular molecular weight value. Above this value, the hysteresis increases with increasing molecular weight of end-grafted polymers. Poly(hydridomethyl-co-dimethylsiloxane)s with varied hydride content (3-100 mol %) exhibit decreasing thickness, decreasing contact angle, and increasing contact angle hysteresis with increasing hydride content. These observations illustrate the importance of molecular mobility in three-phase contact line dynamics on low-hysteresis surfaces. To calibrate our preparative procedure against both monolayers prepared by conventional approaches as well as the recent reports, a series of trialkylsilane (mostly, n-alkyldimethylsilane) monolayers was prepared to determine the reaction time required to achieve the maximum bonding density using dynamic contact angle analysis. Monolayers prepared from hydridosilanes with BCF catalysis have lower bonding densities than those derived from chlorosilanes, and the reactions are more sensitive to alkyl group sterics. This lower bonding density renders greater flexibility to the n-alkyl groups in monolayers and can decrease the contact angle hysteresis.

Molecular simulations of heterogeneous ice nucleation. I. Controlling ice nucleation through surface hydrophilicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cox, Stephen J.; Kathmann, Shawn M.; Slater, B.

2015-05-14

Ice formation is one of the most common and important processes on earth and almost always occurs at the surface of a material. A basic understanding of how the physicochemical properties of a material’s surface affect its ability to form ice has remained elusive. Here, we use molecular dynamics simulations to directly probe heterogeneous ice nucleation at a hexagonal surface of a nanoparticle of varying hydrophilicity. Surprisingly, we find that structurally identical surfaces can both inhibit and promote ice formation and analogous to a chemical catalyst, it is found that an optimal interaction between the surface and the water existsmore » for promoting ice nucleation.We use our microscopic understanding of the mechanism to design a modified surface in silico with enhanced ice nucleating ability. C 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.« less

Advances in modelling of biomimetic fluid flow at different scales

PubMed Central

2011-01-01

The biomimetic flow at different scales has been discussed at length. The need of looking into the biological surfaces and morphologies and both geometrical and physical similarities to imitate the technological products and processes has been emphasized. The complex fluid flow and heat transfer problems, the fluid-interface and the physics involved at multiscale and macro-, meso-, micro- and nano-scales have been discussed. The flow and heat transfer simulation is done by various CFD solvers including Navier-Stokes and energy equations, lattice Boltzmann method and molecular dynamics method. Combined continuum-molecular dynamics method is also reviewed. PMID:21711847

Edge cracks in nickel and aluminium single crystals: A molecular dynamics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandra, Sagar, E-mail: sagarc@barc.gov.in; Chavan, V. M.; Patel, R. J.

A molecular dynamics study of edge cracks in Ni and Al single crystals under mode-I loading conditions is presented. Simulations are performed using embedded-atom method potentials for Ni and Al at a temperature of 0.5 K. The results reveal that Ni and Al show different fracture mechanisms. Overall failure behavior of Ni is brittle, while fracture in Al proceeds through void nucleation and coalescence with a zig-zag pattern of crack growth. The qualitative nature of results is discussed in the context of vacancy-formation energies and surface energies of the two FCC metals.

Fundamental data on the desorption of pure interstellar ices

NASA Astrophysics Data System (ADS)

Brown, Wendy A.; Bolina, Amandeep S.

2007-01-01

The desorption of molecular ices from grain surfaces is important in a number of astrophysical environments including dense molecular clouds, cometary nuclei and the surfaces and atmospheres of some planets. With this in mind, we have performed a detailed investigation of the desorption of pure water, pure methanol and pure ammonia ices from a model dust-grain surface. We have used these results to determine the desorption energy, order of desorption and the pre-exponential factor for the desorption of these molecular ices from our model surface. We find good agreement between our desorption energies and those determined previously; however, our values for the desorption orders, and hence also the pre-exponential factors, are different to those reported previously. The kinetic parameters derived from our data have been used to model desorption on time-scales relevant to astrophysical processes and to calculate molecular residence times, given in terms of population half-life as a function of temperature. These results show the importance of laboratory data for the understanding of astronomical situations whereby icy mantles are warmed by nearby stars and by other dynamical events.

Experiments on the Dynamics of Molecular Processes: a Chronicle of Fifty Years

NASA Astrophysics Data System (ADS)

Boato, Giovanni; Volpi, Gian Gualberto

1999-10-01

This paper reviews the way in which, in the Italy of the years immediately after World War II, interest in the dynamics of molecular processes was awakened. The narrative begins with the work of a small number of chemists and physicists who, in the initial stage, interacted closely. In the course of the years, their interests diverged and younger people joined the newly formed groups. Even now, after half a century, a common approach can still to be seen regarding how to attack problems and perform experiments. Experimental work is discussed, bringing out the common viewpoint of fields as diverse as mass spectrometry, isotope effects, chemical kinetics, molecular beams, molecule-molecule interactions, molecule-ion interactions, molecule-surface interactions, and plasma chemistry.

Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

NASA Astrophysics Data System (ADS)

Awasthi, Shalini; Nair, Nisanth N.

2017-03-01

Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective variables, which severely limits the predictive power of the enhanced sampling approaches. Here we propose a method called Temperature Accelerated Sliced Sampling (TASS) that combines temperature accelerated molecular dynamics with umbrella sampling and metadynamics to sample the collective variable space in an efficient manner. The presented method can sample a large number of collective variables and is advantageous for controlled exploration of broad and unbound free energy basins. TASS is also shown to achieve quick free energy convergence and is practically usable with ab initio molecular dynamics techniques.

Dispersing Zwitterions into Comb Polymers for Nonviral Transfection: Experiments and Molecular Simulation.

PubMed

Ghobadi, Ahmadreza F; Letteri, Rachel; Parelkar, Sangram S; Zhao, Yue; Chan-Seng, Delphine; Emrick, Todd; Jayaraman, Arthi

2016-02-08

Polymer-based gene delivery vehicles benefit from the presence of hydrophilic groups that mitigate the inherent toxicity of polycations and that provide tunable polymer-DNA binding strength and stable complexes (polyplexes). However, hydrophilic groups screen charge, and as such can reduce cell uptake and transfection efficiency. We report the effect of embedding zwitterionic sulfobetaine (SB) groups in cationic comb polymers, using a combination of experiments and molecular simulations. Ring-opening metathesis polymerization (ROMP) produced comb polymers with tetralysine (K4) and SB pendent groups. Dynamic light scattering, zeta potential measurements, and fluorescence-based experiments, together with coarse-grained molecular dynamics simulations, described the effect of SB groups on the size, shape, surface charge, composition, and DNA binding strength of polyplexes formed using these comb polymers. Experiments and simulations showed that increasing SB composition in the comb polymers decreased polymer-DNA binding strength, while simulations indicated that the SB groups distributed throughout the polyplex. This allows polyplexes to maintain a positive surface charge and provide high levels of gene expression in live cells. Notably, comb polymers with nearly 50 mol % SB form polyplexes that exhibit positive surface charge similarly as polyplexes formed from purely cationic comb polymers, indicating the ability to introduce an appreciable amount of SB functionality without screening surface charge. This integrated simulation-experimental study demonstrates the effectiveness of incorporating zwitterions in polyplexes, while guiding the design of new and effective gene delivery vectors.

Reactive Molecular Dynamics Investigations of Alkoxysilane Sol-Gel and Surface Coating Processes

NASA Astrophysics Data System (ADS)

Deetz, Joshua David

The ability to generate nanostructured materials with tailored morphology or chemistry is of great technological interest. One proven method of generating metal-oxide materials, and chemically modifying metal-oxide surfaces is through the reactions of molecular building blocks known as alkoxysilanes. Alkoxysilanes are a class of chemicals which contain one or more organic alkoxy groups bonded to silicon atoms. Alkoxysilane (Si-O-R) chemical groups can undergo reactions to form bridges (Si-O-M) with metal oxides. Due to their ability to "attach" to metal-oxides through condensation reactions, alkoxysilanes have a number of interesting applications, such as: the generation of synthetic siloxane materials through the sol-gel process, and the formation of functionalized surface coatings on metal-oxide surfaces. Despite widespread study of sol-gel and surface coatings processes, it is difficult to predict the morphology of the final products due to the large number of process variables involved, such as precursor molecule structure, solvent effects, solution composition, temperature, and pH. To determine the influence of these variables on the products of sol-gel and coatings processes reactive molecular dynamics simulations are used. A reactive force field was used (ReaxFF) to allow the chemical bonds in simulation to dynamically form and break. The force field parameters were optimized using a parallel optimization scheme with a combination of experimental information, and density functional theory calculations. Polycondensation of alkoxysilanes in mixtures of alcohol and water were studied. Steric effects were observed to influence the rates of hydrolysis and condensation in solutions containing different precursor monomers. By restricting the access of nucleophiles to the central silicon atom, the nucleation rate of siloxanes can be controlled. The influence of solution precursor, water, and methanol composition on reaction rates was explored. It was determined that the rate of alkoxysilane hydrolysis is strongly dependent on the concentration of water. The dynamics of siloxane cluster formation are revealed, which provides insight for experimentalists. The silanization of hydroxylated silica surfaces by alkoxysilanes was modeled in pseudo-infinite liquid solution. Butyl-, octyl-, or dodecylsilanes were exposed to hydroxylated silica surfaces in order to observe the influence of silyl headgroup size on the morphology and formation kinetics of silane films on silica substrates. The radius of gyration and order parameter of the hydrocarbon silyl groups were found to increase with grafting density. This was the first simulation study of the dynamic grafting of alkoxysilanes to a substrate.

PREFACE: Dynamics of wetting Dynamics of wetting

NASA Astrophysics Data System (ADS)

Grest, Gary S.; Oshanin, Gleb; Webb, Edmund B., III

2009-11-01

Capillary phenomena associated with fluids wetting other condensed matter phases have drawn great scientific interest for hundreds of years; consider the recent bicentennial celebration of Thomas Young's paper on equilibrium contact angles, describing the geometric shape assumed near a three phase contact line in terms of the relevant surface energies of the constituent phases [1]. Indeed, nearly a century has passed since the seminal papers of Lucas and Washburn, describing dynamics of capillary imbibition [2, 3]. While it is generally appreciated that dynamics of fluid wetting processes are determined by the degree to which a system is out of capillary equilibrium, myriad complications exist that challenge the fundamental understanding of dynamic capillary phenomena. The topic has gathered much interest from recent Nobel laureate Pierre-Gilles de Gennes, who provided a seminal review of relevant dissipation mechanisms for fluid droplets spreading on solid surfaces [4] Although much about the dynamics of wetting has been revealed, much remains to be learned and intrinsic technological and fundamental interest in the topic drives continuing high levels of research activity. This is enabled partly by improved experimental capabilities for resolving wetting processes at increasingly finer temporal, spatial, and chemical resolution. Additionally, dynamic wetting research advances via higher fidelity computational modeling capabilities, which drive more highly refined theory development. The significance of this topic both fundamentally and technologically has resulted in a number of reviews of research activity in wetting dynamics. One recent example addresses the evaluation of existing wetting dynamics theories from an experimentalist's perspective [5]. A Current Opinion issue was recently dedicated to high temperature capillarity, including dynamics of high temperature spreading [6]. New educational tools have recently emerged for providing instruction in wetting dynamics and the broader field of fluid dynamics [7-9]. Such an active field requires an occasional collective examination of current research to highlight both recent successes and remaining challenges. Herein, we have collected a range of articles to illustrate the broad nature of research associated with understanding dynamics of moving condensed matter three phase contact lines. Despite the breadth of topics examined, certain unifying themes emerge. The role of the substrate surface is critical in determining kinetics of wetting; this is evidenced by the attention given to this in articles herein. McHale et al investigate the role of surface topography on wetting kinetics and how its effect can be incorporated in existing theories describing contact line dynamics. Moosavi et al examine surface topography effects via a mesoscopic hydrodynamics approach. The capillary driven motion of fluid through structures on a surface bears tremendous importance for microfluidics studies and the emerging field of nanofluidics. Blow et al examine this phenomena for liquid imbibition into a geometric array of structures on a solid surface, while Shen et al analyze the effects of surface temperature during boiling and non-boiling conditionson droplet impingement dynamics. Finally, Pesika et al discover a wonderful world of smart surfaces, like gecko adhesion pads. A number of papers utilize computational modeling to explore phenomena underlying wetting dynamics and to consider relevant mechanisms in terms of existing theory for contact line dynamics. Winter et al utilize Monte Carlo simulation techniques and thermodynamic integration methods to test classical theory describing heterogeneous nucleation at a wall near a wetting transition. Qian et al briefly review the Onsager principle of minimum energy dissipation underlying many descriptions of dissipative systems; they then provide a variational approach description of hydrodynamics of moving contact lines and demonstrate the validity of their continuum model via comparison with molecular dynamics simulations.Bertrand et al use large scale molecular dynamics simulations to examine fundamental questions about wetting dynamics and how they depend upon interactions between a liquid drop and solid substrate; in particular, atomic scale mechanisms directly associated with the molecular kinetic theory of wetting are observed and quantified. Sun et al explore, by molecular dynamics simulations, atomistic mechanisms of high temperature contact line advancement for a rapidly spreading liquid droplet. Starov et al discuss general aspects of surface forces and wetting phenomena, while Courbin et al present anoverview of diverse dynamical processes ranging from inertial spreading to viscous imbibition. Mukhopadhyay et al examine the effect of Marangoni and centrifugal forces on the wetting dynamics of thin liquid films and drops. Willis et al analyze an enhanced droplet spreading due to thermal fluctuations. How wetting and contact line dynamics depend upon the complexity of the structure in the liquid is interesting both academically and technologically; Delabre et al illustrate this with a study of wetting of liquid crystals and the role of molecular scale organization. In addition, Mechkov et al explore this realm by studying post-Tanner spreading for nematic droplets and, in general, post-Tanner spreading of liquid droplets governed by the contact line-tension effects. Liang et al focus on spreading dynamics of power-law fluid droplets, while Wei et al discuss dynamics of wetting in viscous Newtonian and non-Newtonian fluids. Yin et al discuss an important issue of reactive wetting in metal-metal systems. We hope that the articles gathered here will permit readers to understand the wide range of condensed matter systems impacted by wetting kinetics and the many complicating factors that emerge in describing contact line dynamics for realistic materials. We wish to thank all the contributing authors for their effort and support of our endeavour. References [1] Young T 1805 Phil. Trans. R. Soc. A 95 65 [2] Lucas R 1918 Kolloidn. Zh. 23 15 [3] Washburn E W 1921 Phys. Rev. 17 273 [4] de Gennes P G 1985 Rev. Mod. Phys. 57 827 [5] Ralston J, Popescu M and Sedev R 2008 Annu. Rev. Mater. Res.38 23 [6] High Temperature Capillarity Focus Issue 2005 Current Opinion in Solid State and Materials Science 9 149-254 [7] Starov V M, Velarde M G and Radke C J 2007 Wetting and Spreading Dynamics (Boca Raton, FL: CRC Press) [8] Golub J 2008 Phys. Today 61 8 [9] Homsby G M (ed) 2008 Multimedia Fluid Mechanics 2nd edn (New York: Cambridge University Press) (Also see www.efluids.com)

Theoretical vibrational sum-frequency generation spectroscopy of water near lipid and surfactant monolayer interfaces. II. Two-dimensional spectra.

PubMed

Roy, S; Gruenbaum, S M; Skinner, J L

2014-12-14

The structural stability and function of biomolecules is strongly influenced by the dynamics and hydrogen bonding of interfacial water. Understanding and characterizing the dynamics of these water molecules require a surface-sensitive technique such as two-dimensional vibrational sum-frequency generation (2DSFG) spectroscopy. We have combined theoretical 2DSFG calculations with molecular dynamics simulations in order to investigate the dynamics of water near different lipid and surfactant monolayer surfaces. We show that 2DSFG can distinguish the dynamics of interfacial water as a function of the lipid charge and headgroup chemistry. The dynamics of water is slow compared to the bulk near water-zwitterionic and water-anionic interfaces due to conformational constraints on interfacial water imposed by strong phosphate-water hydrogen bonding. The dynamics of water is somewhat faster near water-cationic lipid interfaces as no such constraint is present. Using hydrogen bonding and rotational correlation functions, we characterize the dynamics of water as a function of the distance from the interface between water and zwitterionic lipids. We find that there is a transition from bulk-like to interface-like dynamics approximately 7 Å away from a zwitterionic phosphatidylcholine monolayer surface.

Organization of Single Molecule Magnets on Surfaces

NASA Astrophysics Data System (ADS)

Sessoli, Roberta

2006-03-01

The field of magnetic molecular clusters showing slow relaxation of the magnetization has attracted a great interest for the spectacular quantum effects in the dynamics of the magnetization that range from resonant quantum tunneling to topological interferences. Recently these systems, known as Single Molecule Magnets (SMMs), have also been proposed as model systems for the investigation of flame propagation in flammable substances. A renewed interest in SMMs also comes from the possibility to exploit their rich and complex magnetic behavior in nano-spintronics. However, at the crystalline state these molecular materials are substantially insulating. They can however exhibit significant transport properties if the conduction occurs through one molecule connected to two metal electrodes, or through a tunneling mechanism when the SMM is grafted on a conducting surface, as occurs in scanning tunnel microscopy experiments. Molecular compounds can be organized on surfaces thanks to the self assembly technique that exploits the strong affinity of some groups for the surface, e.g. thiols for gold surfaces. However the deposition of large molecules mainly comprising relatively weak coordinative bonds is far from trivial. Several different approaches have started to be investigated. We will briefly review here the strategies developed in a collaboration between the Universities of Florence and Modena. Well isolated molecules on Au(111) surfaces have been obtained with sub-monolayer coverage and different spacers. Organization on a large scale of micrometric structures has been obtained thanks to micro-contact printing. The magnetic properties of the grafted molecules have been investigated through magneto-optical techniques and the results show a significant change in the magnetization dynamics whose origin is still object of investigations.

Structure of a tethered polymer under flow using molecular dynamics and hybrid molecular-continuum simulations

NASA Astrophysics Data System (ADS)

Delgado-Buscalioni, Rafael; Coveney, Peter V.

2006-03-01

We analyse the structure of a single polymer tethered to a solid surface undergoing a Couette flow. We study the problem using molecular dynamics (MD) and hybrid MD-continuum simulations, wherein the polymer and the surrounding solvent are treated via standard MD, and the solvent flow farther away from the polymer is solved by continuum fluid dynamics (CFD). The polymer represents a freely jointed chain (FJC) and is modelled by Lennard-Jones (LJ) beads interacting through the FENE potential. The solvent (modelled as a LJ fluid) and a weakly attractive wall are treated at the molecular level. At large shear rates the polymer becomes more elongated than predicted by existing theoretical scaling laws. Also, along the normal-to-wall direction the structure observed for the FJC is, surprisingly, very similar to that predicted for a semiflexible chain. Comparison with previous Brownian dynamics simulations (which exclude both solvent and wall potential) indicates that these effects are due to the polymer-solvent and polymer-wall interactions. The hybrid simulations are in perfect agreement with the MD simulations, showing no trace of finite size effects. Importantly, the extra cost required to couple the MD and CFD domains is negligible.

Multi-scale modeling to relate Be surface temperatures, concentrations and molecular sputtering yields

NASA Astrophysics Data System (ADS)

Lasa, Ane; Safi, Elnaz; Nordlund, Kai

2015-11-01

Recent experiments and Molecular Dynamics (MD) simulations show erosion rates of Be exposed to deuterium (D) plasma varying with surface temperature and the correlated D concentration. Little is understood how these three parameters relate for Be surfaces, despite being essential for reliable prediction of impurity transport and plasma facing material lifetime in current (JET) and future (ITER) devices. A multi-scale exercise is presented here to relate Be surface temperatures, concentrations and sputtering yields. Kinetic Monte Carlo (MC) code MMonCa is used to estimate equilibrium D concentrations in Be at different temperatures. Then, mixed Be-D surfaces - that correspond to the KMC profiles - are generated in MD, to calculate Be-D molecular erosion yields due to D irradiation. With this new database implemented in the 3D MC impurity transport code ERO, modeling scenarios studying wall erosion, such as RF-induced enhanced limiter erosion or main wall surface temperature scans run at JET, can be revisited with higher confidence. Work supported by U.S. DOE under Contract DE-AC05-00OR22725.

Study of ice cluster impacts on amorphous silica using the ReaxFF reactive force field molecular dynamics simulation method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rahnamoun, A.; Duin, A. C. T. van

We study the dynamics of the collisions between amorphous silica structures and amorphous and crystal ice clusters with impact velocities of 1 km/s, 4 km/s, and 7 km/s using the ReaxFF reactive molecular dynamics simulation method. The initial ice clusters consist of 150 water molecules for the amorphous ice cluster and 128 water molecules for the crystal ice cluster. The ice clusters are collided on the surface of amorphous fully oxidized and suboxide silica. These simulations show that at 1 km/s impact velocities, all the ice clusters accumulate on the surface and at 4 km/s and 7 km/s impact velocities, some of the ice cluster moleculesmore » bounce back from the surface. At 4 km/s and 7 km/s impact velocities, few of the water molecules dissociations are observed. The effect of the second ice cluster impacts on the surfaces which are fully covered with ice, on the mass loss/accumulation is studied. These studies show that at 1 km/s impacts, the entire ice cluster accumulates on the surface at both first and second ice impacts. At higher impact velocities, some ice molecules which after the first ice impacts have been attached to the surface will separate from the surface after the second ice impacts at 7 km/s impact velocity. For the 4 km/s ice cluster impact, ice accumulation is observed for the crystal ice cluster impacts and ice separation is observed for the amorphous ice impacts. Observing the temperatures of the ice clusters during the collisions indicates that the possibility of electron excitement at impact velocities less than 10 km/s is minimal and ReaxFF reactive molecular dynamics simulation can predict the chemistry of these hypervelocity impacts. However, at impact velocities close to 10 km/s the average temperature of the impacting ice clusters increase to about 2000 K, with individual molecules occasionally reaching temperatures of over 8000 K and thus it will be prudent to consider the concept of electron excitation at these higher impact velocities, which goes beyond the current ReaxFF ability.« less

Molecular dynamics simulations study of nano bubble attachment at hydrophobic surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Jiaqi; Dang, Liem X.; Miller, Jan D.

Bubble attachment phenomena are examined using Molecular Dynamics Simulations (MDS) for the first time. The simulation involves a nitrogen nano bubble containing 906 nitrogen molecules in a water phase with 74,000 water molecules at molybdenite surfaces. During a simulation period of 1 ns, film rupture and displacement occurs. The attached nanobubble at the hydrophobic molybdenite face surface results in a contact angle of about 90º. This spontaneous attachment is due to a “water exclusion zone” at the molybdenite face surface and can be explained by a van der Waals (vdW) attractive force, as discussed in the literature. In contrast, themore » film is stable at the hydrophilic quartz (001) surface and the bubble does not attach. Contact angles determined from MD simulations are reported, and these results agree well with experimental and MDS sessile drop results. In this way, film stability and bubble attachment are described with respect to interfacial water structure for surfaces of different polarity. Interfacial water molecules at the hydrophobic molybdenite face surface have relatively weak interactions with the surface when compared to the hydrophilic quartz (001) surface, as revealed by the presence of a 3 Å “water exclusion zone” at the molybdenite/water interface. The molybdenite armchair-edge and zigzag-edge surfaces show a comparably slow process for film rupture and displacement when compared to the molybdenite face surface, which is consistent with their relatively weak hydrophobic character.« less

Molecular mobility of nematic E7 confined to molecular sieves with a low filling degree.

PubMed

Brás, A R; Frunza, S; Guerreiro, L; Fonseca, I M; Corma, A; Frunza, L; Dionísio, M; Schönhals, A

2010-06-14

The nematic liquid crystalline mixture E7 was confined with similar filling degrees to molecular sieves with constant composition but different pore diameters (from 2.8 to 6.8 nm). Fourier transform infrared analysis proved that the E7 molecules interact via the cyanogroup with the pore walls of the molecular sieves. The molecular dynamics of the system was investigated by broadband dielectric spectroscopy (10(-2)-10(9) Hz) covering a wide temperature range of approximately 200 K from temperatures well above the isotropic-nematic transition down to the glass transition of bulk E7. A variety of relaxation processes is observed including two modes that are located close to the bulk behavior in its temperature dependence. For all confined samples, two relaxation processes, at frequencies lower than the processes observed for the bulk, were detected. At lower temperatures, their relaxation rates have different temperature dependencies whereas at higher temperatures, they seem to collapse into one chart. The temperature dependence of the slowest process (S-process) obeys the Vogel-Fulcher-Tammann law indicating a glassy dynamics of the E7 molecules anchored to the pore surface. The pore size dependence of both the Vogel temperature and fragility revealed a steplike transition around 4 nm pore size, which indicates a transition from a strong to a fragile behavior. The process with a relaxation rate in between the bulklike and the S-process (I-process) shows no dependence on the pore size. The agreement of the I-process with the behavior of a 5CB surface layer adsorbed on nonporous silica leads to the assignment of E7 molecules anchored at the outer surface of the microcrystals of the molecular sieves.

Molecular Dynamics Modeling of Ionic Liquids in Electrospray Propulsion

DTIC Science & Technology

2010-06-01

surface equipotential and a correspondes to the model sphere radius. It can also see that the applied voltage is necessary to obtain the surface ...between the tip and extractor, the equipotential line whose angle relative to the x axis is approximately 49 degrees is selected as the Taylor cone surface ...model. Then the electric field on such equipotential line is found by equation 7.5 and used for the distribution along the cone surface . This

Molecular-dynamics simulations of self-assembled monolayers (SAM) on parallel computers

NASA Astrophysics Data System (ADS)

Vemparala, Satyavani

The purpose of this dissertation is to investigate the properties of self-assembled monolayers, particularly alkanethiols and Poly (ethylene glycol) terminated alkanethiols. These simulations are based on realistic interatomic potentials and require scalable and portable multiresolution algorithms implemented on parallel computers. Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing and molecular chain-length. Results show that the alkanethiol chains tilt from the surface normal by a collective angle of 25° along next-nearest neighbor direction at 300K. At 350K the system transforms to a disordered phase characterized by small tilt angle, flexible tilt direction, and random distribution of backbone planes. With increasing lattice spacing, a, the tilt angle increases rapidly from a nearly zero value at a = 4.7A to as high as 34° at a = 5.3A at 300K. We also studied the effect of end groups on the tilt structure of SAM films. We characterized the system with respect to temperature, the alkane chain length, lattice spacing, and the length of the end group. We found that the gauche defects were predominant only in the tails, and the gauche defects increased with the temperature and number of EG units. Effect of electric field on the structure of poly (ethylene glycol) (PEG) terminated alkanethiol self assembled monolayer (SAM) on gold has been studied using parallel molecular dynamics method. An applied electric field triggers a conformational transition from all-trans to a mostly gauche conformation. The polarity of the electric field has a significant effect on the surface structure of PEG leading to a profound effect on the hydrophilicity of the surface. The electric field applied anti-parallel to the surface normal causes a reversible transition to an ordered state in which the oxygen atoms are exposed. On the other hand, an electric field applied in a direction parallel to the surface normal introduces considerable disorder in the system and the oxygen atoms are buried inside.

Copper(II) adsorption on the kaolinite(001) surface: Insights from first-principles calculations and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Kong, Xiang-Ping; Wang, Juan

2016-12-01

The adsorption behavior of Cu(II) on the basal hydroxylated kaolinite(001) surface in aqueous environment was investigated by first-principles calculations and molecular dynamics simulations. Structures of possible monodentate and bidentate inner-sphere adsorption complexes of Cu(II) were examined, and the charge transfer and bonding mechanism were analyzed. Combining the binding energy of complex, the radial distribution function of Cu(II) with oxygen and the extended X-ray absorption fine structure data, monodentate complex on site of surface oxygen with ;upright; hydrogen and bidentate complex on site of two oxygens (one with ;upright; hydrogen and one with ;lying; hydrogen) of single Al center have been found to be the major adsorption species of Cu(II). Both adsorption species are four-coordinated with a square planar geometry. The distribution of surface hydroxyls with ;lying; hydrogen around Cu(II) plays a key role in the structure and stability of adsorption complex. Upon the Mulliken population analysis and partial density of states, charge transfer occurs with Cu(II) accepting some electrons from both surface oxygens and aqua oxygens, and the bonding Cu 3d-O 2p state filling is primarily responsible for the strong covalent interaction of Cu(II) with surface oxygen.

Lead and selenite adsorption at water–goethite interfaces from first principles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leung, Kevin; Criscenti, Louise J.

Here, the complexation of toxic and/or radioactive ions on to mineral surfaces is an important topic in geochemistry. We apply periodic-boundary-conditions density functional theory (DFT) molecular dynamics simulations to examine the coordination of Pb(II),more » $${\\rm SeO}_3^{2-}$$ , and their contact ion pairs to goethite (1 0 1) and (2 1 0) surfaces. The multitude of Pb(II) adsorption sites and possibility of Pb(II)-induced FeOH deprotonation make this a complex problem. At surface sites where Pb(II) is coordinated to three FeO and/or FeOH groups, and with judicious choices of FeOH surface group protonation states, the predicted Fe–Pb distances are in good agreement with EXAFS measurements. Trajectories where Pb(II) is in part coordinated to only two surface Fe–O groups exhibit larger fluctuations in Pb–O distances. Pb(II)/$${\\rm SeO}_3^{2-}$$ contact ion pairs are at least metastable on goethite (2 1 0) surfaces if the $${\\rm SeO}_3^{2-}$$ has a monodentate Se–O–Fe bond. Our DFT-based molecular dynamics calculations are a prerequisite for calculations of finite temperature equilibrium binding constants of Pb(II) and Pb(II)/$${\\rm SeO}_3^{2-}$$ ion pairs to goethite adsorption sites.« less

Lead and selenite adsorption at water–goethite interfaces from first principles

DOE PAGES

Leung, Kevin; Criscenti, Louise J.

2017-08-04

Here, the complexation of toxic and/or radioactive ions on to mineral surfaces is an important topic in geochemistry. We apply periodic-boundary-conditions density functional theory (DFT) molecular dynamics simulations to examine the coordination of Pb(II),more » $${\\rm SeO}_3^{2-}$$ , and their contact ion pairs to goethite (1 0 1) and (2 1 0) surfaces. The multitude of Pb(II) adsorption sites and possibility of Pb(II)-induced FeOH deprotonation make this a complex problem. At surface sites where Pb(II) is coordinated to three FeO and/or FeOH groups, and with judicious choices of FeOH surface group protonation states, the predicted Fe–Pb distances are in good agreement with EXAFS measurements. Trajectories where Pb(II) is in part coordinated to only two surface Fe–O groups exhibit larger fluctuations in Pb–O distances. Pb(II)/$${\\rm SeO}_3^{2-}$$ contact ion pairs are at least metastable on goethite (2 1 0) surfaces if the $${\\rm SeO}_3^{2-}$$ has a monodentate Se–O–Fe bond. Our DFT-based molecular dynamics calculations are a prerequisite for calculations of finite temperature equilibrium binding constants of Pb(II) and Pb(II)/$${\\rm SeO}_3^{2-}$$ ion pairs to goethite adsorption sites.« less

Mass-velocity and size-velocity distributions of ejecta cloud from shock-loaded tin surface using large scale molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Durand, Olivier; Soulard, Laurent

2015-06-01

The mass (volume and areal densities) versus velocity as well as the size versus velocity distributions of a shock-induced cloud of particles are investigated using large scale molecular dynamics (MD) simulations. A generic 3D tin crystal with a sinusoidal free surface roughness is set in contact with vacuum and shock-loaded so that it melts directly on shock. At the reflection of the shock wave onto the perturbations of the free surface, 2D sheets/jets of liquid metal are ejected. The simulations show that the distributions may be described by an analytical model based on the propagation of a fragmentation zone, from the tip of the sheets to the free surface, within which the kinetic energy of the atoms decreases as this zone comes closer to the free surface on late times. As this kinetic energy drives (i) the (self-similar) expansion of the zone once it has broken away from the sheet and (ii) the average size of the particles which result from fragmentation in the zone, the ejected mass and the average size of the particles progressively increase in the cloud as fragmentation occurs closer to the free surface. Though relative to nanometric scales, our model reproduces quantitatively experimental profiles and may help in their analysis.

Solvent Exchange Leading to Nanobubble Nucleation: A Molecular Dynamics Study

PubMed Central

2017-01-01

The solvent exchange procedure has become the most-used protocol to produce surface nanobubbles, while the molecular mechanisms behind the solvent exchange are far from being fully understood. In this paper, we build a simple model and use molecular dynamics simulations to investigate the dynamic characteristics of solvent exchange for producing nanobubbles. We find that at the first stage of solvent exchange, there exists an interface between interchanging solvents of different gas solubility. This interface moves toward the substrate gradually as the exchange process proceeds. Our simulations reveal directed diffusion of gas molecules against the gas concentration gradient, driven by the solubility gradient of the liquid composition across the moving solvent–solvent interface. It is this directed diffusion that causes gas retention and produces a local gas oversaturation much higher near the substrate than far from it. At the second stage of solvent exchange, the high local gas oversaturation leads to bubble nucleation either on the solid surface or in the bulk solution, which is found to depend on the substrate hydrophobicity and the degree of local gas oversaturation. Our findings suggest that solvent exchange could be developed into a standard procedure to produce oversaturation and used to a variety of nucleation applications other than generating nanobubbles. PMID:28742364

Influence of the size and charge of gold nanoclusters on complexation with siRNA: a molecular dynamics simulation study.

PubMed

Mudedla, Sathish Kumar; Azhagiya Singam, Ettayapuram Ramaprasad; Balamurugan, Kanagasabai; Subramanian, Venkatesan

2015-11-11

The complexation of small interfering RNA (siRNA) with positively charged gold nanoclusters has been studied in the present investigation with the help of classical molecular dynamics and steered molecular dynamics simulations accompanied by free energy calculations. The results show that gold nanoclusters form a stable complex with siRNA. The wrapping of siRNA around the gold nanocluster depends on the size and charge on the surface of the gold cluster. The binding pattern of the gold nanocluster with siRNA is also influenced by the presence of another cluster. The interaction between the positively charged amines in the gold nanocluster and the negatively charged phosphate group in the siRNA is responsible for the formation of complexes. The binding free energy value increases with the size of the gold cluster and the number of positive charges present on the surface of the gold nanocluster. The results reveal that the binding energy of small gold nanoclusters increases in the presence of another gold nanocluster while the binding of large gold nanoclusters decreases due to the introduction of another gold nanocluster. Overall, the findings have clearly demonstrated the effect of size and charge of gold nanoclusters on their interaction pattern with siRNA.

Prediction of purification of biopharmeceuticals with molecular dynamics

NASA Astrophysics Data System (ADS)

Ustach, Vincent; Faller, Roland

Purification of biopharmeceuticals remains the most expensive part of protein-based drug production. In ion exchange chromatography (IEX), prediction of the elution ionic strength of host cell and target proteins has the potential to reduce the parameter space for scale-up of protein production. The complex shape and charge distribution of proteins and pores complicates predictions of the interactions in these systems. All-atom molecular dynamics methods are beyond the scope of computational limits for mass transport regimes. We present a coarse-grained model for proteins for prediction of elution pH and ionic strength. By extending the raspberry model for colloid particles to surface shapes and charge distributions of proteins, we can reproduce the behavior of proteins in IEX. The average charge states of titratatable amino acid residues at relevant pH values are determined by extrapolation from all-atom molecular dynamics at pH 7. The pH specific all-atom electrostatic field is then mapped onto the coarse-grained surface beads of the raspberry particle. The hydrodynamics are reproduced with the lattice-Boltzmann scheme. This combination of methods allows very long simulation times. The model is being validated for known elution procedures by comparing the data with experiments. Defense Threat Reduction Agency (Grant Number HDTRA1-15-1-0054).

Multi-scale strategies for dealing with moving contact lines

NASA Astrophysics Data System (ADS)

Smith, Edward R.; Theodorakis, Panagiotis; Craster, Richard V.; Matar, Omar K.

2017-11-01

Molecular dynamics (MD) has great potential to elucidate the dynamics of the moving contact line. As a more fundamental model, it can provide a priori results for fluid-liquid interfaces, surface tension, viscosity, phase change, and near wall stick-slip behaviour which typically show very good agreement to experimental results. However, modelling contact line motion combines all this complexity in a single problem. In this talk, MD simulations of the contact line are compared to the experimental results obtained from studying the dynamics of a sheared liquid bridge. The static contact angles are correctly matched to the experimental data for a range of different electro-wetting results. The moving contact line results are then compared for each of these electro-wetting values. Despite qualitative agreement, there are notable differences between the simulation and experiments. Many MD simulation have studied contact lines, and the sheared liquid bridge, so it is of interest to review the limitations of this setup in light of this discrepancy. A number of factors are discussed, including the inter-molecular interaction model, molecular-scale surface roughness, model of electro-wetting and, perhaps most importantly, the limited system sizes possible using MD simulation. EPSRC, UK, MEMPHIS program Grant (EP/K003976/1), RAEng Research Chair (OKM).

Molecular simulations of heterogeneous ice nucleation. II. Peeling back the layers.

PubMed

Cox, Stephen J; Kathmann, Shawn M; Slater, Ben; Michaelides, Angelos

2015-05-14

Coarse grained molecular dynamics simulations are presented in which the sensitivity of the ice nucleation rate to the hydrophilicity of a graphene nanoflake is investigated. We find that an optimal interaction strength for promoting ice nucleation exists, which coincides with that found previously for a face centered cubic (111) surface. We further investigate the role that the layering of interfacial water plays in heterogeneous ice nucleation and demonstrate that the extent of layering is not a good indicator of ice nucleating ability for all surfaces. Our results suggest that to be an efficient ice nucleating agent, a surface should not bind water too strongly if it is able to accommodate high coverages of water.

Free energy profiles from single-molecule pulling experiments.

PubMed

Hummer, Gerhard; Szabo, Attila

2010-12-14

Nonequilibrium pulling experiments provide detailed information about the thermodynamic and kinetic properties of molecules. We show that unperturbed free energy profiles as a function of molecular extension can be obtained rigorously from such experiments without using work-weighted position histograms. An inverse Weierstrass transform is used to relate the system free energy obtained from the Jarzynski equality directly to the underlying molecular free energy surface. An accurate approximation for the free energy surface is obtained by using the method of steepest descent to evaluate the inverse transform. The formalism is applied to simulated data obtained from a kinetic model of RNA folding, in which the dynamics consists of jumping between linker-dominated folded and unfolded free energy surfaces.

Hamiltonian flow over saddles for exploring molecular phase space structures

NASA Astrophysics Data System (ADS)

Farantos, Stavros C.

2018-03-01

Despite using potential energy surfaces, multivariable functions on molecular configuration space, to comprehend chemical dynamics for decades, the real happenings in molecules occur in phase space, in which the states of a classical dynamical system are completely determined by the coordinates and their conjugate momenta. Theoretical and numerical results are presented, employing alanine dipeptide as a model system, to support the view that geometrical structures in phase space dictate the dynamics of molecules, the fingerprints of which are traced by following the Hamiltonian flow above saddles. By properly selecting initial conditions in alanine dipeptide, we have found internally free rotor trajectories the existence of which can only be justified in a phase space perspective. This article is part of the theme issue `Modern theoretical chemistry'.

Communication: Energy transfer and reaction dynamics for DCl scattering on Au(111): An ab initio molecular dynamics study.

PubMed

Kolb, Brian; Guo, Hua

2016-07-07

Scattering and dissociative chemisorption of DCl on Au(111) are investigated using ab initio molecular dynamics with a slab model, in which the top two layers of Au are mobile. Substantial kinetic energy loss in the scattered DCl is found, but the amount of energy transfer is notably smaller than that observed in the experiment. On the other hand, the dissociative chemisorption probability reproduces the experimental trend with respect to the initial kinetic energy, but is about one order of magnitude larger than the reported initial sticking probability. While the theory-experiment agreement is significantly improved from the previous rigid surface model, the remaining discrepancies are still substantial, calling for further scrutiny in both theory and experiment.

Effect of Surface Oxidation on Interfacial Water Structure at a Pyrite (100) Surface as Studied by Molecular Dynamics Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.

2015-06-01

In the first part of this paper, a Scanning Electron Microscopy and contact angle study of a pyrite surface (100) is reported describing the relationship between surface oxidation and the hydrophilic surface state. In addition to these experimental results, the following simulated surface states were examined using Molecular Dynamics Simulation (MDS): fresh unoxidized (100) surface; polysulfide at the (100) surface; elemental sulfur at the (100) surface. Crystal structures for the polysulfide and elemental sulfur at the (100) surface were simulated using Density Functional Theory (DFT) quantum chemical calculations. The well known oxidation mechanism which involves formation of a metal deficientmore » layer was also described with DFT. Our MDS results of the behavior of interfacial water at the fresh and oxidized pyrite (100) surfaces without/with the presence of ferric hydroxide include simulated contact angles, number density distribution for water, water dipole orientation, water residence time, and hydrogen-bonding considerations. The significance of the formation of ferric hydroxide islands in accounting for the corresponding hydrophilic surface state is revealed not only from experimental contact angle measurements but also from simulated contact angle measurements using MDS. The hydrophilic surface state developed at oxidized pyrite surfaces has been described by MDS, on which basis the surface state is explained based on interfacial water structure. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE funded work performed by Liem X. Dang. Battelle operates the Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES.« less

Low-Dimensional Materials for Optoelectronic and Bioelectronic Applications

NASA Astrophysics Data System (ADS)

Hong, Tu

In this thesis, we first discuss the fundamentals of ab initio electronic structure theory and density functional theory (DFT). We also discuss statistics related to computing thermodynamic averages of molecular dynamics (MD). We then use this theory to analyze and compare the structural, dynamical, and electronic properties of liquid water next to prototypical metals including platinum, graphite, and graphene. Our results are built on Born-Oppenheimer molecular dynamics (BOMD) generated using density functional theory (DFT) which explicitly include van der Waals (vdW) interactions within a first principles approach. All calculations reported use large simulation cells, allowing for an accurate treatment of the water-electrode interfaces. We have included vdW interactions through the use of the optB86b-vdW exchange correlation functional. Comparisons with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional are also shown. We find an initial peak, due to chemisorption, in the density profile of the liquid water-Pt interface not seen in the liquid water-graphite interface, liquid watergraphene interface, nor interfaces studied previously. To further investigate this chemisorption peak, we also report differences in the electronic structure of single water molecules on both Pt and graphite surfaces. We find that a covalent bond forms between the single water molecule and the platinum surface, but not between the single water molecule and the graphite surface. We also discuss the effects that defects and dopants in the graphite and graphene surfaces have on the structure and dynamics of liquid water. Lastly, we introduce artificial neural networks (ANNs), and demonstrate how they can be used to machine learn electronic structure calculations. As a proof of principle, we show the success of an ANN potential energy surfaces for a dimer molecule with a Lennard-Jones potential.

A mapping variable ring polymer molecular dynamics study of condensed phase proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Pierre, Sadrach; Duke, Jessica R.; Hele, Timothy J. H.; Ananth, Nandini

2017-12-01

We investigate the mechanisms of condensed phase proton-coupled electron transfer (PCET) using Mapping-Variable Ring Polymer Molecular Dynamics (MV-RPMD), a recently developed method that employs an ensemble of classical trajectories to simulate nonadiabatic excited state dynamics. Here, we construct a series of system-bath model Hamiltonians for the PCET, where four localized electron-proton states are coupled to a thermal bath via a single solvent mode, and we employ MV-RPMD to simulate state population dynamics. Specifically, for each model, we identify the dominant PCET mechanism, and by comparing against rate theory calculations, we verify that our simulations correctly distinguish between concerted PCET, where the electron and proton transfer together, and sequential PCET, where either the electron or the proton transfers first. This work represents a first application of MV-RPMD to multi-level condensed phase systems; we introduce a modified MV-RPMD expression that is derived using a symmetric rather than asymmetric Trotter discretization scheme and an initialization protocol that uses a recently derived population estimator to constrain trajectories to a dividing surface. We also demonstrate that, as expected, the PCET mechanisms predicted by our simulations are robust to an arbitrary choice of the initial dividing surface.

Interactions between Ether Phospholipids and Cholesterol as Determined by Scattering and Molecular Dynamics Simulations

PubMed Central

Pan, Jianjun; Cheng, Xiaolin; Heberle, Frederick A.; Mostofian, Barmak; Kučerka, Norbert; Drazba, Paul; Katsaras, John

2012-01-01

Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol’s molecular interactions with ether lipids as determined using a combination of small-angle neutron and X-ray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From the analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes, cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts, cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup’s phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules. PMID:23199292

Study of lysozyme mobility and binding free energy during adsorption on a graphene surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakano, C. Masato; Ma, Heng; Wei, Tao, E-mail: twei@lamar.edu

Understanding protein adsorption is a key to the development of biosensors and anti-biofouling materials. Hydration essentially controls the adsorption process on hydrophobic surfaces, but its effect is complicated by various factors. Here, we present an ideal model system to isolate hydration effects—lysozyme adsorption on a flat hydrophobic graphene surface. Our all-atom molecular dynamics and molecular-mechanics/Poisson-Boltzmann surface area computation study reveal that lysozyme on graphene displays much larger diffusivity than in bulk water. Protein's hydration free energy within the first hydration shell is dominated by the protein-water electrostatic interactions and acts as an energy barrier for protein adsorption. On the othermore » hand, the surface tension, especially that from the hydrophobic graphene, can effectively weaken the barrier to promote adsorption.« less

Collective effects of torsion in FtsZ filaments

NASA Astrophysics Data System (ADS)

González de Prado Salas, Pablo; Tarazona, Pedro

2016-04-01

Recent evidence points to the presence of torsion in FtsZ bonds. In addition, experiments with FtsZ mutants on surfaces resulted in new aggregates that cannot be explained by older models for FtsZ dynamics. We use an interaction model for FtsZ derived from molecular dynamics simulations and expand a fine-grained lattice model used to describe FtsZ aggregates on a surface. This new model includes different anchoring angles for the monomers and allows bond twist, two ingredients that oppose each other resulting in a more dynamic and interesting system. We study the role and importance of these conflicting elements and how the aggregates are characterized by the different interaction parameters.

Analysis of the morphology, stability, and folding pathways of ring polymers with supramolecular topological constraints using molecular simulation and nonlinear manifold learning

NASA Astrophysics Data System (ADS)

Wang, Jiang; Ferguson, Andrew

Ring polymers offer a wide range of natural and engineered functions and applications, including as circular bacterial DNA, crown ethers for cation chelation, and ``molecular machines'' such as mechanical nanoswitches. The morphology and dynamics of ring polymers are governed by the chemistry and degree of polymerization of the ring, and intramolecular and supramolecular topological constraints such as knots or mechanically-interlocked rings. We perform molecular dynamics simulations of polyethylene ring polymers as a function of degree of polymerization and in different topological states, including a knotted state, catenane state (two interlocked rings), and borromean state (three interlocked rings). Applying nonlinear manifold learning to our all-atom simulation trajectories, we extract low-dimensional free energy surfaces governing the accessible conformational states and their relative thermodynamic stability. The free energy surfaces reveal how degree of polymerization and topological constraints affect the thermally accessible conformations, chiral symmetry breaking, and folding and collapse pathways of the rings, and present a means to rationally engineer ring size and topology to preferentially stabilize particular conformational states.

Structural Dynamics of Carbon Dots in Water and N, N-Dimethylformamide Probed by All-Atom Molecular Dynamics Simulations.

PubMed

Paloncýová, Markéta; Langer, Michal; Otyepka, Michal

2018-04-10

Carbon dots (CDs), one of the youngest members of the carbon nanostructure family, are now widely experimentally studied for their tunable fluorescence properties, bleaching resistance, and biocompatibility. Their interaction with biomolecular systems has also been explored experimentally. However, many atomistic details still remain unresolved. Molecular dynamics (MD) simulations enabling atomistic and femtosecond resolutions simultaneously are a well-established tool of computational chemistry which can provide useful insights into investigated systems. Here we present a full procedure for performing MD simulations of CDs. We developed a builder for generating CDs of a desired size and with various oxygen-containing surface functional groups. Further, we analyzed the behavior of various CDs differing in size, surface functional groups, and degrees of functionalization by MD simulations. These simulations showed that surface functionalized CDs are stable in a water environment through the formation of an extensive hydrogen bonding network. We also analyzed the internal dynamics of individual layers of CDs and evaluated the role of surface functional groups on CD stability. We observed that carboxyl groups interconnected the neighboring layers and decreased the rate of internal rotations. Further, we monitored changes in the CD shape caused by an excess of charged carboxyl groups or carbonyl groups. In addition to simulations in water, we analyzed the behavior of CDs in the organic solvent DMF, which decreased the stability of pure CDs but increased the level of interlayer hydrogen bonding. We believe that the developed protocol, builder, and parameters will facilitate future studies addressing various aspects of structural features of CDs and nanocomposites containing CDs.

Non-Adiabatic Molecular Dynamics Methods for Materials Discovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Furche, Filipp; Parker, Shane M.; Muuronen, Mikko J.

2017-04-04

The flow of radiative energy in light-driven materials such as photosensitizer dyes or photocatalysts is governed by non-adiabatic transitions between electronic states and cannot be described within the Born-Oppenheimer approximation commonly used in electronic structure theory. The non-adiabatic molecular dynamics (NAMD) methods based on Tully surface hopping and time-dependent density functional theory developed in this project have greatly extended the range of molecular materials that can be tackled by NAMD simulations. New algorithms to compute molecular excited state and response properties efficiently were developed. Fundamental limitations of common non-linear response methods were discovered and characterized. Methods for accurate computations ofmore » vibronic spectra of materials such as black absorbers were developed and applied. It was shown that open-shell TDDFT methods capture bond breaking in NAMD simulations, a longstanding challenge for single-reference molecular dynamics simulations. The methods developed in this project were applied to study the photodissociation of acetaldehyde and revealed that non-adiabatic effects are experimentally observable in fragment kinetic energy distributions. Finally, the project enabled the first detailed NAMD simulations of photocatalytic water oxidation by titania nanoclusters, uncovering the mechanism of this fundamentally important reaction for fuel generation and storage.« less

Structure and property relations of macromolecular self-assemblies at interfaces

NASA Astrophysics Data System (ADS)

Yang, Zhihao

Hydrophilic polymer chains, poly(ethylene glycol) (PEG), are attached to glass surfaces by silylation of the silanol groups on glass surfaces with the omega-(methoxyl terminated PEG) trimethoxysilanes. These tethered polymer chains resemble the self-assembled monolayers (SAMs) of PEG, which exhibit excellent biocompatibility and provide a model system for studying the interactions of proteins with polymer surfaces. The low molecular weight PEGs tend to extend, forming a brush-like monolayer, whereas the longer polymer chains tend to interpenetrate each other, forming a mushroom-like PEG monolayer at the interface. Interactions between a plasma protein, bovine serum albumin, and the PEG-SAMs are investigated in terms of protein adsorption and diffusion on the surfaces by the technique of fluorescence recovery after photobleaching (FRAP). The diffusion and aggregation behaviors of the protein on the two monolayers are found to be quite different despite the similarities in adsorption and desorption behaviors. The results are analyzed with a hypothesis of the hydrated surface dynamics. A method of covalently bonding phospholipid molecules to silica substrates followed by loading with free phospholipids is demonstrated to form well organized and stable phospholipid self-assembled monolayers. Surfaces of such SAMs structurally mimic the aqueous sides of phospholipid bilayer membranes. The dynamics of phospholipids and an adsorbed protein, lipase, in the SAMs are probed with FRAP, in terms of lateral diffusion of both phospholipids and protein molecules. The esterase activity of lipase on the SAM surfaces is confirmed by the hydrolysis reaction of a substrate, umbelliferone stearate, showing such lipid SAMs posess biomembrane functionality in terms of interfacial activation of the membranous enzymes. Dynamics of polyethylene oxide and polypropylene oxide tri-block copolymers, PEO-PPO-PEO and PPO-PEO-PPO, at the air/water interface upon thermal stimulation is studied by surface light scattering, in terms of the dynamic surface tension changes in response to a temperature jump. The characteristic of the surface tension relaxation is found to be highly related to the molecular structure and concentration of the copolymers at the interface.

Activated recombinative desorption: A potential component in mechanisms of spacecraft glow

NASA Technical Reports Server (NTRS)

Cross, J. B.

1985-01-01

The concept of activated recombination of atomic species on surfaces can explain the production of vibrationally and translationally excited desorbed molecular species. Equilibrium statistical mechanics predicts that the molecular quantum state distributions of desorbing molecules is a function of surface temperature only when the adsorption probability is unity and independent of initial collision conditions. In most cases, the adsorption probability is dependent upon initial conditions such as collision energy or internal quantum state distribution of impinging molecules. From detailed balance, such dynamical behavior is reflected in the internal quantum state distribution of the desorbing molecule. This concept, activated recombinative desorption, may offer a common thread in proposed mechanisms of spacecraft glow. Using molecular beam techniques and equipment available at Los Alamos, which includes a high translational energy 0-atom beam source, mass spectrometric detection of desorbed species, chemiluminescence/laser induced fluorescence detection of electronic and vibrationally excited reaction products, and Auger detection of surface adsorbed reaction products, a fundamental study of the gas surface chemistry underlying the glow process is proposed.

Perfect Composition Depth Profiling of Ionic Liquid Surfaces Using High-resolution RBS/ERDA.

PubMed

Nakajima, Kaoru; Zolboo, Enkhbayar; Ohashi, Tomohiro; Lísal, Martin; Kimura, Kenji

2016-01-01

In order to reveal the surface structures of large molecular ionic liquids (ILs), the near-surface elemental depth distributions of 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C n C 1 Im][Tf 2 N], n = 2, 6, 10) were studied using high-resolution Rutherford backscattering spectroscopy (HRBS) in combination with high-resolution elastic recoil detection analysis (HR-ERDA). The elemental depth profiles of all constituent elements, including hydrogen, were derived from HR-ERDA/HRBS measurements, so that the profiles would reproduce both HR-ERDA and HRBS spectra simultaneously. The derived elemental depth profiles agree with state-of-the-art molecular dynamics simulations, indicating the feasibility of this method. A controversy concerning the preferential orientation of [C 2 C 1 Im] at the surface has been resolved by this new combination analysis; namely, the [C 2 C 1 Im] cation has a preferential orientation with the ethyl chain pointing towards the vacuum in the topmost molecular layer.

Potential-based dynamical reweighting for Markov state models of protein dynamics.

PubMed

Weber, Jeffrey K; Pande, Vijay S

2015-06-09

As simulators attempt to replicate the dynamics of large cellular components in silico, problems related to sampling slow, glassy degrees of freedom in molecular systems will be amplified manyfold. It is tempting to augment simulation techniques with external biases to overcome such barriers with ease; biased simulations, however, offer little utility unless equilibrium properties of interest (both kinetic and thermodynamic) can be recovered from the data generated. In this Article, we present a general scheme that harnesses the power of Markov state models (MSMs) to extract equilibrium kinetic properties from molecular dynamics trajectories collected on biased potential energy surfaces. We first validate our reweighting protocol on a simple two-well potential, and we proceed to test our method on potential-biased simulations of the Trp-cage miniprotein. In both cases, we find that equilibrium populations, time scales, and dynamical processes are reliably reproduced as compared to gold standard, unbiased data sets. We go on to discuss the limitations of our dynamical reweighting approach, and we suggest auspicious target systems for further application.

Multiscale Multiphysics and Multidomain Models I: Basic Theory

PubMed Central

Wei, Guo-Wei

2013-01-01

This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field. PMID:25382892

Multiscale Multiphysics and Multidomain Models I: Basic Theory.

PubMed

Wei, Guo-Wei

2013-12-01

This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field.

Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching.

PubMed

Glowacki, David R; Rodgers, W J; Shannon, Robin; Robertson, Struan H; Harvey, Jeremy N

2017-04-28

The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH 3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'. © 2017 The Authors.

Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching

PubMed Central

Rodgers, W. J.; Shannon, Robin; Robertson, Struan H.; Harvey, Jeremy N.

2017-01-01

The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at ‘hotspots’ that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’. PMID:28320908

Quantum Tunneling in Testosterone 6β-Hydroxylation by Cytochrome P450: Reaction Dynamics Calculations Employing Multiconfiguration Molecular-Mechanical Potential Energy Surfaces

NASA Astrophysics Data System (ADS)

Zhang, Yan; Lin, Hai

2009-05-01

Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6β-hydrogen abstraction and the 6β-d1-testosterone 6β-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.

Investigation of the graphene-electrolyte interface in Li-air batteries: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Pavlov, S. V.; Kislenko, S. A.

2018-01-01

In this work the behavior of the main reactants (Li+, O2) of the oxygen reduction reaction (ORR) in acetonitrile solvent near the multi-layer graphene edge has been studied. It was observed by molecular dynamics simulations that the concentration distributions of the Li+ and O2 represent a “chessboard” structure. It was ascertained that the concentrations of the lithium ions and oxygen molecules reach their maximum values near the graphene edges pushed out from the surface, which may act as nucleation centers for the formation of crystalline products of the ORR. The maps of the free energy were estimated for the Li+ and O2. Energy optimal trajectories for the adsorption of oxygen molecules and lithium ions were found. Moreover, the distributions of the electric potential were obtained near the following carbon surfaces: single- and multi-layer graphene edge, graphene plane, which shows the qualitative differences in the double-layer structure.

IgGs are made for walking on bacterial and viral surfaces

NASA Astrophysics Data System (ADS)

Preiner, Johannes; Kodera, Noriyuki; Tang, Jilin; Ebner, Andreas; Brameshuber, Mario; Blaas, Dieter; Gelbmann, Nicola; Gruber, Hermann J.; Ando, Toshio; Hinterdorfer, Peter

2014-07-01

Binding of antibodies to their cognate antigens is fundamental for adaptive immunity. Molecular engineering of antibodies for therapeutic and diagnostic purposes emerges to be one of the major technologies in combating many human diseases. Despite its importance, a detailed description of the nanomechanical process of antibody-antigen binding and dissociation on the molecular level is lacking. Here we utilize high-speed atomic force microscopy to examine the dynamics of antibody recognition and uncover a principle; antibodies do not remain stationary on surfaces of regularly spaced epitopes; they rather exhibit ‘bipedal’ stochastic walking. As monovalent Fab fragments do not move, steric strain is identified as the origin of short-lived bivalent binding. Walking antibodies gather in transient clusters that might serve as docking sites for the complement system and/or phagocytes. Our findings could inspire the rational design of antibodies and multivalent receptors to exploit/inhibit steric strain-induced dynamic effects.

HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

PubMed Central

Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang

2015-01-01

Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL. PMID:25737239

Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics.

PubMed

Kimura, S Roy; Hu, Hai Peng; Ruvinsky, Anatoly M; Sherman, Woody; Favia, Angelo D

2017-06-26

In recent years, molecular dynamics simulations of proteins in explicit mixed solvents have been applied to various problems in protein biophysics and drug discovery, including protein folding, protein surface characterization, fragment screening, allostery, and druggability assessment. In this study, we perform a systematic study on how mixtures of organic solvent probes in water can reveal cryptic ligand binding pockets that are not evident in crystal structures of apo proteins. We examine a diverse set of eight PDB proteins that show pocket opening induced by ligand binding and investigate whether solvent MD simulations on the apo structures can induce the binding site observed in the holo structures. The cosolvent simulations were found to induce conformational changes on the protein surface, which were characterized and compared with the holo structures. Analyses of the biological systems, choice of probes and concentrations, druggability of the resulting induced pockets, and application to drug discovery are discussed here.

Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations.

PubMed

Lee, Michael S; Olson, Mark A

2013-07-28

Implicit solvent models for molecular dynamics simulations are often composed of polar and nonpolar terms. Typically, the nonpolar solvation free energy is approximated by the solvent-accessible-surface area times a constant factor. More sophisticated approaches incorporate an estimate of the attractive dispersion forces of the solvent and∕or a solvent-accessible volume cavitation term. In this work, we confirm that a single volume-based nonpolar term most closely fits the dispersion and cavitation forces obtained from benchmark explicit solvent simulations of fixed protein conformations. Next, we incorporated the volume term into molecular dynamics simulations and find the term is not universally suitable for folding up small proteins. We surmise that while mean-field cavitation terms such as volume and SASA often tilt the energy landscape towards native-like folds, they also may sporadically introduce bottlenecks into the folding pathway that hinder the progression towards the native state.

HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

DOE PAGES

Zhang, Meng; Charles, River; Tong, Huimin; ...

2015-03-04

Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobicmore » environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.« less

Molecular dynamics simulations of bubble formation and cavitation in liquid metals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Insepov, Z.; Hassanein, A.; Bazhirov, T. T.

2007-11-01

Thermodynamics and kinetics of nano-scale bubble formation in liquid metals such as Li and Pb were studied by molecular dynamics (MD) simulations at pressures typical for magnetic and inertial fusion. Two different approaches to bubble formation were developed. In one method, radial densities, pressures, surface tensions, and work functions of the cavities in supercooled liquid lithium were calculated and compared with the surface tension experimental data. The critical radius of a stable cavity in liquid lithium was found for the first time. In the second method, the cavities were created in the highly stretched region of the liquid phase diagram;more » and then the stability boundary and the cavitation rates were calculated in liquid lead. The pressure dependences of cavitation frequencies were obtained over the temperature range 700-2700 K in liquid Pb. The results of MD calculations for cavitation rate were compared with estimates of classical nucleation theory (CNT).« less

HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang

2015-03-01

Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.

A molecular dynamics simulation of solvent effects on the crystal morphology of HMX.

PubMed

Duan, Xiaohui; Wei, Chunxue; Liu, Yonggang; Pei, Chonghua

2010-02-15

The solvent has a large effect on the crystal morphology of the organic explosive compound octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX, C(4)H(8)N(8)O(8)). The attachment energy calculations predict a growth morphology in vacuum dominated by (020), (011), (102 ), (111 ) and (100) crystal forms. Molecular dynamics simulations are performed for these crystal faces of HMX in contact with acetone solvent. A corrected attachment energy model, accounting for the surface chemistry and the associated topography (step structure) of the habit crystal plane, is applied to predict the morphological importance of a crystal surface in solvent. From the solvent-effected attachment energy calculations it follows that the (100) face becomes morphologically more important compared with that in vacuum, while the (020) and (102 ) are not visible at all. This agrees well with the observed experimental HMX morphology grown from the acetone solution.

Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations

NASA Astrophysics Data System (ADS)

Lee, Michael S.; Olson, Mark A.

2013-07-01

Implicit solvent models for molecular dynamics simulations are often composed of polar and nonpolar terms. Typically, the nonpolar solvation free energy is approximated by the solvent-accessible-surface area times a constant factor. More sophisticated approaches incorporate an estimate of the attractive dispersion forces of the solvent and/or a solvent-accessible volume cavitation term. In this work, we confirm that a single volume-based nonpolar term most closely fits the dispersion and cavitation forces obtained from benchmark explicit solvent simulations of fixed protein conformations. Next, we incorporated the volume term into molecular dynamics simulations and find the term is not universally suitable for folding up small proteins. We surmise that while mean-field cavitation terms such as volume and SASA often tilt the energy landscape towards native-like folds, they also may sporadically introduce bottlenecks into the folding pathway that hinder the progression towards the native state.

Molecular dynamics modeling of periodic nanostructuring of metals with a short UV laser pulse under spatial confinement by a water layer

NASA Astrophysics Data System (ADS)

Ivanov, D. S.; Blumenstein, A.; Ihlemann, J.; Simon, P.; Garcia, M. E.; Rethfeld, B.

2017-12-01

The possibility of material surfaces restructuring on the nanoscale due to ultrashort laser pulses has recently found a number of practical applications. It was found experimentally that under spatial confinement due to a liquid layer atop the surface, one can achieve even finer and cleaner structures as compared to that in air or in vacuum. The mechanism of the materials restructuring under the liquid confinement, however, is not clear and its experimental study is limited by the extreme conditions realized during the intense and localized laser energy deposition that takes place on nanometer spatial and picosecond time-scales. In this theoretical work, we suggest a molecular dynamics-based approach that is capable of simulating the processes of periodic nanostructuring with ultrashort UV laser pulse on metals. The theoretical results of the simulations are directly compared with the experimental data on the same spatial and temporal scales.

How nanobubbles lose stability: Effects of surfactants

NASA Astrophysics Data System (ADS)

Xiao, Qianxiang; Liu, Yawei; Guo, Zhenjiang; Liu, Zhiping; Zhang, Xianren

2017-09-01

In contrast to stability theories of nanobubbles, the molecular mechanism of how nanobubbles lose stability is far from being understood. In this work, we try to interpret recent experimental observations that the addition of surfactants destabilizes nanobubbles with an unclear mechanism. Using molecular dynamics simulations, we identify two surfactant-induced molecular mechanisms for nanobubbles losing stability, either through depinning of a contact line or reducing vapor-liquid surface tension. One corresponds to the case with significant adsorption of surfactants on the substrates, which causes depinning of the nanobubble contact line and thus leads to nanobubble instability. The other stresses surfactant adsorption on the vapor-liquid interface of nanobubbles, especially for insoluble surfactants, which reduces the surface tension of the interface and leads to an irreversible liquid-to-vapor phase transition. Our finding can help improve our understanding in nanobubble stability, and the insight presented here has implications for surface nanobubbles involving with other amphiphilic molecules, such as proteins and contaminations.

Effect of peptide length on the conjugation to the gold nanoparticle surface: a molecular dynamic study.

PubMed

Ramezani, Fatemeh; Habibi, Mostafa; Rafii-Tabar, Hashem; Amanlou, Massoud

2015-01-29

Gold nanoparticles now command a great deal of attention for medical applications. Despite the importance of nano-bio interfaces, interaction between peptides and proteins with gold surfaces is not still fully understood, especially in a molecular level. In the present study computational simulation of adsorption of 20 amino acids, in three forms of mono-amino acid, homo di-peptide and homo tri-peptide, on the gold nanoparticles was performed by Gromacs using OPLSAA force field. The flexibility, stability, and size effect of the peptides on the gold nanoparticles were studied as well as the molecular structure of them. According to our results, adsorbed homo tri-peptides on the gold surface had more flexibility, more gyration, and the farthest distance from the GNP in comparison with homo di-peptides and mono-amino acids. Our findings provide new insights into the precise control of interactions between amino acids anchored on the GNPs.

Dynamics of Water in Gemini Surfactant-Based Lyotropic Liquid Crystals

DOE PAGES

McDaniel, Jesse G.; Mantha, Sriteja; Yethiraj, Arun

2016-09-26

The dynamics of water confined to nanometer-sized domains is important in a variety of applications ranging from proton exchange membranes to crowding effects in biophysics. In this work we study the dynamics of water in gemini surfactant-based lyotropic liquid crystals (LLCs) using molecular dynamics simulations. These systems have well characterized morphologies, e.g., hexagonal, gyroid, and lamellar, and the surfaces of the confining regions can be controlled by modifying the headgroup of the surfactants. This allows one to study the effect of topology, functionalization, and interfacial curvature on the dynamics of confined water. Through analysis of the translational diffusion and rotationalmore » relaxation we conclude that the hydration level and resulting confinement lengthscale is the predominate determiner of the rates of water dynamics, and other effects, namely surface functionality and curvature, are largely secondary. In conclusion, this novel analysis of the water dynamics in these LLC systems provides an important comparison for previous studies of water dynamics in lipid bilayers and reverse micelles.« less

The inherent dynamics of a molecular liquid: geodesic pathways through the potential energy landscape of a liquid of linear molecules.

PubMed

Jacobson, Daniel; Stratt, Richard M

2014-05-07

Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation-molecules largely thread their way through narrow channels available in the potential energy landscape.

The inherent dynamics of a molecular liquid: Geodesic pathways through the potential energy landscape of a liquid of linear molecules

NASA Astrophysics Data System (ADS)

Jacobson, Daniel; Stratt, Richard M.

2014-05-01

Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation—molecules largely thread their way through narrow channels available in the potential energy landscape.

Theoretical investigation of interaction of sorbitol molecules with alcohol dehydrogenase in aqueous solution using molecular dynamics simulation.

PubMed

Bahrami, Homayoon; Zahedi, Mansour; Moosavi-Movahedi, Ali Akbar; Azizian, Homa; Amanlou, Massoud

2011-03-01

The nature of protein-sorbitol-water interaction in solution at the molecular level, has been investigated using molecular dynamics simulations. In order to do this task, two molecular dynamics simulations of the protein ADH in solution at room temperature have been carried out, one in the presence (about 0.9 M) and another in the absence of sorbitol. The results show that the sorbitol molecules cluster and move toward the protein, and form hydrogen bonds with protein. Also, coating by sorbitol reduces the conformational fluctuations of the protein compared to the sorbitol-free system. Thus, it is concluded that at moderate concentration of sorbitol solution, sorbitol molecules interact with ADH via many H-bonds that prevent the protein folding. In fact, at more concentrated sorbitol solution, water and sorbitol molecules accumulate around the protein surface and form a continuous space-filling network to reduce the protein flexibility. Namely, in such solution, sorbitol molecules can stabilize a misfolded state of ADH, and prevent the protein from folding to its native structure.

Hydration water dynamics and instigation of protein structuralrelaxation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russo, Daniela; Hura, Greg; Head-Gordon, Teresa

2003-09-01

Until a critical hydration level is reached, proteins do not function. This critical level of hydration is analogous to a similar lack of protein function observed for temperatures below a dynamical temperature range of 180-220K that also is connected to the dynamics of protein surface water. Restoration of some enzymatic activity is observed in partially hydrated protein powders, sometimes corresponding to less than a single hydration layer on the protein surface, which indicates that the dynamical and structural properties of the surface water is intimately connected to protein stability and function. Many elegant studies using both experiment and simulation havemore » contributed important information about protein hydration structure and timescales. The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use experimental quasi-elastic neutron scattering (QENS) and molecular dynamics simulation to investigate hydration water dynamics near a greatly simplified protein system. We consider the hydration water dynamics near the completely deuterated N-acetyl-leucine-methylamide (NALMA) solute, a hydrophobic amino acid side chain attached to a polar blocked polypeptide backbone, as a function of concentration between 0.5M-2.0M under ambient conditions. We note that roughly 50-60% of a folded protein's surface is equally distributed between hydrophobic and hydrophilic domains, domains whose lengths are on the order of a few water diameters, that justify our study of hydration dynamics of this simple model protein system. The QENS experiment was performed at the NIST Center for Neutron Research, using the disk chopper time of flight spectrometer (DCS). In order to separate the translational and rotational components in the spectra, two sets of experiments were carried out using different incident neutron wavelengths of 7.5{angstrom} and 5.5{angstrom} to give two different time resolutions. All the spectra have been measure at room temperature. The spectra were corrected for the sample holder contribution and normalized using the vanadium standard. The resulting data were analyzed with DAVE programs (http://www.ncnr.nist.gov/dave/). The AMBER force field and SPCE water model were used for modeling the NALMA solute and water, respectively. For the analysis of the water dynamics in the NALMA aqueous solutions, we performed simulations of a dispersed solute configuration consistent with our previous structural analysis, where we had primarily focused on the structural organization of these peptide solutions and their connection to protein folding. Further details of the QENS experiment and molecular dynamics simulations are reported elsewhere.« less

Molecular dynamics investigation on adsorption layer of alcohols at the air/brine interface.

PubMed

Nguyen, Cuong V; Phan, Chi M; Ang, Ha M; Nakahara, Hiromichi; Shibata, Osamu; Moroi, Yoshikiyo

2015-01-01

Alcohols are a significant group of surfactants which have been employed extensively in industry to improve the interfacial effects. Recently, the change in surface potential (ΔV) of two isomeric hexanols, methyl isobutyl carbinol (MIBC) and 1-hexanol, was investigated by using an ionizing (241)Am electrode. It clearly showed the opposite effects between MIBC and 1-hexanol in the interfacial zone: one enhanced the presence of cations, whereas the other enhanced the presence of anions. This study employs molecular dynamics simulation to provide new insights into the interactions between alcohol molecules and ions as well as water at the molecular level. The results qualitatively agreed with the experimental data and verified the significance of MIBC branching structure on the molecular arrangement within the interfacial zone. The results also highlighted the role of the second water layer on the interfacial properties.

Tissue organization by cadherin adhesion molecules: dynamic molecular and cellular mechanisms of morphogenetic regulation

PubMed Central

Niessen, Carien M.; Leckband, Deborah; Yap, Alpha S.

2013-01-01

This review addresses the cellular and molecular mechanisms of cadherin-based tissue morphogenesis. Tissue physiology is profoundly influenced by the distinctive organizations of cells in organs and tissues. In metazoa, adhesion receptors of the classical cadherin family play important roles in establishing and maintaining such tissue organization. Indeed, it is apparent that cadherins participate in a range of morphogenetic events that range from support of tissue integrity to dynamic cellular rearrangements. A comprehensive understanding of cadherin-based morphogenesis must then define the molecular and cellular mechanisms that support these distinct cadherin biologies. Here we focus on four key mechanistic elements: the molecular basis for adhesion through cadherin ectodomains; the regulation of cadherin expression at the cell surface; cooperation between cadherins and the actin cytoskeleton; and regulation by cell signaling. We discuss current progress and outline issues for further research in these fields. PMID:21527735

Physics through the 1990s: Atomic, molecular and optical physics

NASA Technical Reports Server (NTRS)

1986-01-01

The volume presents a program of research initiatives in atomic, molecular, and optical physics. The current state of atomic, molecular, and optical physics in the US is examined with respect to demographics, education patterns, applications, and the US economy. Recommendations are made for each field, with discussions of their histories and the relevance of the research to government agencies. The section on atomic physics includes atomic theory, structure, and dynamics; accelerator-based atomic physics; and large facilities. The section on molecular physics includes spectroscopy, scattering theory and experiment, and the dynamics of chemical reactions. The section on optical physics discusses lasers, laser spectroscopy, and quantum optics and coherence. A section elucidates interfaces between the three fields and astrophysics, condensed matter physics, surface science, plasma physics, atmospheric physics, and nuclear physics. Another section shows applications of the three fields in ultra-precise measurements, fusion, national security, materials, medicine, and other topics.

Interactions of polymer surfaces and thin films

NASA Astrophysics Data System (ADS)

Zeng, Hongbo

2007-12-01

Characterization of the adhesion, tribological properties and dynamics of polymer surfaces has been of great interest for many years since polymers are commonly used as adhesive and lubricant coatings to produce both high and low adhesion or friction. Improving our fundamental understanding of the interactions of polymer surfaces at the molecular level is needed to develop further techniques in materials science and chemical engineering. The objectives of my research were to correlate the nano- and micro-scale properties of various polymer thin film and surface phenomena: adhesion, adhesion hysteresis, friction, lubrication, surface deformations, coalescence, spreading, and wear, and identify the fundamental physical forces and mechanisms at the molecular and micro-scales. I studied the adhesion of polymer films at temperatures ranging from below to above the glass transition temperature, Tg. The adhesion hysteresis was found to peak somewhere around Tg, but to also depend on the load, contact time and detachment rate. The results revealed some new scaling relations for the dynamic (rate-dependent) adhesion forces and effective surface energies of polymers. I studied the way polymer surfaces deform during adhesion (coalescence), spreading (wetting) and separation (detachment, rupture, fracture and failure) processes, and characterized the differences (and transition) between liquid-like and solid-like behavior during these processes, e.g., the transition from liquid-to-viscoelastic-to-ductile-to-brittle behavior. Complex and novel transient (dynamic) surface shape changes were found to occur during transitions that involved highly-ordered or disordered fingers, ripples, waves or cracks. A full picture has emerged for the transition from viscous liquid-like to brittle solid-like behavior of adhering and detaching interfaces. Finally, I developed a new experiment technique whereby an electric field can be applied across the two surfaces in a Surface Force Apparatus for the first time, and two types of experiments were performed to measure the normal and/or lateral forces between two surfaces under an E-field.

Computational screening of biomolecular adsorption and self-assembly on nanoscale surfaces.

PubMed

Heinz, Hendrik

2010-05-01

The quantification of binding properties of ions, surfactants, biopolymers, and other macromolecules to nanometer-scale surfaces is often difficult experimentally and a recurring challenge in molecular simulation. A simple and computationally efficient method is introduced to compute quantitatively the energy of adsorption of solute molecules on a given surface. Highly accurate summation of Coulomb energies as well as precise control of temperature and pressure is required to extract the small energy differences in complex environments characterized by a large total energy. The method involves the simulation of four systems, the surface-solute-solvent system, the solute-solvent system, the solvent system, and the surface-solvent system under consideration of equal molecular volumes of each component under NVT conditions using standard molecular dynamics or Monte Carlo algorithms. Particularly in chemically detailed systems including thousands of explicit solvent molecules and specific concentrations of ions and organic solutes, the method takes into account the effect of complex nonbond interactions and rotational isomeric states on the adsorption behavior on surfaces. As a numerical example, the adsorption of a dodecapeptide on the Au {111} and mica {001} surfaces is described in aqueous solution. Copyright 2009 Wiley Periodicals, Inc.

Molecular Dynamics Simulation of Resin Adsorption at Kaolinite Edge Sites: Effect of Surface Deprotonation on Interfacial Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeitler, T. R.; Greathouse, J. A.; Cygan, R. T.

Low-salinity water flooding, a method of enhanced oil recovery, consists of injecting low ionic strength fluids into an oil reservoir in order to detach oil from mineral surfaces in the underlying formation. Although highly successful in practice, the approach is not completely understood at the molecular scale. Molecular dynamics simulations have been used to investigate the effect of surface protonation on the adsorption of an anionic crude oil component on clay mineral edge surfaces. A set of interatomic potentials appropriate for edge simulations has been applied to the kaolinite (010) surface in contact with an aqueous nanopore. Decahydro-2-napthoic acid inmore » its deprotonated form (DHNA –) was used as a representative resin component of crude oil, with monovalent and divalent counterions, to test the observed trends in low-salinity water flooding experiments. Surface models include fully protonated (neutral) and deprotonated (negative) edge sites, which require implementation of a new deprotonation scheme. The surface adsorptive properties of the kaolinite edge under neutral and deprotonated conditions have been investigated for low and high DHNA – concentrations with Na + and Ca 2+ as counterions. The tendency of DHNA – ions to coordinate with divalent (Ca 2+) rather than monovalent (Na +) ions greatly influences adsorption tendencies of the anion. Additionally, the formation of net positively charged surface sites due to Ca 2+ at deprotonated sites results in increased DHNA – adsorption. Divalent cations such as Ca 2+ are able to efficiently bridge surface sites and organic anions. Replacing those cations with monovalent cations such as Na + diminishes the bridging mechanism, resulting in reduced adsorption of the organic species. As a result, a clear trend of decreased DHNA – adsorption is observed in the simulations as Ca 2+ is replaced by Na + for deprotonated surfaces, as would be expected for oil detachment from reservoir formations following a low-salinity flooding event.« less

Molecular Dynamics Simulation of Resin Adsorption at Kaolinite Edge Sites: Effect of Surface Deprotonation on Interfacial Structure

DOE PAGES

Zeitler, T. R.; Greathouse, J. A.; Cygan, R. T.; ...

2017-10-05

Low-salinity water flooding, a method of enhanced oil recovery, consists of injecting low ionic strength fluids into an oil reservoir in order to detach oil from mineral surfaces in the underlying formation. Although highly successful in practice, the approach is not completely understood at the molecular scale. Molecular dynamics simulations have been used to investigate the effect of surface protonation on the adsorption of an anionic crude oil component on clay mineral edge surfaces. A set of interatomic potentials appropriate for edge simulations has been applied to the kaolinite (010) surface in contact with an aqueous nanopore. Decahydro-2-napthoic acid inmore » its deprotonated form (DHNA –) was used as a representative resin component of crude oil, with monovalent and divalent counterions, to test the observed trends in low-salinity water flooding experiments. Surface models include fully protonated (neutral) and deprotonated (negative) edge sites, which require implementation of a new deprotonation scheme. The surface adsorptive properties of the kaolinite edge under neutral and deprotonated conditions have been investigated for low and high DHNA – concentrations with Na + and Ca 2+ as counterions. The tendency of DHNA – ions to coordinate with divalent (Ca 2+) rather than monovalent (Na +) ions greatly influences adsorption tendencies of the anion. Additionally, the formation of net positively charged surface sites due to Ca 2+ at deprotonated sites results in increased DHNA – adsorption. Divalent cations such as Ca 2+ are able to efficiently bridge surface sites and organic anions. Replacing those cations with monovalent cations such as Na + diminishes the bridging mechanism, resulting in reduced adsorption of the organic species. As a result, a clear trend of decreased DHNA – adsorption is observed in the simulations as Ca 2+ is replaced by Na + for deprotonated surfaces, as would be expected for oil detachment from reservoir formations following a low-salinity flooding event.« less

A Comprehensive Study of Hydrogen Adsorbing to Amorphous Water ice: Defining Adsorption in Classical Molecular Dynamics

NASA Astrophysics Data System (ADS)

Dupuy, John L.; Lewis, Steven P.; Stancil, P. C.

2016-11-01

Gas-grain and gas-phase reactions dominate the formation of molecules in the interstellar medium (ISM). Gas-grain reactions require a substrate (e.g., a dust or ice grain) on which the reaction is able to occur. The formation of molecular hydrogen (H2) in the ISM is the prototypical example of a gas-grain reaction. In these reactions, an atom of hydrogen will strike a surface, stick to it, and diffuse across it. When it encounters another adsorbed hydrogen atom, the two can react to form molecular hydrogen and then be ejected from the surface by the energy released in the reaction. We perform in-depth classical molecular dynamics simulations of hydrogen atoms interacting with an amorphous water-ice surface. This study focuses on the first step in the formation process; the sticking of the hydrogen atom to the substrate. We find that careful attention must be paid in dealing with the ambiguities in defining a sticking event. The technical definition of a sticking event will affect the computed sticking probabilities and coefficients. Here, using our new definition of a sticking event, we report sticking probabilities and sticking coefficients for nine different incident kinetic energies of hydrogen atoms [5-400 K] across seven different temperatures of dust grains [10-70 K]. We find that probabilities and coefficients vary both as a function of grain temperature and incident kinetic energy over the range of 0.99-0.22.

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator

NASA Astrophysics Data System (ADS)

Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe; Roux, Benoît

2018-01-01

Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield a significant speedup.

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator.

PubMed

Suh, Donghyuk; Radak, Brian K; Chipot, Christophe; Roux, Benoît

2018-01-07

Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield a significant speedup.

Replica-exchange molecular dynamics simulation of basic fibroblast growth factor adsorption on hydroxyapatite.

PubMed

Liao, Chenyi; Zhou, Jian

2014-06-05

The adsorption of basic fibroblast growth factor (bFGF) on the hydroxyapatite (001) surface was investigated by a combination of replica-exchange molecular dynamics (REMD) and conventional molecular dynamics (CMD) methods. In CMD, the protein cannot readily cross the surface water layer, whereas in REMD, the protein can cross the adsorption barrier from the surface water layer and go through weak, medium, then strong adsorption states with three energetically preferred configurations: heparin-binding-up (HP-up), heparin-binding-middle (HP-middle), and heparin-binding-down (HP-down). The HP-middle orientation, with the strongest adsorption energy (-1149 ± 40 kJ·mol(-1)), has the largest adsorption population (52.1-52.6%) and exhibits the largest conformational charge (RMSD of 0.26 ± 0.01 nm) among the three orientations. The HP-down and HP-up orientations, with smaller adsorption energies of -1022 ± 55 and -894 ± 70 kJ·mol(-1), respectively, have smaller adsorption populations of 27.4-27.7% and 19.7-20.5% and present smaller RMSD values of 0.21 ± 0.01 and 0.19 ± 0.01 nm, respectively. The convergent distribution indicates that nearly half of the population (in the HP-middle orientation) will support both FGF/FGFR and DGR-integrin signaling and another half (in the HP-up and HP-down orientations) will support DGR-integrin signaling. The major population (~80%) has the protein dipole directed outward. In the strong adsorption state, there are usually 2 to 3 basic residues that form the anchoring interactions of 210-332 kJ·mol(-1) per residue or that are accompanied by an acidic residue with an adsorption energy of ~207 kJ·mol(-1). Together, the major bound residues form a triangle or a quadrilateral on the surface and stabilize the adsorption geometrically, which indicates topologic matching between the protein and HAP surfaces.

Simulations of a Membrane-Anchored Peptide: Structure, Dynamics, and Influence on Bilayer Properties

PubMed Central

Jensen, Morten Ø.; Mouritsen, Ole G.; Peters, Günther H.

2004-01-01

A three-dimensional structure of a model decapeptide is obtained by performing molecular dynamics simulations of the peptide in explicit water. Interactions between an N-myristoylated form of the folded peptide anchored to dipalmitoylphosphatidylcholine fluid phase lipid membranes are studied at different applied surface tensions by molecular dynamics simulations. The lipid membrane environment influences the conformational space explored by the peptide. The overall secondary structure of the anchored peptide is found to deviate at times from its structure in aqueous solution through reversible conformational transitions. The peptide is, despite the anchor, highly mobile at the membrane surface with the peptide motion along the bilayer normal being integrated into the collective modes of the membrane. Peptide anchoring moderately alters the lateral compressibility of the bilayer by changing the equilibrium area of the membrane. Although membrane anchoring moderately affects the elastic properties of the bilayer, the model peptide studied here exhibits conformational flexibility and our results therefore suggest that peptide acylation is a feasible way to reinforce peptide-membrane interactions whereby, e.g., the lifetime of receptor-ligand interactions can be prolonged. PMID:15189854

Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions

PubMed Central

Scholes, Natalie S.; Weinzierl, Robert O. J.

2016-01-01

Transcriptional activation domains (ADs) are generally thought to be intrinsically unstructured, but capable of adopting limited secondary structure upon interaction with a coactivator surface. The indeterminate nature of this interface made it hitherto difficult to study structure/function relationships of such contacts. Here we used atomistic accelerated molecular dynamics (aMD) simulations to study the conformational changes of the GCN4 AD and variants thereof, either free in solution, or bound to the GAL11 coactivator surface. We show that the AD-coactivator interactions are highly dynamic while obeying distinct rules. The data provide insights into the constant and variable aspects of orientation of ADs relative to the coactivator, changes in secondary structure and energetic contributions stabilizing the various conformers at different time points. We also demonstrate that a prediction of α-helical propensity correlates directly with the experimentally measured transactivation potential of a large set of mutagenized ADs. The link between α-helical propensity and the stimulatory activity of ADs has fundamental practical and theoretical implications concerning the recruitment of ADs to coactivators. PMID:27175900

Segmental dynamics of polymers in nanoscopic confinements, as probed by simulations of polymer/layered-silicate nanocomposites.

PubMed

Kuppa, V; Foley, T M D; Manias, E

2003-09-01

In this paper we review molecular modeling investigations of polymer/layered-silicate intercalates, as model systems to explore polymers in nanoscopically confined spaces. The atomic-scale picture, as revealed by computer simulations, is presented in the context of salient results from a wide range of experimental techniques. This approach provides insights into how polymeric segmental dynamics are affected by severe geometric constraints. Focusing on intercalated systems, i.e. polystyrene (PS) in 2 nm wide slit-pores and polyethylene-oxide (PEO) in 1 nm wide slit-pores, a very rich picture for the segmental dynamics is unveiled, despite the topological constraints imposed by the confining solid surfaces. On a local scale, intercalated polymers exhibit a very wide distribution of segmental relaxation times (ranging from ultra-fast to ultra-slow, over a wide range of temperatures). In both cases (PS and PEO), the segmental relaxations originate from the confinement-induced local density variations. Additionally, where there exist special interactions between the polymer and the confining surfaces ( e.g., PEO) more molecular mechanisms are identified.

Surface Effect on Oil Transportation in Nanochannel: a Molecular Dynamics Study.

PubMed

Zheng, Haixia; Du, Yonggang; Xue, Qingzhong; Zhu, Lei; Li, Xiaofang; Lu, Shuangfang; Jin, Yakang

2017-12-01

In this work, we investigate the dynamics mechanism of oil transportation in nanochannel using molecular dynamics simulations. It is demonstrated that the interaction between oil molecules and nanochannel has a great effect on the transportation properties of oil in nanochannel. Because of different interactions between oil molecules and channel, the center of mass (COM) displacement of oil in a 6-nm channel is over 30 times larger than that in a 2-nm channel, and the diffusion coefficient of oil molecules at the center of a 6-nm channel is almost two times more than that near the channel surface. Besides, it is found that polarity of oil molecules has the effect on impeding oil transportation, because the electrostatic interaction between polar oil molecules and channel is far larger than that between nonpolar oil molecules and channel. In addition, channel component is found to play an important role in oil transportation in nanochannel, for example, the COM displacement of oil in gold channel is very few due to great interaction between oil and gold substrate. It is also found that nano-sized roughness of channel surface greatly influences the speed and flow pattern of oil. Our findings would contribute to revealing the mechanism of oil transportation in nanochannels and therefore are very important for design of oil extraction in nanochannels.

Effects of Frothers and Oil at Saltwater–Air Interfaces for Oil Separation: Molecular Dynamics Simulations and Experimental Measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chong, Leebyn; Lai, Yungchieh; Gray, McMahan

Separating oil from saltwater is a process relevant to some industries and may be aided by bubble and froth generation. Simulating saltwater–air interfaces adsorbed with surfactants and oil molecules can assist in understanding froth stability to improve separation. Here, combining with surface tension experimental measurements, in this work we employ molecular dynamics with a united-atom force field to linear alkane oil and three surfactant frothers, methyl isobutyl carbinol (MIBC), terpineol, and ethyl glycol butyl ether (EGBE), to investigate their synergistic behaviors for oil separation. The interfacial phenomena were measured for a range of frother surface coverages on saltwater. Density profilesmore » of the hydrophilic and hydrophobic portions of the frothers show an expected orientation of alcohol groups adsorbing to the polar water. A decrease in surface tension with increasing surface coverage of MIBC and terpineol was observed and reflected in experiments where the frother concentration increased. Relations between surface coverage and bulk concentration were observed by comparing the surface tension decreases. Additionally, a range of oil surface coverages was explored when the interface has a thin layer of adsorbed frother molecules. Finally, the obtained results indicate that an increase in surface coverage of oil molecules led to an increase in surface tension for all frother types and the pair correlation functions depicted MIBC and terpineol as having higher distributions with water at closer distances than with oil.« less

Effects of Frothers and Oil at Saltwater–Air Interfaces for Oil Separation: Molecular Dynamics Simulations and Experimental Measurements

DOE PAGES

Chong, Leebyn; Lai, Yungchieh; Gray, McMahan; ...

2017-06-16

Separating oil from saltwater is a process relevant to some industries and may be aided by bubble and froth generation. Simulating saltwater–air interfaces adsorbed with surfactants and oil molecules can assist in understanding froth stability to improve separation. Here, combining with surface tension experimental measurements, in this work we employ molecular dynamics with a united-atom force field to linear alkane oil and three surfactant frothers, methyl isobutyl carbinol (MIBC), terpineol, and ethyl glycol butyl ether (EGBE), to investigate their synergistic behaviors for oil separation. The interfacial phenomena were measured for a range of frother surface coverages on saltwater. Density profilesmore » of the hydrophilic and hydrophobic portions of the frothers show an expected orientation of alcohol groups adsorbing to the polar water. A decrease in surface tension with increasing surface coverage of MIBC and terpineol was observed and reflected in experiments where the frother concentration increased. Relations between surface coverage and bulk concentration were observed by comparing the surface tension decreases. Additionally, a range of oil surface coverages was explored when the interface has a thin layer of adsorbed frother molecules. Finally, the obtained results indicate that an increase in surface coverage of oil molecules led to an increase in surface tension for all frother types and the pair correlation functions depicted MIBC and terpineol as having higher distributions with water at closer distances than with oil.« less

Molecular dynamics modeling and simulation of void growth in two dimensions

NASA Astrophysics Data System (ADS)

Chang, H.-J.; Segurado, J.; Rodríguez de la Fuente, O.; Pabón, B. M.; LLorca, J.

2013-10-01

The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids.

Nanoscale heterogeneity at the aqueous electrolyte-electrode interface

NASA Astrophysics Data System (ADS)

Limmer, David T.; Willard, Adam P.

2015-01-01

Using molecular dynamics simulations, we reveal emergent properties of hydrated electrode interfaces that while molecular in origin are integral to the behavior of the system across long times scales and large length scales. Specifically, we describe the impact of a disordered and slowly evolving adsorbed layer of water on the molecular structure and dynamics of the electrolyte solution adjacent to it. Generically, we find that densities and mobilities of both water and dissolved ions are spatially heterogeneous in the plane parallel to the electrode over nanosecond timescales. These and other recent results are analyzed in the context of available experimental literature from surface science and electrochemistry. We speculate on the implications of this emerging microscopic picture on the catalytic proficiency of hydrated electrodes, offering a new direction for study in heterogeneous catalysis at the nanoscale.

Effect of Sodium Dodecyl Sulfate Surfactant on Methane Hydrate Formation: A Molecular Dynamics Study.

PubMed

Choudhary, Nilesh; Hande, Vrushali R; Roy, Sudip; Chakrabarty, Suman; Kumar, Rajnish

2018-06-28

In experimental studies, it has been observed that the presence of sodium dodecyl sulfate (SDS) significantly increases the kinetics of hydrate formation and the final water-to-hydrate conversion ratio. In this study, we intend to understand the molecular mechanism behind the effect of SDS on the formation of methane hydrate through molecular dynamics simulation. Hydrate formation conditions similar to that of laboratory experiments were chosen to study hydrate growth kinetics in 1 wt % SDS solution. We also investigate the effect of interactions with isolated SDS molecules on methane hydrate growth. It was observed that the hydrophobic tail part of the SDS molecule favorably interacts with the growing hydrate surface and may occupy the partial hydrate cages while the head groups remain exposed to water.

Nonlinear absorption dynamics using field-induced surface hopping: zinc porphyrin in water.

PubMed

Röhr, Merle I S; Petersen, Jens; Wohlgemuth, Matthias; Bonačić-Koutecký, Vlasta; Mitrić, Roland

2013-05-10

We wish to present the application of our field-induced surface-hopping (FISH) method to simulate nonlinear absorption dynamics induced by strong nonresonant laser fields. We provide a systematic comparison of the FISH approach with exact quantum dynamics simulations on a multistate model system and demonstrate that FISH allows for accurate simulations of nonlinear excitation processes including multiphoton electronic transitions. In particular, two different approaches for simulating two-photon transitions are compared. The first approach is essentially exact and involves the solution of the time-dependent Schrödinger equation in an extended manifold of excited states, while in the second one only transiently populated nonessential states are replaced by an effective quadratic coupling term, and dynamics is performed in a considerably smaller manifold of states. We illustrate the applicability of our method to complex molecular systems by simulating the linear and nonlinear laser-driven dynamics in zinc (Zn) porphyrin in the gas phase and in water. For this purpose, the FISH approach is connected with the quantum mechanical-molecular mechanical approach (QM/MM) which is generally applicable to large classes of complex systems. Our findings that multiphoton absorption and dynamics increase the population of higher excited states of Zn porphyrin in the nonlinear regime, in particular in solution, provides a means for manipulating excited-state properties, such as transient absorption dynamics and electronic relaxation. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fibronectin module FN(III)9 adsorption at contrasting solid model surfaces studied by atomistic molecular dynamics.

PubMed

Kubiak-Ossowska, Karina; Mulheran, Paul A; Nowak, Wieslaw

2014-08-21

The mechanism of human fibronectin adhesion synergy region (known as integrin binding region) in repeat 9 (FN(III)9) domain adsorption at pH 7 onto various and contrasting model surfaces has been studied using atomistic molecular dynamics simulations. We use an ionic model to mimic mica surface charge density but without a long-range electric field above the surface, a silica model with a long-range electric field similar to that found experimentally, and an Au {111} model with no partial charges or electric field. A detailed description of the adsorption processes and the contrasts between the various model surfaces is provided. In the case of our model silica surface with a long-range electrostatic field, the adsorption is rapid and primarily driven by electrostatics. Because it is negatively charged (-1e), FN(III)9 readily adsorbs to a positively charged surface. However, due to its partial charge distribution, FN(III)9 can also adsorb to the negatively charged mica model because of the absence of a long-range repulsive electric field. The protein dipole moment dictates its contrasting orientation at these surfaces, and the anchoring residues have opposite charges to the surface. Adsorption on the model Au {111} surface is possible, but less specific, and various protein regions might be involved in the interactions with the surface. Despite strongly influencing the protein mobility, adsorption at these model surfaces does not require wholesale FN(III)9 conformational changes, which suggests that the biological activity of the adsorbed protein might be preserved.

Probing Silica-Biomolecule Interactions by Solid-State NMR and Molecular Dynamics Simulations.

PubMed

Brückner, Stephan Ingmar; Donets, Sergii; Dianat, Arezoo; Bobeth, Manfred; Gutiérrez, Rafael; Cuniberti, Gianaurelio; Brunner, Eike

2016-11-08

Understanding the molecular interactions between inorganic phases such as silica and organic material is fundamental for chromatographic applications, for tailoring silica-enzyme interactions, and for elucidating the mechanisms of biomineralization. The formation, structure, and properties of the organic/inorganic interface is crucial in this context. Here, we investigate the interaction of selectively 13 C-labeled choline with 29 Si-labeled monosilicic acid/silica at the molecular level. Silica/choline nanocomposites were analyzed by solid-state NMR spectroscopy in combination with extended molecular dynamics (MD) simulations to understand the silica/organic interface. Cross-polarization magic angle spinning (CP MAS)-based NMR experiments like 1 H- 13 C CP-REDOR (rotational-echo double resonance), 1 H- 13 C HETCOR (heteronuclear correlation), and 1 H- 29 Si- 1 H double CP are employed to determine spatial parameters. The measurement of 29 Si- 13 C internuclear distances for selectively 13 C-labeled choline provides an experimental parameter that allows the direct verification of MD simulations. Atomistic modeling using classical MD methodologies is performed using the INTERFACE force field. The modeling results are in excellent agreement with the experimental data and reveal the relevant molecular conformations as well as the nature and interplay of the interactions between the choline cation and the silica surface. Electrostatic interactions and hydrogen bonding are both important and depend strongly on the hydration level as well as the charge state of the silica surface.

Molecular Gibbs Surface Excess and CO2-Hydrate Density Determine the Strong Temperature- and Pressure-Dependent Supercritical CO2-Brine Interfacial Tension.

PubMed

Ji, Jiayuan; Zhao, Lingling; Tao, Lu; Lin, Shangchao

2017-06-29

In CO 2 geological storage, the interfacial tension (IFT) between supercritical CO 2 and brine is critical for the storage capacitance design to prevent CO 2 leakage. IFT relies not only on the interfacial molecule properties but also on the environmental conditions at different storage sites. In this paper, supercritical CO 2 -NaCl solution systems are modeled at 343-373 K and 6-35 MPa under the salinity of 1.89 mol/L using molecular dynamics simulations. After computing and comparing the molecular density profile across the interface, the atomic radial distribution function, the molecular orientation distribution, the molecular Gibbs surface excess (derived from the molecular density profile), and the CO 2 -hydrate number density under the above environmental conditions, we confirm that only the molecular Gibbs surface excess of CO 2 molecules and the CO 2 -hydrate number density correlate strongly with the temperature- and pressure-dependent IFTs. We also compute the populations of two distinct CO 2 -hydrate structures (T-type and H-type) and attribute the observed dependence of IFTs to the dominance of the more stable, surfactant-like T-type CO 2 -hydrates at the interface. On the basis of these new molecular mechanisms behind IFT variations, this study could guide the rational design of suitable injecting environmental pressure and temperature conditions. We believe that the above two molecular-level metrics (Gibbs surface excess and hydrate number density) are of great fundamental importance for understanding the supercritical CO 2 -water interface and engineering applications in geological CO 2 storage.