Coulomb interactions in charged fluids.

PubMed

Vernizzi, Graziano; Guerrero-García, Guillermo Iván; de la Cruz, Monica Olvera

2011-07-01

The use of Ewald summation schemes for calculating long-range Coulomb interactions, originally applied to ionic crystalline solids, is a very common practice in molecular simulations of charged fluids at present. Such a choice imposes an artificial periodicity which is generally absent in the liquid state. In this paper we propose a simple analytical O(N(2)) method which is based on Gauss's law for computing exactly the Coulomb interaction between charged particles in a simulation box, when it is averaged over all possible orientations of a surrounding infinite lattice. This method mitigates the periodicity typical of crystalline systems and it is suitable for numerical studies of ionic liquids, charged molecular fluids, and colloidal systems with Monte Carlo and molecular dynamics simulations.

Dynamics of the Rydberg state population of slow highly charged ions impinging a solid surface at arbitrary collision geometry

NASA Astrophysics Data System (ADS)

Nedeljković, N. N.; Majkić, M. D.; Božanić, D. K.; Dojčilović, R. J.

2016-06-01

We consider the population dynamics of the intermediate Rydberg states of highly charged ions (core charge Z\\gg 1, principal quantum number {n}{{A}}\\gg 1) interacting with solid surfaces at arbitrary collision geometry. The recently developed resonant two-state vector model for the grazing incidence (2012 J. Phys. B: At. Mol. Opt. Phys. 45 215202) is extended to the quasi-resonant case and arbitrary angle of incidence. According to the model, the population probabilities depend both on the projectile parallel and perpendicular velocity components, in a complementary way. A cascade neutralization process for {{{Xe}}}Z+ ions, for Z=15{--}45, interacting with a conductive-surface is considered by taking into account the population dynamics. For an arbitrary collision geometry and given range of ionic velocities, a micro-staircase model for the simultaneous calculation of the kinetic energy gain and the charge state of the ion in front of the surface is proposed. The relevance of the obtained results for the explanation of the formation of nanostructures on solid surfaces by slow highly charged ions for normal incidence geometry is briefly discussed.

Modeling the formation of ordered nano-assemblies comprised by dendrimers and linear polyelectrolytes: The role of Coulombic interactions

NASA Astrophysics Data System (ADS)

Eleftheriou, E.; Karatasos, K.

2012-10-01

Models of mixtures of peripherally charged dendrimers with oppositely charged linear polyelectrolytes in the presence of explicit solvent are studied by means of molecular dynamics simulations. Under the influence of varying strength of electrostatic interactions, these systems appear to form dynamically arrested film-like interconnected structures in the polymer-rich phase. Acting like a pseudo-thermodynamic inverse temperature, the increase of the strength of the Coulombic interactions drive the polymeric constituents of the mixture to a gradual dynamic freezing-in. The timescale of the average density fluctuations of the formed complexes initially increases in the weak electrostatic regime reaching a finite limit as the strength of electrostatic interactions grow. Although the models are overall electrically neutral, during this process the dendrimer/linear complexes develop a polar character with an excess charge mainly close to the periphery of the dendrimers. The morphological characteristics of the resulted pattern are found to depend on the size of the polymer chains on account of the distinct conformational features assumed by the complexed linear polyelectrolytes of different length. In addition, the length of the polymer chain appears to affect the dynamics of the counterions, thus affecting the ionic transport properties of the system. It appears, therefore, that the strength of electrostatic interactions together with the length of the linear polyelectrolytes are parameters to which these systems are particularly responsive, offering thus the possibility for a better control of the resulted structure and the electric properties of these soft-colloidal systems.

Critical Dipole Length for the Wetting Transition Due to Collective Water-dipoles Interactions

PubMed Central

Wang, Chunlei; Zhou, Bo; Tu, Yusong; Duan, Manyi; Xiu, Peng; Li, Jingye; Fang, Haiping

2012-01-01

The wetting behavior of water on the solid surfaces is fundamental to various physical, chemical and biological processes. Conventionally, the surface with charges or charge dipoles is hydrophilic, whereas the non-polar surface is hydrophobic though some exceptions were recently reported. Using molecular dynamics simulations, we show that there is a critical length of the charge dipoles on the solid surface. The solid surface still exhibited hydrophobic behavior when the dipole length was less than the critical value, indicating that the water molecules on the solid surface seemed not “feel” attractive interactions from the charge dipoles on the solid surface. Those unexpected observations result from the collective interactions between the water molecules and charge dipoles on the solid surface, where the steric exclusion effect between water molecules greatly reduces the water-dipole interactions. Remarkably, the steric exclusion effect is also important for surfaces with charge dipole lengths greater than this critical length. PMID:22496954

[Molecular Dynamics of N- and C-terminal Interactions during Autoinhibition and Activation of Formin mDial].

PubMed

Orshanskiy, I A; Popinako, A V; Volokh, O I; Shaitan, K V; Sokolova, O S

2015-01-01

With the method of molecular dynamics, pairs of amino acid residues have been identified on the surface of the interacting formin mDial domains: DID-DAD, which are responsible for the autoinhibition of formin, and the GTPase Rho-DID domain, and control activation. It was found that the most stable interactions are ionic interactions between Glu178 residue and Arg248 residue, as well as hydrophobic interactions between Thr175 and Phe247. The strongest interactions proved to be between the DID domain with Rho-GTPase. These interactions are mediated by specific triple ionic interactions between positively charged amino acid in Rho, and a triplet of amino acids in DID, consisting of two negatively charged amino acids, separated by one uncharged. Binding sites for Rho-GTPase and DAD partially overlap, but various amino acids on the DID participate in interactions with different domains. We discuss the possible conformational changes in formin domains during activation and inactivation.

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.

Arginine side chain interactions and the role of arginine as a gating charge carrier in voltage sensitive ion channels

PubMed Central

Armstrong, Craig T.; Mason, Philip E.; Anderson, J. L. Ross; Dempsey, Christopher E.

2016-01-01

Gating charges in voltage-sensing domains (VSD) of voltage-sensitive ion channels and enzymes are carried on arginine side chains rather than lysine. This arginine preference may result from the unique hydration properties of the side chain guanidinium group which facilitates its movement through a hydrophobic plug that seals the center of the VSD, as suggested by molecular dynamics simulations. To test for side chain interactions implicit in this model we inspected interactions of the side chains of arginine and lysine with each of the 19 non-glycine amino acids in proteins in the protein data bank. The arginine guanidinium interacts with non-polar aromatic and aliphatic side chains above and below the guanidinium plane while hydrogen bonding with polar side chains is restricted to in-plane positions. In contrast, non-polar side chains interact largely with the aliphatic part of the lysine side chain. The hydration properties of arginine and lysine are strongly reflected in their respective interactions with non-polar and polar side chains as observed in protein structures and in molecular dynamics simulations, and likely underlie the preference for arginine as a mobile charge carrier in VSD. PMID:26899474

Arginine side chain interactions and the role of arginine as a gating charge carrier in voltage sensitive ion channels

NASA Astrophysics Data System (ADS)

Armstrong, Craig T.; Mason, Philip E.; Anderson, J. L. Ross; Dempsey, Christopher E.

2016-02-01

Gating charges in voltage-sensing domains (VSD) of voltage-sensitive ion channels and enzymes are carried on arginine side chains rather than lysine. This arginine preference may result from the unique hydration properties of the side chain guanidinium group which facilitates its movement through a hydrophobic plug that seals the center of the VSD, as suggested by molecular dynamics simulations. To test for side chain interactions implicit in this model we inspected interactions of the side chains of arginine and lysine with each of the 19 non-glycine amino acids in proteins in the protein data bank. The arginine guanidinium interacts with non-polar aromatic and aliphatic side chains above and below the guanidinium plane while hydrogen bonding with polar side chains is restricted to in-plane positions. In contrast, non-polar side chains interact largely with the aliphatic part of the lysine side chain. The hydration properties of arginine and lysine are strongly reflected in their respective interactions with non-polar and polar side chains as observed in protein structures and in molecular dynamics simulations, and likely underlie the preference for arginine as a mobile charge carrier in VSD.

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

DOE PAGES

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; ...

2017-07-26

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. In this paper, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing tomore » the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. Finally, this suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.« less

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

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

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. In this paper, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing tomore » the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. Finally, this suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.« less

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

NASA Astrophysics Data System (ADS)

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; Mundy, Chistopher J.

2017-10-01

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.

Structure and Liquid Fragility in Sodium Carbonate.

PubMed

Wilson, Mark; Ribeiro, Mauro C C; Wilding, Martin C; Benmore, Chris; Weber, J K R; Alderman, Oliver; Tamalonis, Anthony; Parise, J B

2018-02-01

The relationship between local structure and dynamics is explored for molten sodium carbonate. A flexible fluctuating-charge model, which allows for changes in the shape and charge distribution of the carbonate molecular anion, is developed. The system shows the evolution of highly temperature-dependent complex low-dimensional structures which control the dynamics (and hence the liquid fragility). By varying the molecular anion charge distribution, the key interactions responsible for the formation of these structures can be identified and rationalized. An increase in the mean charge separation within the carbonate ions increases the connectivity of the emerging structures and leads to an increase in the system fragility.

Dynamic model of target charging by short laser pulse interactions

NASA Astrophysics Data System (ADS)

Poyé, A.; Dubois, J.-L.; Lubrano-Lavaderci, F.; D'Humières, E.; Bardon, M.; Hulin, S.; Bailly-Grandvaux, M.; Ribolzi, J.; Raffestin, D.; Santos, J. J.; Nicolaï, Ph.; Tikhonchuk, V.

2015-10-01

A model providing an accurate estimate of the charge accumulation on the surface of a metallic target irradiated by a high-intensity laser pulse of fs-ps duration is proposed. The model is confirmed by detailed comparisons with specially designed experiments. Such a model is useful for understanding the electromagnetic pulse emission and the quasistatic magnetic field generation in laser-plasma interaction experiments.

Dynamic model of target charging by short laser pulse interactions.

PubMed

Poyé, A; Dubois, J-L; Lubrano-Lavaderci, F; D'Humières, E; Bardon, M; Hulin, S; Bailly-Grandvaux, M; Ribolzi, J; Raffestin, D; Santos, J J; Nicolaï, Ph; Tikhonchuk, V

2015-10-01

A model providing an accurate estimate of the charge accumulation on the surface of a metallic target irradiated by a high-intensity laser pulse of fs-ps duration is proposed. The model is confirmed by detailed comparisons with specially designed experiments. Such a model is useful for understanding the electromagnetic pulse emission and the quasistatic magnetic field generation in laser-plasma interaction experiments.

Molecular dynamics simulation of highly charged proteins: Comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions

PubMed Central

Gargallo, Raimundo; Hünenberger, Philippe H.; Avilés, Francesc X.; Oliva, Baldomero

2003-01-01

Molecular dynamics (MD) simulations of the activation domain of porcine procarboxypeptidase B (ADBp) were performed to examine the effect of using the particle-particle particle-mesh (P3M) or the reaction field (RF) method for calculating electrostatic interactions in simulations of highly charged proteins. Several structural, thermodynamic, and dynamic observables were derived from the MD trajectories, including estimated entropies and solvation free energies and essential dynamics (ED). The P3M method leads to slightly higher atomic positional fluctuations and deviations from the crystallographic structure, along with somewhat lower values of the total energy and solvation free energy. However, the ED analysis of the system leads to nearly identical results for both simulations. Because of the strong similarity between the results, both methods appear well suited for the simulation of highly charged globular proteins in explicit solvent. However, the lower computational demand of the RF method in the present implementation represents a clear advantage over the P3M method. PMID:14500874

Molecular dynamics simulations of field emission from a prolate spheroidal tip

NASA Astrophysics Data System (ADS)

Torfason, Kristinn; Valfells, Agust; Manolescu, Andrei

2016-12-01

High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission from a prolate spheroidal tip. The space charge limited current is several times lower than the current calculated with the Fowler-Nordheim formula. The image-charge is taken into account with a spherical approximation, which is good around the top of the tip, i.e., region where the current is generated.

Exciton dynamics of C60-based single-photon emitters explored by Hanbury Brown-Twiss scanning tunnelling microscopy.

PubMed

Merino, P; Große, C; Rosławska, A; Kuhnke, K; Kern, K

2015-09-29

Exciton creation and annihilation by charges are crucial processes for technologies relying on charge-exciton-photon conversion. Improvement of organic light sources or dye-sensitized solar cells requires methods to address exciton dynamics at the molecular scale. Near-field techniques have been instrumental for this purpose; however, characterizing exciton recombination with molecular resolution remained a challenge. Here, we study exciton dynamics by using scanning tunnelling microscopy to inject current with sub-molecular precision and Hanbury Brown-Twiss interferometry to measure photon correlations in the far-field electroluminescence. Controlled injection allows us to generate excitons in solid C60 and let them interact with charges during their lifetime. We demonstrate electrically driven single-photon emission from localized structural defects and determine exciton lifetimes in the picosecond range. Monitoring lifetime shortening and luminescence saturation for increasing carrier injection rates provides access to charge-exciton annihilation dynamics. Our approach introduces a unique way to study single quasi-particle dynamics on the ultimate molecular scale.

Investigations of charged particle motion on the surfaces of dusty, airless solar system bodies (Invited)

NASA Astrophysics Data System (ADS)

Dove, A.; Colwell, J. E.

2013-12-01

Dynamic charging conditions exist on the dusty surfaces of planetary bodies such as the Moon, asteroids, and the moons of Mars. On these so-called 'airless bodies', the motions of dust particles above the surface become complex due to grain-grain and grain-plasma interactions. For example, tribocharging and other charge transfer processes can occur due to relative dust grain movements, and charged dust grains immersed in plasma interact with local electromagnetic forces. This is thought to lead to effects such as the lunar 'horizon glow,' (Rennilson and Criswell, 1974, The Moon, 10) and potential dusty 'fountains' above the lunar surface (Stubbs et al., 2006, Adv. Sp. Res., 37). Regolith grains can be mobilized by impacts or other mechanical disturbances, or simply by the Coulomb force acting on grains. Previous work has increased our theoretical understanding of the behavior of charged particles in these low-gravity environments (i.e. Poppe and Horanyi, 2010, JGR, A115; Colwell et al., 2007, Rev. Geophys., 45 (and references therein)). Experimental work has also analyzed grain surface charging due to plasma or tribocharging (Sickafoose et al., 2001, JGR, 106) and the motion of grains on surfaces in the presence of an electric field (Wang et al., 2009, JGR, 114). Occasionally, there is disagreement between theoretical predictions and observations. We present the results of new laboratory experiments aimed at understanding particle charging and the dynamics of charged particles on the surfaces of airless bodies. In the initial experiments, we analyze the motion of particles in the presence of an electric field in vacuum, either in a bell-jar or in a 0.75-second microgravity drop tower experiment box. Prior to motion, particles may be charged due to triboelectric effects, plasma interactions, or a combination of the two. Motion is induced by shaking or by low-velocity impacts in order to simulate the natural motion of slow-moving objects on regolith surfaces, or induced motion such as that due to a spacecraft. The resulting particle dynamics are tracked using high-speed, high-resolution video. Future exploration on or near the surfaces of airless bodies will certainly experience complications arising from these dusty environments, where particles may contaminate or interfere with the operation of almost any mechanical equipment. By exploring the dynamic behavior of charged particles in these environments, we can work towards solutions that will enable exploration.

Investigations of ultrafast charge dynamics in laser-irradiated targets by a self probing technique employing laser driven protons

NASA Astrophysics Data System (ADS)

Ahmed, H.; Kar, S.; Cantono, G.; Nersisyan, G.; Brauckmann, S.; Doria, D.; Gwynne, D.; Macchi, A.; Naughton, K.; Willi, O.; Lewis, C. L. S.; Borghesi, M.

2016-09-01

The divergent and broadband proton beams produced by the target normal sheath acceleration mechanism provide the unique opportunity to probe, in a point-projection imaging scheme, the dynamics of the transient electric and magnetic fields produced during laser-plasma interactions. Commonly such experimental setup entails two intense laser beams, where the interaction produced by one beam is probed with the protons produced by the second. We present here experimental studies of the ultra-fast charge dynamics along a wire connected to laser irradiated target carried out by employing a 'self' proton probing arrangement - i.e. by connecting the wire to the target generating the probe protons. The experimental data shows that an electromagnetic pulse carrying a significant amount of charge is launched along the wire, which travels as a unified pulse of 10s of ps duration with a velocity close to speed of light. The experimental capabilities and the analysis procedure of this specific type of proton probing technique are discussed.

Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

PubMed Central

Deng, Shaozhong; Xue, Changfeng; Baumketner, Andriy; Jacobs, Donald; Cai, Wei

2013-01-01

This paper extends the image charge solvation model (ICSM) [J. Chem. Phys. 131, 154103 (2009)], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated. PMID:23913979

Designing heteropolymers to fold into unique structures via water-mediated interactions.

PubMed

Jamadagni, Sumanth N; Bosoy, Christian; Garde, Shekhar

2010-10-28

Hydrophobic homopolymers collapse into globular structures in water driven by hydrophobic interactions. Here we employ extensive molecular dynamics simulations to study the collapse of heteropolymers containing one or two pairs of oppositely charged monomers. We show that charging a pair of monomers can dramatically alter the most stable conformations from compact globular to more open hairpin-like. We systematically explore a subset of the sequence space of one- and two-charge-pair polymers, focusing on the locations of the charge pairs. Conformational stability is governed by a balance of hydrophobic interactions, hydration and interactions of charge groups, water-mediated charged-hydrophobic monomer repulsions, and other factors. As a result, placing charge pairs in the middle, away from the hairpin ends, leads to stable hairpin-like structures. Turning off the monomer-water attractions enhances hydrophobic interactions significantly leading to a collapse into compact globular structures even for two-charge-pair heteropolymers. In contrast, the addition of salt leads to open and extended structures, suggesting that solvation of charged monomer sites by salt ions dominates the salt-induced enhancement of hydrophobic interactions. We also test the ability of a predictive scheme based on the additivity of free energy of contact formation. The success of the scheme for symmetric two-charge-pair sequences and the failure for their flipped versions highlight the complexity of the heteropolymer conformation space and of the design problem. Collectively, our results underscore the ability of tuning water-mediated interactions to design stable nonglobular structures in water and present model heteropolymers for further studies in the extended thermodynamic space and in inhomogeneous environments.

Charging of a conducting sphere in a weakly ionized collisional plasma: Temporal dynamics and stationary state

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

Grach, V. S., E-mail: vsgrach@app.sci-nnov.ru; Garasev, M. A.

2015-07-15

We consider the interaction of a isolated conducting sphere with a collisional weakly ionized plasma in an external field. We assume that the plasma consists of two species of ions neglecting of electrons. We take into account charging of the sphere due to sedimentation of plasma ions on it, the field of the sphere charge and the space charge, as well as recombination and molecular diffusion. The nonstationary problem of interaction of the sphere with the surrounding plasma is solved numerically. The temporal dynamics of the sphere charge and plasma perturbations is analyzed, as well as the properties of themore » stationary state. It is shown that the duration of transient period is determined by the recombination time and by the reverse conductivity of ions. The temporal dynamics of the sphere charge and plasma perturbations is determined by the intensity of recombination processes relative to the influence of the space charge field and diffusion. The stationary absolute value of the sphere charge increases linearly with the external electric field, decreases with the relative intensity of recombination processes and increases in the presence of substantial diffusion. The scales of the perturbed region in the plasma are determined by the radius of the sphere, the external field, the effect of diffusion, and the relative intensity of recombination processes. In the limiting case of the absence of molecular diffusion and a strong external field, the properties of the stationary state coincide with those obtained earlier as a result of approximate solution.« less

Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins.

PubMed

Mercadante, Davide; Wagner, Johannes A; Aramburu, Iker V; Lemke, Edward A; Gräter, Frauke

2017-09-12

Molecular dynamics (MD) simulations have valuably complemented experiments describing the dynamics of intrinsically disordered proteins (IDPs), particularly since the proposal of models to solve the artificial collapse of IDPs in silico. Such models suggest redefining nonbonded interactions, by either increasing water dispersion forces or adopting the Kirkwood-Buff force field. These approaches yield extended conformers that better comply with experiments, but it is unclear if they all sample the same intrachain dynamics of IDPs. We have tested this by employing MD simulations and single-molecule Förster resonance energy transfer spectroscopy to sample the dimensions of systems with different sequence compositions, namely strong and weak polyelectrolytes. For strong polyelectrolytes in which charge effects dominate, all the proposed solutions equally reproduce the expected ensemble's dimensions. For weak polyelectrolytes, at lower cutoffs, force fields abnormally alter intrachain dynamics, overestimating excluded volume over chain flexibility or reporting no difference between the dynamics of different chains. The TIP4PD water model alone can reproduce experimentally observed changes in extensions (dimensions), but not quantitatively and with only weak statistical significance. Force field limitations are reversed with increased interaction cutoffs, showing that chain dynamics are critically defined by the presence of long-range interactions. Force field analysis aside, our study provides the first insights into how long-range interactions critically define IDP dimensions and raises the question of which length range is crucial to correctly sample the overall dimensions and internal dynamics of the large group of weakly charged yet highly polar IDPs.

Aggregation and disaggregation dynamics of sedimented and charged superparamagnetic micro-particles in water suspension.

PubMed

Domínguez-García, P; Pastor, J M; Rubio, M A

2011-04-01

This article presents results on the aggregation and disaggregation kinetics on a 1 μm diameter charged superparamagnetic particles dispersed in water under a constant uniaxial magnetic field in experiments with salt (KCl) added to the suspension in order to observe the behaviour of the system when the electrical properties of the particles have been screened. These particles have an electric charge and are confined between two separated 100 μm thick quartz windows, and sediment near the charged bottom wall. The electrostatic interactions that take place in this experimental setup may affect the micro-structure and colloidal stability of the suspension and thus, the dynamics of aggregation and disaggregation.

Point charge representation of multicenter multipole moments in calculation of electrostatic properties

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

1993-01-01

Distributed Point Charge Models (PCM) for CO, (H2O)2, and HS-SH molecules have been computed from analytical expressions using multi-center multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.

Electrostatic, elastic and hydration-dependent interactions in dermis influencing volume exclusion and macromolecular transport.

PubMed

Øien, Alf H; Wiig, Helge

2016-07-07

Interstitial exclusion refers to the limitation of space available for plasma proteins and other macromolecules based on collagen and negatively charged glycosaminoglycans (GAGs) in the interstitial space. It is of particular importance to interstitial fluid and plasma volume regulation. Here we present a novel mechanical and mathematical model of the dynamic interactions of structural elements within the interstitium of the dermis at the microscopic level that may explain volume exclusion of charged and neutral macroparticles. At this level, the interstitium is considered to consist of elements called extracellular matrix (ECM) cells, again containing two main interacting structural components on a fluid background including anions and cations setting up osmotic forces: one smaller GAG component, having an intrinsic expansive electric force, and one bigger collagen component, having an intrinsic elastic force. Because of size differences, the GAG component interacts with a fraction of the collagen component only at normal hydration. This fraction, however, increases with rising hydration as a consequence of the modeled form of the interaction force between the GAGs and collagen. Collagen is locally displaced at variable degrees as hydration changes. Two models of GAGs are considered, having largely different geometries which demands different, but related, forms of GAG-collagen interaction forces. The effects of variable fixed charges on GAGs and of GAG density in tissue are evaluated taking into account observed volume exclusion properties of charged macromolecules as a function of tissue hydration. The presented models may improve our biophysical understanding of acting forces influencing tissue fluid dynamics. Such knowledge is significant when evaluating the transport of electrically charged and neutral macromolecules into and through the interstitium, and therefore to drug uptake and the therapeutic effects of macromolecular agents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dendronized fullerene-porphyrin conjugates in ortho, meta, and para positions: a charge-transfer assay.

PubMed

Krokos, Evangelos; Schubert, Christina; Spänig, Fabian; Ruppert, Michaela; Hirsch, Andreas; Guldi, Dirk M

2012-06-01

The physicochemical characterization, that is, ground and excited state, of a new series of dendronized porphyrin/fullerene electron donor-acceptor conjugates in nonaqueous and aqueous environments is reported. In contrast to previous work, we detail the charge-separation and charge-recombination dynamics in zinc and copper metalloporphyrins as a function of first- and second-generation dendrons as well as a function of ortho, meta, and para substitution. Both have an appreciable impact on the microenvironments of the redox-active constituents, namely the porphyrins and the fullerenes. As a matter of fact, the resulting charge-transfer dynamics were considerably impacted by the interplay between the associated forces that reach from dendron-induced shielding to dipole-charge interactions. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations.

PubMed

Korolev, Nikolay; Yu, Hang; Lyubartsev, Alexander P; Nordenskiöld, Lars

2014-10-01

The positively charged N-terminal histone tails play a crucial role in chromatin compaction and are important modulators of DNA transcription, recombination, and repair. The detailed mechanism of the interaction of histone tails with DNA remains elusive. To model the unspecific interaction of histone tails with DNA, all-atom molecular dynamics (MD) simulations were carried out for systems of four DNA 22-mers in the presence of 20 or 16 short fragments of the H4 histone tail (variations of the 16-23 a. a. KRHRKVLR sequence, as well as the unmodified fragment a. a.13-20, GGAKRHRK). This setup with high DNA concentration, explicit presence of DNA-DNA contacts, presence of unstructured cationic peptides (histone tails) and K(+) mimics the conditions of eukaryotic chromatin. A detailed account of the DNA interactions with the histone tail fragments, K(+) and water is presented. Furthermore, DNA structure and dynamics and its interplay with the histone tail fragments binding are analysed. The charged side chains of the lysines and arginines play major roles in the tail-mediated DNA-DNA attraction by forming bridges and by coordinating to the phosphate groups and to the electronegative sites in the minor groove. Binding of all species to DNA is dynamic. The structure of the unmodified fully-charged H4 16-23 a.a. fragment KRHRKVLR is dominated by a stretched conformation. The H4 tail a. a. fragment GGAKRHRK as well as the H4 Lys16 acetylated fragment are highly flexible. The present work allows capturing typical features of the histone tail-counterion-DNA structure, interaction and dynamics. © 2014 Wiley Periodicals, Inc.

Spin-charge coupled dynamics driven by a time-dependent magnetization

NASA Astrophysics Data System (ADS)

Tölle, Sebastian; Eckern, Ulrich; Gorini, Cosimo

2017-03-01

The spin-charge coupled dynamics in a thin, magnetized metallic system are investigated. The effective driving force acting on the charge carriers is generated by a dynamical magnetic texture, which can be induced, e.g., by a magnetic material in contact with a normal-metal system. We consider a general inversion-asymmetric substrate/normal-metal/magnet structure, which, by specifying the precise nature of each layer, can mimic various experimentally employed setups. Inversion symmetry breaking gives rise to an effective Rashba spin-orbit interaction. We derive general spin-charge kinetic equations which show that such spin-orbit interaction, together with anisotropic Elliott-Yafet spin relaxation, yields significant corrections to the magnetization-induced dynamics. In particular, we present a consistent treatment of the spin density and spin current contributions to the equations of motion, inter alia, identifying a term in the effective force which appears due to a spin current polarized parallel to the magnetization. This "inverse-spin-filter" contribution depends markedly on the parameter which describes the anisotropy in spin relaxation. To further highlight the physical meaning of the different contributions, the spin-pumping configuration of typical experimental setups is analyzed in detail. In the two-dimensional limit the buildup of dc voltage is dominated by the spin-galvanic (inverse Edelstein) effect. A measuring scheme that could isolate this contribution is discussed.

Solvation effects on like-charge attraction.

PubMed

Ghanbarian, Shahzad; Rottler, Jörg

2013-02-28

We present results of molecular dynamics simulations of the electrostatic interaction between two parallel charged rods in the presence of divalent counterions. Such polyelectrolytes have been considered as a simple model for understanding electrostatic interactions in highly charged biomolecules such as DNA. Since there are correlations between the free charge carriers, the phenomenon of like charge attraction appears for specific parameters. We explore the role of solvation effects and the resulting deviations from Coulomb's law on the nanoscale on this peculiar phenomenon. The behavior of the force between the charged rods in a simulation with atomistic representation of water molecules is completely different from a model in which water is modeled as a continuum dielectric. By calculating counterion-rodion pair correlation functions, we find that the presence of water molecules changes the structure of the counterion cloud and results in both qualitative and quantitative changes of the force between highly charged polyelectrolytes.

Manipulating semiconductor colloidal stability through doping.

PubMed

Fleharty, Mark E; van Swol, Frank; Petsev, Dimiter N

2014-10-10

The interface between a doped semiconductor material and electrolyte solution is of considerable fundamental interest, and is relevant to systems of practical importance. Both adjacent domains contain mobile charges, which respond to potential variations. This is exploited to design electronic and optoelectronic sensors, and other enabling semiconductor colloidal materials. We show that the charge mobility in both phases leads to a new type of interaction between semiconductor colloids suspended in aqueous electrolyte solutions. This interaction is due to the electrostatic response of the semiconductor interior to disturbances in the external field upon the approach of two particles. The electrostatic repulsion between two charged colloids is reduced from the one governed by the charged groups present at the particles surfaces. This type of interaction is unique to semiconductor particles and may have a substantial effect on the suspension dynamics and stability.

Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

NASA Astrophysics Data System (ADS)

Carnevale, V.; Raugei, S.

2009-12-01

Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

Vibrational properties of the amide group in acetanilide: A molecular-dynamics study

NASA Astrophysics Data System (ADS)

Campa, Alessandro; Giansanti, Andrea; Tenenbaum, Alexander

1987-09-01

A simplified classical model of acetanilide crystal is built in order to study the mechanisms of vibrational energy transduction in a hydrogen-bonded solid. The intermolecular hydrogen bond is modeled by an electrostatic interaction between neighboring excess charges on hydrogen and oxygen atoms. The intramolecular interaction in the peptide group is provided by a dipole-charge interaction. Forces are calculated up to second-order terms in the atomic displacements from equilibrium positions; the model is thus a chain of nonlinear coupled oscillators. Numerical molecular-dynamics experiments are performed on chain segments of five molecules. The dynamics is ordered, at all temperatures. Energy is widely exchanged between the stretching and the bending of the N-H bond, with characteristic times of the order of 0.2 ps. Energy transduction through the H bond is somewhat slower and of smaller amplitude, and is strongly reduced when the energies of the two bound molecules are very different: This could reduce the dissipation of localized energy fluctuations.

Surface charge effects in protein adsorption on nanodiamonds

NASA Astrophysics Data System (ADS)

Aramesh, M.; Shimoni, O.; Ostrikov, K.; Prawer, S.; Cervenka, J.

2015-03-01

Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids.Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids. Electronic supplementary information (ESI) available: The FTIR spectrum of nanodiamonds, QCM-D profiles of 50 nm nanodiamond adsorption on silica surfaces, QCM-D profiles of protein desorption after rinsing with water (rinsing experiment) and the full FTIR spectrum of proteins before and after adsorption on ND particles. See DOI: 10.1039/c5nr00250h

Fast multipole method using Cartesian tensor in beam dynamic simulation

DOE PAGES

Zhang, He; Huang, He; Li, Rui; ...

2017-03-06

Here, the fast multipole method (FMM) using traceless totally symmetric Cartesian tensor to calculate the Coulomb interaction between charged particles will be presented. The Cartesian tensor-based FMM can be generalized to treat other non-oscillating interactions with the help of the differential algebra or the truncated power series algebra. Issues on implementation of the FMM in beam dynamic simulations are also discussed.

Investigation of electric charge on inertial particle dynamics in turbulence

NASA Astrophysics Data System (ADS)

Lu, Jiang; Shaw, Raymond

2014-11-01

The behavior of electrically charged, inertial particles in homogeneous, isotropic turbulence is investigated. Both like-charged and oppositely-charged particle interactions are considered. Direct numerical simulations (DNS) of turbulence in a periodic box using the pseudospectral numerical method are performed, with Lagrangian tracking of the particles. We study effects of mutual electrostatic repulsion and attraction on the particle dynamics, as quantified by the radial distribution function (RDF) and the radial relative velocity. For the like-charged particle case, the Coulomb force leads to a short range repulsion behavior and an RDF reminiscent of that for a dilute gas. For the oppositely-charged particle case, the Coulomb force increases the RDF beyond that already occurring for neutral inertial particles. For both cases, the relative velocities are calculated as a function of particle separation distance and show distinct deviations from the expected scaling within the dissipation range. This research was supported by NASA Grant NNX113AF90G.

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

Torii, Hajime, E-mail: torii.hajime@shizuoka.ac.jp

The intensity of the band at ∼200 cm{sup −1} (∼6 THz) in the Terahertz spectrum of liquid water mainly arises from the modulations of the extent of intermolecular charge transfer through hydrogen bonds, called intermolecular charge fluxes, occurring upon molecular translations along the O…H hydrogen bonds. To obtain reasonable spectral profiles from simulations, it is necessary to effectively incorporate the effects of those intermolecular charge fluxes, but apparently it is not possible by simple classical molecular dynamics simulations with fixed atomic partial charges even if they are amended by molecular induced dipoles due to intermolecular electrostatic interactions. The present paper showsmore » how we can do reasonably correct spectral simulations, without resorting to fully ab initio molecular dynamics.« less

Luminescent tunable polydots: Charge effects in confined geometry

DOE PAGES

Wijesinghe, Sidath; Maskey, Sabina; Perahia, Dvora; ...

2017-06-28

Long-lived soft nanoparticles, formed by conjugated polymers, constitute a new class of far-from-equilibrium responsive structures for nano-medicine. Tethering ionizable groups to the polymers enables functionality. However concurrently, the ionic groups perturb the delicate balance of interactions that governs these particles. Using fully atomistic molecular dynamics simulations, this study probed the effects of charged groups tethered to poly para phenylene ethynylene substituted by alkyl groups on the polymer conformation and dynamics in confined geometry. As a result, we find that the ionizable groups affect the entire shape of the polydots and impact the conformation and dynamics of the polymer.

Universality and critical behavior of the dynamical Mott transition in a system with long-range interactions

DOE PAGES

Rademaker, Louk; Vinokur, Valerii M.; Galda, Alexey

2017-03-16

Here, we study numerically the voltage-induced breakdown of a Mott insulating phase in a system of charged classical particles with long-range interactions. At half-filling on a square lattice this system exhibits Mott localization in the form of a checkerboard pattern. We find universal scaling behavior of the current at the dynamic Mott insulator-metal transition and calculate scaling exponents corresponding to the transition. Our results are in agreement, up to a difference in universality class, with recent experimental evidence of a dynamic Mott transition in a system of interacting superconducting vortices.

Universality and critical behavior of the dynamical Mott transition in a system with long-range interactions.

PubMed

Rademaker, Louk; Vinokur, Valerii M; Galda, Alexey

2017-03-16

We study numerically the voltage-induced breakdown of a Mott insulating phase in a system of charged classical particles with long-range interactions. At half-filling on a square lattice this system exhibits Mott localization in the form of a checkerboard pattern. We find universal scaling behavior of the current at the dynamic Mott insulator-metal transition and calculate scaling exponents corresponding to the transition. Our results are in agreement, up to a difference in universality class, with recent experimental evidence of a dynamic Mott transition in a system of interacting superconducting vortices.

Detailed Investigations of Interactions between Ionizing Radiation and Neutral Gases

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

Landers, Allen L

We are investigating phenomena that stem from the many body dynamics associated with ionization of an atom or molecule by photon or charged particle. Our program is funded through the Department of Energy EPSCoR Laboratory Partnership Award in collaboration with Lawrence Berkeley National Laboratory. We are using variations on the well established COLTRIMS technique to measure ions and electrons ejected during these interactions. Photoionization measurements take place at the Advanced Light Source at LBNL as part of the ALS-COLTRIMS collaboration with the groups of Reinhard Dörner at Frankfurt and Ali Belkacem at LBNL. Additional experiments on charged particle impact aremore » conducted locally at Auburn University where we are studying the dissociative molecular dynamics following interactions with either ions or electrons over a velocity range of 1 to 12 atomic units.« less

Acyl chain length and charge effect on Tamoxifen-lipid model membrane interactions

NASA Astrophysics Data System (ADS)

Bilge, Duygu; Kazanci, Nadide; Severcan, Feride

2013-05-01

Tamoxifen (TAM), which is an antiestrogenic agent, is widely used during chemotherapy of breast, pancreas, brain and liver cancers. In this study, TAM and model membrane interactions in the form of multilamellar vesicles (MLVs) were studied for lipids containing different acyl chain length and different charge status as a function of different TAM (1, 6, 9 and 15 mol%) concentrations. Zwitterionic lipids namely dipalmitoyl phosphatidylcholine (DPPC), and dimyristoylphosphatidylcholine (DMPC) lipids were used to see the acyl chain length effect and anionic dipalmitoyl phosphtidylglycerol (DPPG) lipid was used to see the charge effect. For this purpose Fourier transform-infrared (FTIR) spectroscopic and differential scanning calorimetric (DSC) techniques have been conducted. For zwitterionic lipid, concentration dependent different action of TAM was observed both in the gel and liquid crystalline phases by significantly increasing the lipid order and decreasing the dynamics for 1 mol% TAM, while decreasing the lipid order and increasing the dynamics of the lipids for higher concentrations (6, 9 and 15 mol%). However, different than neutral lipids, the dynamics and disorder of DPPG liposome increased for all TAM concentrations. The interactions between TAM and head group of multilamellar liposomes was monitored by analyzing the Cdbnd O stretching and PO2- antisymmetric double bond stretching bands. Increasing Tamoxifen concentrations led to a dehydration around these functional groups in the polar part of the lipids. DSC studies showed that for all types of lipids, TAM eliminates the pre-transition, shifts the main phase transition to lower temperatures and broadened the phase transition curve. The results indicate that not the acyl chain length but the charge status of the polar head group induces different effects on lipid membranes order and dynamics.

Dynamic response functions, helical gaps, and fractional charges in quantum wires

NASA Astrophysics Data System (ADS)

Meng, Tobias; Pedder, Christopher J.; Tiwari, Rakesh P.; Schmidt, Thomas L.

We show how experimentally accessible dynamic response functions can discriminate between helical gaps due to magnetic field, and helical gaps driven by electron-electron interactions (''umklapp gaps''). The latter are interesting since they feature gapped quasiparticles of fractional charge e / 2 , and - when coupled to a standard superconductor - an 8 π-Josephson effect and topological zero energy states bound to interfaces. National Research Fund, Luxembourg (ATTRACT 7556175), Deutsche Forschungsgemeinschaft (GRK 1621 and SFB 1143), Swiss National Science Foundation.

Evaluation of reduced point charge models of proteins through Molecular Dynamics simulations: application to the Vps27 UIM-1-Ubiquitin complex.

PubMed

Leherte, Laurence; Vercauteren, Daniel P

2014-02-01

Reduced point charge models of amino acids are designed, (i) from local extrema positions in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions, and (ii) from local maxima positions in promolecular electron density distribution functions. Corresponding charge values are fitted versus all-atom Amber99 MEPs. To easily generate reduced point charge models for protein structures, libraries of amino acid templates are built. The program GROMACS is used to generate stable Molecular Dynamics trajectories of an Ubiquitin-ligand complex (PDB: 1Q0W), under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a nul mass and radius. The results illustrate how the intra- and inter-molecular H-bond interactions are affected by the degree of reduction of the point charge models and give directions for their implementation; a special attention to the atoms selected to locate the virtual sites and to the Coulomb-14 interactions is needed. Results obtained at various temperatures suggest that the use of reduced point charge models allows to probe local potential hyper-surface minima that are similar to the all-atom ones, but are characterized by lower energy barriers. It enables to generate various conformations of the protein complex more rapidly than the all-atom point charge representation. Copyright © 2013 Elsevier Inc. All rights reserved.

Interaction of single-walled carbon nanotubes with poly(propyl ether imine) dendrimers

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

Jayamurugan, G.; Rajesh, Y. B. R. D.; Jayaraman, N.

2011-03-14

We study the complexation of nontoxic, native poly(propyl ether imine) dendrimers with single-walled carbon nanotubes (SWNTs). The interaction was monitored by measuring the quenching of inherent fluorescence of the dendrimer. The dendrimer-nanotube binding also resulted in the increased electrical resistance of the hole doped SWNT, due to charge-transfer interaction between dendrimer and nanotube. This charge-transfer interaction was further corroborated by observing a shift in frequency of the tangential Raman modes of SWNT. We also report the effect of acidic and neutral pH conditions on the binding affinities. Experimental studies were supplemented by all atom molecular dynamics simulations to provide amore » microscopic picture of the dendrimer-nanotube complex. The complexation was achieved through charge transfer and hydrophobic interactions, aided by multitude of oxygen, nitrogen, and n-propyl moieties of the dendrimer.« less

Modeling of electrochemical flow capacitors using Stokesian dynamics

NASA Astrophysics Data System (ADS)

Karzar Jeddi, Mehdi; Luo, Haoxiang; Cummings, Peter; Hatzell, Kelsey

2017-11-01

Electrochemical flow capacitors (EFCs) are supercapacitors designed to store electrical energy in the form of electrical double layer (EDL) near the surface of porous carbon particles. During its operation, a slurry of activated carbon beads and smaller carbon black particles is pumped between two flat and parallel electrodes. In the charging phase, ions in the electrolyte diffuse to the EDL, and electrical charges percolate through the dynamic network of particles from the flat electrodes; during the discharging phase, the process is reversed with the ions released to the bulk fluid and electrical charges percolating back through the network. In these processes, the relative motion and contact of particle of different sizes affect not only the rheology of the slurry but also charge transfer of the percolation network. In this study, we use Stoekesian dynamics simulation to investigate the role of hydrodynamic interactions of packed carbon particles in the charging/discharging behaviors of EFCs. We derived mobility functions for polydisperse spheres near a no-slip wall. A code is implemented and validated, and a simple charging model has been incorporated to represent charge transfer. Theoretical formulation and results demonstration will be presented in this talk.

Quenched dynamics and spin-charge separation in an interacting topological lattice

NASA Astrophysics Data System (ADS)

Barbiero, L.; Santos, L.; Goldman, N.

2018-05-01

We analyze the static and dynamical properties of a one-dimensional topological lattice, the fermionic Su-Schrieffer-Heeger model, in the presence of on-site interactions. Based on a study of charge and spin correlation functions, we elucidate the nature of the topological edge modes, which, depending on the sign of the interactions, either display particles of opposite spin on opposite edges, or a pair and a holon. This study of correlation functions also highlights the strong entanglement that exists between the opposite edges of the system. This last feature has remarkable consequences upon subjecting the system to a quench, where an instantaneous edge-to-edge signal appears in the correlation functions characterizing the edge modes. Besides, other correlation functions are shown to propagate in the bulk according to the light cone imposed by the Lieb-Robinson bound. Our study reveals how one-dimensional lattices exhibiting entangled topological edge modes allow for a nontrivial correlation spreading, while providing an accessible platform to detect spin-charge separation using state-of-the-art experimental techniques.

Elucidating the Ultrafast Dynamics of Photoinduced Charge Separation in Metalloporphyrin-Fullerene Dyads Across the Electromagnetic Spectrum

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

Zhang, J.; Pápai, M.; Hirsch, A.

Metalloporphyrins are prominent building blocks in the synthetic toolbox of advanced photodriven molecular devices. When the central ion is paramagnetic, the relaxation pathways within the manifold of excited states are highly intricate so that unravelling the intramolecular energy and electron transfer processes is usually a very complex task. This fact is critically hampering the development of applications based on the enhanced coupling offered by the electronic exchange interaction. In this work, the dynamics of charge separation in a copper porphyrin-fullerene are studied with several complementary spectroscopic tools across the electromagnetic spectrum (from near infra-red to X-ray wavelengths), each of themmore » providing specific diagnostics. Correlating the various rates clearly demonstrates that the lifetime of the photoinduced charge-separated state exceeds by about 10 fold that of the isolated photoexcited CuII porphyrin. As revealed by the spectral modifications in the XANES region, this stabilization is accompanied by a transient change in covalency around the CuII center, which is induced by an enhanced interaction with the C60 moiety. This experimental finding is further confirmed by state-of-the art calculations using DFT and TD-DFT including dispersion effects that explain the electrostatic and structural origins of this interaction, as the CuIIP cation becomes ruffled and approaches closer to the fullerene in the charge-separated state. From a methodological point of view, these results exemplify the potential of multielectron excitation features in transient X-ray spectra as future diagnostics of sub-femtosecond electronic dynamics. From a practical point of view, this work is paving the way for elucidating out-of-equilibrium electron transfer events coupled to magnetic interaction processes on their intrinsic time-scales.« less

Modulating interactions between ligand-coated nanoparticles and phase-separated lipid bilayers by varying the ligand density and the surface charge.

PubMed

Chen, Xiaojie; Tieleman, D Peter; Liang, Qing

2018-02-01

The interactions between nanoparticles and lipid bilayers are critical in applications of nanoparticles in nanomedicine, cell imaging, toxicology, and elsewhere. Here, we investigate the interactions between nanoparticles coated with neutral and/or charged ligands and phase-separated lipid bilayers using coarse-grained molecular dynamics simulation. Both penetration and adsorption processes as well as the final distribution of the nanoparticles can be readily modulated by varying the ligand density and the surface charge of the nanoparticles. Completely hydrophobic (neutral) nanoparticles with larger size initially preferentially penetrate into the liquid-disordered region of the lipid bilayer and finally transfer into the liquid-ordered region; partially hydrophilic nanoparticles with low or moderate surface charge tend to either distribute in the liquid-disordered region or be adsorbed on the surface of the lipid bilayer, while strongly hydrophilic nanoparticles with high surface charge always reside on the surface of the lipid bilayer. Interactions of the nanoparticles with the lipid bilayers are affected by the surface charge of nanoparticles, hydrophobic mismatch, bending of the ligands, and the packing state of the lipids. Insight in these factors can be used to improve the efficiency of designing nanoparticles for specific applications.

Surface charge effects in protein adsorption on nanodiamonds.

PubMed

Aramesh, M; Shimoni, O; Ostrikov, K; Prawer, S; Cervenka, J

2015-03-19

Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids.

Molecular dynamics simulations on the local order of liquid and amorphous ZnTe

NASA Astrophysics Data System (ADS)

Rino, José Pedro; Borges, Denilson; Mota, Rita C.; Silva, Maurício A. P.

2008-05-01

Molecular dynamics studies of structural and dynamical correlations of molten and vitreous states under several conditions of density and temperature were performed. We use an effective recently proposed interatomic potential, consisting of two- and three-body covalent interactions which has successfully described the structural, dynamical, and structural phase transformation induced by pressure in ZnTe [D. S. Borges and J. P. Rino, Phys. Rev. B 72, 014107 (2005)]. The two-body term of the interaction potential consists of Coulomb interaction resulting from charge transfer, steric repulsion due to atomic sizes, charge-dipole interaction to include the effect of electronic polarizability of anions, and dipole-dipole (van der Waals) interactions. The three-body covalent term is a modification of the Stillinger-Weber potential. Molecular dynamics simulations in isobaric-isenthalpic ensemble have been performed for systems amounting to 4096 and 64 000 particles. Starting from a crystalline zinc-blende (ZB) structure, the system is initially heated until a very homogeneous liquid is obtained. The vitreous zinc telluride phase is attained by cooling the liquid at sufficiently fast cooling rates, while slower cooling rates lead to a disordered ZB crystalline structure. Two- and three-body correlations for the liquid and vitreous phases are analyzed through pair distribution functions, static structure factors, and bond angle distributions. In particular, the neutron static structure factor for the liquid phase is in very good agreement with both the reported experimental data and first-principles simulations.

Make dark matter charged again

NASA Astrophysics Data System (ADS)

Agrawal, Prateek; Cyr-Racine, Francis-Yan; Randall, Lisa; Scholtz, Jakub

2017-05-01

We revisit constraints on dark matter that is charged under a U(1) gauge group in the dark sector, decoupled from Standard Model forces. We find that the strongest constraints in the literature are subject to a number of mitigating factors. For instance, the naive dark matter thermalization timescale in halos is corrected by saturation effects that slow down isotropization for modest ellipticities. The weakened bounds uncover interesting parameter space, making models with weak-scale charged dark matter viable, even with electromagnetic strength interaction. This also leads to the intriguing possibility that dark matter self-interactions within small dwarf galaxies are extremely large, a relatively unexplored regime in current simulations. Such strong interactions suppress heat transfer over scales larger than the dark matter mean free path, inducing a dynamical cutoff length scale above which the system appears to have only feeble interactions. These effects must be taken into account to assess the viability of darkly-charged dark matter. Future analyses and measurements should probe a promising region of parameter space for this model.

Molecular understanding of osmosis in semipermeable membranes.

PubMed

Raghunathan, A V; Aluru, N R

2006-07-14

We investigate single-file osmosis of water through a semipermeable membrane with an uncharged, a positively and a negatively charged nanopore. Molecular dynamics simulations indicate that the osmotic flux through a negatively charged pore (J_) is higher compared to the osmotic flux in a positively charged pore (J+) followed by the osmotic flux in the uncharged pore (J(0)), i.e., J_ > J+ > J(0). The molecular mechanisms governing osmosis, steady state osmosis, and the observed osmotic flux dependence on the nanopore charge are explained by computing all the molecular interactions involved and identifying the molecular interactions that play an important role during and after osmosis. This study helps in a fundamental understanding of osmosis and in the design of advanced nanoporous membranes for various applications of osmosis.

Control of Screening of a Charged Particle in Electrolytic Aqueous Paul Trap

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

Park, Jae Hyun nmn; Krstic, Predrag S

2011-01-01

Individual charged particles could be trapped and confined in the combined radio-frequency and DC quadrupole electric field of an aqueous Paul trap. Viscosity of water improves confinement and extends the range of the trap parameters which characterize the stability of the trap. Electrolyte, if present in aqueous solution, may screen the charged particle and thus partially or fully suppress electrophoretic interaction with the applied filed, possibly reducing it to a generally much weaker dielectrophoretic interaction with an induced dipole. Applying molecular dynamics simulation we show that the quadrupole field has a different affects at the electrolyte ions and at muchmore » heavier charged particle, effectively eliminating the screening effect and reinstating the electrophoretic confinement.« less

Control Of Screening Of A Charged Particle In Electrolytic Aqueous Paul Trap

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

Park, Jae Hyun; Krstic, Predrag S.

2011-06-01

Individual charged particles could be trapped and confined by the combined radio-frequency and DC quadrupole electric field of an aqueous Paul trap. Viscosity of water improves confinement and extends the range of the trap parameters which characterize the stability of the trap. Electrolyte, if present in aqueous solution, may screen the charged particle and thus partially or fully suppress electrophoretic interaction with the applied filed, possibly reducing it to a generally much weaker dielectrophoretic interaction with an induced dipole. Applying molecular dynamics simulation we show that the quadrupole field has a different effect at the electrolyte ions and at muchmore » heavier charged particle, effectively eliminating the screening by electrolyte ions and reinstating the electrophoretic confinement.« less

Early-stage aggregation in three-dimensional charged granular gas.

PubMed

Singh, Chamkor; Mazza, Marco G

2018-02-01

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

Early-stage aggregation in three-dimensional charged granular gas

NASA Astrophysics Data System (ADS)

Singh, Chamkor; Mazza, Marco G.

2018-02-01

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

Probing Polyoxometalate-Protein Interactions Using Molecular Dynamics Simulations.

PubMed

Solé-Daura, Albert; Goovaerts, Vincent; Stroobants, Karen; Absillis, Gregory; Jiménez-Lozano, Pablo; Poblet, Josep M; Hirst, Jonathan D; Parac-Vogt, Tatjana N; Carbó, Jorge J

2016-10-17

The molecular interactions between the Ce IV -substituted Keggin anion [PW 11 O 39 Ce(OH 2 ) 4 ] 3- (CeK) and hen egg-white lysozyme (HEWL) were investigated by molecular dynamics simulations. The analysis of CeK was compared with the Ce IV -substituted Keggin dimer [(PW 11 O 39 ) 2 Ce] 10- (CeK 2 ) and the Zr IV -substituted Lindqvist anion [W 5 O 18 Zr(OH 2 )(OH)] 3- (ZrL) to understand how POM features such as shape, size, charge, or type of incorporated metal ion influence the POM⋅⋅⋅protein interactions. Simulations revealed two regions of the protein in which the CeK anion interacts strongly: cationic sites formed by Arg21 and by Arg45 and Arg68. The POMs chiefly interact with the side chains of the positively charged (arginines, lysines) and the polar uncharged residues (tyrosines, serines, aspargines) via electrostatic attraction and hydrogen bonding with the oxygen atoms of the POM framework. The CeK anion shows higher protein affinity than the CeK 2 and ZrL anions, because it is less hydrophilic and it has the right size and shape for establishing interactions with several residues simultaneously. The larger, more negatively charged CeK 2 anion has a high solvent-accessible surface, which is sub-optimal for the interaction, while the smaller ZrL anion is highly hydrophilic and cannot efficiently interact with several residues simultaneously. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamical Lorentz symmetry breaking in 3D and charge fractionalization

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

Charneski, B.; Gomes, M.; Silva, A. J. da

2009-03-15

We analyze the breaking of Lorentz invariance in a 3D model of fermion fields self-coupled through four-fermion interactions. The low-energy limit of the theory contains various submodels which are similar to those used in the study of graphene or in the description of irrational charge fractionalization.

Phase transitions of a water overlayer on charged graphene: from electromelting to electrofreezing.

PubMed

Zhu, Xueyan; Yuan, Quanzi; Zhao, Ya-Pu

2014-05-21

We show by using molecular dynamics simulations that a water overlayer on charged graphene experiences first-order ice-to-liquid (electromelting), and then liquid-to-ice (electrofreezing) phase transitions with the increase of the charge value. Corresponding to the ice-liquid-ice transition, the variations of the order parameters indicate an order-disorder-order transition. The key to this novel phenomenon is the surface charge induced change of the orientations of water dipoles, which leads to the change of the water-water interactions from being attractive to repulsive at a critical charge value qc. To further uncover how the orientations of water dipoles influence the interaction strength between water molecules, a theoretical model considering both the Coulomb and van der Waals interactions is established. The results show that with the increase of the charge value, the interaction strength between water molecules decreases below qc, then increases above qc. These two inverse processes lead to electromelting and electrofreezing, respectively. Combining this model with the Eyring equation, the diffusion coefficient is obtained, the variation of which is in qualitative agreement with the simulation results. Our findings not only expand our knowledge of the graphene-water interface, but related analyses could also help recognize the controversial role of the surface charge or electric field in promoting phase transitions of water.

Ligand-modulated interactions between charged monolayer-protected Au144 (SR)60 gold nanoparticles in physiological saline

NASA Astrophysics Data System (ADS)

Villarreal, Oscar; Chen, Liao; Whetten, Robert; Yacaman, Miguel

2015-03-01

We studied the interactions of functionalized Au144 nanoparticles (NPs) in a near-physiological environment through all-atom molecular dynamics simulations. The AuNPs were coated with a homogeneous selection of 60 thiolates: 11-mercapto-1-undecanesulfonate, 5-mercapto-1-pentanesulfonate, 5-mercapto-1-pentane-amine, 4-mercapto-benzoate or 4-mercapto-benzamide. These ligands were selected to elucidate how the aggregation behavior depends on the ligands' sign of charge, length, and flexibility. Simulating the dynamics of a pair of identical AuNPs in a cell of saline of 150 mM NaCl in addition to 120 Na+/Cl- counter-ions, we computed the aggregation affinities from the potential of mean force as a function of the pair separation. We found that NPs coated with negatively charged, short ligands have the strongest affinities mediated by multiple Na+ counter-ions residing on a plane in-between the pair and forming ``salt bridges'' to both NPs. Positively charged NPs have weaker affinities, as Cl counter-ions form fewer and weaker salt bridges. The longer ligands' large fluctuations disfavor the forming of salt bridges, enable hydrophobic contact between the exposed hydrocarbon chains and interact at greater separations due to the fact that the screening effect is rather incomplete. Supported by the CONACYT, NIH, NSF and TACC.

Ultrafast dynamics of ligand and substrate interaction in endothelial nitric oxide synthase under Soret excitation.

PubMed

Hung, Chih-Chang; Yabushita, Atsushi; Kobayashi, Takayoshi; Chen, Pei-Feng; Liang, Keng S

2016-01-01

Ultrafast transient absorption spectroscopy of endothelial NOS oxygenase domain (eNOS-oxy) was performed to study dynamics of ligand or substrate interaction under Soret band excitation. Photo-excitation dissociates imidazole ligand in <300fs, then followed by vibrational cooling and recombination within 2ps. Such impulsive bond breaking and late rebinding generate proteinquakes, which relaxes in several tens of picoseconds. The photo excited dynamics of eNOS-oxy with L-arginine substrate mainly occurs at the local site of heme, including ultrafast internal conversion within 400fs, vibrational cooling, charge transfer, and complete ground-state recovery within 1.4ps. The eNOS-oxy without additive is partially bound with water molecule, thus its photoexcited dynamics also shows ligand dissociation in <800fs. Then it followed by vibrational cooling coupled with charge transfer in 4.8ps, and recombination of ligand to distal side of heme in 12ps. Copyright © 2016 Elsevier B.V. All rights reserved.

Weak polyelectrolyte complexation driven by associative charging.

PubMed

Rathee, Vikramjit S; Zervoudakis, Aristotle J; Sidky, Hythem; Sikora, Benjamin J; Whitmer, Jonathan K

2018-03-21

Weak polyelectrolytes are relevant for a wide range of fields; in particular, they have been investigated as "smart" materials for chemical separations and drug delivery. The charges on weak polyelectrolytes are dynamic, causing polymer chains to adopt different equilibrium conformations even with relatively small changes to the surrounding environment. Currently, there exists no comprehensive picture of this behavior, particularly where polymer-polymer interactions have the potential to affect charging properties significantly. In this study, we elucidate the novel interplay between weak polyelectrolyte charging and complexation behavior through coupled molecular dynamics and Monte Carlo simulations. Specifically, we investigate a model of two equal-length and oppositely charging polymer chains in an implicit salt solution represented through Debye-Hückel interactions. The charging tendency of each chain, along with the salt concentration, is varied to determine the existence and extent of cooperativity in charging and complexation. Strong cooperation in the charging of these chains is observed at large Debye lengths, corresponding to low salt concentrations, while at lower Debye lengths (higher salt concentrations), the chains behave in apparent isolation. When the electrostatic coupling is long-ranged, we find that a highly charged chain strongly promotes the charging of its partner chain, even if the environment is unfavorable for an isolated version of that partner chain. Evidence of this phenomenon is supported by a drop in the potential energy of the system, which does not occur at the lower Debye lengths where both potential energies and charge fractions converge for all partner chain charging tendencies. The discovery of this cooperation will be helpful in developing "smart" drug delivery mechanisms by allowing for better predictions for the dissociation point of delivery complexes.

Weak polyelectrolyte complexation driven by associative charging

NASA Astrophysics Data System (ADS)

Rathee, Vikramjit S.; Zervoudakis, Aristotle J.; Sidky, Hythem; Sikora, Benjamin J.; Whitmer, Jonathan K.

2018-03-01

Weak polyelectrolytes are relevant for a wide range of fields; in particular, they have been investigated as "smart" materials for chemical separations and drug delivery. The charges on weak polyelectrolytes are dynamic, causing polymer chains to adopt different equilibrium conformations even with relatively small changes to the surrounding environment. Currently, there exists no comprehensive picture of this behavior, particularly where polymer-polymer interactions have the potential to affect charging properties significantly. In this study, we elucidate the novel interplay between weak polyelectrolyte charging and complexation behavior through coupled molecular dynamics and Monte Carlo simulations. Specifically, we investigate a model of two equal-length and oppositely charging polymer chains in an implicit salt solution represented through Debye-Hückel interactions. The charging tendency of each chain, along with the salt concentration, is varied to determine the existence and extent of cooperativity in charging and complexation. Strong cooperation in the charging of these chains is observed at large Debye lengths, corresponding to low salt concentrations, while at lower Debye lengths (higher salt concentrations), the chains behave in apparent isolation. When the electrostatic coupling is long-ranged, we find that a highly charged chain strongly promotes the charging of its partner chain, even if the environment is unfavorable for an isolated version of that partner chain. Evidence of this phenomenon is supported by a drop in the potential energy of the system, which does not occur at the lower Debye lengths where both potential energies and charge fractions converge for all partner chain charging tendencies. The discovery of this cooperation will be helpful in developing "smart" drug delivery mechanisms by allowing for better predictions for the dissociation point of delivery complexes.

Gyroscopic effect in low-energy classical capture of a rotating quadrupolar diatom by an ion.

PubMed

Dashevskaya, Elena; Litvin, Iliya; Nikitin, Evgueni

2006-03-09

The low-energy capture of homonuclear diatoms by ions is due mainly to the long-range part of the interpartner potential with leading terms that correspond to charge-quadrupole interaction and charge-induced dipole interaction. The capture dynamics is described by the perturbed-rotor adiabatic potentials and the Coriolis interaction between manifold of states that belong to a given value of the intrinsic angular momentum. When the latter is large enough, it can noticeably affect the capture cross section calculated in the adiabatic channel approximation due to the gyroscopic property of a rotating diatom. This paper presents the low-energy (low-temperature) state-selected partial and mean capture cross sections (rate coefficients) for the charge-quadrupole interaction that include the gyroscopic effect (decoupling of intrinsic angular momentum from the collision axis), quantum correction for the diatom rotation, and the correction for the charge-induced dipole interaction. These results complement recent studies on the gyroscopic effect in the quantum regime of diatom-ion capture (Dashevskaya, E. I.; Litvin, I.; Nikitin, E. E.; Troe, J. J. Chem. Phys. 2004, 120, 9989-9997).

Ionic strength independence of charge distributions in solvation of biomolecules

NASA Astrophysics Data System (ADS)

Virtanen, J. J.; Sosnick, T. R.; Freed, K. F.

2014-12-01

Electrostatic forces enormously impact the structure, interactions, and function of biomolecules. We perform all-atom molecular dynamics simulations for 5 proteins and 5 RNAs to determine the dependence on ionic strength of the ion and water charge distributions surrounding the biomolecules, as well as the contributions of ions to the electrostatic free energy of interaction between the biomolecule and the surrounding salt solution (for a total of 40 different biomolecule/solvent combinations). Although water provides the dominant contribution to the charge density distribution and to the electrostatic potential even in 1M NaCl solutions, the contributions of water molecules and of ions to the total electrostatic interaction free energy with the solvated biomolecule are comparable. The electrostatic biomolecule/solvent interaction energies and the total charge distribution exhibit a remarkable insensitivity to salt concentrations over a huge range of salt concentrations (20 mM to 1M NaCl). The electrostatic potentials near the biomolecule's surface obtained from the MD simulations differ markedly, as expected, from the potentials predicted by continuum dielectric models, even though the total electrostatic interaction free energies are within 11% of each other.

Hybrid finite element and Brownian dynamics method for charged particles

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

Huber, Gary A., E-mail: ghuber@ucsd.edu; Miao, Yinglong; Zhou, Shenggao

2016-04-28

Diffusion is often the rate-determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. A previous study introduced a new hybrid diffusion method that couples the strengths of each of these two methods, but was limited by the lack of interactions among the particles; the force on each particle had to be from an external field. This study further develops the method to allow charged particles. The method is derived for a general multidimensional system and is presented usingmore » a basic test case for a one-dimensional linear system with one charged species and a radially symmetric system with three charged species.« less

Interactions in charged colloidal suspensions: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Padidela, Uday Kumar; Behera, Raghu Nath

2017-07-01

Colloidal suspensions are extensively used in everyday life and find several applications in the pharmaceutical, chemical, food industries, etc. We present the classical molecular dynamics simulation results of the structural and transport properties of charged colloidal suspensions as a function of its size, charge and concentration. The system is viewed as a two-component (colloids and counterions) primitive model consisting of spherical colloid particle (macroion) and the counterions (micro-particles), which are treated explicitly. The solvent is treated as dielectric continuum. A systematic trend in the radial distribution functions g(r), potential of mean force W(r), different thermodynamic properties and diffusion coefficients is obtained as a function of colloid charge, size and concentration. An attractive minimum in W(r) is obtained at short interparticle distance.

An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations

NASA Astrophysics Data System (ADS)

Poursina, Mohammad; Anderson, Kurt S.

2014-08-01

This paper presents a novel algorithm to approximate the long-range electrostatic potential field in the Cartesian coordinates applicable to 3D coarse-grained simulations of biopolymers. In such models, coarse-grained clusters are formed via treating groups of atoms as rigid and/or flexible bodies connected together via kinematic joints. Therefore, multibody dynamic techniques are used to form and solve the equations of motion of such coarse-grained systems. In this article, the approximations for the potential fields due to the interaction between a highly negatively/positively charged pseudo-atom and charged particles, as well as the interaction between clusters of charged particles, are presented. These approximations are expressed in terms of physical and geometrical properties of the bodies such as the entire charge, the location of the center of charge, and the pseudo-inertia tensor about the center of charge of the clusters. Further, a novel substructuring scheme is introduced to implement the presented far-field potential evaluations in a binary tree framework as opposed to the existing quadtree and octree strategies of implementing fast multipole method. Using the presented Lagrangian grids, the electrostatic potential is recursively calculated via sweeping two passes: assembly and disassembly. In the assembly pass, adjacent charged bodies are combined together to form new clusters. Then, the potential field of each cluster due to its interaction with faraway resulting clusters is recursively calculated in the disassembly pass. The method is highly compatible with multibody dynamic schemes to model coarse-grained biopolymers. Since the proposed method takes advantage of constant physical and geometrical properties of rigid clusters, improvement in the overall computational cost is observed comparing to the tradition application of fast multipole method.

Understanding the conformational flexibility and electrostatic properties of curcumin in the active site of rhAChE via molecular docking, molecular dynamics, and charge density analysis.

PubMed

Saravanan, Kandasamy; Kalaiarasi, Chinnasamy; Kumaradhas, Poomani

2017-12-01

Acetylcholinesterase (AChE) is an important enzyme responsible for Alzheimer's disease, as per report, keto-enol form of curcumin inhibits this enzyme. The present study aims to understand the binding mechanism of keto-enol curcumin with the recombinant human Acetylcholinesterase (rhAChE) from its conformational flexibility, intermolecular interactions, charge density distribution, and the electrostatic properties at the active site of rhAChE. To accomplish this, a molecular docking analysis of curcumin with the rhAChE was performed, which gives the structure and conformation of curcumin in the active site of rhAChE. Further, the charge density distribution and the electrostatic properties of curcumin molecule (lifted from the active site of rhAChE) were determined from the high level density functional theory (DFT) calculations coupled with the charge density analysis. On the other hand, the curcumin molecule was optimized (gas phase) using DFT method and further, the structure and charge density analysis were also carried out. On comparing the conformation, charge density distribution and the electrostatic potential of the active site form of curcumin with the corresponding gas phase form reveals that the above said properties are significantly altered when curcumin is present in the active site of rhAChE. The conformational stability and the interaction of curcumin in the active site are also studied using molecular dynamics simulation, which shows a large variation in the conformational geometry of curcumin as well as the intermolecular interactions.

Strong influence of coadsorbate interaction on CO desorption dynamics on Ru(0001) probed by ultrafast x-ray spectroscopy and ab initio simulations

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

Xin, H.; LaRue, J.; Oberg, H.

2015-04-16

We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distributionmore » and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.« less

Electron beam interaction with space plasmas.

NASA Astrophysics Data System (ADS)

Krafft, C.; Bolokitin, A. S.

1999-12-01

Active space experiments involving the controlled injection of electron beams and the formation of artificially generated currents can provide in many cases a calibration of natural phenomena connected with the dynamic interaction of charged particles with fields. They have a long history beginning from the launches of small rockets with electron guns in order to map magnetic fields lines in the Earth's magnetosphere or to excite artificial auroras. Moreover, natural beams of charged particles exist in many space and astrophysical plasmas and were identified in situ by several satellites; a few examples are beams connected with solar bursts, planetary foreshocks or suprathermal fluxes traveling in planetary magnetospheres. Many experimental and theoretical works have been performed in order to interpret or plan space experiments involving beam injection as well as to understand the physics of wave-particle interaction, as wave radiation, beam dynamics and background plasma modification.

Interaction of PLGA and trimethyl chitosan modified PLGA nanoparticles with mixed anionic/zwitterionic phospholipid bilayers studied using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Novak, Brian; Astete, Carlos; Sabliov, Cristina; Moldovan, Dorel

2012-02-01

Poly(lactic-co-glycolic acid) (PLGA) is a biodegradable polymer. Nanoparticles of PLGA are commonly used for drug delivery applications. The interaction of the nanoparticles with the cell membrane may influence the rate of their uptake by cells. Both PLGA and cell membranes are negatively charged, so adding positively charged polymers such as trimethyl chitosan (TMC) which adheres to the PLGA particles improves their cellular uptake. The interaction of 3 nm PLGA and TMC-modified-PLGA nanoparticles with lipid bilayers composed of mixtures of phosphatidylcholine and phosphatidylserine lipids was studied using molecular dynamics simulations. The free energy profiles as function of nanoparticles position along the normal direction to the bilayers were calculated, the distribution of phosphatidylserine lipids as a function of distance of the particle from the bilayer was calculated, and the time scale for particle motion in the directions parallel to the bilayer surface was estimated.

Spreading of correlations in the Falicov-Kimball model

NASA Astrophysics Data System (ADS)

Herrmann, Andreas J.; Antipov, Andrey E.; Werner, Philipp

2018-04-01

We study dynamical properties of the one- and two-dimensional Falicov-Kimball model using lattice Monte Carlo simulations. In particular, we calculate the spreading of charge correlations in the equilibrium model and after an interaction quench. The results show a reduction of the light-cone velocity with interaction strength at low temperature, while the phase velocity increases. At higher temperature, the initial spreading is determined by the Fermi velocity of the noninteracting system and the maximum range of the correlations decreases with increasing interaction strength. Charge order correlations in the disorder potential enhance the range of the correlations. We also use the numerically exact lattice Monte Carlo results to benchmark the accuracy of equilibrium and nonequilibrium dynamical cluster approximation calculations. It is shown that the bias introduced by the mapping to a periodized cluster is substantial, and that from a numerical point of view, it is more efficient to simulate the lattice model directly.

Attractive versus repulsive interactions in the Bose-Einstein condensation dynamics of relativistic field theories

NASA Astrophysics Data System (ADS)

Berges, J.; Boguslavski, K.; Chatrchyan, A.; Jaeckel, J.

2017-10-01

We study the impact of attractive self-interactions on the nonequilibrium dynamics of relativistic quantum fields with large occupancies at low momenta. Our primary focus is on Bose-Einstein condensation and nonthermal fixed points in such systems. For a model system, we consider O (N ) -symmetric scalar field theories. We use classical-statistical real-time simulations as well as a systematic 1 /N expansion of the quantum (two-particle-irreducible) effective action to next-to-leading order. When the mean self-interactions are repulsive, condensation occurs as a consequence of a universal inverse particle cascade to the zero-momentum mode with self-similar scaling behavior. For attractive mean self-interactions, the inverse cascade is absent, and the particle annihilation rate is enhanced compared to the repulsive case, which counteracts the formation of coherent field configurations. For N ≥2 , the presence of a nonvanishing conserved charge can suppress number-changing processes and lead to the formation of stable localized charge clumps, i.e., Q balls.

Manipulating quantum coherence of charge states in interacting double-dot Aharonov–Bohm interferometers

NASA Astrophysics Data System (ADS)

Jin, Jinshuang; Wang, Shikuan; Zhou, Jiahuan; Zhang, Wei-Min; Yan, YiJing

2018-04-01

We investigate the dynamics of charge-state coherence in a degenerate double-dot Aharonov–Bohm interferometer with finite inter-dot Coulomb interactions. The quantum coherence of the charge states is found to be sensitive to the transport setup configurations, involving both the single-electron impurity channels and the Coulomb-assisted ones. We numerically demonstrate the emergence of a complete coherence between the two charge states, with the relative phase being continuously controllable through the magnetic flux. Interestingly, a fully coherent charge qubit arises at the double-dots electron pair tunneling resonance condition, where the chemical potential of one electrode is tuned at the center between a single-electron impurity channel and the related Coulomb-assisted channel. This pure quantum state of charge qubit could be experimentally realized at the current–voltage characteristic turnover position, where differential conductance sign changes. We further elaborate the underlying mechanism for both the real-time and the stationary charge-states coherence in the double-dot systems of study.

Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations.

PubMed

Andrews, Casey T; Campbell, Brady A; Elcock, Adrian H

2017-04-11

Given the ubiquitous nature of protein-DNA interactions, it is important to understand the interaction thermodynamics of individual amino acid side chains for DNA. One way to assess these preferences is to perform molecular dynamics (MD) simulations. Here we report MD simulations of 20 amino acid side chain analogs interacting simultaneously with both a 70-base-pair double-stranded DNA and with a 70-nucleotide single-stranded DNA. The relative preferences of the amino acid side chains for dsDNA and ssDNA match well with values deduced from crystallographic analyses of protein-DNA complexes. The estimated apparent free energies of interaction for ssDNA, on the other hand, correlate well with previous simulation values reported for interactions with isolated nucleobases, and with experimental values reported for interactions with guanosine. Comparisons of the interactions with dsDNA and ssDNA indicate that, with the exception of the positively charged side chains, all types of amino acid side chain interact more favorably with ssDNA, with intercalation of aromatic and aliphatic side chains being especially notable. Analysis of the data on a base-by-base basis indicates that positively charged side chains, as well as sodium ions, preferentially bind to cytosine in ssDNA, and that negatively charged side chains, and chloride ions, preferentially bind to guanine in ssDNA. These latter observations provide a novel explanation for the lower salt dependence of DNA duplex stability in GC-rich sequences relative to AT-rich sequences.

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains.

PubMed

Makowski, Mariusz; Liwo, Adam; Scheraga, Harold A

2017-01-19

The physics-based potentials of side-chain-side-chain interactions corresponding to pairs composed of charged and polar, polar and polar, charged and hydrophobic, and hydrophobic and hydrophobic side chains have been determined. A total of 144 four-dimensional potentials of mean force (PMFs) of all possible pairs of molecules modeling these pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expressions were then fitted to the PMFs. Depending on the type of interacting sites, the analytical approximation to the PMF is a sum of terms corresponding to van der Waals interactions and cavity-creation involving the nonpolar sections of the side chains and van der Waals, cavity-creation, and electrostatic (charge-dipole or dipole-dipole) interaction energies and polarization energies involving the charged or polar sections of the side chains. The model used in this work reproduces all features of the interacting pairs. The UNited RESidue force field with the new side-chain-side-chain interaction potentials was preliminarily tested with the N-terminal part of the B-domain of staphylococcal protein A (PDBL 1BDD ; a three-α-helix bundle) and UPF0291 protein YnzC from Bacillus subtilis (PDB: 2HEP ; an α-helical hairpin).

Charge and Spin Dynamics of the Hubbard Chains

NASA Technical Reports Server (NTRS)

Park, Youngho; Liang, Shoudan

1999-01-01

We calculate the local correlation functions of charge and spin for the one-chain and two-chain Hubbard model using density matrix renormalization group method and the recursion technique. Keeping only finite number of states we get good accuracy for the low energy excitations. We study the charge and spin gaps, bandwidths and weights of the spectra for various values of the on-site Coulomb interaction U and the electron filling. In the low energy part, the local correlation functions are different for the charge and spin. The bandwidths are proportional to t for the charge and J for the spin respectively.

Scientific Computation Application Partnerships in Materials and Chemical Sciences, Charge Transfer and Charge Transport in Photoactivated Systems, Developing Electron-Correlated Methods for Excited State Structure and Dynamics in the NWChem Software Suite

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

Cramer, Christopher J.

Charge transfer and charge transport in photoactivated systems are fundamental processes that underlie solar energy capture, solar energy conversion, and photoactivated catalysis, both organometallic and enzymatic. We developed methods, algorithms, and software tools needed for reliable treatment of the underlying physics for charge transfer and charge transport, an undertaking with broad applicability to the goals of the fundamental-interaction component of the Department of Energy Office of Basic Energy Sciences and the exascale initiative of the Office of Advanced Scientific Computing Research.

Electrokinetic and hydrodynamic properties of charged-particles systems. From small electrolyte ions to large colloids

NASA Astrophysics Data System (ADS)

Nägele, G.; Heinen, M.; Banchio, A. J.; Contreras-Aburto, C.

2013-11-01

Dynamic processes in dispersions of charged spherical particles are of importance both in fundamental science, and in technical and bio-medical applications. There exists a large variety of charged-particles systems, ranging from nanometer-sized electrolyte ions to micron-sized charge-stabilized colloids. We review recent advances in theoretical methods for the calculation of linear transport coefficients in concentrated particulate systems, with the focus on hydrodynamic interactions and electrokinetic effects. Considered transport properties are the dispersion viscosity, self- and collective diffusion coefficients, sedimentation coefficients, and electrophoretic mobilities and conductivities of ionic particle species in an external electric field. Advances by our group are also discussed, including a novel mode-coupling-theory method for conduction-diffusion and viscoelastic properties of strong electrolyte solutions. Furthermore, results are presented for dispersions of solvent-permeable particles, and particles with non-zero hydrodynamic surface slip. The concentration-dependent swelling of ionic microgels is discussed, as well as a far-reaching dynamic scaling behavior relating colloidal long- to short-time dynamics.

Molecular dynamic simulation of weakly magnetized complex plasmas

NASA Astrophysics Data System (ADS)

Funk, Dylan; Konopka, Uwe; Thomas, Edward

2017-10-01

A complex plasma consists of the usual plasma components (electrons, ions and neutrals), as well as a heavier component made of solid, micrometer-sized particles. The particles are in general highly charged as a result of the interaction with the other plasma components. The static and dynamic properties of a complex plasma such as its crystal structure or wave properties are influenced by many forces acting on the individual particles such as the dust particle interaction (a screened Coulomb interaction), neutral (Epstein) drag, the particle inertia and various plasma drag or thermophoretic forces. To study the behavior of complex plasmas we setup an experiment accompanying molecular dynamic simulation. We will present the approach taken in our simulation and give an overview of experimental situations that we want to cover with our simulation such as the particle charge under microgravity condition as performed on the PK-4 space experiment, or to study the detailed influences of high magnetic fields. This work was supported by the US Dept. of Energy (DE-SC0016330), NSF (PHY-1613087) and JPL/NASA (JPL-RSA 1571699).

Charge transport calculations by a wave-packet dynamical approach using maximally localized Wannier functions based on density functional theory: Application to high-mobility organic semiconductors

NASA Astrophysics Data System (ADS)

Ishii, Hiroyuki; Kobayashi, Nobuhiko; Hirose, Kenji

2017-01-01

We present a wave-packet dynamical approach to charge transport using maximally localized Wannier functions based on density functional theory including van der Waals interactions. We apply it to the transport properties of pentacene and rubrene single crystals and show the temperature-dependent natures from bandlike to thermally activated behaviors as a function of the magnitude of external static disorder. We compare the results with those obtained by the conventional band and hopping models and experiments.

Space-charge-mediated anomalous ferroelectric switching in P(VDF-TrEE) polymer films.

PubMed

Hu, Weijin; Wang, Zhihong; Du, Yuanmin; Zhang, Xi-Xiang; Wu, Tom

2014-11-12

We report on the switching dynamics of P(VDF-TrEE) copolymer devices and the realization of additional substable ferroelectric states via modulation of the coupling between polarizations and space charges. The space-charge-limited current is revealed to be the dominant leakage mechanism in such organic ferroelectric devices, and electrostatic interactions due to space charges lead to the emergence of anomalous ferroelectric loops. The reliable control of ferroelectric switching in P(VDF-TrEE) copolymers opens doors toward engineering advanced organic memories with tailored switching characteristics.

Thermodynamically consistent Langevin dynamics with spatially correlated noise predicting frictionless regime and transient attraction effect

NASA Astrophysics Data System (ADS)

Majka, M.; Góra, P. F.

2016-10-01

While the origins of temporal correlations in Langevin dynamics have been thoroughly researched, the understanding of spatially correlated noise (SCN) is rather incomplete. In particular, very little is known about the relation between friction and SCN. In this article, starting from the microscopic, deterministic model, we derive the analytical formula for the spatial correlation function in the particle-bath interactions. This expression shows that SCN is the inherent component of binary mixtures, originating from the effective (entropic) interactions. Further, employing this spatial correlation function, we postulate the thermodynamically consistent Langevin equation driven by the Gaussian SCN and calculate the adequate fluctuation-dissipation relation. The thermodynamical consistency is achieved by introducing the spatially variant friction coefficient, which can be also derived analytically. This coefficient exhibits a number of intriguing properties, e.g., the singular behavior for certain types of interactions. Eventually, we apply this new theory to the system of two charged particles in the presence of counter-ions. Such particles interact via the screened-charge Yukawa potential and the inclusion of SCN leads to the emergence of the anomalous frictionless regime. In this regime the particles can experience active propulsion leading to the transient attraction effect. This effect suggests a nonequilibrium mechanism facilitating the molecular binding of the like-charged particles.

A systemic investigation of hydrogen peroxide clusters (H2O2)n (n = 1-6) and liquid-state hydrogen peroxide: based on atom-bond electronegativity equalization method fused into molecular mechanics and molecular dynamics.

PubMed

Yu, Chun-Yang; Yang, Zhong-Zhi

2011-03-31

Hydrogen peroxide (HP) clusters (H(2)O(2))(n) (n = 1-6) and liquid-state HP have been systemically investigated by the newly constructed ABEEM/MM fluctuating charge model. Because of the explicit description of charge distribution and special treatment of the hydrogen-bond interaction region, the ABEEM/MM potential model gives reasonable properties of HP clusters, including geometries, interaction energies, and dipole moments, when comparing with the present ab initio results. Meanwhile, the average dipole moment, static dielectric constant, heats of vaporization, radial distribution function, and diffusion constant for the dynamic properties of liquid HP at 273 K and 1 atm are fairly consistent with the available experimental data. To the best of our knowledge, this is the first theoretical investigation of condensed HP. The properties of HP monomer are studied in detail involving the structure, torsion potentials, molecular orbital analysis, charge distribution, dipole moment, and vibrational frequency.

Rectification of General Relativity, Experimental Verifications, and Errors of the Wheeler School

NASA Astrophysics Data System (ADS)

Lo, C. Y.

2013-09-01

General relativity is not yet consistent. Pauli has misinterpreted Einstein's 1916 equivalence principle that can derive a valid field equation. The Wheeler School has distorted Einstein's 1916 principle to be his 1911 assumption of equivalence, and created new errors. Moreover, errors on dynamic solutions have allowed the implicit assumption of a unique coupling sign that violates the principle of causality. This leads to the space-time singularity theorems of Hawking and Penrose who "refute" applications for microscopic phenomena, and obstruct efforts to obtain a valid equation for the dynamic case. These errors also explain the mistakes in the press release of the 1993 Nobel Committee, who was unaware of the non-existence of dynamic solutions. To illustrate the damages to education, the MIT Open Course Phys. 8.033 is chosen. Rectification of errors confirms that E = mc2 is only conditionally valid, and leads to the discovery of the charge-mass interaction that is experimentally confirmed and subsequently the unification of gravitation and electromagnetism. The charge-mass interaction together with the unification predicts the weight reduction (instead of increment) of charged capacitors and heated metals, and helps to explain NASA's Pioneer anomaly and potentially other anomalies as well.

High-energy e- /e+ spectrometer via coherent interaction in a bent crystal

NASA Astrophysics Data System (ADS)

Bagli, Enrico; Guidi, Vincenzo; Howard, Alexander

2018-01-01

We propose a novel spectrometer based on the crystal channeling effect capable of discriminating between positive and negative particles well beyond the TeV energy scale. The atomic order of a crystalline structure generates an electrostatic field built up by all the atoms in the crystals, which confines charged particle trajectories between neighbouring atomic planes. Through such an interaction in a tiny curved crystal, the same dynamical action on the highest energy particles as that of a huge superconducting magnet is achieved. Depending on the charge sign, points of equilibrium of the oscillatory motion under channeling lie between or on atomic planes for positive and negative particles, respectively, forcing positive particles to stably oscillate far from the planes, while negative ones repeatedly cross them. The different interaction rate with atomic planes causes a tremendous discrepancy between the deflection efficiency of positive and negative particles under channeling. We suggest the use of interactions between charged particles and oriented bent crystals as a novel non-cryogenic passive charge spectrometer to aid the search for dark matter in the Universe in satellite-borne experiment. The limited angular acceptance makes this technique particularly suited for directional local sources of energetic charged particles.

Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates

NASA Astrophysics Data System (ADS)

Arfin, Najmul; Yadav, Avinash Chand; Bohidar, H. B.

2013-11-01

The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement ⟨R2⟩ exhibits a scaling with time as ⟨R2⟩ ˜ tα, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ˜ tβ/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.

Interaction of Charged Patchy Protein Models with Like-Charged Polyelectrolyte Brushes.

PubMed

Yigit, Cemil; Kanduč, Matej; Ballauff, Matthias; Dzubiella, Joachim

2017-01-10

We study the adsorption of charged patchy particle models (CPPMs) on a thin film of a like-charged and dense polyelectrolyte (PE) brush (of 50 monomers per chain) by means of implicit-solvent, explicit-salt Langevin dynamics computer simulations. Our previously introduced set of CPPMs embraces well-defined one- and two-patched spherical globules, each of the same net charge and (nanometer) size, with mono- and multipole moments comparable to those of small globular proteins. We focus on electrostatic effects on the adsorption far away from the isoelectric point of typical proteins, i.e., where charge regulation plays no role. Despite the same net charge of the brush and globule, we observe large binding affinities up to tens of the thermal energy, k B T, which are enhanced by decreasing salt concentration and increasing charge of the patch(es). Our analysis of the distance-resolved potentials of mean force together with a phenomenological description of all leading interaction contributions shows that the attraction is strongest at the brush surface, driven by multipolar, Born (self-energy), and counterion-release contributions, dominating locally over the monopolar and steric repulsions.

Diffusion in Deterministic Interacting Lattice Systems

NASA Astrophysics Data System (ADS)

Medenjak, Marko; Klobas, Katja; Prosen, Tomaž

2017-09-01

We study reversible deterministic dynamics of classical charged particles on a lattice with hard-core interaction. It is rigorously shown that the system exhibits three types of transport phenomena, ranging from ballistic, through diffusive to insulating. By obtaining an exact expressions for the current time-autocorrelation function we are able to calculate the linear response transport coefficients, such as the diffusion constant and the Drude weight. Additionally, we calculate the long-time charge profile after an inhomogeneous quench and obtain diffusive profilewith the Green-Kubo diffusion constant. Exact analytical results are corroborated by Monte Carlo simulations.

Make dark matter charged again

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

Agrawal, Prateek; Cyr-Racine, Francis-Yan; Randall, Lisa

2017-05-01

We revisit constraints on dark matter that is charged under a U(1) gauge group in the dark sector, decoupled from Standard Model forces. We find that the strongest constraints in the literature are subject to a number of mitigating factors. For instance, the naive dark matter thermalization timescale in halos is corrected by saturation effects that slow down isotropization for modest ellipticities. The weakened bounds uncover interesting parameter space, making models with weak-scale charged dark matter viable, even with electromagnetic strength interaction. This also leads to the intriguing possibility that dark matter self-interactions within small dwarf galaxies are extremely large,more » a relatively unexplored regime in current simulations. Such strong interactions suppress heat transfer over scales larger than the dark matter mean free path, inducing a dynamical cutoff length scale above which the system appears to have only feeble interactions. These effects must be taken into account to assess the viability of darkly-charged dark matter. Future analyses and measurements should probe a promising region of parameter space for this model.« less

Electrostatic Interactions and Self-Assembly in Polymeric Systems

NASA Astrophysics Data System (ADS)

Dobrynin, Andrey

Electrostatic interactions between macroions play an important role in different areas ranging from materials science to biophysics. They are main driving forces behind layer-by-layer assembly technique that allows self-assembly of multilayer films from synthetic polyelectrolytes, DNA, proteins and nanoparticles. They are responsible for complexation and reversible gelation between polyelectrolytes and proteins. In this talk, using results of the molecular dynamics simulations and analytical calculations, I will demonstrate what effect electrostatic interactions, counterion condensation and polymer solvent affinity have on a collapse of polyelectrolyte chain in a poor solvent conditions for the polymer backbone, on complexations and reversible gelation between polyelectrolytes and polyamholytes (unstructured proteins), on microphase separation transitions in spherical and planar charged brushes, and on a layer-by-layer assembly of charged nanoparticles and linear polyelectrolytes on charged surfaces. NSF DMR-1004576 DMR-1409710.

Conformational Transitions and Stop-and-Go Nanopore Transport of Single Stranded DNA on Charged Graphene

PubMed Central

Shankla, Manish; Aksimentiev, Aleksei

2014-01-01

Control over interactions with biomolecules holds the key to applications of graphene in biotechnology. One such application is nanopore sequencing, where a DNA molecule is electrophoretically driven through a graphene nanopore. Here, we investigate how interactions of single-stranded DNA and a graphene membrane can be controlled by electrically biasing the membrane. The results of our molecular dynamics simulations suggest that electric charge on graphene can force a DNA homopolymer to adopt a range of strikingly different conformations. The conformational response is sensitive to even very subtle nucleotide modifications, such as DNA methylation. The speed of DNA motion through a graphene nanopore is strongly affected by the graphene charge: a positive charge accelerates the motion whereas a negative charge arrests it. As a possible application of the effect, we demonstrate stop-and-go transport of DNA controlled by the charge of graphene. Such on-demand transport of DNA is essential for realizing nanopore sequencing. PMID:25296960

Applying electric field to charged and polar particles between metallic plates: extension of the Ewald method.

PubMed

Takae, Kyohei; Onuki, Akira

2013-09-28

We develop an efficient Ewald method of molecular dynamics simulation for calculating the electrostatic interactions among charged and polar particles between parallel metallic plates, where we may apply an electric field with an arbitrary size. We use the fact that the potential from the surface charges is equivalent to the sum of those from image charges and dipoles located outside the cell. We present simulation results on boundary effects of charged and polar fluids, formation of ionic crystals, and formation of dipole chains, where the applied field and the image interaction are crucial. For polar fluids, we find a large deviation of the classical Lorentz-field relation between the local field and the applied field due to pair correlations along the applied field. As general aspects, we clarify the difference between the potential-fixed and the charge-fixed boundary conditions and examine the relationship between the discrete particle description and the continuum electrostatics.

Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene

NASA Astrophysics Data System (ADS)

Shankla, Manish; Aksimentiev, Aleksei

2014-10-01

Control over interactions with biomolecules holds the key to applications of graphene in biotechnology. One such application is nanopore sequencing, where a DNA molecule is electrophoretically driven through a graphene nanopore. Here we investigate how interactions of single-stranded DNA and a graphene membrane can be controlled by electrically biasing the membrane. The results of our molecular dynamics simulations suggest that electric charge on graphene can force a DNA homopolymer to adopt a range of strikingly different conformations. The conformational response is sensitive to even very subtle nucleotide modifications, such as DNA methylation. The speed of DNA motion through a graphene nanopore is strongly affected by the graphene charge: a positive charge accelerates the motion, whereas a negative charge arrests it. As a possible application of the effect, we demonstrate stop-and-go transport of DNA controlled by the charge of graphene. Such on-demand transport of DNA is essential for realizing nanopore sequencing.

Studies of dynamic processes related to active experiments in space plasmas

NASA Technical Reports Server (NTRS)

Banks, Peter M.; Neubert, Torsten

1992-01-01

This is the final report for grant NAGw-2055, 'Studies of Dynamic Processes Related to Active Experiments in Space Plasmas', covering research performed at the University of Michigan. The grant was awarded to study: (1) theoretical and data analysis of data from the CHARGE-2 rocket experiment (1keV; 1-46 mA electron beam ejections) and the Spacelab-2 shuttle experiment (1keV; 100 mA); (2) studies of the interaction of an electron beam, emitted from an ionospheric platform, with the ambient neutral atmosphere and plasma by means of a newly developed computer simulation model, relating model predictions with CHARGE-2 observations of return currents observed during electron beam emissions; and (3) development of a self-consistent model for the charge distribution on a moving conducting tether in a magnetized plasma and for the potential structure in the plasma surrounding the tether. Our main results include: (1) the computer code developed for the interaction of electrons beams with the neutral atmosphere and plasma is able to model observed return fluxes to the CHARGE-2 sounding rocket payload; and (2) a 3-D electromagnetic and relativistic particle simulation code was developed.

Charge Carrier Dynamics and pH Effect on Optical Properties of Anionic and Cationic Porphyrin-Graphene Oxide Composites

NASA Astrophysics Data System (ADS)

Bajjou, O.; Bakour, A.; Khenfouch, M.; Baitoul, M.; Mothudi, B.; Maaza, M.; Faulques, E.

2018-02-01

Composites of graphene oxide (GO) functionalized with Sn(V) tetrakis (4-pyridyl)porphyrin (SnTPyP2+) and meso-tetrakis(4-phenylsulfonic acid)porphyrin (H4TPPS4 2- ) were prepared at different pH values.Successful synthesis of water-soluble stable suspension of GO-SnTPyP2+ and GO-H4TPPS4 2-was confirmed using various spectroscopic techniques, including scanning electronic microscopy (SEM), Raman spectroscopy, and ultraviolet-visible (UV-Vis) absorption. Variation of the pH was found to strongly influence the optical properties of the GO-SnTPyP2+ and GO-H4TPPS4 2-composites, as demonstrated by the UV-Vis absorption results. Steady-state photoluminescence (PL) and time-resolved PL (TRPL) results for both composites showed PL quenching and decrease in the exciton mean lifetime, suggesting strong excited-state interactions between the different components. Moreover, charge carrier dynamics study revealed that insertion of GO into both porphyrin derivatives led to faster mean lifetime for excitons with a slight advantage in the case of the cationic porphyrin-GO composite, making it a better choice for charge separation applications thanks to the higher efficiency of charge/energy transfer interactions.

Electrochemical capacitance modulation in an interacting mesoscopic capacitor induced by internal charge transfer

NASA Astrophysics Data System (ADS)

Liu, Wei; He, Jianhong; Guo, Huazhong; Gao, Jie

2018-04-01

We report experiments on the dynamic response of an interacting mesoscopic capacitor consisting of a quantum dot with two confined spin-split levels of the lowest Landau level. In high magnetic fields, states inside the dot are regulated by a mixture of Coulomb interaction and Landau-level quantization, and electrons distribute on two spatially separated regions. Quantum point contact voltage and magnetic field are employed to manipulate the number and distribution of electrons inside the quantum dot. We find that the periodicity of the electrochemical capacitance oscillations is dominated by the charging energy, and their amplitudes, due to internal charge transfer and strong internal capacitive coupling, show rich variations of modulations. Magnetocapacitance displays a sawtoothlike manner and may differ in tooth directions for different voltages, which, we demonstrate, result from a sawtoothlike electrochemical potential change induced by internal charge transfer and field-sensitive electrostatic potential. We further build a charge stability diagram, which, together with all other capacitance properties, is consistently interpreted in terms of a double-dot model. The demonstrated technique is of interest as a tool for fast and sensitive charge state readout of a double-quantum-dot qubit in the gigahertz frequency quantum electronics.

Effective charges of ionic liquid determined self-consistently through combination of molecular dynamics simulation and density-functional theory.

PubMed

Ishizuka, Ryosuke; Matubayasi, Nobuyuki

2017-11-15

A self-consistent scheme combining the molecular dynamics (MD) simulation and density functional theory (DFT) was recently proposed to incorporate the effects of the charge transfer and polarization of ions into non-poralizable force fields of ionic liquids for improved description of energetics and dynamics. The purpose of the present work is to analyze the detailed setups of the MD/DFT scheme by focusing on how the basis set, exchange-correlation (XC) functional, charge-fitting method or force field for the intramolecular and Lennard-Jones interactions affects the MD/DFT results of 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ( [C1mim][NTf2]) and 1-ethyl-3-methylimidazolium glycinate ( [C2mim][Gly]). It was found that the double-zeta valence polarized or larger size of basis set is required for the convergence of the effective charge of the ion. The choice of the XC functional was further not influential as far as the generalized gradient approximation is used. The charge-fitting method and force field govern the accuracy of the MD/DFT scheme, on the other hand. We examined the charge-fitting methods of Blöchl, the iterative Hirshfeld (Hirshfeld-I), and REPEAT in combination with Lopes et al.'s force field and general AMBER force field. There is no single combination of charge fitting and force field that provides good agreements with the experiments, while the MD/DFT scheme reduces the effective charges of the ions and leads to better description of energetics and dynamics compared to the original force field with unit charges. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A New Poisson-Nernst-Planck Model with Ion-Water Interactions for Charge Transport in Ion Channels.

PubMed

Chen, Duan

2016-08-01

In this work, we propose a new Poisson-Nernst-Planck (PNP) model with ion-water interactions for biological charge transport in ion channels. Due to narrow geometries of these membrane proteins, ion-water interaction is critical for both dielectric property of water molecules in channel pore and transport dynamics of mobile ions. We model the ion-water interaction energy based on realistic experimental observations in an efficient mean-field approach. Variation of a total energy functional of the biological system yields a new PNP-type continuum model. Numerical simulations show that the proposed model with ion-water interaction energy has the new features that quantitatively describe dielectric properties of water molecules in narrow pores and are possible to model the selectivity of some ion channels.

Dynamics of two-dimensional monolayer water confined in hydrophobic and charged environments.

PubMed

Kumar, Pradeep; Han, Sungho

2012-09-21

We perform molecular dynamics simulations to study the effect of charged surfaces on the intermediate and long time dynamics of water in nanoconfinements. Here, we use the transferable interaction potential with five points (TIP5P) model of a water molecule confined in both hydrophobic and charged surfaces. For a single molecular layer of water between the surfaces, we find that the temperature dependence of the lateral diffusion constant of water up to very high temperatures remains Arrhenius with a high activation energy. In case of charged surfaces, however, the dynamics of water in the intermediate time regime is drastically modified presumably due to the transient coupling of dipoles of water molecules with electric field fluctuations induced by charges on the confining surfaces. Specifically, the lateral mean square displacements display a distinct super-diffusive behavior at intermediate time scale, defined as the time scale between ballistic and diffusive regimes. This change in the intermediate time-scale dynamics in the charged confinement leads to the enhancement of long-time dynamics as reflected in increasing diffusion constant. We introduce a simple model for a possible explanation of the super-diffusive behavior and find it to be in good agreement with our simulation results. Furthermore, we find that confinement and the surface polarity enhance the low frequency vibration in confinement compared to bulk water. By introducing a new effective length scale of coupling between translational and orientational motions, we find that the length scale increases with the increasing strength of the surface polarity. Further, we calculate the correlation between the diffusion constant and the excess entropy and find a disordering effect of polar surfaces on the structure of water. Finally, we find that the empirical relation between the diffusion constant and the excess entropy holds for a monolayer of water in nanoconfinement.

Mean-field theory of active electrolytes: Dynamic adsorption and overscreening

NASA Astrophysics Data System (ADS)

Frydel, Derek; Podgornik, Rudolf

2018-05-01

We investigate active electrolytes within the mean-field level of description. The focus is on how the double-layer structure of passive, thermalized charges is affected by active dynamics of constituting ions. One feature of active dynamics is that particles adhere to hard surfaces, regardless of chemical properties of a surface and specifically in complete absence of any chemisorption or physisorption. To carry out the mean-field analysis of the system that is out of equilibrium, we develop the "mean-field simulation" technique, where the simulated system consists of charged parallel sheets moving on a line and obeying active dynamics, with the interaction strength rescaled by the number of sheets. The mean-field limit becomes exact in the limit of an infinite number of movable sheets.

Visualizing electron dynamics in organic materials: Charge transport through molecules and angular resolved photoemission

NASA Astrophysics Data System (ADS)

Kümmel, Stephan

Being able to visualize the dynamics of electrons in organic materials is a fascinating perspective. Simulations based on time-dependent density functional theory allow to realize this hope, as they visualize the flow of charge through molecular structures in real-space and real-time. We here present results on two fundamental processes: Photoemission from organic semiconductor molecules and charge transport through molecular structures. In the first part we demonstrate that angular resolved photoemission intensities - from both theory and experiment - can often be interpreted as a visualization of molecular orbitals. However, counter-intuitive quantum-mechanical electron dynamics such as emission perpendicular to the direction of the electrical field can substantially alter the picture, adding surprising features to the molecular orbital interpretation. In a second study we calculate the flow of charge through conjugated molecules. The calculations show in real time how breaks in the conjugation can lead to a local buildup of charge and the formation of local electrical dipoles. These can interact with neighboring molecular chains. As a consequence, collections of ''molecular electrical wires'' can show distinctly different characteristics than ''classical electrical wires''. German Science Foundation GRK 1640.

Investigation of electrostatic behavior of a lactose carrier for dry powder inhalers.

PubMed

Chow, Keat Theng; Zhu, Kewu; Tan, Reginald B H; Heng, Paul W S

2008-12-01

This study aims to elucidate the electrostatic behavior of a model lactose carrier used in dry powder inhaler formulations by examining the effects of ambient relative humidity (RH), aerosolization air flow rate, repeated inhaler use, gelatin capsule and tapping on the specific charge (nC/g) of bulk and aerosolized lactose. Static and dynamic electrostatic charge measurements were performed using a Faraday cage connected to an electrometer. Experiments were conducted inside a walk-in environmental chamber at 25 degrees C and RHs of 20% to 80%. Aerosolization was achieved using air flow rates of 30, 45, 60 and 75 L/min. The initial charges of the bulk and capsulated lactose were a magnitude lower than the charges of tapped or aerosolized lactose. Dynamic charge increased linearly with aerosolization air flow rate and RH. Greater frictional forces at higher air flow rate induced higher electrostatic charges. Increased RH enhanced charge generation. Repeated inhaler use significantly influenced electrostatic charge due to repeated usage. This study demonstrated the significance of interacting influences by variables commonly encountered in the use DPI such as variation in patient's inspiratory flow rate, ambient RH and repeated inhaler use on the electrostatic behavior of a lactose DPI carrier.

Electrohydrodynamic simulation of an electrospray in a colloid thruster

NASA Astrophysics Data System (ADS)

Jugroot, Manish; Forget, Martin; Malardier-Jugroot, Cecile

2012-02-01

A precise understanding of electrosprays is highly interesting as the complexity of micro-technology (such as nano-material processing, spacecraft propulsion and mass-spectrometers) systems increases. A multi-component CFD-based model coupling fluid dynamics, charged species dynamics and electric field is developed. The simulations describe the charged fluid interface with emphasis on the Taylor cone formation and cone-jet transition under the effect of a electric field. The goal is to recapture this transition from a rounded liquid interface into a Taylor cone from an initial uniform distribution, without making assumptions on the behaviour, geometry or charge distribution of the system. The time evolution of the interface highlights the close interaction among space charge, coulombic forces and the surface tension, which appear as governing and competing processes in the transition. The results from the coupled formalism provide valuable insights on the physical phenomena and will be applied to a colloid thruster for small spacecrafts.

Multi-charge-state molecular dynamics and self-diffusion coefficient in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Hou, Yong; Kang, Dongdong; Gao, Cheng; Jin, Fengtao; Yuan, Jianmin

2018-01-01

We present a multi-ion molecular dynamics (MIMD) simulation and apply it to calculating the self-diffusion coefficients of ions with different charge-states in the warm dense matter (WDM) regime. First, the method is used for the self-consistent calculation of electron structures of different charge-state ions in the ion sphere, with the ion-sphere radii being determined by the plasma density and the ion charges. The ionic fraction is then obtained by solving the Saha equation, taking account of interactions among different charge-state ions in the system, and ion-ion pair potentials are computed using the modified Gordon-Kim method in the framework of temperature-dependent density functional theory on the basis of the electron structures. Finally, MIMD is used to calculate ionic self-diffusion coefficients from the velocity correlation function according to the Green-Kubo relation. A comparison with the results of the average-atom model shows that different statistical processes will influence the ionic diffusion coefficient in the WDM regime.

Boundary layer charge dynamics in ionic liquid-ionic polymer transducers

NASA Astrophysics Data System (ADS)

Davidson, Jacob D.; Goulbourne, N. C.

2011-01-01

Ionic polymer transducers (IPTs), also known as ionic polymer-metal composites, are soft sensors and actuators which operate through a coupling of microscale chemical, electrical, and mechanical interactions. The use of an ionic liquid as solvent for an IPT has been shown to dramatically increase transducer lifetime in free-air use, while also allowing for higher applied voltages without electrolysis. In this work, we apply Nernst-Planck/Poisson theory to model charge transport in an ionic liquid IPT by considering a certain fraction of the ionic liquid ions as mobile charge carriers, a phenomenon which is unique to ionic liquid IPTs compared to their water-based counterparts. Numerical simulations are performed using the finite element method to examine how the introduction of another pair of mobile ions affects boundary layer charge dynamics, concentration, and charge density distributions in the electric double layer, and the overall charge transferred and current response of the IPT. Due to interactions with the Nafion ionomer, not all of the ionic liquid ions will function as mobile charge carriers; only a certain fraction will exist as "free" ions. The presence of mobile ionic liquid ions in the transducer will increase the overall charge transferred when a voltage is applied, and cause the current in the transducer to decay more slowly. The additional mobile ions also cause the ionic concentration profiles to exhibit a nonlinear dynamic response, characterized by nonmonotonic ionic concentration profiles in space and time. Although the presence of mobile ionic liquid ions increases the overall amount of charge transferred, this additional charge transfer occurs in a somewhat symmetric manner. Therefore, the additional charge transferred due to the ionic liquid ions does not greatly increase the net bending moment of the transducer; in fact, it is possible that ionic liquid ion movement actually decreases the observed bending response. This suggests that an optimal electromechanical conversion efficiency for bending actuation is achieved by using an ionic liquid where only a relatively small fraction of the ionic liquid ions exist as free ions. Conversely, if it is desired to increase the overall amount of charge transferred, an ionic liquid with a large fraction of free ions should be used. These theoretical considerations are found to be in good qualitative agreement with recent experimental results.

Resonant charge exchange for H-H+ in Debye plasmas

NASA Astrophysics Data System (ADS)

Laricchiuta, Annarita; Colonna, Gianpiero; Capitelli, Mario; Kosarim, Alexander; Smirnov, Boris M.

2017-11-01

The dynamics of resonant charge exchange in proton-hydrogen collisions embedded in plasma is investigated in the framework of the asymptotic approach, modified to account for the effect of Debye-Hückel screening in particle interactions. The cross sections exhibit a marked dependence on the Debye length in regimes of severe plasma confinement. Processes involving excited states H( n)-H+ are also discussed.

Identification of Key Interactions in the Initial Self-Assembly of Amylin in a Membrane Environment.

PubMed

Christensen, Mikkel; Skeby, Katrine K; Schiøtt, Birgit

2017-09-12

Islet amyloid polypeptide, also known as amylin, forms aggregates that reduce the amount of insulin-producing cells in patients with type II diabetes mellitus. Much remains unknown about the process of aggregation and cytotoxicity, but it is known that certain cell membrane components can alter the rate of aggregation. Using atomistic molecular dynamics simulations combined with the highly mobile membrane mimetic model incorporating enhanced sampling of lipid diffusion, we investigate interaction of amylin peptides with the membrane components as well as the self-assembly of amylin. Consistent with experimental evidence, we find that an initial membrane-bound α-helical state folds into stable β-sheet structures upon self-assembly. Our results suggest the following mechanism for the initial phase of amylin self-assembly. The peptides move around on the membrane with the positively charged N-terminus interacting with the negatively charged lipid headgroups. When the peptides start to interact, they partly unfold and break some of the contacts with the membrane. The initial interactions between the peptides are dominated by aromatic and hydrophobic interactions. Oligomers are formed showing both intra- and interpeptide β-sheets, initially with interactions mainly in the C-terminal domain of the peptides. Decreasing the pH to 5.5 is known to inhibit amyloid formation. At low pH, His18 is protonated, adding a fourth positive charge at the peptide. With His18 protonated, no oligomerization is observed in the simulations. The additional charge gives a strong midpoint anchoring of the peptides to negatively charged membrane components, and the peptides experience additional interpeptide repulsion, thereby preventing interactions.

Charge and energy dynamics in photo-excited poly(para-phenylenevinylene) systems

NASA Astrophysics Data System (ADS)

Gisslén, L.; Johansson, A.˚.; Stafström, S.

2004-07-01

We report results from simulations of charge and energy dynamics in poly(para-phenylenevinylene) (PPV) and PPV interacting with C60. The simulations were performed by solving the time-dependent Schrödinger equation and the lattice equation of motion simultaneously and nonadiabatically. The electronic system and the coupling of the electrons to the lattice were described by an extended three-dimensional version of the Su-Schrieffer-Heeger model, which also included an external electric field. Electron and lattice dynamics following electronic excitations at different energies have been simulated. The effect of additional lattice energy was also included in the simulations. Our results show that both exciton diffusion and transitions from high to lower lying excitations are stimulated by increasing the lattice energy. Also field induced charge separation occurs faster if the lattice energy is increased. This separation process is highly nonadiabatic and involves a significant rearrangement of the electron distribution. In the case of PPV coupled to C60, we observe a spontaneous charge separation. The separation time is in this case limited by the local concentration of C60 molecules close to the PPV chain.

Molecular simulation study of feruloyl esterase adsorption on charged surfaces: effects of surface charge density and ionic strength.

PubMed

Liu, Jie; Peng, Chunwang; Yu, Gaobo; Zhou, Jian

2015-10-06

The surrounding conditions, such as surface charge density and ionic strength, play an important role in enzyme adsorption. The adsorption of a nonmodular type-A feruloyl esterase from Aspergillus niger (AnFaeA) on charged surfaces was investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics (AAMD) simulations at different surface charge densities (±0.05 and ±0.16 C·m(-2)) and ionic strengths (0.007 and 0.154 M). The adsorption energy, orientation, and conformational changes were analyzed. Simulation results show that whether AnFaeA can adsorb onto a charged surface is mainly controlled by electrostatic interactions between AnFaeA and the charged surface. The electrostatic interactions between AnFaeA and charged surfaces are weakened when the ionic strength increases. The positively charged surface at low surface charge density and high ionic strength conditions can maximize the utilization of the immobilized AnFaeA. The counterion layer plays a key role in the adsorption of AnFaeA on the negatively charged COOH-SAM. The native conformation of AnFaeA is well preserved under all of these conditions. The results of this work can be used for the controlled immobilization of AnFaeA.

The Interactions Between Three Typical PPCPs and LDH

PubMed Central

Li, Erwei; Liao, Libing; Lv, Guocheng; Li, Zhaohui; Yang, Chengxue; Lu, Yanan

2018-01-01

With a layered structure, layered double hydroxide (LDH) has potential applications in remediation of anionic contaminants, which has been a hot topic for recent years. In this study, a Cl type Mg-Al hydrotalcite (Cl-LDH) was prepared by a co-precipitation method. The adsorption process of three pharmaceuticals and personal care products (PPCPs) [tetracycline (TC), diclofenac sodium (DF), chloramphenicol (CAP)] by Cl-LDH was investigated by X-ray diffraction (XRD), Zeta potential, dynamic light scattering (DLS), BET, Fourier transform infrared (FTIR) spectroscopy, and molecular dynamics simulation. The results showed that the adsorption equilibrium of TC and DF could be reached in 120 min, and the maximum adsorption capacity of the TC and DF were 1.85 and 0.95 mmol/g, respectively. The isothermal adsorption model of TC was fitted with the Freundlich adsorption model, and the isothermal adsorption model of DF was fitted with the Langmuir adsorption model. The adsorption dynamics of TC and DF followed the pseudo-second-order model. The adsorption mechanisms of the three PPCPs into Cl-LDH were different based on the experimental results and molecular dynamics simulation. The TC adsorption on Cl-LDH was accompanied by the electrostatic interactions between the negative charge of TC and the positive charge of Cl-LDH. The uptake of DF was attributed to anion exchange and electrostatic interaction. Cl-LDH does not adsorb CAP due to no electrostatic interaction. The molecular dynamic simulation further confirmed different configurations of three selected PPCPs, which were ultimately responsible for the uptake of PPCPs on Cl-LDH. PMID:29556493

Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models.

PubMed

Leontyev, Igor V; Stuchebrukhov, Alexei A

2014-07-07

Earlier, using phenomenological approach, we showed that in some cases polarizable models of condensed phase systems can be reduced to nonpolarizable equivalent models with scaled charges. Examples of such systems include ionic liquids, TIPnP-type models of water, protein force fields, and others, where interactions and dynamics of inherently polarizable species can be accurately described by nonpolarizable models. To describe electrostatic interactions, the effective charges of simple ionic liquids are obtained by scaling the actual charges of ions by a factor of 1/√(ε(el)), which is due to electronic polarization screening effect; the scaling factor of neutral species is more complicated. Here, using several theoretical models, we examine how exactly the scaling factors appear in theory, and how, and under what conditions, polarizable Hamiltonians are reduced to nonpolarizable ones. These models allow one to trace the origin of the scaling factors, determine their values, and obtain important insights on the nature of polarizable interactions in condensed matter systems.

Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions.

PubMed

Materese, Christopher Kroboth; Goldmon, Christa Charisse; Papoian, Garegin A

2008-08-05

The native state dynamics of the small globular serine protease inhibitor eglin c has been studied in a long 336 ns computer simulation in explicit solvent. We have elucidated the energy landscape explored during the course of the simulation by using Principal Component Analysis. We observe several basins in the energy landscape in which the system lingers for extended periods. Through an iterative process we have generated a tree-like hierarchy of states describing the observed dynamics. We observe a range of divergent contact types including salt bridges, hydrogen bonds, hydrophilic interactions, and hydrophobic interactions, pointing to the frustration between competing interactions. Additionally, we find evidence of competing water-mediated interactions. Divergence in water-mediated interactions may be found to supplement existing direct contacts, but they are also found to be independent of such changes. Water-mediated contacts facilitate interactions between residues of like charge as observed in the simulation. Our results provide insight into the complexity of the dynamic native state of a globular protein and directly probe the residual frustration in the native state.

Fluorescence probe of polypeptide conformational dynamics in gas phase and in solution

NASA Astrophysics Data System (ADS)

Iavarone, Anthony T.; Meinen, Jan; Schulze, Susanne; Parks, Joel H.

2006-07-01

Fluorescence measurements of polypeptides derivatized with the fluorescent dye BODIPY TMR have been used to probe the polypeptide conformational dynamics as a function of temperature and charge state. Measurements of (BODIPY TMR)-[Pro]n-Arg-Trp and (BODIPY TMR)-[Gly-Ser]m-Arg-Trp have been performed for charge states 1+ and 2+ of n = 4 and 10 and m = 2 and 5. The 2+ charge states of both of these polypeptides exhibit similar temperature dependences for equal chain lengths (n = 4, m = 2 and n = 10, m = 5) and suggest conformations dominated by Coulomb repulsion. In the absence of such Coulomb repulsion, the 1+ charge state conformations appear to be characterized by the flexibility of the polypeptide chain for which [Gly-Ser]m > [Pro]n. Comparisons of these gas phase polypeptide measurements with corresponding measurements in solution provide a direct measure of the effects of solvent on the conformational dynamics. The change in fluorescence as a function of temperature in the gas phase is two orders of magnitude greater than that in solution, a dramatic result we attribute to the restrictions on intramolecular dynamics imposed by diffusion-limited kinetics and the lack of shielding by solvent. Measurements were also made of unsolvated Pron peptides without the tryptophan (Trp) residue to isolate the interaction of the fluorescent dye with charges.

Reduced Point Charge Models of Proteins: Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems.

PubMed

Leherte, Laurence; Vercauteren, Daniel P

2017-10-26

We investigate the influence of various solvent models on the structural stability and protein-water interface of three ubiquitin complexes (PDB access codes: 1Q0W , 2MBB , 2G3Q ) modeled using the Amber99sb force field (FF) and two different point charge distributions. A previously developed reduced point charge model (RPCM), wherein each amino acid residue is described by a limited number of point charges, is tested and compared to its all-atom (AA) version. The complexes are solvated in TIP4P-Ew or TIP3P type water molecules, involving either the scaling of the Lennard-Jones protein-O water interaction parameters, or the coarse-grain (CG) SIRAH water description. The best agreements between the RPCM and AA models were obtained for structural, protein-water, and ligand-ubiquitin properties when using the TIP4P-Ew water FF with a scaling factor γ of 0.7. At the RPCM level, a decrease in γ, or the inclusion of SIRAH particles, allows weakening of the protein-water interactions. It results in a slight collapse of the protein structure and a less compact hydration shell and, thus, in a decrease in the number of protein-water and water-water H-bonds. The dynamics of the surface protein atoms and of the water shell molecules are also slightly refrained, which allow the generation of stable RPCM trajectories.

Brownian dynamics simulations of interactions between aldolase and G- or F-actin.

PubMed Central

Ouporov, I V; Knull, H R; Thomasson, K A

1999-01-01

Compartmentation of proteins in cells is important to proper cell function. Interactions of F-actin and glycolytic enzymes is one mechanism by which glycolytic enzymes can compartment. Brownian dynamics (BD) simulations of the binding of the muscle form of the glycolytic enzyme fructose-1,6-bisphosphate aldolase (aldolase) to F- or G-actin provide first-encounter snapshots of these interactions. Using x-ray structures of aldolase, G-actin, and three-dimensional models of F-actin, the electrostatic potential about each protein was predicted by solving the linearized Poisson-Boltzmann equation for use in BD simulations. The BD simulations provided solution complexes of aldolase with F- or G-actin. All complexes demonstrate the close contacts between oppositely charged regions of the protein surfaces. Positively charged surface regions of aldolase (residues Lys 13, 27, 288, 293, and 341 and Arg 257) are attracted to the negatively charged amino terminus (Asp 1 and Glu 2 and 4) and other patches (Asp 24, 25, and 363 and Glu 361, 364, 99, and 100) of actin subunits. According to BD results, the most important factor for aldolase binding to actin is the quaternary structure of aldolase and actin. Two pairs of adjacent aldolase subunits greatly add to the positive electrostatic potential of each other creating a region of attraction for the negatively charged subdomain 1 of the actin subunit that is exposed to solvent in the quaternary F-actin structure. PMID:9876119

Bactericidal action mechanism of negatively charged food grade clove oil nanoemulsions.

PubMed

Majeed, Hamid; Liu, Fei; Hategekimana, Joseph; Sharif, Hafiz Rizwan; Qi, Jing; Ali, Barkat; Bian, Yuan-Yuan; Ma, Jianguo; Yokoyama, Wallace; Zhong, Fang

2016-04-15

Clove oil (CO) anionic nanoemulsions were prepared with varying ratios of CO to canola oil (CA), emulsified and stabilized with purity gum ultra (PGU), a newly developed succinylated waxy maize starch. Interfacial tension measurements showed that CO acted as a co-surfactant and there was a gradual decrease in interfacial tension which favored the formation of small droplet sizes on homogenization until a critical limit (5:5% v/v CO:CA) was reached. Antimicrobial activity of the negatively charged CO nanoemulsion was determined against Gram positive GPB (Listeria monocytogenes and Staphylococcus aureus) and Gram negative GNB (Escherichia coli) bacterial strains using minimum inhibitory concentration (MIC) and a time kill dynamic method. Negatively charged PGU emulsified CO nanoemulsion showed prolonged antibacterial activities against Gram positive bacterial strains. We concluded that negatively charged CO nanoemulsion droplets self-assemble with GPB cell membrane, and facilitated interaction with cellular components of bacteria. Moreover, no electrostatic interaction existed between negatively charged droplets and the GPB membrane. Copyright © 2015 Elsevier Ltd. All rights reserved.

Model improvements to simulate charging in SEM

NASA Astrophysics Data System (ADS)

Arat, K. T.; Klimpel, T.; Hagen, C. W.

2018-03-01

Charging of insulators is a complex phenomenon to simulate since the accuracy of the simulations is very sensitive to the interaction of electrons with matter and electric fields. In this study, we report model improvements for a previously developed Monte-Carlo simulator to more accurately simulate samples that charge. The improvements include both modelling of low energy electron scattering and charging of insulators. The new first-principle scattering models provide a more realistic charge distribution cloud in the material, and a better match between non-charging simulations and experimental results. Improvements on charging models mainly focus on redistribution of the charge carriers in the material with an induced conductivity (EBIC) and a breakdown model, leading to a smoother distribution of the charges. Combined with a more accurate tracing of low energy electrons in the electric field, we managed to reproduce the dynamically changing charging contrast due to an induced positive surface potential.

Coarse-Grained Model for Water Involving a Virtual Site.

PubMed

Deng, Mingsen; Shen, Hujun

2016-02-04

In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones.

Novel foamy origin for singlet fermion masses

NASA Astrophysics Data System (ADS)

Ellis, John; Mavromatos, Nick E.; Nanopoulos, Dimitri V.

2017-10-01

We show how masses for singlet fermions can be generated by interactions with a D-particle model of space-time foam inspired by brane theory. It has been shown previously by one of the authors (N. E. M.) that such interactions may generate dynamically small masses for charged fermions via the recoils of D-particle defects interacting with photons. In this work we consider the direct interactions of D-particle with uncharged singlet fermions such as right-handed neutrinos. Quantum fluctuations of the lattice of D-particles have massless vector (spin-one) excitations that are analogues of phonons. These mediate forces with the singlet fermions, generating large dynamical masses that may be communicated to light neutrinos via the seesaw mechanism.

Aggregation of heteropolyanions in aqueous solutions exhibiting short-range attractions and long-range repulsions

DOE PAGES

Bera, Mrinal K.; Qiao, Baofu; Seifert, Soenke; ...

2015-12-15

Charged colloids and proteins in aqueous solutions interact via short-range attractions and long-range repulsions (SALR) and exhibit complex structural phases. These include homogeneously dispersed monomers, percolated monomers, clusters, and percolated clusters. We report the structural architectures of simple charged systems in the form of spherical, Keggin-type heteropolyanions (HPAs) by small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. Structure factors obtained from the SAXS measurements show that the HPAs interact via SALR. Concentration and temperature dependences of the structure factors for HPAs with –3e (e is the charge of an electron) charge are consistent with a mixture of nonassociated monomersmore » and associated randomly percolated monomers, whereas those for HPAs with –4e and –5e charges exhibit only nonassociated monomers in aqueous solutions. Our experiments show that the increase in magnitude of the charge of the HPAs increases their repulsive interactions and inhibits their aggregation in aqueous solutions. MD simulations were done to reveal the atomistic scale origins of SALR between HPAs. As a result, the short-range attractions result from water or proton-mediated hydrogen bonds between neighboring HPAs, whereas the long-range repulsions are due to the distributions of ions surrounding the HPAs.« less

pH-Sensitive Interactions between Cellulose Nanocrystals and DOPC Liposomes.

PubMed

Navon, Yotam; Radavidson, Harisoa; Putaux, Jean-Luc; Jean, Bruno; Heux, Laurent

2017-09-11

The interaction of 1,2 dioleolyl-sn-glycero-3-phosphatidylcholine (DOPC) vesicles with cellulose nanocrystals (CNCs) using several complementary techniques. Dynamic light scattering, zeta-potential, cryo-transmission electron microscopy and isothermal titration calorimetry (ITC) analyses confirmed the formation of pH-dependent CNC-liposome complexes. ITC was used to characterize the thermodynamic properties of this interaction. Positive values of enthalpy were found at pH lower than 5 where the charge sign of the constituents was opposite. The association was more pronounced at lower pH, as indicated by the higher values of association constant. We suggest that the positive enthalpy is derived from the release of counterions from the particle hydration shell during the association and that the charge of the vesicles plays a significant role in this interaction.

Charge independence, charge symmetry breaking in the S-wave nucleon-nucleon interaction, and renormalization

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

Alvaro Calle Cordon,Manuel Pavon Valderrama,Enrique Ruiz Arriola

2012-02-01

We study the interplay between charge symmetry breaking and renormalization in the NN system for S-waves. We find a set of universality relations which disentangle explicitly the known long distance dynamics from low energy parameters and extend them to the Coulomb case. We analyze within such an approach the One-Boson-Exchange potential and the theoretical conditions which allow to relate the proton-neutron, proton-proton and neutron-neutron scattering observables without the introduction of extra new parameters and providing good phenomenological success.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

PubMed

Wallace, Jason A; Shen, Jana K

2012-11-14

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

PubMed Central

Wallace, Jason A.; Shen, Jana K.

2012-01-01

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pKa values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future. PMID:23163362

Assembling oppositely charged lock and key responsive colloids: A mesoscale analog of adaptive chemistry

PubMed Central

Mihut, Adriana M.; Stenqvist, Björn; Lund, Mikael; Schurtenberger, Peter; Crassous, Jérôme J.

2017-01-01

We have seen a considerable effort in colloid sciences to copy Nature’s successful strategies to fabricate complex functional structures through self-assembly. This includes attempts to design colloidal building blocks and their intermolecular interactions, such as creating the colloidal analogs of directional molecular interactions, molecular recognition, host-guest systems, and specific binding. We show that we can use oppositely charged thermoresponsive particles with complementary shapes, such as spherical and bowl-shaped particles, to implement an externally controllable lock-and-key self-assembly mechanism. The use of tunable electrostatic interactions combined with the temperature-dependent size and shape and van der Waals interactions of these building blocks provides an exquisite control over the selectivity and specificity of the interactions and self-assembly process. The dynamic nature of the mechanism allows for reversibly cycling through various structures that range from weakly structured dense liquids to well-defined molecule-shaped clusters with different configurations through variations in temperature and ionic strength. We link this complex and dynamic self-assembly behavior to the relevant molecular interactions, such as screened Coulomb and van der Waals forces and the geometrical complementarity of the two building blocks, and discuss our findings in the context of the concepts of adaptive chemistry recently introduced to molecular systems. PMID:28929133

Pair interactions of heavy vortices in quantum fluids

NASA Astrophysics Data System (ADS)

Pshenichnyuk, Ivan A.

2018-02-01

The dynamics of quantum vortex pairs carrying heavy doping matter trapped inside their cores is studied. The nonlinear classical matter field formalism is used to build a universal mathematical model of a heavy vortex applicable to different types of quantum mixtures. It is shown how the usual vortex dynamics typical for undoped pairs qualitatively changes when heavy dopants are used: heavy vortices with opposite topological charges (chiralities) attract each other, while vortices with the same charge are repelled. The force responsible for such behavior appears as a result of superposition of vortices velocity fields in the presence of doping substance and can be considered as a special realization of the Magnus effect. The force is evaluated quantitatively and its inverse proportionality to the distance is demonstrated. The mechanism described in this paper gives an example of how a light nonlinear classical field may realize repulsive and attractive interactions between embedded heavy impurities.

Ultrafast collinear scattering and carrier multiplication in graphene.

PubMed

Brida, D; Tomadin, A; Manzoni, C; Kim, Y J; Lombardo, A; Milana, S; Nair, R R; Novoselov, K S; Ferrari, A C; Cerullo, G; Polini, M

2013-01-01

Graphene is emerging as a viable alternative to conventional optoelectronic, plasmonic and nanophotonic materials. The interaction of light with charge carriers creates an out-of-equilibrium distribution, which relaxes on an ultrafast timescale to a hot Fermi-Dirac distribution, that subsequently cools emitting phonons. Although the slower relaxation mechanisms have been extensively investigated, the initial stages still pose a challenge. Experimentally, they defy the resolution of most pump-probe setups, due to the extremely fast sub-100 fs carrier dynamics. Theoretically, massless Dirac fermions represent a novel many-body problem, fundamentally different from Schrödinger fermions. Here we combine pump-probe spectroscopy with a microscopic theory to investigate electron-electron interactions during the early stages of relaxation. We identify the mechanisms controlling the ultrafast dynamics, in particular the role of collinear scattering. This gives rise to Auger processes, including charge multiplication, which is key in photovoltage generation and photodetectors.

An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

NASA Astrophysics Data System (ADS)

Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Xu, Zhenli; Jacobs, Donald; Cai, Wei

2009-10-01

In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.

Charge Carriers Modulate the Bonding of Semiconductor Nanoparticle Dopants As Revealed by Time-Resolved X-ray Spectroscopy

DOE PAGES

Hassan, Asra; Zhang, Xiaoyi; Liu, Xiaohan; ...

2017-08-28

Understanding the electronic structure of doped semiconductors is essential to realize advancements in electronics and in the rational design of nanoscale devices. Here, we report the results of time-resolved X-ray absorption studies on copper-doped cadmium sulfide nanoparticles that provide an explicit description of the electronic dynamics of the dopants. The interaction of a dopant ion and an excess charge carrier is unambiguously observed via monitoring the oxidation state. The experimental data combined with DFT calculations demonstrate that dopant bonding to the host matrix is modulated by its interaction with charge carriers. Additionally, the transient photoluminescence and the kinetics of dopantmore » oxidation reveal the presence of two types of surface-bound ions that create mid-gap states.« less

Charge Carriers Modulate the Bonding of Semiconductor Nanoparticle Dopants As Revealed by Time-Resolved X-ray Spectroscopy

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

Hassan, Asra; Zhang, Xiaoyi; Liu, Xiaohan

Understanding the electronic structure of doped semiconductors is essential to realize advancements in electronics and in the rational design of nanoscale devices. Here, we report the results of time-resolved X-ray absorption studies on copper-doped cadmium sulfide nanoparticles that provide an explicit description of the electronic dynamics of the dopants. The interaction of a dopant ion and an excess charge carrier is unambiguously observed via monitoring the oxidation state. The experimental data combined with DFT calculations demonstrate that dopant bonding to the host matrix is modulated by its interaction with charge carriers. Additionally, the transient photoluminescence and the kinetics of dopantmore » oxidation reveal the presence of two types of surface-bound ions that create mid-gap states.« less

A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing*

PubMed Central

Cordeiro, Tiago N.; García, Jesús; Bernadó, Pau; Millet, Oscar; Pons, Miquel

2015-01-01

The Hha/YmoA nucleoid-associated proteins help selectively silence horizontally acquired genetic material, including pathogenicity and antibiotic resistance genes and their maintenance in the absence of selective pressure. Members of the Hha family contribute to gene silencing by binding to the N-terminal dimerization domain of H-NS and modifying its selectivity. Hha-like proteins and the H-NS N-terminal domain are unusually rich in charged residues, and their interaction is mostly electrostatic-driven but, nonetheless, highly selective. The NMR-based structural model of the complex between Hha/YmoA and the H-NS N-terminal dimerization domain reveals that the origin of the selectivity is the formation of a three-protein charge zipper with interdigitated complementary charged residues from Hha and the two units of the H-NS dimer. The free form of YmoA shows collective microsecond-millisecond dynamics that can by measured by NMR relaxation dispersion experiments and shows a linear dependence with the salt concentration. The number of residues sensing the collective dynamics and the population of the minor form increased in the presence of H-NS. Additionally, a single residue mutation in YmoA (D43N) abolished H-NS binding and the dynamics of the apo-form, suggesting the dynamics and binding are functionally related. PMID:26085102

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

Pramanik, Souvik, E-mail: souvick.in@gmail.com; Ghosh, Subir, E-mail: subir_ghosh2@rediffmail.com; Pal, Probir, E-mail: probirkumarpal@rediffmail.com

In the present paper, dynamics of generalized charged particles are studied in the presence of external electromagnetic interactions. This particular extension of the free relativistic particle model lives in Non-Commutative κ-Minkowski space–time, compatible with Doubly Special Relativity, that is motivated to describe Quantum Gravity effects. Furthermore we have also considered the electromagnetic field to be dynamical and have derived the modified forms of Lienard–Wiechert like potentials for these extended charged particle models. In all the above cases we exploit the new and extended form of κ-Minkowski algebra where electromagnetic effects are incorporated in the lowest order, in the Dirac frameworkmore » of Hamiltonian constraint analysis.« less

Development of a Dynamic Biomechanical Model for Load Carriage: Phase 4, Parts A and B: Development of a Dynamic Biomechanical Model Version 2 of Human Load Carriage

DTIC Science & Technology

2005-08-01

de charge et de comprendre les effets des caractéristiques de conception de systèmes de transport de charge sur la santé et la mobilité humaines...supérieur et le torse inférieur et la force totale de contact. Les travaux sont en cours en vue de l’intégration d’une couche de peau , ce qui...permettrait d’examiner en détail l’interaction au niveau de l’interface équipement- peau . Le but consiste à évaluer les risques de

On the Charge transport regime of crystalline organic semiconductors: diffusion limited by thermal off-diagonal electronic disorder

NASA Astrophysics Data System (ADS)

Troisi, Alessandro

2006-03-01

In organic crystalline semiconductor molecular components are held together by very weak interactions and the transfer integrals between neighboring molecular orbitals are extremely sensitive to small nuclear displacements. We used a mixed quantum chemical and molecular dynamic methodology to assess the effect of thermal structural fluctuations on the modulation of the transfer integrals between close molecules. We have found that the fluctuations of the transfer integrals are of the same order of magnitude of their average value for pentacene and anthracene. This condition makes the band description inadequate because a dynamic localization takes place and the translational symmetry is completely broken for the electronic states. We also present a simple one-dimensional semiclassical model that incorporates the effects of dynamical localization and allows the numerical computation of the charge mobility for ordered organic semiconductors. These results explain several contrasting experimental observations pointing sometimes to a delocalized ``band-like'' transport and sometimes to the existence of strongly localized charge carriers.

Spin-orbit torques in magnetic bilayers

NASA Astrophysics Data System (ADS)

Haney, Paul

2015-03-01

Spintronics aims to utilize the coupling between charge transport and magnetic dynamics to develop improved and novel memory and logic devices. Future progress in spintronics may be enabled by exploiting the spin-orbit coupling present at the interface between thin film ferromagnets and heavy metals. In these systems, applying an in-plane electrical current can induce magnetic dynamics in single domain ferromagnets, or can induce rapid motion of domain wall magnetic textures. There are multiple effects responsible for these dynamics. They include spin-orbit torques and a chiral exchange interaction (the Dzyaloshinskii-Moriya interaction) in the ferromagnet. Both effects arise from the combination of ferromagnetism and spin-orbit coupling present at the interface. There is additionally a torque from the spin current flux impinging on the ferromagnet, arising from the spin hall effect in the heavy metal. Using a combination of approaches, from drift-diffusion to Boltzmann transport to first principles methods, we explore the relative contributions to the dynamics from these different effects. We additionally propose that the transverse spin current is locally enhanced over its bulk value in the vicinity of an interface which is oriented normal to the charge current direction.

Physico-chemical studies on the interaction of dendrimers with lipid bilayers. 1. Effect of dendrimer generation and liposome surface charge.

PubMed

Roy, Biplab; Panda, Amiya Kumar; Parimi, Srinivas; Ametov, Igor; Barnes, Timothy; Prestidge, Clive A

2014-01-01

Studies on the interaction of different generation poly (amido amine) (PAMAM) dendrimers (2G, 4G and 6G) and liposomes of different compositions were carried out by a combined turbidity, dynamic light scattering and atomic force microscopic measurements. Liposomes comprising soy lecithin (SLC, negative surface charge), 1, 2-palmitoyl-sn-glycero-3-phosphatidylcholine (DPPC, mildly positive surface charge), 1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol (DPPG, negatively charged) and a biologically simulated mixture of DPPC + DPPG (7:3, M/M, negatively charged) were used as model bilayers. 30 wt% cholesterol was used in each combination as it is known to control the fluidity of membrane bilayers. Silica was used as a negatively charged hard sphere model with an aim to compare the results. Both the turbidity and hydrodynamic diameter values of all the liposomes, except DPPC, passed through maxima upon the progressive addition of PAMAM; the effect was insignificant in case of DPPC. Formation of dendriosome, a complex formed between dendrimer and liposome, resulted in the charge reversal of the negatively charged liposomes. Interaction between PAMAM and liposome was found to be governed by electrostatic as well as hydrogen bonding. Generation dependent PAMAM activity followed the order: 6G >4G>2G in terms of overall dendrimer concentration. However, interestingly, the order was reverse when PAMAM activity was considered in terms of total end group concentrations. AFM studies reveal the rupture of bilayer structure upon addition of dendrimer.

Sodium dodecyl benzene sulphonate mediated tautomerism of Eriochrome Black-T: Effect of charge transfer interaction

NASA Astrophysics Data System (ADS)

Ghosh, Sumit

2010-11-01

Interaction between anionic surfactant, sodium dodecyl benzene sulphonate, (SDBS) and an anionic dye Eriochrome Black-T, (EBT) has been investigated by visible spectroscopy, conductometry, dynamic light scattering and zeta potential measurements. Spectral changes of EBT observed on addition of SDBS indicate formation of quinone-hydrazone tautomer at pH 7.0, whereas in absence of SDBS this change appears at pH ˜ 9.45. However, at pH 7.0 this change in tautomerism is not observed in presence of sodium dodecyl sulphate (SDS). Experimental results indicate presence of charge transfer interaction between less stable quinone-hydrazone tautomer of EBT and SDBS molecules, which is confirmed using Benesi-Hildebrand and Scott equations.

Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer.

PubMed

Daily, Michael D; Baer, Marcel D; Mundy, Christopher J

2016-03-10

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical force field (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through side chain-side chain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described.

Electron correlation by polarization of interacting densities

NASA Astrophysics Data System (ADS)

Whitten, Jerry L.

2017-02-01

Coulomb interactions that occur in electronic structure calculations are correlated by allowing basis function components of the interacting densities to polarize dynamically, thereby reducing the magnitude of the interaction. Exchange integrals of molecular orbitals are not correlated. The modified Coulomb interactions are used in single-determinant or configuration interaction calculations. The objective is to account for dynamical correlation effects without explicitly introducing higher spherical harmonic functions into the molecular orbital basis. Molecular orbital densities are decomposed into a distribution of spherical components that conserve the charge and each of the interacting components is considered as a two-electron wavefunction embedded in the system acted on by an average field Hamiltonian plus r12-1. A method of avoiding redundancy is described. Applications to atoms, negative ions, and molecules representing different types of bonding and spin states are discussed.

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

DOE PAGES

Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

2017-01-16

Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order ofmore » $$1{{k}_{\\text{B}}}T$$ . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.« less

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

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

Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order ofmore » $$1{{k}_{\\text{B}}}T$$ . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.« less

Electronic structure and partial charge distribution of doxorubicin under different molecular environments

NASA Astrophysics Data System (ADS)

Poudel, Lokendra

Doxorubicin (trade name Adriamycin, abbreviated DOX) is a well-known an- thracyclic chemotherapeutic used in treating a variety of cancers including acute leukemia, lymphoma, multiple myeloma, and a range of stomach, lung, bladder, bone, breast, and ovarian cancers. The purpose of the present work is to study electronic structure, partial charge distribution and interaction energy of DOX under different environments. It provides a framework for better understanding of bioactivity of DOX with DNA. While in this work, we focus on DOX -- DNA interactions; the obtained knowledge could be translated to other drug -- target interactions or biomolecular interactions. The electronic structure and partial charge distribution of DOX in three dierent molecular environments: isolated, solvated, and intercalated into a DNA complex,were studied by rst principles density functional methods. It is shown that the addition of solvating water molecules to DOX and the proximity and interaction with DNA has a signicant impact on the electronic structure as well as the partial charge distribution. The calculated total partial charges for DOX in the three models are 0.0, +0.123 and -0.06 electrons for the isolated, solvated, and intercalated state, respectively. Furthermore, by using the more accurate ab initio partial charge values on every atom in the models, signicant improvement in estimating the DOX-DNA interaction energy is obtained in conjunction with the NAnoscale Molecular Dynamics (NAMD) code. The electronic structure of the DOX-DNA is further elucidated by resolving the total density of states (TDOS) into dierent functional groups of DOX, DNA, water, co-crystallized Spermine molecule, and Na ions. The surface partial charge distribution in the DOX-DNA is calculated and displayed graphically. We conclude that the presence of the solvent as well as the details of the interaction geometry matter greatly in the determination of the stability of the DOX complexion. Ab initio calculations on realistic models are an important step towards a more accurate description of biomolecular interaction and in the eventual understanding of long-range interactions in biomolecular systems.

Dynamics of near-surface electric discharges and mechanisms of their interaction with the airflow

NASA Astrophysics Data System (ADS)

Leonov, Sergey B.; Adamovich, Igor V.; Soloviev, Victor R.

2016-12-01

The main focus of the review is on dynamics and kinetics of near-surface discharge plasmas, such as surface dielectric barrier discharges sustained by AC and repetitively pulsed waveforms, pulsed DC discharges, and quasi-DC discharges, generated in quiescent air and in the airflow. A number of technical issues related to plasma flow control applications are discussed in detail, including discharge development via surface ionization waves, charge transport and accumulation on dielectric surface, discharge contraction, different types of flow perturbations generated by surface discharges, and effect of high-speed flow on discharge dynamics. In the first part of the manuscript, plasma morphology and results of electrical and optical emission spectroscopy measurements are discussed. Particular attention is paid to dynamics of surface charge accumulation and dissipation, both in diffuse discharges and during development of ionization instabilities resulting in discharge contraction. Contraction leads to significant increase of both the surface area of charge accumulation and the energy coupled to the plasma. The use of alternating polarity pulse waveforms accelerates contraction of surface dielectric barrier discharges and formation of filamentary plasmas. The second part discusses the interaction of discharge plasmas with quiescent air and the external airflow. Four major types of flow perturbations have been identified: (1) low-speed near-surface jets generated by electrohydrodynamic interaction (ion wind); (2) spanwise and streamwise vortices formed by both electrohydrodynamic and thermal effects; (3) weak shock waves produced by rapid heating in pulsed discharges on sub-microsecond time scale; and (4) near-surface localized stochastic perturbations, on sub-millisecond time, detected only recently. The mechanism of plasma-flow interaction remains not fully understood, especially in filamentary surface dielectric barrier discharges. Localized quasi-DC surface discharges sustained in a high-speed flow are discussed in the third part of the review. Although dynamics of this type of the discharge is highly transient, due to its strong interaction with the flow, the resultant flow structure is stationary, including the oblique shock and the flow separation region downstream of the discharge. The oblique shock is attached to a time-averaged, wedge-shaped, near-wall plasma layer, with the shock angle controlled by the discharge power, which makes possible changing the flow structure and parameters in a controlled way. Finally, unresolved and open-ended issues are discussed in the summary.

Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Ishioka, T.; Yamada, H.; Miyakawa, T.; Morikawa, R.; Akanuma, S.; Yamagishi, A.; Takasu, M.

2016-12-01

Proteins, which incorporate charged and hydrophobic amino acid residues, are useful as a material of nanotechnology. Among these proteins, IPMDH (3-isopropylmalate dehydrogenase), which has thermal stability, has potential as a material of nanofiber. In this study, we performed coarse-grained molecular dynamics simulation of IPMDH using MARTINI force fields, and we investigated the orientation for the binding of IPMDH. In simulation, we analyzed wild type of IPMDH and the mutated IPMDH proteins, where 13, 20, 27, 332, 335 and 338th amino acid residues are replaced by lysine residues which have positive charge and by glutamic acid residues which have negative charge. Since the binding of mutated IPMDH is advantageous compared with the binding of wild type for one orientation, we suggest that the Coulomb interaction for the binding of IPMDH is important.

A charge-dependent mechanism is responsible for the dynamic accumulation of proteins inside nucleoli.

PubMed

Musinova, Yana R; Kananykhina, Eugenia Y; Potashnikova, Daria M; Lisitsyna, Olga M; Sheval, Eugene V

2015-01-01

The majority of known nucleolar proteins are freely exchanged between the nucleolus and the surrounding nucleoplasm. One way proteins are retained in the nucleoli is by the presence of specific amino acid sequences, namely nucleolar localization signals (NoLSs). The mechanism by which NoLSs retain proteins inside the nucleoli is still unclear. Here, we present data showing that the charge-dependent (electrostatic) interactions of NoLSs with nucleolar components lead to nucleolar accumulation as follows: (i) known NoLSs are enriched in positively charged amino acids, but the NoLS structure is highly heterogeneous, and it is not possible to identify a consensus sequence for this type of signal; (ii) in two analyzed proteins (NF-κB-inducing kinase and HIV-1 Tat), the NoLS corresponds to a region that is enriched for positively charged amino acid residues; substituting charged amino acids with non-charged ones reduced the nucleolar accumulation in proportion to the charge reduction, and nucleolar accumulation efficiency was strongly correlated with the predicted charge of the tested sequences; and (iii) sequences containing only lysine or arginine residues (which were referred to as imitative NoLSs, or iNoLSs) are accumulated in the nucleoli in a charge-dependent manner. The results of experiments with iNoLSs suggested that charge-dependent accumulation inside the nucleoli was dependent on interactions with nucleolar RNAs. The results of this work are consistent with the hypothesis that nucleolar protein accumulation by NoLSs can be determined by the electrostatic interaction of positively charged regions with nucleolar RNAs rather than by any sequence-specific mechanism. Copyright © 2014 Elsevier B.V. All rights reserved.

Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions.

PubMed

Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

2015-08-14

We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

Unveiling the Mode of Interaction of Berberine Alkaloid in Different Supramolecular Confined Environments: Interplay of Surface Charge between Nano-Confined Charged Layer and DNA.

PubMed

Kundu, Niloy; Roy, Arpita; Banik, Debasis; Sarkar, Nilmoni

2016-02-18

In this Article, we demonstrate a detailed characterization of binding interaction of berberine chloride (BBCl) with calf-thymus DNA (CT-DNA) in buffer solution as well as in two differently charged reverse micelles (RMs). The photophyscial properties of this alkaloid have been modulated within these microheterogeneous bioassemblies. The mode of binding of this alkaloid with DNA is of debate to date. However, fluorescence spectroscopic measurements, circular dichroism (CD) measurement, and temperature-dependent study unambiguously establish that BBCl partially intercalates into the DNA base pairs. The nonplanarity imposed by partial saturation in their structure causes the nonclassical types of intercalation into DNA. Besides the intercalation, electrostatic interactions also play a significant role in the binding between BBCl and DNA. DNA structure turns into a condensed form after encapsulation into RMs, which is followed by the CD spectra and microscopy study. The probe location and dynamics in the nanopool of the RMs depended on the electrostatic interaction between the charged surfactants and cationic berberine. The structural alteration of CT-DNA from B form to condensed form and the interplay of surface charge between RMs and DNA determine the interaction between the alkaloid and DNA in RMs. Time-resolved study and fluorescence anisotropy measurements successfully provide the binding interaction of BBCl in the nanopool of the RMs in the absence and in the presence of DNA. This study motivates us to judge further the potential applicability of this alkaloid in other biological systems or other biomimicking organized assemblies.

Dynamic self-assembly of charged colloidal strings and walls in simple fluid flows.

PubMed

Abe, Yu; Zhang, Bo; Gordillo, Leonardo; Karim, Alireza Mohammad; Francis, Lorraine F; Cheng, Xiang

2017-02-22

Colloidal particles can self-assemble into various ordered structures in fluid flows that have potential applications in biomedicine, materials synthesis and encryption. These dynamic processes are also of fundamental interest for probing the general principles of self-assembly under non-equilibrium conditions. Here, we report a simple microfluidic experiment, where charged colloidal particles self-assemble into flow-aligned 1D strings with regular particle spacing near a solid boundary. Using high-speed confocal microscopy, we systematically investigate the influence of flow rates, electrostatics and particle polydispersity on the observed string structures. By studying the detailed dynamics of stable flow-driven particle pairs, we quantitatively characterize interparticle interactions. Based on the results, we construct a simple model that explains the intriguing non-equilibrium self-assembly process. Our study shows that the colloidal strings arise from a delicate balance between attractive hydrodynamic coupling and repulsive electrostatic interaction between particles. Finally, we demonstrate that, with the assistance of transverse electric fields, a similar mechanism also leads to the formation of 2D colloidal walls.

Self-interaction effects on charge-transfer collisions

DOE PAGES

Quashie, Edwin E.; Saha, Bidhan C.; Andrade, Xavier; ...

2017-04-27

In this article, we investigate the role of the self-interaction error in the simulation of collisions using time-dependent density functional theory (TDDFT) and Ehrenfest dynamics. In addition, we compare many different approximations of the exchange and correlation potential, using as a test system the collision of H + + CH 4 at 30 eV. We find that semilocal approximations, like the Perdew-Burke- Ernzerhof (PBE), and even hybrid functionals, such as the Becke, 3-parameter, Lee-Yang-Parr (B3LYP), produce qualitatively incorrect predictions for the scattering of the proton. This discrepancy appears because the self-interaction error allows the electrons to jump too easily tomore » the proton, leading to radically different forces with respect to the non-self-interacting case. Lastly, from our results, we conclude that using a functional that is self-interaction free is essential to properly describing charge-transfer collisions between ions and molecules in TDDFT.« less

DNA packaging in viral capsids with peptide arms.

PubMed

Cao, Qianqian; Bachmann, Michael

2017-01-18

Strong chain rigidity and electrostatic self-repulsion of packed double-stranded DNA in viruses require a molecular motor to pull the DNA into the capsid. However, what is the role of electrostatic interactions between different charged components in the packaging process? Though various theories and computer simulation models were developed for the understanding of viral assembly and packaging dynamics of the genome, long-range electrostatic interactions and capsid structure have typically been neglected or oversimplified. By means of molecular dynamics simulations, we explore the effects of electrostatic interactions on the packaging dynamics of DNA based on a coarse-grained DNA and capsid model by explicitly including peptide arms (PAs), linked to the inner surface of the capsid, and counterions. Our results indicate that the electrostatic interactions between PAs, DNA, and counterions have a significant influence on the packaging dynamics. We also find that the packed DNA conformations are largely affected by the structure of the PA layer, but the packaging rate is insensitive to the layer structure.

Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview.

PubMed

Riniker, Sereina

2018-03-26

In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

Emergent spin electromagnetism induced by magnetization textures in the presence of spin-orbit interaction (invited)

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

Tatara, Gen, E-mail: gen.tatara@riken.jp; Nakabayashi, Noriyuki; Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397 Japan

2014-05-07

Emergent electromagnetic field which couples to electron's spin in ferromagnetic metals is theoretically studied. Rashba spin-orbit interaction induces spin electromagnetic field which is in the linear order in gradient of magnetization texture. The Rashba-induced effective electric and magnetic fields satisfy in the absence of spin relaxation the Maxwell's equations as in the charge-based electromagnetism. When spin relaxation is taken into account besides spin dynamics, a monopole current emerges generating spin motive force via the Faraday's induction law. The monopole is expected to play an important role in spin-charge conversion and in the integration of spintronics into electronics.

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.

Investigation the foam dynamics capacity of SDS in foam generator by affecting the presence of organic and inorganic contaminant

NASA Astrophysics Data System (ADS)

Haryanto, Bode; Siswarni, M. Z.; Sianipar, Yosef C. H.; Sinaga, Tongam M. A.; Bestari, Imam

2017-05-01

The effect of negative charge SDS monomer on its foam capacity with the presence of contaminants was investigated in foam generator. Generally, surfactant with higher concentration has higher foam capacity. The higher concentration will increase the number of monomer then increase the micelles in liquid phase. Increasing the number of monomer with the negative charge is a potential to increase interaction with metal ion with positive charge in solution. The presence of inorganic compound as metal ion with positive charge and organic compound (colloid) as particle of coffee impacting to generate the foam lamella with monomer is evaluated. Foam dynamic capacity of only SDS with variation of CMC, 1 x; 2 x; 3 x have the height 7.5, 8.0 and 8.3 cm respectively with the different range time were investigated. The Height of foam dynamic capacity with the presence of 20 ppm Cd2+ ion contaminant was 8.0, 8.3 and 8.4 cm at the same CMC variation of SDS. The presence of metal ion contaminant within the foam was confirmed by AAS. The black coffee particles and oil as contaminant decreased the foam capacity significantly in comparing to metal ions.

Estimation of Nanodiamond Surface Charge Density from Zeta Potential and Molecular Dynamics Simulations.

PubMed

Ge, Zhenpeng; Wang, Yi

2017-04-20

Molecular dynamics simulations of nanoparticles (NPs) are increasingly used to study their interactions with various biological macromolecules. Such simulations generally require detailed knowledge of the surface composition of the NP under investigation. Even for some well-characterized nanoparticles, however, this knowledge is not always available. An example is nanodiamond, a nanoscale diamond particle with surface dominated by oxygen-containing functional groups. In this work, we explore using the harmonic restraint method developed by Venable et al., to estimate the surface charge density (σ) of nanodiamonds. Based on the Gouy-Chapman theory, we convert the experimentally determined zeta potential of a nanodiamond to an effective charge density (σ eff ), and then use the latter to estimate σ via molecular dynamics simulations. Through scanning a series of nanodiamond models, we show that the above method provides a straightforward protocol to determine the surface charge density of relatively large (> ∼100 nm) NPs. Overall, our results suggest that despite certain limitation, the above protocol can be readily employed to guide the model construction for MD simulations, which is particularly useful when only limited experimental information on the NP surface composition is available to a modeler.

Interaction quantum quenches in the one-dimensional Fermi-Hubbard model

NASA Astrophysics Data System (ADS)

Heidrich-Meisner, Fabian; Bauer, Andreas; Dorfner, Florian; Riegger, Luis; Orso, Giuliano

2016-05-01

We discuss the nonequilibrium dynamics in two interaction quantum quenches in the one-dimensional Fermi-Hubbard model. First, we study the decay of the Néel state as a function of interaction strength. We observe a fast charge dynamics over which double occupancies are built up, while the long-time decay of the staggered moment is controlled by spin excitations, corroborated by the analysis of the entanglement dynamics. Second, we investigate the formation of Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) correlations in a spin-imbalanced system in quenches from the noninteracting case to attractive interactions. Even though the quench puts the system at a finite energy density, peaks at the characteristic FFLO quasimomenta are visible in the quasi-momentum distribution function, albeit with an exponential decay of s-wave pairing correlations. We also discuss the imprinting of FFLO correlations onto repulsively bound pairs and their rapid decay in ramps. Supported by the DFG (Deutsche Forschungsgemeinschaft) via FOR 1807.

Ewald Summation Approach to Potential Models of Aqueous Electrolytes Involving Gaussian Charges and Induced Dipoles: Formal and Simulation Results

DOE PAGES

Chialvo, Ariel A.; Vlcek, Lukas

2014-11-01

We present a detailed derivation of the complete set of expressions required for the implementation of an Ewald summation approach to handle the long-range electrostatic interactions of polar and ionic model systems involving Gaussian charges and induced dipole moments with a particular application to the isobaricisothermal molecular dynamics simulation of our Gaussian Charge Polarizable (GCP) water model and its extension to aqueous electrolytes solutions. The set comprises the individual components of the potential energy, electrostatic potential, electrostatic field and gradient, the electrostatic force and the corresponding virial. Moreover, we show how the derived expressions converge to known point-based electrostatic counterpartsmore » when the parameters, defining the Gaussian charge and induced-dipole distributions, are extrapolated to their limiting point values. Finally, we illustrate the Ewald implementation against the current reaction field approach by isothermal-isobaric molecular dynamics of ambient GCP water for which we compared the outcomes of the thermodynamic, microstructural, and polarization behavior.« less

Peptide adsorption on the hydrophobic surface: A free energy perspective

NASA Astrophysics Data System (ADS)

Sheng, Yuebiao; Wang, Wei; Chen, P.

2011-05-01

Protein adsorption is a very attractive topic which relates to many novel applications in biomaterials, biotechnology and nanotechnology. Ionic complementary peptides are a group of novel nano-biomaterials with many biomedical applications. In this work, molecular dynamics simulations of the ionic-complementary peptide EAK16-II on a hydrophobic graphite surface were performed under neutral, acidic and basic solution conditions. Adsorption free energy contour maps were obtained by analyzing the dynamical trajectories. Hydrophobic interactions were found to govern the adsorption of the first peptide molecule, and both hydrophobic and electrostatic interactions contributed to the adsorption of the second peptide molecule. Especially under acidic and basic solution conditions, interplay existed among chain-chain hydrophobic, chain-surface hydrophobic and chain-chain electrostatic interactions during the adsorption of the second peptide molecule. Non-charged residues were found to lie on the graphite surface, while charged residue side-chains oriented towards the solution after the peptide deposited on the surface. These results provide a basis for understanding peptide adsorption on the hydrophobic surface under different solution conditions, which is useful for novel applications such as bioactive implant devices and drug delivery material design.

Effect of Charged-Magnetic Grains in Protoplanetary Disks

NASA Astrophysics Data System (ADS)

Perry, Jonathan; Matthews, Lorin; Hyde, Truell

Effects of Charged-Magnetic Grains in Protoplanetary Disks Jonathan, Perry, Lorin Swint Matthews, and Truell W. Hyde Center for Astrophysics, Space Physics, and Engi-neering Research, addressPlaceNamePlaceNameplaceBaylor StreetPlaceTypeUniversity, Stree-taddressOne Bear Place 97316 Waco, TX 76798 USA The interaction and growth of dust grains is an important process in early planetesimal formation. The structure of aggregates formed from dust depend largely on the initial properties within the dust population, whether the grains are charged or uncharged, magnetic or non-magnetic. Theoretical simulations exam-ining pair-wise interactions between aggregates indicate that charged magnetic grains exhibit different growth behavior than populations consisting of exclusively charged or exclusively mag-netic grains. This study extends that work to predict how charged-magnetic grains influence grain growth within a protoplanetary disk. An N-body simulation containing various mixtures of dust materials is used to examine the differences in dust coagulation in the presence of charged magnetic aggregates. The growth of the dust aggregates is analyzed to determine the effects that charged magnetic grains contribute to the evolution of the dust cloud. Comparison of the rate of aggregation as well as the dynamic exponent relating mass of a cluster to the elapsed time will both be discussed.

A unifying approach to lattice dynamical and electronic properties of solids

NASA Astrophysics Data System (ADS)

Falter, C.

1988-06-01

A unified analysis of lattice dynamical and electronic properties of solids with special emphasis on the interaction between electrons and phonons is presented. The article is roughly divided into two parts reflecting different points of view. The density response of the electrons provides the link between these parts. In the first part, the microscopic theory in terms of the density response in crystals is discussed. Relations are pointed out between the density response approach and the density functional theory. The latter is used for a representation of the exchange-correlation interaction and the microscopic force constants. Relevant methods, as recently proposed by various authors for the calculation of the density response in inhomogeneous solids are discussed. Particular attention is paid to the development of a renormalized response description. Applications of this method to lattice dynamical and electronic properties are presented. In the second part an alternative physical concept, the quasi-ion approach, is outlined. This concept is shown to provide a microscopic basis for electronic charge localization in crystals and proves the importance of the correlation between crystal symmetry and many-body effects. Is is derived that within linear response theory an appropriate decomposition of the valence charge density leads uniquely to a spatially localized density contribution at the individual ion which follows its motion rigidly. The composite consisting of this partial density and the ion core is taken to be an individual entity, denoted as quasi-ion, from which the crystal is built up. In a certain sense this is a generalization of Ziman's concept of neutral pseudo-atoms being approximately valid in simple metals. New insight into the bonding mechanism and charge relaxation processes is shown to follow from this concept. In particular, we discuss the covalent, ionic and metallic bonding mechanisms, using the localized picture provided by the partial densities, on the same basis. The quasi-ion approach is also applied to the calculation of phonon-induced charge density redistributions and to the construction of a simplified formulation of microscopic lattice dynamics. Investigations of the phonon dispersion for different bonding types are given within a rigid quasi-ion model and extensions of this model are outlined. Among other things, these calculations indicate that bonding dynamics of (covalent) molecules and crystals can be described by relative rotations of the quasi-ions under the condition of rotational invariance of the system. Finally, possible applications of the quasi-ion concept to an approximate formulation of anharmonic lattice dynamics and the interaction between electrons and phonons are discussed. A numerical investigation of this interaction is presented and compared with the results from the rigid-ion model. As a consequence of the quasi-ion concept a consistent calculation of the phonon dispersion, the electronic band structure and the electron-phonon interaction becomes possible.

Mass loading in the solar wind interaction with Venus and Mars

NASA Astrophysics Data System (ADS)

Breus, T. K.; Bauer, S. J.; Krymskii, A. M.; Mitnitskii, V. Ya.

1989-03-01

An analysis of available experimental data and theoretical concepts indicates that the interaction of the solar wind (SW) on the subsolar side with Venus, which has no intrinsic magnetic field, and with Mars, which has a small intrinsic magnetic field, is determined by the solar wind dynamic pressure with a contribution from the neutral planetary atmosphere to this interaction. The pattern of the SW interaction with these planets is different in principle for high and low dynamic pressures of the SW and is related to the varying intensity of ion formation processes (the SW Mass loading effect) in the vicinity of the SW obstacle boundary, which moves for different SW dynamic pressures into regions of different neutral atmosphere density. For moderate or high SW dynamic pressures, the subsolar Martian magnetosphere is also affected by this process. Results of numerical simulations of the SW-Mars interaction for a magnetospheric obstacle boundary at an altitude of 300 km are presented. To estimate the relative role of photoionization and charge exchange processes and their effect on the shock front position, different versions of the mass loading effect were separately calculated.

The aerodynamics of bodies in a rarefied ionized gas with applications to spacecraft environmental dynamics

NASA Technical Reports Server (NTRS)

Stone, N. H.

1981-01-01

The objectives are to provide a parametric description of the electrostatic interaction of a mesosonic, collisionless plasma with conducting bodies on the order of 1 to 10 Debye lengths in size, and to extend this description to the satellite-ionospheric interaction, where possible. Experimental findings include: the wake of the geometrically complex body appears to be a linear superposition of the wakes of its simple geometric components; and vector ion flux measurements show converging ion streams at the wake axis and direct evidence of ion streams deflected from the wake axis by the positive space charge potential associated with the axial ion peak. The extension to the satellite-ionospheric interaction utilizes qualitative scaling and indicates that similar, but smaller amplitude, wake structures may be expected for small or highly charged bodies. However, for large bodies at small potentials, the structure may be diffused by the thermal ion motion and the dispersion resulting for space charge potentials.

Infrared consistency and the weak gravity conjecture

DOE PAGES

Cheung, Clifford; Remmen, Grant N.

2014-12-11

The weak gravity conjecture (WGC) asserts that an Abelian gauge theory coupled to gravity is inconsistent unless it contains a particle of charge q and mass m such that q ≥ m/m Pl. This criterion is obeyed by all known ultraviolet completions and is needed to evade pathologies from stable black hole remnants. In this paper, we explore the WGC from the perspective of low-energy effective field theory. Below the charged particle threshold, the effective action describes a photon and graviton interacting via higher-dimension operators. We derive infrared consistency conditions on the parameters of the effective action using i )more » analyticity of light-by-light scattering, ii ) unitarity of the dynamics of an arbitrary ultraviolet completion, and iii ) absence of superluminality and causality violation in certain non-trivial backgrounds. For convenience, we begin our analysis in three spacetime dimensions, where gravity is non-dynamical but has a physical effect on photon-photon interactions. We then consider four dimensions, where propagating gravity substantially complicates all of our arguments, but bounds can still be derived. Operators in the effective action arise from two types of diagrams: those that involve electromagnetic interactions (parameterized by a charge-to-mass ratio q/m) and those that do not (parameterized by a coefficient γ). In conclusion, infrared consistency implies that q/m is bounded from below for small γ.« less

Charge carrier dynamics and surface plasmon interaction in gold nanorod-blended organic solar cell

NASA Astrophysics Data System (ADS)

Rana, Aniket; Gupta, Neeraj; Lochan, Abhiram; Sharma, G. D.; Chand, Suresh; Kumar, Mahesh; Singh, Rajiv K.

2016-08-01

The inclusion of plasmonic nanoparticles into organic solar cell enhances the light harvesting properties that lead to higher power conversion efficiency without altering the device configuration. This work defines the consequences of the nanoparticle overloading amount and energy transfer process between gold nanorod and polymer (active matrix) in organic solar cells. We have studied the hole population decay dynamics coupled with gold nanorods loading amount which provides better understanding about device performance limiting factors. The exciton and plasmon together act as an interacting dipole; however, the energy exchange between these two has been elucidated via plasmon resonance energy transfer (PRET) mechanism. Further, the charge species have been identified specifically with respect to their energy levels appearing in ultrafast time domain. The specific interaction of these charge species with respective surface plasmon resonance mode, i.e., exciton to transverse mode of oscillation and polaron pair to longitudinal mode of oscillations, has been explained. Thus, our analysis reveals that PRET enhances the carrier population density in polymer via non-radiative process beyond the concurrence of a particular plasmon resonance oscillation mode and polymer absorption range. These findings give new insight and reveal specifically the factors that enhance and control the performance of gold nanorods blended organic solar cells. This work would lead in the emergence of future plasmon based efficient organic electronic devices.

Charge carrier dynamics and surface plasmon interaction in gold nanorod-blended organic solar cell

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

Rana, Aniket; Lochan, Abhiram; Chand, Suresh

The inclusion of plasmonic nanoparticles into organic solar cell enhances the light harvesting properties that lead to higher power conversion efficiency without altering the device configuration. This work defines the consequences of the nanoparticle overloading amount and energy transfer process between gold nanorod and polymer (active matrix) in organic solar cells. We have studied the hole population decay dynamics coupled with gold nanorods loading amount which provides better understanding about device performance limiting factors. The exciton and plasmon together act as an interacting dipole; however, the energy exchange between these two has been elucidated via plasmon resonance energy transfer (PRET)more » mechanism. Further, the charge species have been identified specifically with respect to their energy levels appearing in ultrafast time domain. The specific interaction of these charge species with respective surface plasmon resonance mode, i.e., exciton to transverse mode of oscillation and polaron pair to longitudinal mode of oscillations, has been explained. Thus, our analysis reveals that PRET enhances the carrier population density in polymer via non-radiative process beyond the concurrence of a particular plasmon resonance oscillation mode and polymer absorption range. These findings give new insight and reveal specifically the factors that enhance and control the performance of gold nanorods blended organic solar cells. This work would lead in the emergence of future plasmon based efficient organic electronic devices.« less

Magnon Splitting Induced by Charge Transfer in the Three-Orbital Hubbard Model

NASA Astrophysics Data System (ADS)

Wang, Yao; Huang, Edwin W.; Moritz, Brian; Devereaux, Thomas P.

2018-06-01

Understanding spin excitations and their connection to unconventional superconductivity have remained central issues since the discovery of cuprates. Direct measurement of the dynamical spin structure factor in the parent compounds can provide key information on important interactions relevant in the doped regime, and variations in the magnon dispersion have been linked closely to differences in crystal structure between families of cuprate compounds. Here, we elucidate the relationship between spin excitations and various controlling factors thought to be significant in high-Tc materials by systematically evaluating the dynamical spin structure factor for the three-orbital Hubbard model, revealing differences in the spin dispersion along the Brillouin zone axis and the diagonal. Generally, we find that the absolute energy scale and momentum dependence of the excitations primarily are sensitive to the effective charge-transfer energy, while changes in the on-site Coulomb interactions have little effect on the details of the dispersion. In particular, our result highlights the splitting between spin excitations along the axial and diagonal directions in the Brillouin zone. This splitting decreases with increasing charge-transfer energy and correlates with changes in the apical oxygen position, and general structural variations, for different cuprate families.

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains.

PubMed

Makowski, Mariusz; Liwo, Adam; Sobolewski, Emil; Scheraga, Harold A

2011-05-19

A new model of side-chain-side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parametrized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. © 2011 American Chemical Society

Particle transport through hydrogels is charge asymmetric.

PubMed

Zhang, Xiaolu; Hansing, Johann; Netz, Roland R; DeRouchey, Jason E

2015-02-03

Transport processes within biological polymer networks, including mucus and the extracellular matrix, play an important role in the human body, where they serve as a filter for the exchange of molecules and nanoparticles. Such polymer networks are complex and heterogeneous hydrogel environments that regulate diffusive processes through finely tuned particle-network interactions. In this work, we present experimental and theoretical studies to examine the role of electrostatics on the basic mechanisms governing the diffusion of charged probe molecules inside model polymer networks. Translational diffusion coefficients are determined by fluorescence correlation spectroscopy measurements for probe molecules in uncharged as well as cationic and anionic polymer solutions. We show that particle transport in the charged hydrogels is highly asymmetric, with diffusion slowed down much more by electrostatic attraction than by repulsion, and that the filtering capability of the gel is sensitive to the solution ionic strength. Brownian dynamics simulations of a simple model are used to examine key parameters, including interaction strength and interaction range within the model networks. Simulations, which are in quantitative agreement with our experiments, reveal the charge asymmetry to be due to the sticking of particles at the vertices of the oppositely charged polymer networks. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Dynamics in Complex Coacervates

NASA Astrophysics Data System (ADS)

Perry, Sarah

Understanding the dynamics of a material provides detailed information about the self-assembly, structure, and intermolecular interactions present in a material. While rheological methods have long been used for the characterization of complex coacervate-based materials, it remains a challenge to predict the dynamics for a new system of materials. Furthermore, most work reports only qualitative trends exist as to how parameters such as charge stoichiometry, ionic strength, and polymer chain length impact self-assembly and material dynamics, and there is little information on the effects of polymer architecture or the organization of charges within a polymer. We seek to link thermodynamic studies of coacervation phase behavior with material dynamics through a carefully-controlled, systematic study of coacervate linear viscoelasticity for different polymer chemistries. We couple various methods of characterizing the dynamics of polymer-based complex coacervates, including the time-salt superposition methods developed first by Spruijt and coworkers to establish a more mechanistic strategy for comparing the material dynamics and linear viscoelasticity of different systems. Acknowledgment is made to the Donors of the American Chemical Society Petroleum Research Fund for support of this research.

Brownian Dynamics Simulations of Polyelectrolyte Adsorption in Shear Flow

NASA Astrophysics Data System (ADS)

Panwar, Ajay

2005-03-01

The adsorption of polyelectrolytes onto charged surfaces often occurs in microfludic devices and can influence their operation. We employ Brownian dynamics simulations to investigate the effect of a simple shear flow on the adsorption of an isolated polyelectrolyte molecule onto an oppositely charged surface. The polyelectrolyte is modeled as a freely-jointed bead-rod chain where the total charge is distributed uniformly among all the beads, and the beads are allowed to interact with one another and the charged surface through screened Coulombic interactions. The simulations are performed by placing the chain some distance above the surface, and the adsorption behavior is studied as a function of the screening length. Specifically, we look at the components of the radius of gyration, normal and parallel to the adsorbing surface, as functions of the screening length, both in the absence and presence of the flow. We find that in the absence of flow, the chain lies flat and stretched on the adsorbing surface in the limit of weak screening, but attains free solution behavior in the limit of strong screening. In the presence of a shear flow, the chain orientation in the direction of the flow increases with increasing Weissenberg number over the entire range of screening lengths studied. We also find that increasing the strength of the shear flow leads to an increased contact of the chain with the surface compared to the case when no flow is present.

Time-dependent density functional theory for the charging kinetics of electric double layer containing room-temperature ionic liquids

DOE PAGES

Lian, Cheng; Univ. of California, Riverside, CA; Zhao, Shuangliang; ...

2016-11-29

Understanding the charging kinetics of electric double layers is of fundamental importance for the design and development of novel electrochemical devices such as supercapacitors and field-effect transistors. In this paper, we study the dynamic behavior of room-temperature ionic liquids using a classical time-dependent density functional theory that accounts for the molecular excluded volume effects, the electrostatic correlations, and the dispersion forces. While the conventional models predict a monotonic increase of the surface charge with time upon application of an electrode voltage, our results show that dispersion between ions results in a non-monotonic increase of the surface charge with the durationmore » of charging. Finally and furthermore, we investigate the effects of van der Waals attraction between electrode/ionic-liquid interactions on the charging processes.« less

Charge relaxation and dynamics in organic semiconductors

NASA Astrophysics Data System (ADS)

Kwok, H. L.

2006-08-01

Charge relaxation in dispersive materials is often described in terms of the stretched exponential function (Kohlrausch law). The process can be explained using a "hopping" model which in principle, also applies to charge transport such as current conduction. This work analyzed reported transient photoconductivity data on functionalized pentacene single crystals using a geometric hopping model developed by B. Sturman et al and extracted values (or range of values) on the materials parameters relevant to charge relaxation as well as charge transport. Using the correlated disorder model (CDM), we estimated values of the carrier mobility for the pentacene samples. From these results, we observed the following: i) the transport site density appeared to be of the same order of magnitude as the carrier density; ii) it was possible to extract lower bound values on the materials parameters linked to the transport process; and iii) by matching the simulated charge decay to the transient photoconductivity data, we were able to refine estimates on the materials parameters. The data also allowed us to simulate the stretched exponential decay. Our observations suggested that the stretching index and the carrier mobility were related. Physically, such interdependence would allow one to demarcate between localized molecular interactions and distant coulomb interactions.

Correlated phonons and the Tc-dependent dynamical phonon anomalies

NASA Astrophysics Data System (ADS)

Hakioğlu, T.; Türeci, H.

1997-11-01

Anomalously large low-temperature phonon anharmonicities can lead to static as well as dynamical changes in the low-temperature properties of the electron-phonon system. In this work, we focus our attention on the dynamically generated low-temperature correlations in an interacting electron-phonon system using a self-consistent dynamical approach in the intermediate coupling range. In the context of the model, the polaron correlations are produced by the charge-density fluctuations which are generated dynamically by the electron-phonon coupling. Conversely, the latter is influenced in the presence of the former. The purpose of this work is to examine the dynamics of this dual mechanism between the two using the illustrative Fröhlich model. In particular, the influence of the low-temperature phonon dynamics on the superconducting properties in the intermediate coupling range is investigated. The influence on the Holstein reduction factor as well as the enhancement in the zero-point fluctuations and in the electron-phonon coupling are calculated numerically. We also examine these effects in the presence of superconductivity. Within this model, the contribution of the electron-phonon interaction as one of the important elements in the mechanisms of superconductivity can reach values as high as 15-20% of the characteristic scale of the lattice vibrational energy. The second motivation of this work is to understand the nature of the Tc-dependent temperature anomalies observed in the Debye-Waller factor, dynamical pair correlations, and average atomic vibrational energies for a number of high-temperature superconductors. In our approach we do not claim nor believe that the electron-phonon interaction is the primary mechanism leading to high-temperature superconductivity. Nevertheless, our calculations suggest that the dynamically induced low-temperature phonon correlation model can account for these anomalies and illustrates their possible common origin. Finally, the relevance of incorporating these low-temperature effects into more realistic models of high-temperature superconductivity including both the charge and spin degrees and other similar ideas existing in the literature are discussed.

Oblique Interaction of Dust-ion Acoustic Solitons with Superthermal Electrons in a Magnetized Plasma

NASA Astrophysics Data System (ADS)

Parveen, Shahida; Mahmood, Shahzad; Adnan, Muhammad; Qamar, Anisa

2018-01-01

The oblique interaction between two dust-ion acoustic (DIA) solitons travelling in the opposite direction, in a collisionless magnetized plasma composed of dynamic ions, static dust (positive/negative) charged particles and interialess kappa distributed electrons is investigated. By employing extended Poincaré-Lighthill-Kuo (PLK) method, Korteweg-de Vries (KdV) equations are derived for the right and left moving low amplitude DIA solitons. Their trajectories and corresponding phase shifts before and after their interaction are also obtained. It is found that in negatively charged dusty plasma above the critical dust charged to ion density ratio the positive polarity pulse is formed, while below the critical dust charged density ratio the negative polarity pulse of DIA soliton exist. However it is found that only positive polarity pulse of DIA solitons exist for the positively charged dust particles case in a magnetized nonthermal plasma. The nonlinearity coefficient in the KdV equation vanishes for the negatively charged dusty plasma case for a particular set of parameters. Therefore, at critical plasma density composition for negatively charged dust particles case, the modified Korteweg-de Vries (mKdV) equations having cubic nonlinearity coefficient of the DIA solitons, and their corresponding phase shifts are derived for the left and right moving solitons. The effects of the system parameters including the obliqueness of solitons propagation with respect to magnetic field direction, superthermality of electrons and concentration of positively/negatively static dust charged particles on the phase shifts of the colliding solitons are also discussed and presented numerically. The results are applicable to space magnetized dusty plasma regimes.

Laser-induced electron dynamics including photoionization: A heuristic model within time-dependent configuration interaction theory.

PubMed

Klinkusch, Stefan; Saalfrank, Peter; Klamroth, Tillmann

2009-09-21

We report simulations of laser-pulse driven many-electron dynamics by means of a simple, heuristic extension of the time-dependent configuration interaction singles (TD-CIS) approach. The extension allows for the treatment of ionizing states as nonstationary states with a finite, energy-dependent lifetime to account for above-threshold ionization losses in laser-driven many-electron dynamics. The extended TD-CIS method is applied to the following specific examples: (i) state-to-state transitions in the LiCN molecule which correspond to intramolecular charge transfer, (ii) creation of electronic wave packets in LiCN including wave packet analysis by pump-probe spectroscopy, and, finally, (iii) the effect of ionization on the dynamic polarizability of H(2) when calculated nonperturbatively by TD-CIS.

Molecular dynamics simulations of oxide memory resistors (memristors).

PubMed

Savel'ev, S E; Alexandrov, A S; Bratkovsky, A M; Williams, R Stanley

2011-06-24

Reversible bipolar nanoswitches that can be set and read electronically in a solid-state two-terminal device are very promising for applications. We have performed molecular dynamics simulations that mimic systems with oxygen vacancies interacting via realistic potentials and driven by an external bias voltage. The competing short- and long-range interactions among charged mobile vacancies lead to density fluctuations and short-range ordering, while illustrating some aspects of observed experimental behavior, such as memristor polarity inversion. The simulations show that the 'localized conductive filaments' and 'uniform push/pull' models for memristive switching are actually two extremes of the one stochastic mechanism.

Effect of Structure and Disorder on the Charge Transport in Defined Self-Assembled Monolayers of Organic Semiconductors.

PubMed

Schmaltz, Thomas; Gothe, Bastian; Krause, Andreas; Leitherer, Susanne; Steinrück, Hans-Georg; Thoss, Michael; Clark, Timothy; Halik, Marcus

2017-09-26

Self-assembled monolayer field-effect transistors (SAMFETs) are not only a promising type of organic electronic device but also allow detailed analyses of structure-property correlations. The influence of the morphology on the charge transport is particularly pronounced, due to the confined monolayer of 2D-π-stacked organic semiconductor molecules. The morphology, in turn, is governed by relatively weak van-der-Waals interactions and is thus prone to dynamic structural fluctuations. Accordingly, combining electronic and physical characterization and time-averaged X-ray analyses with the dynamic information available at atomic resolution from simulations allows us to characterize self-assembled monolayer (SAM) based devices in great detail. For this purpose, we have constructed transistors based on SAMs of two molecules that consist of the organic p-type semiconductor benzothieno[3,2-b][1]benzothiophene (BTBT), linked to a C 11 or C 12 alkylphosphonic acid. Both molecules form ordered SAMs; however, our experiments show that the size of the crystalline domains and the charge-transport properties vary considerably in the two systems. These findings were confirmed by molecular dynamics (MD) simulations and semiempirical molecular-orbital electronic-structure calculations, performed on snapshots from the MD simulations at different times, revealing, in atomistic detail, how the charge transport in organic semiconductors is influenced and limited by dynamic disorder.

Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.

PubMed

Takahashi, Masateru; Takahashi, Etsuko; Joudeh, Luay I; Marini, Monica; Das, Gobind; Elshenawy, Mohamed M; Akal, Anastassja; Sakashita, Kosuke; Alam, Intikhab; Tehseen, Muhammad; Sobhy, Mohamed A; Stingl, Ulrich; Merzaban, Jasmeen S; Di Fabrizio, Enzo; Hamdan, Samir M

2018-01-24

The deep-sea brines of the Red Sea are remote and unexplored environments characterized by high temperatures, anoxic water, and elevated concentrations of salt and heavy metals. This environment provides a rare system to study the interplay between halophilic and thermophilic adaptation in biologic macromolecules. The present article reports the first DNA polymerase with halophilic and thermophilic features. Biochemical and structural analysis by Raman and circular dichroism spectroscopy showed that the charge distribution on the protein's surface mediates the structural balance between stability for thermal adaptation and flexibility for counteracting the salt-induced rigid and nonfunctional hydrophobic packing. Salt bridge interactions via increased negative and positive charges contribute to structural stability. Salt tolerance, conversely, is mediated by a dynamic structure that becomes more fixed and functional with increasing salt concentration. We propose that repulsive forces among excess negative charges, in addition to a high percentage of negatively charged random coils, mediate this structural dynamism. This knowledge enabled us to engineer a halophilic version of KOD DNA polymerase.-Takahashi, M., Takahashi, E., Joudeh, L. I., Marini, M., Das, G., Elshenawy, M. M., Akal, A., Sakashita, K., Alam, I., Tehseen, M., Sobhy, M. A., Stingl, U., Merzaban, J. S., Di Fabrizio, E., Hamdan, S. M. Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.

Charged particle dynamics in multiple colliding electromagnetic waves. Survey of random walk, Lévy flights, limit circles, attractors and structurally determinate patterns

NASA Astrophysics Data System (ADS)

Bulanov, S. V.; Esirkepov, T. Zh.; Koga, J. K.; Bulanov, S. S.; Gong, Z.; Yan, X. Q.; Kando, M.

2017-04-01

The multiple colliding laser pulse concept formulated by Bulanov et al. (Phys. Rev. Lett., vol. 104, 2010b, 220404) is beneficial for achieving an extremely high amplitude of coherent electromagnetic field. Since the topology of electric and magnetic fields of multiple colliding laser pulses oscillating in time is far from trivial and the radiation friction effects are significant in the high field limit, the dynamics of charged particles interacting with the multiple colliding laser pulses demonstrates remarkable features corresponding to random walk trajectories, limit circles, attractors, regular patterns and Lévy flights. Under extremely high intensity conditions the nonlinear dissipation mechanism stabilizes the particle motion resulting in the charged particle trajectory being located within narrow regions and in the occurrence of a new class of regular patterns made by the particle ensembles.

Charged particle dynamics in multiple colliding electromagnetic waves. Survey of random walk, Lévy flights, limit circles, attractors and structurally determinate patterns

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

Bulanov, S. V.; Esirkepov, T. Zh.; Koga, J. K.

The multiple colliding laser pulse concept formulated by Bulanovet al.(Phys. Rev. Lett., vol. 104, 2010b, 220404) is beneficial for achieving an extremely high amplitude of coherent electromagnetic field. Since the topology of electric and magnetic fields of multiple colliding laser pulses oscillating in time is far from trivial and the radiation friction effects are significant in the high field limit, the dynamics of charged particles interacting with the multiple colliding laser pulses demonstrates remarkable features corresponding to random walk trajectories, limit circles, attractors, regular patterns and Lévy flights. Lastly, under extremely high intensity conditions the nonlinear dissipation mechanism stabilizes the particle motionmore » resulting in the charged particle trajectory being located within narrow regions and in the occurrence of a new class of regular patterns made by the particle ensembles.« less

Charged particle dynamics in multiple colliding electromagnetic waves. Survey of random walk, Lévy flights, limit circles, attractors and structurally determinate patterns

DOE PAGES

Bulanov, S. V.; Esirkepov, T. Zh.; Koga, J. K.; ...

2017-03-09

The multiple colliding laser pulse concept formulated by Bulanovet al.(Phys. Rev. Lett., vol. 104, 2010b, 220404) is beneficial for achieving an extremely high amplitude of coherent electromagnetic field. Since the topology of electric and magnetic fields of multiple colliding laser pulses oscillating in time is far from trivial and the radiation friction effects are significant in the high field limit, the dynamics of charged particles interacting with the multiple colliding laser pulses demonstrates remarkable features corresponding to random walk trajectories, limit circles, attractors, regular patterns and Lévy flights. Lastly, under extremely high intensity conditions the nonlinear dissipation mechanism stabilizes the particle motionmore » resulting in the charged particle trajectory being located within narrow regions and in the occurrence of a new class of regular patterns made by the particle ensembles.« less

Rate of Bubble Coalescence following Quasi-Static Approach: Screening and Neutralization of the Electric Double Layer

PubMed Central

Katsir, Yael; Marmur, Abraham

2014-01-01

Air-bubble coalescence in aqueous electrolytic solutions, following quasi-static approach, was studied in order to understand its slow rate in purified water and high rate in electrolytic solutions. The former is found to be due to surface charges, originating from the speciation of dissolved CO2, which sustain the electric double layer repulsion. Rapid coalescence in electrolytic solutions is shown to occur via two different mechanisms: (1) neutralization of the carbonaceous, charged species by acids; or (2) screening of the repulsive charge effects by salts and bases. The results do not indicate any ion specificity. They can be explained within the DLVO theory for the van der Waals and electric double layer interactions between particles, in contrast to observations of coalescence following dynamic approach. The present conclusions should serve as a reference point to understanding the dynamic behavior. PMID:24589528

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

Fradkin, D.B.; Hull, L.M.; Laabs, G.W.

The results of dynamic sled track performance testing of advanced tandem configuration shaped-charge warheads against multiple-reactive-element tank armors are presented. Tandem configurations utilizing both currently fielded and experimental shaped-charge warheads were tested. Sled velocities used were between 400 and 1100 ft/s (Mach number 0.35 to 0.95), typical of the terminal approach velocity of TOW-type antitank missiles. High-speed motion pictures (5000 frames/s) of the sled in operation and a typical mock missile'' warhead package approaching the target are shown. Details of the sled design and fabrication and of the warhead package design and fabrication are presented. Sled track instrumentation is discussed.more » This instrumentation includes foil make/break switches and associated time interval meters (TIM) and digital delay units (DDU), magnetic Hall-effect transistors for measuring sled trajectory, and flash x-rays (FXR). Methods for timing the x-rays are presented. Schematic functional diagrams of the experimental setups are also given. Evidence of the ability to accurately time the delay between precursor and main warheads for even very long time delays are presented. FXR pictures illustrate the dynamics of the interaction of the jets with various target elements. The interaction dynamics of the jets is discussed in relation to the overall penetration performance of the tandem warhead. The use of x-ray fluorescence spectroscopy to help diagnose interaction dynamics is illustrated. The results of a test utilizing the missile propulsion rocket motor as a blast shield is presented in this paper. 2 refs., 22 figs.« less

An Acetylation Switch Regulates SUMO-Dependent Protein Interaction Networks

PubMed Central

Ullmann, Rebecca; Chien, Christopher D.; Avantaggiati, Maria Laura; Muller, Stefan

2013-01-01

SUMMARY The attachment of the SUMO modifier to proteins controls cellular signaling pathways through noncovalent binding to SUMO-interaction motifs (SIMs). Canonical SIMs contain a core of hydrophobic residues that bind to a hydrophobic pocket on SUMO. Negatively charged residues of SIMs frequently contribute to binding by interacting with a basic surface on SUMO. Here we define acetylation within this basic interface as a central mechanism for the control of SUMO-mediated interactions. The acetyl-mediated neutralization of basic charges on SUMO prevents binding to SIMs in PML, Daxx, and PIAS family members but does not affect the interaction between RanBP2 and SUMO. Acetylation is controlled by HDACs and attenuates SUMO- and PIAS-mediated gene silencing. Moreover, it affects the assembly of PML nuclear bodies and restrains the recruitment of the corepressor Daxx to these structures. This acetyl-dependent switch thus expands the regulatory repertoire of SUMO signaling and determines the selectivity and dynamics of SUMO-SIM interactions. PMID:22578841

Heterogeneity and dynamics of the ligand recognition mode in purine-sensing riboswitches.

PubMed

Jain, Niyati; Zhao, Liang; Liu, John D; Xia, Tianbing

2010-05-04

High-resolution crystal structures and biophysical analyses of purine-sensing riboswitches have revealed that a network of hydrogen bonding interactions appear to be largey responsible for discrimination of cognate ligands against structurally related compounds. Here we report that by using femtosecond time-resolved fluorescence spectroscopy to capture the ultrafast decay dynamics of the 2-aminopurine base as the ligand, we have detected the presence of multiple conformations of the ligand within the binding pockets of one guanine-sensing and two adenine-sensing riboswitches. All three riboswitches have similar conformational distributions of the ligand-bound state. The known crystal structures represent the global minimum that accounts for 50-60% of the population, where there is no significant stacking interaction between the ligand and bases of the binding pocket, but the hydrogen-bonding cage collectively provides an electronic environment that promotes an ultrafast ( approximately 1 ps) charge transfer pathway. The ligand also samples multiple conformations in which it significantly stacks with either the adenine or the uracil bases of the A21-U75 and A52-U22 base pairs that form the ceiling and floor of the binding pocket, respectively, but favors the larger adenine bases. These alternative conformations with well-defined base stacking interactions are approximately 1-1.5 kcal/mol higher in DeltaG degrees than the global minimum and have distinct charge transfer dynamics within the picosecond to nanosecond time regime. Inside the pocket, the purine ligand undergoes dynamic motion on the low nanosecond time scale, sampling the multiple conformations based on time-resolved anisotropy decay dynamics. These results allowed a description of the energy landscape of the bound ligand with intricate details and demonstrated the elastic nature of the ligand recognition mode by the purine-sensing riboswitches, where there is a dynamic balance between hydrogen bonding and base stacking interactions, yielding the high affinity and specificity by the aptamer domain.

Particle Simulations on Plasma and Dust Environment near Lunar Vertical Holes

NASA Astrophysics Data System (ADS)

Miyake, Y.; Funaki, Y.; Nishino, M. N.

2016-12-01

The Japanese lunar orbiter KAGUYA has revealed the existence of vertical holes on the Moon, which have spatial scales of tens of meters and are possible lava tube skylights. The hole structure has recently received particular attention, because the structure is regarded as evidence for past existence of underground lava flows. Furthermore, the holes have high potential as locations for constructing future lunar bases, because of fewer extra-lunar rays/particles and micrometeorites reaching the hole bottoms. In this sense, these holes are not only of significance in selenology, but are also interesting from the viewpoint of plasma environments. The dayside electrostatic environment near the lunar surface is governed by interactions among the solar wind plasma, photoelectrons, and the charged lunar surface, providing topologically complex boundaries to the plasma. Thus we applied three-dimensional, massively-parallelized, particle-in-cell simulations to the near-hole environment on the Moon. This year we have introduced a horizontal cavern opened at the vertical wall of the hole, assuming the presence of a subsurface lave tube. We will show some preliminary results on the surface potential and its nearly plasma environments. We also started to study the dynamics of submicron-sized charged dust grains around the distinctive landscape. We particularly focus on an effect of a stochastic charging process of such small dust grains. Because of their small surface areas, the dusts will get/lose one elementary charge infrequently, and thus charge amount owned by each dust should be a stochastic variable unlike a widely-known spacecraft charging process. We develop a numerical model of such a charging process, which will be embedded into the test particle analysis of the dust dynamics. We report some results from our simulations on the dust charging process and dynamics around the lunar hole.

Evaluation of molecular dynamics simulation methods for ionic liquid electric double layers.

PubMed

Haskins, Justin B; Lawson, John W

2016-05-14

We investigate how systematically increasing the accuracy of various molecular dynamics modeling techniques influences the structure and capacitance of ionic liquid electric double layers (EDLs). The techniques probed concern long-range electrostatic interactions, electrode charging (constant charge versus constant potential conditions), and electrolyte polarizability. Our simulations are performed on a quasi-two-dimensional, or slab-like, model capacitor, which is composed of a polarizable ionic liquid electrolyte, [EMIM][BF4], interfaced between two graphite electrodes. To ensure an accurate representation of EDL differential capacitance, we derive new fluctuation formulas that resolve the differential capacitance as a function of electrode charge or electrode potential. The magnitude of differential capacitance shows sensitivity to different long-range electrostatic summation techniques, while the shape of differential capacitance is affected by charging technique and the polarizability of the electrolyte. For long-range summation techniques, errors in magnitude can be mitigated by employing two-dimensional or corrected three dimensional electrostatic summations, which led to electric fields that conform to those of a classical electrostatic parallel plate capacitor. With respect to charging, the changes in shape are a result of ions in the Stern layer (i.e., ions at the electrode surface) having a higher electrostatic affinity to constant potential electrodes than to constant charge electrodes. For electrolyte polarizability, shape changes originate from induced dipoles that soften the interaction of Stern layer ions with the electrode. The softening is traced to ion correlations vertical to the electrode surface that induce dipoles that oppose double layer formation. In general, our analysis indicates an accuracy dependent differential capacitance profile that transitions from the characteristic camel shape with coarser representations to a more diffuse profile with finer representations.

On the ultrafast charge migration and subsequent charge directed reactivity in Cl⋯N halogen-bonded clusters following vertical ionization

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

Chandra, Sankhabrata; Bhattacharya, Atanu, E-mail: atanub@ipc.iisc.ernet.in; Periyasamy, Ganga

2015-06-28

In this article, we have presented ultrafast charge transfer dynamics through halogen bonds following vertical ionization of representative halogen bonded clusters. Subsequent hole directed reactivity of the radical cations of halogen bonded clusters is also discussed. Furthermore, we have examined effect of the halogen bond strength on the electron-electron correlation- and relaxation-driven charge migration in halogen bonded complexes. For this study, we have selected A-Cl (A represents F, OH, CN, NH{sub 2}, CF{sub 3}, and COOH substituents) molecules paired with NH{sub 3} (referred as ACl:NH{sub 3} complex): these complexes exhibit halogen bonds. To the best of our knowledge, this ismore » the first report on purely electron correlation- and relaxation-driven ultrafast (attosecond) charge migration dynamics through halogen bonds. Both density functional theory and complete active space self-consistent field theory with 6-31 + G(d, p) basis set are employed for this work. Upon vertical ionization of NCCl⋯NH{sub 3} complex, the hole is predicted to migrate from the NH{sub 3}-end to the ClCN-end of the NCCl⋯NH{sub 3} complex in approximately 0.5 fs on the D{sub 0} cationic surface. This hole migration leads to structural rearrangement of the halogen bonded complex, yielding hydrogen bonding interaction stronger than the halogen bonding interaction on the same cationic surface. Other halogen bonded complexes, such as H{sub 2}NCl:NH{sub 3}, F{sub 3}CCl:NH{sub 3}, and HOOCCl:NH{sub 3}, exhibit similar charge migration following vertical ionization. On the contrary, FCl:NH{sub 3} and HOCl:NH{sub 3} complexes do not exhibit any charge migration following vertical ionization to the D{sub 0} cation state, pointing to interesting halogen bond strength-dependent charge migration.« less

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.

Geometrically Induced Interactions and Bifurcations

NASA Astrophysics Data System (ADS)

Binder, Bernd

2010-01-01

In order to evaluate the proper boundary conditions in spin dynamics eventually leading to the emergence of natural and artificial solitons providing for strong interactions and potentials with monopole charges, the paper outlines a new concept referring to a curvature-invariant formalism, where superintegrability is given by a special isometric condition. Instead of referring to the spin operators and Casimir/Euler invariants as the generator of rotations, a curvature-invariant description is introduced utilizing a double Gudermann mapping function (generator of sine Gordon solitons and Mercator projection) cross-relating two angular variables, where geometric phases and rotations arise between surfaces of different curvature. Applying this stereographic projection to a superintegrable Hamiltonian can directly map linear oscillators to Kepler/Coulomb potentials and/or monopoles with Pöschl-Teller potentials and vice versa. In this sense a large scale Kepler/Coulomb (gravitational, electro-magnetic) wave dynamics with a hyperbolic metric could be mapped as a geodesic vertex flow to a local oscillator singularity (Dirac monopole) with spherical metrics and vice versa. Attracting fixed points and dynamic constraints are given by special isometries with magic precession angles. The nonlinear angular encoding directly provides for a Shannon mutual information entropy measure of the geodesic phase space flow. The emerging monopole patterns show relations to spiral Fresnel holography and Berry/Aharonov-Bohm geometric phases subject to bifurcation instabilities and singularities from phase ambiguities due to a local (entropy) overload. Neutral solitons and virtual patterns emerging and mediating in the overlap region between charged or twisted holographic patterns are visualized and directly assigned to the Berry geometric phase revealing the role of photons, neutrons, and neutrinos binding repulsive charges in Coulomb, strong and weak interaction.

Computational Fluid Dynamics Modeling of the Operation of a Flame Ionization Sensor

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

Huckaby, E.D.; Chorpening, B.T.; Thornton, J.D.

The sensors and controls research group at the United States Department of Energy (DOE) National Energy Technology Laboratory (NETL) is continuing to develop the Combustion Control and Diagnostics Sensor (CCADS) for gas turbine applications. CCADS uses the electrical conduction of the charged species generated during the combustion process to detect combustion instabilities and monitor equivalence ratio. As part of this effort, combustion models are being developed which include the interaction between the electric field and the transport of charged species. The primary combustion process is computed using a flame wrinkling model (Weller et. al. 1998) which is a component ofmore » the OpenFOAM toolkit (Jasak et. al. 2004). A sub-model for the transport of charged species is attached to this model. The formulation of the charged-species model similar that applied by Penderson and Brown (1993) for the simulation of laminar flames. The sub-model consists of an additional flux due to the electric field (drift flux) added to the equations for the charged species concentrations and the solution the electric potential from the resolved charge density. The subgrid interactions between the electric field and charged species transport have been neglected. Using the above procedure, numerical simulations are performed and the results compared with several recent CCADS experiments.« 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.

Non-interacting surface solvation and dynamics in protein-protein interactions.

PubMed

Visscher, Koen M; Kastritis, Panagiotis L; Bonvin, Alexandre M J J

2015-03-01

Protein-protein interactions control a plethora of cellular processes, including cell proliferation, differentiation, apoptosis, and signal transduction. Understanding how and why proteins interact will inevitably lead to novel structure-based drug design methods, as well as design of de novo binders with preferred interaction properties. At a structural and molecular level, interface and rim regions are not enough to fully account for the energetics of protein-protein binding, even for simple lock-and-key rigid binders. As we have recently shown, properties of the global surface might also play a role in protein-protein interactions. Here, we report on molecular dynamics simulations performed to understand solvent effects on protein-protein surfaces. We compare properties of the interface, rim, and non-interacting surface regions for five different complexes and their free components. Interface and rim residues become, as expected, less mobile upon complexation. However, non-interacting surface appears more flexible in the complex. Fluctuations of polar residues are always lower compared with charged ones, independent of the protein state. Further, stable water molecules are often observed around polar residues, in contrast to charged ones. Our analysis reveals that (a) upon complexation, the non-interacting surface can have a direct entropic compensation for the lower interface and rim entropy and (b) the mobility of the first hydration layer, which is linked to the stability of the protein-protein complex, is influenced by the local chemical properties of the surface. These findings corroborate previous hypotheses on the role of the hydration layer in shielding protein-protein complexes from unintended protein-protein interactions. © 2014 Wiley Periodicals, Inc.

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.

Structure and Dynamics of Solvent Landscapes in Charge-Transfer Reactions

NASA Astrophysics Data System (ADS)

Leite, Vitor B. Pereira

The dynamics of solvent polarization plays a major role in the control of charge transfer reactions. The success of Marcus theory describing the solvent influence via a single collective quadratic polarization coordinate has been remarkable. Onuchic and Wolynes have recently proposed (J. Chem Phys 98 (3) 2218, 1993) a simple model demonstrating how a many-dimensional-complex model composed by several dipole moments (representing solvent molecules or polar groups in proteins) can be reduced under the appropriate limits into the Marcus Model. This work presents a dynamical study of the same model, which is characterized by two parameters, an average dipole-dipole interaction as a term associated with the potential energy landscape roughness. It is shown why the effective potential, obtained using a thermodynamic approach, is appropriate for the dynamics of the system. At high temperatures, the system exhibits effective diffusive one-dimensional dynamics, where the Born-Marcus limit is recovered. At low temperatures, a glassy phase appears with a slow non-self-averaging dynamics. At intermediate temperatures, the concept of equivalent diffusion paths and polarization dependence effects are discussed. This approach is extended to treat more realistic solvent models. Real solvents are discussed in terms of simple parameters described above, and an analysis of how different regimes affect the rate of charge transfer is presented. Finally, these ideas are correlated to analogous problems in other areas.

Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids

NASA Astrophysics Data System (ADS)

Pádua, Agílio A. H.

2017-05-01

One important development in interaction potential models, or atomistic force fields, for molecular simulation is the inclusion of explicit polarisation, which represents the induction effects of charged or polar molecules on polarisable electron clouds. Polarisation can be included through fluctuating charges, induced multipoles, or Drude dipoles. This work uses Drude dipoles and is focused on room-temperature ionic liquids, for which fixed-charge models predict too slow dynamics. The aim of this study is to devise a strategy to adapt existing non-polarisable force fields upon addition of polarisation, because induction was already contained to an extent, implicitly, due to parametrisation against empirical data. Therefore, a fraction of the van der Waals interaction energy should be subtracted so that the Lennard-Jones terms only account for dispersion and the Drude dipoles for induction. Symmetry-adapted perturbation theory is used to resolve the dispersion and induction terms in dimers and to calculate scaling factors to reduce the Lennard-Jones terms from the non-polarisable model. Simply adding Drude dipoles to an existing fixed-charge model already improves the prediction of transport properties, increasing diffusion coefficients, and lowering the viscosity. Scaling down the Lennard-Jones terms leads to still faster dynamics and densities that match experiment extremely well. The concept developed here improves the overall prediction of density and transport properties and can be adapted to other models and systems. In terms of microscopic structure of the ionic liquids, the inclusion of polarisation and the down-scaling of Lennard-Jones terms affect only slightly the ordering of the first shell of counterions, leading to small decreases in coordination numbers. Remarkably, the effect of polarisation is major beyond first neighbours, significantly weakening spatial correlations, a structural effect that is certainly related to the faster dynamics of polarisable models.

Single DNA molecules on freestanding and supported cationic lipid bilayers: diverse conformational dynamics controlled by the local bilayer properties

NASA Astrophysics Data System (ADS)

Herold, Christoph; Schwille, Petra; Petrov, Eugene P.

2016-02-01

We present experimental results on the interaction of DNA macromolecules with cationic lipid membranes with different properties, including freestanding membranes in the fluid and gel state, and supported lipid membranes in the fluid state and under conditions of fluid-gel phase coexistence. We observe diverse conformational dynamics of membrane-bound DNA molecules controlled by the local properties of the lipid bilayer. In case of fluid-state freestanding lipid membranes, the behaviour of DNA on the membrane is controlled by the membrane charge density: whereas DNA bound to weakly charged membranes predominantly behaves as a 2D random coil, an increase in the membrane charge density leads to membrane-driven irreversible DNA collapse and formation of subresolution-sized DNA globules. On the other hand, electrostatic binding of DNA macromolecules to gel-state freestanding membranes leads to completely arrested diffusion and conformational dynamics of membrane-adsorbed DNA. A drastically different picture is observed in case of DNA interaction with supported cationic lipid bilayers: When the supported bilayer is in the fluid state, membrane-bound DNA molecules undergo 2D translational Brownian motion and conformational fluctuations, irrespectively of the charge density of the supported bilayer. At the same time, when the supported cationic membrane shows fluid-gel phase coexistence, membrane-bound DNA molecules are strongly attracted to micrometre-sized gel-phase domains enriched with the cationic lipid, which results in 2D compaction of the membrane-bound macromolecules. This DNA compaction, however, is fully reversible, and disappears as soon as the membrane is heated above the fluid-gel coexistence. We also discuss possible biological implications of our experimental findings.

Capacitance, charge dynamics, and electrolyte-surface interactions in functionalized carbide-derived carbon electrodes

DOE PAGES

Dyatkin, Boris; Mamontov, Eugene; Cook, Kevin M.; ...

2015-12-24

Our study analyzed the dynamics of ionic liquid electrolyte inside of defunctionalized, hydrogenated, and aminated pores of carbide-derived carbon supercapacitor electrodes. The approach tailors surface functionalities and tunes nanoporous structures to decouple the influence of pore wall composition on capacitance, ionic resistance, and long-term cyclability. Moreover, quasi-elastic neutron scattering probes the self-diffusion properties and electrode-ion interactions of electrolyte molecules confined in functionalized pores. Room-temperature ionic liquid interactions in confined pores are strongest when the hydrogen-containing groups are present on the surface. This property translates into higher capacitance and greater ion transport through pores during electrochemical cycling. Aminated pores, unlike hydrogenatedmore » pores, do not favorably interact with ionic liquid ions and, subsequently, are outperformed by defunctionalized surfaces.« less

A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation

NASA Astrophysics Data System (ADS)

Saez, David Adrian; Vöhringer-Martinez, Esteban

2015-10-01

S-Adenosylmethionine (AdoMet) is involved in many biological processes as cofactor in enzymes transferring its sulfonium methyl group to various substrates. Additionally, it is used as drug and nutritional supplement to reduce the pain in osteoarthritis and against depression. Due to the biological relevance of AdoMet it has been part of various computational simulation studies and will also be in the future. However, to our knowledge no rigorous force field parameter development for its simulation in biological systems has been reported. Here, we use electronic structure calculations combined with molecular dynamics simulations in explicit solvent to develop force field parameters compatible with the AMBER99 force field. Additionally, we propose new dynamic Hirshfeld-I atomic charges which are derived from the polarized electron density of AdoMet in aqueous solution to describe its electrostatic interactions in biological systems. The validation of the force field parameters and the atomic charges is performed against experimental interproton NOE distances of AdoMet in aqueous solution and crystal structures of AdoMet in the cavity of three representative proteins.

The 3 DLE instrument on ATS-5. [plasma electron counter

NASA Technical Reports Server (NTRS)

Deforest, S. E.

1973-01-01

The performance and operation of the DLE plasma electron counter on board the ATS 5 are described. Two methods of data presentation, microfilm line plots and spectrograms, are discussed along with plasma dynamics, plasma flow velocity, electrostatic charging, and wave-particle interactions.

Ac electroosmotic flows above coplanar electrodes

NASA Astrophysics Data System (ADS)

Kweon Suh, Yong

2009-03-01

Interactive numerical method has been proposed to calculate the ac electroosmotic flows above a pair of coplanar electrodes. The thin electrical triple layer (ETL) has been modeled by an asymptotic theory developed by the authors. The model corresponds to a simple dynamic equation for the surface charge density representing the integrated charge over the inner layer. Interactive calculation of the dynamic equation and the Laplace equation for several periods of ac frequency then yielded steady-state distribution of potential and the potential drop across the Stern and inner layers. The Smoluchowski's slip velocity was then determined from those two set of data and used as the boundary condition for the calculation of the Stokes' flow above the electrodes. We have shown that our solutions compared well with the experimental data reported in the literature. We investigated the effect of various parameters on the slip velocity distribution, such as the ac frequency, the electrode length, the effective Stern-layer thickness and the adsorption coefficients.

Beam dynamics performances and applications of a low-energy electron-beam magnetic bunch compressor

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

Prokop, C. R.; Piot, P.; Carlsten, B. E.

2013-08-01

Many front-end applications of electron linear accelerators rely on the production of temporally compressed bunches. The shortening of electron bunches is often realized with magnetic bunch compressors located in high-energy sections of accelerators. Magnetic compression is subject to collective effects including space charge and self interaction via coherent synchrotron radiation. In this paper we explore the application of magnetic compression to low-energy (~40MeV), high-charge (nC) electron bunches with low normalized transverse emittances (<5@mm).

Dynamics and control of fast ion crystal splitting in segmented Paul traps (Open Access, Publisher’s Version)

DTIC Science & Technology

2014-07-09

operations, in addition to laser - or microwave-driven logic gates. Essential shuttling operations are splitting and merging of linear ion crystals. It is...from stray charges, laser induced charging of the trap [19], trap geometry imperfections or residual ponderomotive forces along the trap axis. The...transfer expressed as the mean phonon number Δ ω¯ = n E / f . We distinguish several regimes of laser –ion interaction: (i) if the vibrational

Interaction and charge transfer between dielectric spheres: Exact and approximate analytical solutions.

PubMed

Lindén, Fredrik; Cederquist, Henrik; Zettergren, Henning

2016-11-21

We present exact analytical solutions for charge transfer reactions between two arbitrarily charged hard dielectric spheres. These solutions, and the corresponding exact ones for sphere-sphere interaction energies, include sums that describe polarization effects to infinite orders in the inverse of the distance between the sphere centers. In addition, we show that these exact solutions may be approximated by much simpler analytical expressions that are useful for many practical applications. This is exemplified through calculations of Langevin type cross sections for forming a compound system of two colliding spheres and through calculations of electron transfer cross sections. We find that it is important to account for dielectric properties and finite sphere sizes in such calculations, which for example may be useful for describing the evolution, growth, and dynamics of nanometer sized dielectric objects such as molecular clusters or dust grains in different environments including astrophysical ones.

Revisiting structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia using QMCF-MD simulation

NASA Astrophysics Data System (ADS)

Hidayat, Yuniawan; Pranowo, Harno Dwi; Armunanto, Ria

2018-05-01

Structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia have been reinvestigated using ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation. The average coordination number of the first solvation consists of 2 ammonia and 4 waters. The mean residence time is less than 2 ps confirming the rapid mobility of ligands. The distance evolution data shows the frequent of ligand exchanges. The second solvation shell shows a more labile structure. The NBO analysis of the first shell structure emphasizes that interaction of K(I)-H2O is stronger than K(I)-NH3. The Wiberg bond confirms a weak electrostatic of ion-ligand interaction.

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

None, None

Coulomb interaction between charged particles inside a bunch is one of the most importance collective effects in beam dynamics, becoming even more significant as the energy of the particle beam is lowered to accommodate analytical and low-Z material imaging purposes such as in the time resolved Ultrafast Electron Microscope (UEM) development currently underway at Michigan State University. In addition, space charge effects are the key limiting factor in the development of ultrafast atomic resolution electron imaging and diffraction technologies and are also correlated with an irreversible growth in rms beam emittance due to fluctuating components of the nonlinear electron dynamics.more » In the short pulse regime used in the UEM, space charge effects also lead to virtual cathode formation in which the negative charge of the electrons emitted at earlier times, combined with the attractive surface field, hinders further emission of particles and causes a degradation of the pulse properties. Space charge and virtual cathode effects and their remediation are core issues for the development of the next generation of high-brightness UEMs. Since the analytical models are only applicable for special cases, numerical simulations, in addition to experiments, are usually necessary to accurately understand the space charge effect. In this paper we will introduce a grid-free differential algebra based multiple level fast multipole algorithm, which calculates the 3D space charge field for n charged particles in arbitrary distribution with an efficiency of O(n), and the implementation of the algorithm to a simulation code for space charge dominated photoemission processes.« less

Enhanced pairing susceptibility in a photodoped two-orbital Hubbard model

NASA Astrophysics Data System (ADS)

Werner, Philipp; Strand, Hugo U. R.; Hoshino, Shintaro; Murakami, Yuta; Eckstein, Martin

2018-04-01

Local spin fluctuations provide the glue for orbital-singlet spin-triplet pairing in the doped Mott insulating regime of multiorbital Hubbard models. At large Hubbard repulsion U , the pairing susceptibility is nevertheless tiny because the pairing interaction cannot overcome the suppression of charge fluctuations. Using nonequilibrium dynamical mean field simulations of the two-orbital Hubbard model, we show that out of equilibrium the pairing susceptibility in this large-U regime can be strongly enhanced by creating a photoinduced population of the relevant charge states. This enhancement is supported by the long lifetime of photodoped charge carriers and a built-in cooling mechanism in multiorbital Hubbard systems.

Ultrafast dynamics of vibrational symmetry breaking in a charge-ordered nickelate

PubMed Central

Coslovich, Giacomo; Kemper, Alexander F.; Behl, Sascha; Huber, Bernhard; Bechtel, Hans A.; Sasagawa, Takao; Martin, Michael C.; Lanzara, Alessandra; Kaindl, Robert A.

2017-01-01

The ability to probe symmetry-breaking transitions on their natural time scales is one of the key challenges in nonequilibrium physics. Stripe ordering represents an intriguing type of broken symmetry, where complex interactions result in atomic-scale lines of charge and spin density. Although phonon anomalies and periodic distortions attest the importance of electron-phonon coupling in the formation of stripe phases, a direct time-domain view of vibrational symmetry breaking is lacking. We report experiments that track the transient multi-terahertz response of the model stripe compound La1.75Sr0.25NiO4, yielding novel insight into its electronic and structural dynamics following an ultrafast optical quench. We find that although electronic carriers are immediately delocalized, the crystal symmetry remains initially frozen—as witnessed by time-delayed suppression of zone-folded Ni–O bending modes acting as a fingerprint of lattice symmetry. Longitudinal and transverse vibrations react with different speeds, indicating a strong directionality and an important role of polar interactions. The hidden complexity of electronic and structural coupling during stripe melting and formation, captured here within a single terahertz spectrum, opens new paths to understanding symmetry-breaking dynamics in solids. PMID:29202025

Ultrafast dynamics of vibrational symmetry breaking in a charge-ordered nickelate

DOE PAGES

Coslovich, Giacomo; Kemper, Alexander F.; Behl, Sascha; ...

2017-11-24

The ability to probe symmetry-breaking transitions on their natural time scales is one of the key challenges in nonequilibrium physics. Stripe ordering represents an intriguing type of broken symmetry, where complex interactions result in atomic-scale lines of charge and spin density. Although phonon anomalies and periodic distortions attest the importance of electron-phonon coupling in the formation of stripe phases, a direct time-domain view of vibrational symmetry breaking is lacking. We report experiments that track the transient multi-terahertz response of the model stripe compound La 1.75Sr 0.25NiO 4, yielding novel insight into its electronic and structural dynamics following an ultrafast opticalmore » quench. We find that although electronic carriers are immediately delocalized, the crystal symmetry remains initially frozen—as witnessed by time-delayed suppression of zone-folded Ni–O bending modes acting as a fingerprint of lattice symmetry. Longitudinal and transverse vibrations react with different speeds, indicating a strong directionality and an important role of polar interactions. As a result, the hidden complexity of electronic and structural coupling during stripe melting and formation, captured here within a single terahertz spectrum, opens new paths to understanding symmetry-breaking dynamics in solids.« less

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

Rai, Durgesh K.; Sharma, Veerendra K.; Anunciado, Divina

The interaction between lipid bilayers and Amyloid β peptide (Aβ) plays a critical role in proliferation of Alzheimer’s disease (AD). AD is expected to affect one in every 85 humans by 2050, and therefore, deciphering the interplay of Aβ and lipid bilayers at the molecular level is of profound importance. In this work, we applied an array of neutron scattering methods to study the structure and dynamics of Aβ(1–40) interacting 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) bilayers. In the structural investigations of lipid bilayer’s response to Aβ binding, Small Angle Neutron Scattering and Neutron Membrane Diffraction revealed that the Aβ anchors firmly to themore » highly charged DMPG bilayers in the interfacial region between water and hydrocarbon chain, and it doesn’t penetrate deeply into the bilayer. This association mode is substantiated by the dynamics studies with high resolution Quasi-Elastic Neutron Scattering experiments, showing that the addition of Aβ mainly affects the slower lateral motion of lipid molecules, especially in the fluid phase, but not the faster internal motion. The results revealed that Aβ associates with the highly charged membrane in surface with limited impact on the structure, but the altered membrane dynamics could have more influence on other membrane processes.« less

Ultrafast dynamics of vibrational symmetry breaking in a charge-ordered nickelate

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

Coslovich, Giacomo; Kemper, Alexander F.; Behl, Sascha

The ability to probe symmetry-breaking transitions on their natural time scales is one of the key challenges in nonequilibrium physics. Stripe ordering represents an intriguing type of broken symmetry, where complex interactions result in atomic-scale lines of charge and spin density. Although phonon anomalies and periodic distortions attest the importance of electron-phonon coupling in the formation of stripe phases, a direct time-domain view of vibrational symmetry breaking is lacking. We report experiments that track the transient multi-terahertz response of the model stripe compound La 1.75Sr 0.25NiO 4, yielding novel insight into its electronic and structural dynamics following an ultrafast opticalmore » quench. We find that although electronic carriers are immediately delocalized, the crystal symmetry remains initially frozen—as witnessed by time-delayed suppression of zone-folded Ni–O bending modes acting as a fingerprint of lattice symmetry. Longitudinal and transverse vibrations react with different speeds, indicating a strong directionality and an important role of polar interactions. As a result, the hidden complexity of electronic and structural coupling during stripe melting and formation, captured here within a single terahertz spectrum, opens new paths to understanding symmetry-breaking dynamics in solids.« less

Blinking correlation in nanocrystal quantum dots probed with novel laser scanning confocal microscopy methods

NASA Astrophysics Data System (ADS)

Hefti, Ryan Alf

Semiconductor quantum dots have a vast array of applications: as fluorescent labels in biological systems, as physical or chemical sensors, as components in photovoltaic technology, and in display devices. An attribute of nearly every quantum dot is its blinking, or fluorescence intermittency, which tends to be a disadvantage in most applications. Despite the fact that blinking has been a nearly universal phenomenon among all types of fluorescent constructs, it is more prevalent in quantum dots than in traditional fluorophores. Furthermore, no unanimously accepted model of quantum dot blinking yet exists. The work encompassed by this dissertation began with an in-depth study of molecular motor protein dynamics in a variety of environments using two specially developed techniques, both of which feature applicability to live cell systems. Parked-beam confocal microscopy was utilized to increase temporal resolution of molecular motor motion dynamics by an order of magnitude over other popular methods. The second technique, fast-scanning confocal microscopy (FSCM), was used for long range observation of motor proteins. While using FSCM on motor protein assays, we discovered an unusual phenomenon. Single quantum dots seemingly communicated with neighboring quantum dots, indicated by a distinct correlation in their blinking patterns. In order to explain this novel correlation phenomenon, the majority of blinking models developed thus far would suggest a dipole-dipole interaction or a Coulomb interaction between singly charged quantum dots. However, our results indicate that the interaction energy is higher than supported by current models, thereby prompting a renewed examination. We propose that the blinking correlation we observed is due to a Coulomb interaction on the order of 3-4 elementary charges per quantum dot and that multiple charging of individual quantum dots may be required to plunge them into a non-emissive state. As a result of charging, charge carriers are displaced into a wide distribution of trap sites in the surrounding matrix, resulting in the expected power-law probability distribution of off times ubiquitous in quantum dots. Our discovery also implies that quantum dot blinking can be controlled, advocating the creation of switchable nanoscale emitters.

Influence of chitosan structure on the formation and stability of DNA-chitosan polyelectrolyte complexes.

PubMed

Strand, Sabina P; Danielsen, Signe; Christensen, Bjørn E; Vårum, Kjell M

2005-01-01

The interactions between DNA and chitosans varying in fractional content of acetylated units (FA), degree of polymerization (DP), and degree of ionization were investigated by several techniques, including an ethidium bromide (EtBr) fluorescence assay, gel retardation, atomic force microscopy, and dynamic and electrophoretic light scattering. The charge density of the chitosan and the number of charges per chain were found to be the dominating factors for the structure and stability of DNA-chitosan complexes. All high molecular weight chitosans condensed DNA into physically stable polyplexes; however, the properties of the complexes were strongly dependent on FA, and thereby the charge density of chitosan. By employing fully charged oligomers of constant charge density, it was shown that the complexation of DNA and stability of the polyplexes is governed by the number of cationic residues per chain. A minimum of 6-9 positive charges appeared necessary to provide interaction strength comparable to that of polycations. In contrast, further increase in the number of charges above 9 did not increase the apparent binding affinity as judged from the EtBr displacement assay. The chitosan oligomers exhibited a pH-dependent interaction with DNA, reflecting the number of ionized amino groups. The complexation of DNA and the stability of oligomer-based polyplexes became reduced above pH 7.4. Such pH-dependent dissociation of polyplexes around the physiological pH is highly relevant in gene delivery applications and might be one of the reasons for the high transfection activity of oligomer-based polyplexes observed.

Soft pair excitations and double-log divergences due to carrier interactions in graphene

NASA Astrophysics Data System (ADS)

Lewandowski, Cyprian; Levitov, L. S.

2018-03-01

Interactions between charge carriers in graphene lead to logarithmic renormalization of observables mimicking the behavior known in (3+1)-dimensional quantum electrodynamics (QED). Here we analyze soft electron-hole (e -h ) excitations generated as a result of fast charge dynamics, a direct analog of the signature QED effect—multiple soft photons produced by the QED vacuum shakeup. We show that such excitations are generated in photon absorption, when a photogenerated high-energy e -h pair cascades down in energy and gives rise to multiple soft e -h excitations. This fundamental process is manifested in a double-log divergence in the emission rate of soft pairs and a characteristic power-law divergence in their energy spectrum of the form 1/ω ln(ω/Δ ) . Strong carrier-carrier interactions make pair production a prominent pathway in the photoexcitation cascade.

Influence of the Location of Attractive Polymer-Pore Interactions on Translocation Dynamics.

PubMed

Ghosh, Bappa; Chaudhury, Srabanti

2018-01-11

We probe the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. We investigate the effect of the strength and location of the polymer-pore interaction using nanopores that are partially charged either at the entry or the exit or on both sides of the pore. We study the change in the translocation time as a function of the strength of the polymer-pore interaction for a given chain length and under the effect of an externally applied field. Under a moderate driving force and a chain length longer than the length of the pore, the translocation time shows a nonmonotonic increase with an increase in the attractive interaction. Also, an interaction on the cis side of the pore can increase the translocation probability. In the presence of an external field and a strong attractive force, the translocation time for shorter chains is independent of the polymer-pore interaction at the entry side of the pore, whereas an interaction on the trans side dominates the translocation process. Our simulation results are rationalized by a qualitative analysis of the free energy landscape for polymer translocation.

Mesoscale magnetism

DOE PAGES

Hoffmann, Axel; Schultheiß, Helmut

2014-12-17

Magnetic interactions give rise to a surprising amount of complexity due to the fact that both static and dynamic magnetic properties are governed by competing short-range exchange interactions and long-range dipolar coupling. Even though the underlying dynamical equations are well established, the connection of magnetization dynamics to other degrees of freedom, such as optical excitations, charge and heat flow, or mechanical motion, make magnetism a mesoscale research problem that is still wide open for exploration. Synthesizing magnetic materials and heterostructures with tailored properties will allow to take advantage of magnetic interactions spanning many length-scales, which can be probed with advancedmore » spectroscopy and microscopy and modeled with multi-scale simulations. Finally, this paper highlights some of the current basic research topics in mesoscale magnetism, which beyond their fundamental science impact are also expected to influence applications ranging from information technologies to magnetism based energy conversion.« less

Charged groups at binding interfaces of the PsbO subunit of photosystem II: A combined bioinformatics and simulation study.

PubMed

Del Val, Coral; Bondar, Ana-Nicoleta

2017-06-01

PsbO is an extrinsic subunit of photosystem II engaged in complex binding interactions within photosystem II. At the interface between PsbO, D1 and D2 subunits of photosystem II, a cluster of charged and polar groups of PsbO is part of an extended hydrogen-bond network thought to participate in proton transfer. The precise role of specific amino acid residues at this complex binding interface remains a key open question. Here, we address this question by carrying out extensive bioinformatics analyses and molecular dynamics simulations of PsbO proteins with mutations at the binding interface. We find that PsbO proteins from cyanobacteria vs. plants have specific preferences for the number and composition of charged amino acid residues that may ensure that PsbO proteins avoid aggregation and expose long unstructured loops for binding to photosystem II. A cluster of conserved charged groups with dynamic hydrogen bonds provides PsbO with structural plasticity at the binding interface with photosystem II. Copyright © 2017. Published by Elsevier B.V.

Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films

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

Mohammadi, Erfan; Zhao, Chuankai; Meng, Yifei

Solution processable semiconducting polymers have been under intense investigations due to their diverse applications from printed electronics to biomedical devices. However, controlling the macromolecular assembly across length scales during solution coating remains a key challenge, largely due to the disparity in timescales of polymer assembly and high-throughput printing/coating. Herein we propose the concept of dynamic templating to expedite polymer nucleation and the ensuing assembly process, inspired by biomineralization templates capable of surface reconfiguration. Molecular dynamic simulations reveal that surface reconfigurability is key to promoting template–polymer interactions, thereby lowering polymer nucleation barrier. Employing ionic-liquid-based dynamic template during meniscus-guided coating results inmore » highly aligned, highly crystalline donor-acceptor polymer thin films over large area (41cm 2) and promoted charge transport along both the polymer backbone and the π-π stacking direction in field-effect transistors. We further demonstrate that the charge transport anisotropy can be reversed by tuning the degree of polymer backbone alignment.« less

Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films

PubMed Central

Mohammadi, Erfan; Zhao, Chuankai; Meng, Yifei; Qu, Ge; Zhang, Fengjiao; Zhao, Xikang; Mei, Jianguo; Zuo, Jian-Min; Shukla, Diwakar; Diao, Ying

2017-01-01

Solution processable semiconducting polymers have been under intense investigations due to their diverse applications from printed electronics to biomedical devices. However, controlling the macromolecular assembly across length scales during solution coating remains a key challenge, largely due to the disparity in timescales of polymer assembly and high-throughput printing/coating. Herein we propose the concept of dynamic templating to expedite polymer nucleation and the ensuing assembly process, inspired by biomineralization templates capable of surface reconfiguration. Molecular dynamic simulations reveal that surface reconfigurability is key to promoting template–polymer interactions, thereby lowering polymer nucleation barrier. Employing ionic-liquid-based dynamic template during meniscus-guided coating results in highly aligned, highly crystalline donor–acceptor polymer thin films over large area (>1 cm2) and promoted charge transport along both the polymer backbone and the π–π stacking direction in field-effect transistors. We further demonstrate that the charge transport anisotropy can be reversed by tuning the degree of polymer backbone alignment. PMID:28703136

Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films

DOE PAGES

Mohammadi, Erfan; Zhao, Chuankai; Meng, Yifei; ...

2017-07-13

Solution processable semiconducting polymers have been under intense investigations due to their diverse applications from printed electronics to biomedical devices. However, controlling the macromolecular assembly across length scales during solution coating remains a key challenge, largely due to the disparity in timescales of polymer assembly and high-throughput printing/coating. Herein we propose the concept of dynamic templating to expedite polymer nucleation and the ensuing assembly process, inspired by biomineralization templates capable of surface reconfiguration. Molecular dynamic simulations reveal that surface reconfigurability is key to promoting template–polymer interactions, thereby lowering polymer nucleation barrier. Employing ionic-liquid-based dynamic template during meniscus-guided coating results inmore » highly aligned, highly crystalline donor-acceptor polymer thin films over large area (41cm 2) and promoted charge transport along both the polymer backbone and the π-π stacking direction in field-effect transistors. We further demonstrate that the charge transport anisotropy can be reversed by tuning the degree of polymer backbone alignment.« less

The differential algebra based multiple level fast multipole algorithm for 3D space charge field calculation and photoemission simulation

DOE PAGES

None, None

2015-09-28

Coulomb interaction between charged particles inside a bunch is one of the most importance collective effects in beam dynamics, becoming even more significant as the energy of the particle beam is lowered to accommodate analytical and low-Z material imaging purposes such as in the time resolved Ultrafast Electron Microscope (UEM) development currently underway at Michigan State University. In addition, space charge effects are the key limiting factor in the development of ultrafast atomic resolution electron imaging and diffraction technologies and are also correlated with an irreversible growth in rms beam emittance due to fluctuating components of the nonlinear electron dynamics.more » In the short pulse regime used in the UEM, space charge effects also lead to virtual cathode formation in which the negative charge of the electrons emitted at earlier times, combined with the attractive surface field, hinders further emission of particles and causes a degradation of the pulse properties. Space charge and virtual cathode effects and their remediation are core issues for the development of the next generation of high-brightness UEMs. Since the analytical models are only applicable for special cases, numerical simulations, in addition to experiments, are usually necessary to accurately understand the space charge effect. In this paper we will introduce a grid-free differential algebra based multiple level fast multipole algorithm, which calculates the 3D space charge field for n charged particles in arbitrary distribution with an efficiency of O(n), and the implementation of the algorithm to a simulation code for space charge dominated photoemission processes.« less

Microscopic theory for coupled atomistic magnetization and lattice dynamics

NASA Astrophysics Data System (ADS)

Fransson, J.; Thonig, D.; Bessarab, P. F.; Bhattacharjee, S.; Hellsvik, J.; Nordström, L.

2017-12-01

A coupled atomistic spin and lattice dynamics approach is developed which merges the dynamics of these two degrees of freedom into a single set of coupled equations of motion. The underlying microscopic model comprises local exchange interactions between the electron spin and magnetic moment and the local couplings between the electronic charge and lattice displacements. An effective action for the spin and lattice variables is constructed in which the interactions among the spin and lattice components are determined by the underlying electronic structure. In this way, expressions are obtained for the electronically mediated couplings between the spin and lattice degrees of freedom, besides the well known interatomic force constants and spin-spin interactions. These former susceptibilities provide an atomistic ab initio description for the coupled spin and lattice dynamics. It is important to notice that this theory is strictly bilinear in the spin and lattice variables and provides a minimal model for the coupled dynamics of these subsystems and that the two subsystems are treated on the same footing. Questions concerning time-reversal and inversion symmetry are rigorously addressed and it is shown how these aspects are absorbed in the tensor structure of the interaction fields. By means of these results regarding the spin-lattice coupling, simple explanations of ionic dimerization in double-antiferromagnetic materials, as well as charge density waves induced by a nonuniform spin structure, are given. In the final parts, coupled equations of motion for the combined spin and lattice dynamics are constructed, which subsequently can be reduced to a form which is analogous to the Landau-Lifshitz-Gilbert equations for spin dynamics and a damped driven mechanical oscillator for the ionic motion. It is important to notice, however, that these equations comprise contributions that couple these descriptions into one unified formulation. Finally, Kubo-like expressions for the discussed exchanges in terms of integrals over the electronic structure and, moreover, analogous expressions for the damping within and between the subsystems are provided. The proposed formalism and types of couplings enable a step forward in the microscopic first principles modeling of coupled spin and lattice quantities in a consistent format.

Intracellular dynamics of cationic and anionic polystyrene nanoparticles without direct interaction with mitotic spindle and chromosomes.

PubMed

Liu, Yuexian; Li, Wei; Lao, Fang; Liu, Ying; Wang, Liming; Bai, Ru; Zhao, Yuliang; Chen, Chunying

2011-11-01

The fate of nanomaterials with different sizes and charges in mitotic cells is of great importance but seldom explored. Herein we investigate the intracellular fate of negatively charged carboxylated polystyrene (COOH-PS) and positively charged amino-modified polystyrene (NH(2)-PS) nanoparticles of three different diameters (50, 100 and 500 nm) on cancer HeLa cells and normal NIH 3T3 cells during the cell cycles. The results showed that all the fluorescent PS nanoparticles differing in size and/or charge did not interact with chromosome reorganization and cytoskeleton assembly during the mitotic process in live cells. They neither disturbed chromosome reorganization nor affected the cytoskeleton reassembly in both normal and cancer cells. However, NH(2)-PS at the size of 50 nm caused G1 phase delay and a decrease of cyclin (D, E) expression, respectively. Moreover, NH(2)-PS displayed higher cellular toxicity and NH(2)-PS of 50 nm disturbed the integrity of cell membranes. Both cationic and anionic PS nanoparticles had a more pronounced effect on normal NIH 3T3 cells than cancer HeLa cell. Our research provides insight into the dynamic fate, intracellular behavior, and the effects of nanoparticles on spindle and chromosomes during cell division, which will enable the optimization of design and selection of much safer nanoparticles for lower risk to human health and widely medical applications. Copyright © 2011 Elsevier Ltd. All rights reserved.

Interactions of hydrogen with amorphous hafnium oxide

NASA Astrophysics Data System (ADS)

Kaviani, Moloud; Afanas'ev, Valeri V.; Shluger, Alexander L.

2017-02-01

We used density functional theory (DFT) calculations to study the interaction of hydrogen with amorphous hafnia (a -HfO2 ) using a hybrid exchange-correlation functional. Injection of atomic hydrogen, its diffusion towards electrodes, and ionization can be seen as key processes underlying charge instability of high-permittivity amorphous hafnia layers in many applications. Hydrogen in many wide band gap crystalline oxides exhibits negative-U behavior (+1 and -1 charged states are thermodynamically more stable than the neutral state) . Our results show that in a -HfO2 hydrogen is also negative-U, with charged states being the most thermodynamically stable at all Fermi level positions. However, metastable atomic hydrogen can share an electron with intrinsic electron trapping precursor sites [Phys. Rev. B 94, 020103 (2016)., 10.1103/PhysRevB.94.020103] forming a [etr -+O -H ] center, which is lower in energy on average by about 0.2 eV. These electron trapping sites can affect both the dynamics and thermodynamics of the interaction of hydrogen with a -HfO2 and the electrical behavior of amorphous hafnia films in CMOS devices.

The simulation study of protein-protein interfaces based on the 4-helix bundle structure

NASA Astrophysics Data System (ADS)

Fukuda, Masaki; Komatsu, Yu; Morikawa, Ryota; Miyakawa, Takeshi; Takasu, Masako; Akanuma, Satoshi; Yamagishi, Akihiko

2013-02-01

Docking of two protein molecules is induced by intermolecular interactions. Our purposes in this study are: designing binding interfaces on the two proteins, which specifically interact to each other; and inducing intermolecular interactions between the two proteins by mixing them. A 4-helix bundle structure was chosen as a scaffold on which binding interfaces were created. Based on this scaffold, we designed binding interfaces involving charged and nonpolar amino acid residues. We performed molecular dynamics (MD) simulation to identify suitable amino acid residues for the interfaces. We chose YciF protein as the scaffold for the protein-protein docking simulation. We observed the structure of two YciF protein molecules (I and II), and we calculated the distance between centroids (center of gravity) of the interfaces' surface planes of the molecules I and II. We found that the docking of the two protein molecules can be controlled by the number of hydrophobic and charged amino acid residues involved in the interfaces. Existence of six hydrophobic and five charged amino acid residues within an interface were most suitable for the protein-protein docking.

Effects of polymer graft properties on protein adsorption and transport in ion exchange chromatography: a multiscale modeling study.

PubMed

Basconi, Joseph E; Carta, Giorgio; Shirts, Michael R

2015-04-14

Multiscale simulation is used to study the adsorption of lysozyme onto ion exchangers obtained by grafting charged polymers into a porous matrix, in systems with various polymer properties and strengths of electrostatic interaction. Molecular dynamics simulations show that protein partitioning into the polymer-filled pore space increases with the overall charge content of the polymers, while the diffusivity in the pore space decreases. However, the combination of greatly increased partitioning and modestly decreased diffusion results in macroscopic transport rates that increase as a function of charge content, as the large concentration driving force due to enhanced pore space partitioning outweighs the reduction in the pore space diffusivity. Matrices having greater charge associated with the grafted polymers also exhibit more diffuse intraparticle concentration profiles during transient adsorption. In systems with a high charge content per polymer and a low protein loading, the polymers preferentially partition toward the surface due to favorable interactions with the surface-bound protein. These results demonstrate the potential of multiscale modeling to illuminate qualitative trends between molecular properties and the adsorption equilibria and kinetic properties observable on macroscopic scales.

Hydration of Li+ -ion in atom-bond electronegativity equalization method-7P water: a molecular dynamics simulation study.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-02-22

We have carried out molecular dynamics simulations of a Li(+) ion in water over a wide range of temperature (from 248 to 368 K). The simulations make use of the atom-bond electronegativity equalization method-7P water model, a seven-site flexible model with fluctuating charges, which has accurately reproduced many bulk water properties. The recently constructed Li(+)-water interaction potential through fitting to the experimental and ab initio gas-phase binding energies and to the measured structures for Li(+)-water clusters is adopted in the simulations. ABEEM was proposed and developed in terms of partitioning the electron density into atom and bond regions and using the electronegativity equalization method (EEM) and the density functional theory (DFT). Based on a combination of the atom-bond electronegativity equalization method and molecular mechanics (ABEEM/MM), a new set of water-water and Li(+)-water potentials, successfully applied to ionic clusters Li(+)(H(2)O)(n)(n=1-6,8), are further investigated in an aqueous solution of Li(+) in the present paper. Two points must be emphasized in the simulations: first, the model allows for the charges on the interacting sites fluctuating as a function of time; second, the ABEEM-7P model has applied the parameter k(lp,H)(R(lp,H)) to explicitly describe the short-range interaction of hydrogen bond in the hydrogen bond interaction region, and has a new description for the hydrogen bond. The static, dynamic, and thermodynamic properties have been studied in detail. In addition, at different temperatures, the structural properties such as radial distribution functions, and the dynamical properties such as diffusion coefficients and residence times of the water molecules in the first hydration shell of Li(+), are also simulated well. These simulation results show that the ABEEM/MM-based water-water and Li(+)-water potentials appear to be robust giving the overall characteristic hydration properties in excellent agreement with experiments and other molecular dynamics simulations on similar system.

Hamiltonian structure of classical N-body systems of finite-size particles subject to EM interactions

NASA Astrophysics Data System (ADS)

Cremaschini, C.; Tessarotto, M.

2012-01-01

An open issue in classical relativistic mechanics is the consistent treatment of the dynamics of classical N-body systems of mutually interacting particles. This refers, in particular, to charged particles subject to EM interactions, including both binary interactions and self-interactions ( EM-interacting N- body systems). The correct solution to the question represents an overriding prerequisite for the consistency between classical and quantum mechanics. In this paper it is shown that such a description can be consistently obtained in the context of classical electrodynamics, for the case of a N-body system of classical finite-size charged particles. A variational formulation of the problem is presented, based on the N -body hybrid synchronous Hamilton variational principle. Covariant Lagrangian and Hamiltonian equations of motion for the dynamics of the interacting N-body system are derived, which are proved to be delay-type ODEs. Then, a representation in both standard Lagrangian and Hamiltonian forms is proved to hold, the latter expressed by means of classical Poisson Brackets. The theory developed retains both the covariance with respect to the Lorentz group and the exact Hamiltonian structure of the problem, which is shown to be intrinsically non-local. Different applications of the theory are investigated. The first one concerns the development of a suitable Hamiltonian approximation of the exact equations that retains finite delay-time effects characteristic of the binary interactions and self-EM-interactions. Second, basic consequences concerning the validity of Dirac generator formalism are pointed out, with particular reference to the instant-form representation of Poincaré generators. Finally, a discussion is presented both on the validity and possible extension of the Dirac generator formalism as well as the failure of the so-called Currie "no-interaction" theorem for the non-local Hamiltonian system considered here.

Swelling properties of montmorillonite and beidellite clay minerals from molecular simulation: Comparison of temperature interlayer cation, and charge location effects

DOE PAGES

Teich-McGoldrick, Stephanie L.; Greathouse, Jeffery A.; Jove-Colon, Carlos F.; ...

2015-08-27

In this study, the swelling properties of smectite clay minerals are relevant to many engineering applications including environmental remediation, repository design for nuclear waste disposal, borehole stability in drilling operations, and additives for numerous industrial processes and commercial products. We used molecular dynamics and grand canonical Monte Carlo simulations to study the effects of layer charge location, interlayer cation, and temperature on intracrystalline swelling of montmorillonite and beidellite clay minerals. For a beidellite model with layer charge exclusively in the tetrahedral sheet, strong ion–surface interactions shift the onset of the two-layer hydrate to higher water contents. In contrast, for amore » montmorillonite model with layer charge exclusively in the octahedral sheet, weaker ion–surface interactions result in the formation of fully hydrated ions (two-layer hydrate) at much lower water contents. Clay hydration enthalpies and interlayer atomic density profiles are consistent with the swelling results. Water adsorption isotherms from grand canonical Monte Carlo simulations are used to relate interlayer hydration states to relative humidity, in good agreement with experimental findings.« less

Molecular-Scale Investigation of Heavy Metal Ions at a Charged Langmuir Monolayer

NASA Astrophysics Data System (ADS)

Rock, William; Qiao, Baofu; Uysal, Ahmet; Bu, Wei; Lin, Binhua

Solvent extraction - the surfactant-aided preferential transfer of a species from an aqueous to an organic phase - is an important technique used in heavy and precious metal refining and reprocessing. Solvent extraction requires transfer through an oil/water interface, and interfacial interactions are expected to control transfer kinetics and phase stability, yet these key interactions are poorly understood. Langmuir monolayers with charged headgroups atop concentrated salt solutions containing heavy metal ions act as a model of solvent extraction interfaces; studies of ions at a charged surface are also fundamentally important to many other phenomena including protein solvation, mineral surface chemistry, and electrochemistry. We probe these charged interfaces using a variety of surface-sensitive techniques - vibrational sum frequency generation (VSFG) spectroscopy, x-ray reflectivity (XRR), x-ray fluorescence near total reflection (XFNTR), and grazing incidence diffraction (GID). We integrate experiments with Molecular Dynamics (MD) simulations to uncover the molecular-level interfacial structure. This work is supported by the U.S. DOE, BES, Contract DE-AC02-06CH11357. ChemMatCARS is supported by NSF/CHE-1346572.

Dependence of Interaction Free Energy between Solutes on an External Electrostatic Field

PubMed Central

Yang, Pei-Kun

2013-01-01

To explore the athermal effect of an external electrostatic field on the stabilities of protein conformations and the binding affinities of protein-protein/ligand interactions, the dependences of the polar and hydrophobic interactions on the external electrostatic field, −Eext, were studied using molecular dynamics (MD) simulations. By decomposing Eext into, along, and perpendicular to the direction formed by the two solutes, the effect of Eext on the interactions between these two solutes can be estimated based on the effects from these two components. Eext was applied along the direction of the electric dipole formed by two solutes with opposite charges. The attractive interaction free energy between these two solutes decreased for solutes treated as point charges. In contrast, the attractive interaction free energy between these two solutes increased, as observed by MD simulations, for Eext = 40 or 60 MV/cm. Eext was applied perpendicular to the direction of the electric dipole formed by these two solutes. The attractive interaction free energy was increased for Eext = 100 MV/cm as a result of dielectric saturation. The force on the solutes along the direction of Eext computed from MD simulations was greater than that estimated from a continuum solvent in which the solutes were treated as point charges. To explore the hydrophobic interactions, Eext was applied to a water cluster containing two neutral solutes. The repulsive force between these solutes was decreased/increased for Eext along/perpendicular to the direction of the electric dipole formed by these two solutes. PMID:23852018

Molecular dynamics simulations on the effect of size and shape on the interactions between negative Au18(SR)14, Au102(SR)44 and Au144(SR)60 nanoparticles in physiological saline.

PubMed

Villareal, Oscar D; Rodriguez, Roberto A; Yu, Lili; Wambo, Thierry O

2016-08-20

Molecular dynamics simulations employing all-atom force fields have become a reliable way to study binding interactions quantitatively for a wide range of systems. In this work, we employ two recently developed methods for the calculation of dissociation constants K D between gold nanoparticles (AuNPs) of different sizes in a near-physiological environment through the potential of mean force (PMF) formalism: the method of geometrical restraints developed by Woo et al. and formalized by Gumbart et al. and the method of hybrid Steered Molecular Dynamics (hSMD). Obtaining identical results (within the margin of error) from both approaches on the negatively charged Au 18 (SR) 14 NP, functionalized by the negatively charged 4-mercapto-benzoate (pMBA) ligand, we draw parallels between their energetic and entropic interactions. By applying the hSMD method on Au 102 (SR) 44 and Au 144 (SR) 60 , both of them near-spherical in shape and functionalized by pMBA, we study the effects of size and shape on the binding interactions. Au 18 binds weakly with K D = 13 mM as a result of two opposing effects: its large surface curvature hindering the formation of salt bridges, and its large ligand density on preferential orientations favoring their formation. On the other hand, Au 102 binds more strongly with K D = 30 μM and Au 144 binds the strongest with K D = 3.2 nM .

Collective charge excitations and the metal-insulator transition in the square lattice Hubbard-Coulomb model

DOE PAGES

Ulybyshev, Maksim; Winterowd, Christopher; Zafeiropoulos, Savvas

2017-11-09

Here in this article, we discuss the nontrivial collective charge excitations (plasmons) of the extended square lattice Hubbard model. Using a fully nonperturbative approach, we employ the hybrid Monte Carlo algorithm to simulate the system at half-filling. A modified Backus-Gilbert method is introduced to obtain the spectral functions via numerical analytic continuation. We directly compute the single-particle density of states which demonstrates the formation of Hubbard bands in the strongly correlated phase. The momentum-resolved charge susceptibility also is computed on the basis of the Euclidean charge-density-density correlator. In agreement with previous extended dynamical mean-field theory studies, we find that, atmore » high strength of the electron-electron interaction, the plasmon dispersion develops two branches.« less

Collective charge excitations and the metal-insulator transition in the square lattice Hubbard-Coulomb model

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

Ulybyshev, Maksim; Winterowd, Christopher; Zafeiropoulos, Savvas

Here in this article, we discuss the nontrivial collective charge excitations (plasmons) of the extended square lattice Hubbard model. Using a fully nonperturbative approach, we employ the hybrid Monte Carlo algorithm to simulate the system at half-filling. A modified Backus-Gilbert method is introduced to obtain the spectral functions via numerical analytic continuation. We directly compute the single-particle density of states which demonstrates the formation of Hubbard bands in the strongly correlated phase. The momentum-resolved charge susceptibility also is computed on the basis of the Euclidean charge-density-density correlator. In agreement with previous extended dynamical mean-field theory studies, we find that, atmore » high strength of the electron-electron interaction, the plasmon dispersion develops two branches.« less

Molecular dynamics investigation of the ionic liquid/enzyme interface: application to engineering enzyme surface charge.

PubMed

Burney, Patrick R; Nordwald, Erik M; Hickman, Katie; Kaar, Joel L; Pfaendtner, Jim

2015-04-01

Molecular simulations of the enzymes Candida rugosa lipase and Bos taurus α-chymotrypsin in aqueous ionic liquids 1-butyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium ethyl sulfate were used to study the change in enzyme-solvent interactions induced by modification of the enzyme surface charge. The enzymes were altered by randomly mutating lysine surface residues to glutamate, effectively decreasing the net surface charge by two for each mutation. These mutations resemble succinylation of the enzyme by chemical modification, which has been shown to enhance the stability of both enzymes in ILs. After establishing that the enzymes were stable on the simulated time scales, we focused the analysis on the organization of the ionic liquid substituents about the enzyme surface. Calculated solvent charge densities show that for both enzymes and in both solvents that changing positively charged residues to negative charge does indeed increase the charge density of the solvent near the enzyme surface. The radial distribution of IL constituents with respect to the enzyme reveals decreased interactions with the anion are prevalent in the modified systems when compared to the wild type, which is largely accompanied by an increase in cation contact. Additionally, the radial dependence of the charge density and ion distribution indicates that the effect of altering enzyme charge is confined to short range (≤1 nm) ordering of the IL. Ultimately, these results, which are consistent with that from prior experiments, provide molecular insight into the effect of enzyme surface charge on enzyme stability in ILs. © 2015 Wiley Periodicals, Inc.

Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome.

PubMed

Beard, D A; Schlick, T

2001-01-01

Much progress has been achieved on quantitative assessment of electrostatic interactions on the all-atom level by molecular mechanics and dynamics, as well as on the macroscopic level by models of continuum solvation. Bridging of the two representations-an area of active research-is necessary for studying integrated functions of large systems of biological importance. Following perspectives of both discrete (N-body) interaction and continuum solvation, we present a new algorithm, DiSCO (Discrete Surface Charge Optimization), for economically describing the electrostatic field predicted by Poisson-Boltzmann theory using a discrete set of Debye-Hückel charges distributed on a virtual surface enclosing the macromolecule. The procedure in DiSCO relies on the linear behavior of the Poisson-Boltzmann equation in the far zone; thus contributions from a number of molecules may be superimposed, and the electrostatic potential, or equivalently the electrostatic field, may be quickly and efficiently approximated by the summation of contributions from the set of charges. The desired accuracy of this approximation is achieved by minimizing the difference between the Poisson-Boltzmann electrostatic field and that produced by the linearized Debye-Hückel approximation using our truncated Newton optimization package. DiSCO is applied here to describe the salt-dependent electrostatic environment of the nucleosome core particle in terms of several hundred surface charges. This representation forms the basis for modeling-by dynamic simulations (or Monte Carlo)-the folding of chromatin. DiSCO can be applied more generally to many macromolecular systems whose size and complexity warrant a model resolution between the all-atom and macroscopic levels. Copyright 2000 John Wiley & Sons, Inc.

Effect of the charge surface distribution on the flow field induced by a dielectric barrier discharge actuator

NASA Astrophysics Data System (ADS)

Cristofolini, Andrea; Neretti, Gabriele; Borghi, Carlo A.

2013-08-01

The Electro-Hydro-Dynamics (EHD) interaction induced by a surface dielectric barrier discharge in the aerodynamic boundary layer at one atmosphere still air has been investigated. Three different geometrical configurations of the actuator have been utilized. In the first configuration, an electrode pair separated by a 2 mm dielectric sheet has been used. The second and the third configurations have been obtained by adding a third electrode on the upper side of the dielectric surface. This electrode has been placed downstream of the upper electrode and has been connected to ground or has been left floating. Three different dielectric materials have been utilized. The high voltage upper electrode was fed by an a.c. electric tension. Measurements of the dielectric surface potential generated by the charge deposition have been done. The discharge has been switched off after positive and negative phases of the plasma current (the current phase was characterized by a positive or a negative value, respectively). The measurements have been carried out after both phases. The charge distribution strongly depended on the switching off phase and was heavily affected by the geometrical configuration. A remarkable decrease of the charge deposited on the dielectric surface has been detected when the third electrode was connected to ground. Velocity profiles were obtained by using a Pitot probe. They showed that the presence of the third electrode limits the fluid dynamics performance of the actuator. A relation between the charge surface distribution and the EHD interaction phenomenon has been found. Imaging of the plasma has been done to evaluate the discharge structure and the extension of the plasma in the configurations investigated.

Density functional theory and molecular dynamics study of the uranyl ion (UO₂)²⁺.

PubMed

Rodríguez-Jeangros, Nicolás; Seminario, Jorge M

2014-03-01

The detection of uranium is very important, especially in water and, more importantly, in the form of uranyl ion (UO₂)²⁺, which is one of its most abundant moieties. Here, we report analyses and simulations of uranyl in water using ab initio modified force fields for water with improved parameters and charges of uranyl. We use a TIP4P model, which allows us to obtain accurate water properties such as the boiling point and the second and third shells of water molecules in the radial distribution function thanks to a fictitious charge that corrects the 3-point models by reproducing the exact dipole moment of the water molecule. We also introduced non-bonded interaction parameters for the water-uranyl intermolecular force field. Special care was taken in testing the effect of a range of uranyl charges on the structure of uranyl-water complexes. Atomic charges of the solvated ion in water were obtained using density functional theory (DFT) calculations taking into account the presence of nitrate ions in the solution, forming a neutral ensemble. DFT-based force fields were calculated in such a way that water properties, such as the boiling point or the pair distribution function stand. Finally, molecular dynamics simulations of a water box containing uranyl cations and nitrate anions are performed at room temperature. The three peaks in the oxygen-oxygen radial distribution function for water were found to be kept in the presence of uranyl thanks to the improvement of interaction parameters and charges. Also, we found three shells of water molecules surrounding the uranyl ion instead of two as was previously thought.

Lattice dynamical and dielectric properties of L-amino acids

NASA Astrophysics Data System (ADS)

Tulip, P. R.; Clark, S. J.

2006-08-01

We present the results of ab initio calculations of the lattice dynamical and dielectric properties of the L-amino acids L-alanine, L-leucine, and L-isoleucine. Normal-mode frequencies and dielectric permittivity tensors are obtained using density-functional perturbation theory implemented within the plane-wave pseudopotential approximation. IR spectra are calculated and are used to analyze the effects of intermolecular interactions and zwitterionization upon the lattice dynamics. It is found that vibronic modes associated with the carboxy and amino functional groups undergo modification from their free-molecule values due to the presence of hydrogen bonds. The role of macroscopic electric fields set up by zone-center normal modes in the lattice dynamics is investigated by analysis of the Born effective charge. Calculated permittivity tensors are found to be greater than would be obtained by a naive use of the isolated molecular values, indicating the role of intermolecular interactions in increasing molecular polarizability.

Modeling hole transport in wet and dry DNA.

PubMed

Pavanello, Michele; Adamowicz, Ludwik; Volobuyev, Maksym; Mennucci, Benedetta

2010-04-08

We present a DFT/classical molecular dynamics model of DNA charge conductivity. The model involves a temperature-driven, hole-hopping charge transfer and includes the time-dependent nonequilibrium interaction of DNA with its molecular environment. We validate our method against a variety of hole transport experiments. The method predicts a significant hole-transfer slowdown of approximately 35% from dry to wet DNA with and without electric field bias. In addition, in agreement with experiments, it also predicts an insulating behavior of (GC)(N) oligomers for 40 < N < 1000, depending on the experimental setup.

Effect of PDGF-B aptamer on PDGFRβ/PDGF-B interaction: Molecular dynamics study.

PubMed

Vu, Cong Quang; Rotkrua, Pichayanoot; Soontornworajit, Boonchoy; Tantirungrotechai, Yuthana

2018-06-01

PDGFRβ/PDGF-B interaction plays a role in angiogenesis, and is mandatory in wound healing and cancer treatment. It has been reported that the PDGF-B aptamer was able to bind to PDGF-B, thus regulating the angiogenesis. However, the binding interaction between the aptamer and the growth factor, including the binding sites, has not been well investigated. This study applied a molecular dynamics (MD) simulation to investigate the aptamer-growth factor interaction in the presence or absence of a receptor (PDGFRβ). Characterization of the structure of an aptamer-growth factor complex revealed binding sites from each section in the complex. Upon the complex formation, PDGF-B and its aptamer exhibited less flexibility in their molecular movement, as indicated by the minimum values of RMSD, RMSF, loop-to-loop distance, and the summation of PCA eigenvalues. Our study of residue pairwise interaction demonstrated that the binding interaction was mainly contributed by electrostatic interaction between the positively-charged amino acid and the negatively-charged phosphate backbone. The role of the PDGF-B aptamer in PDGFRβ/PDGF-B interaction was also investigated. We demonstrated that the stability of the Apt-PDGF-B complex could prevent the presence of a competitor, of PDGFRβ, interrupting the binding process. Because the aptamer was capable of binding with PDGF-B, and blocking the growth factor from the PDGFRβ, it could down regulate the consequent signaling pathway. We provide evidence that the PDGF-BB aptamer is a promising molecule for regulation of angiogenesis. The MD study provides a molecular understanding to modification of the aptamer binding interaction, which could be used in a number of medical applications. Copyright © 2018 Elsevier Inc. All rights reserved.

Near-Field Nanoscopy of Metal-Insulator Phase Transitions Towards Synthesis of Novel Correlated Transition Metal Oxides and Their Interaction with Plasmon Resonances

DTIC Science & Technology

2016-01-05

and to utilize the phase transtion states of VO2 to control and manipulate local plasmon resonaces. First, we imaged the charge dynamics in (MIT) of...Then we studied the interaction of VO2 with plasmons . Both the film VO2 and the crystal VO2 were 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 13...Novel Correlated Transition Metal Oxides and Their Interaction with Plasmon Resonances The views, opinions and/or findings contained in this report are

Asymmetric Wormholes via Electrically Charged Lightlike Branes

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

Guendelman, E.; Kaganovich, A.; Nissimov, E.

2010-06-17

We consider a self-consistent Einstein-Maxwell-Kalb-Ramond system in the bulk D = 4 space-time interacting with a variable-tension electrically charged lightlike brane. The latter serves both as a material and charge source for gravity and electromagnetism, as well as it dynamically generates a bulk space varying cosmological constant. We find an asymmetric wormhole solution describing two 'universes' with different spherically symmetric black-hole-type geometries connected through a 'throat' occupied by the lightlike brane. The electrically neutral 'left universe' comprises the exterior region of Schwarzschild-de-Sitter (or pure Schwarzschild) space-time above the inner(Schwarzschild-type) horizon, whereas the electrically charged 'right universe' consists of the exteriormore » Reissner-Nordstroem (or Reissner-Nordstroem-de-Sitter) black hole region beyond the outer Reissner-Nordstroem horizon. All physical parameters of the wormhole are uniquely determined by two free parameters - the electric charge and Kalb-Ramond coupling of the lightlike brane.« less

Charge-transfer dynamics and nonlocal dielectric permittivity tuned with metamaterial structures as solvent analogues

NASA Astrophysics Data System (ADS)

Lee, Kwang Jin; Xiao, Yiming; Woo, Jae Heun; Kim, Eunsun; Kreher, David; Attias, André-Jean; Mathevet, Fabrice; Ribierre, Jean-Charles; Wu, Jeong Weon; André, Pascal

2017-07-01

Charge transfer (CT) is a fundamental and ubiquitous mechanism in biology, physics and chemistry. Here, we evidence that CT dynamics can be altered by multi-layered hyperbolic metamaterial (HMM) substrates. Taking triphenylene:perylene diimide dyad supramolecular self-assemblies as a model system, we reveal longer-lived CT states in the presence of HMM structures, with both charge separation and recombination characteristic times increased by factors of 2.4 and 1.7--that is, relative variations of 140 and 73%, respectively. To rationalize these experimental results in terms of driving force, we successfully introduce image dipole interactions in Marcus theory. The non-local effect herein demonstrated is directly linked to the number of metal-dielectric pairs, can be formalized in the dielectric permittivity, and is presented as a solid analogue to local solvent polarity effects. This model and extra PH3T:PC60BM results show the generality of this non-local phenomenon and that a wide range of kinetic tailoring opportunities can arise from substrate engineering. This work paves the way toward the design of artificial substrates to control CT dynamics of interest for applications in optoelectronics and chemistry.

Stochastic collective dynamics of charged-particle beams in the stability regime

NASA Astrophysics Data System (ADS)

Petroni, Nicola Cufaro; de Martino, Salvatore; de Siena, Silvio; Illuminati, Fabrizio

2001-01-01

We introduce a description of the collective transverse dynamics of charged (proton) beams in the stability regime by suitable classical stochastic fluctuations. In this scheme, the collective beam dynamics is described by time-reversal invariant diffusion processes deduced by stochastic variational principles (Nelson processes). By general arguments, we show that the diffusion coefficient, expressed in units of length, is given by λcN, where N is the number of particles in the beam and λc the Compton wavelength of a single constituent. This diffusion coefficient represents an effective unit of beam emittance. The hydrodynamic equations of the stochastic dynamics can be easily recast in the form of a Schrödinger equation, with the unit of emittance replacing the Planck action constant. This fact provides a natural connection to the so-called ``quantum-like approaches'' to beam dynamics. The transition probabilities associated to Nelson processes can be exploited to model evolutions suitable to control the transverse beam dynamics. In particular we show how to control, in the quadrupole approximation to the beam-field interaction, both the focusing and the transverse oscillations of the beam, either together or independently.

The chaperone-histone partnership: for the greater good of histone traffic and chromatin plasticity.

PubMed

Hondele, Maria; Ladurner, Andreas G

2011-12-01

Histones are highly positively charged proteins that wrap our genome. Their surface properties also make them prone to nonspecific interactions and aggregation. A class of proteins known as histone chaperones is dedicated to safeguard histones by aiding their proper incorporation into nucleosomes. Histone chaperones facilitate ordered nucleosome assembly and disassembly reactions through the formation of semi-stable histone-chaperone intermediates without requiring ATP, but merely providing a complementary protein surface for histones to dynamically interact with. Recurrent 'chaperoning' mechanisms involve the masking of the histone's positive charge and the direct blocking of crucial histone surface sites, including those required for H3-H4 tetramerization or the binding of nucleosomal DNA. This shielding prevents histones from engaging in premature or unwanted interactions with nucleic acids and other cellular components. In this review, we analyze recent structural studies on chaperone-histone interactions and discuss the implications of this vital partnership for nucleosome assembly and disassembly pathways. Copyright © 2011 Elsevier Ltd. All rights reserved.

Kinetics of aggregation in charged nanoparticle solutions driven by different mechanisms

NASA Astrophysics Data System (ADS)

Abbas, S.; Yadav, I.; Kumar, Sugam; Aswal, V. K.; Kohlbrecher, J.

2017-05-01

The structure and kinetics during aggregation of anionic silica nanoparticles as induced through different mechanisms have been studied by dynamic light scattering (DLS) and small-angle neutron scattering (SANS). Three different additives, namely an electrolyte (NaCl), cationic protein (lysozyme) and non-ionic surfactant (C12E10) were used to initiate nanoparticle aggregation. Electrolyte induced aggregation can be explained by DLVO interaction, whereas depletion interaction (non-DLVO interaction) is found responsible for nanoparticle aggregation in case of non-ionic surfactant. Unlike these two cases, strong electrostatic attraction between nanoparticle and oppositely charged protein results into protein-mediated nanoparticle aggregation. The electrolyte induced aggregation show quite slow aggregation rate whereas protein mediated as well as surfactant induced aggregation takes place almost instantaneously. The significant differences observed in the kinetics are explained based on range of interactions responsible for the aggregation. In spite of differences in mechanism and kinetics, the nanoparticle clusters are found to have similar fractal morphology (fractal dimension ˜ 2.5) in all the three cases.

Coulomb repulsion in short polypeptides.

PubMed

Norouzy, Amir; Assaf, Khaleel I; Zhang, Shuai; Jacob, Maik H; Nau, Werner M

2015-01-08

Coulomb repulsion between like-charged side chains is presently viewed as a major force that impacts the biological activity of intrinsically disordered polypeptides (IDPs) by determining their spatial dimensions. We investigated short synthetic models of IDPs, purely composed of ionizable amino acid residues and therefore expected to display an extreme structural and dynamic response to pH variation. Two synergistic, custom-made, time-resolved fluorescence methods were applied in tandem to study the structure and dynamics of the acidic and basic hexapeptides Asp6, Glu6, Arg6, Lys6, and His6 between pH 1 and 12. (i) End-to-end distances were obtained from the short-distance Förster resonance energy transfer (sdFRET) from N-terminal 5-fluoro-l-tryptophan (FTrp) to C-terminal Dbo. (ii) End-to-end collision rates were obtained for the same peptides from the collision-induced fluorescence quenching (CIFQ) of Dbo by FTrp. Unexpectedly, the very high increase of charge density at elevated pH had no dynamical or conformational consequence in the anionic chains, neither in the absence nor in the presence of salt, in conflict with the common view and in partial conflict with accompanying molecular dynamics simulations. In contrast, the cationic peptides responded to ionization but with surprising patterns that mirrored the rich individual characteristics of each side chain type. The contrasting results had to be interpreted, by considering salt screening experiments, N-terminal acetylation, and simulations, in terms of an interplay of local dielectric constant and peptide-length dependent side chain charge-charge repulsion, side chain functional group solvation, N-terminal and side chain charge-charge repulsion, and side chain-side chain as well as side chain-backbone interactions. The common picture that emerged is that Coulomb repulsion between water-solvated side chains is efficiently quenched in short peptides as long as side chains are not in direct contact with each other or the main chain.

Proteins with Novel Structure, Function and Dynamics

NASA Technical Reports Server (NTRS)

Pohorille, Andrew

2014-01-01

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Conformational flexibility of domain III of annexin V: the effect of pH and binding to membrane-water interfaces

NASA Astrophysics Data System (ADS)

Sopkova, Jana; Vincent, Michel; Takahashi, Maza; Lewit-Bentley, Anita; Gallay, Jacques

1999-05-01

Steady-state and time-resolved fluorescence of the single tryptophan residue (W187) of annexin V show that the conformation and the dynamics of domain III are strongly modified upon binding of the protein to negatively charged phospholipid vesicles in the presence of calcium, or upon incorporation into reverse micelles of water/sodium bis(2- ethylhexyl) sulfosuccinate (AOT) in iso-octane. In the protein at neutral pH, W187 is slightly mobile and buried in a hydrophobic pocket. It becomes more mobile and is moved in a more polar environment when the protein interacts with the model membranes. In each condition, the heterogeneity of the fluorescence intensity decay of W187 is likely due to the co- existence of local conformers with different dynamics. A similar change of conformation and dynamics can be provoked by mild acidic pH. This suggests that electrostatic interactions are important for the folding of domain III. An interplay of salt bridges implying charged amino-acid side-chains at the protein surface in domain III can be observed in the crystal structure. Local pH modifications at the membrane surface can therefore be responsible for the observed conformational change. The high flexibility of domain III in the membrane- bound protein suggests moreover that this domain may not be crucial for the interaction of the protein with the membrane, in agreement with recent atomic force microscope results (Reviakine et al., 1998, J. Struct. Biol. 121, 356-362).

Tuning of protein-surfactant interaction to modify the resultant structure.

PubMed

Mehan, Sumit; Aswal, Vinod K; Kohlbrecher, Joachim

2015-09-01

Small-angle neutron scattering and dynamic light scattering studies have been carried out to examine the interaction of bovine serum albumin (BSA) protein with different surfactants under varying solution conditions. We show that the interaction of anionic BSA protein (pH7) with surfactant and the resultant structure are strongly modified by the charge head group of the surfactant, ionic strength of the solution, and mixed surfactants. The protein-surfactant interaction is maximum when two components are oppositely charged, followed by components being similarly charged through the site-specific binding, and no interaction in the case of a nonionic surfactant. This interaction of protein with ionic surfactants is characterized by the fractal structure representing a bead-necklace structure of micellelike clusters adsorbed along the unfolded protein chain. The interaction is enhanced with ionic strength only in the case of site-specific binding of an anionic surfactant with an anionic protein, whereas it is almost unchanged for other complexes of cationic and nonionic surfactants with anionic proteins. Interestingly, the interaction of BSA protein with ionic surfactants is significantly suppressed in the presence of nonionic surfactant. These results with mixed surfactants thus can be used to fold back the unfolded protein as well as to prevent surfactant-induced protein unfolding. For different solution conditions, the results are interpreted in terms of a change in fractal dimension, the overall size of the protein-surfactant complex, and the number of micelles attached to the protein. The interplay of electrostatic and hydrophobic interactions is found to govern the resultant structure of complexes.

Tuning of protein-surfactant interaction to modify the resultant structure

NASA Astrophysics Data System (ADS)

Mehan, Sumit; Aswal, Vinod K.; Kohlbrecher, Joachim

2015-09-01

Small-angle neutron scattering and dynamic light scattering studies have been carried out to examine the interaction of bovine serum albumin (BSA) protein with different surfactants under varying solution conditions. We show that the interaction of anionic BSA protein (p H 7 ) with surfactant and the resultant structure are strongly modified by the charge head group of the surfactant, ionic strength of the solution, and mixed surfactants. The protein-surfactant interaction is maximum when two components are oppositely charged, followed by components being similarly charged through the site-specific binding, and no interaction in the case of a nonionic surfactant. This interaction of protein with ionic surfactants is characterized by the fractal structure representing a bead-necklace structure of micellelike clusters adsorbed along the unfolded protein chain. The interaction is enhanced with ionic strength only in the case of site-specific binding of an anionic surfactant with an anionic protein, whereas it is almost unchanged for other complexes of cationic and nonionic surfactants with anionic proteins. Interestingly, the interaction of BSA protein with ionic surfactants is significantly suppressed in the presence of nonionic surfactant. These results with mixed surfactants thus can be used to fold back the unfolded protein as well as to prevent surfactant-induced protein unfolding. For different solution conditions, the results are interpreted in terms of a change in fractal dimension, the overall size of the protein-surfactant complex, and the number of micelles attached to the protein. The interplay of electrostatic and hydrophobic interactions is found to govern the resultant structure of complexes.

THE EFFECTS OF PARTIAL CONDENSATION AROUND IONS IN ELECTRIC FLUID DYNAMIC ENERGY CONVERSION PROCESSES.

DTIC Science & Technology

theoretically. Negative ions are produced by a corona discharge from a needle placed along the axis of a nozzle. A dense air-vapor mixture is...interaction with the gas molecules to an electrode of high potential. The effectiveness of the viscous coupling depends on the charge mobility being

Hybrid particle-field molecular dynamics simulation for polyelectrolyte systems.

PubMed

Zhu, You-Liang; Lu, Zhong-Yuan; Milano, Giuseppe; Shi, An-Chang; Sun, Zhao-Yan

2016-04-14

To achieve simulations on large spatial and temporal scales with high molecular chemical specificity, a hybrid particle-field method was proposed recently. This method is developed by combining molecular dynamics and self-consistent field theory (MD-SCF). The MD-SCF method has been validated by successfully predicting the experimentally observable properties of several systems. Here we propose an efficient scheme for the inclusion of electrostatic interactions in the MD-SCF framework. In this scheme, charged molecules are interacting with the external fields that are self-consistently determined from the charge densities. This method is validated by comparing the structural properties of polyelectrolytes in solution obtained from the MD-SCF and particle-based simulations. Moreover, taking PMMA-b-PEO and LiCF3SO3 as examples, the enhancement of immiscibility between the ion-dissolving block and the inert block by doping lithium salts into the copolymer is examined by using the MD-SCF method. By employing GPU-acceleration, the high performance of the MD-SCF method with explicit treatment of electrostatics facilitates the simulation study of many problems involving polyelectrolytes.

Changes in conformational dynamics of basic side chains upon protein–DNA association

PubMed Central

Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani; Roy, Sourav; Pettitt, B. Montgometry; Iwahara, Junji

2016-01-01

Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein–DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1–DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains. PMID:27288446

Designing effective anticancer-radiopeptides. A Molecular Dynamics study of their interaction with model tumor and healthy cell membranes.

PubMed

Capozzi, E; Aureli, S; Minicozzi, V; Rossi, G C; Stellato, F; Morante, S

2018-06-06

One of the greatest merit of the use of radiopeptides in oncology is their selectivity which, however, brings about the drawback that each radiopeptide is specific for a given tumor type. To overcome this problem the direction currently taken in drug design is that of radiolabelling peptide hormones (or their analogues), relying on their intrinsic ability to bind to specific receptors in precise areas of the human body, at the cost, however, of a poor selectivity against healthy cells. We present here an extensive Molecular Dynamics study of a promising alternative inspired by the mechanism through which antimicrobial peptides interact with the negatively charged bacterial membranes. Appropriately modifying the human antimicrobial peptide, LL-37, we designed a functionalized radionuclide carrier capable of binding more strongly to the negatively charged (model) tumor membranes than to the neutral healthy ones. The mechanism behind this behaviour relies on the fact that at the slight acidic pH surrounding tumor tissues the histidines belonging to the peptide get protonated thus making it positively charged. We have investigated by an extended numerical study the way in which this artificial peptide interacts with models of tumor and healthy cell membranes, proving by Potential Mean Force calculations that the affinity of the peptide to model tumor membranes is significantly larger than to healthy ones. These features (high affinity and generic tumor selectivity) recommend antimicrobial derived customized carriers as promising theranostic constructs in cancer diagnostic and therapy. Copyright © 2018 Elsevier B.V. All rights reserved.

General Method to Determine the Flux of Charged Molecules through Nanopores Applied to β-Lactamase Inhibitors and OmpF.

PubMed

Ghai, Ishan; Pira, Alessandro; Scorciapino, Mariano Andrea; Bodrenko, Igor; Benier, Lorraine; Ceccarelli, Matteo; Winterhalter, Mathias; Wagner, Richard

2017-03-16

A major challenge in the discovery of the new antibiotics against Gram-negative bacteria is to achieve sufficiently fast permeation in order to avoid high doses causing toxic side effects. So far, suitable assays for quantifying the uptake of charged antibiotics into bacteria are lacking. We apply an electrophysiological zero-current assay using concentration gradients of β-lactamase inhibitors combined with single-channel conductance to quantify their flux rates through OmpF. Molecular dynamic simulations provide in addition details on the interactions between the nanopore wall and the charged solutes. In particular, the interaction barrier for three β-lactamase inhibitors is surprisingly as low as 3-5 kcal/mol and only slightly above the diffusion barrier of ions such as chloride. Within our macroscopic constant field model, we determine that at a zero-membrane potential a concentration gradient of 10 μM of avibactam, sulbactam, or tazobactam can create flux rates of roughly 620 molecules/s per OmpF trimer.

Interface-driven spin-torque ferromagnetic resonance by Rashba coupling at the interface between nonmagnetic materials

DOE PAGES

Jungfleisch, M. B.; Zhang, W.; Sklenar, J.; ...

2016-06-20

The Rashba-Edelstein effect stems from the interaction between the electron's spin and its momentum induced by spin-orbit interaction at an interface or a surface. It was shown that the inverse Rashba-Edelstein effect can be used to convert a spin current into a charge current. Here, we demonstrate the reverse process of a charge-to spin-current conversion at a Bi/Ag Rashba interface. We show that this interface-driven spin current can drive an adjacent ferromagnet to resonance. We employ a spin-torque ferromagnetic resonance excitation/detection scheme which was developed originally for a bulk spin-orbital effect, the spin Hall effect. In our experiment, the directmore » Rashba-Edelstein effect generates an oscillating spin current from an alternating charge current driving the magnetization precession in a neighboring permalloy (Py, Ni 80Fe 20) layer. As a result, electrical detection of the magnetization dynamics is achieved by a rectificationmechanism of the time dependent multilayer resistance arising from the anisotropic magnetoresistance.« less

Atomistic Time-Domain Simulations of Light-Harvesting and Charge-Transfer Dynamics in Novel Nanoscale Materials for Solar Hydrogen Production.

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

Prezhdo, Oleg V.

2012-03-22

Funded by the DOE grant (i) we continued to study and analyze the atomistic detail of the electron transfer (ET) across the chromophore-TiO2 interface in Gratzel cell systems for solar hydrogen production. (ii) We extensively investigated the nature of photoexcited states and excited state dynamics in semiconductor quantum dots (QD) designed for photovoltaic applications. (iii) We continued a newly initiated research direction focusing on excited state properties and electron-phonon interactions in nanoscale carbon materials. Over the past year, the results of the DOE funded research were summarized in 3 review articles. 12 original manuscripts were written. The research results weremore » reported in 28 invited talks at conferences and university seminars. 20 invitations were accepted for talks in the near future. 2 symposia at national and international meetings have being organized this year on topics closely related to the DOE funded project, and 2 more symposia have been planned for the near future. We summarized the insights into photoinduced dynamics of semiconductor QDs, obtained from our time-domain ab initio studies. QDs exhibit both molecular and bulk properties. Unlike either bulk or molecular materials, QD properties can be modified continuously by changing QD shape and size. However, the chemical and physical properties of molecular and bulk materials often contradict each other, which can lead to differing viewpoints about the behavior of QDs. For example, the molecular view suggests strong electron-hole and charge-phonon interactions, as well as slow energy relaxation due to mismatch between electronic energy gaps and phonon frequencies. In contrast, the bulk view advocates that the kinetic energy of quantum confinement is greater than electron-hole interactions, that charge-phonon coupling is weak, and that the relaxation through quasi-continuous bands is rapid. By synthesizing the bulk and molecular viewpoints, we clarified the controversies and provided a unified atomistic picture of the nature and dynamics of photoexcited states in semiconductor QDs. We also summarized our recent findings about the photoinduced electron dynamics at the chromophore-semiconductor interfaces from a time-domain ab initio perspective. The interface provides the foundation for a new, promising type of solar cell and presents a fundamentally important case study for several fields, including photo-, electro- and analytical chemistries, molecular electronics, and photography. Further, the interface offers a classic example of an interaction between an organic molecular species and an inorganic bulk material. Scientists employ different concepts and terminologies to describe molecular and solid states of matter, and these differences make it difficult to describe the interface with a single model. At the basic atomistic level of description, however, this challenge can be largely overcome. Recent advances in non-adiabatic molecular dynamics and time-domain density functional theory have created a unique opportunity for simulating the ultrafast, photoinduced processes on a computer very similar to the way that they occur in nature. These state-of-the-art theoretical tools offered a comprehensive picture of a variety of electron transfer processes that occur at the interface, including electron injection from the chromophore to the semiconductor, electron relaxation and delocalization inside the semiconductor, back-transfer of the electron to the chromophore and to the electrolyte, and regeneration of the neutral chromophore by the electrolyte. The ab initio time-domain modeling is particularly valuable for understanding these dynamic features of the ultrafast electron transfer processes, which cannot be represented by a simple rate description. We demonstrated using symmetry adapted cluster theory with configuration interaction (SAC-CI) that charging of small PbSe nanocrystals (NCs) greatly modifies their electronic states and optical excitations. Conduction and valence band transitions that are not available in neutral NCs dominate low energy electronic excitations and show weak optical activity. At higher energies these transitions mix with both single excitons (SEs) and multiple excitons (MEs) associated with transitions across the band-gap. As a result, both SEs and MEs are significantly blue-shifted, and ME generation is drastically hampered. The overall contribution of MEs to the electronic excitations of the charged NCs is small even at very high energies. The calculations supported the recent view that the observed strong dependence of the ME yields on the experimental conditions is likely due to the effects of NC charging. The electron-hole excitonic nature of high energy states was investigated in neutral and charged Si clusters, motivated by the ME generation (MEG) process that is highly debated in photovoltaic literature.« less

Electrodynamics of Lipid Membrane Interactions in the Presence of Zwitterionic Buffers

PubMed Central

Koerner, Megan M.; Palacio, Luis A.; Wright, Johnnie W.; Schweitzer, Kelly S.; Ray, Bruce D.; Petrache, Horia I.

2011-01-01

Due to thermal motion and molecular polarizability, electrical interactions in biological systems have a dynamic character. Zwitterions are dipolar molecules that typically are highly polarizable and exhibit both a positive and a negative charge depending on the pH of the solution. We use multilamellar structures of common lipids to identify and quantify the effects of zwitterionic buffers that go beyond the control of pH. We use the fact that the repeat spacing of multilamellar lipid bilayers is a sensitive and accurate indicator of the force balance between membranes. We show that common buffers can in fact charge up neutral membranes. However, this electrostatic effect is not immediately recognized because of the concomitant modification of dispersion (van der Waals) forces. We show that although surface charging can be weak, electrostatic forces are significant even at large distances because of reduced ionic screening and reduced van der Waals attraction. The zwitterionic interactions that we identify are expected to be relevant for interfacial biological processes involving lipid bilayers, and for a wide range of biomaterials, including amino acids, detergents, and pharmaceutical drugs. An appreciation of zwitterionic electrodynamic character can lead to a better understanding of molecular interactions in biological systems and in soft materials in general. PMID:21767488

Evidences of Changes in Surface Electrostatic Charge Distribution during Stabilization of HPV16 Virus-Like Particles

PubMed Central

Vega, Juan F.; Vicente-Alique, Ernesto; Núñez-Ramírez, Rafael; Wang, Yang; Martínez-Salazar, Javier

2016-01-01

The stabilization of human papillomavirus type 16 virus-like particles has been examined by means of different techniques including dynamic and static light scattering, transmission electron microscopy and electrophoretic mobility. All these techniques provide different and often complementary perspectives about the aggregation process and generation of stabilized virus-like particles after a period of time of 48 hours at a temperature of 298 K. Interestingly, static light scattering results point towards a clear colloidal instability in the initial systems, as suggested by a negative value of the second virial coefficient. This is likely related to small repulsive electrostatic interactions among the particles, and in agreement with relatively small absolute values of the electrophoretic mobility and, hence, of the net surface charges. At this initial stage the small repulsive interactions are not able to compensate binding interactions, which tend to aggregate the particles. As time proceeds, an increase of the size of the particles is accompanied by strong increases, in absolute values, of the electrophoretic mobility and net surface charge, suggesting enhanced repulsive electrostatic interactions and, consequently, a stabilized colloidal system. These results show that electrophoretic mobility is a useful methodology that can be applied to screen the stabilization factors for virus-like particles during vaccine development. PMID:26885635

Inelastic neutron scattering and molecular simulation of the dynamics of interlayer water in smectite clay minerals

DOE PAGES

Cygan, Randall T.; Daemen, Luke L.; Ilgen, Anastasia G.; ...

2015-11-16

The study of mineral–water interfaces is of great importance to a variety of applications including oil and gas extraction, gas subsurface storage, environmental contaminant treatment, and nuclear waste repositories. Understanding the fundamentals of that interface is key to the success of those applications. Confinement of water in the interlayer of smectite clay minerals provides a unique environment to examine the interactions among water molecules, interlayer cations, and clay mineral surfaces. Smectite minerals are characterized by a relatively low layer charge that allows the clay to swell with increasing water content. Montmorillonite and beidellite varieties of smectite were investigated to comparemore » the impact of the location of layer charge on the interlayer structure and dynamics. Inelastic neutron scattering of hydrated and dehydrated cation-exchanged smectites was used to probe the dynamics of the interlayer water (200–900 cm –1 spectral region) and identify the shift in the librational edge as a function of the interlayer cation. Molecular dynamics simulations of equivalent phases and power spectra, derived from the resulting molecular trajectories, indicate a general shift in the librational behavior with interlayer cation that is generally consistent with the neutron scattering results for the monolayer hydrates. Both neutron scattering and power spectra exhibit librational structures affected by the location of layer charge and by the charge of the interlayer cation. Furthermore, divalent cations (Ba 2+ and Mg 2+) characterized by large hydration enthalpies typically exhibit multiple broad librational peaks compared to monovalent cations (Cs + and Na +), which have relatively small hydration enthalpies.« less

Understanding the influence of solvent field and fluctuations on the stability of photo-induced charge-separated state in molecular triad

NASA Astrophysics Data System (ADS)

Balamurugan, D.; Aquino, Adelia; Lischka, Hans; Dios, Francis; Flores, Lionel; Cheung, Margaret

2013-03-01

Molecular triad composed of fullerene, porphyrin, and carotene is an artificial analogue of natural photosynthetic system and is considered for applications in solar energy conversion because of its ability to produce long-lived photo-induced charge separated state. The goal of the present multiscale simulation is to understand how the stability of photo-induced charge-separated state in molecular triad is influenced by a polar organic solvent, namely tetrahydrofuran (THF). The multiscale approach is based on combined quantum, classical molecular dynamics, and statistical physics calculations. The quantum chemical calculations were performed on the triad using the second order algebraic diagrammatic perturbation and time-dependent density functional theory. Molecular dynamics simulations were performed on triad in a box of THF solvent with the replica exchange method. The two methods on different length and time scales are bridged through an important sampling technique. We have analyzed the free energy landscape, structural fluctuations, and the long- range electrostatic interactions between triad and solvent molecules. The results suggest that the polarity and re-organization of the solvent is critical in stabilization of charge-separated state in triad. Supported by DOE (DE-FG02-10ER16175)

Ion size effects on the electrokinetics of spherical particles in salt-free concentrated suspensions

NASA Astrophysics Data System (ADS)

Roa, Rafael; Carrique, Felix; Ruiz-Reina, Emilio

2012-02-01

In this work we study the influence of the counterion size on the electrophoretic mobility and on the dynamic mobility of a suspended spherical particle in a salt-free concentrated colloidal suspension. Salt-free suspensions contain charged particles and the added counterions that counterbalance their surface charge. A spherical cell model approach is used to take into account particle-particle electro-hydrodynamic interactions in concentrated suspensions. The finite size of the counterions is considered including an entropic contribution, related with the excluded volume of the ions, in the free energy of the suspension, giving rise to a modified counterion concentration profile. We are interested in studying the linear response of the system to an electric field, thus we solve the different electrokinetic equations by using a linear perturbation scheme. We find that the ionic size effect is quite important for moderate to high particles charges at a given particle volume fraction. In addition for such particle surface charges, both the electrophoretic mobility and the dynamic mobility suffer more important changes the larger the particle volume fraction for each ion size. The latter effects are more relevant the larger the ionic size.

Liouville master equation for multi-electron dynamics during ion-surface interactions

NASA Astrophysics Data System (ADS)

Wirtz, L.; Reinhold, C. O.; Lemell, C.; Burgdorfer, J.

2003-05-01

We present a simulation of the neutralization of highly charged ions in front of a LiF(100) surface including the close-collision regime above the surface. Our approach employs a Monte-Carlo solution of the Liouville master equation for the joint probability density of the ionic motion and the electronic population of the projectile and the target surface. It includes single as well as double particle-hole (de)excitation processes and incorporates electron correlation effects through the conditional dynamics of population strings. The input in terms of elementary one- and two-electron transfer rates is determined from CTMC calculations as well as quantum mechanical Auger calculations. For slow projectiles and normal incidence, the ionic motion depends sensitively on the interplay between image acceleration towards the surface and repulsion by an ensemble of positive hole charges in the surface (``trampoline effect"). For Ne10+ ions we find that image acceleration dominates and no collective backscattering high above the surface takes place. For grazing incidence, our simulation delineates the pathways to complete neutralization. In accordance with recent experimental observations, most ions are reflected as neutrals or even as singly charged negative particles, irrespective of the charge state of the incoming ion.

Accumulation of phosphatidylcholine on gut mucosal surface is not dominated by electrostatic interactions.

PubMed

Korytowski, Agatha; Abuillan, Wasim; Amadei, Federico; Makky, Ali; Gumiero, Andrea; Sinning, Irmgard; Gauss, Annika; Stremmel, Wolfgang; Tanaka, Motomu

2017-05-01

The accumulation of phosphatidylcholine (PC) in the intestinal mucus layer is crucial for the protection of colon epithelia from the bacterial attack. It has been reported that the depletion of PC is a distinct feature of ulcerative colitis. Here we addressed the question how PC interacts with its binding proteins, the mucins, which may establish the hydrophobic barrier against colonic microbiota. In the first step, the interactions of dioleoylphosphatidylcholine (DOPC) with two mucin preparations from porcine stomach, have been studied using dynamic light scattering, zeta potential measurement, and Langmuir isotherms, suggesting that mucin binds to the surface of DOPC vesicles. The enthalpy of mucin-PC interaction could be determined by isothermal titration calorimetry. The high affinity to PC found for both mucin types seems reasonable, as they mainly consist of mucin 2, a major constituent of the flowing mucus. Moreover, by the systematic variation of net charges, we concluded that the zwitterionic DOPC has the strongest binding affinity that cannot be explained within the electrostatic interactions between charged molecules. Copyright © 2017 Elsevier B.V. All rights reserved.

The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA

PubMed Central

Law, Michael J.; Linde, Michael E.; Chambers, Eric J.; Oubridge, Chris; Katsamba, Phinikoula S.; Nilsson, Lennart; Haworth, Ian S.; Laird-Offringa, Ite A.

2006-01-01

Previous kinetic investigations of the N-terminal RNA recognition motif (RRM) domain of spliceosomal protein U1A, interacting with its RNA target U1 hairpin II, provided experimental evidence for a ‘lure and lock’ model of binding in which electrostatic interactions first guide the RNA to the protein, and close range interactions then lock the two molecules together. To further investigate the ‘lure’ step, here we examined the electrostatic roles of two sets of positively charged amino acids in U1A that do not make hydrogen bonds to the RNA: Lys20, Lys22 and Lys23 close to the RNA-binding site, and Arg7, Lys60 and Arg70, located on ‘top’ of the RRM domain, away from the RNA. Surface plasmon resonance-based kinetic studies, supplemented with salt dependence experiments and molecular dynamics simulation, indicate that Lys20 predominantly plays a role in association, while nearby residues Lys22 and Lys23 appear to be at least as important for complex stability. In contrast, kinetic analyses of residues away from the RNA indicate that they have a minimal effect on association and stability. Thus, well-positioned positively charged residues can be important for both initial complex formation and complex maintenance, illustrating the multiple roles of electrostatic interactions in protein–RNA complexes. PMID:16407334

Interplay of polyelectrolytes with different adsorbing surfaces

NASA Astrophysics Data System (ADS)

Xie, Feng

We study the adsorption of polyelectrolytes from solution onto different adsorbing surfaces, focusing on the electrostatic interactions. Measurements of the surface excess, fractional ionization of chargeable groups, segmental orientation, and adsorption kinetics were made using Fourier transform infrared spectroscopy in the mode of attenuated total reflection. Different adsorbing surfaces, from single solid surfaces, solid surfaces modified with adsorbed polymer layer, to fluid-like surfaces-biomembranes were adopted. Both atomic force microscopy (AFM) and fluorescent techniques were employed to investigate the fluid-like surfaces in the absence and in the presence of polyelectrolytes. The work focuses on three primary issues: (i) the charge regulation of weak polyelectrolytes on both homogeneous and heterogeneous surfaces, (ii) the dynamics of adsorption when the surface possesses reciprocal mobility, i.e., biomembrane surface, and (iii) the structural and dynamical properties of the fluid-like surfaces interacting with polyelectrolytes. We find that the ionization of chargeable groups in weak polyelectrolytes is controlled by the charge balance between the adsorbates and the surfaces. A new interpretation of ionization in the adsorbed layer provides a new insight into the fundamental problem of whether ions of opposite charge associate or remain separate. Bjerrum length is found to be a criterion for the onset of surface ionization suppression, which helps to predict and control the conformation transition of proteins. In addition to the effect of different surfaces on the adsorption behavior of polyelectrolytes, we also focused on the response of the surfaces to the adsorbates. Chains that encountered sparsely-covered surfaces spread to maximize the number of segment-surface contacts at rates independent of the molar mass. Surface reconstruction rather than molar mass of the adsorbing molecules appeared to determine the rate of spreading. This contrasts starkly with traditional polymer adsorption onto surfaces whose structure is "frozen" and unresponsive. Finally, preliminary studies on dynamical properties of biomembrane surfaces interacting with polyelectrolytes are presented, using fluorescence correlation spectroscopy (FCS). The significance is to characterize domains induced by polyelectrolyte binding.

Nonlinear evolution and final fate of (charged) superradiant instability

NASA Astrophysics Data System (ADS)

Green, Stephen; Bosch, Pablo; Lehner, Luis

2016-03-01

We describe the full nonlinear development of the superradiant instability for a charged massless scalar field, coupled to general relativity and electromagnetism, in the vicinity of a Reissner-Nordstrom-AdS black hole. The presence of the negative cosmological constant provides a natural context for considering perfectly reflecting boundary conditions and studying the dynamics as the scalar field interacts repeateadly with the black hole. At early times, small superradiant perturbations grow as expected from linearized studies. Backreaction then causes the black hole to lose charge and mass until the perturbation becomes nonsuperradiant, with the final state described by a stable hairy black hole. For large gauge coupling, the instability extracts a large amount of charge per unit mass, resulting in greater entropy increase. We discuss the implications of the observed behavior for the general problem of superradiance in black hole spacetimes.

Effect of Valence of Counterions on the Structure of Charged Membranes, a Computer Simulation Study

NASA Astrophysics Data System (ADS)

Qiao, Baofu; Olvera de La Cruz, Monica

2012-02-01

Phospholipids have been investigated for a long period, due to its ability of self-assembling into bilayer structures which resemble biological membranes. But most of the studies have been limited on the neutral phosphatidylcholine based lipids. The understanding of charged membranes (e.g., phosphatidylserine) is very limited due to the repulsion between the charged groups on lipids. In the present work, we investigated the effect of different counter-ions on the structures of charged membranes formed by 1,2-dilauroyl-sn-glycoro-3-phospho-L-serine. Three kinds of counterions were investigated, from monovalent, to divalent, to trivalent ions. Molecular dynamics simulations were performed at all-atom level. We have calculated the area per lipid. And the interaction between counterions and COO^- groups was found to dominate over that between counterions and PO4^- groups.

NERNST Vortex Potential Of A Genetic Oscillator

NASA Astrophysics Data System (ADS)

Garnett, Merrill; Jones, Bill

The vortex is a dynamic spiral. In molecular biology these have not been reported. We report a vortex compound, with oscillating energy. Toroglobulin (1) transfers 416 mv. to histone. This histone reductase enriches charge in the chromosome in spool proteins around which DNA is coiled. Controlling chromosome charge introduces energetics to gene compression. Impedance spectroscopy shows symmetric oscillations. Specific frequencies show amplitude increases. The Mott-Schottky scans show frequency bands. Histone bands are electronically reduced by Toroglobulin by 416 mv. The Nernst potentials of chemical systems correlate electric gradient to concentration gradients of charged particles. Charge polarization refers to laminar alignment. In formation of the Toroglobulin Ginzburg-Landau vortex, the polarization follows filament curvatures which spiral back on themselves. The magnetic dipoles achieve interactive resonance (esr). This spiral resonator with magnetic interfaces produces the measured Nernst potential.

Nonlinear dynamics of resonant electrons interacting with coherent Langmuir waves

NASA Astrophysics Data System (ADS)

Tobita, Miwa; Omura, Yoshiharu

2018-03-01

We study the nonlinear dynamics of resonant particles interacting with coherent waves in space plasmas. Magnetospheric plasma waves such as whistler-mode chorus, electromagnetic ion cyclotron waves, and hiss emissions contain coherent wave structures with various discrete frequencies. Although these waves are electromagnetic, their interaction with resonant particles can be approximated by equations of motion for a charged particle in a one-dimensional electrostatic wave. The equations are expressed in the form of nonlinear pendulum equations. We perform test particle simulations of electrons in an electrostatic model with Langmuir waves and a non-oscillatory electric field. We solve equations of motion and study the dynamics of particles with different values of inhomogeneity factor S defined as a ratio of the non-oscillatory electric field intensity to the wave amplitude. The simulation results demonstrate deceleration/acceleration, thermalization, and trapping of particles through resonance with a single wave, two waves, and multiple waves. For two-wave and multiple-wave cases, we describe the wave-particle interaction as either coherent or incoherent based on the probability of nonlinear trapping.

A numerical study of neutral-plasma interaction in magnetically confined plasmas

NASA Astrophysics Data System (ADS)

Taheri, S.; Shumlak, U.; King, J. R.

2017-10-01

Interactions between plasma and neutral species can have a large effect on the dynamic behavior of magnetically confined plasma devices, such as the edge region of tokamaks and the plasma formation of Z-pinches. The presence of neutrals can affect the stability of the pinch and change the dynamics of the pinch collapse, and they can lead to deposition of high energy particles on the first wall. However, plasma-neutral interactions can also have beneficial effects such as quenching the disruptions in tokamaks. In this research a reacting plasma-neutral model, which combines a magnetohydrodynamic (MHD) plasma model with a gas dynamic neutral fluid model, is used to study the interaction between plasma and neutral gas. Incorporating this model into NIMROD allows the study of electron-impact ionization, radiative recombination, and resonant charge-exchange in plasma-neutral systems. An accelerated plasma moving through a neutral gas background is modeled in both a parallel plate and a coaxial electrode configuration to explore the effect of neutral gas in pinch-like devices. This work is supported by a Grant from US DOE.

Tracking gas-liquid coexistence in fluids of charged soft dumbbells.

PubMed

Braun, Heiko; Hentschke, Reinhard

2009-10-01

The existence of gas-liquid coexistence in dipolar fluids with no other contribution to attractive interaction than dipole-dipole interaction is a basic and open question in the theory of fluids. Recent Monte Carlo work by Camp and co-workers indicates that a fluid of charged hard dumbbells does exhibit gas-liquid (g-l) coexistence. This system has the potential to answer the above fundamental question because the charge-to-charge separation, d , on the dumbbells may be reduced to, at least in principle, yield the dipolar fluid limit. Using the molecular-dynamics technique we present simulation results for the g-l critical point of charged soft dumbbells at fixed dipole moment as function of d . We do find a g-l critical point at finite temperature even at the smallest d value (10;{-4}) . Reversible aggregation appears to play less a role than in related model systems as d becomes small. Consequently attempts to interpret the simulation results using either an extension of Flory's lattice theory for polymer systems, which includes reversible assembly of monomers into chains, or the defect model for reversible networks proposed by Tlusty and Safran are not successful. The overall best qualitative interpretation of the critical parameters is obtained by considering the dumbbells as dipoles immersed in a continuum dielectric.

Brownian dynamics simulations of simplified cytochrome c molecules in the presence of a charged surface

NASA Astrophysics Data System (ADS)

Gorba, C.; Geyer, T.; Helms, V.

2004-07-01

Simulations were performed for up to 150 simplified spherical horse heart cytochrome c molecules in the presence of a charged surface, which serves as an approximate model for a lipid membrane. Screened electrostatic and short-ranged attractive as well as repulsive van der Waals forces for interparticle and particle-membrane interactions are utilized in the simulations. At a distance from the membrane, where particle-membrane interactions are negligible, the simulation is coupled to a noninteraction continuum analogous to a heat bath [Geyer et al., J. Chem. Phys. 120, 4573 (2004)]. From the particles' density profiles perpendicular to the planar surface binding isotherms are derived and compared to experimental results [Heimburg et al. (1999)]. Using a negatively charged structureless membrane surface a saturation effect was found for relatively large particle concentrations. Since biological membranes often contain membrane proteins, we also studied the influence of additional charges on our model membrane mimicking bacterial reaction centers. We find that the onset of the saturation occurs for much lower concentrations and is sensitive to the detailed implementation. Therefore we suggest that local distortion of membrane planarity (undulation), or lipid demixing, or the presence of charged integral membrane proteins create preferential binding sites on the membrane. Only then do we observe saturation at physiological concentrations.

Glass transition of soft colloids

NASA Astrophysics Data System (ADS)

Philippe, Adrian-Marie; Truzzolillo, Domenico; Galvan-Myoshi, Julian; Dieudonné-George, Philippe; Trappe, Véronique; Berthier, Ludovic; Cipelletti, Luca

2018-04-01

We explore the glassy dynamics of soft colloids using microgels and charged particles interacting by steric and screened Coulomb interactions, respectively. In the supercooled regime, the structural relaxation time τα of both systems grows steeply with volume fraction, reminiscent of the behavior of colloidal hard spheres. Computer simulations confirm that the growth of τα on approaching the glass transition is independent of particle softness. By contrast, softness becomes relevant at very large packing fractions when the system falls out of equilibrium. In this nonequilibrium regime, τα depends surprisingly weakly on packing fraction, and time correlation functions exhibit a compressed exponential decay consistent with stress-driven relaxation. The transition to this novel regime coincides with the onset of an anomalous decrease in local order with increasing density typical of ultrasoft systems. We propose that these peculiar dynamics results from the combination of the nonequilibrium aging dynamics expected in the glassy state and the tendency of colloids interacting through soft potentials to refluidize at high packing fractions.

Interaction of N-vortex structures in a continuum, including atmosphere, hydrosphere and plasma

NASA Astrophysics Data System (ADS)

Belashov, Vasily Yu.

2017-10-01

The results of analysis and numerical simulation of evolution and interaction of the N-vortex structures of various configuration and different vorticities in the continuum including atmosphere, hydrosphere and plasma are presented. It is found that in dependence on initial conditions the regimes of weak interaction with quasi-stationary evolution and active interaction with the "phase intermixing", when the evolution can lead to formation of complex forms of vorticity regions, are realized in the N-vortex systems. For the 2-vortex interaction the generalized critical parameter determining qualitative character of interaction of vortices is introduced. It is shown that for given initial conditions its value divides modes of active interaction and quasi-stationary evolution. The results of simulation of evolution and interaction of the two-dimensional and three-dimensional vortex structures, including such phenomena as dynamics of the atmospheric synoptic vortices of cyclonic types and tornado, hydrodynamic 4-vortex interaction and also interaction in the systems of a type of "hydrodynamic vortex - dust particles" are presented. The applications of undertaken approach to the problems of such plasma systems as streams of charged particles in a uniform magnetic field B and plasma clouds in the ionosphere are considered. It is shown that the results obtained have obvious applications in studies of the dynamics of the vortex structures dynamics in atmosphere, hydrosphere and plasma.

Investigation of the charge-orbital ordering mechanism in single-layered Pr0.5Ca1.5MnO4

NASA Astrophysics Data System (ADS)

Rangkuti, C. N.; Majidi, M. A.

2018-04-01

Motivated by the experimental study of half-doped single-layered Pr0.5Ca1.5MnO4 showing charge, orbital, and spin orderings [1], we propose a model to theoretically study the system to explain such ordering phenomena. The ground state electron configuration reveals that the charges form a checkerboard pattern with alternating Mn3+/Mn4+ sites, while the orbitals are aligned in zigzag chains [1, 2]. We calculate the ground state energy of this system to find the most preferable configuration by comparing three types of configurations (charge-unordered, charge-ordered, and charge-orbital-ordered states). The calculations are based on a tight-binding model representing effective electron hoppings among Mn ions in MnO2-plane. We take into account the horizontally- and vertically-oriented orbital and spin degrees of freedom at Mn sites. We assume that the hopping integral values depend on the relative orientation between the corresponding orbitals of adjacent Mn ions. The interaction terms we incorporate into our effective Hamiltonian include inter-orbital, intra-orbital Hubbard repulsions, and Jahn-Teller distortion [2]. We absorb the exchange interaction between spins into local self-energy that we calculate within dynamical mean field algorithm [2]. Within our model we show a circumstance in which the charge-orbital ordered configuration has the lowest energy, consistent with the ground state ordering revealed by the experimental data.

Explicit ions/implicit water generalized Born model for nucleic acids

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

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

Ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model, and utilizes a non-standard approach to defining the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes – disconnected dielectric boundary around the solute-ion or ion-ion pairs. Fully analytical description of all energymore » components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force (PMF) for Na+-Cl− ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of DNA duplex; these differences in the counterion binding patters were shown earlier to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with homopolymeric poly(dA·dT) DNA duplex with modified (de-methylated) and native Thymine bases are used to explore the physics behind CoHex-Thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-Thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range, and may be important to consider in the context of methylation effects on DNA condensation.« less

Explicit ions/implicit water generalized Born model for nucleic acids

NASA Astrophysics Data System (ADS)

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

2018-05-01

The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes—disconnected dielectric boundary around the solute-ion or ion-ion pairs. A fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na+-Cl- ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of the RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of the DNA duplex; these differences in the counterion binding patters were earlier shown to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with the homopolymeric poly(dA.dT) DNA duplex with modified (de-methylated) and native thymine bases are used to explore the physics behind CoHex-thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range and may be important to consider in the context of methylation effects on DNA condensation.

Interactions between ionic liquid surfactant [C12mim]Br and DNA in dilute brine.

PubMed

He, Yunfei; Shang, Yazhuo; Liu, Zhenhai; Shao, Shuang; Liu, Honglai; Hu, Ying

2013-01-01

Interactions between ionic liquid surfactant [C(12)mim]Br and DNA in dilute brine were investigated in terms of various experimental methods and molecular dynamics (MD) simulation. It was shown that the aggregation of [C(12)mim]Br on DNA chains is motivated not only by electrostatic attractions between DNA phosphate groups and [C(12)mim]Br headgroups but also by hydrophobic interactions among [C(12)mim]Br alkyl chains. Isothermal titration calorimetry analysis indicated that the [C(12)mim]Br aggregation in the presence and absence of DNA are both thermodynamically favored driven by enthalpy and entropy. DNA undergoes size transition and conformational change induced by [C(12)mim]Br, and the charges of DNA are neutralized by the added [C(12)mim]Br. Various microstructures were observed such as DNA with loose coil conformation in nature state, necklace-like structures, and compact spherical aggregates. MD simulation showed that the polyelectrolyte collapses upon the addition of oppositely charged surfactants and the aggregation of surfactants around the polyelectrolyte was reaffirmed. The simulation predicted the gradual neutralization of the negatively charged polyelectrolyte by the surfactant, consistent with the experimental results. Copyright © 2012 Elsevier B.V. All rights reserved.

A new force field including charge directionality for TMAO in aqueous solution

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

Usui, Kota; Nagata, Yuki, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de; Hunger, Johannes

We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (O{sub TMAO}) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O{sub TMAO} to mimic the O{sub TMAO} lone pairs and we migrate the negative charge on the O{sub TMAO} to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasingmore » TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.« less

Non-Maxwellian and magnetic field effects in complex plasma wakes★

NASA Astrophysics Data System (ADS)

Ludwig, Patrick; Jung, Hendrik; Kählert, Hanno; Joost, Jan-Philip; Greiner, Franko; Moldabekov, Zhandos; Carstensen, Jan; Sundar, Sita; Bonitz, Michael; Piel, Alexander

2018-05-01

In a streaming plasma, negatively charged dust particles create complex charge distributions on the downstream side of the particle, which are responsible for attractive forces between the like-charged particles. This wake phenomenon is studied by means of refined linear response theory and molecular dynamics simulations as well as in experiments. Particular attention is paid to non-Maxwellian velocity distributions that are found in the plasma sheath and to situations with strong magnetic fields, which are becoming increasingly important. Non-Maxwellian distributions and strong magnetic fields result in a substantial damping of the oscillatory wake potential. The interaction force in particle pairs is explored with the phase-resolved resonance method, which demonstrates the non-reciprocity of the interparticle forces in unmagnetized and magnetized systems.

Lattice dynamics of solid N2 with an ab initio intermolecular potential

NASA Astrophysics Data System (ADS)

Luty, T.; van der Avoird, A.; Berns, R. M.

1980-11-01

We have performed harmonic and self-consistent phonon lattice dynamics calculations for α and γ N2 crystals using an intermolecular potential from ab initio calculations. This potential contains electrostatic (multipole) interactions, up to all R-9 terms inclusive, anisotropic dispersion interactions up to all R-10 terms inclusive, and anisotropic overlap interactions caused by charge penetration and exchange between the molecules. The lattice constants, cohesion energy, the frequencies of the translational phonon modes and the Grüneisen parameters for the librational modes are in good agreement with experimental values, confirming the quality of the potential. The frequencies of the librational modes and those of the mixed modes are less well reproduced, especially at temperatures near the α-β phase transition. Probably, the self-consistent phonon method used does not fully account for the anharmonicity in the librations.

Study of polycation effects on erythrocyte agglutination mediated by anti-glycophorins using microscopic image digital analysis

NASA Astrophysics Data System (ADS)

Riquelme, B.; Dumas, D.; Relancio, F.; Fontana, A.; Alessi, A.; Foresto, P.; Grandfils, C.; Stoltz, J.; Valverde, J.

2006-04-01

The aim of this work was to study synthetic polycation effects on erythrocyte agglutination mediated by anti-glycophorin using image digital analysis. Polycations are oligomers or polymers of natural or synthetic origin, which bear a great number of positive charges at pH 7.4. Several of these polycations are nowadays used in clinic for human and veterinary purposes. New applications of polycations to the development of new drug delivery systems are investigated, in order to promote the drug absorption through the gastro-intestinal and blood brain barriers. However, up to now, there are no clear relationships between macromolecular features of polycations (molecular weight, mean charge density, charge repartition, etc.) and their interactions with blood elements (which bear superficial negative charges). The interaction on the red blood cell membrane with synthetic polycations having well-controlled macromolecular features and functionalized with pendent polyethylene glycol segments was investigated. The alterations over stationary and dynamic viscoelastic properties of erythrocyte membranes were analyzed through laser diffractometry. Image digital analysis was used to study erythrocyte agglutination mediated by anti-glycophorin. Results show different reactivities of the polycations on the erythrocyte membrane. These findings could provide more information about the mechanisms of polycation interaction on erythrocyte membranes. We consider that this work could provide useful tools to understand and improve the haemocompatibility of polycations and enlarge their potential in clinic.

Counterintuitive cooperative endocytosis of like-charged nanoparticles in cellular internalization: computer simulation and experiment

NASA Astrophysics Data System (ADS)

Li, Ye; Yuan, Bing; Yang, Kai; Zhang, Xianren; Yan, Bing; Cao, Dapeng

2017-02-01

The nanoparticles (NPs) functionalized with charged ligands are of particular significance due to their potential drug/gene delivery and biomedical applications. However, the molecular mechanism of endocytosis of the charged NPs by cells, especially the effect of the NP-NP and NP-biomembrane interactions on the internalization pathways is still poorly understood. In this work, we systematically investigate the internalization behaviors of the positively charged NPs by combining experiment technology and dissipative particle dynamics (DPD) simulation. We experimentally find an interesting but highly counterintuitive phenomenon, i.e. the multiple positively charged NPs prefer to enter cells cooperatively although the like-charged NPs have obvious electrostatic repulsion. Furthermore, we adopt the DPD simulation to confirm the experimental findings, and reveal that the mechanism of the cooperative endocytosis between like-charged NPs is definitely caused by the interplay of particle size, the charged ligand density on particle surface and local concentration of NPs. Importantly, we not only observe the normal cooperative endocytosis of like-charged NPs in cell biomembrane like neutral NP case, but also predict the ‘bud’ cooperative endocytosis of like-charged NPs which is absence in the neutral NP case. The results indicate that electrostatic repulsion between the positively charged nanoparticles plays an important role in the ‘bud’ cooperative endocytosis of like-charged NPs.

Nanostructure of propylammonium nitrate in the presence of poly(ethylene oxide) and halide salts

NASA Astrophysics Data System (ADS)

Stefanovic, Ryan; Webber, Grant B.; Page, Alister J.

2018-05-01

Nanoscale structure of protic ionic liquids is critical to their utility as molecular electrochemical solvents since it determines the capacity to dissolve salts and polymers such as poly(ethylene oxide) (PEO). Here we use quantum chemical molecular dynamics simulations to investigate the impact of dissolved halide anions on the nanostructure of an archetypal nanostructured protic ionic liquid, propylammonium nitrate (PAN), and how this impacts the solvation of a model PEO polymer. At the molecular level, PAN is nanostructured, consisting of charged/polar and uncharged/nonpolar domains. The charged domain consists of the cation/anion charge groups, and is formed by their electrostatic interaction. This domain solvophobically excludes the propyl chains on the cation, which form a distinct, self-assembled nonpolar domain within the liquid. Our simulations demonstrate that the addition of Cl- and Br- anions to PAN disrupts the structure within the PAN charged domain due to competition between nitrate and halide anions for the ammonium charge centre. This disruption increases with halide concentration (up to 10 mol. %). However, at these concentrations, halide addition has little effect on the structure of the PAN nonpolar domain. Addition of PEO to pure PAN also disrupts the structure within the charged domain of the liquid due to hydrogen bonding between the charge groups and the terminal PEO hydroxyl groups. There is little other association between the PEO structure and the surrounding ionic liquid solvent, with strong PEO self-interaction yielding a compact, coiled polymer morphology. Halide addition results in greater association between the ionic liquid charge centres and the ethylene oxide components of the PEO structure, resulting in reduced conformational flexibility, compared to that observed in pure PAN. Similarly, PEO self-interactions increase in the presence of Cl- and Br- anions, compared to PAN, indicating that the addition of halide salts to PAN decreases its utility as a molecular solvent for polymers such as PEO.

A New Kinetic Simulation Model with Self-Consistent Calculation of Regolith Layer Charging for Moon-Plasma Interactions

NASA Astrophysics Data System (ADS)

Han, D.; Wang, J.

2015-12-01

The moon-plasma interactions and the resulting surface charging have been subjects of extensive recent investigations. While many particle-in-cell (PIC) based simulation models have been developed, all existing PIC simulation models treat the surface of the Moon as a boundary condition to the plasma flow. In such models, the surface of the Moon is typically limited to simple geometry configurations, the surface floating potential is calculated from a simplified current balance condition, and the electric field inside the regolith layer cannot be resolved. This paper presents a new full particle PIC model to simulate local scale plasma flow and surface charging. A major feature of this new model is that the surface is treated as an "interface" between two mediums rather than a boundary, and the simulation domain includes not only the plasma but also the regolith layer and the bedrock underneath it. There are no limitations on the surface shape. An immersed-finite-element field solver is applied which calculates the regolith surface floating potential and the electric field inside the regolith layer directly from local charge deposition. The material property of the regolith layer is also explicitly included in simulation. This new model is capable of providing a self-consistent solution to the plasma flow field, lunar surface charging, the electric field inside the regolith layer and the bedrock for realistic surface terrain. This new model is applied to simulate lunar surface-plasma interactions and surface charging under various ambient plasma conditions. The focus is on the lunar terminator region, where the combined effects from the low sun elevation angle and the localized plasma wake generated by plasma flow over a rugged terrain can generate strongly differentially charged surfaces and complex dust dynamics. We discuss the effects of the regolith properties and regolith layer charging on the plasma flow field, dust levitation, and dust transport.

Electric Double-Layer Structure in Primitive Model Electrolytes. Comparing Molecular Dynamics with Local-Density Approximations

DOE PAGES

Giera, Brian; Lawrence Livermore National Lab.; Henson, Neil; ...

2015-02-27

We evaluate the accuracy of local-density approximations (LDAs) using explicit molecular dynamics simulations of binary electrolytes comprised of equisized ions in an implicit solvent. The Bikerman LDA, which considers ions to occupy a lattice, poorly captures excluded volume interactions between primitive model ions. Instead, LDAs based on the Carnahan–Starling (CS) hard-sphere equation of state capture simulated values of ideal and excess chemical potential profiles extremely well, as is the relationship between surface charge density and electrostatic potential. Excellent agreement between the EDL capacitances predicted by CS-LDAs and computed in molecular simulations is found even in systems where ion correlations drivemore » strong density and free charge oscillations within the EDL, despite the inability of LDAs to capture the oscillations in the detailed EDL profiles.« less

Oppositely charged colloids out of equilibrium

NASA Astrophysics Data System (ADS)

Vissers, T.

2010-11-01

Colloids are particles with a size in the range of a few nanometers up to several micrometers. Similar to atomic and molecular systems, they can form gases, liquids, solids, gels and glasses. Colloids can be used as model systems because, unlike molecules, they are sufficiently large to be studied directly with light microscopy and move sufficiently slow to study their dynamics. In this thesis, we study binary systems of polymethylmethacrylate (PMMA) colloidal particles suspended in low-polar solvent mixtures. Since the ions can still partially dissociate, a surface charge builds up which causes electrostatic interactions between the colloids. By carefully tuning the conditions inside the suspension, we make two kinds of particles oppositely charged. To study our samples, we use Confocal Laser Scanning Microscopy (CLSM). The positively and negatively charged particles can be distinguished by a different fluorescent dye. Colloids constantly experience a random motion resulting from random kicks of surrounding solvent molecules. When the attractions between the oppositely charged particles are weak, the particles can attach and detach many times and explore a lot of possible configurations and the system can reach thermodynamic equilibrium. For example, colloidal ‘ionic’ crystals consisting of thousands to millions of particles can form under the right conditions. When the attractions are strong, the system can become kinetically trapped inside a gel-like state. We observe that when the interactions change again, crystals can even emerge again from this gel-like phase. By using local order parameters, we quantitatively study the crystallization of colloidal particles and identify growth defects inside the crystals. We also study the effect of gravity on the growth of ionic crystals by using a rotating stage. We find that sedimentation can completely inhibit crystal growth and plays an important role in crystallization from the gel-like state. The surface potential and charge are studied by electrophoresis. Here, the velocity of the particles is measured while they are moving in an electric field. Using our real-space CLSM setup, we find that for a single-component system, the charge on the particles decreases with increasing volume fraction. Apart from structures that oppositely charged particles form close to thermodynamic equilibrium, we also study pattern formation when the system is driven out of equilibrium by an electric field. When oppositely charged particles are driven in opposite directions, the collisions between them cause particle of the same kind to form lanes. By combining our CLSM experiments with Brownian dynamics computer simulations, we study the structure and the dynamics of the suspension on the single-particle level. We find that the number of particles in a lane increases continuously with the field strength. By studying the dynamics and fluctuations parallel and perpendicular to the electric field direction, we identify the key mechanism of lane-formation. We show that pattern formation can easily become more complicated when we introduce alternating current (AC) fields. In addition to the formation of lanes parallel to the field-axis, bands of like-charged particles can form perpendicular to it. When the particles are sufficiently mobile, the system can be remixed again by changing the frequency. When AC-fields with higher field strengths are used, we show that complex patterns, including rotating instabilities, can emerge. The results in this thesis yield fundamental insight in electrophoresis, crystallization and pattern formation when systems are driven out of equilibrium. The results on lane- and band-formation can be relevant for the design of electronic ink (e-ink), where electrically driven oppositely charged particles are used to change the image on a piece of electronic paper.

Ultrafast non-radiative dynamics of atomically thin MoSe 2

DOE PAGES

Lin, Ming -Fu; Kochat, Vidya; Krishnamoorthy, Aravind; ...

2017-10-17

Non-radiative energy dissipation in photoexcited materials and resulting atomic dynamics provide a promising pathway to induce structural phase transitions in two-dimensional materials. However, these dynamics have not been explored in detail thus far because of incomplete understanding of interaction between the electronic and atomic degrees of freedom, and a lack of direct experimental methods to quantify real-time atomic motion and lattice temperature. Here, we explore the ultrafast conversion of photoenergy to lattice vibrations in a model bi-layered semiconductor, molybdenum diselenide, MoSe 2. Specifically, we characterize sub-picosecond lattice dynamics initiated by the optical excitation of electronic charge carriers in the highmore » electron-hole plasma density regime. Our results focuses on the first ten picosecond dynamics subsequent to photoexcitation before the onset of heat transfer to the substrate, which occurs on a ~100 picosecond time scale. Photoinduced atomic motion is probed by measuring the time dependent Bragg diffraction of a delayed mega-electronvolt femtosecond electron beam. Transient lattice temperatures are characterized through measurement of Bragg peak intensities and calculation of the Debye-Waller factor (DWF). These measurements show a sub-picosecond decay of Bragg diffraction and a correspondingly rapid rise in lattice temperatures. We estimate a high quantum yield for the conversion of excited charge carrier energy to lattice motion under our experimental conditions, indicative of a strong electron-phonon interaction. First principles nonadiabatic quantum molecular dynamics simulations (NAQMD) on electronically excited MoSe 2 bilayers reproduce the observed picosecond-scale increase in lattice temperature and ultrafast conversion of photoenergy to lattice vibrations. Calculation of excited-state phonon dispersion curves suggests that softened vibrational modes in the excited state are involved in efficient and rapid energy transfer between the electronic system and the lattice.« less

Ultrafast non-radiative dynamics of atomically thin MoSe 2

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

Lin, Ming -Fu; Kochat, Vidya; Krishnamoorthy, Aravind

Non-radiative energy dissipation in photoexcited materials and resulting atomic dynamics provide a promising pathway to induce structural phase transitions in two-dimensional materials. However, these dynamics have not been explored in detail thus far because of incomplete understanding of interaction between the electronic and atomic degrees of freedom, and a lack of direct experimental methods to quantify real-time atomic motion and lattice temperature. Here, we explore the ultrafast conversion of photoenergy to lattice vibrations in a model bi-layered semiconductor, molybdenum diselenide, MoSe 2. Specifically, we characterize sub-picosecond lattice dynamics initiated by the optical excitation of electronic charge carriers in the highmore » electron-hole plasma density regime. Our results focuses on the first ten picosecond dynamics subsequent to photoexcitation before the onset of heat transfer to the substrate, which occurs on a ~100 picosecond time scale. Photoinduced atomic motion is probed by measuring the time dependent Bragg diffraction of a delayed mega-electronvolt femtosecond electron beam. Transient lattice temperatures are characterized through measurement of Bragg peak intensities and calculation of the Debye-Waller factor (DWF). These measurements show a sub-picosecond decay of Bragg diffraction and a correspondingly rapid rise in lattice temperatures. We estimate a high quantum yield for the conversion of excited charge carrier energy to lattice motion under our experimental conditions, indicative of a strong electron-phonon interaction. First principles nonadiabatic quantum molecular dynamics simulations (NAQMD) on electronically excited MoSe 2 bilayers reproduce the observed picosecond-scale increase in lattice temperature and ultrafast conversion of photoenergy to lattice vibrations. Calculation of excited-state phonon dispersion curves suggests that softened vibrational modes in the excited state are involved in efficient and rapid energy transfer between the electronic system and the lattice.« less

Charge-dependent conformations and dynamics of pamam dendrimers revealed by neutron scattering and molecular dynamics

NASA Astrophysics Data System (ADS)

Wu, Bin

Neutron scattering and fully atomistic molecular dynamics (MD) are employed to investigate the structural and dynamical properties of polyamidoamine (PAMAM) dendrimers with ethylenediamine (EDA) core under various charge conditions. Regarding to the conformational characteristics, we focus on scrutinizing density profile evolution of PAMAM dendrimers as the molecular charge of dendrimer increases from neutral state to highly charged condition. It should be noted that within the context of small angle neutron scattering (SANS), the dendrimers are composed of hydrocarbon component (dry part) and the penetrating water molecules. Though there have been SANS experiments that studied the charge-dependent structural change of PAMAM dendrimers, their results were limited to the collective behavior of the aforementioned two parts. This study is devoted to deepen the understanding towards the structural responsiveness of intra-molecular polymeric and hydration parts separately through advanced contrast variation SANS data analysis scheme available recently and unravel the governing principles through coupling with MD simulations. Two kinds of acids, namely hydrochloric and sulfuric acids, are utilized to tune the pH condition and hence the molecular charge. As far as the dynamical properties, we target at understanding the underlying mechanism that leads to segmental dynamic enhancement observed from quasielstic neutron scattering (QENS) experiment previously. PAMAM dendrimers have a wealth of potential applications, such as drug delivery agency, energy harvesting medium, and light emitting diodes. More importantly, it is regarded as an ideal system to test many theoretical predictions since dendrimers conjugate both colloid-like globular shape and polymer-like flexible chains. This Ph.D. research addresses two main challenges in studying PAMAM dendrimers. Even though neutron scattering is an ideal tool to study this PAMAM dendrimer solution due to its matching temporal and spatial instrumental scales, understanding experimental results involves extensive and difficult data analysis based on liquid theory and condensed matter physics. Therefore, a model that successfully describes the inter- and intra-dendrimer correlations is crucial in obtaining and delivering reliable information. On the other hand, making meaningful comparisons between molecular dynamics and neutron scattering is a fundamental challenge to link simulations and experiments at the nano-scale. This challenge stems from our approach to utilize MD simulation to explain the underlying mechanism of experimental observation. The SANS measurements were conducted on a series of SANS spectrometers including the Extended Q-Range Small-Angle Neutron Scattering Diffractometer (EQ-SANS) and the General-Purpose Small-Angle Neutron Scattering Diffractometer (GP-SANS) at the Oak Ridge National Laboratory (ORNL), and NG7 Small Angle Neutron Scattering Spectrometer at National Institute of Standards (NIST) and Technology in U.S.A., large dynamic range small-angle diffractometer D22 at Institut Laue-Langevin (ILL) in France, and 40m-SANS Spectrometer at Korea Atomic Energy Research Institute (KAERI) in Korea. On the other hand, the Amber molecular dynamics simulation package is utilized to carry out the computational study. In this dissertation, the following observations have been revealed. The previously developed theoretical model for polyelectrolyte dendrimers are adopted to analyze SANS measurements and superb model fitting quality is found. Coupling with advanced contrast variation small angle neutron scattering (CVSANS) data analysis scheme reported recently, the intra-dendrimer hydration and hydrocarbon components distributions are revealed experimentally. The results indeed indicate that the maximum density is located in the molecular center rather than periphery, which is consistent to previous SANS studies and the back-folding picture of PAMAM dendrimers. According to this picture, at neutral condition, the exterior residues folding back into interior would necessarily lead to higher entropy and equivalently lower free energy and thereby is energetically favored. As one decreases the pH condition of PAMAM dendrimers, the constituent residues would carry positive charges. The resultant inter-residue Coulomb repulsion would naturally result in conformational evolution. We found from CVSANS analysis that when dendrimers are charged by different acids, this conformational evolution is not the same. For dendrimers charged by DCl, the mass is seen to relocate from molecular interior to periphery. Nevertheless, those acidified by D 2SO4 exhibit surprisingly minor structural change under variation of molecular charge. To explain the above observation, we performed MD simulations and calculated the excess free energy of Cl- and SO 42- counterions. The binding between sulfate ions and charged amines of PAMAM dendrimers are found to be much stronger than the case for chlorides. This more energetic binding would serve as better screening effect among charged residues. Consequently, electrostatic repulsion triggered outstretching tendency is effectively diminished. In order to make direct comparison between MD simulations and neutron scattering experiments, we proposed and implemented a rigorous method, which incorporates the contribution from those invasive water molecules, to calculate scattering functions of a single PAMAM dendrimer using equilibrium MD trajectories. The bridge between neutron scattering experiments and MD simulation is successfully established. Aside from structural comparisons between MD simulations and experiments, we utilized MD simulation to decipher the previously reported QENS experimental observation that the segmental dynamics of PAMAM dendrimer would enhance with increasing molecular charge. We pursued the mechanism from the perspective of hydrocarbon component of dendrimer and solvent (water) interaction as a form similar to hydrogen bonding. It is found that the population of this bonding would increase and the corresponding relaxation would slow down as molecular charge increases. We perceive that through more and longer interaction between penetrating water molecules and polymeric part of dendrimer, the dynamics of latter could be enhanced.

Modeling the Electrostatics of Hollow Shell Suspensions: Ion Distribution, Pair Interactions, and Many-Body Effects.

PubMed

Hallez, Yannick; Meireles, Martine

2016-10-11

Electrostatic interactions play a key role in hollow shell suspensions as they determine their structure, stability, thermodynamics, and rheology and also the loading capacity of small charged species for nanoreservoir applications. In this work, fast, reliable modeling strategies aimed at predicting the electrostatics of hollow shells for one, two, and many colloids are proposed and validated. The electrostatic potential inside and outside a hollow shell with a finite thickness and a specific permittivity is determined analytically in the Debye-Hückel (DH) limit. An expression for the interaction potential between two such hollow shells is then derived and validated numerically. It follows a classical Yukawa form with an effective charge depending on the shell geometry, permittivity, and inner and outer surface charge densities. The predictions of the Ornstein-Zernike (OZ) equation with this pair potential to determine equations of state are then evaluated by comparison to results obtained with a Brownian dynamics algorithm coupled to the resolution of the linearized Poisson-Boltzmann and Laplace equations (PB-BD simulations). The OZ equation based on the DLVO-like potential performs very well in the dilute regime as expected, but also quite well, and more surprisingly, in the concentrated regime in which full spheres exhibit significant many-body effects. These effects are shown to vanish for shells with small thickness and high permittivity. For highly charged hollow shells, we propose and validate a charge renormalization procedure. Finally, using PB-BD simulations, we show that the cell model predicts the ion distribution inside and outside hollow shells accurately in both electrostatically dilute and concentrated suspensions. We then determine the shell loading capacity as a function of salt concentration, volume fraction, and surface charge density for nanoreservoir applications such as drug delivery, sensing, or smart coatings.

Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise.

PubMed

Liu, Chaoren; Beratan, David N; Zhang, Peng

2016-04-21

System-environment interactions are essential in determining charge-transfer (CT) rates and mechanisms. We developed a computationally accessible method, suitable to simulate CT in flexible molecules (i.e., DNA) with hundreds of sites, where the system-environment interactions are explicitly treated with numerical noise modeling of time-dependent site energies and couplings. The properties of the noise are tunable, providing us a flexible tool to investigate the detailed effects of correlated thermal fluctuations on CT mechanisms. The noise is parametrizable by molecular simulation and quantum calculation results of specific molecular systems, giving us better molecular resolution in simulating the system-environment interactions than sampling fluctuations from generic spectral density functions. The spatially correlated thermal fluctuations among different sites are naturally built-in in our method but are not readily incorporated using approximate spectral densities. Our method has quantitative accuracy in systems with small redox potential differences (

The Charge of Neoliberal Brigade and Higher Education in India

ERIC Educational Resources Information Center

Kumar, Ravi

2012-01-01

This paper looks at the state of higher education in India--in terms of policies and the trajectory that it has taken in the aftermath of neoliberalisation of the economy. Through studying the discourses that construct the edifice of the educational complex in the country, it unravels the dynamics of how economy, politics and education interact.…

Sodium dopants in helium clusters: Structure, equilibrium and submersion kinetics

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

Calvo, F.

Alkali impurities bind to helium nanodroplets very differently depending on their size and charge state, large neutral or charged dopants being wetted by the droplet whereas small neutral impurities prefer to reside aside. Using various computational modeling tools such as quantum Monte Carlo and path-integral molecular dynamics simulations, we have revisited some aspects of the physical chemistry of helium droplets interacting with sodium impurities, including the onset of snowball formation in presence of many-body polarization forces, the transition from non-wetted to wetted behavior in larger sodium clusters, and the kinetics of submersion of small dopants after sudden ionization.

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

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

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for coarse grained models of electrolyte solution. Here, we provide rigorous definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation (DFT-MD) and isolate the effects of charge and cavitation,more » comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to highly unphysical values for the solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry (CHA) for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation. We would like to thank Thomas Beck, Shawn Kathmann, Richard Remsing and John Weeks for helpful discussions. Computing resources were generously allocated by PNNL's Institutional Computing program. This research also used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. TTD, GKS, and CJM were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle for the U.S. Department of Energy.« less

Interactions of the Auxilin-1 PTEN-like Domain with Model Membranes Result in Nanoclustering of Phosphatidyl Inositol Phosphates

PubMed Central

Kalli, Antreas C.; Morgan, Gareth; Sansom, Mark S.P.

2013-01-01

Auxilin-1 is a neuron-specific membrane-binding protein involved in a late stage of clathrin-mediated endocytosis. It recruits Hsc70, thus initiating uncoating of the clathrin-coated vesicles. Interactions of auxilin-1 with the vesicle membrane are crucial for this function and are mediated via an N-terminal PTEN-like domain. We have used multiscale molecular dynamics simulations to probe the interactions of the auxilin-1 PTEN-like domain with lipid bilayers containing differing phospholipid composition, including bilayers containing phosphatidyl inositol phosphates. Our results suggest a novel, to our knowledge, model for the auxilin/membrane encounter and subsequent interactions. Negatively charged lipids (especially PIP2) enhance binding of auxilin to lipid bilayers and facilitate its correct orientation relative to the membrane. Mutations in three basic residues (R301E/R307E/K311E) of the C2 subdomain of the PTEN-like domain perturbed its interaction with the bilayer, changing its orientation. The interaction of membrane-bound auxilin-1 PTEN-like domain with negatively charged lipid headgroups results in nanoclustering of PIP2 molecules in the adjacent bilayer leaflet. PMID:23823232

Charge-mediated Fab-Fc interactions in an IgG1 antibody induce reversible self-association, cluster formation, and elevated viscosity.

PubMed

Arora, Jayant; Hu, Yue; Esfandiary, Reza; Sathish, Hasige A; Bishop, Steven M; Joshi, Sangeeta B; Middaugh, C Russell; Volkin, David B; Weis, David D

Concentration-dependent reversible self-association (RSA) of monoclonal antibodies (mAbs) poses a challenge to their pharmaceutical development as viable candidates for subcutaneous delivery. While the role of the antigen-binding fragment (Fab) in initiating RSA is well-established, little evidence supports the involvement of the crystallizable fragment (Fc). In this report, a variety of biophysical tools, including hydrogen exchange mass spectrometry, are used to elucidate the protein interface of such non-covalent protein-protein interactions. Using dynamic and static light scattering combined with viscosity measurements, we find that an IgG1 mAb (mAb-J) undergoes RSA primarily through electrostatic interactions and forms a monomer-dimer-tetramer equilibrium. We provide the first direct experimental mapping of the interface formed between the Fab and Fc domains of an antibody at high protein concentrations. Charge distribution heterogeneity between the positively charged interface spanning complementarity-determining regions CDR3H and CDR2L in the Fab and a negatively charged region in C H 3/Fc domain mediates the RSA of mAb-J. When arginine and NaCl are added, they disrupt RSA of mAb-J and decrease the solution viscosity. Fab-Fc domain interactions between mAb monomers may promote the formation of large transient antibody complexes that ultimately cause increases in solution viscosity. Our findings illustrate how limited specific arrangements of amino-acid residues can cause mAbs to undergo RSA at high protein concentrations and how conserved regions in the Fc portion of the antibody can also play an important role in initiating weak and transient protein-protein interactions.

Thermodynamic and Structural Properties of Methanol-Water Solutions Using Non-Additive Interaction Models

PubMed Central

Zhong, Yang; Warren, G. Lee; Patel, Sandeep

2014-01-01

We study bulk structural and thermodynamic properties of methanol-water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P-FQ potential for water-water interactions, and the CHARMM-based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol-methanol and methanol-water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self-diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol-water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol-water gas-phase interaction energy for the lowest-energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P-FQ water are predicted to be −5.6±0.2 kcal/mole, in respectable agreement with the experimental value of −5.1 kcal/mole. With respect to solution micro-structure, the present cluster analysis suggests that the micro-scale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bi-percolating network structure. PMID:18074339

Highly Dynamic Anion-Quadrupole Networks in Proteins.

PubMed

Kapoor, Karan; Duff, Michael R; Upadhyay, Amit; Bucci, Joel C; Saxton, Arnold M; Hinde, Robert J; Howell, Elizabeth E; Baudry, Jerome

2016-11-01

The dynamics of anion-quadrupole (or anion-π) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (Protein Data Bank entry 1EP0 ), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-π and anion-π-π) are formed by the protein during the simulated trajectory, which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1.6 kcal/mol per pair. Some anion-π interactions are predicted to form during the trajectory, extending the number of anion-quadrupole interactions beyond those predicted from crystal structure analysis. At the same time, some anion-π pairs observed in the crystal structure exhibit marginal stability. Overall, most anion-π interactions alternate between an "on" state, with significantly stabilizing energies, and an "off" state, with marginal or null stabilizing energies. The way proteins possibly compensate for transient loss of anion-quadrupole interactions is characterized in the RmlC aspartate 84-phenylalanine 112 anion-quadrupole pair observed in the crystal structure. A double-mutant cycle analysis of the thermal stability suggests a possible loss of anion-π interactions compensated by variations of hydration of the residues and formation of compensating electrostatic interactions. These results suggest that near-planar anion-quadrupole pairs can exist, sometimes transiently, which may play a role in maintaining the structural stability and function of the protein, in an otherwise very dynamic interplay of a nonbonded interaction network as well as solvent effects.

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.

On the dual equivalence of the self-dual and topologically massive /B∧F models coupled to dynamical fermionic matter

NASA Astrophysics Data System (ADS)

Menezes, R.; Nascimento, J. R. S.; Ribeiro, R. F.; Wotzasek, C.

2002-06-01

We study the equivalence between the /B∧F self-dual (SDB∧F) and the /B∧F topologically massive (TMB∧F) models including the coupling to dynamical, U(1) charged fermionic matter. This is done through an iterative procedure of gauge embedding that produces the dual mapping. In the interactive cases, the minimal coupling adopted for both vector and tensor fields in the self-dual representation is transformed into a non-minimal magnetic like coupling in the topologically massive representation but with the currents swapped. It is known that to establish this equivalence a current-current interaction term is needed to render the matter sector unchanged. We show that both terms arise naturally from the embedding procedure.

Charge and spin control of ultrafast electron and hole dynamics in single CdSe/ZnSe quantum dots

NASA Astrophysics Data System (ADS)

Hinz, C.; Gumbsheimer, P.; Traum, C.; Holtkemper, M.; Bauer, B.; Haase, J.; Mahapatra, S.; Frey, A.; Brunner, K.; Reiter, D. E.; Kuhn, T.; Seletskiy, D. V.; Leitenstorfer, A.

2018-01-01

We study the dynamics of photoexcited electrons and holes in single negatively charged CdSe/ZnSe quantum dots with two-color femtosecond pump-probe spectroscopy. An initial characterization of the energy level structure is performed at low temperatures and magnetic fields of up to 5 T. Emission and absorption resonances are assigned to specific transitions between few-fermion states by a theoretical model based on a configuration interaction approach. To analyze the dynamics of individual charge carriers, we initialize the quantum system into excited trion states with defined energy and spin. Subsequently, the time-dependent occupation of the trion ground state is monitored by spectrally resolved differential transmission measurements. We observe subpicosecond dynamics for a hole excited to the D shell. The energy dependence of this D -to-S shell intraband transition is investigated in quantum dots of varying size. Excitation of an electron-hole pair in the respective p shells leads to the formation of singlet and triplet spin configurations. Relaxation of the p -shell singlet is observed to occur on a time scale of a few picoseconds. Pumping of p -shell triplet transitions opens up two pathways with distinctly different scattering times. These processes are shown to be governed by the mixing of singlet and triplet states due to exchange interactions enabling simultaneous electron and hole spin flips. To isolate the relaxation channels, we align the spin of the residual electron by a magnetic field and employ laser pulses of defined helicity. This step provides ultrafast preparation of a fully inverted trion ground state of the quantum dot with near unity probability, enabling deterministic addition of a single photon to the probe pulse. Therefore our experiments represent a significant step towards using single quantum emitters with well-controled inversion to manipulate the photon statistics of ultrafast light pulses.

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).

Dynamic Responses and Initial Decomposition under Shock Loading: A DFTB Calculation Combined with MSST Method for β-HMX with Molecular Vacancy.

PubMed

He, Zheng-Hua; Chen, Jun; Ji, Guang-Fu; Liu, Li-Min; Zhu, Wen-Jun; Wu, Qiang

2015-08-20

Despite extensive efforts on studying the decomposition mechanism of HMX under extreme condition, an intrinsic understanding of mechanical and chemical response processes, inducing the initial chemical reaction, is not yet achieved. In this work, the microscopic dynamic response and initial decomposition of β-HMX with (1 0 0) surface and molecular vacancy under shock condition, were explored by means of the self-consistent-charge density-functional tight-binding method (SCC-DFTB) in conjunction with multiscale shock technique (MSST). The evolutions of various bond lengths and charge transfers were analyzed to explore and understand the initial reaction mechanism of HMX. Our results discovered that the C-N bond close to major axes had less compression sensitivity and higher stretch activity. The charge was transferred mainly from the N-NO2 group along the minor axes and H atom to C atom during the early compression process. The first reaction of HMX primarily initiated with the fission of the molecular ring at the site of the C-N bond close to major axes. Further breaking of the molecular ring enhanced intermolecular interactions and promoted the cleavage of C-H and N-NO2 bonds. More significantly, the dynamic response behavior clearly depended on the angle between chemical bond and shock direction.

Bacterial Adhesion under Static and Dynamic Conditions

PubMed Central

Rijnaarts, Huub H. M.; Norde, Willem; Bouwer, Edward J.; Lyklema, Johannes; Zehnder, Alexander J. B.

1993-01-01

The deposition of various pseudomonads and coryneform bacteria with different hydrophobicities (water contact angles) and negative cell surface charges on negatively charged Teflon and glass surfaces was investigated. The levels of deposition varied between 5.0 × 104 and 1.6 × 107 cells cm-2 and between 5.0 × 104 and 3.6 × 107 cells cm-2 for dynamic column and static batch systems, respectively, indicating that there was a wide variation in physicochemical interactions. Batch and column results were compared in order to better distinguish between hydrodynamic and other system-dependent influences and method-independent physicochemical interactions. Despite the shorter suspension-solid contact time in columns (1 h) than in batch systems (4 h), the level of deposition (expressed as the number of cells that adhered) divided by the applied ambient cell concentration was 4.12 ± 1.63 times higher in columns than in batch sytems for 15 of 22 strain-surface combinations studied. This demonstrates that transport of microbial particles from bulk liquid to surfaces is more efficient in dynamic columns (transport dominated by convection and diffusion) than in static batch systems (transport by diffusion only). The relative constancy of this ratio for the 15 combinations shows that physicochemical interactions affect adhesion similarly in the two systems. The deviating deposition behavior of the other seven strain-surface combinations could be attributed to method-dependent effects resulting from specific cell characteristics (e.g., to the presence of capsular polymers, to an ability to aggregate, to large cell sizes, or to a tendency to desorb after passage through an air-liquid interface). Images PMID:16349063

Charge carrier trapping and acoustic phonon modes in single CdTe nanowires.

PubMed

Lo, Shun Shang; Major, Todd A; Petchsang, Nattasamon; Huang, Libai; Kuno, Masaru K; Hartland, Gregory V

2012-06-26

Semiconductor nanostructures produced by wet chemical synthesis are extremely heterogeneous, which makes single particle techniques a useful way to interrogate their properties. In this paper the ultrafast dynamics of single CdTe nanowires are studied by transient absorption microscopy. The wires have lengths of several micrometers and lateral dimensions on the order of 30 nm. The transient absorption traces show very fast decays, which are assigned to charge carrier trapping into surface defects. The time constants vary for different wires due to differences in the energetics and/or density of surface trap sites. Measurements performed at the band edge compared to the near-IR give slightly different time constants, implying that the dynamics for electron and hole trapping are different. The rate of charge carrier trapping was observed to slow down at high carrier densities, which was attributed to trap-state filling. Modulations due to the fundamental and first overtone of the acoustic breathing mode were also observed in the transient absorption traces. The quality factors for these modes were similar to those measured for metal nanostructures, and indicate a complex interaction with the environment.

Ultrafast optical excitations in supramolecular metallacycles with charge transfer properties.

PubMed

Flynn, Daniel C; Ramakrishna, Guda; Yang, Hai-Bo; Northrop, Brian H; Stang, Peter J; Goodson, Theodore

2010-02-03

New organometallic materials such as two-dimensional metallacycles and three-dimensional metallacages are important for the development of novel optical, electronic, and energy related applications. In this article, the ultrafast dynamics of two different platinum-containing metallacycles have been investigated by femtosecond fluorescence upconversion and transient absorption. These measurements were carried out in an effort to probe the charge transfer dynamics and the rate of intersystem crossing in metallacycles of different geometries and dimensions. The processes of ultrafast intersystem crossing and charge transfer vary between the two different classes of metallacyclic systems studied. For rectangular anthracene-containing metallacycles, the electronic coupling between adjacent ligands was relatively weak, whereas for the triangular phenanthrene-containing structures, there was a clear interaction between the conjugated ligand and the metal complex center. The transient lifetimes increased with increasing conjugation in that case. The results show that differences in the dimensionality and structure of metallacycles result in different optical properties, which may be utilized in the design of nonlinear optical materials and potential new, longer-lived excited state materials for further electronic applications.

Stochastic Lagrangian dynamics for charged flows in the E-F regions of ionosphere

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

Tang Wenbo; Mahalov, Alex

2013-03-15

We develop a three-dimensional numerical model for the E-F region ionosphere and study the Lagrangian dynamics for plasma flows in this region. Our interest rests on the charge-neutral interactions and the statistics associated with stochastic Lagrangian motion. In particular, we examine the organizing mixing patterns for plasma flows due to polarized gravity wave excitations in the neutral field, using Lagrangian coherent structures (LCS). LCS objectively depict the flow topology-the extracted attractors indicate generation of ionospheric density gradients, due to accumulation of plasma. Using Lagrangian measures such as the finite-time Lyapunov exponents, we locate the Lagrangian skeletons for mixing in plasma,more » hence where charged fronts are expected to appear. With polarized neutral wind, we find that the corresponding plasma velocity is also polarized. Moreover, the polarized velocity alone, coupled with stochastic Lagrangian motion, may give rise to polarized density fronts in plasma. Statistics of these trajectories indicate high level of non-Gaussianity. This includes clear signatures of variance, skewness, and kurtosis of displacements taking polarized structures aligned with the gravity waves, and being anisotropic.« less

Nonlinear Evolution and Final Fate of Charged Anti-de Sitter Black Hole Superradiant Instability

NASA Astrophysics Data System (ADS)

Bosch, Pablo; Green, Stephen R.; Lehner, Luis

2016-04-01

We describe the full nonlinear development of the superradiant instability for a charged massless scalar field coupled to general relativity and electromagnetism, in the vicinity of a Reissner-Nordström-anti-de Sitter black hole. The presence of the negative cosmological constant provides a natural context for considering perfectly reflecting boundary conditions and studying the dynamics as the scalar field interacts repeatedly with the black hole. At early times, small superradiant perturbations grow as expected from linearized studies. Backreaction then causes the black hole to lose charge and mass until the perturbation becomes nonsuperradiant, with the final state described by a stable hairy black hole. For large gauge coupling, the instability extracts a large amount of charge per unit mass, resulting in greater entropy increase. We discuss the implications of the observed behavior for the general problem of superradiance in black hole spacetimes.

Nonlinear Evolution and Final Fate of Charged Anti-de Sitter Black Hole Superradiant Instability.

PubMed

Bosch, Pablo; Green, Stephen R; Lehner, Luis

2016-04-08

We describe the full nonlinear development of the superradiant instability for a charged massless scalar field coupled to general relativity and electromagnetism, in the vicinity of a Reissner-Nordström-anti-de Sitter black hole. The presence of the negative cosmological constant provides a natural context for considering perfectly reflecting boundary conditions and studying the dynamics as the scalar field interacts repeatedly with the black hole. At early times, small superradiant perturbations grow as expected from linearized studies. Backreaction then causes the black hole to lose charge and mass until the perturbation becomes nonsuperradiant, with the final state described by a stable hairy black hole. For large gauge coupling, the instability extracts a large amount of charge per unit mass, resulting in greater entropy increase. We discuss the implications of the observed behavior for the general problem of superradiance in black hole spacetimes.

A Monte Carlo modeling on charging effect for structures with arbitrary geometries

NASA Astrophysics Data System (ADS)

Li, C.; Mao, S. F.; Zou, Y. B.; Li, Yong Gang; Zhang, P.; Li, H. M.; Ding, Z. J.

2018-04-01

Insulating materials usually suffer charging effects when irradiated by charged particles. In this paper, we present a Monte Carlo study on the charging effect caused by electron beam irradiation for sample structures with any complex geometry. When transporting in an insulating solid, electrons encounter elastic and inelastic scattering events; the Mott cross section and a Lorentz-type dielectric function are respectively employed to describe such scatterings. In addition, the band gap and the electron–long optical phonon interaction are taken into account. The electronic excitation in inelastic scattering causes generation of electron–hole pairs; these negative and positive charges establish an inner electric field, which in turn induces the drift of charges to be trapped by impurities, defects, vacancies etc in the solid, where the distributions of trapping sites are assumed to have uniform density. Under charging conditions, the inner electric field distorts electron trajectories, and the surface electric potential dynamically alters secondary electron emission. We present, in this work, an iterative modeling method for a self-consistent calculation of electric potential; the method has advantages in treating any structure with arbitrary complex geometry, in comparison with the image charge method—which is limited to a quite simple boundary geometry. Our modeling is based on: the combination of the finite triangle mesh method for an arbitrary geometry construction; a self-consistent method for the spatial potential calculation; and a full dynamic description for the motion of deposited charges. Example calculations have been done to simulate secondary electron yield of SiO2 for a semi-infinite solid, the charging for a heterostructure of SiO2 film grown on an Au substrate, and SEM imaging of a SiO2 line structure with rough surfaces and SiO2 nanoparticles with irregular shapes. The simulations have explored interesting interlaced charge layer distribution underneath the nanoparticle surface and the mechanism by which it is produced.

Elucidation of amyloid beta-protein oligomerization mechanisms: discrete molecular dynamics study.

PubMed

Urbanc, B; Betnel, M; Cruz, L; Bitan, G; Teplow, D B

2010-03-31

Oligomers of amyloid beta-protein (Abeta) play a central role in the pathology of Alzheimer's disease. Of the two predominant Abeta alloforms, Abeta(1-40) and Abeta(1-42), Abeta(1-42) is more strongly implicated in the disease. We elucidated the structural characteristics of oligomers of Abeta(1-40) and Abeta(1-42) and their Arctic mutants, [E22G]Abeta(1-40) and [E22G]Abeta(1-42). We simulated oligomer formation using discrete molecular dynamics (DMD) with a four-bead protein model, backbone hydrogen bonding, and residue-specific interactions due to effective hydropathy and charge. For all four peptides under study, we derived the characteristic oligomer size distributions that were in agreement with prior experimental findings. Unlike Abeta(1-40), Abeta(1-42) had a high propensity to form paranuclei (pentameric or hexameric) structures that could self-associate into higher-order oligomers. Neither of the Arctic mutants formed higher-order oligomers, but [E22G]Abeta(1-40) formed paranuclei with a similar propensity to that of Abeta(1-42). Whereas the best agreement with the experimental data was obtained when the charged residues were modeled as solely hydrophilic, further assembly from spherical oligomers into elongated protofibrils was induced by nonzero electrostatic interactions among the charged residues. Structural analysis revealed that the C-terminal region played a dominant role in Abeta(1-42) oligomer formation whereas Abeta(1-40) oligomerization was primarily driven by intermolecular interactions among the central hydrophobic regions. The N-terminal region A2-F4 played a prominent role in Abeta(1-40) oligomerization but did not contribute to the oligomerization of Abeta(1-42) or the Arctic mutants. The oligomer structure of both Arctic peptides resembled Abeta(1-42) more than Abeta(1-40), consistent with their potentially more toxic nature.

Electron-flux infrared response to varying π-bond topology in charged aromatic monomers

PubMed Central

Álvaro Galué, Héctor; Oomens, Jos; Buma, Wybren Jan; Redlich, Britta

2016-01-01

The interaction of delocalized π-electrons with molecular vibrations is key to charge transport processes in π-conjugated organic materials based on aromatic monomers. Yet the role that specific aromatic motifs play on charge transfer is poorly understood. Here we show that the molecular edge topology in charged catacondensed aromatic hydrocarbons influences the Herzberg-Teller coupling of π-electrons with molecular vibrations. To this end, we probe the radical cations of picene and pentacene with benchmark armchair- and zigzag-edges using infrared multiple-photon dissociation action spectroscopy and interpret the recorded spectra via quantum-chemical calculations. We demonstrate that infrared bands preserve information on the dipolar π-electron-flux mode enhancement, which is governed by the dynamical evolution of vibronically mixed and correlated one-electron configuration states. Our results reveal that in picene a stronger charge π-flux is generated than in pentacene, which could justify the differences of electronic properties of armchair- versus zigzag-type families of technologically relevant organic molecules. PMID:27577323

Accurate van der Waals coefficients from density functional theory

PubMed Central

Tao, Jianmin; Perdew, John P.; Ruzsinszky, Adrienn

2012-01-01

The van der Waals interaction is a weak, long-range correlation, arising from quantum electronic charge fluctuations. This interaction affects many properties of materials. A simple and yet accurate estimate of this effect will facilitate computer simulation of complex molecular materials and drug design. Here we develop a fast approach for accurate evaluation of dynamic multipole polarizabilities and van der Waals (vdW) coefficients of all orders from the electron density and static multipole polarizabilities of each atom or other spherical object, without empirical fitting. Our dynamic polarizabilities (dipole, quadrupole, octupole, etc.) are exact in the zero- and high-frequency limits, and exact at all frequencies for a metallic sphere of uniform density. Our theory predicts dynamic multipole polarizabilities in excellent agreement with more expensive many-body methods, and yields therefrom vdW coefficients C6, C8, C10 for atom pairs with a mean absolute relative error of only 3%. PMID:22205765

Ultrafast dynamics of multi-exciton state coupled to coherent vibration in zinc chlorin aggregates for artificial photosynthesis.

PubMed

Shi, Tongchao; Liu, Zhengzheng; Miyatake, Tomohiro; Tamiaki, Hitoshi; Kobayashi, Takayoshi; Zhang, Zeyu; Du, Juan; Leng, Yuxin

2017-11-27

Ultrafast vibronic dynamics induced by the interaction of the Frenkel exciton with the coherent molecular vibrations in a layer-structured zinc chlorin aggregates prepared for artificial photosynthesis have been studied by 7.1 fs real-time vibrational spectroscopy with multi-spectrum detection. The fast decay of 100 ± 5fs is ascribed to the relaxation from the higher multi-exciton state (MES) to the one-exciton state, and the slow one of 863 ± 70fs is assigned to the relaxation from Q-exciton state to the dark nonfluorescent charge-transfer (CT) state, respectively. In addition, the wavelength dependences of the exciton-vibration coupling strength are found to follow the zeroth derivative of the transient absorption spectra of the exciton. It could be explained in term of the transition dipole moment modulated by dynamic intensity borrowing between the B transition and the Q transition through the vibronic interactions.

Changes in conformational dynamics of basic side chains upon protein-DNA association.

PubMed

Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani; Roy, Sourav; Pettitt, B Montgometry; Iwahara, Junji

2016-08-19

Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein-DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1-DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Spin dynamics in helical molecules with nonlinear interactions

NASA Astrophysics Data System (ADS)

Díaz, E.; Albares, P.; Estévez, P. G.; Cerveró, J. M.; Gaul, C.; Diez, E.; Domínguez-Adame, F.

2018-04-01

It is widely admitted that the helical conformation of certain chiral molecules may induce a sizable spin selectivity observed in experiments. Spin selectivity arises as a result of the interplay between a helicity-induced spin–orbit coupling (SOC) and electric dipole fields in the molecule. From the theoretical point of view, different phenomena might affect the spin dynamics in helical molecules, such as quantum dephasing, dissipation and the role of metallic contacts. With a few exceptions, previous studies usually neglect the local deformation of the molecule about the carrier, but this assumption seems unrealistic to describe charge transport in molecular systems. We introduce an effective model describing the electron spin dynamics in a deformable helical molecule with weak SOC. We find that the electron–lattice interaction allows the formation of stable solitons such as bright solitons with well defined spin projection onto the molecule axis. We present a thorough study of these bright solitons and analyze their possible impact on the spin dynamics in deformable helical molecules.

Structure and hydration of membranes embedded with voltage-sensing domains.

PubMed

Krepkiy, Dmitriy; Mihailescu, Mihaela; Freites, J Alfredo; Schow, Eric V; Worcester, David L; Gawrisch, Klaus; Tobias, Douglas J; White, Stephen H; Swartz, Kenton J

2009-11-26

Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly charged S1-S4 voltage-sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated ion channels. Here we use neutron diffraction, solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1-S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations and cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings indicate that voltage sensors have evolved to interact with the lipid membrane while keeping energetic and structural perturbations to a minimum, and that water penetrates the membrane, to hydrate charged residues and shape the transmembrane electric field.

Structure and hydration of membranes embedded with voltage-sensing domains

PubMed Central

Krepkiy, Dmitriy; Mihailescu, Mihaela; Freites, J. Alfredo; Schow, Eric V.; Worcester, David L.; Gawrisch, Klaus; Tobias, Douglas; White, Stephen H.; Swartz, Kenton J.

2009-01-01

Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly-charged S1–S4 voltage-sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated potassium channels. Here we use neutron diffraction, solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1–S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations, cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings reveal that voltage sensors have evolved to interact with the lipid membrane while keeping the energetic and structural perturbations to a minimum, and that water penetrates into the membrane to hydrate charged residues and shape the transmembrane electric field. PMID:19940918

A Neutron View of Proteins in Lipid Bilayers

NASA Astrophysics Data System (ADS)

White, Stephen

2012-02-01

Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly-charged S1-S4 voltage- sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated potassium channels. We have used neutron diffraction, solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1-S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations, cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings reveal that voltage sensors have evolved to interact with the lipid membrane while keeping the energetic and structural perturbations to a minimum, and that water penetrates into the membrane to hydrate charged residues and shape the transmembrane electric field.

Modulating weak interactions for molecular recognition: a dynamic combinatorial analysis for assessing the contribution of electrostatics to the stability of CH-π bonds in water.

PubMed

Jiménez-Moreno, Ester; Gómez, Ana M; Bastida, Agatha; Corzana, Francisco; Jiménez-Oses, Gonzalo; Jiménez-Barbero, Jesús; Asensio, Juan Luis

2015-03-27

Electrostatic and charge-transfer contributions to CH-π complexes can be modulated by attaching electron-withdrawing substituents to the carbon atom. While clearly stabilizing in the gas phase, the outcome of this chemical modification in water is more difficult to predict. Herein we provide a definitive and quantitative answer to this question employing a simple strategy based on dynamic combinatorial chemistry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Translocation of a heterogeneous polymer

PubMed Central

Mirigian, Stephen; Wang, Yanbo; Muthukumar, Murugappan

2012-01-01

We present results on the sequence dependence of translocation kinetics for a partially charged heteropolymer moving through a very thin pore using theoretical tools and Langevin dynamics simulational techniques. The chain is composed of two types of monomers of differing frictional interaction with the pore and charge. We present exact analytical expressions for passage probability, mean first passage time, and mean successful passage times for both reflecting/absorbing and absorbing/absorbing boundary conditions, showing rich and unexpected dependence of translocation behavior on charge fraction, distribution along the chain, and electric field configuration. We find excellent qualitative and good quantitative agreement between theoretical and simulation results. Surprisingly, there emerges a threshold charge fraction of a diblock copolymer beyond which the success rate of translocation is independent of charge fraction. Also, the mean successful translocation time of a diblock copolymer displays non-monotonic behavior with increasing length of the charged block; there is an optimum length of the charged block where the mean translocation rate is the slowest; and there can be a substantial range of higher charge fractions which make the translocation slower than even a minimally charged chain. Additionally, we find for a fixed total charge on the chain, finer distribution along the backbone significantly decreases mean translocation time. PMID:22897308

Dynamics of glycoprotein charge in the evolutionary history of human influenza.

PubMed

Arinaminpathy, Nimalan; Grenfell, Bryan

2010-12-30

Influenza viruses show a significant capacity to evade host immunity; this is manifest both as large occasional jumps in the antigenic phenotype of viral surface molecules and in gradual antigenic changes leading to annual influenza epidemics in humans. Recent mouse studies show that avidity for host cells can play an important role in polyclonal antibody escape, and further that electrostatic charge of the hemagglutinin glycoprotein can contribute to such avidity. We test the role of glycoprotein charge on sequence data from the three major subtypes of influenza A in humans, using a simple method of calculating net glycoprotein charge. Of all subtypes, H3N2 in humans shows a striking pattern of increasing positive charge since its introduction in 1968. Notably, this trend applies to both hemagglutinin and neuraminidase glycoproteins. In the late 1980s hemagglutinin charge reached a plateau, while neuraminidase charge started to decline. We identify key groups of amino acid sites involved in this charge trend. To our knowledge these are the first indications that, for human H3N2, net glycoprotein charge covaries strongly with antigenic drift on a global scale. Further work is needed to elucidate how such charge interacts with other immune escape mechanisms, such as glycosylation, and we discuss important questions arising for future study.

A quantum dot close to Stoner instability: The role of the Berry phase

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

Saha, Arijit, E-mail: arijitsahahri@gmail.com; Gefen, Yuval; Burmistrov, Igor

2012-10-15

The physics of a quantum dot with electron-electron interactions is well captured by the so called 'Universal Hamiltonian' if the dimensionless conductance of the dot is much higher than unity. Within this scheme interactions are represented by three spatially independent terms which describe the charging energy, the spin-exchange and the interaction in the Cooper channel. In this paper we concentrate on the exchange interaction and generalize the functional bosonization formalism developed earlier for the charging energy. This turned out to be challenging as the effective bosonic action is formulated in terms of a vector field and is non-abelian due tomore » the non-commutativity of the spin operators. Here we develop a geometric approach which is particularly useful in the mesoscopic Stoner regime, i.e., when the strong exchange interaction renders the system close to the Stoner instability. We show that it is sufficient to sum over the adiabatic paths of the bosonic vector field and, for these paths, the crucial role is played by the Berry phase. Using these results we were able to calculate the magnetic susceptibility of the dot. The latter, in close vicinity of the Stoner instability point, matches very well with the exact solution [I.S. Burmistrov, Y. Gefen, M.N. Kiselev, JETP Lett. 92 (2010) 179]. - Highlights: Black-Right-Pointing-Pointer We consider a conducting QD whose dynamics is governed by exchange interaction. Black-Right-Pointing-Pointer We study the model within the 'Universal Hamiltonian' framework. Black-Right-Pointing-Pointer The ensuing bosonic action is non-abelian (hence non-trivial). Black-Right-Pointing-Pointer We find that the low energy dynamics is governed by a fluctuating Berry phase term. Black-Right-Pointing-Pointer We calculate the partition function and the zero frequency magnetic susceptibility.« less

Neutron Scattering Studies of the Interplay of Amyloid β Peptide(1–40) and An Anionic Lipid 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol

DOE PAGES

Rai, Durgesh K.; Sharma, Veerendra K.; Anunciado, Divina; ...

2016-08-09

The interaction between lipid bilayers and Amyloid β peptide (Aβ) plays a critical role in proliferation of Alzheimer’s disease (AD). AD is expected to affect one in every 85 humans by 2050, and therefore, deciphering the interplay of Aβ and lipid bilayers at the molecular level is of profound importance. In this work, we applied an array of neutron scattering methods to study the structure and dynamics of Aβ(1–40) interacting 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) bilayers. In the structural investigations of lipid bilayer’s response to Aβ binding, Small Angle Neutron Scattering and Neutron Membrane Diffraction revealed that the Aβ anchors firmly to themore » highly charged DMPG bilayers in the interfacial region between water and hydrocarbon chain, and it doesn’t penetrate deeply into the bilayer. This association mode is substantiated by the dynamics studies with high resolution Quasi-Elastic Neutron Scattering experiments, showing that the addition of Aβ mainly affects the slower lateral motion of lipid molecules, especially in the fluid phase, but not the faster internal motion. The results revealed that Aβ associates with the highly charged membrane in surface with limited impact on the structure, but the altered membrane dynamics could have more influence on other membrane processes.« less

Dermaseptin 01 as antimicrobial peptide with rich biotechnological potential: study of peptide interaction with membranes containing Leishmania amazonensis lipid-rich extract and membrane models.

PubMed

Salay, Luiz C; Nobre, Thatyane M; Colhone, Marcelle C; Zaniquelli, Maria E D; Ciancaglini, Pietro; Stabeli, Rodrigo G; Leite, José Roberto S A; Zucolotto, Valtencir

2011-10-01

This article addresses the interactions of the synthetic antimicrobial peptide dermaseptin 01 (GLWSTIKQKGKEAAIAAA- KAAGQAALGAL-NH(2) , DS 01) with phospholipid (PL) monolayers comprising (i) a lipid-rich extract of Leishmania amazonensis (LRE-La), (ii) zwitterionic PL (dipalmitoylphosphatidylcholine, DPPC), and (iii) negatively charged PL (dipalmitoylphosphatidylglycerol, DPPG). The degree of interaction of DS 01 with the different biomembrane models was quantified from equilibrium and dynamic liquid-air interface parameters. At low peptide concentrations, interactions between DS 01 and zwitterionic PL, as well as with the LRE-La monolayers were very weak, whereas with negatively charged PLs the interactions were stronger. For peptide concentrations above 1 µg/ml, a considerable expansion of negatively charged monolayers occurred. In the case of DPPC, it was possible to return to the original lipid area in the condensed phase, suggesting that the peptide was expelled from the monolayer. However, in the case of DPPG, the average area per lipid molecule in the presence of DS 01 was higher than pure PLs even at high surface pressures, suggesting that at least part of DS 01 remained incorporated in the monolayer. For the LRE-La monolayers, DS 01 also remained in the monolayer. This is the first report on the antiparasitic activity of AMPs using Langmuir monolayers of a natural lipid extract from L. amazonensis. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.

Theoretical Studies of Interactions between O-Phosphorylated and Standard Amino-Acid Side-Chain Models in Water

PubMed Central

Wiśniewska, Marta; Sobolewski, Emil; Ołdziej, Stanisław; Liwo, Adam; Scheraga, Harold A.; Makowski, Mariusz

2015-01-01

Phosphorylation is a common post-translational modification of the amino-acid side chains (serine, tyrosine, and threonine) that contain hydroxyl groups. The transfer of the negatively charged phosphate group from an ATP molecule to such amino-acid side chains leads to changes in the local conformations of proteins and the pattern of interactions with other amino-acid side-chains. A convenient characteristic of the side chain–side chain interactions in the context of an aqueous environment is the potential of mean force (PMF) in water. A series of umbrella-sampling molecular dynamic (MD) simulations with the AMBER force field were carried out for pairs of O-phosphorylated serine (pSer), threonine (pThr), and tyrosine, (pTyr) with natural amino acids in a TIP3P water model as a solvent at 298 K. The weighted-histogram analysis method was used to calculate the four-dimensional potentials of mean force. The results demonstrate that the positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the relative orientation depend on the character of the interacting pairs. More distinct minima are observed for oppositely charged pairs such as, e.g., O-phosphorylated side-chains and positively charged ones, such as the side-chains of lysine and arginine. PMID:26100791

Towards a First-Principles Determination of Effective Coulomb Interactions in Correlated Electron Materials: Role of Intershell Interactions

NASA Astrophysics Data System (ADS)

Seth, Priyanka; Hansmann, Philipp; van Roekeghem, Ambroise; Vaugier, Loig; Biermann, Silke

2017-08-01

The determination of the effective Coulomb interactions to be used in low-energy Hamiltonians for materials with strong electronic correlations remains one of the bottlenecks for parameter-free electronic structure calculations. We propose and benchmark a scheme for determining the effective local Coulomb interactions for charge-transfer oxides and related compounds. Intershell interactions between electrons in the correlated shell and ligand orbitals are taken into account in an effective manner, leading to a reduction of the effective local interactions on the correlated shell. Our scheme resolves inconsistencies in the determination of effective interactions as obtained by standard methods for a wide range of materials, and allows for a conceptual understanding of the relation of cluster model and dynamical mean field-based electronic structure calculations.

Towards a First-Principles Determination of Effective Coulomb Interactions in Correlated Electron Materials: Role of Intershell Interactions.

PubMed

Seth, Priyanka; Hansmann, Philipp; van Roekeghem, Ambroise; Vaugier, Loig; Biermann, Silke

2017-08-04

The determination of the effective Coulomb interactions to be used in low-energy Hamiltonians for materials with strong electronic correlations remains one of the bottlenecks for parameter-free electronic structure calculations. We propose and benchmark a scheme for determining the effective local Coulomb interactions for charge-transfer oxides and related compounds. Intershell interactions between electrons in the correlated shell and ligand orbitals are taken into account in an effective manner, leading to a reduction of the effective local interactions on the correlated shell. Our scheme resolves inconsistencies in the determination of effective interactions as obtained by standard methods for a wide range of materials, and allows for a conceptual understanding of the relation of cluster model and dynamical mean field-based electronic structure calculations.

Deep eutectic solvents: similia similibus solvuntur?

PubMed

Zahn, Stefan

2017-02-01

Deep eutectic solvents, mixtures of an organic compound and a salt with a deep eutectic melting point, are promising cheap and eco-friendly alternatives to ionic liquids. Ab initio molecular dynamics simulations of reline, a mixture consisting of urea and choline chloride, reveal that not solely hydrogen bonds allow similar interactions between both constituents. The chloride anion and the oxygen atom of urea also show a similar spatial distribution close to the cationic core of choline due to a similar charge located on both atoms. As a result of multiple similar interactions, clusters migrating together cannot be observed in reline which supports the hypothesis similia similibus solvuntur. In contrast to previous suggestions, the interaction of the hydroxyl group of choline with a hydrogen bond acceptor is overall rigid. Fast hydrogen bond acceptor dynamics is facilitated by the hydrogen atoms in the trans position to the carbonyl group of urea which contributes to the low melting point of reline.

Dynamic Charge Storage in Ionic Liquids-Filled Nanopores: Insight from a Computational Cyclic Voltammetry Study.

PubMed

He, Yadong; Huang, Jingsong; Sumpter, Bobby G; Kornyshev, Alexei A; Qiao, Rui

2015-01-02

Understanding the dynamic charge storage in nanoporous electrodes with room-temperature ionic liquid electrolytes is essential for optimizing them to achieve supercapacitors with high energy and power densities. Herein, we report coarse-grained molecular dynamics simulations of the cyclic voltammetry of supercapacitors featuring subnanometer pores and model ionic liquids. We show that the cyclic charging and discharging of nanopores are governed by the interplay between the external field-driven ion transport and the sloshing dynamics of ions inside of the pore. The ion occupancy along the pore length depends strongly on the scan rate and varies cyclically during charging/discharging. Unlike that at equilibrium conditions or low scan rates, charge storage at high scan rates is dominated by counterions while the contribution by co-ions is marginal or negative. These observations help explain the perm-selective charge storage observed experimentally. We clarify the mechanisms underlying these dynamic phenomena and quantify their effects on the efficiency of the dynamic charge storage in nanopores.

Attraction between like-charged monovalent ions.

PubMed

Zangi, Ronen

2012-05-14

Ions with like-charges repel each other with a magnitude given by the Coulomb law. The repulsion is also known to persist in aqueous solutions albeit factored by the medium's dielectric constant. In this paper, we report results from molecular dynamics simulations of alkali halides salt solutions indicating an effective attraction between some of the like-charged monovalent ions. The attraction is observed between anions, as well as between cations, leading to the formation of dimers with lifetimes on the order of few picoseconds. Two mechanisms have been identified to drive this counterintuitive attraction. The first is exhibited by high-charge density ions, such as fluoride, at low salt concentrations, yielding effective attractions with magnitude up to the order of 1-2 kT. In this case, the stronger local electric field generated when the two ions are in contact augments the alignment of neighboring waters toward the ions. This results in a gain of substantial favorable ion-water interaction energy. For fluorides, this interaction constitutes the major change among the different energy components compensating for the anion-anion repulsion, and therefore, rendering like-charge association possible. The second mechanism involves mediation by counterions, the attractions increase with salt concentration and are characterized by small magnitudes. In particular, clusters of ion triplets, in which a counterion is either bridging the two like-charged ions or is paired to only one of them, are formed. Although these two mechanisms may not yield net attractions in many cases, they might still be operational and significant, explaining effective repulsions between like-charged ions with magnitudes much smaller than expected based on continuum electrostatics.

Economic Development and the Market Place for Education: Dynamics of the International Schools Sector in Shanghai, China

ERIC Educational Resources Information Center

Yamato, Yoko; Bray, Mark

2006-01-01

To some extent, all schools operate in a market place; but the interaction with the market place may be particularly evident in the international schools sector, since many such schools are operated by foundations or private companies which charge fees. This article focuses on the distinctive market place of Shanghai, China, which has undergone…

LO-TO splittings, effective charges and interactions in electro-optic meta-nitroaniline crystal as studied by polarized IR reflection and transmission spectra

NASA Astrophysics Data System (ADS)

Szostak, M. M.; Le Calvé, N.; Romain, F.; Pasquier, B.

1994-10-01

The polarized IR reflection spectra of the meta-nitroaniline ( m-NA) single crystal along the a, b and c crystallographic axes as well as the b and c polarized transmission spectra have been measured in the 100-400 cm -1 region. The LO-TO splitting values have been calculated from the reflection spectra by fitting them with the four parameter dielectric function. The dipole moment derivatives, relevant to dynamic effective charges, of the vibrations have also been calculated and used to check the applicability of the oriented gas model (OGM) to reflection spectra. The discrepancies from the OGM have been discussed in terms of vibronic couplings, weak hydrogen bondings (HB) and intramolecular charge transfer.

Development of a Charge-Implicit ReaxFF Potential for Hydrocarbon Systems.

PubMed

Kański, Michał; Maciążek, Dawid; Postawa, Zbigniew; Ashraf, Chowdhury M; van Duin, Adri C T; Garrison, Barbara J

2018-01-18

Molecular dynamics (MD) simulations continue to make important contributions to understanding chemical and physical processes. Concomitant with the growth of MD simulations is the need to have interaction potentials that both represent the chemistry of the system and are computationally efficient. We propose a modification to the ReaxFF potential for carbon and hydrogen that eliminates the time-consuming charge equilibration, eliminates the acknowledged flaws of the electronegativity equalization method, includes an expanded training set for condensed phases, has a repulsive wall for simulations of energetic particle bombardment, and is compatible with the LAMMPS code. This charge-implicit ReaxFF potential is five times faster than the conventional ReaxFF potential for a simulation of keV particle bombardment with a sample size of over 800 000 atoms.

Dark Matter and the elusive Z' in a dynamical Inverse Seesaw scenario

DOE PAGES

De Romeri, Valentina; Fernandez-Martinez, Enrique; Gehrlein, Julia; ...

2017-10-24

The Inverse Seesaw naturally explains the smallness of neutrino masses via an approximate $B-L$ symmetry broken only by a correspondingly small parameter. In this work the possible dynamical generation of the Inverse Seesaw neutrino mass mechanism from the spontaneous breaking of a gauged $U(1)$ $B-L$ symmetry is investigated. Interestingly, the Inverse Seesaw pattern requires a chiral content such that anomaly cancellation predicts the existence of extra fermions belonging to a dark sector with large, non-trivial, charges under the $U(1)$ $B-L$. We investigate the phenomenology associated to these new states and find that one of them is a viable dark mattermore » candidate with mass around the TeV scale, whose interaction with the Standard Model is mediated by the $Z'$ boson associated to the gauged $U(1)$ $B-L$ symmetry. Given the large charges required for anomaly cancellation in the dark sector, the $B-L$ $Z'$ interacts preferentially with this dark sector rather than with the Standard Model. This suppresses the rate at direct detection searches and thus alleviates the constraints on $Z'$-mediated dark matter relic abundance. Furthermore, the collider phenomenology of this elusive $Z'$ is also discussed.« less

Reinforcing the membrane-mediated mechanism of action of the anti-tuberculosis candidate drug thioridazine with molecular simulations

NASA Astrophysics Data System (ADS)

Kopec, Wojciech; Khandelia, Himanshu

2014-02-01

Thioridazine is a well-known dopamine-antagonist drug with a wide range of pharmacological properties ranging from neuroleptic to antimicrobial and even anticancer activity. Thioridazine is a critical component of a promising multi-drug therapy against M. tuberculosis. Amongst the various proposed mechanisms of action, the cell membrane-mediated one is peculiarly tempting due to the distinctive feature of phenothiazine drug family to accumulate in selected body tissues. In this study, we employ long-scale molecular dynamics simulations to investigate the interactions of three different concentrations of thioridazine with zwitterionic and negatively charged model lipid membranes. Thioridazine partitions into the interfacial region of membranes and modifies their structural and dynamic properties, however dissimilarly so at the highest membrane-occurring concentration, that appears to be obtainable only for the negatively charged bilayer. We show that the origin of such changes is the drug induced decrease of the interfacial tension, which ultimately leads to the significant membrane expansion. Our findings support the hypothesis that the phenothiazines therapeutic activity may arise from the drug-membrane interactions, and reinforce the wider, emerging view of action of many small, bioactive compounds.

Anomalous transport of charged dust grains in a magnetized collisional plasma: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Bezbaruah, Pratikshya; Das, Nilakshi

2018-05-01

Anomalous diffusion of charged dust grains immersed in a plasma in the presence of strong ion-neutral collision, flowing ions, and a magnetic field has been observed. Molecular Dynamics simulation confirms the deviation from normal diffusion in an ensemble of dust grains probed in laboratory plasma chambers. Collisional effects are significant in governing the nature of diffusion. In order to have a clear idea on the transport of particles in a real experimental situation, the contribution of streaming ions and the magnetic field along with collision is considered through the relevant interaction potential. The nonlinear evolution of Mean Square Displacement is an indication of the modification in particle trajectories due to several effects as mentioned above. It is found that strong collision and ion flow significantly affect the interparticle interaction potential in the presence of the magnetic field and lead to the appearance of the asymmetric type of Debye Hückel (D H) potential. Due to the combined effect of the magnetic field, ion flow, and collision, dusty plasma exhibits a completely novel behavior. The coupling parameter Γ enhances the asymmetric D H type potential arising due to ion flow, and this may drive the system to a disordered state.

Dark Matter and the elusive Z' in a dynamical Inverse Seesaw scenario

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

De Romeri, Valentina; Fernandez-Martinez, Enrique; Gehrlein, Julia

The Inverse Seesaw naturally explains the smallness of neutrino masses via an approximate $B-L$ symmetry broken only by a correspondingly small parameter. In this work the possible dynamical generation of the Inverse Seesaw neutrino mass mechanism from the spontaneous breaking of a gauged $U(1)$ $B-L$ symmetry is investigated. Interestingly, the Inverse Seesaw pattern requires a chiral content such that anomaly cancellation predicts the existence of extra fermions belonging to a dark sector with large, non-trivial, charges under the $U(1)$ $B-L$. We investigate the phenomenology associated to these new states and find that one of them is a viable dark mattermore » candidate with mass around the TeV scale, whose interaction with the Standard Model is mediated by the $Z'$ boson associated to the gauged $U(1)$ $B-L$ symmetry. Given the large charges required for anomaly cancellation in the dark sector, the $B-L$ $Z'$ interacts preferentially with this dark sector rather than with the Standard Model. This suppresses the rate at direct detection searches and thus alleviates the constraints on $Z'$-mediated dark matter relic abundance. Furthermore, the collider phenomenology of this elusive $Z'$ is also discussed.« less

Surface-charge-governed electrolyte transport in carbon nanotubes

NASA Astrophysics Data System (ADS)

Xue, Jian-Ming; Guo, Peng; Sheng, Qian

2015-08-01

The transport behavior of pressure-driven aqueous electrolyte solution through charged carbon nanotubes (CNTs) is studied by using molecular dynamics simulations. The results reveal that the presence of charges around the nanotube can remarkably reduce the flow velocity as well as the slip length of the aqueous solution, and the decreasing of magnitude depends on the number of surface charges and distribution. With 1-M KCl solution inside the carbon nanotube, the slip length decreases from 110 nm to only 14 nm when the number of surface charges increases from 0 to 12 e. This phenomenon is attributed to the increase of the solid-liquid friction force due to the electrostatic interaction between the charges and the electrolyte particles, which can impede the transports of water molecules and electrolyte ions. With the simulation results, we estimate the energy conversion efficiency of nanofluidic battery based on CNTs, and find that the highest efficiency is only around 30% but not 60% as expected in previous work. Project supported by the National Natural Science Foundation of China (Grant Nos. 11375031 and 11335003).

Interlayer‐State‐Coupling Dependent Ultrafast Charge Transfer in MoS2/WS2 Bilayers

PubMed Central

Zhang, Jin; Hong, Hao; Lian, Chao; Ma, Wei; Xu, Xiaozhi; Zhou, Xu; Fu, Huixia

2017-01-01

Light‐induced interlayer ultrafast charge transfer in 2D heterostructures provides a new platform for optoelectronic and photovoltaic applications. The charge separation process is generally hypothesized to be dependent on the interlayer stackings and interactions, however, the quantitative characteristic and detailed mechanism remain elusive. Here, a systematical study on the interlayer charge transfer in model MoS2/WS2 bilayer system with variable stacking configurations by time‐dependent density functional theory methods is demonstrated. The results show that the slight change of interlayer geometry can significantly modulate the charge transfer time from 100 fs to 1 ps scale. Detailed analysis further reveals that the transfer rate in MoS2/WS2 bilayers is governed by the electronic coupling between specific interlayer states, rather than the interlayer distances, and follows a universal dependence on the state‐coupling strength. The results establish the interlayer stacking as an effective freedom to control ultrafast charge transfer dynamics in 2D heterostructures and facilitate their future applications in optoelectronics and light harvesting. PMID:28932669

Brownian dynamics simulations of polyelectrolyte adsorption in shear flow with hydrodynamic interaction

NASA Astrophysics Data System (ADS)

Hoda, Nazish; Kumar, Satish

2007-12-01

The adsorption of single polyelectrolyte molecules in shear flow is studied using Brownian dynamics simulations with hydrodynamic interaction (HI). Simulations are performed with bead-rod and bead-spring chains, and electrostatic interactions are incorporated through a screened Coulombic potential with excluded volume accounted for by the repulsive part of a Lennard-Jones potential. A correction to the Rotne-Prager-Yamakawa tensor is derived that accounts for the presence of a planar wall. The simulations show that migration away from an uncharged wall, which is due to bead-wall HI, is enhanced by increases in the strength of flow and intrachain electrostatic repulsion, consistent with kinetic theory predictions. When the wall and polyelectrolyte are oppositely charged, chain behavior depends on the strength of electrostatic screening. For strong screening, chains get depleted from a region close to the wall and the thickness of this depletion layer scales as N1/3Wi2/3 at high Wi, where N is the chain length and Wi is the Weissenberg number. At intermediate screening, bead-wall electrostatic attraction competes with bead-wall HI, and it is found that there is a critical Weissenberg number for desorption which scales as N-1/2κ-3(lB∣σq∣)3/2, where κ is the inverse screening length, lB is the Bjerrum length, σ is the surface charge density, and q is the bead charge. When the screening is weak, adsorbed chains are observed to align in the vorticity direction at low shear rates due to the effects of repulsive intramolecular interactions. At higher shear rates, the chains align in the flow direction. The simulation method and results of this work are expected to be useful for a number of applications in biophysics and materials science in which polyelectrolyte adsorption plays a key role.

Role of Adsorbed Water on Charge Carrier Dynamics in Photoexcited TiO2

PubMed Central

2017-01-01

Overall photocatalytic water splitting is one of the most sought after processes for sustainable solar-to-chemical energy conversion. The efficiency of this process strongly depends on charge carrier recombination and interaction with surface adsorbates at different time scales. Here, we investigated how hydration of TiO2 P25 affects dynamics of photogenerated electrons at the millisecond to minute time scale characteristic for chemical reactions. We used rapid scan diffuse-reflectance infrared Fourier transform spectroscopy (DRIFTS). The decay of photogenerated electron absorption was substantially slower in the presence of associated water. For hydrated samples, the charge carrier recombination rates followed an Arrhenius-type behavior in the temperature range of 273–423 K; these became temperature-independent when the material was dehydrated at temperatures above 423 K or cooled below 273 K. A DFT+U analysis revealed that hydrogen bonding with adsorbed water stabilizes surface-trapped holes at anatase TiO2(101) facet and lowers the barriers for hole migration. Hence, hole mobility should be higher in the hydrated material than in the dehydrated system. This demonstrates that adsorbed associated water can efficiently stabilize photogenerated charge carriers in nanocrystalline TiO2 and suppress their recombination at the time scale up to minutes. PMID:28413570

Numerical modelling of the Luna-Glob lander electric charging on the lunar surface with SPIS-DUST

NASA Astrophysics Data System (ADS)

Kuznetsov, I. A.; Hess, S. L. G.; Zakharov, A. V.; Cipriani, F.; Seran, E.; Popel, S. I.; Lisin, E. A.; Petrov, O. F.; Dolnikov, G. G.; Lyash, A. N.; Kopnin, S. I.

2018-07-01

One of the complicating factors of the future robotic and human lunar landing missions is the influence of the dust. The upper insulating regolith layer is electrically charged by the solar ultraviolet radiation and the flow of solar wind particles. Resulted electric charge and thus surface potential depend on the lunar local time, latitude and the electrical properties of the regolith. Understanding of mechanisms of the dust electric charging, dust levitation and electric charging of a lander on the lunar surface is essential for interpretation of measurements of the instruments of the Luna-Glob lander payload, e.g. the Dust Impact sensor and the Langmuir Probe. One of the tools, which allows simulating the electric charging of the regolith and lander and also the transport and deposition of the dust particles on the lander surface, is the recently developed Spacecraft Plasma Interaction Software toolkit, called the SPIS-DUST. This paper describes the SPIS-DUST numerical simulation of the interaction between the solar wind plasma, ultraviolet radiation, regolith and a lander and presents as result qualitative and quantitative data of charging the surfaces, plasma sheath and its influence on spacecraft sensors, dust dynamics. The model takes into account the geometry of the Luna-Glob lander, the electric properties of materials used on the lander surface, as well as Luna-Glob landing place. Initial conditions are chosen using current theoretical models of formation of dusty plasma exosphere and levitating charged dust particles. Simulation for the three cases (local lunar noon, evening and sunset) showed us the surrounding plasma sheath around the spacecraft which gives a significant potential bias in the spacecraft vicinity. This bias influences on the spacecraft sensors but with SPIS software we can estimate the potential of uninfluenced plasma with the data from the plasma sensors (Langmuir probes). SPIS-DUST modification allows us to get the dust dynamics properties. For our three cases we've obtained the dust densities around the spacecraft and near the surface of the Moon. As another practical result of this work we can count a suggestion of improving of dusty plasma instrument for the next mission: it must be valuable to relocate the plasma sensors to a distant boom at some distance from the spacecraft.

Study on structures and properties of ammonia clusters (NH3)n (n=1-5) and liquid ammonia in terms of ab initio method and atom-bond electronegativity equalization method ammonia-8P fluctuating charge potential model.

PubMed

Yu, Ling; Yang, Zhong-Zhi

2010-05-07

Structures, binding energies, and vibrational frequencies of (NH(3))(n) (n=2-5) isomers and dynamical properties of liquid ammonia have been explored using a transferable intermolecular potential eight point model including fluctuating charges and flexible body based on a combination of the atom-bond electronegativity equalization and molecular (ABEEM) mechanics (ABEEM ammonia-8P) in this paper. The important feature of this model is to divide the charge sites of one ammonia molecule into eight points region containing four atoms, three sigma bonds, and a lone pair, and allows the charges in system to fluctuate responding to the ambient environment. Due to the explicit descriptions of charges and special treatment of hydrogen bonds, the results of equilibrium geometries, dipole moments, cluster interaction energies, vibrational frequencies for the gas phase of small ammonia clusters, and radial distribution function for liquid ammonia calculated with the ABEEM ammonia-8P potential model are in good agreement with those measured by available experiments and those obtained from high level ab initio calculations. The properties of ammonia dimer are studied in detail involving the structure and one-dimensional, two-dimensional potential energy surface. As for interaction energies, the root mean square deviation is 0.27 kcal/mol, and the linear correlation coefficient reaches 0.994.

Diffusional interaction behavior of NSAIDs in lipid bilayer membrane using molecular dynamics (MD) simulation: Aspirin and Ibuprofen.

PubMed

Sodeifian, Gholamhossein; Razmimanesh, Fariba

2018-05-10

In this research, for the first time, molecular dynamics (MD) method was used to simulate aspirin and ibuprofen at various concentrations and in neutral and charged states. Effects of the concentration (dosage), charge state, and existence of an integral protein in the membrane on the diffusion rate of drug molecules into lipid bilayer membrane were investigated on 11 systems, for which the parameters indicating diffusion rate and those affecting the rate were evaluated. Considering the diffusion rate, a suitable score was assigned to each system, based on which, analysis of variance (ANOVA) was performed. By calculating the effect size of the indicative parameters and total scores, an optimum system with the highest diffusion rate was determined. Consequently, diffusion rate controlling parameters were obtained: the drug-water hydrogen bond in protein-free systems and protein-drug hydrogen bond in the systems containing protein.

Incorporation of the TIP4P water model into a continuum solvent for computing solvation free energy

NASA Astrophysics Data System (ADS)

Yang, Pei-Kun

2014-10-01

The continuum solvent model is one of the commonly used strategies to compute solvation free energy especially for large-scale conformational transitions such as protein folding or to calculate the binding affinity of protein-protein/ligand interactions. However, the dielectric polarization for computing solvation free energy from the continuum solvent is different than that obtained from molecular dynamic simulations. To mimic the dielectric polarization surrounding a solute in molecular dynamic simulations, the first-shell water molecules was modeled using a charge distribution of TIP4P in a hard sphere; the time-averaged charge distribution from the first-shell water molecules were estimated based on the coordination number of the solute, and the orientation distribution of the first-shell waters and the intermediate water molecules were treated as that of a bulk solvent. Based on this strategy, an equation describing the solvation free energy of ions was derived.

Electrostatic Interactions at the Dimer Interface Stabilize the E. coli β Sliding Clamp.

PubMed

Purohit, Anirban; England, Jennifer K; Douma, Lauren G; Tondnevis, Farzaneh; Bloom, Linda B; Levitus, Marcia

2017-08-22

Sliding clamps are ring-shaped oligomeric proteins that encircle DNA and associate with DNA polymerases for processive DNA replication. The dimeric Escherichia coli β-clamp is closed in solution but must adopt an open conformation to be assembled onto DNA by a clamp loader. To determine what factors contribute to the stability of the dimer interfaces in the closed conformation and how clamp dynamics contribute to formation of the open conformation, we identified conditions that destabilized the dimer and measured the effects of these conditions on clamp dynamics. We characterized the role of electrostatic interactions in stabilizing the β-clamp interface. Increasing salt concentration results in decreased dimer stability and faster subunit dissociation kinetics. The equilibrium dissociation constant of the dimeric clamp varies with salt concentration as predicted by simple charge-screening models, indicating that charged amino acids contribute to the remarkable stability of the interface at physiological salt concentrations. Mutation of a charged residue at the interface (Arg-103) weakens the interface significantly, whereas effects are negligible when a hydrophilic (Ser-109) or a hydrophobic (Ile-305) amino acid is mutated instead. It has been suggested that clamp opening by the clamp loader takes advantage of spontaneous opening-closing fluctuations at the clamp's interface, but our time-resolved fluorescence and fluorescence correlation experiments rule out conformational fluctuations that lead to a significant fraction of open states. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A fast multipole method combined with a reaction field for long-range electrostatics in molecular dynamics simulations: The effects of truncation on the properties of water

NASA Astrophysics Data System (ADS)

Mathias, Gerald; Egwolf, Bernhard; Nonella, Marco; Tavan, Paul

2003-06-01

We present a combination of the structure adapted multipole method with a reaction field (RF) correction for the efficient evaluation of electrostatic interactions in molecular dynamics simulations under periodic boundary conditions. The algorithm switches from an explicit electrostatics evaluation to a continuum description at the maximal distance that is consistent with the minimum image convention, and, thus, avoids the use of a periodic electrostatic potential. A physically motivated switching function enables charge clusters interacting with a given charge to smoothly move into the solvent continuum by passing through the spherical dielectric boundary surrounding this charge. This transition is complete as soon as the cluster has reached the so-called truncation radius Rc. The algorithm is used to examine the dependence of thermodynamic properties and correlation functions on Rc in the three point transferable intermolecular potential water model. Our test simulations on pure liquid water used either the RF correction or a straight cutoff and values of Rc ranging from 14 Å to 40 Å. In the RF setting, the thermodynamic properties and the correlation functions show convergence for Rc increasing towards 40 Å. In the straight cutoff case no such convergence is found. Here, in particular, the dipole-dipole correlation functions become completely artificial. The RF description of the long-range electrostatics is verified by comparison with the results of a particle-mesh Ewald simulation at identical conditions.

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains

PubMed Central

Han, Wei; Schulten, Klaus

2012-01-01

PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 – 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 – 30 μs simulations, to its native states (Cα RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins. PMID:23204949

Ab initio study on the structural and electronic properties of water surrounding a multifunctional nanoprobe

NASA Astrophysics Data System (ADS)

Xia, Xiuli; Shao, Yuanzhi

2018-02-01

We report the magneto-electric behavior of a dual-modality biomedical nanoprobe, a ternary nanosystem consisting of gold and gadolinia clusters and water molecules, with the effect of both nanoclusters on the structural and electronic properties of water. The hydrogen-oxygen bond lengths and angles as well as electronic charges of water molecules surrounding both nanoclusters were calculated using Hubbard U corrected density functional theory aided by molecular dynamics approach. The calculations reveal existence of a magneto-electric interaction between gold and gadolinium oxide nanoclusters, which influences the physical properties of surrounding water remarkably. A broader (narrower) distribution of Hsbnd O bond lengths (Hsbnd Osbnd H bond angles) was observed at the presence of either gold or gadolinia nanoclusters. The presence of Gd6O9 cluster leads to the larger charges of neighbour oxygen atoms. The distribution of oxygen atom charges becomes border when both Gd6O9 and Au13 clusters coexist. Ab initio calculation provides a feasible approach to explore the most essential interactions among functional components of a multimodal nanoprobe applied in aqueous environment.

Neural evidence for moral intuition and the temporal dynamics of interactions between emotional processes and moral cognition.

PubMed

Gui, Dan-Yang; Gan, Tian; Liu, Chao

2016-01-01

Behavioral and neurological studies have revealed that emotions influence moral cognition. Although moral stimuli are emotionally charged, the time course of interactions between emotions and moral judgments remains unknown. In the present study, we investigated the temporal dynamics of the interaction between emotional processes and moral cognition. The results revealed that when making moral judgments, the time course of the event-related potential (ERP) waveform was significantly different between high emotional arousal and low emotional arousal contexts. Different stages of processing were distinguished, showing distinctive interactions between emotional processes and moral reasoning. The precise time course of moral intuition and moral reasoning sheds new light on theoretical models of moral psychology. Specifically, the N1 component (interpreted as representing moral intuition) did not appear to be influenced by emotional arousal. However, the N2 component and late positive potential were strongly affected by emotional arousal; the slow wave was influenced by both emotional arousal and morality, suggesting distinct moral processing at different emotional arousal levels.

Exact wave packet dynamics of singlet fission in unsubstituted and substituted polyene chains within long-range interacting models

NASA Astrophysics Data System (ADS)

Prodhan, Suryoday; Ramasesha, S.

2017-08-01

Singlet fission (SF) is a potential pathway for significant enhancement of efficiency in organic solar cells (OSC). In this paper, we study singlet fission in a pair of polyene molecules in two different stacking arrangements employing exact many-body wave packet dynamics. In the noninteracting model, the SF yield is absent. The individual molecules are treated within Hubbard and Pariser-Parr-Pople (PPP) models and the interaction between them involves transfer terms, intersite electron repulsions, and site-charge-bond-charge repulsion terms. Initial wave packet is constructed from excited singlet state of one molecule and ground state of the other. Time development of this wave packet under the influence of intermolecular interactions is followed within the Schrödinger picture by an efficient predictor-corrector scheme. In unsubstituted Hubbard and PPP chains, 2 1A excited singlet state leads to significant SF yield while the 1 1B state gives negligible fission yield. On substitution by donor-acceptor groups of moderate strength, the lowest excited state will have sufficient 2 1A character and hence results in significant SF yield. Because of rapid internal conversion, the nature of the lowest excited singlet will determine the SF contribution to OSC efficiency. Furthermore, we find the fission yield depends considerably on the stacking arrangement of the polyene molecules.

The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

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

Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca

2014-01-01

Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of themore » simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.« less

Cations Modulate Actin Bundle Mechanics, Assembly Dynamics, and Structure.

PubMed

Castaneda, Nicholas; Zheng, Tianyu; Rivera-Jacquez, Hector J; Lee, Hyun-Ju; Hyun, Jaekyung; Balaeff, Alexander; Huo, Qun; Kang, Hyeran

2018-04-12

Actin bundles are key factors in the mechanical support and dynamic reorganization of the cytoskeleton. High concentrations of multivalent counterions promote bundle formation through electrostatic attraction between actin filaments that are negatively charged polyelectrolytes. In this study, we evaluate how physiologically relevant divalent cations affect the mechanical, dynamic, and structural properties of actin bundles. Using a combination of total internal reflection fluorescence microscopy, transmission electron microscopy, and dynamic light scattering, we demonstrate that divalent cations modulate bundle stiffness, length distribution, and lateral growth. Molecular dynamics simulations of an all-atom model of the actin bundle reveal specific actin residues coordinate cation-binding sites that promote the bundle formation. Our work suggests that specific cation interactions may play a fundamental role in the assembly, structure, and mechanical properties of actin bundles.

Charge-transfer modified embedded atom method dynamic charge potential for Li-Co-O system

NASA Astrophysics Data System (ADS)

Kong, Fantai; Longo, Roberto C.; Liang, Chaoping; Nie, Yifan; Zheng, Yongping; Zhang, Chenxi; Cho, Kyeongjae

2017-11-01

To overcome the limitation of conventional fixed charge potential methods for the study of Li-ion battery cathode materials, a dynamic charge potential method, charge-transfer modified embedded atom method (CT-MEAM), has been developed and applied to the Li-Co-O ternary system. The accuracy of the potential has been tested and validated by reproducing a variety of structural and electrochemical properties of LiCoO2. A detailed analysis on the local charge distribution confirmed the capability of this potential for dynamic charge modeling. The transferability of the potential is also demonstrated by its reliability in describing Li-rich Li2CoO2 and Li-deficient LiCo2O4 compounds, including their phase stability, equilibrium volume, charge states and cathode voltages. These results demonstrate that the CT-MEAM dynamic charge potential could help to overcome the challenge of modeling complex ternary transition metal oxides. This work can promote molecular dynamics studies of Li ion cathode materials and other important transition metal oxides systems that involve complex electrochemical and catalytic reactions.

Charge-transfer modified embedded atom method dynamic charge potential for Li-Co-O system.

PubMed

Kong, Fantai; Longo, Roberto C; Liang, Chaoping; Nie, Yifan; Zheng, Yongping; Zhang, Chenxi; Cho, Kyeongjae

2017-11-29

To overcome the limitation of conventional fixed charge potential methods for the study of Li-ion battery cathode materials, a dynamic charge potential method, charge-transfer modified embedded atom method (CT-MEAM), has been developed and applied to the Li-Co-O ternary system. The accuracy of the potential has been tested and validated by reproducing a variety of structural and electrochemical properties of LiCoO 2 . A detailed analysis on the local charge distribution confirmed the capability of this potential for dynamic charge modeling. The transferability of the potential is also demonstrated by its reliability in describing Li-rich Li 2 CoO 2 and Li-deficient LiCo 2 O 4 compounds, including their phase stability, equilibrium volume, charge states and cathode voltages. These results demonstrate that the CT-MEAM dynamic charge potential could help to overcome the challenge of modeling complex ternary transition metal oxides. This work can promote molecular dynamics studies of Li ion cathode materials and other important transition metal oxides systems that involve complex electrochemical and catalytic reactions.

On the different roles of anions and cations in the solvation of enzymes in ionic liquids.

PubMed

Klähn, Marco; Lim, Geraldine S; Seduraman, Abirami; Wu, Ping

2011-01-28

The solvation of the enzyme Candida antarctica lipase B (CAL-B) was studied in eight different ionic liquids (ILs). The influence of enzyme-ion interactions on the solvation of CAL-B and the structure of the enzyme-IL interface are analyzed. CAL-B and ILs are described with molecular dynamics (MD) simulations in combination with an atomistic empirical force field. The considered cations are based on imidazolium or guanidinium that are paired with nitrate, tetrafluoroborate or hexafluorophosphate anions. The interactions of CAL-B with ILs are dominated by Coulomb interactions with anions, while the second largest contribution stems from van der Waals interactions with cations. The enzyme-ion interaction strength is determined by the ion size and the magnitude of the ion surface charge. The solvation of CAL-B in ILs is unfavorable compared to water because of large formation energies for the CAL-B solute cages in ILs. The internal energy in the IL and of CAL-B increases linearly with the enzyme-ion interaction strength. The average electrostatic potential on the surface of CAL-B is larger in ILs than in water, due to a weaker screening of charged enzyme residues. Ion densities increased moderately in the vicinity of charged residues and decreased close to non-polar residues. An aggregation of long alkyl chains close to non-polar regions and the active site entrance of CAL-B are observed in one IL that involved long non-polar decyl groups. In ILs that contain 1-butyl-3-methylimidazolium cations, the diffusion of one or two cations into the active site of CAL-B occurs during MD simulations. This suggests a possible obstruction of the active site in these ILs. Overall, the results indicate that small ions lead to a stronger electrostatic screening within the solvent and stronger interactions with the enzyme. Also a large ion surface charge, when more hydrophilic ions are used, increases enzyme-IL interactions. An increase of these interactions destabilizes the enzyme and impedes enzyme solvation due to an increase in solute cage formation energies.

Relating Trp-Glu dipeptide fluorescence to molecular conformation: the role of the discrete Chi 1 and Chi 2 angles.

PubMed

Eisenberg, Azaria Solomon; Juszczak, Laura J

2013-07-05

Molecular dynamics (MD), coupled with fluorescence data for charged dipeptides of tryptophanyl glutamic acid (Trp-Glu), reveal a detailed picture of how specific conformation affects fluorescence. Fluorescence emission spectra and time-resolved emission measurements have been collected for all four charged species. MD simulations 20 to 30 ns in length have also been carried out for the Trp-Glu species, as simulation provides aqueous phase conformational data that can be correlated with the fluorescence data. The calculations show that each dipeptide species is characterized by a similar set of six, discrete Chi 1, Chi 2 dihedral angle pairs. The preferred Chi 1 angles--60°, 180°, and 300°--play the significant role in positioning the terminal amine relative to the indole ring. A Chi 1 angle of 60° results in the arching of the backbone over the indole ring and no interaction of the ring with the terminal amine. Chi 1 values of 180° and 300° result in an extension of the backbone away from the indole ring and a NH3 cation-π interaction with indole. This interaction is believed responsible for charge transfer quenching. Two fluorescence lifetimes and their corresponding amplitudes correlate with the Chi 1 angle probability distribution for all four charged Trp-Glu dipeptides. Fluorescence emission band maxima are also consistent with the proposed pattern of terminal amine cation quenching of fluorescence. Copyright © 2013 Wiley Periodicals, Inc.

Effect of Charge Localization on the Effective Hyperfine Interaction in Organic Semiconducting Polymers

NASA Astrophysics Data System (ADS)

Geng, Rugang; Subedi, Ram C.; Luong, Hoang M.; Pham, Minh T.; Huang, Weichuan; Li, Xiaoguang; Hong, Kunlun; Shao, Ming; Xiao, Kai; Hornak, Lawrence A.; Nguyen, Tho D.

2018-02-01

Hyperfine interaction (HFI), originating from the coupling between spins of charge carriers and nuclei, has been demonstrated to strongly influence the spin dynamics of localized charges in organic semiconductors. Nevertheless, the role of charge localization on the HFI strength in organic thin films has not yet been experimentally investigated. In this study, the statistical relation hypothesis that the effective HFI of holes in regioregular poly(3-hexylthiophene) (P3HT) is proportional to 1 /N0.5 has been examined, where N is the number of the random nuclear spins within the envelope of the hole wave function. First, by studying magnetoconductance in hole-only devices made by isotope-labeled P3HT we verify that HFI is indeed the dominant spin interaction in P3HT. Second, assuming that holes delocalize fully over the P3HT polycrystalline domain, the strength of HFI is experimentally demonstrated to be proportional to 1 /N0.52 in excellent agreement with the statistical relation. Third, the HFI of electrons in P3HT is about 3 times stronger than that of holes due to the stronger localization of the electrons. Finally, the effective HFI in organic light emitting diodes is found to be a superposition of effective electron and hole HFI. Such a statistical relation may be generally applied to other semiconducting polymers. This Letter may provide great benefits for organic optoelectronics, chemical reaction kinetics, and magnetoreception in biology.

Effect of Charge Localization on the Effective Hyperfine Interaction in Organic Semiconducting Polymers.

PubMed

Geng, Rugang; Subedi, Ram C; Luong, Hoang M; Pham, Minh T; Huang, Weichuan; Li, Xiaoguang; Hong, Kunlun; Shao, Ming; Xiao, Kai; Hornak, Lawrence A; Nguyen, Tho D

2018-02-23

Hyperfine interaction (HFI), originating from the coupling between spins of charge carriers and nuclei, has been demonstrated to strongly influence the spin dynamics of localized charges in organic semiconductors. Nevertheless, the role of charge localization on the HFI strength in organic thin films has not yet been experimentally investigated. In this study, the statistical relation hypothesis that the effective HFI of holes in regioregular poly(3-hexylthiophene) (P3HT) is proportional to 1/N^{0.5} has been examined, where N is the number of the random nuclear spins within the envelope of the hole wave function. First, by studying magnetoconductance in hole-only devices made by isotope-labeled P3HT we verify that HFI is indeed the dominant spin interaction in P3HT. Second, assuming that holes delocalize fully over the P3HT polycrystalline domain, the strength of HFI is experimentally demonstrated to be proportional to 1/N^{0.52} in excellent agreement with the statistical relation. Third, the HFI of electrons in P3HT is about 3 times stronger than that of holes due to the stronger localization of the electrons. Finally, the effective HFI in organic light emitting diodes is found to be a superposition of effective electron and hole HFI. Such a statistical relation may be generally applied to other semiconducting polymers. This Letter may provide great benefits for organic optoelectronics, chemical reaction kinetics, and magnetoreception in biology.

Effects of the bond polarity on the structural and dynamical properties of silica-like liquids

NASA Astrophysics Data System (ADS)

Pafong Sanjon, E.; Drossel, B.; Vogel, M.

2018-03-01

Silica is a network-forming liquid that shares many properties with water due to its tetrahedral structure. It undergoes a transition from a fragile to a strong liquid as the temperature is decreased, which is accompanied by a structural change to lower density and higher tetrahedral order. In order to disentangle the effects of Coulomb and van der Waals interactions on the structure and dynamics of liquid silica, we modify the bond polarity by changing the partial charges assigned to each atom. Using molecular dynamics simulations, we show that density, tetrahedral order, and structural relaxation times decrease when reducing bond polarity. Moreover, we find that the density maximum and the fragile-to-strong transition move to lower temperatures until they eventually vanish when the partial charges are decreased below approximately 75% of their regular value. Irrespective of whether strong or fragile behavior exists, structural relaxation is governed by hopping motion at sufficiently low temperatures. As long as there is a strong regime, the energy barrier associated with strong dynamics decreases with decreasing partial charges, but the dependence on the bond polarity differs from that of the activation energy in the Arrhenius regime at high temperatures. We show that the fragile-to-strong transition is associated with structural changes occurring between the first and second coordination shells that lead to a decrease in density and an increase in tetrahedral order. In particular, independent of the value of the partial charges, the distribution of the local structures is the same at this dynamic crossover, but we find no evidence that the effect occurs upon crossing the Widom line. In the fragile regime at intermediate temperatures, the relaxation times are well described by a previously proposed model which decomposes the apparent activation energy into a constant single-particle contribution and a temperature-dependent collective contribution. However, our results for silica-like melts do not obey several common relations of the model parameters reported for molecular glass formers.

Fractional Dynamics of Single File Diffusion in Dusty Plasma Ring

NASA Astrophysics Data System (ADS)

Muniandy, S. V.; Chew, W. X.; Asgari, H.; Wong, C. S.; Lim, S. C.

2011-11-01

Single file diffusion (SFD) refers to the constrained motion of particles in quasi-one-dimensional channel such that the particles are unable to pass each other. Possible SFD of charged dust confined in biharmonic annular potential well with screened Coulomb interaction is investigated. Transition from normal diffusion to anomalous sub-diffusion behaviors is observed. Deviation from SFD's mean square displacement scaling behavior of 1/2-exponent may occur in strongly interacting systems. A phenomenological model based on fractional Langevin equation is proposed to account for the anomalous SFD behavior in dusty plasma ring.

Kinetic effects on the transition to relativistic self-induced transparency in laser-driven ion acceleration

NASA Astrophysics Data System (ADS)

Siminos, Evangelos; Svedung Wettervik, Benjamin; Grech, Mickael; Fülöp, Tünde

2016-10-01

We study kinetic effects responsible for the transition to relativistic self-induced transparency in the interaction of a circularly-polarized laser-pulse with an overdense plasma and their relation to hole-boring and ion acceleration. It is shown, using particle-in-cell simulations and an analysis of separatrices in single-particle phase-space, that this transition is mediated by the complex interplay of fast electron dynamics and ion motion at the initial stage of the interaction. It thus depends on the ion charge-to-mass ratio and can be controlled by varying the laser temporal profile. Moreover, we find a new regime in which a transition from relativistic transparency to hole-boring occurs dynamically during the course of the interaction. It is shown that, for a fixed laser intensity, this dynamic transition regime allows optimal ion acceleration in terms of both energy and energy spread. This work was supported by the Knut and Alice Wallenberg Foundation (pliona project) and the European Research Council (ERC-2014-CoG Grant 647121).

Dynamic spin injection into a quantum well coupled to a spin-split bound state

NASA Astrophysics Data System (ADS)

Maslova, N. S.; Rozhansky, I. V.; Mantsevich, V. N.; Arseyev, P. I.; Averkiev, N. S.; Lähderanta, E.

2018-05-01

We present a theoretical analysis of dynamic spin injection due to spin-dependent tunneling between a quantum well (QW) and a bound state split in spin projection due to an exchange interaction or external magnetic field. We focus on the impact of Coulomb correlations at the bound state on spin polarization and sheet density kinetics of the charge carriers in the QW. The theoretical approach is based on kinetic equations for the electron occupation numbers taking into account high order correlation functions for the bound state electrons. It is shown that the on-site Coulomb repulsion leads to an enhanced dynamic spin polarization of the electrons in the QW and a delay in the carriers tunneling into the bound state. The interplay of these two effects leads to nontrivial dependence of the spin polarization degree, which can be probed experimentally using time-resolved photoluminescence experiments. It is demonstrated that the influence of the Coulomb interactions can be controlled by adjusting the relaxation rates. These findings open a new way of studying the Hubbard-like electron interactions experimentally.

The role of nonbonded interactions in the conformational dynamics of organophosphorous hydrolase adsorbed onto functionalized mesoporous silica surfaces.

PubMed

Gomes, Diego E B; Lins, Roberto D; Pascutti, Pedro G; Lei, Chenghong; Soares, Thereza A

2010-01-14

The enzyme organophosphorous hydrolase (OPH) catalyzes the hydrolysis of a wide variety of organophosphorous compounds with high catalytic efficiency and broad substrate specificity. The immobilization of OPH in functionalized mesoporous silica (FMS) surfaces increases significantly its catalytic specific activity, as compared to the enzyme in solution, with important applications for the detection and decontamination of insecticides and chemical warfare agents. Experimental measurements of immobilization efficiency as a function of the charge and coverage percentage of different functional groups have been interpreted as electrostatic forces being the predominant interactions underlying the adsorption of OPH onto FMS surfaces. Explicit solvent molecular dynamics simulations have been performed for OPH in bulk solution and adsorbed onto two distinct interaction potential models of the FMS functional groups to investigate the relative contributions of nonbonded interactions to the conformational dynamics and adsorption of the protein. Our results support the conclusion that electrostatic interactions are responsible for the binding of OPH to the FMS surface. However, these results also show that van der Waals forces are detrimental for interfacial adhesion. In addition, it is found that OPH adsorption onto the FMS models favors a protein conformation whose active site is fully accessible to the substrate, in contrast to the unconfined protein.

Surface potential-governed cellular osteogenic differentiation on ferroelectric polyvinylidene fluoride trifluoroethylene films.

PubMed

Tang, Bolin; Zhang, Bo; Zhuang, Junjun; Wang, Qi; Dong, Lingqing; Cheng, Kui; Weng, Wenjian

2018-07-01

Surface potential of biomaterials can dramatically influence cellular osteogenic differentiation. In this work, a wide range of surface potential on ferroelectric polyvinylidene fluoride trifluoroethylene (P(VDF-TrFE)) films was designed to get insight into the interfacial interaction of cell-charged surface. The P(VDF-TrFE) films poled by contact electric poling at various electric fields obtained well stabilized surface potential, with wide range from -3 to 915 mV. The osteogenic differentiation level of cells cultured on the films was strongly dependent on surface potential and reached the optimum at 391 mV in this system. Binding specificity assay indicated that surface potential could effectively govern the binding state of the adsorbed fibronectin (FN) with integrin. Molecular dynamic (MD) simulation further revealed that surface potential brought a significant difference in the relative distance between RGD and synergy PHSRN sites of adsorbed FN, resulting in a distinct integrin-FN binding state. These results suggest that the full binding of integrin α5β1 with both RGD and PHSRN sites of FN possesses a strong ability to activate osteogenic signaling pathway. This work sheds light on the underlying mechanism of osteogenic differentiation behavior on charged material surfaces, and also provides a guidance for designing a reasonable charged surface to enhance osteogenic differentiation. The ferroelectric P(VDF-TrFE) films with steady and a wide range of surface potential were designed to understand underlying mechanism of cell-charged surface interaction. The results showed that the charged surface well favored upregulation of osteogenic differentiation of MC3T3-E1 cells, and more importantly, a highest level occurred on the film with a moderate surface potential. Experiments and molecular dynamics simulation demonstrated that the surface potential could govern fibronectin conformation and then the integrin-fibronectin binding. We propose that a full binding state of integrin α5β1 with fibronectin induces effective activation of integrin-mediated FAK/ERK signaling pathway to upregulate cellular osteogenic differentiation. This work provides a guidance for designing a reasonable charged surface to enhance osteogenic differentiation. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules.

PubMed

Mondal, Saptarsi; Chaterjee, Soumit; Halder, Ritaban; Jana, Biman; Singh, Prashant Chandra

2017-08-17

Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (C═O and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules.

First interactions between hydrogen and stress-induced reverse transformation of Ni-Ti superelastic alloy

NASA Astrophysics Data System (ADS)

Yokoyama, Ken'ichi; Hashimoto, Tatsuki; Sakai, Jun'ichi

2017-11-01

The first dynamic interactions between hydrogen and the stress-induced reverse transformation have been investigated by performing an unloading test on a Ni-Ti superelastic alloy subjected to hydrogen charging under a constant applied strain in the elastic deformation region of the martensite phase. Upon unloading the specimen, charged with a small amount of hydrogen, no change in the behaviour of the stress-induced reverse transformation is observed in the stress-strain curve, although the behaviour of the stress-induced martensite transformation changes. With increasing amount of hydrogen charging, the critical stress for the reverse transformation markedly decreases. Eventually, for a larger amount of hydrogen charging, the reverse transformation does not occur, i.e. there is no recovery of the superelastic strain. The residual martensite phase on the side surface of the unloaded specimen is confirmed by X-ray diffraction. Upon training before the unloading test, the properties of the reverse transformation slightly recover after ageing in air at room temperature. The present study indicates that to change the behaviour of the reverse transformation a larger amount of hydrogen than that for the martensite transformation is necessary. In addition, it is likely that a substantial amount of hydrogen in solid solution more strongly suppresses the reverse transformation than hydrogen trapped at defects, thereby stabilising the martensite phase.

Dynamical formation of a Reissner-Nordström black hole with scalar hair in a cavity

NASA Astrophysics Data System (ADS)

Sanchis-Gual, Nicolas; Degollado, Juan Carlos; Herdeiro, Carlos; Font, José A.; Montero, Pedro J.

2016-08-01

In a recent Letter [Sanchis-Gual et al., Phys. Rev. Lett. 116, 141101 (2016)], we presented numerical relativity simulations, solving the full Einstein-Maxwell-Klein-Gordon equations, of superradiantly unstable Reissner-Nordström black holes (BHs), enclosed in a cavity. Low frequency, spherical perturbations of a charged scalar field trigger this instability. The system's evolution was followed into the nonlinear regime, until it relaxed into an equilibrium configuration, found to be a hairy BH: a charged horizon in equilibrium with a scalar field condensate, whose phase is oscillating at the (final) critical frequency. Here, we investigate the impact of adding self-interactions to the scalar field. In particular, we find sufficiently large self-interactions suppress the exponential growth phase, known from linear theory, and promote a nonmonotonic behavior of the scalar field energy. Furthermore, we discuss in detail the influence of the various parameters in this model: the initial BH charge, the initial scalar perturbation, the scalar field charge, the mass, and the position of the cavity's boundary (mirror). We also investigate the "explosive" nonlinear regime previously reported to be akin to a bosenova. A mode analysis shows that the "explosions" can be interpreted as the decay into the BH of modes that exit the superradiant regime.

In situ measurements of Saturn’s ionosphere show that it is dynamic and interacts with the rings

NASA Astrophysics Data System (ADS)

Wahlund, J.-E.; Morooka, M. W.; Hadid, L. Z.; Persoon, A. M.; Farrell, W. M.; Gurnett, D. A.; Hospodarsky, G.; Kurth, W. S.; Ye, S.-Y.; Andrews, D. J.; Edberg, N. J. T.; Eriksson, A. I.; Vigren, E.

2018-01-01

The ionized upper layer of Saturn’s atmosphere, its ionosphere, provides a closure of currents mediated by the magnetic field to other electrically charged regions (for example, rings) and hosts ion-molecule chemistry. In 2017, the Cassini spacecraft passed inside the planet’s rings, allowing in situ measurements of the ionosphere. The Radio and Plasma Wave Science instrument detected a cold, dense, and dynamic ionosphere at Saturn that interacts with the rings. Plasma densities reached up to 1000 cubic centimeters, and electron temperatures were below 1160 kelvin near closest approach. The density varied between orbits by up to two orders of magnitude. Saturn’s A- and B-rings cast a shadow on the planet that reduced ionization in the upper atmosphere, causing a north-south asymmetry.

A Hamiltonian Model of Dissipative Wave-particle Interactions and the Negative-mass Effect

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

A. Zhmoginov

2011-02-07

The effect of radiation friction is included in the Hamiltonian treatment of wave-particle interactions with autoresonant phase-locking, yielding a generalized canonical approach to the problem of dissipative dynamics near a nonlinear resonance. As an example, the negativemass eff ect exhibited by a charged particle in a pump wave and a static magnetic field is studied in the presence of the friction force due to cyclotron radiation. Particles with negative parallel masses m! are shown to transfer their kinetic energy to the pump wave, thus amplifying it. Counterintuitively, such particles also undergo stable dynamics, decreasing their transverse energy monotonically due tomore » cyclotron cooling, whereas some of those with positive m! undergo cyclotron heating instead, extracting energy from the pump wave.« less

A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics.

PubMed

Jha, Prateek K; Sknepnek, Rastko; Guerrero-García, Guillermo Iván; Olvera de la Cruz, Monica

2010-10-12

We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys. 2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of electrolytes. Our GPU implementation is significantly faster than the CPU implementation of the Ewald method for small to a sizable number of particles (∼10(5)). Thermodynamic and structural properties of monovalent and divalent hydrated salts in the bulk are calculated for a wide range of ionic concentrations. An excellent agreement between the two methods was found at the level of electrostatic energy, heat capacity, radial distribution functions, and integrated charge of the electrolytes.

Regimes of electrostatic collapse of a highly charged polyelectrolyte in a poor solvent.

PubMed

Tom, Anvy Moly; Vemparala, Satyavani; Rajesh, R; Brilliantov, Nikolai V

2017-03-01

We perform extensive molecular dynamics simulations of a highly charged, collapsed, flexible polyelectrolyte chain in a poor solvent for the case when the electrostatic interactions, characterized by the reduced Bjerrum length l B , are strong. We find the existence of several sub-regimes in the dependence of the gyration radius of the chain R g on l B characterized by R g ∼ l. In contrast to a good solvent, the exponent γ for a poor solvent crucially depends on the size and valency of the counterions. To explain the different sub-regimes, we generalize the existing counterion fluctuation theory by including a more complete account of all possible volume interactions in the free energy of the polyelectrolyte chain. We also show that the presence of condensed counterions modifies the effective attraction among the chain monomers and modulates the sign of the second virial coefficient under poor solvent conditions.

Ion transport and structural dynamics in homologous ammonium and phosphonium-based room temperature ionic liquids

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

Griffin, Philip J., E-mail: pgrif@seas.upenn.edu; Holt, Adam P.; Tsunashima, Katsuhiko

2015-02-28

Charge transport and structural dynamics in a homologous pair of ammonium and phosphonium based room temperature ionic liquids (ILs) have been characterized over a wide temperature range using broadband dielectric spectroscopy and quasi-elastic light scattering spectroscopy. We have found that the ionic conductivity of the phosphonium based IL is significantly enhanced relative to the ammonium homolog, and this increase is primarily a result of a lower glass transition temperature and higher ion mobility. Additionally, these ILs exhibit pronounced secondary relaxations which are strongly influenced by the atomic identity of the cation charge center. While the secondary relaxation in the phosphoniummore » IL has the expected Arrhenius temperature dependence characteristic of local beta relaxations, the corresponding relaxation process in the ammonium IL was found to exhibit a mildly non-Arrhenius temperature dependence in the measured temperature range—indicative of molecular cooperativity. These differences in both local and long-range molecular dynamics are a direct reflection of the subtly different inter-ionic interactions and mesoscale structures found in these homologous ILs.« less

Ion transport and structural dynamics in homologous ammonium and phosphonium-based room temperature ionic liquids

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

Griffin, Phillip J.; Holt, Adam P.; Tsunashima, Katsuhiko

2015-02-01

Charge transport and structural dynamics in a homologous pair of ammonium and phosphonium based room temperature ionic liquids (ILs) have been characterized over a wide temperature range using broadband dielectric spectroscopy and quasi-elastic light scattering spectroscopy. We have found that the ionic conductivity of the phosphonium based IL is significantly enhanced relative to the ammonium homolog, and this increase is primarily a result of a lower glass transition temperature and higher ion mobility. Additionally, these ILs exhibit pronounced secondary relaxations which are strongly influenced by the atomic identity of the cation charge center. While the secondary relaxation in the phosphoniummore » IL has the expected Arrhenius temperature dependence characteristic of local beta relaxations, the corresponding relaxation process in the ammonium IL was found to exhibit a mildly non-Arrhenius temperature dependence in the measured temperature range-indicative of molecular cooperativity. These differences in both local and long-range molecular dynamics are a direct reflection of the subtly different inter-ionic interactions and mesoscale structures found in these homologous ILs.« less

Hydration and Ion Pairing in Aqueous Mg2+ and Zn2+ Solutions: Force-Field Description Aided by Neutron Scattering Experiments and Ab Initio Molecular Dynamics Simulations.

PubMed

Duboué-Dijon, Elise; Mason, Philip E; Fischer, Henry E; Jungwirth, Pavel

2018-04-05

Magnesium and zinc dications possess the same charge and have an almost identical size, yet they behave very differently in aqueous solutions and play distinct biological roles. It is thus crucial to identify the origins of such different behaviors and to assess to what extent they can be captured by force-field molecular dynamics simulations. In this work, we combine neutron scattering experiments in a specific mixture of H 2 O and D 2 O (the so-called null water) with ab initio molecular dynamics simulations to probe the difference in the hydration structure and ion-pairing properties of chloride solutions of the two cations. The obtained data are used as a benchmark to develop a scaled-charge force field for Mg 2+ that includes electronic polarization in a mean field way. We show that using this electronic continuum correction we can describe aqueous magnesium chloride solutions well. However, in aqueous zinc chloride specific interaction terms between the ions need to be introduced to capture ion pairing quantitatively.

Metal nanoparticle-graphene oxide composites: Photophysical properties and sensing applications

NASA Astrophysics Data System (ADS)

Murphy, Sean J.

Composite nanomaterials allow for attractive properties of multiple functional components to be combined. Fundamental understanding of the interaction between different nanomaterials, their surroundings, and nearby molecular species is pertinent for implementation into devices. Metal nanoparticles have been used for their optical properties in many applications including stained glass, cancer therapy, solar steam generation, surface enhanced Raman spectroscopy (SERS), and catalysis. Carbon-based nanomaterials such as graphene and carbon nanotubes show potential for a wide variety of applications including solar energy harvesting, chemical sensors, and electronics. Combining useful and in some cases new properties of composite nanomaterials offers exciting opportunities in fundamental science and device development. In this dissertation, I aim to address understanding photoinduced interaction between porphyrin and silver nanoparticles, inter-sheet interaction between stacked graphene oxide (GO) sheets in thin films, complexation of reduced GO with Raman active target molecule in SERS applications, and efficacy of graphene-metal nanoparticle composites for sensing applications. Molecule-metal nanoparticle composite material made up of photoactive porphyrin and silver nanoparticles was studied using various spectroscopic tools. UV-visible absorption and surface enhanced Raman spectroscopic results suggest formation of a charge-transfer complex for porphyrin-silver nanoparticle composite. Ultrafast transient absorption and fluorescence upconversion spectroscopies further corroborate electronic interaction by providing evidence for excited state electron transfer between porphyrin and silver nanoparticles. Understanding electronic interaction between adsorbed photoactive molecules and metal nanoparticles may be of use for applications in photocatalysis or light-energy harvesting. Graphene oxide (GO) thin films have been prepared and studied using transient absorption microscopy (TAM). Transient absorption microscopy correlated with atomic force microscope allows for the morphological properties of GO thin film to be related to optical properties, namely dynamics of photoexcited carriers in GO. Results suggest short-timescale (ps -- ˜1 ns) dynamics of charge carriers in GO are affected very little by interaction with the glass substrate on which GO is placed. Also, the stack thickness or number of stacked GO sheets does not play a large role in the short-timescale dynamics of GO charge carriers. GO or reduced GO (RGO)-silver nanoparticles composites were produced using different methods: (1) chemical reduction of silver ion precursor and (2) photocatalytic reduction of GO and silver ion using TiO2 nanoparticles. Optical and morphological properties of composites were studied using spectroscopy and electron microscopy revealing a degree of control in metal nanoparticle growth and loading on the surface of RGO. Nanocomposites were shown to be capable of complexing with or adsorbing target molecular species. Complexation and adsorption are corroborated with demonstration that the composite nanomaterials act as effective SERRS sensors taking advantage of localized surface plasmon resonance of metal nanoparticles and the ability of RGO to interact with molecular and ionic species.

Hyperbolic metamaterial nanostructures to tune charge-transfer dynamics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lee, Kwang Jin; Xiao, Yiming; Woo, Jae Heun; Kim, Eun Sun; Kreher, David; Attias, André-Jean; Mathevet, Fabrice; Ribierre, Jean-Charles; Wu, Jeong Weon; André, Pascal

2016-09-01

Charge transfer (CT) is an essential phenomenon relevant to numerous fields including biology, physics and chemistry.1-5 Here, we demonstrate that multi-layered hyperbolic metamaterial (HMM) substrates alter organic semiconductor CT dynamics.6 With triphenylene:perylene diimide dyad supramolecular self-assemblies prepared on HMM substrates, we show that both charge separation (CS) and charge recombination (CR) characteristic times are increased by factors of 2.5 and 1.6, respectively, resulting in longer-lived CT states. We successfully rationalize the experimental data by extending Marcus theory framework with dipole image interactions tuning the driving force. The number of metal-dielectric pairs alters the HMM interfacial effective dielectric constant and becomes a solid analogue to solvent polarizability. Based on the experimental results and extended Marcus theory framework, we find that CS and CR processes are located in normal and inverted regions on Marcus parabola diagram, respectively. The model and further PH3T:PCBM data show that the phenomenon is general and that molecular and substrate engineering offer a wide range of kinetic tailoring opportunities. This work opens the path toward novel artificial substrates designed to control CT dynamics with potential applications in fields including optoelectronics, organic solar cells and chemistry. 1. Marcus, Rev. Mod. Phys., 1993, 65, 599. 2. Marcus, Phys. Chem. Chem. Phys., 2012, 14, 13729. 3. Lambert, et al., Nat. Phys., 2012, 9, 10. 4. C. Clavero, Nat. Photon., 2014, 8, 95. 5. A. Canaguier-Durand, et al., Angew. Chem. Int. Ed., 2013, 52, 10533. 6. K. J. Lee, et al., Submitted, 2015, arxiv.org/abs/1510.08574.

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

NASA Astrophysics Data System (ADS)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

Carrier dynamics and the role of surface defects: Designing a photocatalyst for gas-phase CO 2 reduction

DOE PAGES

Hoch, Laura B.; Szymanski, Paul; Ghuman, Kulbir Kaur; ...

2016-11-28

In 2O 3-x(OH) y nanoparticles have been shown to function as an effective gas-phase photocatalyst for the reduction of CO 2 to CO via the reverse water–gas shift reaction. Their photocatalytic activity is strongly correlated to the number of oxygen vacancy and hydroxide defects present in the system. To better understand how such defects interact with photogenerated electrons and holes in these materials, we have studied the relaxation dynamics of In 2O 3-x(OH) y nanoparticles with varying concentration of defects using two different excitation energies corresponding to above-band-gap (318-nm) and near-band-gap (405-nm) excitations. Our results demonstrate that defects play amore » significant role in the excited-state, charge relaxation pathways. Higher defect concentrations result in longer excited-state lifetimes, which are attributed to improved charge separation. This correlates well with the observed trends in the photocatalytic activity. These results are further supported by density-functional theory calculations, which confirm the positions of oxygen vacancy and hydroxide defect states within the optical band gap of indium oxide. This enhanced understanding of the role these defects play in determining the optoelectronic properties and charge carrier dynamics can provide valuable insight toward the rational development of more efficient photocatalytic materials for CO 2 reduction.« less

Carrier dynamics and the role of surface defects: Designing a photocatalyst for gas-phase CO 2 reduction

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

Hoch, Laura B.; Szymanski, Paul; Ghuman, Kulbir Kaur

In 2O 3-x(OH) y nanoparticles have been shown to function as an effective gas-phase photocatalyst for the reduction of CO 2 to CO via the reverse water–gas shift reaction. Their photocatalytic activity is strongly correlated to the number of oxygen vacancy and hydroxide defects present in the system. To better understand how such defects interact with photogenerated electrons and holes in these materials, we have studied the relaxation dynamics of In 2O 3-x(OH) y nanoparticles with varying concentration of defects using two different excitation energies corresponding to above-band-gap (318-nm) and near-band-gap (405-nm) excitations. Our results demonstrate that defects play amore » significant role in the excited-state, charge relaxation pathways. Higher defect concentrations result in longer excited-state lifetimes, which are attributed to improved charge separation. This correlates well with the observed trends in the photocatalytic activity. These results are further supported by density-functional theory calculations, which confirm the positions of oxygen vacancy and hydroxide defect states within the optical band gap of indium oxide. This enhanced understanding of the role these defects play in determining the optoelectronic properties and charge carrier dynamics can provide valuable insight toward the rational development of more efficient photocatalytic materials for CO 2 reduction.« less

A Technology-Enhanced Unit of Modeling Static Electricity: Integrating scientific explanations and everyday observations

NASA Astrophysics Data System (ADS)

Shen, Ji; Linn, Marcia C.

2011-08-01

What trajectories do students follow as they connect their observations of electrostatic phenomena to atomic-level visualizations? We designed an electrostatics unit, using the knowledge integration framework to help students link observations and scientific ideas. We analyze how learners integrate ideas about charges, charged particles, energy, and observable events. We compare learning enactments in a typical school and a magnet school in the USA. We use pre-tests, post-tests, embedded notes, and delayed post-tests to capture the trajectories of students' knowledge integration. We analyze how visualizations help students grapple with abstract electrostatics concepts such as induction. We find that overall students gain more sophisticated ideas. They can interpret dynamic, interactive visualizations, and connect charge- and particle-based explanations to interpret observable events. Students continue to have difficulty in applying the energy-based explanation.

Origin of higher affinity to RNA of the N-terminal RNA-binding domain than that of the C-terminal one of a mouse neural protein, musashi1, as revealed by comparison of their structures, modes of interaction, surface electrostatic potentials, and backbone dynamics.

PubMed

Miyanoiri, Youhei; Kobayashi, Hisanori; Imai, Takao; Watanabe, Michinao; Nagata, Takashi; Uesugi, Seiichi; Okano, Hideyuki; Katahira, Masato

2003-10-17

Musashi1 is an RNA-binding protein abundantly expressed in the developing mouse central nervous system. Its restricted expression in neural precursor cells suggests that it is involved in maintenance of the character of progenitor cells. Musashi1 contains two ribonucleoprotein-type RNA-binding domains (RBDs), RBD1 and RBD2, the affinity to RNA of RBD1 being much higher than that of RBD2. We previously reported the structure and mode of interaction with RNA of RBD2. Here, we have determined the structure and mode of interaction with RNA of RBD1. We have also analyzed the surface electrostatic potential and backbone dynamics of both RBDs. The two RBDs exhibit the same ribo-nucleoprotein-type fold and commonly make contact with RNA on the beta-sheet side. On the other hand, there is a remarkable difference in surface electrostatic potential, the beta-sheet of RBD1 being positively charged, which is favorable for binding negatively charged RNA, but that of RBD2 being almost neutral. There is also a difference in backbone dynamics, the central portion of the beta-sheet of RBD1 being flexible, but that of RBD2 not being flexible. The flexibility of RBD1 may be utilized in the recognition process to facilitate an induced fit. Thus, comparative studies have revealed the origin of the higher affinity of RBD1 than that of RBD2 and indicated that the affinity of an RBD to RNA is not governed by its fold alone but is also determined by its surface electrostatic potential and/or backbone dynamics. The biological role of RBD2 with lower affinity is also discussed.

Charging of insulators by multiply-charged-ion impact probed by slowing down of fast binary-encounter electrons

NASA Astrophysics Data System (ADS)

de Filippo, E.; Lanzanó, G.; Amorini, F.; Cardella, G.; Geraci, E.; Grassi, L.; La Guidara, E.; Lombardo, I.; Politi, G.; Rizzo, F.; Russotto, P.; Volant, C.; Hagmann, S.; Rothard, H.

2010-12-01

The interaction of ion beams with insulators leads to charging-up phenomena, which at present are under investigation in connection with guiding phenomena in nanocapillaries with possible application in nanofocused beams. We studied the charging dynamics of insulating foil targets [Mylar, polypropylene (PP)] irradiated with swift ion beams (C, O, Ag, and Xe at 40, 23, 40, and 30 MeV/u, respectively) via the measurement of the slowing down of fast binary-encounter electrons. Also, sandwich targets (Mylar covered with a thin Au layer on both surfaces) and Mylar with Au on only one surface were used. Fast-electron spectra were measured by the time-of-flight method at the superconducting cyclotron of Laboratori Nazionali del Sud (LNS) Catania. The charge buildup leads to target-material-dependent potentials of the order of 6.0 kV for Mylar and 2.8 kV for PP. The sandwich targets, surprisingly, show the same behavior as the insulating targets, whereas a single Au layer on the electron and ion exit side strongly suppresses the charging phenomenon. The accumulated number of projectiles needed for charging up is inversely proportional to electronic energy loss. Thus, the charging up is directly related to emission of secondary electrons.

Using a water-confined carbon nanotube to probe the electricity of sequential charged segments of macromolecules

NASA Astrophysics Data System (ADS)

Wang, Yu; Zhao, Yan-Jiao; Huang, Ji-Ping

2012-07-01

The detection of macromolecular conformation is particularly important in many physical and biological applications. Here we theoretically explore a method for achieving this detection by probing the electricity of sequential charged segments of macromolecules. Our analysis is based on molecular dynamics simulations, and we investigate a single file of water molecules confined in a half-capped single-walled carbon nanotube (SWCNT) with an external electric charge of +e or -e (e is the elementary charge). The charge is located in the vicinity of the cap of the SWCNT and along the centerline of the SWCNT. We reveal the picosecond timescale for the re-orientation (namely, from one unidirectional direction to the other) of the water molecules in response to a switch in the charge signal, -e → +e or +e → -e. Our results are well understood by taking into account the electrical interactions between the water molecules and between the water molecules and the external charge. Because such signals of re-orientation can be magnified and transported according to Tu et al. [2009 Proc. Natl. Acad. Sci. USA 106 18120], it becomes possible to record fingerprints of electric signals arising from sequential charged segments of a macromolecule, which are expected to be useful for recognizing the conformations of some particular macromolecules.

Measurements of Lunar Dust Charging Properties by Electron Impact

NASA Technical Reports Server (NTRS)

Abbas, Mian M.; Tankosic, Dragana; Craven, Paul D.; Schneider, Todd A.; Vaughn, Jason A.; LeClair, Andre; Spann, James F.; Norwood, Joseph K.

2009-01-01

Dust grains in the lunar environment are believed to be electrostatically charged predominantly by photoelectric emissions resulting from solar UV radiation on the dayside, and on the nightside by interaction with electrons in the solar wind plasma. In the high vacuum environment on the lunar surface with virtually no atmosphere, the positive and negative charge states of micron/submicron dust grains lead to some unusual physical and dynamical dust phenomena. Knowledge of the electrostatic charging properties of dust grains in the lunar environment is required for addressing their hazardous effect on the humans and mechanical systems. It is well recognized that the charging properties of individual small micron size dust grains are substantially different from the measurements on bulk materials. In this paper we present the results of measurements on charging of individual Apollo 11 and Apollo 17 dust grains by exposing them to mono-energetic electron beams in the 10-100 eV energy range. The charging/discharging rates of positively and negatively charged particles of approx. 0.1 to 5 micron radii are discussed in terms of the sticking efficiencies and secondary electron yields. The secondary electron emission process is found to be a complex and effective charging/discharging mechanism for incident electron energies as low as 10-25 eV, with a strong dependence on particle size. Implications of the laboratory measurements on the nature of dust grain charging in the lunar environment are discussed.

Adsorption of hydrophobin on different self-assembled monolayers: the role of the hydrophobic dipole and the electric dipole.

PubMed

Peng, Chunwang; Liu, Jie; Zhao, Daohui; Zhou, Jian

2014-09-30

In this work, the adsorptions of hydrophobin (HFBI) on four different self-assembled monolayers (SAMs) (i.e., CH3-SAM, OH-SAM, COOH-SAM, and NH2-SAM) were investigated by parallel tempering Monte Carlo and molecular dynamics simulations. Simulation results indicate that the orientation of HFBI adsorbed on neutral surfaces is dominated by a hydrophobic dipole. HFBI adsorbs on the hydrophobic CH3-SAM through its hydrophobic patch and adopts a nearly vertical hydrophobic dipole relative to the surface, while it is nearly horizontal when adsorbed on the hydrophilic OH-SAM. For charged SAM surfaces, HFBI adopts a nearly vertical electric dipole relative to the surface. HFBI has the narrowest orientation distribution on the CH3-SAM, and thus can form an ordered monolayer and reverse the wettability of the surface. For HFBI adsorption on charged SAMs, the adsorption strength weakens as the surface charge density increases. Compared with those on other SAMs, a larger area of the hydrophobic patch is exposed to the solution when HFBI adsorbs on the NH2-SAM. This leads to an increase of the hydrophobicity of the surface, which is consistent with the experimental results. The binding of HFBI to the CH3-SAM is mainly through hydrophobic interactions, while it is mediated through a hydration water layer near the surface for the OH-SAM. For the charged SAM surfaces, the adsorption is mainly induced by electrostatic interactions between the charged surfaces and the oppositely charged residues. The effect of a hydrophobic dipole on protein adsorption onto hydrophobic surfaces is similar to that of an electric dipole for charged surfaces. Therefore, the hydrophobic dipole may be applied to predict the probable orientations of protein adsorbed on hydrophobic surfaces.

Effective charges and virial pressure of concentrated macroion solutions

DOE PAGES

Boon, Niels; Guerrero-García, Guillermo Ivan; van Roij, René; ...

2015-07-13

The stability of colloidal suspensions is crucial in a wide variety of processes, including the fabrication of photonic materials and scaffolds for biological assemblies. The ionic strength of the electrolyte that suspends charged colloids is widely used to control the physical properties of colloidal suspensions. The extensively used two-body Derjaguin-Landau-Verwey-Overbeek (DLVO) approach allows for a quantitative analysis of the effective electrostatic forces between colloidal particles. DLVO relates the ionic double layers, which enclose the particles, to their effective electrostatic repulsion. Nevertheless, the double layer is distorted at high macroion volume fractions. Therefore, DLVO cannot describe the many-body effects that arisemore » in concentrated suspensions. In this paper, we show that this problem can be largely resolved by identifying effective point charges for the macroions using cell theory. This extrapolated point charge (EPC) method assigns effective point charges in a consistent way, taking into account the excluded volume of highly charged macroions at any concentration, and thereby naturally accounting for high volume fractions in both salt-free and added-salt conditions. We provide an analytical expression for the effective pair potential and validate the EPC method by comparing molecular dynamics simulations of macroions and monovalent microions that interact via Coulombic potentials to simulations of macroions interacting via the derived EPC effective potential. The simulations reproduce the macroion-macroion spatial correlation and the virial pressure obtained with the EPC model. Finally, our findings provide a route to relate the physical properties such as pressure in systems of screened Coulomb particles to experimental measurements.« less

The influence of ligand charge and length on the assembly of Brome mosaic virus derived virus-like particles with magnetic core

NASA Astrophysics Data System (ADS)

Mieloch, Adam A.; Krecisz, Monika; Rybka, Jakub D.; Strugała, Aleksander; Krupiński, Michał; Urbanowicz, Anna; Kozak, Maciej; Skalski, Bohdan; Figlerowicz, Marek; Giersig, Michael

2018-03-01

Virus-like particles (VLPs) have sparked a great interest in the field of nanobiotechnology and nanomedicine. The introduction of superparamagnetic nanoparticles (SPIONs) as a core, provides potential use of VLPs in the hyperthermia therapy, MRI contrast agents and magnetically-powered delivery agents. Magnetite NPs also provide a significant improvement in terms of VLPs stability. Moreover employing viral structural proteins as self-assembling units has opened a new paths for targeted therapy, drug delivery systems, vaccines design, and many more. In many cases, the self-assembly of a virus strongly depends on electrostatic interactions between positively charged groups of the capsid proteins and negatively charged nucleic acid. This phenomenon imposes the negative net charge as a key requirement for the core nanoparticle. In our experiments, Brome mosaic virus (BMV) capsid proteins isolated from infected plants Hordeum vulgare were used. Superparamagnetic iron oxide nanoparticles (Fe3O4) with 15 nm in diameter were synthesized by thermal decomposition and functionalized with COOH-PEG-PL polymer or dihexadecylphosphate (DHP) in order to provide water solubility and negative charge required for the assembly. Nanoparticles were characterized by Transmission Electron Microscopy (TEM), Dynamic Light Scattering (DLS), Zeta Potential, Fourier Transformed Infrared Spectroscopy (FTIR) and Superconducting Quantum Interference Device (SQUID) magnetometry. TEM and DLS study were conducted to verify VLPs creation. This study demonstrates that the increase of negative surface charge is not a sufficient factor determining successful assembly. Additional steric interactions provided by longer ligands are crucial for the assembly of BMV SPION VLPs and may enhance the colloidal stability.

Classical Electrodynamics: Lecture notes

NASA Astrophysics Data System (ADS)

Likharev, Konstantin K.

2018-06-01

Essential Advanced Physics is a series comprising four parts: Classical Mechanics, Classical Electrodynamics, Quantum Mechanics and Statistical Mechanics. Each part consists of two volumes, Lecture notes and Problems with solutions, further supplemented by an additional collection of test problems and solutions available to qualifying university instructors. This volume, Classical Electrodynamics: Lecture notes is intended to be the basis for a two-semester graduate-level course on electricity and magnetism, including not only the interaction and dynamics charged point particles, but also properties of dielectric, conducting, and magnetic media. The course also covers special relativity, including its kinematics and particle-dynamics aspects, and electromagnetic radiation by relativistic particles.

Trion formation dynamics in monolayer transition metal dichalcogenides

DOE PAGES

Singh, Akashay; Moody, Galan; Schaibley, John R.; ...

2016-01-05

Here, we report charged exciton (trion) formation dynamics in doped monolayer transition metal dichalcogenides, specifically molybdenum diselenide (MoSe 2), using resonant two-color pump-probe spectroscopy. When resonantly pumping the exciton transition, trions are generated on a picosecond time scale through exciton-electron interaction. As the pump energy is tuned from the high energy to low energy side of the inhomogeneously broadened exciton resonance, the trion formation time increases by ~50%. This feature can be explained by the existence of both localized and delocalized excitons in a disordered potential and suggests the existence of an exciton mobility edge in transition metal dichalcogenides.

Comparison of Molecular Dynamics with Classical Density Functional and Poisson–Boltzmann Theories of the Electric Double Layer in Nanochannels

PubMed Central

2012-01-01

Comparisons are made among Molecular Dynamics (MD), Classical Density Functional Theory (c-DFT), and Poisson–Boltzmann (PB) modeling of the electric double layer (EDL) for the nonprimitive three component model (3CM) in which the two ion species and solvent molecules are all of finite size. Unlike previous comparisons between c-DFT and Monte Carlo (MC), the present 3CM incorporates Lennard-Jones interactions rather than hard-sphere and hard-wall repulsions. c-DFT and MD results are compared over normalized surface charges ranging from 0.2 to 1.75 and bulk ion concentrations from 10 mM to 1 M. Agreement between the two, assessed by electric surface potential and ion density profiles, is found to be quite good. Wall potentials predicted by PB begin to depart significantly from c-DFT and MD for charge densities exceeding 0.3. Successive layers are observed to charge in a sequential manner such that the solvent becomes fully excluded from each layer before the onset of the next layer. Ultimately, this layer filling phenomenon results in fluid structures, Debye lengths, and electric surface potentials vastly different from the classical PB predictions. PMID:23316120

Floquet theory of microwave absorption by an impurity in the two-dimensional electron gas

NASA Astrophysics Data System (ADS)

Chepelianskii, Alexei D.; Shepelyansky, Dima L.

2018-03-01

We investigate the dynamics of a two-dimensional electron gas (2DEG) under circular polarized microwave radiation in the presence of dilute localized impurities. Inspired by recent developments on Floquet topological insulators we obtain the Floquet wave functions of this system which allow us to predict the microwave absorption and charge density responses of the electron gas; we demonstrate how these properties can be understood from the underlying semiclassical dynamics even for impurities with a size of around a magnetic length. The charge density response takes the form of a rotating charge density vortex around the impurity that can lead to a significant renormalization of the external microwave field which becomes strongly inhomogeneous on the scale of a cyclotron radius around the impurity. We show that this inhomogeneity can suppress the circular polarization dependence which is theoretically expected for microwave induced resistance oscillations but which was not observed in experiments on semiconducting 2DEGs. Our explanation for this so far unexplained polarization independence has close similarities with the Azbel'-Kaner effect in metals where the interaction length between the microwave field and conduction electrons is much smaller than the cyclotron radius due to skin effect generating harmonics of the cyclotron resonance.

Potential of mean force between identical charged nanoparticles immersed in a size-asymmetric monovalent electrolyte

NASA Astrophysics Data System (ADS)

Guerrero-García, Guillermo Iván; González-Mozuelos, Pedro; de la Cruz, Mónica Olvera

2011-10-01

In a previous theoretical and simulation study [G. I. Guerrero-García, E. González-Tovar, and M. Olvera de la Cruz, Soft Matter 6, 2056 (2010)], it has been shown that an asymmetric charge neutralization and electrostatic screening depending on the charge polarity of a single nanoparticle occurs in the presence of a size-asymmetric monovalent electrolyte. This effect should also impact the effective potential between two macroions suspended in such a solution. Thus, in this work we study the mean force and the potential of mean force between two identical charged nanoparticles immersed in a size-asymmetric monovalent electrolyte, showing that these results go beyond the standard description provided by the well-known Derjaguin-Landau-Verwey-Overbeek theory. To include consistently the ion-size effects, molecular dynamics (MD) simulations and liquid theory calculations are performed at the McMillan-Mayer level of description in which the solvent is taken into account implicitly as a background continuum with the suitable dielectric constant. Long-range electrostatic interactions are handled properly in the simulations via the well established Ewald sums method and the pre-averaged Ewald sums approach, originally proposed for homogeneous ionic fluids. An asymmetric behavior with respect to the colloidal charge polarity is found for the effective interactions between two identical nanoparticles. In particular, short-range attractions are observed between two equally charged nanoparticles, even though our model does not include specific interactions; these attractions are greatly enhanced for anionic nanoparticles immersed in standard electrolytes where cations are smaller than anions. Practical implications of some of the presented results are also briefly discussed. A good accord between the standard Ewald method and the pre-averaged Ewald approach is attained, despite the fact that the ionic system studied here is certainly inhomogeneous. In general, good agreement between the liquid theory approach and MD simulations is also found.

Determining the Critical Dose Threshold of Electron-Induced Electron Yield for Minimally Charged Highly Insulating Materials

NASA Astrophysics Data System (ADS)

Hoffmann, Ryan; Dennison, J. R.; Abbott, Jonathan

2006-03-01

When incident energetic electrons interact with a material, they excite electrons within the material to escape energies. The electron emission is quantified as the ratio of emitted electrons to incident particle flux, termed electron yield. Measuring the electron yield of insulators is difficult due to dynamic surface charge accumulation which directly affects landing energies and the potential barrier that emitted electrons must overcome. Our recent measurements of highly insulating materials have demonstrated significant changes in total yield curves and yield decay curves for very small electron doses equivalent to a trapped charge density of <10^10 electrons /cm^3. The Chung-Everhart theory provides a basic model for the behavior of the electron emission spectra which we relate to yield decay curves as charge is allowed to accumulate. Yield measurements as a function of dose for polyimide (Kapton^TM) and microcrystalline SiO2 will be presented. We use our data and model to address the question of whether there is a minimal dose threshold at which the accumulated charge no longer affects the yield.

Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

PubMed

Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

2014-12-12

Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ionic Structure at Dielectric Interfaces

NASA Astrophysics Data System (ADS)

Jing, Yufei

The behavior of ions in liquids confined between macromolecules determines the outcome of many nanoscale assembly processes in synthetic and biological materials such as colloidal dispersions, emulsions, hydrogels, DNA, cell membranes, and proteins. Theoretically, the macromolecule-liquid boundary is often modeled as a dielectric interface and an important quantity of interest is the ionic structure in a liquid confined between two such interfaces. The knowledge gleaned from the study of ionic structure in such models can be useful in several industrial applications, such as biosensors, lithium-ion batteries double-layer supercapacitors for energy storage and seawater desalination. Electrostatics plays a critical role in the development of such functional materials. Many of the functions of these materials, result from charge and composition heterogeneities. There are great challenges in solving electrostatics problems in heterogeneous media with arbitrary shapes because electrostatic interactions remains unknown but depend on the particular density of charge distributions. Charged molecules in heterogeneous media affect the media's dielectric response and hence the interaction between the charges is unknown since it depends on the media and on the geometrical properties of the interfaces. To determine the properties of heterogeneous systems including crucial effects neglected in classical mean field models such as the hard core of the ions, the dielectric mismatch and interfaces with arbitrary shapes. The effect of hard core interactions accounts properly for short range interactions and the effect of local dielectric heterogeneities in the presence of ions and/or charged molecules for long-range interactions are both analyzed via an energy variational principle that enables to update charges and the medium's response in the same simulation time step. In particular, we compute the ionic structure in a model system of electrolyte confined by two planar dielectric interfaces using molecular dynamics(MD) simulations and compared it with liquid state theory result. We explore the effects of high electrolyte concentrations, multivalent ions, and dielectric contrasts on the ionic distributions. We observe the presence of non-monotonous ionic density profiles leading to structure deformation in the fluid which is attributed to the competition between electrostatic and steric (entropic) interactions. We find that thermal forces that arise from symmetry breaking at the interfaces can have a profound effect on the ionic structure and can oftentimes overwhelm the influence of dielectric discontinuity. The combined effect of ionic correlations and inhomogeneous dielectric permittivity significantly changes the character of effective interaction between two interfaces. We show that, in concentrated electrolytes with confinement, it is imperative to take into account the finite-size of the ions as well as proper description of electrostatic interactions in heterogeneous media, which is not fully fulfilled by Poisson-Boltzmann based approaches. The effect of electric field at interface between two immiscible electrolyte solutions is studied as well. The classical Poisson-Boltzmann theory has been widely used to describe the corresponding ionic distribution, even though it neglects the polarization and ion correlations typical of these charged systems. Using Monte Carlo simulations, we provide an enhanced description of an oil-water interface in the presence of an electric field without needing any adjustable parameter, including realistic ionic sizes, ion correlations, and image charges. Our data agree with experimental measurements of excess surface tension for a wide range of electrolyte concentrations of LiCl and TBATPB (tetrabutylammonium-tetraphenylborate), contrasting with the result of the classical non-linear Poisson-Boltzmann theory. More importantly, we show that the size-asymmetry between small Li+ and large Cl- ions can significantly increase the electric field near the liquid interface, or can even reverse it locally, at high salt concentrations in the aqueous phase. These observations suggest a novel trapping/release mechanism of charged nanoparticles at oil-water interfaces in the vicinity of the point of zero charge. In addition, we study the effects of size asymmetry and charge asymmetry on ion distribution at a dielectric interface using coarse-grained MD based on an energy variational principle. The goal is to explore charge amplification with exact consideration of surface polarization. We find that both size asymmetry and charge asymmetry lead to charge separation at the interfaces. In addition, charge separation is enhanced by interface polarization. We are currently extending the research to charged interfaces that has broad applications such as batteries and supercapacitors for energy storage.

Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method.

PubMed

Kan, Zigui; Zhu, Qiang; Yang, Lijiang; Huang, Zhixiong; Jin, Biaobing; Ma, Jing

2017-05-04

Conformation of cellulose with various degree of polymerization of n = 1-12 in ionic liquid 1,3-dimethylimidazolium chloride ([C 1 mim]Cl) and the intermolecular interaction between them was studied by means of molecular dynamics (MD) simulations with fixed-charge and charge variable polarizable force fields, respectively. The integrated tempering enhanced sampling method was also employed in the simulations in order to improve the sampling efficiency. Cellulose undergoes significant conformational changes from a gaseous right-hand helical twist along the long axis to a flexible conformation in ionic liquid. The intermolecular interactions between cellulose and ionic liquid were studied by both infrared spectrum measurements and theoretical simulations. Designated by their puckering parameters, the pyranose rings of cellulose oligomers are mainly arranged in a chair conformation. With the increase in the degree of polymerization of cellulose, the boat and skew-boat conformations of cellulose appear in the MD simulations, especially in the simulations with polarization model. The number and population of hydrogen bonds between the cellulose and the chloride anions show that chloride anion is prone to form HBs whenever it approaches the hydroxyl groups of cellulose and, thus, each hydroxyl group is fully hydrogen bonded to the chloride anion. MD simulations with polarization model presented more abundant conformations than that with nonpolarization model. The application of the enhanced sampling method further enlarged the conformational spaces that could be visited by facilitating the system escaping from the local minima. It was found that the electrostatics interactions between the cellulose and ionic liquid contribute more to the total interaction energies than the van der Waals interactions. Although the interaction energy between the cellulose and anion is about 2.9 times that between the cellulose and cation, the role of cation is non-negligible. In contrast, the interaction energy between the cellulose and water is too weak to dissolve cellulose in water.

Interactions of Multimodal Ligands with Proteins: Insights into Selectivity Using Molecular Dynamics Simulations.

PubMed

Parimal, Siddharth; Garde, Shekhar; Cramer, Steven M

2015-07-14

Fundamental understanding of protein-ligand interactions is important to the development of efficient bioseparations in multimodal chromatography. Here we employ molecular dynamics (MD) simulations to investigate the interactions of three different proteins--ubiquitin, cytochrome C, and α-chymotrypsinogen A, sampling a range of charge from +1e to +9e--with two multimodal chromatographic ligands containing similar chemical moieties--aromatic, carboxyl, and amide--in different structural arrangements. We use a spherical harmonic expansion to analyze ligand and individual moiety density profiles around the proteins. We find that the Capto MMC ligand, which contains an additional aliphatic group, displays stronger interactions than Nuvia CPrime ligand with all three proteins. Studying the ligand densities at the moiety level suggests that hydrophobic interactions play a major role in determining the locations of high ligand densities. Finally, the greater structural flexibility of the Capto MMC ligand compared to that of the Nuvia cPrime ligand allows for stronger structural complementarity and enables stronger hydrophobic interactions. These subtle and not-so-subtle differences in binding affinities and modalities for multimodal ligands can result in significantly different binding behavior towards proteins with important implications for bioprocessing.

Identification of Binding Modes for Amino Naphthalene 2-Cyanoacrylate (ANCA) Probes to Amyloid Fibrils from Molecular Dynamics Simulations.

PubMed

He, Huan; Xu, Juan; Cheng, Dan-Yang; Fu, Li; Ge, Yu-Shu; Jiang, Feng-Lei; Liu, Yi

2017-02-16

The amino naphthalene 2-cyanoacrylate (ANCA) probe is a kind of fluorescent amyloid binding probe that can report different fluorescence emissions when bound to various amyloid deposits in tissue, while their interactions with amyloid fibrils remain unclear due to the insoluble nature of amyloid fibrils. Here, all-atom molecular dynamics simulations were used to investigate the interaction between ANCA probes with three different amyloid fibrils. Two common binding modes of ANCA probes on Aβ40 amyloid fibrils were identified by cluster analysis of multiple simulations. The van der Waals and electrostatic interactions were found to be major driving forces for the binding. Atomic contacts analysis and binding free energy decomposition results suggested that the hydrophobic part of ANCA mainly interacts with aromatic side chains on the fibril surface and the hydrophilic part mainly interacts with positive charged residues in the β-sheet region. By comparing the binding modes with different fibrils, we can find that ANCA adopts different conformations while interacting with residues of different hydrophobicity, aromaticity, and electrochemical properties in the β-sheet region, which accounts for its selective mechanism toward different amyloid fibrils.

A Continuum Method for Determining Membrane Protein Insertion Energies and the Problem of Charged Residues

PubMed Central

Choe, Seungho; Hecht, Karen A.; Grabe, Michael

2008-01-01

Continuum electrostatic approaches have been extremely successful at describing the charged nature of soluble proteins and how they interact with binding partners. However, it is unclear whether continuum methods can be used to quantitatively understand the energetics of membrane protein insertion and stability. Recent translation experiments suggest that the energy required to insert charged peptides into membranes is much smaller than predicted by present continuum theories. Atomistic simulations have pointed to bilayer inhomogeneity and membrane deformation around buried charged groups as two critical features that are neglected in simpler models. Here, we develop a fully continuum method that circumvents both of these shortcomings by using elasticity theory to determine the shape of the deformed membrane and then subsequently uses this shape to carry out continuum electrostatics calculations. Our method does an excellent job of quantitatively matching results from detailed molecular dynamics simulations at a tiny fraction of the computational cost. We expect that this method will be ideal for studying large membrane protein complexes. PMID:18474636

Observation of finite-wavelength screening in high-energy-density matter

DOE PAGES

Chapman, D. A.; Vorberger, J.; Fletcher, L. B.; ...

2015-04-23

A key component for the description of charged particle systems is the screening of the Coulomb interaction between charge carriers. First investigated in the 1920s by Debye and Hückel for electrolytes, charge screening is important for determining the structural and transport properties of matter as diverse as astrophysical and laboratory plasmas, nuclear matter such as quark-gluon plasmas, electrons in solids, planetary cores and charged macromolecules. For systems with negligible dynamics, screening is still mostly described using a Debye–Hückel-type approach. Here, we report the novel observation of a significant departure from the Debye–Hückel-type model in high-energy-density matter by probing laser-driven, shock-compressedmore » plastic with high-energy X-rays. We use spectrally resolved X-ray scattering in a geometry that enables direct investigation of the screening cloud, and demonstrate that the observed elastic scattering amplitude is only well described within a more general approach.« less

Monolayer optical memory cells based on artificial trap-mediated charge storage and release

NASA Astrophysics Data System (ADS)

Lee, Juwon; Pak, Sangyeon; Lee, Young-Woo; Cho, Yuljae; Hong, John; Giraud, Paul; Shin, Hyeon Suk; Morris, Stephen M.; Sohn, Jung Inn; Cha, Seungnam; Kim, Jong Min

2017-03-01

Monolayer transition metal dichalcogenides are considered to be promising candidates for flexible and transparent optoelectronics applications due to their direct bandgap and strong light-matter interactions. Although several monolayer-based photodetectors have been demonstrated, single-layered optical memory devices suitable for high-quality image sensing have received little attention. Here we report a concept for monolayer MoS2 optoelectronic memory devices using artificially-structured charge trap layers through the functionalization of the monolayer/dielectric interfaces, leading to localized electronic states that serve as a basis for electrically-induced charge trapping and optically-mediated charge release. Our devices exhibit excellent photo-responsive memory characteristics with a large linear dynamic range of ~4,700 (73.4 dB) coupled with a low OFF-state current (<4 pA), and a long storage lifetime of over 104 s. In addition, the multi-level detection of up to 8 optical states is successfully demonstrated. These results represent a significant step toward the development of future monolayer optoelectronic memory devices.

Polyelectrolyte properties of single stranded DNA measured using SAXS and single molecule FRET: beyond the wormlike chain model

PubMed Central

Meisburger, Steve P.; Sutton, Julie L.; Chen, Huimin; Pabit, Suzette A.; Kirmizialtin, Serdal; Elber, Ron; Pollack, Lois

2013-01-01

Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with worm like chain models, but non base-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and di-valent salt. We report measurements of the form factor and interparticle interactions using SAXS, end to end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent Molecular Dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers. PMID:23606337

Targeting EphA2-Sam and Its Interactome: Design and Evaluation of Helical Peptides Enriched in Charged Residues.

PubMed

Mercurio, Flavia A; Marasco, Daniela; Di Natale, Concetta; Pirone, Luciano; Costantini, Susan; Pedone, Emilia M; Leone, Marilisa

2016-11-17

The EphA2 receptor controls diverse physiological and pathological conditions and its levels are often upregulated in cancer. Targeting receptor overexpression, through modulation of endocytosis and consequent degradation, appears to be an appealing strategy for attacking tumor malignancy. In this scenario, the Sam domain of EphA2 plays a pivotal role because it is the site where protein regulators of endocytosis and stability are recruited by means of heterotypic Sam-Sam interactions. Because EphA2-Sam heterotypic complexes are largely based on electrostatic contacts, we have investigated the possibility of attacking these interactions with helical peptides enriched in charged residues. Several peptide sequences with high predicted helical propensities were designed, and detailed conformational analyses were conducted by diverse techniques including NMR, CD, and molecular dynamics (MD) simulations. Interaction studies were also performed by NMR, surface plasmon resonance (SPR), and microscale thermophoresis (MST) and led to the identification of two peptides capable of binding to the first Sam domain of Odin. These molecules represent early candidates for the generation of efficient Sam domain binders and antagonists of Sam-Sam interactions involving EphA2. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental simulation of magma-carbonate interaction beneath Mt. Vesuvius, Italy

NASA Astrophysics Data System (ADS)

Jolis, E. M.; Freda, C.; Troll, V. R.; Deegan, F. M.; Blythe, L. S.; McLeod, C. L.; Davidson, J. P.

2013-11-01

We simulated the process of magma-carbonate interaction beneath Mt. Vesuvius in short duration piston-cylinder experiments under controlled magmatic conditions (from 0 to 300 s at 0.5 GPa and 1,200 °C), using a Vesuvius shoshonite composition and upper crustal limestone and dolostone as starting materials. Backscattered electron images and chemical analysis (major and trace elements and Sr isotopes) of sequential experimental products allow us to identify the textural and chemical evolution of carbonated products during the assimilation process. We demonstrate that melt-carbonate interaction can be extremely fast (minutes), and results in dynamic contamination of the host melt with respect to Ca, Mg and 87Sr/86Sr, coupled with intense CO2 vesiculation at the melt-carbonate interface. Binary mixing between carbonate and uncontaminated melt cannot explain the geochemical variations of the experimental charges in full and convection and diffusion likely also operated in the charges. Physical mixing and mingling driven by exsolving volatiles seems to be a key process to promote melt homogenisation. Our results reinforce hypotheses that magma-carbonate interaction is a relevant and ongoing process at Mt. Vesuvius and one that may operate not only on a geological, but on a human timescale.

Adaptive Quantum Control of Charge Motion in Semiconductor Heterostructures

NASA Astrophysics Data System (ADS)

Reitze, David

1998-05-01

Quantum control of electronic wavepacket motion and interactions using ultrafast lasers has moved from the conceptual stage to reality, in large part driven by advances in quantum control theory (R. J. Gordon and S. A. Rice, Ann. Rev. Phys. Chem. (1997), in press.) (M. Shapiro and P. Brumer, J. Chem. Soc. Faraday Trans. V93, 1263 (1997).) (D. Neuhauser and H. Rabitz, Acc. Chem. Res. V26, 496 (1993).) and experimental pulse shaping methods (A. M. Weiner, D. E. Leaird, G. P. Wiederrecht, and K. A. Nelson, Science V247, 412 (1990).) (A. Efimov, C. Schaffer, and D. H. Reitze, J. Opt. Soc. Am VB12, 1968 (1995).). Here, we apply these methods to controlling charge motion in semiconductor heterostructures. Control of coherent charge dynamics in heterostructures enjoys an advantage in that spatial potential profiles can be adjusted almost arbitrarily. Thus, control of charge motion can be exerted by tailoring both the temporal and spatial interactions of the charges with the controlling optical and static fields. In this talk, we demonstrate an experimental feedback loop which adaptively shapes fs pulses in a quantum contol pump-probe experiment, apply it to the control of coherent wavepacket motion in DC-biased asymmetric double quantum well(ADQW) structures, and compare to theoretical predictions of quantum control in ADQWs (N. M. Beach, D. H. Reitze, and J. L. Krause, submitted to Opt. Exp.) (J. L. Krause, D. H. Reitze, G. D. Sanders, A. Kuznetsov, and C. J. Stanton, to appear in Phys. Rev. B).

Dynamical photo-induced electronic properties of molecular junctions

NASA Astrophysics Data System (ADS)

Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

2018-03-01

Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.

Role of Dynamically Frustrated Bond Disorder in a Li + Superionic Solid Electrolyte

DOE PAGES

Adelstein, Nicole; Wood, Brandon C.

2016-09-16

Inorganic lithium solid electrolytes are critical components in next-generation solid-state batteries, yet the fundamental nature of the cation-anion interactions and their relevance for ionic conductivity in these materials remains enigmatic. Here, we employ first-principles molecular dynamics simulations to explore the interplay between chemistry, structure, and functionality of a highly conductive Li + solid electrolyte, Li3InBr6. Using local-orbital projections to dynamically track the evolution of the electronic charge density, the simulations reveal rapid, correlated fluctuations between cation-anion interactions with different degrees of directional covalent character. These chemical bond dynamics are shown to correlate with Li + mobility, and are enabled thermallymore » by intrinsic frustration between the preferred geometries of chemical bonding and lattice symmetry. We suggest that the fluctuating chemical environment from the polarizable anions functions similar to a solvent, contributing to the superionic behavior of Li 3InBr 6 by temporarily stabilizing configurations favorable for migrating Li +. The generality of these conclusions for understanding solid electrolytes and key factors governing the superionic phase transition is discussed.« less

Impact of environment on dynamics of exciton complexes in a WS2 monolayer

NASA Astrophysics Data System (ADS)

Jakubczyk, Tomasz; Nogajewski, Karol; Molas, Maciej R.; Bartos, Miroslav; Langbein, Wolfgang; Potemski, Marek; Kasprzak, Jacek

2018-07-01

Scientific curiosity to uncover original optical properties and functionalities of atomically thin semiconductors, stemming from unusual Coulomb interactions in the two-dimensional geometry and multi-valley band structure, drives the research on monolayers of transition metal dichalcogenides (TMDs). While recent works ascertained the exotic energetic schemes of exciton complexes in TMDs, we here infer their unusual coherent dynamics occurring on subpicosecond time scale. The dynamics is largely affected by the disorder landscape on the submicron scale, thus can be uncovered using four-wave mixing in the frequency domain, which enables microscopic investigations and imaging. Focusing on a WS2 monolayer, we observe that exciton coherence is lost primarily due to interaction with phonons and relaxation processes towards optically dark excitonic states. Notably, when temperature is low and disorder weak, excitons large coherence volume results in enhanced oscillator strength, allowing to reach the regime of radiatively limited dephasing. Additionally, we observe long valley coherence for the negatively charged exciton complex. We therefore elucidate the crucial role of exciton environment in the TMDs on its dynamics and show that revealed mechanisms are ubiquitous within this family.

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.

Ionization of short polymethacrylic acid: titration, DLS, and model calculations.

PubMed

Pohlmeier, A; Haber-Pohlmeier, S

2004-05-15

In this work the charging of polymethacrylic acid in excess electrolyte solution is investigated experimentally by titration and dynamic light scattering. The results are analyzed by a penetrable sphere model, which employs the Poisson-Boltzmann equation for the description of electrostatic interactions and takes into account specific binding of H+ and Na+. The evaluation of the DLS data yields two relaxation modes. The slow mode is present only at finite degrees of charging and is therefore caused by collective diffusion. The fast mode, which corresponds to diffusion coefficients in the range from (1.1 to 1.5) x 10(-10) m2 s(-1), is present over the whole pH range. This reflects the diffusional dynamics of the polyion itself and allows the calculation of hydrodynamic radii for equivalent spheres (RH). These increase from 1.5 nm at pH 2.14 up to 1.8 nm for a degree of deprotonation alpha=0.47 at pH 5.86. With a further increase of pH the radii slightly decrease to 1.6 nm. Setting the radius of the penetrable sphere equal to RH, we can successfully model the overall charging curve with logK0H=4.85 and logK0Na=-0.6. This means that weak complexes of the type COO---Na are formed, which reduce the effective charge inside the polyelectrolyte coil.

Coupled electron-nuclear dynamics: Charge migration and charge transfer initiated near a conical intersection

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

Mendive-Tapia, David; Vacher, Morgane; Bearpark, Michael J.

Coupled electron-nuclear dynamics, implemented using the Ehrenfest method, has been used to study charge migration with fixed nuclei, together with charge transfer when nuclei are allowed to move. Simulations were initiated at reference geometries of neutral benzene and 2-phenylethylamine (PEA), and at geometries close to potential energy surface crossings in the cations. Cationic eigenstates, and the so-called sudden approximation, involving removal of an electron from a correlated ground-state wavefunction for the neutral species, were used as initial conditions. Charge migration without coupled nuclear motion could be observed if the Ehrenfest simulation, using the sudden approximation, was started near a conicalmore » intersection where the states were both strongly coupled and quasi-degenerate. Further, the main features associated with charge migration were still recognizable when the nuclear motion was allowed to couple. In the benzene radical cation, starting from the reference neutral geometry with the sudden approximation, one could observe sub-femtosecond charge migration with a small amplitude, which results from weak interaction with higher electronic states. However, we were able to engineer large amplitude charge migration, with a period between 10 and 100 fs, corresponding to oscillation of the electronic structure between the quinoid and anti-quinoid cationic electronic configurations, by distorting the geometry along the derivative coupling vector from the D{sub 6h} Jahn-Teller crossing to lower symmetry where the states are not degenerate. When the nuclear motion becomes coupled, the period changes only slightly. In PEA, in an Ehrenfest trajectory starting from the D{sub 2} eigenstate and reference geometry, a partial charge transfer occurs after about 12 fs near the first crossing between D{sub 1}, D{sub 2} (N{sup +}-Phenyl, N-Phenyl{sup +}). If the Ehrenfest propagation is started near this point, using the sudden approximation without coupled nuclear motion, one observes an oscillation of the spin density – charge migration – between the N atom and the phenyl ring with a period of 4 fs. When the nuclear motion becomes coupled, this oscillation persists in a damped form, followed by an effective charge transfer after 30 fs.« less

Coupled electron-nuclear dynamics: Charge migration and charge transfer initiated near a conical intersection

NASA Astrophysics Data System (ADS)

Mendive-Tapia, David; Vacher, Morgane; Bearpark, Michael J.; Robb, Michael A.

2013-07-01

Coupled electron-nuclear dynamics, implemented using the Ehrenfest method, has been used to study charge migration with fixed nuclei, together with charge transfer when nuclei are allowed to move. Simulations were initiated at reference geometries of neutral benzene and 2-phenylethylamine (PEA), and at geometries close to potential energy surface crossings in the cations. Cationic eigenstates, and the so-called sudden approximation, involving removal of an electron from a correlated ground-state wavefunction for the neutral species, were used as initial conditions. Charge migration without coupled nuclear motion could be observed if the Ehrenfest simulation, using the sudden approximation, was started near a conical intersection where the states were both strongly coupled and quasi-degenerate. Further, the main features associated with charge migration were still recognizable when the nuclear motion was allowed to couple. In the benzene radical cation, starting from the reference neutral geometry with the sudden approximation, one could observe sub-femtosecond charge migration with a small amplitude, which results from weak interaction with higher electronic states. However, we were able to engineer large amplitude charge migration, with a period between 10 and 100 fs, corresponding to oscillation of the electronic structure between the quinoid and anti-quinoid cationic electronic configurations, by distorting the geometry along the derivative coupling vector from the D6h Jahn-Teller crossing to lower symmetry where the states are not degenerate. When the nuclear motion becomes coupled, the period changes only slightly. In PEA, in an Ehrenfest trajectory starting from the D2 eigenstate and reference geometry, a partial charge transfer occurs after about 12 fs near the first crossing between D1, D2 (N+-Phenyl, N-Phenyl+). If the Ehrenfest propagation is started near this point, using the sudden approximation without coupled nuclear motion, one observes an oscillation of the spin density - charge migration - between the N atom and the phenyl ring with a period of 4 fs. When the nuclear motion becomes coupled, this oscillation persists in a damped form, followed by an effective charge transfer after 30 fs.

Unraveling the Agglomeration Mechanism in Charged Block Copolymer and Surfactant Complexes

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

Borreguero, Jose M.; Pincus, Philip A.; Sumpter, Bobby G.

Here, we report a molecular dynamics simulation investigation of self-assembly and complex formation of charged-neutral double hydrophilic and hydrophobic-hydrophilic block copolymers (BCP) with oppositely charged surfactants. Furthermore, the structure of the surfactant micelles and the BCP aggregation on the micelle surface is systematically studied for five different BCP volume fractions that also mimics a reduction of the surfactant concentration. The local electrostatic interactions between the oppositely charged species encourage the formation of core-shell structures between the surfactant micelles where the surfactants form the cores and the charged blocks of the BCP form the corona. The emergent morphologies of these aggregatesmore » are contingent upon the nature of the BCP neutral blocks. The hydrophilic neutral blocks agglomerate with the micelles as hairy colloidal structures while the hydrophobic neutrals agglomerate in lamellar structures with the surfactant micelles. The distribution of counterion charges along the simulation box show a close-to-normal density distribution for the hydrophilic neutral blocks and a binodal distribution for hydrophobic neutral blocks. No specific surfactant concentration dependent scaling relation is observed as opposed to the simpler case of homo-polyelectrolytes.« less

Unraveling the Agglomeration Mechanism in Charged Block Copolymer and Surfactant Complexes

DOE PAGES

Borreguero, Jose M.; Pincus, Philip A.; Sumpter, Bobby G.; ...

2017-01-27

Here, we report a molecular dynamics simulation investigation of self-assembly and complex formation of charged-neutral double hydrophilic and hydrophobic-hydrophilic block copolymers (BCP) with oppositely charged surfactants. Furthermore, the structure of the surfactant micelles and the BCP aggregation on the micelle surface is systematically studied for five different BCP volume fractions that also mimics a reduction of the surfactant concentration. The local electrostatic interactions between the oppositely charged species encourage the formation of core-shell structures between the surfactant micelles where the surfactants form the cores and the charged blocks of the BCP form the corona. The emergent morphologies of these aggregatesmore » are contingent upon the nature of the BCP neutral blocks. The hydrophilic neutral blocks agglomerate with the micelles as hairy colloidal structures while the hydrophobic neutrals agglomerate in lamellar structures with the surfactant micelles. The distribution of counterion charges along the simulation box show a close-to-normal density distribution for the hydrophilic neutral blocks and a binodal distribution for hydrophobic neutral blocks. No specific surfactant concentration dependent scaling relation is observed as opposed to the simpler case of homo-polyelectrolytes.« less

Femtosecond dynamics of energetic electrons in high intensity laser-matter interactions

NASA Astrophysics Data System (ADS)

Pompili, R.; Anania, M. P.; Bisesto, F.; Botton, M.; Castellano, M.; Chiadroni, E.; Cianchi, A.; Curcio, A.; Ferrario, M.; Galletti, M.; Henis, Z.; Petrarca, M.; Schleifer, E.; Zigler, A.

2016-10-01

Highly energetic electrons are generated at the early phases of the interaction of short-pulse high-intensity lasers with solid targets. These escaping particles are identified as the essential core of picosecond-scale phenomena such as laser-based acceleration, surface manipulation, generation of intense magnetic fields and electromagnetic pulses. Increasing the number of the escaping electrons facilitate the late time processes in all cases. Up to now only indirect evidences of these important forerunners have been recorded, thus no detailed study of the governing mechanisms was possible. Here we report, for the first time, direct time-dependent measurements of energetic electrons ejected from solid targets by the interaction with a short-pulse high-intensity laser. We measured electron bunches up to 7 nanocoulombs charge, picosecond duration and 12 megaelectronvolts energy. Our ’snapshots’ capture their evolution with an unprecedented temporal resolution, demonstrat- ing a significant boost in charge and energy of escaping electrons when increasing the geometrical target curvature. These results pave the way toward significant improvement in laser acceleration of ions using shaped targets allowing the future development of small scale laser-ion accelerators.

Nambu mechanism of dynamical symmetry breaking by the top quark

NASA Astrophysics Data System (ADS)

Pham, Xuan-Yem

1990-05-01

It may be possible that the gauge symmetry breaking of the standard electroweak interactions is not due to the elementary scalar Higgs fields but has a dynamic origin intimately involving the top quark. A prototype of this dynamical scenario is the Nambu and Jona-Lasinio model in which both the top quark and the gauge bosons become massive by some strong attractive nonlinear interactions similar to the gap energy produced in BCS superconductivity. Self-consistent equations for the charged Goldstone boson and for the vector meson are used to get an upper bound for the top quark mass. In the bubble approximation of keeping only fermion loops, we obtain an equation relating the top quark mass to the W boson one; from the top mass is found to be around 84 GeV. Its typical dominant decay mode t→W+s then follows. Also discussed are distinctive signatures of the scalar overlinett bound state identified as the physical Higgs particle whose mass is twice that of the top quark.

Molecular dynamics simulation and NMR investigation of the association of the β-blockers atenolol and propranolol with a chiral molecular micelle

NASA Astrophysics Data System (ADS)

Morris, Kevin F.; Billiot, Eugene J.; Billiot, Fereshteh H.; Hoffman, Charlene B.; Gladis, Ashley A.; Lipkowitz, Kenny B.; Southerland, William M.; Fang, Yayin

2015-08-01

Molecular dynamics simulations and NMR spectroscopy were used to compare the binding of two β-blocker drugs to the chiral molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The molecular micelle is used as a chiral selector in capillary electrophoresis. This study is part of a larger effort to understand the mechanism of chiral recognition in capillary electrophoresis by characterizing the molecular micelle binding of chiral compounds with different geometries and charges. Propranolol and atenolol were chosen because their structures are similar, but their chiral interactions with the molecular micelle are different. Molecular dynamics simulations showed both propranolol enantiomers inserted their aromatic rings into the molecular micelle core and that (S)-propranolol associated more strongly with the molecular micelle than (R)-propranolol. This difference was attributed to stronger molecular micelle hydrogen bonding interactions experienced by (S)-propranolol. Atenolol enantiomers were found to bind near the molecular micelle surface and to have similar molecular micelle binding free energies.

Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties

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

Doktorova, Milka; Heberle, Frederick A.; Kingston, Richard L.

Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein’s matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here in this paper, using a broad set of in vitro and in silico techniques we addressed molecularmore » mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.« less

Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties

DOE PAGES

Doktorova, Milka; Heberle, Frederick A.; Kingston, Richard L.; ...

2017-11-07

Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein’s matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here in this paper, using a broad set of in vitro and in silico techniques we addressed molecularmore » mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.« less

Structure and Dynamics of Antifreeze Protein--Model Membrane Interactions: A Combined Spectroscopic and Molecular Dynamics Study.

PubMed

Kar, Rajiv K; Mroue, Kamal H; Kumar, Dinesh; Tejo, Bimo A; Bhunia, Anirban

2016-02-11

Antifreeze proteins (AFPs) are the key biomolecules that enable species to survive under subzero temperature conditions. The physiologically relevant activities of AFPs are based on the adsorption to ice crystals, followed by the inhibition of subsequent crystal layer growth of ice, routed with depression in freezing point in a noncolligative manner. The functional attributes governing the mechanism by which AFPs inhibit freezing of body fluids in bacteria, fungi, plants, and fishes are mainly attributed to their adsorption onto the surface of ice within the physiological system. Importantly, AFPs are also known for their application in cryopreservation of biological samples that might be related to membrane interaction. To date, there is a paucity of information detailing the interaction of AFPs with membrane structures. Here, we focus on elucidating the biophysical properties of the interactions between AFPs and micelle models that mimic the membrane system. Micelle model systems of zwitterionic DPC and negatively charged SDS were utilized in this study, against which a significant interaction is experienced by two AFP molecules, namely, Peptide 1m and wfAFP (the popular AFP sourced from winter flounder). Using low- and high-resolution biophysical characterization techniques, such as circular dichroism (CD) and NMR spectroscopy, a strong evidence for the interactions of these AFPs with the membrane models is revealed in detail and is corroborated by in-depth residue-specific information derived from molecular dynamics simulation. Altogether, these results not only strengthen the fact that AFPs interact actively with membrane systems, but also demonstrate that membrane-associated AFPs are dynamic and capable of adopting a number of conformations rendering fluidity to the system.

Photoinduced Bandgap Renormalization and Exciton Binding Energy Reduction in WS2.

PubMed

Cunningham, Paul D; Hanbicki, Aubrey T; McCreary, Kathleen M; Jonker, Berend T

2017-12-26

Strong Coulomb attraction in monolayer transition metal dichalcogenides gives rise to tightly bound excitons and many-body interactions that dominate their optoelectronic properties. However, this Coulomb interaction can be screened through control of the surrounding dielectric environment as well as through applied voltage, which provides a potential means of tuning the bandgap, exciton binding energy, and emission wavelength. Here, we directly show that the bandgap and exciton binding energy can be optically tuned by means of the intensity of the incident light. Using transient absorption spectroscopy, we identify a sub-picosecond decay component in the excited-state dynamics of WS 2 that emerges for incident photon energies above the A-exciton resonance, which originates from a nonequilibrium population of charge carriers that form excitons as they cool. The generation of this charge-carrier population exhibits two distinct energy thresholds. The higher threshold is coincident with the onset of continuum states and therefore provides a direct optical means of determining both the bandgap and exciton binding energy. Using this technique, we observe a reduction in the exciton binding energy from 310 ± 30 to 220 ± 20 meV as the excitation density is increased from 3 × 10 11 to 1.2 × 10 12 photons/cm 2 . This reduction is due to dynamic dipolar screening of Coulomb interactions by excitons, which is the underlying physical process that initiates bandgap renormalization and leads to the insulator-metal transition in monolayer transition metal dichalcogenides.

Defect interactions in anisotropic two-dimensional fluids

NASA Astrophysics Data System (ADS)

Stannarius, Ralf; Harth, Kirsten

Disclinations in liquid crystals bear striking analogies to defect structures in a wide variety of physical systems, they are excellent models to study fundamental properties of defect interactions. Freely suspended smectic C films behave like quasi 2D polar nematics. An experimental procedure is introduced to capture high-strength disclinations in localized spots. After they are released in a controlled way, the motion of the mutually repelling topological charges is studied. We demonstrate that the classical models, based on elastic one-constant approximation, fail to describe their dynamics correctly. In realistic liquid crystals, the models work only in ideal configurations. In general, additional director walls modify interactions substantially. Funded by DFG within project STA 425/28-1.

Smart Adaptive Socket to Improve Fit and Relieve Pain in Wounded Warriors

DTIC Science & Technology

2016-10-01

applications were developed for wireless interaction with the socket system firmware. A control algorithm was designed and tested. Clinical trial...interface, Dynamic segmental volume control, Wireless connection, Pressure control system. 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18...charging jack, and power button are included in the design. A Bluetooth 4 radio is also included to allow for advanced user control via smartphone. The

The effect of dynamical Bloch oscillations on optical-field-induced current in a wide-gap dielectric

NASA Astrophysics Data System (ADS)

Földi, P.; Benedict, M. G.; Yakovlev, V. S.

2013-06-01

We consider the motion of charge carriers in a bulk wide-gap dielectric interacting with a few-cycle laser pulse. A semiclassical model based on Bloch equations is applied to describe the emerging time-dependent macroscopic currents for laser intensities close to the damage threshold. At such laser intensities, electrons can reach edges of the first Brillouin zone even for electron-phonon scattering rates as high as those known for SiO2. We find that, whenever this happens, Bragg-like reflections of electron waves, also known as Bloch oscillations, affect the dependence of the charge displaced by the laser pulse on its carrier-envelope phase.

Concerted manipulation of laser plasma dynamics with two laser pulses

NASA Astrophysics Data System (ADS)

Braenzel, J.; Andreev, A. A.; Ehrentraut, L.; Sommer, D.; Schnürer, M.

2017-05-01

In this article we present experimental results from a counter-propagating two laser pulse experiment at high intensity and using ultrathin gold and plastic foil targets. We applied one laser pulse as a pre-pulse with an intensity of up to 1x1018 W/cm2. By this method we manipulated the pre-plasma of the foil target with which the stronger laser pulse with an intensity of 6x1019W/cm2 interacts. This alters significantly subsequent processes from the laser plasma interaction which we show the ion acceleration and high harmonic generation. On the one hand, the maximum kinetic ion energy and the maximum charge state for gold ions decline due to the pre-heating of the target in the time range of few ps, on the other hand the number of accelerated ions is increased. For the same parameter range we detected a significant raise of the high harmonic emission. Moreover, we present first experimental observations, that when the second laser pulse is applied as a counter-propagating post-pulse the energy distribution of accelerated carbon ions is charge selective altered. Our findings indicate that using this method a parametric optimization can be achieved, which promises new insights about the concurrent processes of the laser plasma dynamics.

Exploring the Electronic Landscape at Interfaces and Junctions in Semiconductor Nanowire Devices with Subsurface Local Probing of Carrier Dynamics

NASA Astrophysics Data System (ADS)

McGuckin, Terrence

The solid state devices that are pervasive in our society, are based on building blocks composed of interfaces between materials and junctions that manipulate how charge carriers behave in a device. As the dimensions of these devices are reduced to the nanoscale, surfaces and interfaces play a larger role in the behavior of carriers in devices and must be thoroughly investigated to understand not only the material properties but how these materials interact. Separating the effects of these different building blocks is a challenge, as most testing methods measure the performance of the whole device. Semiconductor nanowires represent an excellent test system to explore the limits of size and novel device structures. The behavior of charge carriers in semiconductor nanowire devices under operational conditions is investigated using local probing technique electron beam induced current (EBIC). The behavior of locally excited carriers are driven by the forces of drift, from electric fields within a device at junctions, surfaces, contacts and, applied voltage bias, and diffusion. This thesis presents the results of directly measuring these effects spatially with nanometer resolution, using EBIC in Ge, Si, and complex heterostructure GaAs/AlGaAs nanowire devices. Advancements to the EBIC technique, have pushed the resolution from tens of nanometers down to 1 to 2 nanometers. Depth profiling and tuning of the interaction volume allows for the separating the signal originating from the surface and the interior of the nanowire. Radial junctions and variations in bands can now be analyzed including core/shell hetero-structures. This local carrier probing reveals a number of surprising behaviors; Most notably, directly imaging the evolution of surface traps filling with electrons causing bandbending at the surface of Ge nanowires that leads to an enhancement in the charge separation of electrons and holes, and extracting different characteristic lengths from GaAs and AlGaAs in core/shell nanowires. For new and emerging solid state materials, understanding charge carrier dynamics is crucial to designing functional devices. Presented here are examples of the wide application of EBIC, and its variants, through imaging domains in ferroelectric materials, local electric fields and defects in 2D semiconductor material MoS2, and gradients in doping profiles of solar cells. Measuring the local behavior of carrier dynamics, EBIC has the potential to be a key metrology technique in correlative microscopy, enabling a deeper understanding of materials and how they interact within devices.

In situ measurements of Saturn's ionosphere show that it is dynamic and interacts with the rings.

PubMed

Wahlund, J-E; Morooka, M W; Hadid, L Z; Persoon, A M; Farrell, W M; Gurnett, D A; Hospodarsky, G; Kurth, W S; Ye, S-Y; Andrews, D J; Edberg, N J T; Eriksson, A I; Vigren, E

2018-01-05

The ionized upper layer of Saturn's atmosphere, its ionosphere, provides a closure of currents mediated by the magnetic field to other electrically charged regions (for example, rings) and hosts ion-molecule chemistry. In 2017, the Cassini spacecraft passed inside the planet's rings, allowing in situ measurements of the ionosphere. The Radio and Plasma Wave Science instrument detected a cold, dense, and dynamic ionosphere at Saturn that interacts with the rings. Plasma densities reached up to 1000 cubic centimeters, and electron temperatures were below 1160 kelvin near closest approach. The density varied between orbits by up to two orders of magnitude. Saturn's A- and B-rings cast a shadow on the planet that reduced ionization in the upper atmosphere, causing a north-south asymmetry. Copyright © 2018, American Association for the Advancement of Science.

Solid-State Division progress report for period ending March 31, 1983

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

Green, P.H.; Watson, D.M.

1983-09-01

Progress and activities are reported on: theoretical solid-state physics (surfaces; electronic, vibrational, and magnetic properties; particle-solid interactions; laser annealing), surface and near-surface properties of solids (surface, plasma-material interactions, ion implantation and ion-beam mixing, pulsed-laser and thermal processing), defects in solids (radiation effects, fracture, impurities and defects, semiconductor physics and photovoltaic conversion), transport properties of solids (fast-ion conductors, superconductivity, mass and charge transport in materials), neutron scattering (small-angle scattering, lattice dynamics, magnetic properties, structure and instrumentation), and preparation and characterization of research materials (growth and preparative methods, nuclear waste forms, special materials). (DLC)

Single-molecule dynamics in nanofabricated traps

NASA Astrophysics Data System (ADS)

Cohen, Adam

2009-03-01

The Anti-Brownian Electrokinetic trap (ABEL trap) provides a means to immobilize a single fluorescent molecule in solution, without surface attachment chemistry. The ABEL trap works by tracking the Brownian motion of a single molecule, and applying feedback electric fields to induce an electrokinetic motion that approximately cancels the Brownian motion. We present a new design for the ABEL trap that allows smaller molecules to be trapped and more information to be extracted from the dynamics of a single molecule than was previously possible. In particular, we present strategies for extracting dynamically fluctuating mobilities and diffusion coefficients, as a means to probe dynamic changes in molecular charge and shape. If one trapped molecule is good, many trapped molecules are better. An array of single molecules in solution, each immobilized without surface attachment chemistry, provides an ideal test-bed for single-molecule analyses of intramolecular dynamics and intermolecular interactions. We present a technology for creating such an array, using a fused silica plate with nanofabricated dimples and a removable cover for sealing single molecules within the dimples. With this device one can watch the shape fluctuations of single molecules of DNA or study cooperative interactions in weakly associating protein complexes.

Self-consistent analysis of radiation and relativistic electron beam dynamics in a helical wiggler using Lienard-Wiechert fields

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

Tecimer, M.; Elias, L.R.

1995-12-31

Lienard-Wiechert (LW) fields, which are exact solutions of the Wave Equation for a point charge in free space, are employed to formulate a self-consistent treatment of the electron beam dynamics and the evolution of the generated radiation in long undulators. In a relativistic electron beam the internal forces leading to the interaction of the electrons with each other can be computed by means of retarded LW fields. The resulting electron beam dynamics enables us to obtain three dimensional radiation fields starting from an initial incoherent spontaneous emission, without introducing a seed wave at start-up. Based on the formalism employed here,more » both the evolution of the multi-bucket electron phase space dynamics in the beam body as well as edges and the relative slippage of the radiation with respect to the electrons in the considered short bunch are naturally embedded into the simulation model. In this paper, we present electromagnetic radiation studies, including multi-bucket electron phase dynamics and angular distribution of radiation in the time and frequency domain produced by a relativistic short electron beam bunch interacting with a circularly polarized magnetic undulator.« less

First-Principles Molecular Dynamics Study on the Electric-double layer Capacitance of Water-MXene interfaces

NASA Astrophysics Data System (ADS)

Ando, Yasunobu; Otani, Minoru

MXenes are a new, large family of layered materials synthesized from MAX phases by simple chemical treatments. Due to their enormous variations, MXenes have attracted great attention as promising candidates as anode materials for next-generation secondary batteries. Unfortunately, the specific capacitance of MXenes supercapacitors is lower than that of active-carbon ones. Theoretical investigation of the electric-double layer (EDL) at electrode interfaces is necessary to improve their capacitance. First-principles molecular dynamics (FPMD) simulation based on the density functional theory (DFT) is performed to estimate the EDL capacitance from a potential profile V(z) and a charge distribution q(z) induced by the ions at water-Ti2CTx (T =O, F) interfaces. Potential profiles V(z) of both Ti2CO2 and Ti2CF2 decrease about 1.0 eV steeply in a region of only 3 Å from a Ti layer, which is the same profile at the platinum interfaces. On the other hand, induced charge distribution q(z) depends on the species of surface termination. Induced electrons are introduced at Ti layers in the case of O surface termination. However, Ti2CF2 is not capable to store electrons at Ti layers because it is mono-valence anions. It indicates that effective surface-position of MXenes depends on the surface terminations. Our results are revealed that small induced charge leads the low EDL capacitance at MXene interfaces. This is because interface polarization due to strong interaction between water and Ti2CTx induces net charge. The surface net charge hinders the introduction of ion-induced charges.

MOLSIM: A modular molecular simulation software

PubMed Central

Jurij, Reščič

2015-01-01

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25994597

Interaction between the NS4B amphipathic helix, AH2, and charged lipid headgroups alters membrane morphology and AH2 oligomeric state--Implications for the Hepatitis C virus life cycle.

PubMed

Ashworth Briggs, Esther L; Gomes, Rafael G B; Elhussein, Malaz; Collier, William; Findlow, I Stuart; Khalid, Syma; McCormick, Chris J; Williamson, Philip T F

2015-08-01

The non-structural protein 4B (NS4B) from Hepatitis C virus (HCV) plays a pivotal role in the remodelling of the host cell's membranes, required for the formation of the viral replication complex where genome synthesis occurs. NS4B is an integral membrane protein that possesses a number of domains vital for viral replication. Structural and biophysical studies have revealed that one of these, the second amphipathic N-terminal helix (AH2), plays a key role in these remodelling events. However, there is still limited understanding of the mechanism through which AH2 promotes these changes. Here we report on solid-state NMR and molecular dynamics studies that demonstrate that AH2 promotes the clustering of negatively charged lipids within the bilayer, a process that reduces the strain within the bilayer facilitating the remodelling of the lipid bilayer. Furthermore, the presence of negatively charged lipids within the bilayer appears to promote the disassociation of AH2 oligomers, highlighting a potential role for lipid recruitment in regulating NS protein interactions. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Attitude stabilization of a spacecraft equipped with large electrostatic protection screens

NASA Astrophysics Data System (ADS)

Nikitin, D. Yu.; Tikhonov, A. A.

2018-05-01

A satellite with a system of three electrostatic radiation protection (ERP) screens is under consideration. The screens are constructed as electrostatically charged toroidal shields with characteristic size of order equal to 100 m. The interaction of electric charge with the Earth's magnetic field (EMF) give rise to the Lorentz torque acting upon a satellite attitude motion. As the sizes of ERP system are large, we derive the Lorentz torque taking into account the complex form of ERP screens and gradient of the EMF in the screen volume. It is assumed that the satellite center of charge coincides with the satellite mass center. The EMF is modeled by the straight magnetic dipole. In the paper we investigate the usage of Lorentz torque for passive attitude stabilization for satellite in a circular equatorial orbit. Mathematical model for attitude dynamics of a satellite equipped with ERP interacting with the EMF is derived and first integral of corresponding differential equations is constructed. The straight equilibrium position of the satellite in the orbital frame is found. Sufficient conditions for stability of satellite equilibrium position are constructed with the use of the first integral. The gravity gradient torque is taken into account. The satellite equilibrium stability domain is constructed.

Coulombic interactions on the deposition and rotational mobility distributions of dyes in polyelectrolyte multilayer thin films.

PubMed

Li, Ye; Yip, Wai Tak

2004-12-07

We employed negatively charged fluorescein (FL), positively charged rhodamine 6G (R6G), and neutral Nile Red (NR) as molecular probes to investigate the influence of Coulombic interaction on their deposition into and rotational mobility inside polyelectrolyte multilayer (PEM) films. The entrapment efficiency of the dyes reveals that while Coulombic repulsion has little effect on dye deposition, Coulombic attraction can dramatically enhance the loading efficiency of dyes into a PEM film. By monitoring the emission polarization of single dye molecules in polyethylenimine (PEI) films, the percentages of mobile R6G, NR, and FL were determined to be 87 +/- 4%, 76 +/- 5%, and 68 +/- 3%, respectively. These mobility distributions suggest that cationic R6G enjoys the highest degree of rotational freedom, whereas anionic FL shows the least mobility because of Coulombic attraction toward cationic PEI. Regardless of charges, this high percentage of mobile molecules is in stark contrast to the 5-40% probe mobility reported from spun-cast polymer films, indicating that our PEI films contain more free volume and display richer polymer dynamics. These observations demonstrate the potential of using isolated fluorescent probes to interrogate the internal structure of a PEM film at a microscopic level.

K4[Fe(CN)6] immobilized anion sensitive protonated amine functionalized polysilsesquioxane films for ultra-low electrochemical detection of dsDNA.

PubMed

Silambarasan, Krishnamoorthy; Narendra Kumar, Alam Venugopal; Joseph, James

2016-03-14

Charge transport in polymeric films bound by redox reagents is a topic of current interest. The dynamics of electroinactive ions across the interface is studied by immobilizing ferrocyanide anion in a polysilsesquioxanes (PSQs) modified electrode. Redox reagents can stay in the polymeric film by either physical forces or electrostatic binding. The present work describes the immobilization of ferro/ferricyanide redox couples in PSQ films possessing protonated amine functional groups by electrostatic interactions. Charge transport in [Fe(CN)6](4-)-PSQs film was found to be anion dependent, and its formal potential value varied with the relative hydrophilic or hydrophobic nature of the anion used in the supporting electrolyte, unlike the observed dependence on solution cation for electrodes modified with metal hexacyanoferrates (Prussian Blue analogues). The [Fe(CN)6](4-) bound PSQs films were extensively characterized by varying different supporting electrolytes anions using cyclic voltammetry. The redox peak currents were linearly proportional to the square root of the scan rate, implying that the transport of charge carriers is accompanied with redox ion diffusion and electron hopping in a confined space. dsDNA molecules were found to interact with this polymer matrix through anionic phosphate groups. Both voltammetry and A.C. impedance spectroscopy studies revealed that these interactions could be exploited for the determination of ultra-low level (0.5 attomolar) of dsDNA present in aqueous solution.

Thermoelectric properties of an interacting quantum dot based heat engine

NASA Astrophysics Data System (ADS)

Erdman, Paolo Andrea; Mazza, Francesco; Bosisio, Riccardo; Benenti, Giuliano; Fazio, Rosario; Taddei, Fabio

2017-06-01

We study the thermoelectric properties and heat-to-work conversion performance of an interacting, multilevel quantum dot (QD) weakly coupled to electronic reservoirs. We focus on the sequential tunneling regime. The dynamics of the charge in the QD is studied by means of master equations for the probabilities of occupation. From here we compute the charge and heat currents in the linear response regime. Assuming a generic multiterminal setup, and for low temperatures (quantum limit), we obtain analytical expressions for the transport coefficients which account for the interplay between interactions (charging energy) and level quantization. In the case of systems with two and three terminals we derive formulas for the power factor Q and the figure of merit Z T for a QD-based heat engine, identifying optimal working conditions which maximize output power and efficiency of heat-to-work conversion. Beyond the linear response we concentrate on the two-terminal setup. We first study the thermoelectric nonlinear coefficients assessing the consequences of large temperature and voltage biases, focusing on the breakdown of the Onsager reciprocal relation between thermopower and Peltier coefficient. We then investigate the conditions which optimize the performance of a heat engine, finding that in the quantum limit output power and efficiency at maximum power can almost be simultaneously maximized by choosing appropriate values of electrochemical potential and bias voltage. At last we study how energy level degeneracy can increase the output power.

Extreme disorder in an ultrahigh-affinity protein complex

NASA Astrophysics Data System (ADS)

Borgia, Alessandro; Borgia, Madeleine B.; Bugge, Katrine; Kissling, Vera M.; Heidarsson, Pétur O.; Fernandes, Catarina B.; Sottini, Andrea; Soranno, Andrea; Buholzer, Karin J.; Nettels, Daniel; Kragelund, Birthe B.; Best, Robert B.; Schuler, Benjamin

2018-03-01

Molecular communication in biology is mediated by protein interactions. According to the current paradigm, the specificity and affinity required for these interactions are encoded in the precise complementarity of binding interfaces. Even proteins that are disordered under physiological conditions or that contain large unstructured regions commonly interact with well-structured binding sites on other biomolecules. Here we demonstrate the existence of an unexpected interaction mechanism: the two intrinsically disordered human proteins histone H1 and its nuclear chaperone prothymosin-α associate in a complex with picomolar affinity, but fully retain their structural disorder, long-range flexibility and highly dynamic character. On the basis of closely integrated experiments and molecular simulations, we show that the interaction can be explained by the large opposite net charge of the two proteins, without requiring defined binding sites or interactions between specific individual residues. Proteome-wide sequence analysis suggests that this interaction mechanism may be abundant in eukaryotes.

The complex nature of calcium cation interactions with phospholipid bilayers

PubMed Central

Melcrová, Adéla; Pokorna, Sarka; Pullanchery, Saranya; Kohagen, Miriam; Jurkiewicz, Piotr; Hof, Martin; Jungwirth, Pavel; Cremer, Paul S.; Cwiklik, Lukasz

2016-01-01

Understanding interactions of calcium with lipid membranes at the molecular level is of great importance in light of their involvement in calcium signaling, association of proteins with cellular membranes, and membrane fusion. We quantify these interactions in detail by employing a combination of spectroscopic methods with atomistic molecular dynamics simulations. Namely, time-resolved fluorescent spectroscopy of lipid vesicles and vibrational sum frequency spectroscopy of lipid monolayers are used to characterize local binding sites of calcium in zwitterionic and anionic model lipid assemblies, while dynamic light scattering and zeta potential measurements are employed for macroscopic characterization of lipid vesicles in calcium-containing environments. To gain additional atomic-level information, the experiments are complemented by molecular simulations that utilize an accurate force field for calcium ions with scaled charges effectively accounting for electronic polarization effects. We demonstrate that lipid membranes have substantial calcium-binding capacity, with several types of binding sites present. Significantly, the binding mode depends on calcium concentration with important implications for calcium buffering, synaptic plasticity, and protein-membrane association. PMID:27905555

The complex nature of calcium cation interactions with phospholipid bilayers

NASA Astrophysics Data System (ADS)

Melcrová, Adéla; Pokorna, Sarka; Pullanchery, Saranya; Kohagen, Miriam; Jurkiewicz, Piotr; Hof, Martin; Jungwirth, Pavel; Cremer, Paul S.; Cwiklik, Lukasz

2016-12-01

Understanding interactions of calcium with lipid membranes at the molecular level is of great importance in light of their involvement in calcium signaling, association of proteins with cellular membranes, and membrane fusion. We quantify these interactions in detail by employing a combination of spectroscopic methods with atomistic molecular dynamics simulations. Namely, time-resolved fluorescent spectroscopy of lipid vesicles and vibrational sum frequency spectroscopy of lipid monolayers are used to characterize local binding sites of calcium in zwitterionic and anionic model lipid assemblies, while dynamic light scattering and zeta potential measurements are employed for macroscopic characterization of lipid vesicles in calcium-containing environments. To gain additional atomic-level information, the experiments are complemented by molecular simulations that utilize an accurate force field for calcium ions with scaled charges effectively accounting for electronic polarization effects. We demonstrate that lipid membranes have substantial calcium-binding capacity, with several types of binding sites present. Significantly, the binding mode depends on calcium concentration with important implications for calcium buffering, synaptic plasticity, and protein-membrane association.

Interactions of lysozyme in concentrated electrolyte solutions from dynamic light-scattering measurements.

PubMed Central

Kuehner, D E; Heyer, C; Rämsch, C; Fornefeld, U M; Blanch, H W; Prausnitz, J M

1997-01-01

The diffusion of hen egg-white lysozyme has been studied by dynamic light scattering in aqueous solutions of ammonium sulfate as a function of protein concentration to 30 g/liter. Experiments were conducted under the following conditions: pH 4-7 and ionic strength 0.05-5.0 M. Diffusivity data for ionic strengths up to 0.5 M were interpreted in the context of a two-body interaction model for monomers. From this analysis, two potential-of-mean-force parameters, the effective monomer charge, and the Hamaker constant were obtained. At higher ionic strength, the data were analyzed using a model that describes the diffusion coefficient of a polydisperse system of interacting protein aggregates in terms of an isodesmic, indefinite aggregation equilibrium constant. Data analysis incorporated multicomponent virial and hydrodynamic effects. The resulting equilibrium constants indicate that lysozyme does not aggregate significantly as ionic strength increases, even at salt concentrations near the point of salting-out precipitation. PMID:9414232

Near UV-Visible electronic absorption originating from charged amino acids in a monomeric protein† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00880e

PubMed Central

Prasad, Saumya; Mandal, Imon; Singh, Shubham; Paul, Ashim; Mandal, Bhubaneswar

2017-01-01

Electronic absorption spectra of proteins are primarily characterized over the ultraviolet region (185–320 nm) of the electromagnetic spectrum. While recent studies on peptide aggregates have revealed absorption beyond 350 nm, monomeric proteins lacking aromatic amino acids, disulphide bonds, and active site prosthetic groups are expected to remain optically silent beyond 250 nm. Here, in a joint theoretical and experimental investigation, we report the distinctive UV-Vis absorption spectrum between 250 nm [ε = 7338 M–1 cm–1] and 800 nm [ε = 501 M–1 cm–1] in a synthetic 67 residue protein (α3C), in monomeric form, devoid of aromatic amino acids. Systematic control studies with high concentration non-aromatic amino acid solutions revealed significant absorption beyond 250 nm for charged amino acids which constitute over 50% of the sequence composition in α3C. Classical atomistic molecular dynamics (MD) simulations of α3C reveal dynamic interactions between multiple charged sidechains of Lys and Glu residues present in α3C. Time-dependent density functional theory calculations on charged amino acid residues sampled from the MD trajectories of α3C reveal that the distinctive absorption features of α3C may arise from two different types of charge transfer (CT) transitions involving spatially proximal Lys/Glu amino acids. Specifically, we show that the charged amino (NH3+)/carboxylate (COO–) groups of Lys/Glu sidechains act as electronic charge acceptors/donors for photoinduced electron transfer either from/to the polypeptide backbone or to each other. Further, the sensitivity of the CT spectra to close/far/intermediate range of encounters between sidechains of Lys/Glu owing to the three dimensional protein fold can create the long tail in the α3C absorption profile between 300 and 800 nm. Finally, we experimentally demonstrate the sensitivity of α3C absorption spectrum to temperature and pH-induced changes in protein structure. Taken together, our investigation significantly expands the pool of spectroscopically active biomolecular chromophores and adds an optical 250–800 nm spectral window, which we term ProCharTS (Protein Charge Transfer Spectra), for label free probes of biomolecular structure and dynamics. PMID:28970921

Energy and structure of bonds in the interaction of organic anions with layered double hydroxide nanosheets: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Tsukanov, A. A.; Psakhie, S. G.

2016-01-01

The application of hybrid and hierarchical nanomaterials based on layered hydroxides and oxyhydroxides of metals is a swiftly progressing field in biomedicine. Layered double hydroxides (LDH) possess a large specific surface area, significant surface electric charge and biocompatibility. Their physical and structural properties enable them to adsorb various kinds of anionic species and to transport them into cells. However, possible side effects resulting from the interaction of LDH with anions of the intercellular and intracellular medium need to be considered, since such interaction can potentially disrupt ion transport, signaling processes, apoptosis, nutrition and proliferation of living cells. In the present paper molecular dynamics is used to determine the energies of interaction of organic anions (aspartic acid, glutamic acid and bicarbonate) with a fragment of layered double hydroxide Mg/Al-LDH. The average number of hydrogen bonds between the anions and the hydroxide surface and characteristic binding configurations are determined. Possible effects of LDH on the cell resulting from binding of protein fragments and replacement of native intracellular anions with delivered anions are considered.

Pion single and double charge exchange in the resonance region: Dynamical corrections

NASA Astrophysics Data System (ADS)

Johnson, Mikkel B.; Siciliano, E. R.

1983-04-01

We consider pion-nucleus elastic scattering and single- and double-charge-exchange scattering to isobaric analog states near the (3,3) resonance within an isospin invariant framework. We extend previous theories by introducing terms into the optical potential U that are quadratic in density and consistent with isospin invariance of the strong interaction. We study the sensitivity of single and double charge exchange angular distributions to parameters of the second-order potential both numerically, by integrating the Klein-Gordon equation, and analytically, by using semiclassical approximations that explicate the dependence of the exact numerical results to the parameters of U. The magnitude and shape of double charge exchange angular distributions are more sensitive to the isotensor term in U than has been hitherto appreciated. An examination of recent experimental data shows that puzzles in the shape of the 18O(π+, π-)18Ne angular distribution at 164 MeV and in the A dependence of the forward double charge exchange scattering on 18O, 26Mg, 42Ca, and 48Ca at the same energy may be resolved by adding an isotensor term in U. NUCLEAR REACTIONS Scattering theory for elastic, single-, and double-charge-exchange scattering to IAS in the region of the P33 resonance. Second-order effects on charge-exchange calculations of σ(A, θ).

Quantum dynamics at finite temperature: Time-dependent quantum Monte Carlo study

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

Christov, Ivan P., E-mail: ivan.christov@phys.uni-sofia.bg

2016-08-15

In this work we investigate the ground state and the dissipative quantum dynamics of interacting charged particles in an external potential at finite temperature. The recently devised time-dependent quantum Monte Carlo (TDQMC) method allows a self-consistent treatment of the system of particles together with bath oscillators first for imaginary-time propagation of Schrödinger type of equations where both the system and the bath converge to their finite temperature ground state, and next for real time calculation where the dissipative dynamics is demonstrated. In that context the application of TDQMC appears as promising alternative to the path-integral related techniques where the realmore » time propagation can be a challenge.« less

On the molecular dynamics in the hurricane interactions with its environment

NASA Astrophysics Data System (ADS)

Meyer, Gabriel; Vitiello, Giuseppe

2018-06-01

By resorting to the Burgers model for hurricanes, we study the molecular motion involved in the hurricane dynamics. We show that the Lagrangian canonical formalism requires the inclusion of the environment degrees of freedom. This also allows the description of the motion of charged particles. In view of the role played by moist convection, cumulus and cloud water droplets in the hurricane dynamics, we discuss on the basis of symmetry considerations the role played by the molecular electrical dipoles and the formation of topologically non-trivial structures. The mechanism of energy storage and dissipation, the non-stationary time dependent Ginzburg-Landau equation and the vortex equation are studied. Finally, we discuss the fractal self-similarity properties of hurricanes.

Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer

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

Daily, Michael D.; Baer, Marcel D.; Mundy, Christopher J.

2016-03-10

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids usingmore » a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical forcefield (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through sidechain-sidechain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described. MDD was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory. Research was funded by the Laboratory Directed Research and Development program at Pacific Northwest National Laboratory. MDB acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Material & Engineering. CJM acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.« less

Interaction between electrically charged droplets in microgravity

NASA Astrophysics Data System (ADS)

Brandenbourger, Martin; Caps, Herve; Hardouin, Jerome; Vitry, Youen; Boigelot, Bernard; Dorbolo, Stephane; Grasp Team; Beams Collaboration

2015-11-01

The past ten years, electrically charged droplets have been studied tremendously for their applications in industry (electrospray, electrowetting,...). However, charged droplets are also present in nature. Indeed, it has been shown that the droplets falling from thunderclouds possess an excess of electric charges. Moreover, some research groups try to use the electrical interaction between drops in order to control the coalescence between cloud droplets and control rain generation. The common way to study this kind of system is to make hypothesis on the interaction between two charged drops. Then, these hypothesis are extended to a system of thousands of charged droplets. Thanks to microgravity conditions, we were able to study the interaction between two electrically charged droplets. In practice, the charged droplets were propelled one in front of the other at low speed (less than 1 m/s). The droplets trajectory is studied for various charges and volumes. The repulsion between two charged drops is correctly fitted by a simple Coulomb repulsion law. In the case of attractive interactions, we discuss the collisions observed as a function of the droplets speed, volume and electric charges. Thanks to FNRS for financial support.

Capacitance of Nanoporous Carbon-Based Supercapacitors Is a Trade-Off between the Concentration and the Separability of the Ions.

PubMed

Burt, Ryan; Breitsprecher, Konrad; Daffos, Barbara; Taberna, Pierre-Louis; Simon, Patrice; Birkett, Greg; Zhao, X S; Holm, Christian; Salanne, Mathieu

2016-10-06

Nanoporous carbon-based supercapacitors store electricity through adsorption of ions from the electrolyte at the surface of the electrodes. Room temperature ionic liquids, which show the largest ion concentrations among organic liquid electrolytes, should in principle yield larger capacitances. Here, we show by using electrochemical measurements that the capacitance is not significantly affected when switching from a pure ionic liquid to a conventional organic electrolyte using the same ionic species. By performing additional molecular dynamics simulations, we interpret this result as an increasing difficulty of separating ions of opposite charges when they are more concentrated, that is, in the absence of a solvent that screens the Coulombic interactions. The charging mechanism consistently changes with ion concentration, switching from counterion adsorption in the diluted organic electrolyte to ion exchange in the pure ionic liquid. Contrarily to the capacitance, in-pore diffusion coefficients largely depend on the composition, with a noticeable slowing of the dynamics in the pure ionic liquid.

Statistical against dynamical PLF fission as seen by the IMF-IMF correlation functions and comparisons with CoMD model

NASA Astrophysics Data System (ADS)

Pagano, E. V.; Acosta, L.; Auditore, L.; Cap, T.; Cardella, G.; Colonna, M.; De Filippo, E.; Geraci, E.; Gnoffo, B.; Lanzalone, G.; Maiolino, C.; Martorana, N.; Pagano, A.; Papa, M.; Piasecki, E.; Pirrone, S.; Politi, G.; Porto, F.; Quattrocchi, L.; Rizzo, F.; Russotto, P.; Trifiro’, A.; Trimarchi, M.; Siwek-Wilczynska, K.

2018-05-01

In nuclear reactions at Fermi energies two and multi particles intensity interferometry correlation methods are powerful tools in order to pin down the characteristic time scale of the emission processes. In this paper we summarize an improved application of the fragment-fragment correlation function in the specific physics case of heavy projectile-like (PLF) binary massive splitting in two fragments of intermediate mass(IMF). Results are shown for the reverse kinematics reaction 124 Sn+64 Ni at 35 AMeV that has been investigated by using the forward part of CHIMERA multi-detector. The analysis was performed as a function of the charge asymmetry of the observed couples of IMF. We show a coexistence of dynamical and statistical components as a function of the charge asymmetry. Transport CoMD simulations are compared with the data in order to pin down the timescale of the fragments production and the relevant ingredients of the in medium effective interaction used in the transport calculations.

Ionic Adsorption and Desorption of CNT Nanoropes

PubMed Central

Shang, Jun-Jun; Yang, Qing-Sheng; Yan, Xiao-Hui; He, Xiao-Qiao; Liew, Kim-Meow

2016-01-01

A nanorope is comprised of several carbon nanotubes (CNTs) with different chiralities. A molecular dynamic model is built to investigate the ionic adsorption and desorption of the CNT nanoropes. The charge distribution on the nanorope is obtained by using a modified gradient method based on classical electrostatic theory. The electrostatic interactions among charged carbon atoms are calculated by using the Coulomb law. It was found here that the charged nanorope can adsorb heavy metal ions, and the adsorption and desorption can be realized by controlling the strength of applied electric field. The distance between the ions and the nanorope as well as the amount of ions have an effect on the adsorption capacity of the nanorope. The desorption process takes less time than that of adsorption. The study indicates that the CNT nanorope can be used as a core element of devices for sewage treatment. PMID:28335306

Evidence of the charge-density wave state in polypyrrole nanotubes

DOE PAGES

Sarma, Abhisakh; Sanyal, Milan K.; Littlewood, Peter B.

2015-04-13

Here, we present a detailed investigation of the low-frequency dielectric and conductivity properties of conducting polymer nanowires. Our results, obtained by connecting ~10 7 nanowires in parallel, show that these polypyrrole nanowires behave like conventional charge-density wave (CDW) materials, in their nonlinear and dynamic response, together with scaling of relaxation time and conductivity. The observed Arrhenius law for both these quantities gives a CDW gap of 3.5 meV in the regime of temperature (~40 K) in which the CDW state survives. We find good agreement with a theory of weakly pinned CDW, screened by thermally excited carriers across the CDWmore » gap. The identification of polymer nanowires as CDW provides us a model system to investigate charge ordering owing to electrostatic interaction, relevant to a variety of systems from dusty plasma to molecular biology.« less

Tunable aqueous virtual micropore.

PubMed

Park, Jae Hyun; Guan, Weihua; Reed, Mark A; Krstić, Predrag S

2012-03-26

A charged microparticle can be trapped in an aqueous environment by forming a narrow virtual pore--a cylindrical space region in which the particle motion in the radial direction is limited by forces emerging from dynamical interactions of the particle charge and dipole moment with an external radiofrequency quadrupole electric field. If the particle satisfies the trap stability criteria, its mean motion is reduced exponentially with time due to the viscosity of the aqueous environment; thereafter the long-time motion of particle is subject only to random, Brownian fluctuations, whose magnitude, influenced by the electrophoretic and dielectrophoretic effects and added to the particle size, determines the radius of the virtual pore, which is demonstrated by comparison of computer simulations and experiment. The measured size of the virtual nanopore could be utilized to estimate the charge of a trapped micro-object. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adsorption of charged protein residues on an inorganic nanosheet: Computer simulation of LDH interaction with ion channel

NASA Astrophysics Data System (ADS)

Tsukanov, Alexey A.; Psakhie, Sergey G.

2016-08-01

Quasi-two-dimensional and hybrid nanomaterials based on layered double hydroxides (LDH), cationic clays, layered oxyhydroxides and hydroxides of metals possess large specific surface area and strong electrostatic properties with permanent or pH-dependent electric charge. Such nanomaterials may impact cellular electrostatics, changing the ion balance, pH and membrane potential. Selective ion adsorption/exchange may alter the transmembrane electrochemical gradient, disrupting potential-dependent cellular processes. Cellular proteins as a rule have charged residues which can be effectively adsorbed on the surface of layered hydroxide based nanomaterials. The aim of this study is to attempt to shed some light on the possibility and mechanisms of protein "adhesion" an LDH nanosheet and to propose a new direction in anticancer medicine, based on physical impact and strong electrostatics. An unbiased molecular dynamics simulation was performed and the combined process free energy estimation (COPFEE) approach was used.

Electrostatically Directed Self-Assembly of Ultrathin Supramolecular Polymer Microcapsules

PubMed Central

Parker, Richard M; Zhang, Jing; Zheng, Yu; Coulston, Roger J; Smith, Clive A; Salmon, Andrew R; Yu, Ziyi; Scherman, Oren A; Abell, Chris

2015-01-01

Supramolecular self-assembly offers routes to challenging architectures on the molecular and macroscopic scale. Coupled with microfluidics it has been used to make microcapsules—where a 2D sheet is shaped in 3D, encapsulating the volume within. In this paper, a versatile methodology to direct the accumulation of capsule-forming components to the droplet interface using electrostatic interactions is described. In this approach, charged copolymers are selectively partitioned to the microdroplet interface by a complementary charged surfactant for subsequent supramolecular cross-linking via cucurbit[8]uril. This dynamic assembly process is employed to selectively form both hollow, ultrathin microcapsules and solid microparticles from a single solution. The ability to dictate the distribution of a mixture of charged copolymers within the microdroplet, as demonstrated by the single-step fabrication of distinct core–shell microcapsules, gives access to a new generation of innovative self-assembled constructs. PMID:26213532

Ionic Adsorption and Desorption of CNT Nanoropes.

PubMed

Shang, Jun-Jun; Yang, Qing-Sheng; Yan, Xiao-Hui; He, Xiao-Qiao; Liew, Kim-Meow

2016-09-28

A nanorope is comprised of several carbon nanotubes (CNTs) with different chiralities. A molecular dynamic model is built to investigate the ionic adsorption and desorption of the CNT nanoropes. The charge distribution on the nanorope is obtained by using a modified gradient method based on classical electrostatic theory. The electrostatic interactions among charged carbon atoms are calculated by using the Coulomb law. It was found here that the charged nanorope can adsorb heavy metal ions, and the adsorption and desorption can be realized by controlling the strength of applied electric field. The distance between the ions and the nanorope as well as the amount of ions have an effect on the adsorption capacity of the nanorope. The desorption process takes less time than that of adsorption. The study indicates that the CNT nanorope can be used as a core element of devices for sewage treatment.

Ultrafast spin exchange-coupling torque via photo-excited charge-transfer processes

NASA Astrophysics Data System (ADS)

Ma, X.; Fang, F.; Li, Q.; Zhu, J.; Yang, Y.; Wu, Y. Z.; Zhao, H. B.; Lüpke, G.

2015-10-01

Optical control of spin is of central importance in the research of ultrafast spintronic devices utilizing spin dynamics at short time scales. Recently developed optical approaches such as ultrafast demagnetization, spin-transfer and spin-orbit torques open new pathways to manipulate spin through its interaction with photon, orbit, charge or phonon. However, these processes are limited by either the long thermal recovery time or the low-temperature requirement. Here we experimentally demonstrate ultrafast coherent spin precession via optical charge-transfer processes in the exchange-coupled Fe/CoO system at room temperature. The efficiency of spin precession excitation is significantly higher and the recovery time of the exchange-coupling torque is much shorter than for the demagnetization procedure, which is desirable for fast switching. The exchange coupling is a key issue in spin valves and tunnelling junctions, and hence our findings will help promote the development of exchange-coupled device concepts for ultrafast coherent spin manipulation.

Dust in Jupiter's magnetosphere. I - Physical processes. II - Origin of the ring. III - Time variations. IV - Effect on magnetospheric electrons and ions

NASA Technical Reports Server (NTRS)

Morfill, G. E.; Gruen, E.; Johnson, T. V.

1980-01-01

The physical processes acting on charged microscopic dust grains in the Jovian atmosphere involve electromagnetic forces which dominate dust particle dynamics and diffusion across field lines resulting from random charge fluctuations of the dust grains. A model of the Jovian ring hypothesizes that the 'visible' ring particles are produced by erosive collisions between an assumed population of kilometer-sized parent bodies and submicron-sized magnetospheric dust particles. Fluctuations in the ring topology and intensity are determined over various time scales, showing that the ring is a quasipermanent and quasistable characteristic of the Jovian system. Finally, the interaction of the Jovian energetic belt electrons and the Jovian plasma with an ambient dust population is examined; the distribution of dust ejected from Io in the inner magnetosphere and losses of magnetospheric ions and electrons due to direct collisions with charged dust particles are calculated.

Supramolecular gating of ion transport in nanochannels.

PubMed

Kumar, B V V S Pavan; Rao, K Venkata; Sampath, S; George, Subi J; Eswaramoorthy, Muthusamy

2014-11-24

Several covalent strategies towards surface charge-reversal in nanochannels have been reported with the purpose of manipulating ion transport. However, covalent routes lack dynamism, modularity and post-synthetic flexibility, and hence restrict their applicability in different environments. Here, we introduce a facile non-covalent approach towards charge-reversal in nanochannels (<10 nm) using strong charge-transfer interactions between dicationic viologen (acceptor) and trianionic pyranine (donor). The polarity of ion transport was switched from anion selective to ambipolar to cation selective by controlling the extent of viologen bound to the pyranine. We could also regulate the ion transport with respect to pH by selecting a donor with pH-responsive functional groups. The modularity of this approach further allows facile integration of various functional groups capable of responding to stimuli such as light and temperature to modulate the transport of ions as well as molecules. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the exchange-hole model of London dispersion forces

NASA Astrophysics Data System (ADS)

Ángyán, János G.

2007-07-01

First-principles derivation is given for the heuristic exchange-hole model of London dispersion forces by Becke and Johnson [J. Chem. Phys. 122, 154104 (2005)]. A one-term approximation is used for the dynamic charge density response function, and it is shown that a central nonempirical ingredient of the approximate nonexpanded dispersion energy is the charge density autocorrelation function, a two-particle property, related to the exchange-correlation hole. In the framework of a dipolar approximation of the Coulomb interaction around the molecular origin, one obtains the so-called Salem-Tang-Karplus approximation to the C6 dispersion coefficient. Alternatively, by expanding the Coulomb interaction around the center of charge (centroid) of the exchange-correlation hole associated with each point in the molecular volume, a multicenter expansion is obtained around the centroids of electron localization domains, always in terms of the exchange-correlation hole. In order to get a formula analogous to that of Becke and Johnson, which involves the exchange-hole only, further assumptions are needed, related to the difficulties of obtaining the expectation value of a two-electron operator from a single determinant. Thus a connection could be established between the conventional fluctuating charge density model of London dispersion forces and the notion of the "exchange-hole dipole moment" shedding some light on the true nature of the approximations implicit in the Becke-Johnson model.

X-ray Pump–Probe Investigation of Charge and Dissociation Dynamics in Methyl Iodine Molecule

DOE PAGES

Fang, Li; Xiong, Hui; Kukk, Edwin; ...

2017-05-19

Molecular dynamics is of fundamental interest in natural science research. The capability of investigating molecular dynamics is one of the various motivations for ultrafast optics. Here, we present our investigation of photoionization and nuclear dynamics in methyl iodine (CH 3I) molecule with an X-ray pump X-ray probe scheme. The pump–probe experiment was realized with a two-mirror X-ray split and delay apparatus. Time-of-flight mass spectra at various pump–probe delay times were recorded to obtain the time profile for the creation of high charge states via sequential ionization and for molecular dissociation. We observed high charge states of atomic iodine up tomore » 29+, and visualized the evolution of creating these high atomic ion charge states, including their population suppression and enhancement as the arrival time of the second X-ray pulse was varied. We also show the evolution of the kinetics of the high charge states upon the timing of their creation during the ionization-dissociation coupled dynamics. We demonstrate the implementation of X-ray pump–probe methodology for investigating X-ray induced molecular dynamics with femtosecond temporal resolution. The results indicate the footprints of ionization that lead to high charge states, probing the long-range potential curves of the high charge states.« less

Traversing the folding pathway of proteins using temperature-aided cascade molecular dynamics with conformation-dependent charges.

PubMed

Jani, Vinod; Sonavane, Uddhavesh; Joshi, Rajendra

2016-07-01

Protein folding is a multi-micro second time scale event and involves many conformational transitions. Crucial conformational transitions responsible for biological functions of biomolecules are difficult to capture using current state-of-the-art molecular dynamics (MD) simulations. Protein folding, being a stochastic process, witnesses these transitions as rare events. Many new methodologies have been proposed for observing these rare events. In this work, a temperature-aided cascade MD is proposed as a technique for studying the conformational transitions. Folding studies for Engrailed homeodomain and Immunoglobulin domain B of protein A have been carried out. Using this methodology, the unfolded structures with RMSD of 20 Å were folded to a structure with RMSD of 2 Å. Three sets of cascade MD runs were carried out using implicit solvation, explicit solvation, and charge updation scheme. In the charge updation scheme, charges based on the conformation obtained are calculated and are updated in the topology file. In all the simulations, the structure of 2 Å was reached within a few nanoseconds using these methods. Umbrella sampling has been performed using snapshots from the temperature-aided cascade MD simulation trajectory to build an entire conformational transition pathway. The advantage of the method is that the possible pathways for a particular reaction can be explored within a short duration of simulation time and the disadvantage is that the knowledge of the start and end state is required. The charge updation scheme adds the polarization effects in the force fields. This improves the electrostatic interaction among the atoms, which may help the protein to fold faster.

Effect of spin traps on charge transport in low-bandgap copolymer:fullerene composites

NASA Astrophysics Data System (ADS)

Krinichnyi, Victor I.; Yudanova, Evgeniya I.; Bogatyrenko, Victor R.

2017-12-01

Light-Induced EPR study of magnetic, relaxation and dynamic parameters of spin charge carriers background photoinduced in bulk heterojunctions of composites formed by poly[2,7-(9,9-dioctylfluorene)-alt-4,7-bis(thiophen-2-yl)benzo-2,1,3-thiadiazole] (PFO-DBT) and poly[N-9‧-heptadecanyl-2,7-carbazole-alt-5,5-(4‧,7‧-di-2-thienyl-2‧,1‧,3‧-benzothiadiazole)] (PCDTBT) with methanofullerene [6,6]-phenyl-C61-butyric acid methyl ester is described. A part of polarons is captured by deep spin traps whose number and energy depth are governed by the structure, morphology of a copolymer matrix and also by the photon energy. Both the composites exhibit photo-response within photon energy/wavelength 1.32-3.14 eV/940-395 nm region which is wider than that of other polymer composites. Magnetic, relaxation and dynamics parameters of spin charge carriers were shown to be governed by their exchange interaction and photon energy. Specific morphology of the composites causes selectivity of these parameters to the photon energy. It was shown that the anisotropy of spin mobility through bulk heterojunctions reflects the system dimensionality and is governed by the photon properties. The replacement of the PFO-DBT backbone by the PCDTBT matrix leads increases the ordering of a copolymer, decreases the number of spin traps and changes a mechanism of charge recombination. The decay of free charge carriers was interpreted in terms of the trapping-detrapping spin diffusion in bulk heterojunctions.

Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape.

PubMed

Ghaemi, Zhaleh; Guzman, Irisbel; Gnutt, David; Luthey-Schulten, Zaida; Gruebele, Martin

2017-09-14

U1A protein-stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape toward a specific binding site. We show by using molecular dynamics simulations that deletion of two long-range electrostatic interactions (K22Q and K50Q) leads to mutant-specific alternative RNA bound states. One of these states preserves short-range interactions with aromatic residues in the original binding site, while the other one does not. We test the computational prediction with experimental temperature-jump kinetics using a tryptophan probe in the U1A-RNA binding site. The two mutants show the distinct predicted kinetic behaviors. Thus, the stem loop 2 RNA has multiple binding sites on a rough RNA-protein binding landscape. We speculate that the rough protein-RNA binding landscape, when biased to different local minima by electrostatics, could be one way that protein-RNA interactions evolve toward new binding sites and novel function.

Dynamic Colloidal Molecules Maneuvered by Light-Controlled Janus Micromotors.

PubMed

Gao, Yirong; Mou, Fangzhi; Feng, Yizheng; Che, Shengping; Li, Wei; Xu, Leilei; Guan, Jianguo

2017-07-12

In this work, we propose and demonstrate a dynamic colloidal molecule that is capable of moving autonomously and performing swift, reversible, and in-place assembly dissociation in a high accuracy by manipulating a TiO 2 /Pt Janus micromotor with light irradiation. Due to the efficient motion of the TiO 2 /Pt Janus motor and the light-switchable electrostatic interactions between the micromotor and colloidal particles, the colloidal particles can be captured and assembled one by one on the fly, subsequently forming into swimming colloidal molecules by mimicking space-filling models of simple molecules with central atoms. The as-demonstrated dynamic colloidal molecules have a configuration accurately controlled and stabilized by regulating the time-dependent intensity of UV light, which controls the stop-and-go motion of the colloidal molecules. The dynamic colloidal molecules are dissociated when the light irradiation is turned off due to the disappearance of light-switchable electrostatic interaction between the motor and the colloidal particles. The strategy for the assembly of dynamic colloidal molecules is applicable to various charged colloidal particles. The simulated optical properties of a dynamic colloidal molecule imply that the results here may provide a novel approach for in-place building functional microdevices, such as microlens arrays, in a swift and reversible manner.

Interactions between charged nanoparticles and giant vesicles fabricated from inverted-headgroup lipids

NASA Astrophysics Data System (ADS)

Wang, Lu; Malmstadt, Noah

2017-10-01

The surface chemistry of the cell membrane plays an important role in how cells interact with particulate species. These interactions are dictated in large part by lipid headgroup charge. To investigate the nature of electrostatic interactions between lipid bilayers and nanoparticles in solution, we studied nanoparticles interacting with the zwitterionic lipid 1,2-dioleoyl-glycero-3-phosphocholine (DOPC), and its inverted-headgroup analog DOCP. These interactions were investigated by fabricating giant unilamellar vesicles (GUVs) with DOPC lipids and DOCP lipids respectively, and introducing nanoparticles to suspensions of both. GUVs displayed various deformational modes depending on the charge and size of the nanoparticles as well as the compositions of the GUVs. The differences in the responses of the two lipid species illuminate how the phosphate and choline groups on the lipid interact with charged nanoparticles. This study suggests that the phosphate group dominates the lipid-nanoparticle electrostatic interaction. We speculate that the formation of water clathrate structures around the choline group inhibits interactions between negatively charged nanoparticles and the positively charged choline.

Atomic partial charges on CH{sub 3}NH{sub 3}PbI{sub 3} from first-principles electronic structure calculations

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

Madjet, Mohamed E., E-mail: mmadjet@qf.org.qa; El-Mellouhi, Fedwa; Carignano, Marcelo A.

We calculated the partial charges in methylammonium (MA) lead-iodide perovskite CH{sub 3}NH{sub 3}PbI{sub 3} in its different crystalline phases using different first-principles electronic charge partitioning approaches, including the Bader, ChelpG, and density-derived electrostatic and chemical (DDEC) schemes. Among the three charge partitioning methods, the DDEC approach provides chemically intuitive and reliable atomic charges for this material, which consists of a mixture of transition metals, halide ions, and organic molecules. The DDEC charges are also found to be robust against the use of hybrid functionals and/or upon inclusion of spin–orbit coupling or dispersive interactions. We calculated explicitly the atomic charges withmore » a special focus on the dipole moment of the MA molecules within the perovskite structure. The value of the dipole moment of the MA is reduced with respect to the isolated molecule due to charge redistribution involving the inorganic cage. DDEC charges and dipole moment of the organic part remain nearly unchanged upon its rotation within the octahedral cavities. Our findings will be of both fundamental and practical importance, as the accurate and consistent determination of the atomic charges is important in order to understand the average equilibrium distribution of the electrons and to help in the development of force fields for larger scale atomistic simulations to describe static, dynamic, and thermodynamic properties of the material.« less

Charge dynamics of the antiferromagnetically ordered Mott insulator

NASA Astrophysics Data System (ADS)

Han, Xing-Jie; Liu, Yu; Liu, Zhi-Yuan; Li, Xin; Chen, Jing; Liao, Hai-Jun; Xie, Zhi-Yuan; Normand, B.; Xiang, Tao

2016-10-01

We introduce a slave-fermion formulation in which to study the charge dynamics of the half-filled Hubbard model on the square lattice. In this description, the charge degrees of freedom are represented by fermionic holons and doublons and the Mott-insulating characteristics of the ground state are the consequence of holon-doublon bound-state formation. The bosonic spin degrees of freedom are described by the antiferromagnetic Heisenberg model, yielding long-ranged (Néel) magnetic order at zero temperature. Within this framework and in the self-consistent Born approximation, we perform systematic calculations of the average double occupancy, the electronic density of states, the spectral function and the optical conductivity. Qualitatively, our method reproduces the lower and upper Hubbard bands, the spectral-weight transfer into a coherent quasiparticle band at their lower edges and the renormalisation of the Mott gap, which is associated with holon-doublon binding, due to the interactions of both quasiparticle species with the magnons. The zeros of the Green function at the chemical potential give the Luttinger volume, the poles of the self-energy reflect the underlying quasiparticle dispersion with a spin-renormalised hopping parameter and the optical gap is directly related to the Mott gap. Quantitatively, the square-lattice Hubbard model is one of the best-characterised problems in correlated condensed matter and many numerical calculations, all with different strengths and weaknesses, exist with which to benchmark our approach. From the semi-quantitative accuracy of our results for all but the weakest interaction strengths, we conclude that a self-consistent treatment of the spin-fluctuation effects on the charge degrees of freedom captures all the essential physics of the antiferromagnetic Mott-Hubbard insulator. We remark in addition that an analytical approximation with these properties serves a vital function in developing a full understanding of the fundamental physics of the Mott state, both in the antiferromagnetic insulator and at finite temperatures and dopings.

Living with dementia: communicating with an older person and her family.

PubMed

Long, A; Slevin, E

1999-01-01

This article is designed to explore and examine the key components of communication that emerged during the interactional analysis of a role play that took place in the classroom. The 'actors' were nurses who perceived the interaction to reflect an everyday encounter in a hospital ward. Permission to tape the interaction was sought and given by all persons involved. The principal 'players' in the scenario were: the patient, a 70-year-old-woman who had been admitted with dementia, her son and daughter, and the nurse in charge of the ward. The fundamental dynamics of the use of power and restriction, truth telling, family stress, interpersonal conflict, ageism, sexism, empathy and humanism surfaced during the analysis. The findings show that therapeutic communication should be the foundation on which nursing should stand. The article continues with an exploration of the theoretical frameworks that guided the analysis of interaction and concludes by suggesting tentatively some meaningful implications for nursing practice. It plans to furnish provocative new insights into the sometimes covert communication dynamics occurring within the nurse-patient relationship. Finally, it aims to generate discussion on this little-charted realm of human social interaction.

Wavelet analysis of particle density functions in nucleus-nucleus interactions

NASA Astrophysics Data System (ADS)

Manna, S. K.; Haldar, P. K.; Mali, P.; Mukhopadhyay, A.; Singh, G.

A continuous wavelet analysis is performed for pattern recognition of the pseudorapidity density profile of singly charged particles produced in 16O+Ag/Br and 32S+Ag/Br interactions, each at an incident energy of 200 GeV per nucleon in the laboratory system. The experiments are compared with a model prediction based on the ultra-relativistic quantum molecular dynamics (UrQMD). To eliminate the contribution coming from known source(s) of particle cluster formation like Bose-Einstein correlation (BEC), the UrQMD output is modified by “an algorithm that mimics the BEC as an after burner.” We observe that for both interactions particle clusters are found at same pseudorapidity locations at all scales. However, the cluster locations in the 16O+Ag/Br interaction are different from those found in the 32S+Ag/Br interaction. Significant differences between experiments and simulations are revealed in the wavelet pseudorapidity spectra that can be interpreted as the preferred pseudorapidity values and/or scales of the pseudorapidity interval at which clusters of particles are formed. The observed discrepancy between experiment and corresponding simulation should therefore be interpreted in terms of some kind of nontrivial dynamics of multiparticle production.