Shapiro like steps reveals molecular nanomagnets’ spin dynamics

International Nuclear Information System (INIS)

Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid

2015-01-01

We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields

Dynamically polarized hydrogen target as a broadband, wavelength-independent thermal neutron spin polarizer

International Nuclear Information System (INIS)

Zhao Jinkui; Garamus, Vasil M.; Mueller, Wilhelm; Willumeit, Regine

2005-01-01

A hydrogen-rich sample with dynamically polarized hydrogen nuclei was tested as a wavelength-independent neutron transmission spin polarizer. The experiment used a modified setup of the dynamic nuclear polarization target station at the GKSS research center. The standard solvent sample at the GKSS DNP station was used. It is 2.8mm thick and consists of 43.4wt% water, 54.6wt% glycerol, and 2wt% of EHBA-Cr(v) complex. The wavelength of the incident neutrons for the transmission experiment was λ=8.1A with Δλ/λ=10%. The polarization of neutron beam after the target sample was analyzed with a supermirror analyzer. A neutron polarization of -52% was achieved at the hydrogen polarization of -69%. Further experiments will test the feasibility of other hydrogen-rich materials, such as methane, as the polarizer. A theoretical calculation shows that a polarized methane target would allow over 95% neutron polarizations with more than 30% transmission

Dynamic nuclear polarization of irradiated target materials

International Nuclear Information System (INIS)

Seely, M.L.

1982-01-01

Polarized nucleon targets used in high energy physics experiments usually employ the method of dynamic nuclear polarization (DNP) to polarize the protons or deuterons in an alcohol. DNP requires the presence of paramagnetic centers, which are customarily provided by a chemical dopant. These chemically doped targets have a relatively low polarizable nucleon content and suffer from loss of polarization when subjected to high doses of ionizing radiation. If the paramagnetic centers formed when the target is irradiated can be used in the DNP process, it becomes possible to produce targets using materials which have a relatively high polarizable nucleon content, but which are not easily doped by chemical means. Furthermore, the polarization of such targets may be much more radiation resistant. Dynamic nuclear polarization in ammonia, deuterated ammonia, ammonium hydroxide, methylamine, borane ammonia, butonal, ethane and lithium borohydride has been studied. These studies were conducted at the Stanford Linear Accelerator Center using the Yale-SLAC polarized target system. Results indicate that the use of ammonia and deuterated ammonia as polarized target materials would make significant increases in polarized target performance possible

Electron Interference in Molecular Circular Polarization Attosecond XUV Photoionization

Directory of Open Access Journals (Sweden)

Kai-Jun Yuan

2015-01-01

Full Text Available Two-center electron interference in molecular attosecond photoionization processes is investigated from numerical solutions of time-dependent Schrödinger equations. Both symmetric H\\(_2^+\\ and nonsymmetric HHe\\(^{2+}\\ one electron diatomic systems are ionized by intense attosecond circularly polarized XUV laser pulses. Photoionization of these molecular ions shows signature of interference with double peaks (minima in molecular attosecond photoelectron energy spectra (MAPES at critical angles \\(\\vartheta_c\\ between the molecular \\(\\textbf{R}\\ axis and the photoelectron momentum \\(\\textbf{p}\\. The interferences are shown to be a function of the symmetry of electronic states and the interference patterns are sensitive to the molecular orientation and pulse polarization. Such sensitivity offers possibility for imaging of molecular structure and orbitals.

Polarization of far-infrared radiation from molecular clouds

Science.gov (United States)

Novak, G.; Gonatas, D. P.; Hildebrand, R. H.; Platt, S. R.; Dragovan, M.

1989-01-01

The paper reports measurements of the polarization of far-infrared emission from dust in nine molecular clouds. Detections were obtained in Mon R2, in the Kleinmann-Low (KL) nebula in Orion, and in Sgr A. Upper limits were set for six other clouds. A comparison of the 100 micron polarization of KL with that previously measured at 270 microns provides new evidence that the polarization is due to emission from magnetically aligned dust grains. Comparing the results for Orion with measurements at optical wavelengths, it is inferred that the magnetic field direction in the outer parts of the Orion cloud is the same as that in the dense core. This direction is nearly perpendicular to the ridge of molecular emission and is parallel to both the molecular outflow in KL and the axis of rotation of the cloud core. In Mon R2, the field direction which the measurements imply does not agree withthat derived from 0.9-2.2 micron polarimetry. The discrepancy is attributed to scattering in the near-infrared. In Orion and Sgr A, where comparisons are possible, the measurements are in good agreement with 10 micron polarization measurements.

Spin polarized electron tunneling and magnetoresistance in molecular junctions.

Science.gov (United States)

Szulczewski, Greg

2012-01-01

This chapter reviews tunneling of spin-polarized electrons through molecules positioned between ferromagnetic electrodes, which gives rise to tunneling magnetoresistance. Such measurements yield important insight into the factors governing spin-polarized electron injection into organic semiconductors, thereby offering the possibility to manipulate the quantum-mechanical spin degrees of freedom for charge carriers in optical/electrical devices. In the first section of the chapter a brief description of the Jullière model of spin-dependent electron tunneling is reviewed. Next, a brief description of device fabrication and characterization is presented. The bulk of the review highlights experimental studies on spin-polarized electron tunneling and magnetoresistance in molecular junctions. In addition, some experiments describing spin-polarized scanning tunneling microscopy/spectroscopy on single molecules are mentioned. Finally, some general conclusions and prospectus on the impact of spin-polarized tunneling in molecular junctions are offered.

SUBMILLIMETER POLARIZATION SPECTRUM IN THE VELA C MOLECULAR CLOUD

Energy Technology Data Exchange (ETDEWEB)

Gandilo, Natalie N. [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George Street Toronto, ON M5S 3H4 (Canada); Ade, Peter A. R.; Pascale, Enzo [Cardiff University, School of Physics and Astronomy, Queens Buildings, The Parade, Cardiff, CF24 3AA (United Kingdom); Angilè, Francesco E.; Devlin, Mark J.; Dober, Bradley; Galitzki, Nicholas; Klein, Jeffrey [Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA, 19104 (United States); Ashton, Peter; Fissel, Laura M.; Matthews, Tristan G.; Novak, Giles [Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 (United States); Benton, Steven J. [Department of Physics, Princeton University, Jadwin Hall, Princeton, NJ 08544 (United States); Fukui, Yasuo [Department of Physics and Astrophysics, Nagoya University, Nagoya 464-8602 (Japan); Korotkov, Andrei L. [Department of Physics, Brown University, 182 Hope Street, Providence, RI, 02912 (United States); Li, Zhi-Yun [Department of Astronomy, University of Virginia, 530 McCormick Road, Charlottesville, VA 22904 (United States); Martin, Peter G. [CITA, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Moncelsi, Lorenzo [California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125 (United States); Nakamura, Fumitaka [National Astronomical Observatory, Mitaka, Tokyo 181-8588 (Japan); Netterfield, Calvin B., E-mail: ngandil1@jhu.edu [Department of Physics and Astronomy, Johns Hopkins University, 3701 San Martin Drive, Baltimore, Maryland (United States); and others

2016-06-20

Polarization maps of the Vela C molecular cloud were obtained at 250, 350, and 500 μ m during the 2012 flight of the balloon-borne telescope BLASTPol. These measurements are used in conjunction with 850 μ m data from Planck to study the submillimeter spectrum of the polarization fraction for this cloud. The spectrum is relatively flat and does not exhibit a pronounced minimum at λ ∼ 350 μ m as suggested by previous measurements of other molecular clouds. The shape of the spectrum does not depend strongly on the radiative environment of the dust, as quantified by the column density or the dust temperature obtained from Herschel data. The polarization ratios observed in Vela C are consistent with a model of a porous clumpy molecular cloud being uniformly heated by the interstellar radiation field.

Experimental and molecular dynamics study on the inhibition performance of some nitrogen containing compounds for iron corrosion

International Nuclear Information System (INIS)

Khaled, K.F.

2010-01-01

A molecular dynamics study for the adsorption of three benzimidazole derivatives and their inhibition characteristics was studied using chemical (weight loss) and electrochemical measurements (potentiodynamic polarization and electrochemical impedance spectroscopy, EIS). Electrochemical measurements results revealed that the inhibition efficiencies increased with the concentration of inhibitors. Results obtained from weight loss, dc polarization and ac impedance measurements are in reasonably good agreement and show increased inhibitor efficiency with increasing inhibitor concentration. The molecular dynamics calculations showed that the higher the binding energy between the inhibitor and metal surface, the higher the inhibition efficiency. Also, the higher the adsorption energy, the higher the inhibition efficiency. The molecular dynamics study revealed that the benzimidazole ring as well as the side chain are the active sites in these inhibitors and they can absorb on Fe surface by donating electrons to Fe d-orbital.

Dynamic nuclear polarization tests in some polymers for polarized targets

International Nuclear Information System (INIS)

Brandt, B. van den; Hautle, P.; Konter, J.A.; Mango, S.; Bunyatova, E.I.

1998-01-01

The results of dynamic polarization tests in polyethylene (PE) and ethylene propylene copolymer (EPC), doped with the stable free radical 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO), are presented. Sizable proton polarizations have been achieved in a magnetic field of 2.5 T at a temperature below 0.3 K and 5T at 1 K

The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces

Science.gov (United States)

Aviat, Félix; Lagardère, Louis; Piquemal, Jean-Philip

2017-10-01

In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.

NMR dispersion measurement of dynamic nuclear polarization

International Nuclear Information System (INIS)

Davies, K.; Cox, S.F.J.

1978-01-01

The feasibility of monitoring dynamic nuclear polarization from the NMR dispersive susceptibility is examined. Two prototype instruments are tested in a polarized proton target using organic target material. The more promising employs a tunnel diode oscillator, inside the target cavity, and should provide a precise polarization measurement working at a frequency far enough from the main resonance for the disturbance of the measured polarization to be negligible. Other existing methods for measuring target polarization are briefly reviewed. (author)

A sensitive fluorescent probe for the polar solvation dynamics at protein-surfactant interfaces.

Science.gov (United States)

Singh, Priya; Choudhury, Susobhan; Singha, Subhankar; Jun, Yongwoong; Chakraborty, Sandipan; Sengupta, Jhimli; Das, Ranjan; Ahn, Kyo-Han; Pal, Samir Kumar

2017-05-17

Relaxation dynamics at the surface of biologically important macromolecules is important taking into account their functionality in molecular recognition. Over the years it has been shown that the solvation dynamics of a fluorescent probe at biomolecular surfaces and interfaces account for the relaxation dynamics of polar residues and associated water molecules. However, the sensitivity of the dynamics depends largely on the localization and exposure of the probe. For noncovalent fluorescent probes, localization at the region of interest in addition to surface exposure is an added challenge compared to the covalently attached probes at the biological interfaces. Here we have used a synthesized donor-acceptor type dipolar fluorophore, 6-acetyl-(2-((4-hydroxycyclohexyl)(methyl)amino)naphthalene) (ACYMAN), for the investigation of the solvation dynamics of a model protein-surfactant interface. A significant structural rearrangement of a model histone protein (H1) upon interaction with anionic surfactant sodium dodecyl sulphate (SDS) as revealed from the circular dichroism (CD) studies is nicely corroborated in the solvation dynamics of the probe at the interface. The polarization gated fluorescence anisotropy of the probe compared to that at the SDS micellar surface clearly reveals the localization of the probe at the protein-surfactant interface. We have also compared the sensitivity of ACYMAN with other solvation probes including coumarin 500 (C500) and 4-(dicyanomethylene)-2-methyl-6-(p-dimethylamino-styryl)-4H-pyran (DCM). In comparison to ACYMAN, both C500 and DCM fail to probe the interfacial solvation dynamics of a model protein-surfactant interface. While C500 is found to be delocalized from the protein-surfactant interface, DCM becomes destabilized upon the formation of the interface (protein-surfactant complex). The timescales obtained from this novel probe have also been compared with other femtosecond resolved studies and molecular dynamics simulations.

Generating highly polarized nuclear spins in solution using dynamic nuclear polarization

DEFF Research Database (Denmark)

Wolber, J.; Ellner, F.; Fridlund, B.

2004-01-01

A method to generate strongly polarized nuclear spins in solution has been developed, using Dynamic Nuclear Polarization (DNP) at a temperature of 1.2K, and at a field of 3.354T, corresponding to an electron spin resonance frequency of 94GHz. Trityl radicals are used to directly polarize 13C...... and other low-γ nuclei. Subsequent to the DNP process, the solid sample is dissolved rapidly with a warm solvent to create a solution of molecules with highly polarized nuclear spins. Two main applications are proposed: high-resolution liquid state NMR with enhanced sensitivity, and the use...

Active Polar Gels: a Paradigm for Cytoskeletal Dynamics

Science.gov (United States)

Julicher, Frank

2006-03-01

The cytoskeleton of eucaryotic cells is an intrinsically dynamic network of rod-like filaments. Active processes on the molecular scale such as the action of motor proteins and the polymerization and depolymerization of filaments drive active dynamic behaviors while consuming chemical energy in the form of a fuel. Such emergent dynamics is regulated by the cell and is important for many cellular processes such as cell locomotion and cell division. From a general point of view the cytoskeleton represents an active gel-like material with interesting material properties. We present a general theory of active viscoelastic materials made of polar filaments which is motivated by the the cytoskeleton. The continuous consumption of a fuel generates a non- equilibrium state characterized by the generation of flows and stresses. Our theory can be applied to experiments in which cytoskeletal patterns are set in motion by active processes such as those which are at work in cells. It can also capture generic aspects of the flows and stress profiles which occur during cell locomotion.

Dynamics of actin cables in polarized growth of the filamentous fungus Aspergillus nidulans

Directory of Open Access Journals (Sweden)

Anna eBergs

2016-05-01

Full Text Available Highly polarized growth of filamentous fungi requires a continuous supply of proteins and lipids to the hyphal tip. This transport is managed by vesicle trafficking via the actin and microtubule cytoskeletons and their associated motor proteins. Particularly, actin cables originating from the hyphal tip are essential for hyphal growth. Although specific marker proteins to visualize actin cables have been developed in filamentous fungi, the exact organization and dynamics of actin cables has remained elusive. Here we visualized actin cables using tropomyosin (TpmA and Lifeact fused to fluorescent proteins in Aspergillus nidulans and studied the dynamics and regulation. GFP tagged TpmA visualized dynamic actin cables formed from the hyphal tip with cycles of elongation and shrinkage. The elongation and shrinkage rates of actin cables were similar and approximately 0.6 μm/s. Comparison of actin markers revealed that high concentrations of Lifeact reduced actin dynamics. Simultaneous visualization of actin cables and microtubules suggests temporally and spatially coordinated polymerization and depolymerization between the two cytoskeletons. Our results provide new insights into the molecular mechanism of ordered polarized growth regulated by actin cables and microtubules.

Effect of the R dependence of laser-induced polarizability on molecular dynamic alignment in an intense femtosecond laser field

International Nuclear Information System (INIS)

Chen Jianxin; Cui Xiaomei; Huang Bomin; Wu Hongchun; Zhuo Shuangmu

2006-01-01

In the rotation equation of the angle θ between the molecular axis and the laser polarization direction, the dependence of laser-induced polarizability on the molecular internuclear distance R is considered. The effect of the R dependence of laser-induced polarizability on molecular dynamic alignment in an intense femtosecond laser field is investigated with 20 and 100 fs laser pulses for N 2 molecules and with 60 and 100 fs laser pulses for Br 2 molecules at intensities of 5x10 14 W cm -2 and 5x10 15 W cm -2 . This effect exists and only occurs during the dissociative process after the molecule is ionized. It enhances the degrees of molecular dynamic alignment and is more significant in reorienting the angular distributions of molecules towards the laser polarization direction in the conditions of high laser intensity and short pulse length. Compared with the N 2 molecule, the effect of the R dependence of laser-induced polarizability on molecular dynamic alignment for Br 2 is stronger. The reasons are presented and discussed

The Kinesin Adaptor Calsyntenin-1 Organizes Microtubule Polarity and Regulates Dynamics during Sensory Axon Arbor Development

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Mary C. Halloran

2017-04-01

Full Text Available Axon growth and branching, and development of neuronal polarity are critically dependent on proper organization and dynamics of the microtubule (MT cytoskeleton. MTs must organize with correct polarity for delivery of diverse cargos to appropriate subcellular locations, yet the molecular mechanisms regulating MT polarity remain poorly understood. Moreover, how an actively branching axon reorganizes MTs to direct their plus ends distally at branch points is unknown. We used high-speed, in vivo imaging of polymerizing MT plus ends to characterize MT dynamics in developing sensory axon arbors in zebrafish embryos. We find that axonal MTs are highly dynamic throughout development, and that the peripheral and central axons of sensory neurons show differences in MT behaviors. Furthermore, we show that Calsyntenin-1 (Clstn-1, a kinesin adaptor required for sensory axon branching, also regulates MT polarity in developing axon arbors. In wild type neurons the vast majority of MTs are directed in the correct plus-end-distal orientation from early stages of development. Loss of Clstn-1 causes an increase in MTs polymerizing in the retrograde direction. These misoriented MTs most often are found near growth cones and branch points, suggesting Clstn-1 is particularly important for organizing MT polarity at these locations. Together, our results suggest that Clstn-1, in addition to regulating kinesin-mediated cargo transport, also organizes the underlying MT highway during axon arbor development.

Polarized neutron inelastic scattering experiments on spin dynamics

International Nuclear Information System (INIS)

Kakurai, Kazuhisa

2016-01-01

The principles of polarized neutron scattering are introduced and examples of polarized neutron inelastic scattering experiments on spin dynamics investigation are presented. These examples should demonstrate the importance of the polarized neutron utilization for the investigation of non-trivial magnetic ground and excited states in frustrated and low dimensional quantum spin systems. (author)

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

Science.gov (United States)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses

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Jinxiang Xi

2018-03-01

Full Text Available Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of

Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses.

Science.gov (United States)

Xi, Jinxiang; Hu, Qin; Zhao, Linlin; Si, Xiuhua April

2018-03-27

Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD) simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of high-polarity

A concurrent multiscale micromorphic molecular dynamics

International Nuclear Information System (INIS)

Li, Shaofan; Tong, Qi

2015-01-01

In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation

Dynamical nuclear polarization using multi-colour control of color centers in diamond

Energy Technology Data Exchange (ETDEWEB)

Yang, Pengcheng [Huazhong University of Science and Technology, School of Physics, Wuhan (China); Huazhong University of Science and Technology, Center for Quantum Optical Science, Wuhan (China); Plenio, Martin B. [Universitaet Ulm, Institut fuer Theoretische Physik, Ulm (Germany); Universitaet Ulm, Center for Integrated Quantum Science and Technology, Ulm (Germany); Cai, Jianming [Huazhong University of Science and Technology, School of Physics, Wuhan (China); Huazhong University of Science and Technology, Center for Quantum Optical Science, Wuhan (China); Universitaet Ulm, Institut fuer Theoretische Physik, Ulm (Germany); Universitaet Ulm, Center for Integrated Quantum Science and Technology, Ulm (Germany)

2016-12-15

Dynamical nuclear polarization (DNP) transfers the polarization of electron spins at cryogenic temperatures to achieve strong nuclear polarization for applications in nuclear magnetic resonance. Recently introduced approaches employ optical pumping of nitrogen-vacancy (NV) centers in diamond to achieve DNP even at ambient temperatures. In such schemes microwave radiation is used to establish a Hartmann-Hahn condition between the NV electron spin and proximal nuclear spins to facilitate polarization transfer. For a single monochromatic microwave driving field, the Hartmann-Hahn condition cannot be satisfied for an ensemble of NV centers due to inhomogeneous broadening and reduces significantly the overall efficiency of dynamical nuclear polarization using an ensemble of NV centers. Here, we adopt generalized Hartmann-Hahn type dynamical nuclear polarization schemes by applying microwave driving fields with (multiple) time-modulated frequencies. We show that it is possible to enhance the effective coupling between an ensemble of NV center spins with inhomogeneous broadening and nuclear spins, thereby improving significantly the overall efficiency of dynamical nuclear polarization. This approach can also be used to achieve dynamical nuclear polarization of an ensemble of nuclei with a distribution of Larmor frequencies, which would be helpful in magnetic resonance spectroscopy using a single NV spin sensor. (orig.)

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

Science.gov (United States)

Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal

2016-08-23

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Boosting the Amount of Molecular Information Through Polarized Resolved Resonance Raman Scattering

DEFF Research Database (Denmark)

Hassing, Søren

2017-01-01

and near-infrared absorption spectroscopy, i.e. only the spectral distribution is analysed. The goal of the present chapter is to demonstrate that the amount of molecular information (also for solutions and powders) can be increased considerably by analysing also the polarization of the Raman and resonance...... Ramanscattered light. The goal is achieved through: (1) a discussion of the basic properties of Raman scattering with special focus on polarization and polarization dispersion. The discussion includes the rotational invariants of Raman tensors, the non-commuting generator approach to molecular symmetry as a tool...... for construction of state and Raman tensors for single molecules and dimers and higher aggregates and thereby predict the polarization; (2) a discussion of two illustrative case studies: Case study 1: Aggregation of haemoglobin in red blood cells (RBC); and Case study 2: In vitro polarization resolved RRS study...

Interaction of lysozyme with a tear film lipid layer model: A molecular dynamics simulation study.

Science.gov (United States)

Wizert, Alicja; Iskander, D Robert; Cwiklik, Lukasz

2017-12-01

The tear film is a thin multilayered structure covering the cornea. Its outermost layer is a lipid film underneath of which resides on an aqueous layer. This tear film lipid layer (TFLL) is itself a complex structure, formed by both polar and nonpolar lipids. It was recently suggested that due to tear film dynamics, TFLL contains inhomogeneities in the form of polar lipid aggregates. The aqueous phase of tear film contains lachrymal-origin proteins, whereby lysozyme is the most abundant. These proteins can alter TFLL properties, mainly by reducing its surface tension. However, a detailed nature of protein-lipid interactions in tear film is not known. We investigate the interactions of lysozyme with TFLL in molecular details by employing coarse-grained molecular dynamics simulations. We demonstrate that lysozyme, due to lateral restructuring of TFLL, is able to penetrate the tear lipid film embedded in inverse micellar aggregates. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular dynamics in porous media studied by nuclear magnetic resonance techniques

International Nuclear Information System (INIS)

Mattea, C.

2006-01-01

Field cycling NMR relaxometry was used to study dynamics of fluids under confinement in different scenarios: fluids flowing through porous media, fluids partially filling porous media and polymer melts in nanoscopic pores. Diffusion in partially filled porous media was also studied with the aid of an NMR diffusometry technique. It is shown that hydrodynamic flow influences the spin-lattice relaxation rate of water confined in mesoscopic porous media under certain conditions. The effect is predicted by an analytical theory and Monte Carlo simulations, and confirmed experimentally by field-cycling NMR relaxometry. Field-cycling NMR relaxometry has been applied to polar and non polar adsorbates in partially filled silica porous glasses. The dependence of the spin-lattice relaxation rate on the filling degree shows that limits for slow and fast exchange between different phases can be distinguished and identified depending on the pore size and polarity of the solvents. Diffusion in the same unsaturated systems was studied with the aid of NMR diffusometry technique. The effective diffusion coefficient of solvents with different polarities displays opposite tendencies as a function of the liquid content. A two-phase fast exchange model including Knudsen and ordinary diffusion and different effective tortuosities is presented accounting for these phenomena. In the case of polymer melts confined in narrow artificial tubes of a porous solid matrix with variable diameter (9 to 57 nm), the characteristics of reptation were experimentally verified using proton field cycling NMR relaxometry technique. This observation is independent of the molecular mass and pore size. In bulk, the same polymer melts show either Rouse or renormalized Rouse dynamics, depending on the molecular mass. The polymers under confinement show features specific for reptation even with a pore diameter 15 times larger than the Flory radius while bulk melts of the same polymers do not. (orig.)

Many-body kinetics of dynamic nuclear polarization by the cross effect

Science.gov (United States)

Karabanov, A.; Wiśniewski, D.; Raimondi, F.; Lesanovsky, I.; Köckenberger, W.

2018-03-01

Dynamic nuclear polarization (DNP) is an out-of-equilibrium method for generating nonthermal spin polarization which provides large signal enhancements in modern diagnostic methods based on nuclear magnetic resonance. A particular instance is cross-effect DNP, which involves the interaction of two coupled electrons with the nuclear spin ensemble. Here we develop a theory for this important DNP mechanism and show that the nonequilibrium nuclear polarization buildup is effectively driven by three-body incoherent Markovian dissipative processes involving simultaneous state changes of two electrons and one nucleus. We identify different parameter regimes for effective polarization transfer and discuss under which conditions the polarization dynamics can be simulated by classical kinetic Monte Carlo methods. Our theoretical approach allows simulations of the polarization dynamics on an individual spin level for ensembles consisting of hundreds of nuclear spins. The insight obtained by these simulations can be used to find optimal experimental conditions for cross-effect DNP and to design tailored radical systems that provide optimal DNP efficiency.

Molecular potentials and relaxation dynamics

International Nuclear Information System (INIS)

Karo, A.M.

1981-01-01

The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy

Active Polar Two-Fluid Macroscopic Dynamics

Science.gov (United States)

Pleiner, Harald; Svensek, Daniel; Brand, Helmut R.

2014-03-01

We study the dynamics of systems with a polar dynamic preferred direction. Examples include the pattern-forming growth of bacteria (in a solvent, shoals of fish (moving in water currents), flocks of birds and migrating insects (flying in windy air). Because the preferred direction only exists dynamically, but not statically, the macroscopic variable of choice is the macroscopic velocity associated with the motion of the active units. We derive the macroscopic equations for such a system and discuss novel static, reversible and irreversible cross-couplings connected to this second velocity. We find a normal mode structure quite different compared to the static descriptions, as well as linear couplings between (active) flow and e.g. densities and concentrations due to the genuine two-fluid transport derivatives. On the other hand, we get, quite similar to the static case, a direct linear relation between the stress tensor and the structure tensor. This prominent ``active'' term is responsible for many active effects, meaning that our approach can describe those effects as well. In addition, we also deal with explicitly chiral systems, which are important for many active systems. In particular, we find an active flow-induced heat current specific for the dynamic chiral polar order.

Self-Sustaining Dynamical Nuclear Polarization Oscillations in Quantum Dots

DEFF Research Database (Denmark)

Rudner, Mark Spencer; Levitov, Leonid

2013-01-01

Early experiments on spin-blockaded double quantum dots revealed robust, large-amplitude current oscillations in the presence of a static (dc) source-drain bias. Despite experimental evidence implicating dynamical nuclear polarization, the mechanism has remained a mystery. Here we introduce......) and nuclear spin diffusion, which governs dynamics of the spatial profile of nuclear polarization. The proposed framework naturally explains the differences in phenomenology between vertical and lateral quantum dot structures as well as the extremely long oscillation periods....

Molecular Diagnosis of Classical Rabies Virus in Polar Foxes in Greeenland

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Strandbygaard, Bertel

Classical rabies virus continues to circulate in polar foxes in Greenland. Within the last 5 years more than 30 animals, mainly polar foxes have been tested positive for rabies. In this study, brain samples from this period were assessed for the presence of rabies viral RNA using molecular...

THE KEY ROLE OF SOLAR DYNAMICS IN THE CHROMOSPHERIC HANLE POLARIZATION

Energy Technology Data Exchange (ETDEWEB)

Carlin, E. S.; Bianda, M., E-mail: escarlin@irsol.ch [Istituto Ricerche Solari Locarno, 6600 Locarno (Switzerland)

2016-11-01

The quantum theory of polarized light allows one to model scattering in the solar atmosphere for inferring its properties. This powerful approach has revealed two key long-standing problems in solar physics: the puzzling dilemmas between theory and observations in several anomalously polarized spectral lines and the need for inferring the ubiquitous weak chromospheric magnetic fields, which requires discriminating the Hanle effect in dynamic optically thick plasmas. However, the ever-present dynamics, i.e., the temporal evolution of heatings and macroscopic motions, has been widely disregarded when modeling and interpreting the scattering polarization. This has hindered a consistent theoretical solution to the puzzle while falsifying the Hanle diagnosis. Here, we show that the dynamical evolution is a keystone for solving both problems because its systematic impact allows an explanation of the observations from “anomalous” instantaneous polarization signals. Evolution accounted for, we reproduce amplitudes and (spectral and spatial) shapes of the Ca i 4227 Å polarization at solar disk center, identifying a restrictive arrangement of magnetic fields, kinematics, heatings, and spatio-temporal resolution. We find that the joint action of dynamics, Hanle effect, and low temporal resolutions mimics Zeeman linear polarization profiles, the true weak-field Zeeman signals being negligible. Our results allow reinterpretation of many polarization signals of the solar spectra and support time-dependent scattering polarization as a powerful tool for deciphering the spatio-temporal distribution of chromospheric heatings and fields. This approach may be a key aid in developing the Hanle diagnosis for the solar atmosphere.

Molecular polarization potential maps of the nucleic acid bases

International Nuclear Information System (INIS)

Alkorta, I.; Perez, J.J.

1996-01-01

Ab initio calculations at the SCF level were carried out to compute the polarization potential map NM of the nucleic acid bases: cytosine, thymine, uracil, adedine, and guanine. For this purpose, the Dunning's 9s5p basis set contracted to a split-valence, was selected to perform the calculations. The molecular polarization potential (MPP) at each point was evaluated by the difference between the interaction energy of the molecule with a unit point charge and the molecular electrostatic potential (MEP) at that point. MEPS and MPPS for the different molecules were computed with a density of 5 points/Angstrom 2 on the van der Waals surface of each molecule, defined using the van der Waals radii. Due to the symmetry of the molecules, only half the points were computed. The total number of points calculated was 558 for cytosine, 621 for thymine, 526 for uracil, 666 for adenine, and 699 for guanine. The results of these calculations are analyzed in terms of their implications on the molecular interactions between pairs of nucleic acid bases. 23 refs., 5 figs., 1 tab

Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

International Nuclear Information System (INIS)

Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

1992-09-01

Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

Polarization dynamics in nonlinear anisotropic fibers

International Nuclear Information System (INIS)

Komarov, Andrey; Komarov, Konstantin; Meshcheriakov, Dmitry; Amrani, Foued; Sanchez, Francois

2010-01-01

We give an extensive study of polarization dynamics in anisotropic fibers exhibiting a third-order index nonlinearity. The study is performed in the framework of the Stokes parameters with the help of the Poincare sphere. Stationary states are determined, and their stability is investigated. The number of fixed points and their stability depend on the respective magnitude of the linear and nonlinear birefringence. A conservation relation analogous to the energy conservation in mechanics allows evidencing a close analogy between the movement of the polarization in the Poincare sphere and the motion of a particle in a potential well. Two distinct potentials are found, leading to the existence of two families of solutions, according to the sign of the total energy of the equivalent mechanical system. The mechanical analogy allows us to fully characterize the solutions and also to determine analytically the associated beat lengths. General analytical solutions are given for the two families in terms of Jacobi's functions. The intensity-dependent transmission of a fiber placed between two crossed polarizers is calculated. Optimal conditions for efficient nonlinear switching compatible with mode-locking applications are determined. The general case of a nonlinear fiber ring with an intracavity polarizer placed between two polarization controllers is also considered.

Modification of -Adenosyl--Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation

Directory of Open Access Journals (Sweden)

Usman Sumo Friend Tambunan

2017-04-01

Full Text Available Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world’s population in tropical and subtropical countries. Nonstructural protein 5 (NS5 methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S -adenosyl- l -methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2′OH, resulting in S -adenosyl- l -homocysteine (SAH. The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity test. The 2 simulations were performed using Molecular Operating Environment (MOE 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356 based on ΔG binding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever.

Study of lanthanide tri-cations in aqueous solution by molecular dynamic

International Nuclear Information System (INIS)

Duvail, M.

2007-11-01

This is essentially a lanthanide tri-cation hydration study by means of classical molecular dynamics (CLMD) simulations using explicit polarization. Explicit polarization is calculated with a Car-Parrinello type of dynamics on induced dipoles, which decreases the CPU time as compared to the self-consistent resolution. Several pair interaction potentials are parametrized from ab initio calculations (MP2) and tested for the La 3+ -OH 2 interaction. The best results are obtained with an exponential-6 Buckingham potential. Next, the La 3+ -OH 2 interaction potential parameters are extrapolated to the other Ln 3+ -OH 2 interactions, only by using the ionic radii. The CLMD results reproduce the reliable experimental data (EXAFS distances), and the sigmoidal variation of the coordination number (with S shape), from 9 for La 3+ to 8 for Lu 3+ . This variation is explained by the linear variation of DrG0 (9,298) vs. atomic number. Insights are also given on the Co 2+ hydration, CPMD simulations, reconstruction of EXAFS signal from MD simulations, and OH - complexation of La 3+ in aqueous solution. (author)

A novel polarization demodulation method using polarization beam splitter (PBS) for dynamic pressure sensor

Science.gov (United States)

Su, Yang; Zhou, Hua; Wang, Yiming; Shen, Huiping

2018-03-01

In this paper we propose a new design to demodulate polarization properties induced by pressure using a PBS (polarization beam splitter), which is different with traditional polarimeter based on the 4-detector polarization measurement approach. The theoretical model is established by Muller matrix method. Experimental results confirm the validity of our analysis. Proportional relationships and linear fit are found between output signal and applied pressure. A maximum sensitivity of 0.092182 mv/mv is experimentally achieved and the frequency response exhibits a <0.14 dB variation across the measurement bandwidth. The sensitivity dependence on incident SOP (state of polarization) is investigated. The simple and all-fiber configuration, low-cost and high speed potential make it promising for fiber-based dynamic pressure sensing.

Dynamic polarization of 19F in a fluorinated alcohol

International Nuclear Information System (INIS)

Hill, D.; Kasprzyk, T.; Jarmer, J.J.; Penttilae, S.; Krumpolc, M.; Hoffmann, G.W.; Purcell, M.

1988-01-01

We have studied microwave dynamic cooling of 19 F and 1 H nuclei in mixtures of 1,1,1,3,3,3-hexafluoro-2-propanol and water, doped with Cr(V) complex. Equal spin temperatures of the two nuclei are produced, and the highest spin polarizations (/approximately/80%) are found in mixtures near the eutectic ratio. The high fluorine content and polarization make this a suitable material for polarized nuclear scattering experiments. 11 refs., 3 figs., 1 tab

Molecular dynamics simulations of ferroelectric domain formation by oxygen vacancy

Science.gov (United States)

Zhu, Lin; You, Jeong Ho; Chen, Jinghong; Yeo, Changdong

2018-05-01

An oxygen vacancy, known to be detrimental to ferroelectric properties, has been investigated numerically for the potential uses to control ferroelectric domains in films using molecular dynamics simulations based on the first-principles effective Hamiltonian. As an electron donor, an oxygen vacancy generates inhomogeneous electrostatic and displacement fields which impose preferred polarization directions near the oxygen vacancy. When the oxygen vacancies are placed at the top and bottom interfaces, the out-of-plane polarizations are locally developed near the interfaces in the directions away from the interfaces. These polarizations from the interfaces are in opposite directions so that the overall out-of-plane polarization becomes significantly reduced. In the middle of the films, the in-plane domains are formed with containing 90° a 1/a 2 domain walls and the films are polarized along the [1 1 0] direction even when no electric field is applied. With oxygen vacancies placed at the top interface only, the films exhibit asymmetric hysteresis loops, confirming that the oxygen vacancies are one of the possible sources of ferroelectric imprint. It has been qualitatively demonstrated that the domain structures in the imprint films can be turned on and off by controlling an external field along the thickness direction. This study shows qualitatively that the oxygen vacancies can be utilized for tuning ferroelectric domain structures in films.

Dipole-Oriented Molecular Solids Can Undergo a Phase Change and Still Maintain Electrical Polarization

Energy Technology Data Exchange (ETDEWEB)

Glavic, Artur G [ORNL; Cassidy, Andrew M [ORNL; Jorgensen, Mads Ry Ry [University of Aarhus, Denmark; Lauter, Valeria [ORNL; Rosu-Finsen, Alexander [Heriot-Watt University, Edinburgh, UK; Lasne, Jérôme [Heriot-Watt University, Edinburgh, UK; Jorgensen, Jakob [Aarhus University, Denmark; Iversen, Bo [ORNL; McCoustra, Martin [Heriot-Watt University, Edinburgh, UK; Field, David [University of Aarhus, Denmark

2016-10-02

It has recently been demonstrated that nanoscale molecular films can spontaneously assemble to self-generate intrinsic electric fields that can exceed 10⁸ V/m. These electric fields originate from polarization charges in the material that arise because the films self-assemble to orient molecular dipole moments. This has been called the spontelectric effect. Such growth of spontaneously polarized layers of molecular solids has implications for our understanding of how intermolecular interactions dictate the structure of molecular materials used in a range of applications, for example, molecular semiconductors, sensors, and catalysts. In this paper, we present the first in situ structural characterization of a representative spontelectric solid, nitrous oxide. Infrared spectroscopy, temperature-programmed desorption, and neutron reflectivity measurements demonstrate that polarized films of nitrous oxide undergo a structural phase transformation upon heating above 48 K. A mean-field model can be used to describe quantitatively the magnitude of the spontaneously generated field as a function of film-growth temperature, and this model also recreates the phase change. Finally, this reinforces the spontelectric model as a means of describing long-range dipole–dipole interactions and points to a new type of ordering in molecular thin films.

In silico study of amphiphilic nanotubes based on cyclic peptides in polar and non-polar solvent

DEFF Research Database (Denmark)

Vijayakumar, Vinodhkumar; Vijayaraj, Ramadoss; Peters, Günther H.J.

2016-01-01

The stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation ...

Dynamically polarized samples for neutron protein crystallography at the Spallation Neutron Source

International Nuclear Information System (INIS)

Zhao, Jinkui; Pierce, Josh; Robertson, J. L.; Herwig, Kenneth W.; Myles, Dean; Cuneo, Matt; Li, Le; Meilleur, Flora; Standaert, Bob

2016-01-01

To prepare for the next generation neutron scattering instruments for the planned second target station at the Spallation Neutron Source (SNS) and to broaden the scientific impact of neutron protein crystallography at the Oak Ridge National Laboratory, we have recently ramped up our efforts to develop a dynamically polarized target for neutron protein crystallography at the SNS. Proteins contain a large amount of hydrogen which contributes to incoherent diffraction background and limits the sensitivity of neutron protein crystallography. This incoherent background can be suppressed by using polarized neutron diffraction, which in the same time also improves the coherent diffraction signal. Our plan is to develop a custom Dynamic Nuclear Polarization (DNP) setup tailored to neutron protein diffraction instruments. Protein crystals will be polarized at a magnetic field of 5 T and temperatures of below 1 K. After the dynamic polarization process, the sample will be brought to a frozen-spin mode in a 0.5 T holding field and at temperatures below 100 mK. In a parallel effort, we are also investigating various ways of incorporating polarization agents needed for DNP, such as site specific spin labels, into protein crystals. (paper)

Modelling dust polarization observations of molecular clouds through MHD simulations

Science.gov (United States)

King, Patrick K.; Fissel, Laura M.; Chen, Che-Yu; Li, Zhi-Yun

2018-03-01

The BLASTPol observations of Vela C have provided the most detailed characterization of the polarization fraction p and dispersion in polarization angles S for a molecular cloud. We compare the observed distributions of p and S with those obtained in synthetic observations of simulations of molecular clouds, assuming homogeneous grain alignment. We find that the orientation of the mean magnetic field relative to the observer has a significant effect on the p and S distributions. These distributions for Vela C are most consistent with synthetic observations where the mean magnetic field is close to the line of sight. Our results point to apparent magnetic disorder in the Vela C molecular cloud, although it can be due to either an inclination effect (i.e. observing close to the mean field direction) or significant field tangling from strong turbulence/low magnetization. The joint correlations of p with column density and of S with column density for the synthetic observations generally agree poorly with the Vela C joint correlations, suggesting that understanding these correlations requires a more sophisticated treatment of grain alignment physics.

Dissolution Dynamic Nuclear Polarization capability study with fluid path

DEFF Research Database (Denmark)

Malinowski, Ronja Maja; Lipsø, Hans Kasper Wigh; Lerche, Mathilde Hauge

2016-01-01

Signal enhancement by hyperpolarization is a way of overcoming the low sensitivity in magnetic resonance; MRI in particular. One of the most well-known methods, dissolution Dynamic Nuclear Polarization, has been used clinically in cancer patients. One way of ensuring a low bioburden of the hyperp......Signal enhancement by hyperpolarization is a way of overcoming the low sensitivity in magnetic resonance; MRI in particular. One of the most well-known methods, dissolution Dynamic Nuclear Polarization, has been used clinically in cancer patients. One way of ensuring a low bioburden...... of the hyperpolarized product is by use of a closed fluid path that constitutes a barrier to contamination. The fluid path can be filled with the pharmaceuticals, i.e. imaging agent and solvents, in a clean room, and then stored or immediately used at the polarizer. In this study, we present a method of filling...

A Single-Cell Biochemistry Approach Reveals PAR Complex Dynamics during Cell Polarization.

Science.gov (United States)

Dickinson, Daniel J; Schwager, Francoise; Pintard, Lionel; Gotta, Monica; Goldstein, Bob

2017-08-21

Regulated protein-protein interactions are critical for cell signaling, differentiation, and development. For the study of dynamic regulation of protein interactions in vivo, there is a need for techniques that can yield time-resolved information and probe multiple protein binding partners simultaneously, using small amounts of starting material. Here we describe a single-cell protein interaction assay. Single-cell lysates are generated at defined time points and analyzed using single-molecule pull-down, yielding information about dynamic protein complex regulation in vivo. We established the utility of this approach by studying PAR polarity proteins, which mediate polarization of many animal cell types. We uncovered striking regulation of PAR complex composition and stoichiometry during Caenorhabditis elegans zygote polarization, which takes place in less than 20 min. PAR complex dynamics are linked to the cell cycle by Polo-like kinase 1 and govern the movement of PAR proteins to establish polarity. Our results demonstrate an approach to study dynamic biochemical events in vivo. Copyright © 2017 Elsevier Inc. All rights reserved.

Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering

Czech Academy of Sciences Publication Activity Database

Kohagen, Miriam; Mason, Philip E.; Jungwirth, Pavel

2016-01-01

Roč. 120, č. 8 (2016), s. 1454-1460 ISSN 1520-6106 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : molecular dynamics * neutron scattering * agueous sodium chloride Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.177, year: 2016

Dynamics of gas-phase transient species studied by dissociative photodetachment of molecular anions

OpenAIRE

Lu, Zhou

2007-01-01

Gas-phase transient species, such as the CH₃CO₂ and HOCO free radicals, play important roles in combustion and environment chemistry. In this thesis work, the dynamics of these two radicals were studied by dissociative photodetachment (DPD) of the negative ions, CH₃CO₂-С and HOCO⁻, respectively. The experiments were carried out with a fast-ion-beam photoelectron-photofragment coincidence (PPC) spectrometer. Mass-selected molecular anions in a fast ion beam were intercepted by a linearly polar...

Polarization dependent effects in photo-fragmentation dynamics of free molecules

International Nuclear Information System (INIS)

Mocellin, A.; Marinho, R.R.T.; Coutinho, L.H.; Burmeister, F.; Wiesner, K.; Naves de Brito, A.

2003-01-01

We present multicoincidence spectra of nitrogen, formic acid and methyl methacrylate. We demonstrate how to probe the local symmetry of molecular orbitals from molecules core excited with linearly polarized synchrotron radiation. The intensity distribution of the photoelectron photo-ion photo-ion coincidence (PEPIPICO) spectrum reflects the selectivity and localization of core excitation by polarized light. By simulating the spectra the angular dependence of the fragmentation is determined

Polarization dependent effects in photo-fragmentation dynamics of free molecules

Energy Technology Data Exchange (ETDEWEB)

Mocellin, A.; Marinho, R.R.T.; Coutinho, L.H.; Burmeister, F.; Wiesner, K.; Naves de Brito, A

2003-04-01

We present multicoincidence spectra of nitrogen, formic acid and methyl methacrylate. We demonstrate how to probe the local symmetry of molecular orbitals from molecules core excited with linearly polarized synchrotron radiation. The intensity distribution of the photoelectron photo-ion photo-ion coincidence (PEPIPICO) spectrum reflects the selectivity and localization of core excitation by polarized light. By simulating the spectra the angular dependence of the fragmentation is determined.

Ejectile polarization and nuclear orbitals

International Nuclear Information System (INIS)

Ohnishi, A.; Maruyama, T.; Horiuchi, H.

1992-01-01

Ejectile polarization phenomena are studied by the use of 'Quantum Molecular Dynamics plus external mean field' model. It is shown that the far-side contribution increases as the incident energy increases or the target charge decreases. The incident energy and the target dependence of ejectile polarization data is reproduced qualitatively. The near- and far-side contributions themselves are calculated to be almost monotone functions of ejectile momentum as is predicted in a simple projectile fragmentation scheme without the assumption that the linear and angular momentum transfers are negligible, and their statistical average results in various shapes in ejectile polarization

Modification of S-Adenosyl-l-Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation.

Science.gov (United States)

Tambunan, Usman Sumo Friend; Nasution, Mochammad Arfin Fardiansyah; Azhima, Fauziah; Parikesit, Arli Aditya; Toepak, Erwin Prasetya; Idrus, Syarifuddin; Kerami, Djati

2017-01-01

Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world's population in tropical and subtropical countries. Nonstructural protein 5 (NS5) methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S -adenosyl-l-methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2'OH, resulting in S -adenosyl-l-homocysteine (SAH). The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity) test. The 2 simulations were performed using Molecular Operating Environment (MOE) 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356) based on ΔG binding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever.

Molecular dynamics simulation of the ionic liquid N-octylpyridinium tetrafluoroborate and acetonitrile: Thermodynamic and structural properties

Science.gov (United States)

Zhou, Siwen; Zhu, Guanglai; Kang, Xianqu; Li, Qiang; Sha, Maolin; Cui, Zhifeng; Xu, Xinsheng

2018-06-01

Using molecular dynamics simulation, the research obtained the thermodynamic properties and microstructures of the mixture of N-octylpyridinium tetrafluoroborate and acetonitrile, including density, self-diffusion coefficients, excess properties, radial distribution functions (RDFs) and spatial distribution functions (SDFs). Both RDFs and SDFs indicate that the local microstructure of the polar region is different from the nonpolar region with different mole fraction of ionic liquids. Acetonitrile could increase the order of the polar regions. While with acetonitrile increasing, the orderliness of the nonpolar region increases firstly and then decreases. In relatively dilute solution, ionic liquids were dispersed to form small aggregates wrapped by acetonitrile.

Incident angle dependence of reactions between graphene and hydrogen atom by molecular dynamics simulation

International Nuclear Information System (INIS)

Saito, Seiki; Nakamura, Hiroaki; Ito, Atsushi

2010-01-01

Incident angle dependence of reactions between graphene and hydrogen atoms are obtained qualitatively by classical molecular dynamics simulation under the NVE condition with modified Brenner reactive empirical bond order (REBO) potential. Chemical reaction depends on two parameters, i.e., polar angle θ and azimuthal angle φ of the incident hydrogen. From the simulation results, it is found that the reaction rates strongly depend on polar angle θ. Reflection rate becomes larger with increasing θ, and the θ dependence of adsorption rate is also found. The θ dependence is caused by three dimensional structure of the small potential barrier which covers adsorption sites. φ dependence of penetration rate is also found for large θ. (author)

Color molecular dynamics for dense matter

International Nuclear Information System (INIS)

Maruyama, Toshiki; Hatsuda, Tetsuo

2000-01-01

We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)

Lattice dynamics and molecular dynamics simulation of complex materials

International Nuclear Information System (INIS)

Chaplot, S.L.

1997-01-01

In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

Molecular orientation in aligned electrospun polyimide nanofibers by polarized FT-IR spectroscopy.

Science.gov (United States)

Yang, Haoqi; Jiang, Shaohua; Fang, Hong; Hu, Xiaowu; Duan, Gaigai; Hou, Haoqing

2018-07-05

Quantitative explanation on the improved mechanical properties of aligned electrospun polyimide (PI) nanofibers as the increased imidization temperatures is highly required. In this work, polarized FT-IR spectroscopy is applied to solve this problem. Based on the polarized FT-IR spectroscopy and the molecular model in the fibers, the length of the repeat unit of PI molecule, the angle between the fiber axis and the symmetric stretching direction of carbonyl group on the imide ring, and the angle between the PI molecular axis and fiber axis are all investigated. The Mark-Howink equation is used to calculate the number-average molar mass of PI molecules. The orientation states of PI molecules in the electrospun nanofibers are studied from the number-average molar mass of PI molecules and the average fiber diameter. Quantitative analysis of the orientation factor of PI molecules in the electrospun nanofibers is performed by polarized FT-IR spectroscopy. Copyright © 2018 Elsevier B.V. All rights reserved.

Molecular dynamics for irradiation driven chemistry

DEFF Research Database (Denmark)

Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

2016-01-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

Substructured multibody molecular dynamics.

Energy Technology Data Exchange (ETDEWEB)

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

2006-11-01

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

Local Polar Fluctuations in Lead Halide Perovskite Crystals

Science.gov (United States)

Yaffe, Omer; Guo, Yinsheng; Tan, Liang Z.; Egger, David A.; Hull, Trevor; Stoumpos, Constantinos C.; Zheng, Fan; Heinz, Tony F.; Kronik, Leeor; Kanatzidis, Mercouri G.; Owen, Jonathan S.; Rappe, Andrew M.; Pimenta, Marcos A.; Brus, Louis E.

2017-03-01

Hybrid lead-halide perovskites have emerged as an excellent class of photovoltaic materials. Recent reports suggest that the organic molecular cation is responsible for local polar fluctuations that inhibit carrier recombination. We combine low-frequency Raman scattering with first-principles molecular dynamics (MD) to study the fundamental nature of these local polar fluctuations. Our observations of a strong central peak in the cubic phase of both hybrid (CH3 NH3 PbBr3 ) and all-inorganic (CsPbBr3 ) lead-halide perovskites show that anharmonic, local polar fluctuations are intrinsic to the general lead-halide perovskite structure, and not unique to the dipolar organic cation. MD simulations indicate that head-to-head Cs motion coupled to Br face expansion, occurring on a few hundred femtosecond time scale, drives the local polar fluctuations in CsPbBr3 .

Local Polar Fluctuations in Lead Halide Perovskite Crystals

Energy Technology Data Exchange (ETDEWEB)

Yaffe, Omer; Guo, Yinsheng; Tan, Liang Z.; Egger, David A.; Hull, Trevor; Stoumpos, Constantinos C.; Zheng, Fan; Heinz, Tony F.; Kronik, Leeor; Kanatzidis, Mercouri G.; Owen, Jonathan S.; Rappe, Andrew M.; Pimenta, Marcos A.; Brus, Louis E.

2017-03-01

Hybrid lead-halide perovskites have emerged as an excellent class of photovoltaic materials. Recent reports suggest that the organic molecular cation is responsible for local polar fluctuations that inhibit carrier recombination. We combine low-frequency Raman scattering with first-principles molecular dynamics (MD) to study the fundamental nature of these local polar fluctuations. Our observations of a strong central peak in the cubic phase of both hybrid (CH3NH3PbBr3) and all-inorganic (CsPbBr3) leadhalide perovskites show that anharmonic, local polar fluctuations are intrinsic to the general lead-halide perovskite structure, and not unique to the dipolar organic cation. MD simulations indicate that head-tohead Cs motion coupled to Br face expansion, occurring on a few hundred femtosecond time scale, drives the local polar fluctuations in CsPbBr3.

Quantum mechanical aspects of dynamical neutron polarization

International Nuclear Information System (INIS)

Betz, T.; Badurek, G.; Jericha, E.

2007-01-01

Dynamic Neutron Polarization (DNP) is a concept which allows to achieve complete polarization of slow neutrons, virtually without any loss of intensity. There the neutrons pass through a combination of a static and a rotating magnetic field in resonance, like in a standard NMR apparatus. Depending on their initial spin state, they end up with different kinetic energies and therefore different velocity. In a succeeding magnetic precession field this distinction causes a different total precession angle. Tuning the field strength can lead to a final state where two original anti-parallel spin states are aligned parallel and hence to polarization. The goal of this work is to describe the quantum mechanical aspects of DNP and to work out the differences to the semi-classical treatment. We show by quantum mechanical means, that the concept works and DNP is feasible, indeed. Therefore, we have to take a closer look to the behavior of neutron wave functions in magnetic fields. In the first Section we consider a monochromatic continuous beam. The more realistic case of a pulsed, polychromatic beam requires a time-dependent field configuration and will be treated in the second Section. In particular the spatial separation of the spin up- and down-states is considered, because it causes an effect of polarization damping so that one cannot achieve a fully polarized final state. This effect is not predicted by the semi-classical treatment of DNP. However, this reduction of polarization is very small and can be neglected in realistic DNP-setups

Avoiding polar catastrophe in the growth of polarly orientated nickel perovskite thin films by reactive oxide molecular beam epitaxy

International Nuclear Information System (INIS)

Yang, H. F.; Liu, Z. T.; Fan, C. C.; Xiang, P.; Zhang, K. L.; Li, M. Y.; Liu, J. S.; Yao, Q.; Shen, D. W.

2016-01-01

By means of the state-of-the-art reactive oxide molecular beam epitaxy, we synthesized (001)- and (111)-orientated polar LaNiO 3 thin films. In order to avoid the interfacial reconstructions induced by polar catastrophe, screening metallic Nb-doped SrTiO 3 and iso-polarity LaAlO 3 substrates were chosen to achieve high-quality (001)-orientated films in a layer-by-layer growth mode. For largely polar (111)-orientated films, we showed that iso-polarity LaAlO 3 (111) substrate was more suitable than Nb-doped SrTiO 3 . In situ reflection high-energy electron diffraction, ex situ high-resolution X-ray diffraction, and atomic force microscopy were used to characterize these films. Our results show that special attentions need to be paid to grow high-quality oxide films with polar orientations, which can prompt the explorations of all-oxide electronics and artificial interfacial engineering to pursue intriguing emergent physics like proposed interfacial superconductivity and topological phases in LaNiO 3 based superlattices.

An Investigation of Molecular Docking and Molecular Dynamic Simulation on Imidazopyridines as B-Raf Kinase Inhibitors

Directory of Open Access Journals (Sweden)

Huiding Xie

2015-11-01

Full Text Available In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD simulation and binding free energy (ΔGbind calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA, and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

Science.gov (United States)

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

Approximation of quantum observables by molecular dynamics simulations

KAUST Repository

Sandberg, Mattias

2016-01-01

In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

Approximation of quantum observables by molecular dynamics simulations

KAUST Repository

Sandberg, Mattias

2016-01-06

In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

Antiferroelectric polarization switching and dynamic scaling of energy storage: A Monte Carlo simulation

Science.gov (United States)

Huang, B. Y.; Lu, Z. X.; Zhang, Y.; Xie, Y. L.; Zeng, M.; Yan, Z. B.; Liu, J.-M.

2016-05-01

The polarization-electric field hysteresis loops and the dynamics of polarization switching in a two-dimensional antiferroelectric (AFE) lattice submitted to a time-oscillating electric field E(t) of frequency f and amplitude E0, is investigated using Monte Carlo simulation based on the Landau-Devonshire phenomenological theory on antiferroelectrics. It is revealed that the AFE double-loop hysteresis area A, i.e., the energy loss in one cycle of polarization switching, exhibits the single-peak frequency dispersion A(f), suggesting the unique characteristic time for polarization switching, which is independent of E0 as long as E0 is larger than the quasi-static coercive field for the antiferroelectric-ferroelectric transitions. However, the dependence of recoverable stored energy W on amplitude E0 seems to be complicated depending on temperature T and frequency f. A dynamic scaling behavior of the energy loss dispersion A(f) over a wide range of E0 is obtained, confirming the unique characteristic time for polarization switching of an AFE lattice. The present simulation may shed light on the dynamics of energy storage and release in AFE thin films.

Simulation and Automation of Microwave Frequency Control in Dynamic Nuclear Polarization for Solid Polarized Targets

Science.gov (United States)

Perera, Gonaduwage; Johnson, Ian; Keller, Dustin

2017-09-01

Dynamic Nuclear Polarization (DNP) is used in most of the solid polarized target scattering experiments. Those target materials must be irradiated using microwaves at a frequency determined by the difference in the nuclear Larmor and electron paramagnetic resonance (EPR) frequencies. But the resonance frequency changes with time as a result of radiation damage. Hence the microwave frequency should be adjusted accordingly. Manually adjusting the frequency can be difficult, and improper adjustments negatively impact the polarization. In order to overcome these difficulties, two controllers were developed which automate the process of seeking and maintaining the optimal frequency: one being a standalone controller for a traditional DC motor and the other a LabVIEW VI for a stepper motor configuration. Further a Monte-Carlo simulation was developed which can accurately model the polarization over time as a function of microwave frequency. In this talk, analysis of the simulated data and recent improvements to the automated system will be presented. DOE.

Polymer friction Molecular Dynamics

DEFF Research Database (Denmark)

Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

Opposite photo-induced deformations in azobenzene-containing polymers with different molecular architecture: Molecular dynamics study

International Nuclear Information System (INIS)

Ilnytskyi, Jaroslav M.; Neher, Dieter; Saphiannikova, Marina

2011-01-01

Photo-induced deformations in azobenzene-containing polymers (azo-polymers) are central to a number of applications, such as optical storage and fabrication of diffractive elements. The microscopic nature of the underlying opto-mechanical coupling is yet not clear. In this study, we address the experimental finding that the scenario of the effects depends on molecular architecture of the used azo-polymer. Typically, opposite deformations in respect to the direction of light polarization are observed for liquid crystalline and amorphous azo-polymers. In this study, we undertake molecular dynamics simulations of two different models that mimic these two types of azo-polymers. We employ hybrid force field modeling and consider only trans-isomers of azobenzene, represented as Gay-Berne sites. The effect of illumination on the orientation of the chromophores is considered on the level of orientational hole burning and emphasis is given to the resulting deformation of the polymer matrix. We reproduce deformations of opposite sign for the two models being considered here and discuss the relevant microscopic mechanisms in both cases.

Mapping 180° polar domains using electron backscatter diffraction and dynamical scattering simulations

Energy Technology Data Exchange (ETDEWEB)

Burch, Matthew J.; Fancher, Chris M.; Patala, Srikanth [Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC (United States); De Graef, Marc [Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburg, PA (United States); Dickey, Elizabeth C. [Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC (United States)

2017-02-15

A novel technique, which directly and nondestructively maps polar domains using electron backscatter diffraction (EBSD) is described and demonstrated. Through dynamical diffraction simulations and quantitative comparison to experimental EBSD patterns, the absolute orientation of a non-centrosymmetric crystal can be determined. With this information, the polar domains of a material can be mapped. The technique is demonstrated by mapping the non-ferroelastic, or 180°, ferroelectric domains in periodically poled LiNbO{sub 3} single crystals. Further, the authors demonstrate the possibility of mapping polarity using this technique in other polar materials system. - Highlights: • A novel technique to directly polar domains utilizing EBSD is demonstrated. • The technique relies on dynamical diffraction simulations of EBSD patterns. • The technique is demonstrated by mapping 180° domains in LiNbO{sub 3} single crystals. • Further application of this technique to other materials classes is discussed.

ALMA’s Polarized View of 10 Protostars in the Perseus Molecular Cloud

Science.gov (United States)

Cox, Erin G.; Harris, Robert J.; Looney, Leslie W.; Li, Zhi-Yun; Yang, Haifeng; Tobin, John J.; Stephens, Ian

2018-03-01

We present 870 μm ALMA dust polarization observations of 10 young Class 0/I protostars in the Perseus Molecular Cloud. At ∼0.″35 (80 au) resolution, all of our sources show some degree of polarization, with most (9/10) showing significantly extended emission in the polarized continuum. Each source has incredibly intricate polarization signatures. In particular, all three disk-candidates have polarization vectors roughly along the minor axis, which is indicative of polarization produced by dust scattering. On ∼100 au scales, the polarization is at a relatively low level (≲1%) and is quite ordered. In sources with significant envelope emission, the envelope is typically polarized at a much higher (≳5%) level and has a far more disordered morphology. We compute the cumulative probability distributions for both the small (disk-scale) and large (envelope-scale) polarization percentage. We find that the two are intrinsically different, even after accounting for the different detection thresholds in the high/low surface brightness regions. We perform Kolmogorov–Smirnov and Anderson–Darling tests on the distributions of angle offsets of the polarization from the outflow axis. We find disk-candidate sources are different from the non-disk-candidate sources. We conclude that the polarization on the 100 au scale is consistent with the signature of dust scattering for disk-candidates and that the polarization on the envelope-scale in all sources may come from another mechanism, most likely magnetically aligned grains.

Polarization: A must for fusion

Directory of Open Access Journals (Sweden)

Didelez J.-P.

2013-11-01

Full Text Available The complete polarization of DT fuel would increase the fusion reactivity by 50% in magnetic as well as in inertial confinements. The persistence of polarization in a fusion process could be tested, using a terawatt laser hitting a polarized HD target. The polarized deuterons heated in the plasma induced by the laser can fuse producing a 3He and a neutron in the final state. The angular distribution of the emitted neutrons and the change in the corresponding total Cross Section (CS can sign the polarization persistence. The polarization of solid H2, D2 or T2 Hydrogen isotopes is very difficult. However, it has been possible to polarize HD, a hetero-molecular form of Hydrogen, by static polarization, at very low temperature and very high field. The radioactivity of DT molecules forbids there high polarization by the static method, therefore one has to develop the Dynamic Nuclear Polarization (DNP by RF transitions. The DNP of HD has been investigated in the past. The magnetic properties of HD and DT molecules are very similar, it is therefore expected that any polarization result obtained with HD could be extrapolated to DT.

Effects of film polarities on InN growth by molecular-beam epitaxy

International Nuclear Information System (INIS)

Xu, K.; Yoshikawa, A.

2003-01-01

Effects of the film polarity on InN growth were investigated in molecular-beam epitaxy (MBE). It was found that N-polarity InN could be grown at higher temperatures than In-polarity one. For the In-polarity films, which were grown on Ga-polar GaN template, the highest growth temperature was limited below 500 deg. C, and the surface morphology and crystal quality tended to be poor mainly because of the tolerated low growth temperature. While for the N-polarity InN films, which were grown on MBE-grown N-polar GaN, the growth temperature could be as high as 600 deg. C. The step-flow-like growth morphology was achieved for the InN films grown with N polarity at 580 deg. C. The resulting full widths of half maximum of x-ray rocking curve around InN (002) and (102) reflections were about 200-250 and 950-1100 arc sec, respectively. The photoluminescence of the InN films peaked at 0.697 eV. The recording Hall mobility of InN film grown in N polarity is 1400 cm 2 /V s with a background carrier concentration of 1.56x10 18 cm -3 at room temperature. For both-polarity films, we found N-rich condition was necessary for the stable InN growth

Next generation extended Lagrangian first principles molecular dynamics.

Science.gov (United States)

Niklasson, Anders M N

2017-08-07

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

Directory of Open Access Journals (Sweden)

Lin Lin

2013-12-01

Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

A Molecular Dynamics Study of Lunasin | Singh | South African ...

African Journals Online (AJOL)

A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

The influence of non-polar lipids on tear film dynamics

KAUST Repository

Bruna, M.

2014-04-04

© 2014 Cambridge University Press. In this paper we examine the effect that physiological non-polar lipids, residing on the surface of an aqueous tear film, have on the film evolution. In our model we track the evolution of the thickness of the non-polar lipid layer, the thickness of the aqueous layer and the concentration of polar lipids which reside at the interface between the two. We also utilise a force balance in the non-polar lipid layer in order to determine its velocity. We show how to obtain previous models in the literature from our model by making particular choices of the parameters. We see the formation of boundary layers in some of these submodels, across which the concentration of polar lipid and the non-polar lipid velocity and film thickness vary. We solve our model numerically for physically realistic parameter values, and we find that the evolution of the aqueous layer and the polar lipid layer are similar to that described by previous authors. However, there are interesting dynamics for the non-polar lipid layer. The effects of altering the key parameters are highlighted and discussed. In particular, we see that the Marangoni number plays a key role in determining how far over the eye the non-polar lipid spreads.

Molecular dynamics simulation of nonlinear spectroscopies of intermolecular motions in liquid water.

Science.gov (United States)

Yagasaki, Takuma; Saito, Shinji

2009-09-15

elucidated by introducing the "translation-free" molecular dynamics simulation. The isotropic pump-probe signal and the polarization anisotropy decay show fast transfer of the librational energy to the surrounding water molecules, followed by relaxation to the hot ground state. These theoretical methods do not require frequently used assumptions and can thus be called ab initio methods; together with multidimensional nonlinear spectroscopies, they provide powerful methods for examining the inter- and intramolecular details of water dynamics.

Near equilibrium dynamics and one-dimensional spatial—temporal structures of polar active liquid crystals

International Nuclear Information System (INIS)

Yang Xiao-Gang; Wang Qi; Forest, M. Gregory

2014-01-01

We systematically explore near equilibrium, flow-driven, and flow-activity coupled dynamics of polar active liquid crystals using a continuum model. Firstly, we re-derive the hydrodynamic model to ensure the thermodynamic laws are obeyed and elastic stresses and forces are consistently accounted. We then carry out a linear stability analysis about constant steady states to study near equilibrium dynamics around the steady states, revealing long-wave instability inherent in this model system and how active parameters in the model affect the instability. We then study model predictions for one-dimensional (1D) spatial—temporal structures of active liquid crystals in a channel subject to physical boundary conditions. We discuss the model prediction in two selected regimes, one is the viscous stress dominated regime, also known as the flow-driven regime, while the other is the full regime, in which all active mechanisms are included. In the viscous stress dominated regime, the polarity vector is driven by the prescribed flow field. Dynamics depend sensitively on the physical boundary condition and the type of the driven flow field. Bulk-dominated temporal periodic states and spatially homogeneous states are possible under weak anchoring conditions while spatially inhomogeneous states exist under strong anchoring conditions. In the full model, flow-orientation interaction generates a host of planar as well as out-of-plane spatial—temporal structures related to the spontaneous flows due to the molecular self-propelled motion. These results provide contact with the recent literature on active nematic suspensions. In addition, symmetry breaking patterns emerge as the additional active viscous stress due to the polarity vector is included in the force balance. The inertia effect is found to limit the long-time survival of spatial structures to those with small wave numbers, i.e., an asymptotic coarsening to long wave structures. A rich set of mechanisms for generating

Organization of lipids in the tear film: a molecular-level view.

Directory of Open Access Journals (Sweden)

Alicja Wizert

Full Text Available Biophysical properties of the tear film lipid layer are studied at the molecular level employing coarse grain molecular dynamics (MD simulations with a realistic model of the human tear film. In this model, polar lipids are chosen to reflect the current knowledge on the lipidome of the tear film whereas typical Meibomian-origin lipids are included in the thick non-polar lipids subphase. Simulation conditions mimic those experienced by the real human tear film during blinks. Namely, thermodynamic equilibrium simulations at different lateral compressions are performed to model varying surface pressure, and the dynamics of the system during a blink is studied by non-equilibrium MD simulations. Polar lipids separate their non-polar counterparts from water by forming a monomolecular layer whereas the non-polar molecules establish a thick outermost lipid layer. Under lateral compression, the polar layer undulates and a sorting of polar lipids occurs. Moreover, formation of three-dimensional aggregates of polar lipids in both non-polar and water subphases is observed. We suggest that these three-dimensional structures are abundant under dynamic conditions caused by the action of eye lids and that they act as reservoirs of polar lipids, thus increasing stability of the tear film.

Polarization measurements of auroral kilometric radiation by Dynamics Explorer-1

International Nuclear Information System (INIS)

Shawhan, S.D.; Gurnett, D.A.

1982-01-01

The plasma wave instrument (PWI) on the Dynamics Explorer-1 has been used to measure polarization of auroral kilometric radiation (AKR) at frequencies of 50 to 400 kHz in both the northern and the southern nightside auroral regions at altitudes of 1 to 3 R/sub E/ above the AKR source regions. The AKR polarization sense is found to be the same as the right hand polarized auroral hiss found in the frequency range of 0.8 to 6.4 kHz. Consequently, these unambiguous direct polarization measurements of AKR lead to the conclusion that AKR escapes the magnetosphere in the R-X mode. Since DE-1 is close to the source region, it can be inferred that AKR is generated predominately in the R-X mode

First Observation of the Submillimeter Polarization Spectrum in a Translucent Molecular Cloud

Science.gov (United States)

Ashton, Peter C.; Ade, Peter A. R.; Angilè, Francesco E.; Benton, Steven J.; Devlin, Mark J.; Dober, Bradley; Fissel, Laura M.; Fukui, Yasuo; Galitzki, Nicholas; Gandilo, Natalie N.; Klein, Jeffrey; Korotkov, Andrei L.; Li, Zhi-Yun; Martin, Peter G.; Matthews, Tristan G.; Moncelsi, Lorenzo; Nakamura, Fumitaka; Netterfield, Calvin B.; Novak, Giles; Pascale, Enzo; Poidevin, Frédérick; Santos, Fabio P.; Savini, Giorgio; Scott, Douglas; Shariff, Jamil A.; Soler, Juan D.; Thomas, Nicholas E.; Tucker, Carole E.; Tucker, Gregory S.; Ward-Thompson, Derek

2018-04-01

Polarized emission from aligned dust is a crucial tool for studies of magnetism in the ISM, but a troublesome contaminant for studies of cosmic microwave background polarization. In each case, an understanding of the significance of the polarization signal requires well-calibrated physical models of dust grains. Despite decades of progress in theory and observation, polarized dust models remain largely underconstrained. During its 2012 flight, the balloon-borne telescope BLASTPol obtained simultaneous broadband polarimetric maps of a translucent molecular cloud at 250, 350, and 500 μm. Combining these data with polarimetry from the Planck 850 μm band, we have produced a submillimeter polarization spectrum, the first for a cloud of this type. We find the polarization degree to be largely constant across the four bands. This result introduces a new observable with the potential to place strong empirical constraints on ISM dust polarization models in a previously inaccessible density regime. Compared to models by Draine & Fraisse, our result disfavors two of their models for which all polarization arises due only to aligned silicate grains. By creating simple models for polarized emission in a translucent cloud, we verify that extinction within the cloud should have only a small effect on the polarization spectrum shape, compared to the diffuse ISM. Thus, we expect the measured polarization spectrum to be a valid check on diffuse ISM dust models. The general flatness of the observed polarization spectrum suggests a challenge to models where temperature and alignment degree are strongly correlated across major dust components.

Theory of coherent dynamic nuclear polarization in quantum dots

DEFF Research Database (Denmark)

Neder, Izhar; Rudner, Mark Spencer; Halperin, Bertrand

2014-01-01

We consider the production of dynamic nuclear spin polarization (DNP) in a two-electron double quantum dot, in which the electronic levels are repeatedly swept through a singlet-triplet avoided crossing. Our analysis helps to elucidate the intriguing interplay between electron-nuclear hyperfine...

Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

Energy Technology Data Exchange (ETDEWEB)

Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

2014-10-15

The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

Negative circular polarization dynamics in InP/InGaP quantum dots

Science.gov (United States)

Nekrasov, S. V.; Kusrayev, Yu G.; Akimov, I. A.; Korenev, V. L.; Langer, L.; Salewski, M.

2016-08-01

Photoluminescence (PL) negative circular polarization (NCP) dynamics of InP/InGaP quantum dots (QDs) was studied. Time resolved measurements of PL demonstrated that NCP vanishes, when transverse magnetic field is applied, while oscillations of polarization (that are typical for both low-dimensional and bulk materials) do not occur. Hole g-factor spread in the QD ensemble was supposed to be the most probable reason for such NCP magnetic field behavior. The dependence of NCP dynamics on the repetition period of excitation laser pulses was investigated. In case of fairly small repetition period (T = 13.3 ns) long living NCP (13.3 ns < t < 133 ns) was detected, what was ascribed to resident electron spin orientation, accumulated during many laser pulses. In that regime more than one luminescence polarization decay time exist.

Negative circular polarization dynamics in InP/InGaP quantum dots

International Nuclear Information System (INIS)

Nekrasov, S V; Kusrayev, Yu G; Akimov, I A; Korenev, V L; Langer, L; Salewski, M

2016-01-01

Photoluminescence (PL) negative circular polarization (NCP) dynamics of InP/InGaP quantum dots (QDs) was studied. Time resolved measurements of PL demonstrated that NCP vanishes, when transverse magnetic field is applied, while oscillations of polarization (that are typical for both low-dimensional and bulk materials) do not occur. Hole g-factor spread in the QD ensemble was supposed to be the most probable reason for such NCP magnetic field behavior. The dependence of NCP dynamics on the repetition period of excitation laser pulses was investigated. In case of fairly small repetition period (T = 13.3 ns) long living NCP (13.3 ns < t < 133 ns) was detected, what was ascribed to resident electron spin orientation, accumulated during many laser pulses. In that regime more than one luminescence polarization decay time exist. (paper)

Surface Effect on Oil Transportation in Nanochannel: a Molecular Dynamics Study.

Science.gov (United States)

Zheng, Haixia; Du, Yonggang; Xue, Qingzhong; Zhu, Lei; Li, Xiaofang; Lu, Shuangfang; Jin, Yakang

2017-12-01

In this work, we investigate the dynamics mechanism of oil transportation in nanochannel using molecular dynamics simulations. It is demonstrated that the interaction between oil molecules and nanochannel has a great effect on the transportation properties of oil in nanochannel. Because of different interactions between oil molecules and channel, the center of mass (COM) displacement of oil in a 6-nm channel is over 30 times larger than that in a 2-nm channel, and the diffusion coefficient of oil molecules at the center of a 6-nm channel is almost two times more than that near the channel surface. Besides, it is found that polarity of oil molecules has the effect on impeding oil transportation, because the electrostatic interaction between polar oil molecules and channel is far larger than that between nonpolar oil molecules and channel. In addition, channel component is found to play an important role in oil transportation in nanochannel, for example, the COM displacement of oil in gold channel is very few due to great interaction between oil and gold substrate. It is also found that nano-sized roughness of channel surface greatly influences the speed and flow pattern of oil. Our findings would contribute to revealing the mechanism of oil transportation in nanochannels and therefore are very important for design of oil extraction in nanochannels.

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

Science.gov (United States)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

TE-TM dynamics in a semiconductor laser subject to polarization-rotated optical feedback

International Nuclear Information System (INIS)

Heil, T.; Uchida, A.; Davis, P.; Aida, T.

2003-01-01

We present a comprehensive experimental characterization of the dynamics of semiconductor lasers subject to polarization-rotated optical feedback. We find oscillatory instabilities appearing for large feedback levels and disappearing at large injection currents, which we classify in contrast to the well-known conventional optical-feedback-induced dynamics. In addition, we compare our experiments to theoretical results of a single-mode model assuming incoherence of the optical feedback, and we identify differences concerning the average power of the laser. Hence, we develop an alternative model accounting for both polarizations, where the emission of the dominant TE mode is injected with delay into the TM mode of the laser. Numerical simulations using this model show good qualitative agreement with our experimental results, correctly reproducing the parameter dependences of the dynamics. Finally, we discuss the application of polarization-rotated-feedback induced instabilities in chaotic carrier communication systems

Extensive molecular differences between anterior- and posterior-half-sclerotomes underlie somite polarity and spinal nerve segmentation

Directory of Open Access Journals (Sweden)

Keynes Roger J

2009-05-01

Full Text Available Abstract Background The polarization of somite-derived sclerotomes into anterior and posterior halves underlies vertebral morphogenesis and spinal nerve segmentation. To characterize the full extent of molecular differences that underlie this polarity, we have undertaken a systematic comparison of gene expression between the two sclerotome halves in the mouse embryo. Results Several hundred genes are differentially-expressed between the two sclerotome halves, showing that a marked degree of molecular heterogeneity underpins the development of somite polarity. Conclusion We have identified a set of genes that warrant further investigation as regulators of somite polarity and vertebral morphogenesis, as well as repellents of spinal axon growth. Moreover the results indicate that, unlike the posterior half-sclerotome, the central region of the anterior-half-sclerotome does not contribute bone and cartilage to the vertebral column, being associated instead with the development of the segmented spinal nerves.

Thermally driven molecular linear motors - A molecular dynamics study

DEFF Research Database (Denmark)

Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence

2009-01-01

We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...

Spin-polarized transport properties of a pyridinium-based molecular spintronics device

Science.gov (United States)

Zhang, J.; Xu, B.; Qin, Z.

2018-05-01

By applying a first-principles approach based on non-equilibrium Green's functions combined with density functional theory, the transport properties of a pyridinium-based "radical-π-radical" molecular spintronics device are investigated. The obvious negative differential resistance (NDR) and spin current polarization (SCP) effect, and abnormal magnetoresistance (MR) are obtained. Orbital reconstruction is responsible for novel transport properties such as that the MR increases with bias and then decreases and that the NDR being present for both parallel and antiparallel magnetization configurations, which may have future applications in the field of molecular spintronics.

Are Amyloid Fibrils RNA-Traps? A Molecular Dynamics Perspective

Directory of Open Access Journals (Sweden)

Massimiliano Meli

2018-06-01

Full Text Available The self-assembly of proteins and peptides into amyloids is a key feature of an increasing number of diseases. Amyloid fibrils display a unique surface reactivity endowing the sequestration of molecules such as MicroRNAs, which can be the active moiety of the toxic action. To test this hypothesis we studied the recognition between a model RNA and two different steric zipper spines using molecular dynamics simulations. We found that the interaction occurs and displays peptide-sequence dependence. Interestingly, interactions with polar zipper surfaces such as the formed by SNQNNF are more stable and favor the formation of β-barrel like complexes resembling the structures of toxic oligomers. These sequence-structure-recognition relationships of the two different assemblies may be exploited for the design of compounds targeting the fibers or competing with RNA-amyloid attachment

Molecular Memory of Morphologies by Septins during Neuron Generation Allows Early Polarity Inheritance.

Science.gov (United States)

Boubakar, Leila; Falk, Julien; Ducuing, Hugo; Thoinet, Karine; Reynaud, Florie; Derrington, Edmund; Castellani, Valérie

2017-08-16

Transmission of polarity established early during cell lineage history is emerging as a key process guiding cell differentiation. Highly polarized neurons provide a fascinating model to study inheritance of polarity over cell generations and across morphological transitions. Neural crest cells (NCCs) migrate to the dorsal root ganglia to generate neurons directly or after cell divisions in situ. Using live imaging of vertebrate embryo slices, we found that bipolar NCC progenitors lose their polarity, retracting their processes to round for division, but generate neurons with bipolar morphology by emitting processes from the same locations as the progenitor. Monitoring the dynamics of Septins, which play key roles in yeast polarity, indicates that Septin 7 tags process sites for re-initiation of process growth following mitosis. Interfering with Septins blocks this mechanism. Thus, Septins store polarity features during mitotic rounding so that daughters can reconstitute the initial progenitor polarity. Copyright © 2017 Elsevier Inc. All rights reserved.

Daple Coordinates Planar Polarized Microtubule Dynamics in Ependymal Cells and Contributes to Hydrocephalus

Directory of Open Access Journals (Sweden)

Maki Takagishi

2017-07-01

Full Text Available Motile cilia in ependymal cells, which line the cerebral ventricles, exhibit a coordinated beating motion that drives directional cerebrospinal fluid (CSF flow and guides neuroblast migration. At the apical cortex of these multi-ciliated cells, asymmetric localization of planar cell polarity (PCP proteins is required for the planar polarization of microtubule dynamics, which coordinates cilia orientation. Daple is a disheveled-associating protein that controls the non-canonical Wnt signaling pathway and cell motility. Here, we show that Daple-deficient mice present hydrocephalus and their ependymal cilia lack coordinated orientation. Daple regulates microtubule dynamics at the anterior side of ependymal cells, which in turn orients the cilial basal bodies required for the directional cerebrospinal fluid flow. These results demonstrate an important role for Daple in planar polarity in motile cilia and provide a framework for understanding the mechanisms and functions of planar polarization in the ependymal cells.

Adaptive polarization image fusion based on regional energy dynamic weighted average

Institute of Scientific and Technical Information of China (English)

ZHAO Yong-qiang; PAN Quan; ZHANG Hong-cai

2005-01-01

According to the principle of polarization imaging and the relation between Stokes parameters and the degree of linear polarization, there are much redundant and complementary information in polarized images. Since man-made objects and natural objects can be easily distinguished in images of degree of linear polarization and images of Stokes parameters contain rich detailed information of the scene, the clutters in the images can be removed efficiently while the detailed information can be maintained by combining these images. An algorithm of adaptive polarization image fusion based on regional energy dynamic weighted average is proposed in this paper to combine these images. Through an experiment and simulations,most clutters are removed by this algorithm. The fusion method is used for different light conditions in simulation, and the influence of lighting conditions on the fusion results is analyzed.

The emergence of sarcomeric, graded-polarity and spindle-like patterns in bundles of short cytoskeletal polymers and two opposite molecular motors

International Nuclear Information System (INIS)

Craig, E M; Dey, S; Mogilner, A

2011-01-01

We use linear stability analysis and numerical solutions of partial differential equations to investigate pattern formation in the one-dimensional system of short dynamic polymers and one (plus-end directed) or two (one is plus-end, another minus-end directed) molecular motors. If polymer sliding and motor gliding rates are slow and/or the polymer turnover rate is fast, then the polymer-motor bundle has mixed polarity and homogeneous motor distribution. However, if motor gliding is fast, a sarcomeric pattern with periodic bands of alternating polymer polarity separated by motor aggregates evolves. On the other hand, if polymer sliding is fast, a graded-polarity bundle with motors at the center emerges. In the presence of the second, minus-end directed motor, the sarcomeric pattern is more ubiquitous, while the graded-polarity pattern is destabilized. However, if the minus-end motor is weaker than the plus-end directed one, and/or polymer nucleation is autocatalytic, and/or long polymers are present in the bundle, then a spindle-like architecture with a sorted-out polarity emerges with the plus-end motors at the center and minus-end motors at the edges. We discuss modeling implications for actin-myosin fibers and in vitro and meiotic spindles.

The enhanced spin-polarized transport behaviors through cobalt benzene-porphyrin-benzene molecular junctions: the effect of functional groups

Science.gov (United States)

Cheng, Jue-Fei; Zhou, Liping; Wen, Zhongqian; Yan, Qiang; Han, Qin; Gao, Lei

2017-05-01

The modification effects of the groups amino (NH2) and nitro (NO2) on the spin polarized transport properties of the cobalt benzene-porphyrin-benzene (Co-BPB) molecule coupled to gold (Au) nanowire electrodes are investigated by the nonequilibrium Green’s function method combined with the density functional theory. The calculation results show that functional groups can lead to the significant spin-filter effect, enhanced low-bias negative differential resistance (NDR) behavior and novel reverse rectifying effect in Co-BPB molecular junction. The locations and types of functional groups have distinct influences on spin-polarized transport performances. The configuration with NH2 group substituting H atom in central porphyrin ring has larger spin-down current compared to that with NO2 substitution. And Co-BPB molecule junction with NH2 group substituting H atom in side benzene ring shows reverse rectifying effect. Detailed analyses confirm that NH2 and NO2 group substitution change the spin-polarized transferred charge, which makes the highest occupied molecular orbitals (HOMO) of spin-down channel of Co-BPB closer to the Fermi level. And the shift of HOMO strengthens the spin-polarized coupling between the molecular orbitals and the electrodes, leading to the enhanced spin-polarized behavior. Our findings might be useful in the design of multi-functional molecular devices in the future.

Simulation of generation and dynamics of polarization singularities with circular Airy beams.

Science.gov (United States)

Ye, Dong; Peng, Xinyu; Zhou, Muchun; Xin, Yu; Song, Minmin

2017-11-01

The generation and dynamics of polarization singularities have been underresearched for years, while the focusing property of the topological configuration has not been explored much. In this paper, we simulated the generation of low-order polarization singularities with a circular Airy beam and explored the focusing property of the synthetic light field during propagation due to the autofocusing of the component. Our work researched the focusing properties of the polarization singularity configuration, which may help to develop its application prospect.

Introduction to Molecular Dynamics and Accelerated Molecular Dynamics

International Nuclear Information System (INIS)

Perez, Danny

2012-01-01

We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.

Chemically induced dynamic electron polarization. Pulse radiolysis of aqueous solutions of alcohols

International Nuclear Information System (INIS)

Trifunac, A.D.; Thurnauer, M.C.

1975-01-01

The radical pair model of chemically induced dynamic electron polarization (CIDEP) is experimentally verified. Aqueous solutions of alcohols were irradiated with 3 MeV electrons and observed with time resolved electron paramagnetic resonance (EPR) spectroscopy. Relative line intensities of the polarized EPR spectra of radicals from methanol and especially ethylene glycol, alone and in the presence of radicals from compounds containing halogens, illustrates the polarization dependence on the g-factor differences between the radical pair components. The observation of the relative polarization enhancement in the various lines of the multiline EPR spectra illustrates the polarization dependence on the hyperfine terms. Intrinsic enhancements are calculated and are shown to be proportional to the observed enhancement, showing that the radical pair model of CIDEP is qualitatively correct

Higher-Order Extended Lagrangian Born-Oppenheimer Molecular Dynamics for Classical Polarizable Models.

Science.gov (United States)

Albaugh, Alex; Head-Gordon, Teresa; Niklasson, Anders M N

2018-02-13

Generalized extended Lagrangian Born-Oppenheimer molecular dynamics (XLBOMD) methods provide a framework for fast iteration-free simulations of models that normally require expensive electronic ground state optimizations prior to the force evaluations at every time step. XLBOMD uses dynamically driven auxiliary degrees of freedom that fluctuate about a variationally optimized ground state of an approximate "shadow" potential which approximates the true reference potential. While the requirements for such shadow potentials are well understood, constructing such potentials in practice has previously been ad hoc, and in this work, we present a systematic development of XLBOMD shadow potentials that match the reference potential to any order. We also introduce a framework for combining friction-like dissipation for the auxiliary degrees of freedom with general-order integration, a combination that was not previously possible. These developments are demonstrated with a simple fluctuating charge model and point induced dipole polarization models.

Current-driven dynamics in molecular-scale devices

International Nuclear Information System (INIS)

Seideman, Tamar

2003-01-01

We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)

Characterization of molecularly imprinted polymers using a new polar solvent titration method.

Science.gov (United States)

Song, Di; Zhang, Yagang; Geer, Michael F; Shimizu, Ken D

2014-07-01

A new method of characterizing molecularly imprinted polymers (MIPs) was developed and tested, which provides a more accurate means of identifying and measuring the molecular imprinting effect. In the new polar solvent titration method, a series of imprinted and non-imprinted polymers were prepared in solutions containing increasing concentrations of a polar solvent. The polar solvent additives systematically disrupted the templation and monomer aggregation processes in the prepolymerization solutions, and the extent of disruption was captured by the polymerization process. The changes in binding capacity within each series of polymers were measured, providing a quantitative assessment of the templation and monomer aggregation processes in the imprinted and non-imprinted polymers. The new method was tested using three different diphenyl phosphate imprinted polymers made using three different urea functional monomers. Each monomer had varying efficiencies of templation and monomer aggregation. The new MIP characterization method was found to have several advantages. To independently verify the new characterization method, the MIPs were also characterized using traditional binding isotherm analyses. The two methods appeared to give consistent conclusions. First, the polar solvent titration method is less susceptible to false positives in identifying the imprinting effect. Second, the method is able to differentiate and quantify changes in binding capacity, as measured at a fixed guest and polymer concentration, arising from templation or monomer aggregation processes in the prepolymerization solution. Third, the method was also easy to carry out, taking advantage of the ease of preparing MIPs. Copyright © 2014 John Wiley & Sons, Ltd.

Molecular Dynamics Studies of Nanofluidic Devices

DEFF Research Database (Denmark)

Zambrano Rodriguez, Harvey Alexander

of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...

1H chemically induced dynamic nuclear polarization in the photodecomposition of uranyl carboxylates

International Nuclear Information System (INIS)

Rykov, S.V.; Khudyakov, I.V.; Skakovsky, E.D.; Burrows, H.D.; Formosinho, S.J.; Miguel, M. da G.M.

1991-01-01

Chemically induced dynamic nuclear polarization ( 1 H CIDNP) has been observed during photolysis of uranyl salts of pivalic, propionic, and acetic acids in D 2 O solution, [ 2 H 6 ]acetone, [ 2 H 4 ]methanol, or in some other solvent. The multiplet polarization of isobutene and isobutane protons has been found under photolysis of deoxygenated pivalate solution. The polarized compounds are formed in the triplet pairs of tert-butyl free radicals. 1 H Emission of the tert-butylperoxyl group and emission of 1 H from isobutene have been recorded under photolysis of air-saturated pivalate solutions. The CIDNP of butane protons stays as a multiplet. Such changes in the presence of air/oxygen have arisen apparently because of the formation of tert-butylperoxyl free radical and its reaction with tert-butyl radical products, i.e. hydroperoxide (peroxide) and isobutene. Isobutene probably forms a complex with molecular oxygen which has a very short proton relaxation time. During the photolysis of uranyl pivalate in the presence of p-benzoquinone (5 x 10 -2 -0.1 mol dm -3 ) we have not observed any CIDNP, whereas under p-benzoquinone concentrations of 10 -3 -10 -2 mol dm -3 the CIDNP from both hydroquinone and p-benzoquinone has been followed. Photolysis of uranyl propionate has led to CIDNP from butane protons. An emission from methyl group protons of a compound with an ethylperoxyl fragment in the presence of air/oxygen has been observed. The same polarization picture has arisen under interaction of photoexcited uranyl with propionic acid. During the photolysis of uranyl acetate at relatively low concentrations (10 -2 mol dm -3 ) a CIDNP very similar to that registered for uranyl propionate was recorded. The ethyl fragment is probably obtained in reactions for two methyl radicals formed from acetate with the parent uranyl acetate, namely hydrogen-atom abstraction and addition reactions. (author)

Dynamically Polarized Sample for Neutron Scattering At the Spallation Neutron Source

International Nuclear Information System (INIS)

Pierce, Josh; Zhao, J. K.; Crabb, Don

2009-01-01

The recently constructed Spallation Neutron Source at the Oak Ridge National Laboratory is quickly becoming the world's leader in neutron scattering sciences. In addition to the world's most intense pulsed neutron source, we are continuously constructing state of the art neutron scattering instruments as well as sample environments to address today and tomorrow's challenges in materials research. The Dynamically Polarized Sample project at the SNS is aimed at taking maximum advantage of polarized neutron scattering from polarized samples, especially biological samples that are abundant in hydrogen. Polarized neutron scattering will allow us drastically increase the signal to noise ratio in experiments such as neutron protein crystallography. The DPS project is near completion and all key components have been tested. Here we report the current status of the project.

Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La(3+).

Science.gov (United States)

Terrier, Cyril; Vitorge, Pierre; Gaigeot, Marie-Pierre; Spezia, Riccardo; Vuilleumier, Rodolphe

2010-07-28

Structural and electronic properties of La(3+) immersed in bulk water have been assessed by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations. Correct structural properties, i.e., La(III)-water distances and La(III) coordination number, can be obtained within the framework of Car-Parrinello simulations providing that both the La pseudopotential and conditions of the dynamics (fictitious mass and time step) are carefully set up. DFT-MD explicitly treats electronic densities and is shown here to provide a theoretical justification to the necessity of including polarization when studying highly charged cations such as lanthanoids(III) with classical MD. La(3+) was found to strongly polarize the water molecules located in the first shell, giving rise to dipole moments about 0.5 D larger than those of bulk water molecules. Finally, analyzing Kohn-Sham orbitals, we found La(3+) empty 4f orbitals extremely compact and to a great extent uncoupled from the water conduction band, while the 5d empty orbitals exhibit mixing with unoccupied states of water.

Theoretical Concepts in Molecular Photodissociation Dynamics

DEFF Research Database (Denmark)

Henriksen, Niels Engholm

1995-01-01

This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...

Stable isotope-resolved analysis with quantitative dissolution dynamic nuclear polarization

DEFF Research Database (Denmark)

Lerche, Mathilde Hauge; Yigit, Demet; Frahm, Anne Birk

2018-01-01

Metabolite profiles and their isotopomer distributions can be studied non-invasively in complex mixtures with NMR. The advent of dissolution Dynamic Nuclear Polarization (dDNP) and isotope enrichment add sensitivity and resolution to such met-abolic studies. Metabolic pathways and networks can be...

First principles molecular dynamics without self-consistent field optimization

International Nuclear Information System (INIS)

Souvatzis, Petros; Niklasson, Anders M. N.

2014-01-01

We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations

Impact of molecular packing on electronic polarization in organic crystals: the case of pentacene vs TIPS-pentacene.

Science.gov (United States)

Ryno, Sean M; Risko, Chad; Brédas, Jean-Luc

2014-04-30

Polarization energy corresponds to the stabilization of the cation or anion state of an atom or molecule when going from the gas phase to the solid state. The decrease in ionization energy and increase in electron affinity in the solid state are related to the (electronic and nuclear) polarization of the surrounding atoms and molecules in the presence of a charged entity. Here, through a combination of molecular mechanics and quantum mechanics calculations, we evaluate the polarization energies in two prototypical organic semiconductors, pentacene and 6,13-bis(2-(tri-isopropylsilyl)ethynyl)pentacene (TIPS-pentacene). Comparison of the results for the two systems reveals the critical role played by the molecular packing configurations in the determination of the polarization energies and provides physical insight into the experimental data reported by Lichtenberger and co-workers (J. Amer. Chem. Soc. 2010, 132, 580; J. Phys. Chem. C 2010, 114, 13838). Our results underline that the impact of packing configurations, well established in the case of the charge-transport properties, also extends to the polarization properties of π-conjugated materials.

Molecular dynamics and diffusion a compilation

CERN Document Server

Fisher, David

2013-01-01

The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...

Extended Lagrangian Excited State Molecular Dynamics.

Science.gov (United States)

Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

2018-02-13

An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

Advances in molecular vibrations and collision dynamics molecular clusters

CERN Document Server

Bacic, Zatko

1998-01-01

This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...

The Telemachus mission: dynamics of the polar sun and heliosphere

Science.gov (United States)

Roelof, E.

Telemachus in Greek mythology was the faithful son of Ulysses. The Telemachus mission is envisioned as the next logical step in the exploration of the polar regions of the Sun and heliosphere so excitingly initiated by the ESA/NASA Ulysses mission. Telemachus is a polar solar-heliospheric mission described in the current NASA Sun-Earth Connections Roadmap (2003-2028) that has successfully undergone two Team X studies by NASA/JPL. The pioneering observations from Ulysses transformed our perception of the structure and dynamics of these polar regions through which flow the solar wind, magnetic fields and energetic particles that eventually populate most of the volume of the heliosphere. Ulysses carried only fields and particles detectors. Telemachus, in addition to modern versions of such essential in situ instruments, will carry imagers that will give solar astronomers a new viewpoint on coronal mass ejections and solar flares, as well as their first purely polar views of the photospheric magnetic field, thereby providing new helioseismology to probe the interior of the Sun. Unlike the RTG-powered Ulysses, the power for Telemachus will come simply from solar panels. Gravity assist encounters with Venus and Earth (twice) will yield ˜5 years of continuous in-ecliptic cruise science between 0.7 AU and 3.3 AU that will powerfully complement other contemporary solar-heliospheric missions. The Jupiter gravity assist, followed by a perihelion burn ˜8 years after launch, will place Telemachus in a permanent ˜0.2 AU by 2.5 AU heliographic polar orbit (inclination >80 deg) whose period will be 1.5 years. Telemachus will then pass over the solar poles at ˜0.4 AU (compared to 1.4 AU for Ulysses) and spend ˜2 weeks above 60 deg on each polar pass (alternating perihelions between east and west limbs as viewed from Earth). In 14 polar passes during a 10.5 year solar cycle, Telemachus would accumulate over half a year of polar science data. During the remainder of the time, it

Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

Indian Academy of Sciences (India)

Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

Broadband cross-polarization-based heteronuclear dipolar recoupling for structural and dynamic NMR studies of rigid and soft solids

International Nuclear Information System (INIS)

Kharkov, B. B.; Chizhik, V. I.; Dvinskikh, S. V.

2016-01-01

Dipolar recoupling is an essential part of current solid-state NMR methodology for probing atomic-resolution structure and dynamics in solids and soft matter. Recently described magic-echo amplitude- and phase-modulated cross-polarization heteronuclear recoupling strategy aims at efficient and robust recoupling in the entire range of coupling constants both in rigid and highly dynamic molecules. In the present study, the properties of this recoupling technique are investigated by theoretical analysis, spin-dynamics simulation, and experimentally. The resonance conditions and the efficiency of suppressing the rf field errors are examined and compared to those for other recoupling sequences based on similar principles. The experimental data obtained in a variety of rigid and soft solids illustrate the scope of the method and corroborate the results of analytical and numerical calculations. The technique benefits from the dipolar resolution over a wider range of coupling constants compared to that in other state-of-the-art methods and thus is advantageous in studies of complex solids with a broad range of dynamic processes and molecular mobility degrees

Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

Czech Academy of Sciences Publication Activity Database

Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel

2016-01-01

Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016

Visualizing Energy on Target: Molecular Dynamics Simulations

Science.gov (United States)

2017-12-01

ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

Nonadiabatic electron wavepacket dynamics behind molecular autoionization

Science.gov (United States)

Matsuoka, Takahide; Takatsuka, Kazuo

2018-01-01

A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

Ultrafast molecular dynamics illuminated with synchrotron radiation

International Nuclear Information System (INIS)

Bozek, John D.; Miron, Catalin

2015-01-01

Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.

Rheology via nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Hoover, W.G.

1982-10-01

The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference

First-principles molecular dynamics for metals

International Nuclear Information System (INIS)

Fernando, G.W.; Qian, G.; Weinert, M.; Davenport, J.W.

1989-01-01

A Car-Parrinello-type first-principles molecular-dynamics approach capable of treating the partial occupancy of electronic states that occurs at the Fermi level in a metal is presented. The algorithms used to study metals are both simple and computationally efficient. We also discuss the connection between ordinary electronic-structure calculations and molecular-dynamics simulations as well as the role of Brillouin-zone sampling. This extension should be useful not only for metallic solids but also for solids that become metals in their liquid and/or amorphous phases

How Dynamic Visualization Technology Can Support Molecular Reasoning

Science.gov (United States)

Levy, Dalit

2013-01-01

This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

Surface activation of cyclo olefin polymer by oxygen plasma discharge: a molecular dynamics study

International Nuclear Information System (INIS)

Soberon, Felipe

2014-01-01

Thermoplastic substrates made of cyclo olefin polymer (COP) are treated with oxygen plasma discharges to introduce polar groups at the surface. This is the first step in the process of surface functionalization of COP substrates used in biosensor devices. A molecular dynamics model of basic COP structure is implemented using the second-generation reactive empirical bond order (REBO) potentials for hydrocarbon–oxygen interactions. The model includes covalent bond and Van der Waals interactions. The bombardment of a COP surface with mono-energetic atomic oxygen ions, energy in the range 1-35 eV, is simulated and reported here. The dynamics of the substrate modification reveals that the substrate top layer is de-hydrogenated and subsequently builds up an oxygen–carbon matrix layer, ∼10 Å thick. Analysis of the modified substrates indicates that surface yield is predominantly peroxide groups. (paper)

Increasing Spin Coherence in Nanodiamond via Dynamic Nuclear Polarization

Science.gov (United States)

Gaebel, Torsten; Rej, Ewa; Boele, Thomas; Waddington, David; Reilly, David

Nanodiamonds are of interest for quantum information technology, as metrological sensors, and more recently as a probe of biological environments. Here we present results examining how intrinsic defects can be used for dynamic nuclear polarization that leads to a dramatic increase in both T1 and T2 for 13C spins in nanodiamond. Mechanisms to explain this enhancement are discussed.

Physical adsorption and molecular dynamics

International Nuclear Information System (INIS)

Cohan, N.V.

1981-01-01

Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.) [pt

Molecular dynamics study of the coordination sphere of trivalent lanthanum in a highly concentrated LiCl aqueous solution: A combined classical and ab initio approach

International Nuclear Information System (INIS)

Vuilleumier, R.; Petit, L.; Maldivi, P.; Adamo, C.

2008-01-01

The first coordination sphere of trivalent lanthanum in a highly concentrated (14 M) lithium chloride solution is studied with a combination of classical molecular dynamics and density functional theory based first principle molecular dynamics. This method enables us to obtain a solvation shell of La 3+ containing 2 chloride ions and 6 water molecules. After refinement using first principle molecular dynamics, the resulting cation-water and cation-anion distances are in very good agreement with experiment. The 2 Cl - and the 6 water molecules arrange in a square anti-prism around La 3+ . Exchange of water molecules was also observed in the first-principle simulation, with an intermediate structure comprising 7 water molecules stable for 2.5 ps. Finally, evaluation of dipole moments using maximally localized Wannier functions shows a substantial polarization of the chloride anions and the water molecules in the first solvation shell of trivalent lanthanum. (authors)

Ferroelectric Polarization Switching Dynamics and Domain Growth of Triglycine Sulfate and Imidazolium Perchlorate

KAUST Repository

Ma, He; Gao, Wenxiu; Wang, Junling; Wu, Tao; Yuan, Guoliang; Liu, Junming; Liu, Zhiguo

2016-01-01

The weak bond energy and large anisotropic domain wall energy induce many special characteristics of the domain nucleation, growth, and polarization switch in triglycine sulfate (TGS) and imidazolium perchlorate (IM), two typical molecular

Molecular dynamics for dense matter

International Nuclear Information System (INIS)

Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro

2012-01-01

We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear “pasta”, i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)

Molecular dynamics for dense matter

Science.gov (United States)

Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

2012-08-01

We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.

Influence of temperature on spin polarization dynamics in dilute nitride semiconductors—Role of nonparamagnetic centers

Energy Technology Data Exchange (ETDEWEB)

Baranowski, M.; Misiewicz, J. [Laboratory for Optical Spectroscopy of Nanostructures, Department of Experimental Physics, Wroclaw University of Technology, Wybrzeze, Wyspianskiego 27, 50-370 Wroclaw (Poland)

2015-10-21

We report theoretical studies of spin polarization dynamics in dilute nitride semiconductors. We develop a commonly used rate equation model [Lagarde et al., Phys. Status Solidi A 204, 208 (2007) and Kunold et al. Phys. Rev. B 83, 165202 (2011)] to take into account the influence of shallow localizing states on the temperature dependence of spin polarization dynamics and a spin filtering effect. Presented investigations show that the experimentally observed temperature dependence of a spin polarization lifetime in dilute nitrides can be related to the electron capture process by shallow localizing states without paramagnetic properties. This process reduces the efficiency of spin filtering effect by deep paramagnetic centers, especially at low temperatures.

Dynamic Nuclear Polarization and other magnetic ideas at EPFL.

Science.gov (United States)

Bornet, Aurélien; Milani, Jonas; Wang, Shutao; Mammoli, Daniele; Buratto, Roberto; Salvi, Nicola; Segaw, Takuya F; Vitzthum, Veronika; Miéville, Pascal; Chinthalapalli, Srinivas; Perez-Linde, Angel J; Carnevale, Diego; Jannin, Sami; Caporinia, Marc; Ulzega, Simone; Rey, Martial; Bodenhausen, Geoffrey

2012-01-01

Although nuclear magnetic resonance (NMR) can provide a wealth of information, it often suffers from a lack of sensitivity. Dynamic Nuclear Polarization (DNP) provides a way to increase the polarization and hence the signal intensities in NMR spectra by transferring the favourable electron spin polarization of paramagnetic centres to the surrounding nuclear spins through appropriate microwave irradiation. In our group at EPFL, two complementary DNP techniques are under investigation: the combination of DNP with magic angle spinning at temperatures near 100 K ('MAS-DNP'), and the combination of DNP at 1.2 K with rapid heating followed by the transfer of the sample to a high-resolution magnet ('dissolution DNP'). Recent applications of MAS-DNP to surfaces, as well as new developments of magnetization transfer of (1)H to (13)C at 1.2 K prior to dissolution will illustrate the work performed in our group. A second part of the paper will give an overview of some 'non-enhanced' activities of our laboratory in liquid- and solid-state NMR.

NMR of insensitive nuclei enhanced by dynamic nuclear polarization.

Science.gov (United States)

Miéville, Pascal; Jannin, Sami; Helm, Lothar; Bodenhausen, Geoffrey

2011-01-01

Despite the powerful spectroscopic information it provides, Nuclear Magnetic Resonance (NMR) spectroscopy suffers from a lack of sensitivity, especially when dealing with nuclei other than protons. Even though NMR can be applied in a straightforward manner when dealing with abundant protons of organic molecules, it is very challenging to address biomolecules in low concentration and/or many other nuclei of the periodic table that do not provide as intense signals as protons. Dynamic Nuclear Polarization (DNP) is an important technique that provides a way to dramatically increase signal intensities in NMR. It consists in transferring the very high electron spin polarization of paramagnetic centers (usually at low temperature) to the surrounding nuclear spins with appropriate microwave irradiation. DNP can lead to an enhancement of the nuclear spin polarization by up to four orders of magnitude. We present in this article some basic concepts of DNP, describe the DNP apparatus at EPFL, and illustrate the interest of the technique for chemical applications by reporting recent measurements of the kinetics of complexation of 89Y by the DOTAM ligand.

Diverging effects of isotopic fractionation upon molecular diffusion of noble gases in water: mechanistic insights through ab initio molecular dynamics simulations.

Science.gov (United States)

Pinto de Magalhães, Halua; Brennwald, Matthias S; Kipfer, Rolf

2017-03-22

Atmospheric noble gases are routinely used as natural tracers to analyze gas transfer processes in aquatic systems. Their isotopic ratios can be employed to discriminate between different physical transport mechanisms by comparison to the unfractionated atmospheric isotope composition. In many applications of aquatic systems molecular diffusion was thought to cause a mass dependent fractionation of noble gases and their isotopes according to the square root ratio of their masses. However, recent experiments focusing on isotopic fractionation within a single element challenged this broadly accepted assumption. The determined fractionation factors of Ne, Ar, Kr and Xe isotopes revealed that only Ar follows the prediction of the so-called square root relation, whereas within the Ne, Kr and Xe elements no mass-dependence was found. The reason for this unexpected divergence of Ar is not yet understood. The aim of our computational exercise is to establish the molecular-resolved mechanisms behind molecular diffusion of noble gases in water. We make the hypothesis that weak intermolecular interactions are relevant for the dynamical properties of noble gases dissolved in water. Therefore, we used ab initio molecular dynamics to explicitly account for the electronic degrees of freedom. Depending on the size and polarizability of the hydrophobic particles such as noble gases, their motion in dense and polar liquids like water is subject to different diffusive regimes: the inter-cavity hopping mechanism of small particles (He, Ne) breaks down if a critical particle size achieved. For the case of large particles (Kr, Xe), the motion through the water solvent is governed by mass-independent viscous friction leading to hydrodynamical diffusion. Finally, Ar falls in between the two diffusive regimes, where particle dispersion is propagated at the molecular collision time scale of the surrounding water molecules.

Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

Science.gov (United States)

2014-01-01

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

The rotational temperature of polar molecular ions in Coulomb crystals

International Nuclear Information System (INIS)

Bertelsen, Anders; Joergensen, Solvejg; Drewsen, Michael

2006-01-01

With MgH + ions as a test case, we investigate to what extent the rotational motion of smaller polar molecular ions sympathetically cooled into Coulomb crystals in linear Paul traps couples to the translational motions of the ion ensemble. By comparing the results obtained from rotational resonance-enhanced multiphoton photo-dissociation experiments with data from theoretical simulations, we conclude that the effective rotational temperature exceeds the translational temperature (<100 mK) by more than two orders of magnitude, indicating a very weak coupling. (letter to the editor)

Convergence of environment polarization effects in multiscale modeling of excitation energies

DEFF Research Database (Denmark)

Beerepoot, Maarten; Steindal, Arnfinn Hykkerud; Ruud, Kenneth

2014-01-01

We present a systematic investigation of the influence of polarization effects from a surrounding medium on the excitation energies of a chromophore. We use a combined molecular dynamics and polarizable embedding time-dependent density functional theory (PE-TD-DFT) approach for chromophores in pr...

Dynamic nuclear polarization of nucleic acid with endogenously bound manganese

International Nuclear Information System (INIS)

Wenk, Patricia; Kaushik, Monu; Richter, Diane; Vogel, Marc; Suess, Beatrix; Corzilius, Björn

2015-01-01

We report the direct dynamic nuclear polarization (DNP) of 13 C nuclei of a uniformly [ 13 C, 15 N]-labeled, paramagnetic full-length hammerhead ribozyme (HHRz) complex with Mn 2+ where the enhanced polarization is fully provided by the endogenously bound metal ion and no exogenous polarizing agent is added. A 13 C enhancement factor of ε = 8 was observed by intra-complex DNP at 9.4 T. In contrast, “conventional” indirect and direct DNP experiments were performed using AMUPol as polarizing agent where we obtained a 1 H enhancement factor of ε ≈ 250. Comparison with the diamagnetic (Mg 2+ ) HHRz complex shows that the presence of Mn 2+ only marginally influences the (DNP-enhanced) NMR properties of the RNA. Furthermore two-dimensional correlation spectra ( 15 N– 13 C and 13 C– 13 C) reveal structural inhomogeneity in the frozen, amorphous state indicating the coexistence of several conformational states. These demonstrations of intra-complex DNP using an endogenous metal ion as well as DNP-enhanced MAS NMR of RNA in general yield important information for the development of new methods in structural biology

Molecular dynamics with deterministic and stochastic numerical methods

CERN Document Server

Leimkuhler, Ben

2015-01-01

This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications.  Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...

High-Frequency Dynamic Nuclear Polarization in the Nuclear Rotating Frame

DEFF Research Database (Denmark)

Farrar, C. T.; Hall, D. A.; Gerfen, G. J.

2000-01-01

A proton dynamic nuclear polarization (DNP) NMR signal enhancement (ϵ) close to thermal equilibrium, ϵ = 0.89, has been obtained at high field (B0 = 5 T, νepr = 139.5 GHz) using 15 mM trityl radical in a 40:60 water/glycerol frozen solution at 11 K. The electron-nuclear polarization transfer...... is performed in the nuclear rotating frame with microwave irradiation during a nuclear spin-lock pulse. The growth of the signal enhancement is governed by the rotating frame nuclear spin–lattice relaxation time (T1ρ), which is four orders of magnitude shorter than the nuclear spin–lattice relaxation time (T1n......). Due to the rapid polarization transfer in the nuclear rotating frame the experiment can be recycled at a rate of 1/T1ρ and is not limited by the much slower lab frame nuclear spin–lattice relaxation rate (1/T1n). The increased repetition rate allowed in the nuclear rotating frame provides an effective...

Quantum master equation method based on the broken-symmetry time-dependent density functional theory: application to dynamic polarizability of open-shell molecular systems.

Science.gov (United States)

Kishi, Ryohei; Nakano, Masayoshi

2011-04-21

A novel method for the calculation of the dynamic polarizability (α) of open-shell molecular systems is developed based on the quantum master equation combined with the broken-symmetry (BS) time-dependent density functional theory within the Tamm-Dancoff approximation, referred to as the BS-DFTQME method. We investigate the dynamic α density distribution obtained from BS-DFTQME calculations in order to analyze the spatial contributions of electrons to the field-induced polarization and clarify the contributions of the frontier orbital pair to α and its density. To demonstrate the performance of this method, we examine the real part of dynamic α of singlet 1,3-dipole systems having a variety of diradical characters (y). The frequency dispersion of α, in particular in the resonant region, is shown to strongly depend on the exchange-correlation functional as well as on the diradical character. Under sufficiently off-resonant condition, the dynamic α is found to decrease with increasing y and/or the fraction of Hartree-Fock exchange in the exchange-correlation functional, which enhances the spin polarization, due to the decrease in the delocalization effects of π-diradical electrons in the frontier orbital pair. The BS-DFTQME method with the BHandHLYP exchange-correlation functional also turns out to semiquantitatively reproduce the α spectra calculated by a strongly correlated ab initio molecular orbital method, i.e., the spin-unrestricted coupled-cluster singles and doubles.

Molecular ions, Rydberg spectroscopy and dynamics

International Nuclear Information System (INIS)

Jungen, Ch.

2015-01-01

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

Molecular ions, Rydberg spectroscopy and dynamics

Energy Technology Data Exchange (ETDEWEB)

Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

2015-01-22

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

Effect of driving voltage polarity on dynamic response characteristics of electrowetting liquid lens

Science.gov (United States)

Na, Xie; Ning, Zhang; Rong-Qing, Xu

2018-05-01

A test device is developed for studying the dynamic process of an electrowetting liquid lens. By analyzing the light signals through the liquid lens, the dynamical properties of the lens are investigated. In our experiment, three types of pulse, i.e., sine, bipolar pulse, and single pulse signals, are employed to drive the liquid lens, and the dynamic characteristics of the lens are subsequently analyzed. The results show that the positive and negative polarities of the driving voltage can cause a significant difference in the response of the liquid lens; meanwhile, the lens’s response to the negative polarity of the driving voltage is clearer. We use the theory of charge restraint to explain this phenomenon, and it is concluded that the negative ions are more easily restrained by a dielectric layer. This work gives direct guidance for practical applications based on an electrowetting liquid lens.

Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

Directory of Open Access Journals (Sweden)

Renata De Paris

2015-01-01

Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

Fast, high-fidelity, all-optical and dynamically-controlled polarization gate using room-temperature atomic vapor

Energy Technology Data Exchange (ETDEWEB)

Li, Runbing [National Institute of Standards and Technology, Gaithersburg, Maryland 20899 (United States); State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China); Center for Cold Atom Physics, Chinese Academy of Sciences, Wuhan 430071 (China); Zhu, Chengjie [National Institute of Standards and Technology, Gaithersburg, Maryland 20899 (United States); School of Physics Science and Engineering, Tongji University, Shanghai 200092 (China); Deng, L.; Hagley, E. W. [National Institute of Standards and Technology, Gaithersburg, Maryland 20899 (United States)

2014-10-20

We demonstrate a fast, all-optical polarization gate in a room-temperature atomic medium. Using a Polarization-Selective-Kerr-Phase-Shift (PSKPS) technique, we selectively write a π phase shift to one circularly-polarized component of a linearly-polarized input signal field. The output signal field maintains its original strength but acquires a 90° linear polarization rotation, demonstrating fast, high-fidelity, dynamically-controlled polarization gate operation. The intensity of the polarization-switching field used in this PKSPK-based polarization gate operation is only 2 mW/cm{sup 2}, which would be equivalent to 0.5 nW of light power (λ = 800 nm) confined in a typical commercial photonic hollow-core fiber. This development opens a realm of possibilities for potential future extremely low light level telecommunication and information processing systems.

Haber Process Made Efficient by Hydroxylated Graphene: Ab Initio Thermochemistry and Reactive Molecular Dynamics.

Science.gov (United States)

Chaban, Vitaly V; Prezhdo, Oleg V

2016-07-07

The Haber-Bosch process is the main industrial method for producing ammonia from diatomic nitrogen and hydrogen. We use a combination of ab initio thermochemical analysis and reactive molecular dynamics to demonstrate that a significant increase in the ammonia production yield can be achieved using hydroxylated graphene and related species. Exploiting the polarity difference between N2/H2 and NH3, as well as the universal proton acceptor behavior of NH3, we demonstrate a strong shift of the equilibrium of the Haber-Bosch process toward ammonia (ca. 50 kJ mol(-1) enthalpy gain and ca. 60-70 kJ mol(-1) free energy gain). The modified process is of significant importance to the chemical industry.

X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.

Science.gov (United States)

Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G; Gao, Jiali

2009-02-17

A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Å(3), and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born-Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from -0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible.

Interfacial polarization phenomena in organic molecular films

International Nuclear Information System (INIS)

Iwamoto, Mitsumasa; Manaka, Takaaki

2006-01-01

Electrostatic phenomena occurring at the interface between metal/organic and organic/organic materials are discussed from the viewpoint of dielectrics physics. Focusing on two important origins of surface polarization phenomena, orientational ordering of polar molecules and displacement of excess charges at the interface, surface polarization phenomena of organic thin films are discussed. To define the orientational order of polar molecules, orientational order parameters are introduced, and surface polarization due to the alignment of dipoles is expressed. The generation of Maxwell displacement current (MDC) and optical second harmonic generation (SHG) that are specific for surface organic monomolecular films are discussed, and some experimental evidence are shown. As an extension of the concept of surface Fermi level introduced to discuss the electrostatic phenomena due to electron transfer at the interface between metal-organic insulators, the surface Fermi level is extended to the discussion on the electrostatic phenomena of organic semiconductor materials on metals. In this paper, some experimental evidence of surface polarization originating from polar molecules and displacement of excess charges are shown. After that, with consideration of these surface phenomena, single electron tunneling of organic films are briefly discussed in association with surface polarization phenomena

A fermionic molecular dynamics technique to model nuclear matter

International Nuclear Information System (INIS)

Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

2009-01-01

Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)

Dynamical photo-induced electronic properties of molecular junctions

Science.gov (United States)

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.

Dynamical processes in atomic and molecular physics

CERN Document Server

Ogurtsov, Gennadi

2012-01-01

Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece

Theory and application of quantum molecular dynamics

CERN Document Server

Zeng Hui Zhang, John

1999-01-01

This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli

Dynamics and Thermodynamics of Molecular Machines

DEFF Research Database (Denmark)

Golubeva, Natalia

2014-01-01

to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...

Spin Dynamics in Highly Spin Polarized Co1-xFexS2

Science.gov (United States)

Hoch, Michael J. R.; Kuhns, Philip L.; Moulton, William G.; Reyes, Arneil P.; Lu, Jun; Wang, Lan; Leighton, Chris

2006-09-01

Highly spin polarized or half-metallic systems are of considerable current interest because of their potential for spin injection in spintronics applications. The ferromagnet (FM) CoS2 is close to being a half-metal. Recent theoretical and experimental work has shown that the alloys Co1-xFexS2 (0.07 < x < 0.9) are highly spin polarized at low temperatures. The Fe concentration may be used to tune the spin polarization. Using 59Co FM- NMR we have investigated the spin dynamics in this family of alloys and have obtained information on the evolution of the d-band density of states at the Fermi level with x in the range 0 to 0.3. The results are compared with available theoretical predictions.

Molecular dynamics simulations of ter-pyridine, BTP, and their complexes with La3+, Eu3+ and Lu3+

International Nuclear Information System (INIS)

Guilbaud, P.; Dognon, J.P.

2000-01-01

This poster presents molecular dynamics simulations performed to study ter-pyridine and bis-triazinyl-pyridine with lanthanide cations for the gas phase and for water solution. Different counter-ions have been tested in order to assess their influence on complexes structures and stabilities in both phases. For stable complexes, Gibbs free energy calculations have been achieved to estimate the selectivity of these complexes towards the lanthanide cations. Finally, some tests have been done adding a polarization term in the potential energy in order to have a more precise description of interaction energies. (authors)

Multiple time step integrators in ab initio molecular dynamics

International Nuclear Information System (INIS)

Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

2014-01-01

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

Charge-Transfer States in Organic Solar Cells: Understanding the Impact of Polarization, Delocalization, and Disorder

KAUST Repository

Zheng, Zilong; Tummala, Naga Rajesh; Fu, Yao-Tsung; Coropceanu, Veaceslav; Bredas, Jean-Luc

2017-01-01

pentacene molecules and three C60 molecules allows us to take explicitly into account the electronic polarization effects. These complexes are extracted from a bilayer architecture modeled by molecular dynamics simulations and evaluated by means

Molecular thermodynamics of nonideal fluids

CERN Document Server

Lee, Lloyd L

2013-01-01

Molecular Thermodynamics of Nonideal Fluids serves as an introductory presentation for engineers to the concepts and principles behind and the advances in molecular thermodynamics of nonideal fluids. The book covers related topics such as the laws of thermodynamics; entropy; its ensembles; the different properties of the ideal gas; and the structure of liquids. Also covered in the book are topics such as integral equation theories; theories for polar fluids; solution thermodynamics; and molecular dynamics. The text is recommended for engineers who would like to be familiarized with the concept

Cluster formation restricts dynamic nuclear polarization of xenon in solid mixtures

DEFF Research Database (Denmark)

Kuzma, N. N.; Pourfathi, M.; Kara, H.

2012-01-01

During dynamic nuclear polarization (DNP) at 1.5 K and 5 T, Xe-129 nuclear magnetic resonance (NMR) spectra of a homogeneous xenon/1-propanol/trityl-radical solid mixture exhibit a single peak, broadened by H-1 neighbors. A second peak appears upon annealing for several hours at 125 K. Its...

Dynamic nuclear polarization of nucleic acid with endogenously bound manganese

Energy Technology Data Exchange (ETDEWEB)

Wenk, Patricia [University of Tübingen, Werner Siemens Imaging Center and Department of Preclinical Imaging and Radiopharmacy (Germany); Kaushik, Monu; Richter, Diane [Goethe University, Institute of Physical und Theoretical Chemistry, Institute of Biophysical Chemistry und Center for Biomolecular Magnetic Resonance (BMRZ) (Germany); Vogel, Marc; Suess, Beatrix [Technical University Darmstadt, Department of Biology (Germany); Corzilius, Björn, E-mail: corzilius@em.uni-frankfurt.de [Goethe University, Institute of Physical und Theoretical Chemistry, Institute of Biophysical Chemistry und Center for Biomolecular Magnetic Resonance (BMRZ) (Germany)

2015-09-15

We report the direct dynamic nuclear polarization (DNP) of {sup 13}C nuclei of a uniformly [{sup 13}C,{sup 15}N]-labeled, paramagnetic full-length hammerhead ribozyme (HHRz) complex with Mn{sup 2+} where the enhanced polarization is fully provided by the endogenously bound metal ion and no exogenous polarizing agent is added. A {sup 13}C enhancement factor of ε = 8 was observed by intra-complex DNP at 9.4 T. In contrast, “conventional” indirect and direct DNP experiments were performed using AMUPol as polarizing agent where we obtained a {sup 1}H enhancement factor of ε ≈ 250. Comparison with the diamagnetic (Mg{sup 2+}) HHRz complex shows that the presence of Mn{sup 2+} only marginally influences the (DNP-enhanced) NMR properties of the RNA. Furthermore two-dimensional correlation spectra ({sup 15}N–{sup 13}C and {sup 13}C–{sup 13}C) reveal structural inhomogeneity in the frozen, amorphous state indicating the coexistence of several conformational states. These demonstrations of intra-complex DNP using an endogenous metal ion as well as DNP-enhanced MAS NMR of RNA in general yield important information for the development of new methods in structural biology.

Dynamic signature of molecular association in methanol

International Nuclear Information System (INIS)

Bertrand, C. E.; Copley, J. R. D.; Faraone, A.; Self, J. L.

2016-01-01

Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD 3 OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.

Molecular dynamics for fermions

International Nuclear Information System (INIS)

Feldmeier, H.; Schnack, J.

2000-02-01

The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)

Pattern recognition in molecular dynamics. [FORTRAN

Energy Technology Data Exchange (ETDEWEB)

Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)

1977-07-01

An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.

Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel

DEFF Research Database (Denmark)

Bjelkmar, Pär; Niemelä, Perttu S; Vattulainen, Ilpo

2009-01-01

transitions occur in membrane proteins-not to mention numerous applications in drug design. Here, we present a full 1 micros atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements......Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how...... and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations....

Dynamic polarization in paramagnetic solids and microscopic correlation functions

International Nuclear Information System (INIS)

Boucher, Jean-Paul

1972-01-01

The different effects of Dynamic Nuclear Polarization in paramagnetic solids are described by means of a single thermodynamic formalism. In the case of large exchange interactions, the Overhauser effect correlated with nuclear relaxation time measurements can provide a way of studying correlation functions between electronic spins. This method is used to study the low-frequency behaviour of the microscopic spectral density which should diverge as ω → 0, in the case of a linear exchange chain. (author) [fr

The Venus Emissivity Mapper - Investigating the Atmospheric Structure and Dynamics of Venus' Polar Region

Science.gov (United States)

Widemann, T.; Marcq, E.; Tsang, C.; Mueller, N. T.; Kappel, D.; Helbert, J.; Dyar, M. D.; Smrekar, S. E.

2017-12-01

Venus' climate evolution is driven by the energy balance of its global cloud layers. Venus displays the best-known case of polar vortices evolving in a fast-rotating atmosphere. Polar vortices are pervasive in the Solar System and may also be present in atmosphere-bearing exoplanets. While much progress has been made since the early suggestion that the Venus clouds are H2O-H2SO4 liquid droplets (Young 1973), several cloud parameters are still poorly constrained, particularly in the lower cloud layer and optically thicker polar regions. The average particle size is constant over most of the planet but increases toward the poles. This indicates that cloud formation processes are different at latitudes greater than 60°, possibly as a result of the different dynamical regimes that exist in the polar vortices (Carlson et al. 1993, Wilson et al. 2008, Barstow et al. 2012). Few wind measurements exist in the polar region due to unfavorable viewing geometry of currently available observations. Cloud-tracking data indicate circumpolar circulation close to solid-body rotation. E-W winds decrease to zero velocity close to the pole. N-S circulation is marginal, with extremely variable morphology and complex vorticity patterns (Sanchez-Lavega et al. 2008, Luz et al. 2011, Garate-Lopez et al. 2013). The Venus Emissivity Mapper (VEM; Helbert et al., 2016) proposed for NASA's Venus Origins Explorer (VOX) and the ESA M5/EnVision orbiters has the capability to better constrain the microphysics (vertical, horizontal, time dependence of particle size distribution, or/and composition) of the lower cloud particles in three spectral bands at 1.195, 1.310 and 1.510 μm at a spatial resolution of 10 km. Circular polar orbit geometry would provide an unprecedented study of both polar regions within the same mission. In addition, VEM's pushbroom method will allow short timescale cloud dynamics to be assessed, as well as local wind speeds, using repeated imagery at 90 minute intervals

Crystallography and Molecular Arrangement of Polymorphic Monolayer J-Aggregates of a Cyanine Dye: Multiangle Polarized Light Fluorescence Optical Microscopy Study.

Science.gov (United States)

Prokhorov, Valery V; Pozin, Sergey I; Perelygina, Olga M; Mal'tsev, Eugene I

2018-04-24

The molecular orientation in monolayer J-aggregates of 3,3-di(γ-sulfopropyl)-5,5-dichlorotiamonomethinecyanine dye has been precisely estimated using improved linear polarization measurements in the fluorescence microscope in which a multiangle set of polarization data is obtained using sample rotation. The estimated molecular orientation supplemented with the previously established crystallographic constraints based on the analysis of the well-developed two-dimensional J-aggregate shapes unambiguously indicate the staircase type of molecular arrangement for striplike J-aggregates with the staircases oriented along strips. The molecular transition dipoles are inclined at an angle of ∼25° to the strip direction, whereas the characteristic strip vertex angle ∼45° is formed by the [100] and [1-10] directions of the monoclinic unit cell. Measurements of the geometry of partially unwound tubes and their polarization properties support the model of tube formation by close-packed helical winding of flexible monolayer strips. In the tubes, the long molecular axes are oriented at a small angle in the range of 5-15° to the normal to the tube axis providing low bending energy. At a nanoscale, high-resolution atomic force microscopy imaging of J-aggregate monolayers reveals a complex quasi-one-dimensional organization.

Pulsed recording of anisotropy and holographic polarization gratings in azo-polymethacrylates with different molecular architectures

DEFF Research Database (Denmark)

Forcén, Patricia; Oriol, Luis; Alcala, Rafael

2008-01-01

Recording of anisotropy and holographic polarization gratings using 532 nm, 4 ns light pulses has been carried out in thin films of polymers with the same azobenzene content (20 wt %) and different molecular architectures. Random and block copolymers comprising azobenzene and methylmethacrylate (...

Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

Institute of Scientific and Technical Information of China (English)

Chengzhen Sun; Bofeng Bai

2017-01-01

Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

Using polarized Raman spectroscopy and the pseudospectral method to characterize molecular structure and function

Science.gov (United States)

Weisman, Andrew L.

Electronic structure calculation is an essential approach for determining the structure and function of molecules and is therefore of critical interest to physics, chemistry, and materials science. Of the various algorithms for calculating electronic structure, the pseudospectral method is among the fastest. However, the trade-off for its speed is more up-front programming and testing, and as a result, applications using the pseudospectral method currently lag behind those using other methods. In Part I of this dissertation, we first advance the pseudospectral method by optimizing it for an important application, polarized Raman spectroscopy, which is a well-established tool used to characterize molecular properties. This is an application of particular importance because often the easiest and most economical way to obtain the polarized Raman spectrum of a material is to simulate it; thus, utilization of the pseudospectral method for this purpose will accelerate progress in the determination of molecular properties. We demonstrate that our implementation of Raman spectroscopy using the pseudospectral method results in spectra that are just as accurate as those calculated using the traditional analytic method, and in the process, we derive the most comprehensive formulation to date of polarized Raman intensity formulas, applicable to both crystalline and isotropic systems. Next, we apply our implementation to determine the orientations of crystalline oligothiophenes -- a class of materials important in the field of organic electronics -- achieving excellent agreement with experiment and demonstrating the general utility of polarized Raman spectroscopy for the determination of crystal orientation. In addition, we derive from first-principles a method for using polarized Raman spectra to establish unambiguously whether a uniform region of a material is crystalline or isotropic. Finally, we introduce free, open-source software that allows a user to determine any of a

Classical and quantum molecular dynamics in NMR spectra

CERN Document Server

Szymański, Sławomir

2018-01-01

The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

The molecular orientation of CO on Pd(1 1 1): a polarization-dependent SFG study

Science.gov (United States)

Galletto, Paolo; Unterhalt, Holger; Rupprechter, Günther

2003-01-01

The molecular orientation of carbon monoxide adsorbed on Pd(1 1 1) was examined by sum frequency generation (SFG) vibrational spectroscopy utilizing different polarization combinations of the visible and SFG light. This allows to determine the CO tilt angle with respect to the substrate, provided that a proper optical model for the interface can be defined. It is demonstrated that it is essential to invoke the βaac hyperpolarizability into the analysis and that polarization-dependent SFG of CO/Pd(1 1 1) yields information on βaac/ βccc rather than the tilt angle.

Hyperchaotic Dynamics for Light Polarization in a Laser Diode

Science.gov (United States)

Bonatto, Cristian

2018-04-01

It is shown that a highly randomlike behavior of light polarization states in the output of a free-running laser diode, covering the whole Poincaré sphere, arises as a result from a fully deterministic nonlinear process, which is characterized by a hyperchaotic dynamics of two polarization modes nonlinearly coupled with a semiconductor medium, inside the optical cavity. A number of statistical distributions were found to describe the deterministic data of the low-dimensional nonlinear flow, such as lognormal distribution for the light intensity, Gaussian distributions for the electric field components and electron densities, Rice and Rayleigh distributions, and Weibull and negative exponential distributions, for the modulus and intensity of the orthogonal linear components of the electric field, respectively. The presented results could be relevant for the generation of single units of compact light source devices to be used in low-dimensional optical hyperchaos-based applications.

Multiscale equation-free algorithms for molecular dynamics

Science.gov (United States)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

Dynamics of cell polarity in tissue morphogenesis: a comparative view from Drosophila and Ciona [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Michael T. Veeman

2016-06-01

Full Text Available Tissues in developing embryos exhibit complex and dynamic rearrangements that shape forming organs, limbs, and body axes. Directed migration, mediolateral intercalation, lumen formation, and other rearrangements influence the topology and topography of developing tissues. These collective cell behaviors are distinct phenomena but all involve the fine-grained control of cell polarity. Here we review recent findings in the dynamics of polarized cell behavior in both the Drosophila ovarian border cells and the Ciona notochord. These studies reveal the remarkable reorganization of cell polarity during organ formation and underscore conserved mechanisms of developmental cell polarity including the Par/atypical protein kinase C (aPKC and planar cell polarity pathways. These two very different model systems demonstrate important commonalities but also key differences in how cell polarity is controlled in tissue morphogenesis. Together, these systems raise important, broader questions on how the developmental control of cell polarity contributes to morphogenesis of diverse tissues across the metazoa.

Ferroelectric Polarization Switching Dynamics and Domain Growth of Triglycine Sulfate and Imidazolium Perchlorate

KAUST Repository

Ma, He

2016-04-10

The weak bond energy and large anisotropic domain wall energy induce many special characteristics of the domain nucleation, growth, and polarization switch in triglycine sulfate (TGS) and imidazolium perchlorate (IM), two typical molecular ferroelectrics. Their domain nucleation and polarization switch are rather slower than those of conventional oxide ferroelectrics, which may be due to the weaker bond energy of hydrogen bond or van der Waals bond than that of ionic bond. These chemical bonds dominate the elastic energy, with the latter being an important component of domain wall energy and playing an important role in domain nucleation and domain growth. The ratio of anisotropic domain wall energy to Gibbs free energy is large in TGS and IM, which allows a favorable domain shape and a special domain evolution under a certain electric field. Therefore, this study not only sheds light on the physical nature but also indicates the application direction for molecular ferroelectrics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Scalable Molecular Dynamics for Large Biomolecular Systems

Directory of Open Access Journals (Sweden)

Robert K. Brunner

2000-01-01

Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

Resonances in field-cycling NMR on molecular crystals. (reversible) Spin dynamics or (irreversible) relaxation?; Resonanzen in Field-Cycling-NMR an Molekuelkristallen. (reversible) Spindynamik oder (irreversible) Relaxation?

Energy Technology Data Exchange (ETDEWEB)

Tacke, Christian

2015-07-01

Multi spin systems with spin 1/2 nuclei and dipolar coupled quadrupolar nuclei can show so called ''quadrupolar dips''. There are two main reasons for this behavior: polarization transfer and relaxation. They look quite alike and without additional research cannot be differentiated easily in most cases. These two phenomena have quite different physical and theoretical backgrounds. For no or very slow dynamics, polarization transfer will take place, which is energy conserving inside the spin system. This effect can entirely be described using quantum mechanics on the spin system. Detailed knowledge about the crystallography is needed, because this affects the relevant hamiltonians directly. For systems with fast enough dynamics, relaxation takes over, and the energy flows from the spin system to the lattice; thus a more complex theoretical description is needed. This description has to include a dynamic model, usually in the form of a spectral density function. Both models should include detailed modelling of the complete spin system. A software library was developed to be able to model complex spin systems. It allows to simulate polarization transfer or relaxation effects. NMR measurements were performed on the protonic conductor K{sub 3}H(SO{sub 4}){sub 2}. A single crystal shows sharp quadrupolar dips at room temperature. Dynamics could be excluded using relaxation measurements and literature values. Thus, a polarization transfer analysis was used to describe those dips with good agreement. As a second system, imidazolium based molecular crystals were analyzed. The quadrupolar dips were expected to be caused by polarization transfer; this was carefully analyzed and found not to be true. A relaxation based analysis shows good agreement with the measured data in the high temperature area. It leverages a two step spectral density function, which indicates two distinct dynamic processes happening in this system.

Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

Science.gov (United States)

Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

2015-05-01

Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

Idealized numerical modeling of polar mesocyclones dynamics diagnosed by energy budget

Science.gov (United States)

Sergeev, Dennis; Stepanenko, Victor

2014-05-01

Polar mesocyclones (MC) refer to a wide class of mesoscale vortices occuring poleward of the main polar front [1]. Their subtype - polar low - is commonly known for its intensity, that can result in windstorm damage of infrastructure in high latitudes. The observational data sparsity and the small size of polar MCs are major limitations for the clear understanding and numerical prediction of the evolution of these objects. The origin of polar MCs is still a matter of uncertainty, though the recent numerical investigations have exposed a strong dependence of the polar mesocyclone development upon the magnitude of baroclinicity and upon the water vapor concentration in the atmosphere. However, most of the previous studies focused on the individual polar low (the so-called case studies), with too many factors affecting it simultaneously and none of them being dominant in polar MC generation. This study focuses on the early stages of polar MC development within an idealized numerical experiments with mesoscale atmospheric model, where it is possible to look deeper into each single physical process. Our aim is to explain the role of such mechanisms as baroclinic instability or diabatic heating by comparing their contribution to the structure and dynamics of the vortex. The baroclinic instability, as reported by many researchers [2], can be a crucial factor in a MC's life cycle, especially in polar regions. Besides the baroclinic instability several diabatic processes can contribute to the energy generation that fuels a polar mesocyclone. One of the key energy sources in polar regions is surface heat fluxes. The other is the moisture content in the atmosphere that can affect the development of the disturbance by altering the latent heat release. To evaluate the relative importance of the diabatic and baroclinic energy sources for the development of the polar mesocyclone we apply energy diagnostics. In other words, we examine the rate of change of the kinetic energy (that

Lagrangian dynamics of spinning particles and polarized media in general relativity

International Nuclear Information System (INIS)

Bailey, Ian.

1980-01-01

The dynamic laws governing spinning multipole test particles and polarized media with internal spin are derived from both variational principles and the multipole formalism of extended bodies. The general form of the Lagrangian equations of motion is derived for a spinning multipole particle in given external fields. The author then considers the dynamics of a continuous medium with internal spin and multipole structure. From a four-dimensional action integral the field equations relating to fields generated by the medium to its bulk properties are derived, together with the balance laws expressing conservation of total four-momentum and spin. A natural splitting of the total energy-momentum tensor into matter and field parts is adopted that leads to a generalized Minkowski electromagnetic energy tensor. In both the electromagnetic and the gravitational field equations the source terms contain polarization contributions. It is shown that the multipole formalism may be used to formulate the same equations of motion, balance laws and decomposition of total energy-momentum as those resulting from variational principles

Theory of attosecond delays in molecular photoionization.

Science.gov (United States)

Baykusheva, Denitsa; Wörner, Hans Jakob

2017-03-28

We present a theoretical formalism for the calculation of attosecond delays in molecular photoionization. It is shown how delays relevant to one-photon-ionization, also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole matrix elements provided by molecular quantum scattering theory. These results are used to derive formulae for the delays measured by two-photon attosecond interferometry based on an attosecond pulse train and a dressing femtosecond infrared pulse. These effective delays are first expressed in the molecular frame where maximal information about the molecular photoionization dynamics is available. The effects of averaging over the emission direction of the electron and the molecular orientation are introduced analytically. We illustrate this general formalism for the case of two polyatomic molecules. N 2 O serves as an example of a polar linear molecule characterized by complex photoionization dynamics resulting from the presence of molecular shape resonances. H 2 O illustrates the case of a non-linear molecule with comparably simple photoionization dynamics resulting from a flat continuum. Our theory establishes the foundation for interpreting measurements of the photoionization dynamics of all molecules by attosecond metrology.

Molecular quantum dynamics. From theory to applications

International Nuclear Information System (INIS)

Gatti, Fabien

2014-01-01

An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the

Molecular quantum dynamics. From theory to applications

Energy Technology Data Exchange (ETDEWEB)

Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253

2014-09-01

An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible

Frozen Acrylamide Gels as Dynamic Nuclear Polarization Matrices.

KAUST Repository

Viger-Gravel, Jasmine; Berruyer, Pierrick; Gajan, David; Basset, Jean-Marie; Lesage, Anne; Tordo, Paul; Ouari, Olivier; Emsley, Lyndon

2017-01-01

We show that aqueous acrylamide gels can be used to provide dynamic nuclear polarization (DNP) NMR signal enhancements of around 200 at 9.4 T and 100 K. The enhancements are shown to increase with cross linker concentration and low concentrations of the AMUPol biradical. We show that this DNP matrix can be used in situations where conventional incipient wetness methods fail, such as to obtain DNP surface enhanced NMR spectra from inorganic nanoparticles. In particular, we obtain 113Cd spectra from CdTe-COOH NPs in minutes. The spectra clearly indicate a highly-disordered cadmium rich surface.

Frozen Acrylamide Gels as Dynamic Nuclear Polarization Matrices.

KAUST Repository

Viger-Gravel, Jasmine

2017-05-24

We show that aqueous acrylamide gels can be used to provide dynamic nuclear polarization (DNP) NMR signal enhancements of around 200 at 9.4 T and 100 K. The enhancements are shown to increase with cross linker concentration and low concentrations of the AMUPol biradical. We show that this DNP matrix can be used in situations where conventional incipient wetness methods fail, such as to obtain DNP surface enhanced NMR spectra from inorganic nanoparticles. In particular, we obtain 113Cd spectra from CdTe-COOH NPs in minutes. The spectra clearly indicate a highly-disordered cadmium rich surface.

Excited-state molecular photoionization dynamics

International Nuclear Information System (INIS)

Pratt, S.T.

1995-01-01

This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)

Symmetry of quantum molecular dynamics

International Nuclear Information System (INIS)

Burenin, A.V.

2002-01-01

The paper reviews the current state-of-art in describing quantum molecular dynamics based on symmetry principles alone. This qualitative approach is of particular interest as the only method currently available for a broad and topical class of problems in the internal dynamics of molecules. Besides, a molecule is a physical system whose collective internal motions are geometrically structured, and its perturbation theory description requires a symmetry analysis of this structure. The nature of the geometrical symmetry groups crucial for the closed formulation of the qualitative approach is discussed [ru

Molecular dynamics modeling of polymer flammability

International Nuclear Information System (INIS)

Nyden, M.R.; Brown, J.E.; Lomakin, S.M.

1992-01-01

Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)

Electron-nuclear dynamics of molecular systems

International Nuclear Information System (INIS)

Diz, A.; Oehrn, Y.

1994-01-01

The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

Science.gov (United States)

Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

2015-04-21

Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

Magnetic Switching of a Single Molecular Magnet due to Spin-Polarized Current

OpenAIRE

Misiorny, Maciej; Barnas, Józef

2006-01-01

Magnetic switching of a single molecular magnet (SMM) due to spin-polarized current flowing between ferromagnetic metallic electrodes is investigated theoretically. Magnetic moments of the electrodes are assumed to be collinear and parallel to the magnetic easy axis of the molecule. Electrons tunneling through a barrier between magnetic leads are coupled to the SMM via exchange interaction. The current flowing through the system as well as the spin relaxation times of the SMM are calculated f...

Dynamics of molecular superrotors in an external magnetic field

Science.gov (United States)

Korobenko, Aleksey; Milner, Valery

2015-08-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

International Nuclear Information System (INIS)

Balliou, A.; Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N.; Tsikritzis, D.; Kennou, S.

2014-01-01

In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW 12 O 40 3− , as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

Observation of strongly forbidden solid effect dynamic nuclear polarization transitions via electron-electron double resonance detected NMR

Energy Technology Data Exchange (ETDEWEB)

Smith, Albert A.; Corzilius, Björn; Haze, Olesya; Swager, Timothy M.; Griffin, Robert G., E-mail: rgg@mit.edu [Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

2013-12-07

We present electron paramagnetic resonance experiments for which solid effect dynamic nuclear polarization transitions were observed indirectly via polarization loss on the electron. This use of indirect observation allows characterization of the dynamic nuclear polarization (DNP) process close to the electron. Frequency profiles of the electron-detected solid effect obtained using trityl radical showed intense saturation of the electron at the usual solid effect condition, which involves a single electron and nucleus. However, higher order solid effect transitions involving two, three, or four nuclei were also observed with surprising intensity, although these transitions did not lead to bulk nuclear polarization—suggesting that higher order transitions are important primarily in the transfer of polarization to nuclei nearby the electron. Similar results were obtained for the SA-BDPA radical where strong electron-nuclear couplings produced splittings in the spectrum of the indirectly observed solid effect conditions. Observation of high order solid effect transitions supports recent studies of the solid effect, and suggests that a multi-spin solid effect mechanism may play a major role in polarization transfer via DNP.

Correlated, Static and Dynamic Polarizabilities of Small Molecules. Comparison of Four "Black Box" Methods

DEFF Research Database (Denmark)

Dalskov, Erik K.; Sauer, Stephan P. A.

1998-01-01

Molecular static and dynamic polarizabilities for thirteen small molecules have been calculated using four "black box" ab initio methods, the random phase approximation, RPA, the second-order polarization propagator approximation, SOPPA, the second-order polarization propagator approximation...

Anandamide-ceramide interactions in a membrane environment: Molecular dynamic simulations data.

Science.gov (United States)

Di Scala, Coralie; Mazzarino, Morgane; Yahi, Nouara; Varini, Karine; Garmy, Nicolas; Fantini, Jacques; Chahinian, Henri

2017-10-01

Anandamide is a lipid neurotransmitter that interacts with various plasma membrane lipids. The data here consists of molecular dynamics simulations of anandamide, C18-ceramide and cholesterol performed in vacuo and within a hydrated palmitoyl-oleoyl-phosphatidylcholine (POPC)/cholesterol membrane. Several models of anandamide/cholesterol and anandamide/ceramide complexes are presented. The energy of interaction and the nature of the intermolecular forces involved in each of these complexes are detailed. The impact of water molecules hydrating the POPC/cholesterol membrane for the stability of the anandamide/cholesterol and anandamide/ceramide complexes is also analyzed. From a total number of 1920 water molecules stochatiscally merged with the lipid matrix, 48 were eventually redistributed around the polar head groups of the anandamide/ceramide complex, whereas only 15 reached with the anandamide/cholesterol complex. The interpretation of this dataset is presented in the accompanying article "Ceramide binding to anandamide increases its half-life and potentiates its cytotoxicity in human neuroblastoma cells" [1].

Expansion and Polarity Sorting in Microtubule-Dynein Bundles(WHAT IS LIFE? THE NEXT 100 YEARS OF YUKAWA'S DREAM)

OpenAIRE

Assaf, ZEMEL; Alex, MOGILNER; Department of Neurobiology, Physiology and Behavior, University of California; Department of Neurobiology, Physiology and Behavior, University of California

2008-01-01

Interactions of multiple molecular motors with dynamic polymers, such as actin and microtubules, form the basis for many processes in the cell cytoskeleton. One example is the active 'sorting' of microtubule bundles by dynein molecular motors into aster-like arrays of microtubules; in these bundles dynein motors cross-link and slide neighboring microtubules apart. A number of models have been suggested to quantify the active dynamics of cross-linked bundles of polar filaments. In the case of ...

Molecular dynamics simulations of the structure and single-particle dynamics of mixtures of divalent salts and ionic liquids

Energy Technology Data Exchange (ETDEWEB)

Gómez-González, Víctor; Docampo-Álvarez, Borja; Gallego, Luis J.; Varela, Luis M., E-mail: luismiguel.varela@usc.es [Grupo de Nanomateriais e Materia Branda, Departamento de Física da Materia Condensada, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela (Spain); Cabeza, Oscar [Facultade de Ciencias, Universidade da Coruña, Campus A Zapateira s/n, E-15008 A Coruña (Spain); Fedorov, Maxim [Department of Physics, Scottish University Physics Alliance (SUPA), University of Strathclyde, John Anderson Bldg., 107 Rottenrow East, Glasgow G4 0NG (United Kingdom); Lynden-Bell, Ruth M. [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)

2015-09-28

We report a molecular dynamics study of the structure and single-particle dynamics of mixtures of a protic (ethylammonium nitrate) and an aprotic (1-butyl-3-methylimidazolium hexaflurophosphate [BMIM][PF{sub 6}]) room-temperature ionic liquids doped with magnesium and calcium salts with a common anion at 298.15 K and 1 atm. The solvation of these divalent cations in dense ionic environments is analyzed by means of apparent molar volumes of the mixtures, radial distribution functions, and coordination numbers. For the protic mixtures, the effect of salt concentration on the network of hydrogen bonds is also considered. Moreover, single-particle dynamics of the salt cations is studied by means of their velocity autocorrelation functions and vibrational densities of states, explicitly analyzing the influence of salt concentration, and cation charge and mass on these magnitudes. The effect of the valency of the salt cation on these properties is considered comparing the results with those for the corresponding mixtures with lithium salts. We found that the main structural and dynamic features of the local solvation of divalent cations in ionic liquids are similar to those of monovalent salts, with cations being localized in the polar nanoregions of the bulk mixture coordinated in monodentate and bidentate coordination modes by the [NO{sub 3}]{sup −} and [PF{sub 6}]{sup −} anions. However, stronger electrostatic correlations of these polar nanoregions than in mixtures with salts with monovalent cations are found. The vibrational modes of the ionic liquid (IL) are seen to be scarcely affected by the addition of the salt, and the effect of mass and charge on the vibrational densities of states of the dissolved cations is reported. Cation mass is seen to exert a deeper influence than charge on the low-frequency vibrational spectra, giving a red shift of the vibrational modes and a virtual suppression of the higher energy vibrational modes for the heavier Ca{sup 2

Molecular dynamics simulations of the structure and single-particle dynamics of mixtures of divalent salts and ionic liquids

International Nuclear Information System (INIS)

Gómez-González, Víctor; Docampo-Álvarez, Borja; Gallego, Luis J.; Varela, Luis M.; Cabeza, Oscar; Fedorov, Maxim; Lynden-Bell, Ruth M.

2015-01-01

We report a molecular dynamics study of the structure and single-particle dynamics of mixtures of a protic (ethylammonium nitrate) and an aprotic (1-butyl-3-methylimidazolium hexaflurophosphate [BMIM][PF 6 ]) room-temperature ionic liquids doped with magnesium and calcium salts with a common anion at 298.15 K and 1 atm. The solvation of these divalent cations in dense ionic environments is analyzed by means of apparent molar volumes of the mixtures, radial distribution functions, and coordination numbers. For the protic mixtures, the effect of salt concentration on the network of hydrogen bonds is also considered. Moreover, single-particle dynamics of the salt cations is studied by means of their velocity autocorrelation functions and vibrational densities of states, explicitly analyzing the influence of salt concentration, and cation charge and mass on these magnitudes. The effect of the valency of the salt cation on these properties is considered comparing the results with those for the corresponding mixtures with lithium salts. We found that the main structural and dynamic features of the local solvation of divalent cations in ionic liquids are similar to those of monovalent salts, with cations being localized in the polar nanoregions of the bulk mixture coordinated in monodentate and bidentate coordination modes by the [NO 3 ] − and [PF 6 ] − anions. However, stronger electrostatic correlations of these polar nanoregions than in mixtures with salts with monovalent cations are found. The vibrational modes of the ionic liquid (IL) are seen to be scarcely affected by the addition of the salt, and the effect of mass and charge on the vibrational densities of states of the dissolved cations is reported. Cation mass is seen to exert a deeper influence than charge on the low-frequency vibrational spectra, giving a red shift of the vibrational modes and a virtual suppression of the higher energy vibrational modes for the heavier Ca 2+ cations. No qualitative

Femtochemistry and femtobiology ultrafast dynamics in molecular science

CERN Document Server

Douhal, Abderrazzak

2002-01-01

This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol

Conformity, Anticonformity and Polarization of Opinions: Insights from a Mathematical Model of Opinion Dynamics

Directory of Open Access Journals (Sweden)

Tyll Krueger

2017-07-01

Full Text Available Understanding and quantifying polarization in social systems is important because of many reasons. It could for instance help to avoid segregation and conflicts in the society or to control polarized debates and predict their outcomes. In this paper, we present a version of the q-voter model of opinion dynamics with two types of responses to social influence: conformity (like in the original q-voter model and anticonformity. We put the model on a social network with the double-clique topology in order to check how the interplay between those responses impacts the opinion dynamics in a population divided into two antagonistic segments. The model is analyzed analytically, numerically and by means of Monte Carlo simulations. Our results show that the system undergoes two bifurcations as the number of cross-links between cliques changes. Below the first critical point, consensus in the entire system is possible. Thus, two antagonistic cliques may share the same opinion only if they are loosely connected. Above that point, the system ends up in a polarized state.

Molecular dynamics simulation of ribosome jam

KAUST Repository

Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

2011-01-01

We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We

Ultrafast spectroscopy on DNA-cleavage by endonuclease in molecular crowding.

Science.gov (United States)

Singh, Priya; Choudhury, Susobhan; Dutta, Shreyasi; Adhikari, Aniruddha; Bhattacharya, Siddhartha; Pal, Debasish; Pal, Samir Kumar

2017-10-01

The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG. We have also labelled the enzyme by a well-known fluorescent probe 8-anilino-1-naphthalenesulfonic acid ammonium salt (ANS) to study the molecular mechanism of the protein-DNA association through exited state relaxation of the probe in absence (dictated by polarity) and presence of EB in the DNA (dictated by Förster resonance energy transfer (FRET)). The overall and local structures of the protein in presence of PEG have been followed by circular dichroism and time resolved polarization gated spectroscopy respectively. The enhanced dynamical flexibility of protein in presence of PEG as revealed from excited state lifetime and polarization gated anisotropy of ANS has been correlated with the stronger DNA-binding for the higher nuclease activity. We have also used conventional experimental strategy of agarose gel electrophoresis to monitor DNA-cleavage and found consistent results of enhanced nuclease activities both on synthetic 20-mer oligonucleotide and long genomic DNA from calf thymus. Copyright © 2017 Elsevier B.V. All rights reserved.

Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

DEFF Research Database (Denmark)

Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore

2010-01-01

We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations...... of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...

Spin filtering neutrons with a proton target dynamically polarized using photo-excited triplet states

International Nuclear Information System (INIS)

Haag, M.; Brandt, B. van den; Eichhorn, T.R.; Hautle, P.; Wenckebach, W.Th.

2012-01-01

In a test of principle a neutron spin filter has been built, which is based on dynamic nuclear polarization (DNP) using photo-excited triplet states. This DNP method has advantages over classical concepts as the requirements for cryogenic equipment and magnets are much relaxed: the spin filter is operated in a field of 0.3 T at a temperature of about 100 K and has performed reliably over periods of several weeks. The neutron beam was also used to analyze the polarization of the target employed as a spin filter. We obtained an independent measurement of the proton spin polarization of ∼0.13 in good agreement with the value determined with NMR. Moreover, the neutron beam was used to measure the proton spin polarization as a function of position in the naphthalene sample. The polarization was found to be homogeneous, even at low laser power, in contradiction to existing models describing the photo-excitation process.

Dynamics of molecular superrotors in an external magnetic field

International Nuclear Information System (INIS)

Korobenko, Aleksey; Milner, Valery

2015-01-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

Science.gov (United States)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

Kinetics from Replica Exchange Molecular Dynamics Simulations.

Science.gov (United States)

Stelzl, Lukas S; Hummer, Gerhard

2017-08-08

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

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

DEFF Research Database (Denmark)

Papaleo, Elena

2015-01-01

that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

Molecular dynamics in drug design: new generations of compstatin analogs.

Science.gov (United States)

Tamamis, Phanourios; López de Victoria, Aliana; Gorham, Ronald D; Bellows-Peterson, Meghan L; Pierou, Panayiota; Floudas, Christodoulos A; Morikis, Dimitrios; Archontis, Georgios

2012-05-01

We report the computational and rational design of new generations of potential peptide-based inhibitors of the complement protein C3 from the compstatin family. The binding efficacy of the peptides is tested by extensive molecular dynamics-based structural and physicochemical analysis, using 32 atomic detail trajectories in explicit water for 22 peptides bound to human, rat or mouse target protein C3, with a total of 257 ns. The criteria for the new design are: (i) optimization for C3 affinity and for the balance between hydrophobicity and polarity to improve solubility compared to known compstatin analogs; and (ii) development of dual specificity, human-rat/mouse C3 inhibitors, which could be used in animal disease models. Three of the new analogs are analyzed in more detail as they possess strong and novel binding characteristics and are promising candidates for further optimization. This work paves the way for the development of an improved therapeutic for age-related macular degeneration, and other complement system-mediated diseases, compared to known compstatin variants. © 2012 John Wiley & Sons A/S.

AceCloud: Molecular Dynamics Simulations in the Cloud.

Science.gov (United States)

Harvey, M J; De Fabritiis, G

2015-05-26

We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

Tunable 13C/1H dual channel matching circuit for dynamic nuclear polarization system with cross-polarization

DEFF Research Database (Denmark)

Rybalko, Oleksandr; Bowen, Sean; Zhurbenko, Vitaliy

2016-01-01

In this paper we report initial results of design and practical implementation of tuning and matching circuit to estimate a performance of Dynamic Nuclear Polarization (DNP) at a magnetic field of 6.7 T. It is shown that developed circuit for signal observation is compact, easy to make and provides....... Measurement results with a tuning and matching circuit prototype are presented including obtained spectra (13C and 1H) and estimation of the signal-to-noise ratio....

Dynamics of Molecular Gyroscopes Created by Strong Optical Fields

Science.gov (United States)

Mullin, Amy

2015-03-01

We explore the behavior of molecules in ultra-high angular momentum states prepared in an optical centrifuge and detected with transient IR absorption spectroscopy. In the optical centrifuge, the polarizable electron cloud of molecules interacts with the electric field of linearly polarized light that angularly accelerates over the time of the optical pulse. The centrifuge pulse is generated by combining oppositely chirped pulsed of light. Trapped molecules are driven into high angular momentum states that are spatially oriented with the optical field and have energies far above the average at 300 K. High resolution transient IR spectroscopy reveals the dynamics of collisional energy transfer for the super-rotors. Polarization-dependent studies show that the initial angular momentum orientation persists for many collisions, indicating that molecules in an optical centrifuge behave as quantum gyroscopes. Time-dependent population and energy profiles for individual J- states give information about the dynamics of super-rotors. Research support provided by NSF and the University of Maryland.

Molecular dynamics simulations of RNA motifs

Czech Academy of Sciences Publication Activity Database

Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.

2002-01-01

Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics

Monte Carlo-molecular dynamics simulations for two-dimensional magnets

International Nuclear Information System (INIS)

Kawabata, C.; takeuchi, M.; Bishop, A.R.

1985-01-01

A combined Monte Carlo-molecular dynamics simulation technique is used to study the dynamic structure factor on a square lattice for isotropic Heisenberg and planar classical ferromagnetic spin Hamiltonians

High-field Overhauser dynamic nuclear polarization in silicon below the metal-insulator transition.

Science.gov (United States)

Dementyev, Anatoly E; Cory, David G; Ramanathan, Chandrasekhar

2011-04-21

Single crystal silicon is an excellent system to explore dynamic nuclear polarization (DNP), as it exhibits a continuum of properties from metallic to insulating as a function of doping concentration and temperature. At low doping concentrations DNP has been observed to occur via the solid effect, while at very high-doping concentrations an Overhauser mechanism is responsible. Here we report the hyperpolarization of (29)Si in n-doped silicon crystals, with doping concentrations in the range of (1-3) × 10(17) cm(-3). In this regime exchange interactions between donors become extremely important. The sign of the enhancement in our experiments and its frequency dependence suggest that the (29)Si spins are directly polarized by donor electrons via an Overhauser mechanism within exchange-coupled donor clusters. The exchange interaction between donors only needs to be larger than the silicon hyperfine interaction (typically much smaller than the donor hyperfine coupling) to enable this Overhauser mechanism. Nuclear polarization enhancement is observed for a range of donor clusters in which the exchange energy is comparable to the donor hyperfine interaction. The DNP dynamics are characterized by a single exponential time constant that depends on the microwave power, indicating that the Overhauser mechanism is a rate-limiting step. Since only about 2% of the silicon nuclei are located within 1 Bohr radius of the donor electron, nuclear spin diffusion is important in transferring the polarization to all the spins. However, the spin-diffusion time is much shorter than the Overhauser time due to the relatively weak silicon hyperfine coupling strength. In a 2.35 T magnetic field at 1.1 K, we observed a DNP enhancement of 244 ± 84 resulting in a silicon polarization of 10.4 ± 3.4% following 2 h of microwave irradiation.

Molecular dynamics and Monte Carlo calculations in statistical mechanics

International Nuclear Information System (INIS)

Wood, W.W.; Erpenbeck, J.J.

1976-01-01

Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references

Enhancement of molecular NMR signal induced by polarization transfer from laser-polarized 129Xe

International Nuclear Information System (INIS)

Sun Xianping

2001-01-01

There is a large non-equilibrium nuclear polarization and a longer relaxation time in the laser-polarized 129 Xe produced by means of optical pumping and spin exchange. The characteristics of the laser-polarized 129 Xe permit the transfer of the polarization to enhance the atomic nuclear spin in liquid, solid and surface of solid molecules. Therefore, the sensitivity in nuclear magnetic resonance measurements for the molecules is enhanced and applications in the investigations of materials and surface sciences are expanded. The progress in the investigations of materials and surface sciences are expanded. The progress in the investigations of the polarization transfer between laser-polarized 129 Xe and the atomic nuclei in the molecules, the relative physics and the measurement of some parameters are introduced

Dynamic cholesteric liquid crystal superstructures photoaligned by one-step polarization holography

Science.gov (United States)

Li, Sen-Sen; Shen, Yuan; Chang, Zhen-Ni; Li, Wen-Song; Xu, Yan-Chao; Fan, Xing-Yu; Chen, Lu-Jian

2017-12-01

A convenient approach to modulate the fingerprint textures of methyl red (MR) doped cholesteric liquid crystals by asymmetric photoalignment in the green-light waveband is presented, resulting in the generation of voltage-controllable helical superstructures. The interaction between the MR molecules and the incident light polarization determines the initial twisted planar geometry, providing a multivariant control over the stripe directions of fingerprint textures by applying a proper electric field. The key factors for precise manipulation of fingerprint stripes in a predictable and rewritable manner are analyzed theoretically and investigated experimentally, which involves the alignment asymmetry, the ratio of cell gap to natural pitch length, and the chirality of chiral dopant. Dynamic periodic fingerprint textures in shapes of dashed curve and dashed line are further demonstrated by utilizing a facile one-step polarization holography process using two beams with orthogonal circular and orthogonal linear polarizations, respectively. It is believed that the practical approach described in this study would enrich the research contents of self-assembled hierarchical superstructures using soft liquid crystal building blocks.

Polarization recovery through scattering media.

Science.gov (United States)

de Aguiar, Hilton B; Gigan, Sylvain; Brasselet, Sophie

2017-09-01

The control and use of light polarization in optical sciences and engineering are widespread. Despite remarkable developments in polarization-resolved imaging for life sciences, their transposition to strongly scattering media is currently not possible, because of the inherent depolarization effects arising from multiple scattering. We show an unprecedented phenomenon that opens new possibilities for polarization-resolved microscopy in strongly scattering media: polarization recovery via broadband wavefront shaping. We demonstrate focusing and recovery of the original injected polarization state without using any polarizing optics at the detection. To enable molecular-level structural imaging, an arbitrary rotation of the input polarization does not degrade the quality of the focus. We further exploit the robustness of polarization recovery for structural imaging of biological tissues through scattering media. We retrieve molecular-level organization information of collagen fibers by polarization-resolved second harmonic generation, a topic of wide interest for diagnosis in biomedical optics. Ultimately, the observation of this new phenomenon paves the way for extending current polarization-based methods to strongly scattering environments.

Intense field stabilization in circular polarization: Three-dimensional time-dependent dynamics

International Nuclear Information System (INIS)

Choi, Dae-Il; Chism, Will

2002-01-01

We investigate the stabilization of hydrogen atoms in a circularly polarized laser field. We use a three-dimensional, time-dependent approach to study the quantum dynamics of hydrogen atoms subject to high-intensity, short-wavelength, laser pulses. We find an enhanced survival probability as the field is increased under fixed envelope conditions. We also confirm wave packet behaviors previously seen in two-dimensional time-dependent computations

ImaEdge - a platform for quantitative analysis of the spatiotemporal dynamics of cortical proteins during cell polarization.

Science.gov (United States)

Zhang, Zhen; Lim, Yen Wei; Zhao, Peng; Kanchanawong, Pakorn; Motegi, Fumio

2017-12-15

Cell polarity involves the compartmentalization of the cell cortex. The establishment of cortical compartments arises from the spatial bias in the activity and concentration of cortical proteins. The mechanistic dissection of cell polarity requires the accurate detection of dynamic changes in cortical proteins, but the fluctuations of cell shape and the inhomogeneous distributions of cortical proteins greatly complicate the quantitative extraction of their global and local changes during cell polarization. To address these problems, we introduce an open-source software package, ImaEdge, which automates the segmentation of the cortex from time-lapse movies, and enables quantitative extraction of cortical protein intensities. We demonstrate that ImaEdge enables efficient and rigorous analysis of the dynamic evolution of cortical PAR proteins during Caenorhabditis elegans embryogenesis. It is also capable of accurate tracking of varying levels of transgene expression and discontinuous signals of the actomyosin cytoskeleton during multiple rounds of cell division. ImaEdge provides a unique resource for quantitative studies of cortical polarization, with the potential for application to many types of polarized cells.This article has an associated First Person interview with the first authors of the paper. © 2017. Published by The Company of Biologists Ltd.

Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties

Czech Academy of Sciences Publication Activity Database

Fojtíková, J.; Kalvoda, L.; Sedlák, Petr

2015-01-01

Roč. 128, č. 4 (2015), s. 637-639 ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.525, year: 2015 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf

Nanotribology investigations with classical molecular dynamics

NARCIS (Netherlands)

Solhjoo, Soheil

2017-01-01

This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu, H.G.; Muckerman, J.T.

2010-06-01

The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

Directory of Open Access Journals (Sweden)

Mingyuan Xu

2018-05-01

Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

Science.gov (United States)

Cawkwell, M J; Niklasson, Anders M N

2012-10-07

Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

Molecular Dynamics Simulations to Investigate the Binding Mode of the Natural Product Liphagal with Phosphoinositide 3-Kinase α

Directory of Open Access Journals (Sweden)

Yanjuan Gao

2016-06-01

Full Text Available Phosphatidylinositol 3-kinase α (PI3Kα is an attractive target for anticancer drug design. Liphagal, isolated from the marine sponge Aka coralliphaga, possesses the special “liphagane” meroterpenoid carbon skeleton and has been demonstrated as a PI3Kα inhibitor. Molecular docking and molecular dynamics simulations were performed to explore the dynamic behaviors of PI3Kα binding with liphagal, and free energy calculations and energy decomposition analysis were carried out by use of molecular mechanics/Poisson-Boltzmann (generalized Born surface area (MM/PB(GBSA methods. The results reveal that the heteroatom rich aromatic D-ring of liphagal extends towards the polar region of the binding site, and the D-ring 15-hydroxyl and 16-hydroxyl form three hydrogen bonds with Asp810 and Tyr836. The cyclohexyl A-ring projects up into the upper pocket of the lipophilic region, and the hydrophobic/van der Waals interactions with the residues Met772, Trp780, Ile800, Ile848, Val850, Met922, Phe930, Ile932 could be the key interactions for the affinity of liphagal to PI3Kα. Thus, a new strategy for the rational design of more potent analogs of liphagal against PI3Kα is provided. Our proposed PI3Kα/liphagal binding mode would be beneficial for the discovery of new active analogs of liphagal against PI3Kα.

Modeling ramp compression experiments using large-scale molecular dynamics simulation.

Energy Technology Data Exchange (ETDEWEB)

Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

2011-10-01

Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

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

Science.gov (United States)

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.

Optical polarimetry and molecular line studies of L1157 dark molecular cloud

Science.gov (United States)

Sharma, Ekta; Soam, Archana; Gopinathan, Maheswar

2018-04-01

Filaments are omnipresent in molecular clouds which are believed to fragment into cores. The detailed process of the evolution from filaments to cores depends critically on the physical conditions in the star forming region. This study aims at characterising gas motions using velocity structure and finding the dynamical importance of magnetic fields in the filament morphology. The plane-of-the-sky component of the magnetic field has been measured using optical polarization of the background stars. The orientation is found to be almost perpendicular to the filament implying its dynamical importance in the evolution of the cloud. Optical polarimetric results match very well with the sub millimetre polarization angles obtained in the inner core regions. The magnetic fields are found to have an orientation of 130° east with respect to north. The angular offset between the outflow axis and the magnetic field direction is found to be 25°. Values for parameters like the excitation temperature, optical depth and column densities have been derived using molecular lines. Optically thick lines show non-gaussian features. The non-thermal widths tell about the presence of turbulent motions whereas the C180 lines follow Gaussian features almost at all the locations observed in the filament.

Einstein-aether theory: dynamics of relativistic particles with spin or polarization in a Gödel-type universe

Energy Technology Data Exchange (ETDEWEB)

Balakin, Alexander B.; Popov, Vladimir A., E-mail: alexander.balakin@kpfu.ru, E-mail: vladipopov@mail.ru [Department of General Relativity and Gravitation, Institute of Physics, Kazan Federal University, Kremlevskaya str. 18, Kazan 420008 (Russian Federation)

2017-04-01

In the framework of the Einstein-aether theory we consider a cosmological model, which describes the evolution of the unit dynamic vector field with activated rotational degree of freedom. We discuss exact solutions of the Einstein-aether theory, for which the space-time is of the Gödel-type, the velocity four-vector of the aether motion is characterized by a non-vanishing vorticity, thus the rotational vectorial modes can be associated with the source of the universe rotation. The main goal of our paper is to study the motion of test relativistic particles with a vectorial internal degree of freedom (spin or polarization), which is coupled to the unit dynamic vector field. The particles are considered as the test ones in the given space-time background of the Gödel-type; the spin (polarization) coupling to the unit dynamic vector field is modeled using exact solutions of three types. The first exact solution describes the aether with arbitrary Jacobson's coupling constants; the second one relates to the case, when the Jacobson's constant responsible for the vorticity is vanishing; the third exact solution is obtained using three constraints for the coupling constants. The analysis of the exact expressions, which are obtained for the particle momentum and for the spin (polarization) four-vector components, shows that the interaction of the spin (polarization) with the unit vector field induces a rotation, which is additional to the geodesic precession of the spin (polarization) associated with the universe rotation as a whole.

A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

KAUST Repository

Neumann, Philipp; Tchipev, Nikola

2012-01-01

We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm

Dynamic nuclear polarization by frequency modulation of a tunable gyrotron of 260GHz.

Science.gov (United States)

Yoon, Dongyoung; Soundararajan, Murari; Cuanillon, Philippe; Braunmueller, Falk; Alberti, Stefano; Ansermet, Jean-Philippe

2016-01-01

An increase in Dynamic Nuclear Polarization (DNP) signal intensity is obtained with a tunable gyrotron producing frequency modulation around 260GHz at power levels less than 1W. The sweep rate of frequency modulation can reach 14kHz, and its amplitude is fixed at 50MHz. In water/glycerol glassy ice doped with 40mM TEMPOL, the relative increase in the DNP enhancement was obtained as a function of frequency-sweep rate for several temperatures. A 68 % increase was obtained at 15K, thus giving a DNP enhancement of about 80. By employing λ/4 and λ/8 polarizer mirrors, we transformed the polarization of the microwave beam from linear to circular, and achieved an increase in the enhancement by a factor of about 66% for a given power. Copyright © 2015 Elsevier Inc. All rights reserved.

Reactive surface organometallic complexes observed using dynamic nuclear polarization surface enhanced NMR spectroscopy

KAUST Repository

Pump, Eva; Viger-Gravel, Jasmine; Abou-Hamad, Edy; Samantaray, Manoja; Hamzaoui, Bilel; Gurinov, Andrei; Anjum, Dalaver H.; Gajan, David; Lesage, Anne; Bendjeriou-Sedjerari, Anissa; Emsley, Lyndon; Basset, Jean-Marie

2016-01-01

Dynamic Nuclear Polarization Surface Enhanced NMR Spectroscopy (DNP SENS) is an emerging technique that allows access to high-sensitivity NMR spectra from surfaces. However, DNP SENS usually requires the use of radicals as an exogenous source of polarization, which has so far limited applications for organometallic surface species to those that do not react with the radicals. Here we show that reactive surface species can be studied if they are immobilized inside porous materials with suitably small windows, and if bulky nitroxide bi-radicals (here TEKPol) are used as the polarization source and which cannot enter the pores. The method is demonstrated by obtaining significant DNP enhancements from highly reactive complelxes [(equivalent to Si-O-)W(Me)(5)] supported on MCM-41, and effects of pore size (6.0, 3.0 and 2.5 nm) on the performance are discussed.

Reactive surface organometallic complexes observed using dynamic nuclear polarization surface enhanced NMR spectroscopy

KAUST Repository

Pump, Eva

2016-08-15

Dynamic Nuclear Polarization Surface Enhanced NMR Spectroscopy (DNP SENS) is an emerging technique that allows access to high-sensitivity NMR spectra from surfaces. However, DNP SENS usually requires the use of radicals as an exogenous source of polarization, which has so far limited applications for organometallic surface species to those that do not react with the radicals. Here we show that reactive surface species can be studied if they are immobilized inside porous materials with suitably small windows, and if bulky nitroxide bi-radicals (here TEKPol) are used as the polarization source and which cannot enter the pores. The method is demonstrated by obtaining significant DNP enhancements from highly reactive complelxes [(equivalent to Si-O-)W(Me)(5)] supported on MCM-41, and effects of pore size (6.0, 3.0 and 2.5 nm) on the performance are discussed.

Molecular dynamics simulations of proton-ordered water confined in low-diameter carbon nanotubes.

Science.gov (United States)

Li, Shujuan; Schmidt, Burkhard

2015-03-21

The present work deals with molecular dynamics simulations of water confined in single-walled carbon nanotubes (CNTs), with emphasis on the proton-ordering of water and its polarization. First, the water occupancy of open-ended armchair and zigzag CNTs immersed in water under ambient NPT conditions is calculated for various water models, and for varying Lennard-Jones parameters of the water-carbon interaction. As a function of the CNT diameter, the water density displays several oscillations before converging to the bulk value. Based on these results, the water structures encapsulated in 10 nm long armchair CNTs (n,n) with 5 ≤ n ≤ 10, are investigated under NVT conditions. Inside the smallest nanotubes (n = 5, 6) highly ferroelectric (FE), quasi-one-dimensional water chains are found while inside the other CNTs water molecules assemble into single-walled ice nanotubes (INTs). There are several, near-degenerate minimum energy INT structures: single helical structures were found for 7 ≤ n ≤ 10, in all cases in FE arrangement. In addition, a double helical INT structure was found for n = 8 with an even higher polarization. Prism-like structures were found only for 8 ≤ n ≤ 10 with various FE, ferrielectric (FI), and antiferroelectric (AF, n = 9, 10) proton ordering. The coexistence of the nearly iso-energetic FE, FI, and AF INT structures separated by high barriers renders the molecular dynamics highly metastable, typically with nanosecond timescales at room temperature. Hence, the replica exchange simulation method is used to obtain populations of different INT states at finite temperatures. Many of the FE INT structures confined in low-diameter CNTs are still prevalent at room temperature. Both helix-helix and helix-prism structural transitions are detected which can be either continuous (around 470 K for n = 8) or discontinuous (at 218 K for n = 9). Also melting-like transitions are found in which the INT structures are disrupted leading to a loss of FE

Formation of molecular complexes of salicylic acid, acetylsalicylic acid, and methyl salicylate in a mixture of supercritical carbon dioxide with a polar cosolvent

Science.gov (United States)

Petrenko, V. E.; Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.

2015-08-01

The solvate structures formed by salicylic acid, acetylsalicylic acid, and methyl salicylate in supercritical (SC) carbon dioxide with a polar cosolvent (methanol, 0.03 mole fractions) at a density of 0.7 g/cm3 and a temperature of 318 K were studied by the molecular dynamics method. Salicylic and acetylsalicylic acids were found to form highly stable hydrogen-bonded complexes with methanol via the hydrogen atom of the carboxyl group. For methyl salicylate in which the carboxyl hydrogen is substituted by a methyl radical, the formation of stable hydrogen bonds with methanol was not revealed. The contribution of other functional groups of the solute to the interactions with the cosolvent was much smaller. An analysis of correlations between the obtained data and the literature data on the cosolvent effect on the solubility of the compounds in SC CO2 showed that the dissolving ability of SC CO2 with respect to a polar organic substance in the presence of a cosolvent increased only when stable hydrogen-bonded complexes are formed between this substance and the cosolvent.

Dynamic nuclear-polarization studies of paramagnetic species in solution

International Nuclear Information System (INIS)

Glad, W.E.

1982-07-01

Dynamic Nuclear Polarization (DNP) was used to measure the electron spin lattice relaxation times, T 1 , of transition metal ions in aqueous solution. Saturation which is induced in the electron spin system is transferred to the solvent proton spins by dipole-dipole interactions. The change in the polarization of the proton spins is much larger than it is in the electron spins. The change in proton polarization is easily measured by proton Nuclear Magnetic Resonance (NMR). In one experimental arrangement the sample solution was continuously flowed through a microwave cavity to the NMR coil. The NMR was observed with a continuous wave NMR spectrometer. In a second arrangement the whole sample tube was moved from within the microwave cavity to the NMR coil in less than 40 ms by a blast of compressed air. The NMR was then observed with a pulse-Fourier-transform spectrometer. With the second arrangement a mean-square microwave magnetic field at the sample of more than 10 G 2 is obtainable with 14 W of microwave power. Measurements of DNP at 9 GHz were made on aqueous solutions of VO 2+ , Mn 2+ , Cr(CN) 6 3- , Cu 2+ and Cu(ethylenediamine) 2 (H 2 0) 2 2+ ions from 3 to 60 0 C. It was also possible to observe DNP on resolved proton resonances from mixed water-acetonitrile solutions of VO 2+ and Cr(CN) 6 3- ions

Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite

KAUST Repository

Yoon, Seyoon; Monteiro, Paulo J.M.

2013-01-01

The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current

Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

DEFF Research Database (Denmark)

Toxvaerd, Søren

2001-01-01

Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

Dynamic nuclear polarization and optimal control spatial-selective 13C MRI and MRS

DEFF Research Database (Denmark)

Vinding, Mads Sloth; Laustsen, Christoffer; Maximov, Ivan I.

2013-01-01

. This is achieved through the development of spatial-selective single-shot spiral-readout MRI and MRS experiments combined with dynamic nuclear polarization hyperpolarized [1-13C]pyruvate on a 4.7T pre-clinical MR scanner. The method stands out from related techniques by facilitating anatomic shaped region...

molecular dynamics simulations and quantum chemical calculations

African Journals Online (AJOL)

ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.

Invariant molecular-dynamics approach to structural phase transitions

International Nuclear Information System (INIS)

Wentzcovitch, R.M.

1991-01-01

Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

International Nuclear Information System (INIS)

Aradi, Balint; Frauenheim, Thomas

2015-01-01

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology

Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package

Science.gov (United States)

Dizkirici, Ayten; Tekpinar, Mustafa

2015-03-01

GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

Science.gov (United States)

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

NMR investigations of molecular dynamics

Science.gov (United States)

Palmer, Arthur

2011-03-01

NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

Excitation dynamics and relaxation in a molecular heterodimer

International Nuclear Information System (INIS)

Balevičius, V.; Gelzinis, A.; Abramavicius, D.; Mančal, T.; Valkunas, L.

2012-01-01

Highlights: ► Dynamics of excitation within a heterogenous molecular dimer. ► Excited states can be swapped due to different reorganization energies of monomers. ► Conventional excitonic basis becomes renormalized due to interaction with the bath. ► Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the molecular excitation energy gap, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.

The nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Hoover, W.G.

1992-03-01

MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments

Reaction dynamics of molecular hydrogen on silicon surfaces

DEFF Research Database (Denmark)

Bratu, P.; Brenig, W.; Gross, A.

1996-01-01

of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...

Identification of potent inhibitors against snake venom metalloproteinase (SVMP) using molecular docking and molecular dynamics studies.

Science.gov (United States)

Chinnasamy, Sathishkumar; Chinnasamy, Selvakkumar; Nagamani, Selvaraman; Muthusamy, Karthikeyan

2015-01-01

Snake venom metalloproteinase (SVMP) (Echis coloratus (Carpet viper) is a multifunctional enzyme that is involved in producing several symptoms that follow a snakebite, such as severe local hemorrhage, nervous system effects and tissue necrosis. Because the three-dimensional (3D) structure of SVMP is not known, models were constructed, and the best model was selected based on its stereo-chemical quality. The stability of the modeled protein was analyzed through molecular dynamics (MD) simulation studies. Structure-based virtual screening was performed, and 15 potential molecules with the highest binding energies were selected. Further analysis was carried out with induced fit docking, Prime/MM-GBSA (ΔGBind calculations), quantum-polarized ligand docking, and density functional theory calculations. Further, the stability of the lead molecules in the SVMP-active site was examined using MD simulation. The results showed that the selected lead molecules were highly stable in the active site of SVMP. Hence, these molecules could potentially be selective inhibitors of SVMP. These lead molecules can be experimentally validated, and their backbone structural scaffold could serve as building blocks in designing drug-like molecules for snake antivenom.

Accretion dynamics and polarized x-ray emission of magnetized neutron stars

International Nuclear Information System (INIS)

Arons, J.

1991-01-01

The basic ideas of accretion onto magnetized neutron stars are outlined. These are applied to a simple model of the structure of the plasma mound sitting at the magnetic poles of such as star, in which upward diffusion of photons is balanced by their downward advection. This steady flow model of the plasma's dynamical state is used to compute the emission of polarized X-rays from the optically thick, birefringent medium. The linear polarization of the continuum radiation emerging from the quasi-static mound is found to be as much as 40% at some rotation phases, but is insensitive to the geometry of the accretion flow. The role of the accretion shock, whose detailed polarimetric and spectral characteristics have yet to be calculated, is emphasized as the final determinant of the properties of the emerging X-rays. Some results describing the fully time dependent dynamics of the flow are also presented. In particular, steady flow onto a neutron star is shown to exhibit formation of ''photon bubbles,'' regions of greatly reduced plasma density filled with radiation which form and rise on millisecond time scales. The possible role of these complex structures in the flow for the formation of the emergent spectrum is briefly outlined

Accretion dynamics and polarized X-ray emission of magnetized neutron stars

Science.gov (United States)

Arons, Jonathan

1991-01-01

The basic ideas of accretion onto magnetized neutron stars are outlined. These are applied to a simple model of the structure of the plasma mound sitting at the magnetic poles of such a star, in which upward diffusion of photons is balanced by their downward advection. This steady flow model of the plasma's dynamical state is used to compute the emission of polarized X-raysfrom the optically thick, birefringent medium. The linear polarization of the continuum radiation emerging from the quasi-static mound is found to be as much as 40 percent at some rotation phases, but is insensitive to the geometry of the accretion flow. The role of the accretion shock, whose detailed polarimetric and spectral characteristics have yet to be calculated, is emphasized as the final determinant of the properties of the emerging X-rays. Some results describing the fully time dependent dynamics of the flow are also presented. In particular, steady flow onto a neutron star is shown to exhibit formation of 'photon bubbles', regions of greatly reduced plasma density filled with radiation which form and rise on millisecond time scale. The possible role of these complex structures in the flow for the formation of the emergent spectrum is briefly outlined.

State-to-state dynamics of molecular energy transfer

Energy Technology Data Exchange (ETDEWEB)

Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)

1993-12-01

The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

Line-shape theory and molecular dynamics in collision-induced light scattering

International Nuclear Information System (INIS)

Balucani, U.; Tognetti, V.; Vallauri, R.

1979-01-01

Molecular-dynamics studies in argon at 148 amagats are presented for gaining information on the dynamical properties responsible for the depolarized light scattering from simple fluids. The total and pair-correlation functions are computed within the simple dipole--induced-dipole model of polarizability anisotropy. The pair spectral shape is derived. These results are compared with a theoretical analysis based on a continued-fraction approach. The necessary frequency moments are calculated both in the low-density limit and taking into account first-order density corrections, and compared with the molecular-dynamics data. The agreement between the theoretical spectra and molecular-dynamics data shows the validity of the memory-function approach. The comparison with the real experimental results allows one to test the relevant physical contributions to the polarizability anisotropy

Coulomb interactions via local dynamics: a molecular-dynamics algorithm

International Nuclear Information System (INIS)

Pasichnyk, Igor; Duenweg, Burkhard

2004-01-01

We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

DEFF Research Database (Denmark)

Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

2012-01-01

In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

Science.gov (United States)

Hu, Hao; Liu, Haiyan

2013-05-30

Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.

Polarization Dependent Dynamics of CO2 Trapped in AN Optical Centrifuge

Science.gov (United States)

Toro, Carlos; Echebiri, Geraldine; Liu, Qingnan; Mullin, Amy S.

2012-06-01

An optical centrifuge (Yuan {et al}. {PNAS} 2011, 108, 6872) has been employed to prepare carbon dioxide molecules in very high rotational states (``hot'' rotors, J ˜220) in order to investigate how collisions relax ensembles of molecules with an overall angular momentum that is spatially oriented. We have performed polarization-dependent high resolution transient IR absorption measurements to study the spatial dependence of the relaxation dynamics. Our results show that the net angular momentum of the initially centrifuged molecules persists for at least 10 gas kinetic collisions and that the translational energy distributions are dependent on the probe orientation and polarization. These studies indicate that the centrifuged molecules tend to maintain the orientation of their initial angular momentum for the first set of collisions and that relatively large changes in J are involved in the first collisions.

Dynamics of Venus' Southern hemisphere and South Polar Vortex from VIRTIS data obtained during the Venus Expres Mission

Science.gov (United States)

Hueso, R.; Garate-Lopez, I.; Sanchez-Lavega, A.

2011-12-01

The VIRTIS instrument onboard Venus Express observes Venus in two channels (visible and infrared) obtaining spectra and multi-wavelength images of the planet. The images have been used to trace the motions of the atmosphere at different layers of clouds [1-3]. We review the VIRTIS cloud image data and wind results obtained by different groups [1-3] and we present new results concerning the morphology and evolution of the South Polar Vortex at the upper and lower cloud levels with data covering the first 900 days of the mission. We present wind measurements of the South hemisphere obtained by cloud tracking individual cloud features and higher-resolution wind results of the polar region covering the evolution of the South polar vortex. The later were obtained by an image correlation algorithm run under human supervision to validate the data. We present day-side data of the upper clouds obtained at 380 and 980 nm sensitive to altitudes of 66-70 km, night-side data in the near infrared at 1.74 microns of the lower cloud (45-50 km) and day and night-side data obtained in the thermal infrared (wavelengths of 3.8 and 5.1 microns) which covers the dynamical evolution of Venus South Polar vortex at the cloud tops (66-70 km). We explore the different dynamics associated to the varying morphology of the vortex, its dynamical structure at different altitudes, the variability of the global wind data of the southern hemisphere and the interrelation of the polar vortex dynamics with the wind dynamics at subpolar and mid-latitudes. Acknowledgements: Work funded by Spanish MICIIN AYA2009-10701 with FEDER support and Grupos Gobierno Vasco IT-464-07. References [1] A. Sánchez-Lavega et al., Geophys. Res. Lett. 35, L13204, (2008). [2] D. Luz et al., Science, 332, 577-580 (2011). [3] R. Hueso, et al., Icarus doi:10.1016/j.icarus.2011.04.020 (2011)

Polar bear population dynamics in the southern Beaufort Sea during a period of sea ice decline.

Science.gov (United States)

Bromaghin, Jeffrey F; Mcdonald, Trent L; Stirling, Ian; Derocher, Andrew E; Richardson, Evan S; Regehr, Eric V; Douglas, David C; Durner, George M; Atwood, Todd; Amstrup, Steven C

2015-04-01

In the southern Beaufort Sea of the United States and Canada, prior investigations have linked declines in summer sea ice to reduced physical condition, growth, and survival of polar bears (Ursus maritimus). Combined with projections of population decline due to continued climate warming and the ensuing loss of sea ice habitat, those findings contributed to the 2008 decision to list the species as threatened under the U.S. Endangered Species Act. Here, we used mark-recapture models to investigate the population dynamics of polar bears in the southern Beaufort Sea from 2001 to 2010, years during which the spatial and temporal extent of summer sea ice generally declined. Low survival from 2004 through 2006 led to a 25-50% decline in abundance. We hypothesize that low survival during this period resulted from (1) unfavorable ice conditions that limited access to prey during multiple seasons; and possibly, (2) low prey abundance. For reasons that are not clear, survival of adults and cubs began to improve in 2007 and abundance was comparatively stable from 2008 to 2010, with ~900 bears in 2010 (90% CI 606-1212). However, survival of subadult bears declined throughout the entire period. Reduced spatial and temporal availability of sea ice is expected to increasingly force population dynamics of polar bears as the climate continues to warm. However, in the short term, our findings suggest that factors other than sea ice can influence survival. A refined understanding of the ecological mechanisms underlying polar bear population dynamics is necessary to improve projections of their future status and facilitate development of management strategies.

Dynamic polarization by coulomb excitation in the closed formalism for heavy ion scattering

International Nuclear Information System (INIS)

Frahn, W.E.; Hill, T.F.

1978-01-01

We present a closed-form treatment of the effects of dynamic polarization by Coulomb excitation on the elastic scattering of deformed heavy ions. We assume that this interaction can be represented by an absorptive polarization potential. The relatively long range of this potential entails a relatively slow variation of the associated reflection function in l-space. This feature leads to a simple generalization of the closed formula derived previously for the elastic scattering amplitude of spherical heavy nuclei. We use both the polarization potential of Love et al. and the recent improved potential of Baltz et al. to derive explicit expressions for the associated reflection functions in a Coulomb-distorted eikonal approximation. As an example we analyze the elastic scattering of 90-MeV 18 O ions by 184 W and show that both results give a quantitative description of the data. (orig.) [de

Polarized proton spin density images the tyrosyl radical locations in bovine liver catalase

Directory of Open Access Journals (Sweden)

Oliver Zimmer

2016-09-01

Full Text Available A tyrosyl radical, as part of the amino acid chain of bovine liver catalase, supports dynamic proton spin polarization (DNP. Finding the position of the tyrosyl radical within the macromolecule relies on the accumulation of proton polarization close to it, which is readily observed by polarized neutron scattering. The nuclear scattering amplitude due to the polarization of protons less than 10 Å distant from the tyrosyl radical is ten times larger than the amplitude of magnetic neutron scattering from an unpaired polarized electron of the same radical. The direction of DNP was inverted every 5 s, and the initial evolution of the intensity of polarized neutron scattering after each inversion was used to identify those tyrosines which have assumed a radical state. Three radical sites, all of them close to the molecular centre and the haem, appear to be equally possible. Among these is tyr-369, the radical state of which had previously been proven by electron paramagnetic resonance.

MiR-146a modulates macrophage polarization by inhibiting Notch1 pathway in RAW264.7 macrophages.

Science.gov (United States)

Huang, Cheng; Liu, Xue-Jiao; QunZhou; Xie, Juan; Ma, Tao-Tao; Meng, Xiao-Ming; Li, Jun

2016-03-01

Macrophages are heterogeneous and plastic cells which are able to undergo dynamic transition between M1 and M2 polarized phenotypes in response to the microenvironment signals. However, the underlying molecular mechanisms of macrophage polarization are still obscure. In the current study, it was revealed that miR-146a might play a pivotal role in macrophage polarization. As our results indicated, miR-146a was highly expressed in M2 macrophages rather than M1 macrophages. Over-expression of miR-146a resulted in significantly decreased production of pro-inflammatory cytokines including iNOS and TNF-α in M1 macrophages, while increased production of M2 marker genes such as Arg1 and CD206 in M2 macrophages. In contrast, knockdown of miR-146a promoted M1 macrophage polarization but diminished M2 macrophage polarization. Mechanistically, it was revealed that miR-146a modulated macrophage polarization by targeting Notch1. Of note, PPARγ was responsible as another target for miR-146a-mediated macrophage polarization. Taken together, it was suggested that miR-146a might serve as a molecular regulator in macrophage polarization and is a potential therapeutic target for inflammatory diseases. Copyright © 2016 Elsevier B.V. All rights reserved.

An approach to spin-resolved molecular gas microscopy

Science.gov (United States)

Covey, Jacob P.; De Marco, Luigi; Acevedo, Óscar L.; Rey, Ana Maria; Ye, Jun

2018-04-01

Ultracold polar molecules are an ideal platform for studying many-body physics with long-range dipolar interactions. Experiments in this field have progressed enormously, and several groups are pursuing advanced apparatus for manipulation of molecules with electric fields as well as single-atom-resolved in situ detection. Such detection has become ubiquitous for atoms in optical lattices and tweezer arrays, but has yet to be demonstrated for ultracold polar molecules. Here we present a proposal for the implementation of site-resolved microscopy for polar molecules, and specifically discuss a technique for spin-resolved molecular detection. We use numerical simulation of spin dynamics of lattice-confined polar molecules to show how such a scheme would be of utility in a spin-diffusion experiment.

Study of lanthanide tri-cations in aqueous solution by molecular dynamic; Etude des trications lanthanide en solution aqueuse par dynamique moleculaire

Energy Technology Data Exchange (ETDEWEB)

Duvail, M

2007-11-15

This is essentially a lanthanide tri-cation hydration study by means of classical molecular dynamics (CLMD) simulations using explicit polarization. Explicit polarization is calculated with a Car-Parrinello type of dynamics on induced dipoles, which decreases the CPU time as compared to the self-consistent resolution. Several pair interaction potentials are parametrized from ab initio calculations (MP2) and tested for the La{sup 3+}-OH{sub 2} interaction. The best results are obtained with an exponential-6 Buckingham potential. Next, the La{sup 3+}-OH{sub 2} interaction potential parameters are extrapolated to the other Ln{sup 3+}-OH{sub 2} interactions, only by using the ionic radii. The CLMD results reproduce the reliable experimental data (EXAFS distances), and the sigmoidal variation of the coordination number (with S shape), from 9 for La{sup 3+} to 8 for Lu{sup 3+}. This variation is explained by the linear variation of DrG0 (9,298) vs. atomic number. Insights are also given on the Co{sup 2+} hydration, CPMD simulations, reconstruction of EXAFS signal from MD simulations, and OH{sup -} complexation of La{sup 3+} in aqueous solution. (author)

Ab initio molecular dynamics in a finite homogeneous electric field.

Science.gov (United States)

Umari, P; Pasquarello, Alfredo

2002-10-07

We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

Reciprocal and dynamic polarization of planar cell polarity core components and myosin

Science.gov (United States)

Newman-Smith, Erin; Kourakis, Matthew J; Reeves, Wendy; Veeman, Michael; Smith, William C

2015-01-01

The Ciona notochord displays planar cell polarity (PCP), with anterior localization of Prickle (Pk) and Strabismus (Stbm). We report that a myosin is polarized anteriorly in these cells and strongly colocalizes with Stbm. Disruption of the actin/myosin machinery with cytochalasin or blebbistatin disrupts polarization of Pk and Stbm, but not of myosin complexes, suggesting a PCP-independent aspect of myosin localization. Wash out of cytochalasin restored Pk polarization, but not if done in the presence of blebbistatin, suggesting an active role for myosin in core PCP protein localization. On the other hand, in the pk mutant line, aimless, myosin polarization is disrupted in approximately one third of the cells, indicating a reciprocal action of core PCP signaling on myosin localization. Our results indicate a complex relationship between the actomyosin cytoskeleton and core PCP components in which myosin is not simply a downstream target of PCP signaling, but also required for PCP protein localization. DOI: http://dx.doi.org/10.7554/eLife.05361.001 PMID:25866928

Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

International Nuclear Information System (INIS)

Bresme, F.; Armstrong, J.

2014-01-01

We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation

Structure and dynamics of H{sub 2}O vis-á-vis phenylalanine recognition at a DPPC lipid membrane via interfacial H-bond types: Insights from polarized FT-IRRAS and ADMP simulations

Energy Technology Data Exchange (ETDEWEB)

Sarangi, Nirod Kumar; Ramesh, Nivarthi; Patnaik, Archita [Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036 (India)

2015-01-14

Preferential and enantioselective interactions of L-/D-Phenylalanine (L-Phe and D-Phe) and butoxycarbonyl-protected L-/D-Phenylalanine (LPA and DPA) as guest with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (L-DPPC) as host were tapped by using real time Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS). Polarization-modulated FT-IRRAS of DPPC monolayers above the phenylalanine modified subphases depicted fine structure/conformation differences under considerations of controlled 2D surface pressure. Selective molecular recognition of D-enantiomer over L-enantiomer driven by the DPPC head group via H-bonding and electrostatic interactions was evident spectroscopically. Accordingly, binding constants (K) of 145, 346, 28, and 56 M{sup −1} for LPA, DPA, L-Phe, and D-Phe, respectively, were estimated. The real time FT-IRRAS water bands were strictly conformation sensitive. The effect of micro-solvation on the structure and stability of the 1:1 diastereomeric L-lipid⋯, LPA/DPA and L-lipid⋯, (L/D)-Phe adducts was investigated with the aid of Atom-centered Density Matrix Propagation (ADMP), a first principle quantum mechanical molecular dynamics approach. The phosphodiester fragment was the primary site of hydration where specific solvent interactions were simulated through single- and triple- “water-phosphate” interactions, as water cluster’s “tetrahedral dice” to a “trimeric motif” transformation as a partial de-clusterization was evident. Under all the hydration patterns considered in both static and dynamic descriptions of density functional theory, L-lipid/D-amino acid enantiomer adducts continued to be stable structures while in dynamic systems, water rearranged without getting “squeezed-out” in the process of recognition. In spite of the challenging computational realm of this multiscale problem, the ADMP simulated molecular interactions complying with polarized vibrational spectroscopy unraveled a novel route to chiral

Modifying Poisson equation for near-solute dielectric polarization and solvation free energy

Energy Technology Data Exchange (ETDEWEB)

Yang, Pei-Kun, E-mail: peikun@isu.edu.tw

2016-06-15

Highlights: • We modify the Poisson equation. • The dielectric polarization was calculated from the modified Poisson equation. • The solvation free energies of the solutes were calculated from the dielectric polarization. • The calculated solvation free energies were similar to those obtained from MD simulations. - Abstract: The dielectric polarization P is important for calculating the stability of protein conformation and the binding affinity of protein–protein/ligand interactions and for exploring the nonthermal effect of an external electric field on biomolecules. P was decomposed into the product of the electric dipole moment per molecule p; bulk solvent density N{sub bulk}; and relative solvent molecular density g. For a molecular solute, 4πr{sup 2}p(r) oscillates with the distance r to the solute, and g(r) has a large peak in the near-solute region, as observed in molecular dynamics (MD) simulations. Herein, the Poisson equation was modified for computing p based on the modified Gauss’s law of Maxwell’s equations, and the potential of the mean force was used for computing g. For one or two charged atoms in a water cluster, the solvation free energies of the solutes obtained by these equations were similar to those obtained from MD simulations.

The use of molecular dynamics to simulate the temperature dependence of the calculated absorption spectrum for Nd3+ :YAG

International Nuclear Information System (INIS)

Klintenberg, M.; Thomas, J.O.; Edvardsson, S.

1998-01-01

Full text: We have previously shown that the use of molecular dynamics (MD) and the inclusion of configuration interaction (CI) effects are important when simulating polarized absorption spectra for rare-earth doped compounds. In this work, we focus on how well the MD approach can account for the temperature dependence of the calculated absorption spectrum for Nd 3+ :YAG (yttrium aluminium garnet), using the standard MD pair-potential of the Born-Mayer-Huggins form. All simulated spectra are compared to the corresponding experimental spectra. The results indicate that the simple pair-potential must be replaced by a many-body potential to describe the motion of the ions sufficiently accurately

Low-Temperature Dynamic Nuclear Polarization at 9.4 Tesla With a 30 Milliwatt Microwave Source

Science.gov (United States)

Thurber, Kent R.; Yau, Wai-Ming; Tycko, Robert

2010-01-01

Dynamic nuclear polarization (DNP) can provide large signal enhancements in nuclear magnetic resonance (NMR) by transfer of polarization from electron spins to nuclear spins. We discuss several aspects of DNP experiments at 9.4 Tesla (400 MHz resonant frequency for 1H, 264 GHz for electron spins in organic radicals) in the 7–80 K temperature range, using a 30 mW, frequency-tunable microwave source and a quasi-optical microwave bridge for polarization control and low-loss microwave transmission. In experiments on frozen glycerol/water doped with nitroxide radicals, DNP signal enhancements up to a factor of 80 are observed (relative to 1H NMR signals with thermal equilibrium spin polarization). The largest sensitivity enhancements are observed with a new triradical dopant, DOTOPA-TEMPO. Field modulation with a 10 G root-mean-squared amplitude during DNP increases the nuclear spin polarizations by up to 135%. Dependencies of 1H NMR signal amplitudes, nuclear spin relaxation times, and DNP build-up times on the dopant and its concentration, temperature, microwave power, and modulation frequency are reported and discussed. The benefits of low-temperature DNP can be dramatic: the 1H spin polarization is increased approximately 1000-fold at 7 K with DNP, relative to thermal polarization at 80 K. PMID:20392658

Fermionic molecular dynamics for colliding and decaying nuclei

International Nuclear Information System (INIS)

Feldmeier, H.; Schnack, J.

1993-11-01

Fermionic Molecular Dynamics models a system of fermions by means of a trial many-body state composed of an antisymmetrized product of single-particle states which are localized gaussians in coordinate and momentum space. The parameters specifying them are the analogue to the variables in classical molecular dynamics. The time-dependent variational principle yields the equations of motion which are solved for collisions of 12 C+ 12 C and deexcitations of 12 C. The collisions show a great variety of phenomena including explosion, sequential fragmentation and multifragmentation. The deexcitation for nuclei with E * /A ∼ 5MeV is dominated by particle evaporation on time scales of the order of 10 -20 s or longer. (orig.)

Optical spectra and lattice dynamics of molecular crystals

CERN Document Server

Zhizhin, GN

1995-01-01

The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.

Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids

International Nuclear Information System (INIS)

De Leeuw, S.W.; Brakkee, M.J.D.

1990-01-01

Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs

Modifications to 8x8 dynamical theory: Polarizations redefined according to x-ray diffraction convention

International Nuclear Information System (INIS)

Macrander, A.T.; Blasdell, R.C.

1993-09-01

Dynamical x-ray diffraction theory can be cast in matrix form. In recent years, an 8x8 matrix theory was developed that treated asymmetric reflections from strained crystals. The polarization of the incident, specularly reflected, reflected diffracted, transmitted diffracted, and transmitted electromagnetic wave fields were all defined as s or p. That is, polarizations were defined with respect to the plane containing the incident beam direction and the surface normal. The authors present modifications of the theory to treat σ and π polarizations for Bragg diffraction from asymmetric planes, that is, for polarizations defined with respect to the plane containing the incident beam direction and the reciprocal lattice vector for Bragg diffraction. They present results of this theory for unstrained crystals in the inclined geometry. In this geometry the incident beam wavevector, the reciprocal lattice vector, and the surface normal are not coplanar. The inclined crystal geometry appears promising for use in a high-heat-load monochromator for undulator radiation at the Advanced Photon Source. As expected, they find a weak π-polarization component in the diffracted beam when the polarization of the incident beam is pure σ

Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

Energy Technology Data Exchange (ETDEWEB)

Lambert, F

2007-08-15

The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

Science.gov (United States)

Cooke, Ben; Schmidler, Scott C

2008-10-28

We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.

Orthonormal Wavelet Bases for Quantum Molecular Dynamics

International Nuclear Information System (INIS)

Tymczak, C.; Wang, X.

1997-01-01

We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society

Non-Adiabatic Molecular Dynamics Methods for Materials Discovery

Energy Technology Data Exchange (ETDEWEB)

Furche, Filipp [Univ. of California, Irvine, CA (United States); Parker, Shane M. [Univ. of California, Irvine, CA (United States); Muuronen, Mikko J. [Univ. of California, Irvine, CA (United States); Roy, Saswata [Univ. of California, Irvine, CA (United States)

2017-04-04

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

Molecular MRI based on hyper-polarized xenon

International Nuclear Information System (INIS)

Tassali, Nawal

2012-01-01

Magnetic Resonance Imaging (MRI) has a high importance in medicine as it enables the observation of the organs inside the body without the use of radiative or invasive techniques. However it is known to suffer from poor sensitivity. To circumvent this limitation, a key solution resides in the use of hyper-polarized species. Among the entities with which we can drastically increase nuclear polarization, xenon has very specific properties through its interactions with its close environment that lead to a wide chemical shift bandwidth. The goal is thus to use it as a tracer. This PhD thesis focuses on the concept of 129 Xe MRI-based sensors for the detection of biological events. In this approach, hyper-polarized xenon is vectorized to biological targets via functionalized host systems, and then localized thanks to fast dedicated MRI sequences. The conception and set-up of a spin-exchange optical pumping device is first described. Then studies about the interaction of the hyper-polarized noble gas with new cryptophanes susceptible to constitute powerful host molecules are detailed. Also the implementation of recent MRI sequences optimized for the transient character of the hyper-polarization and taking profit of the xenon in-out exchange is described. Applications of this approach for the detection of metallic ions and cellular receptors are studied. Finally, our first in vivo results on a small animal model are presented. (author) [fr

Molecular dynamics simulations of disjoining pressure effects in ultra-thin water films on a metal surface

Science.gov (United States)

Hu, Han; Sun, Ying

2013-11-01

Disjoining pressure, the excess pressure in an ultra-thin liquid film as a result of van der Waals interactions, is important in lubrication, wetting, flow boiling, and thin film evaporation. The classic theory of disjoining pressure is developed for simple monoatomic liquids. However, real world applications often utilize water, a polar liquid, for which fundamental understanding of disjoining pressure is lacking. In the present study, molecular dynamics (MD) simulations are used to gain insights into the effect of disjoining pressure in a water thin film. Our MD models were firstly validated against Derjaguin's experiments on gold-gold interactions across a water film and then verified against disjoining pressure in an argon thin film using the Lennard-Jones potential. Next, a water thin film adsorbed on a gold surface was simulated to examine the change of vapor pressure with film thickness. The results agree well with the classic theory of disjoining pressure, which implies that the polar nature of water molecules does not play an important role. Finally, the effects of disjoining pressure on thin film evaporation in nanoporous membrane and on bubble nucleation are discussed.

Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes

NARCIS (Netherlands)

Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes

2007-01-01

This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the

Molecular dynamics for reactions of heterogeneous catalysis

NARCIS (Netherlands)

Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

1991-01-01

An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.

Electron paramagnetic resonance and dynamic nuclear polarization of char suspensions: surface science and oximetry

DEFF Research Database (Denmark)

Clarkson, R B; Odintsov, B M; Ceroke, P J

1998-01-01

; they can be calibrated and used for oximetry. Biological stability and low toxicity make chars good sensors for in vivo measurements. Scalar and dipolar interactions of water protons at the surfaces of chars may be utilized to produce dynamic nuclear polarization (DNP) of the nuclear spin population...

Study of excess carrier dynamics in polar, semi-polar, and non-polar (In,Ga)N epilayers and QWs

Energy Technology Data Exchange (ETDEWEB)

Aleksiejunas, R. [Institute of Applied Research, Vilnius University, Sauletekio Ave. 9-III, 10222 Vilnius (Lithuania); Laser Research Center, Vilnius University, Sauletekio Ave. 10, 10222 Vilnius (Lithuania); Lubys, L.; Jarasiunas, K. [Institute of Applied Research, Vilnius University, Sauletekio Ave. 9-III, 10222 Vilnius (Lithuania); Vengris, M. [Laser Research Center, Vilnius University, Sauletekio Ave. 10, 10222 Vilnius (Lithuania); Wernicke, T.; Hoffmann, V.; Netzel, C.; Knauer, A.; Weyers, M. [Ferdinand-Braun-Institut, Leibniz-Institut fuer Hoechstfrequenztechnik, Gustav-Kirchhoff-Str. 4, 12498 Berlin (Germany); Kneissl, M. [Ferdinand-Braun-Institut, Leibniz-Institut fuer Hoechstfrequenztechnik, Gustav-Kirchhoff-Str. 4, 12498 Berlin (Germany); Institute of Solid State Physics, Technische Universitaet Berlin, Hardenbergstr. 36, 10623 Berlin (Germany)

2011-07-15

We studied carrier recombination and diffusion in GaN/sapphire templates, (In,Ga)N layers, and (In,Ga)N quantum well structures oriented along the polar [0001], semi-polar [11-22], and non-polar [11-20] orientations by means of light induced transient grating, differential transmission, and photoluminescence optical techniques. We show that the lifetime of excess carriers drops by orders of magnitude when changing the orientation from polar to non-polar, both in GaN templates and (In,Ga)N layers. We attribute the shorter lifetime to carrier trapping by extended structural defects that are more abundant in non-polar grown samples. In addition, we observe pronounced carrier localization effects in the semi- and non-polar layers. We show that thick (In,Ga)N layers inherit the properties of the GaN templates. However, the thin quantum well structures show a lower carrier trapping activity. So, a better electrical quality can be assumed as compared to the thick (In,Ga)N layers. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Molecular dynamics simulations on PGLa using NMR orientational constraints

Energy Technology Data Exchange (ETDEWEB)

Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

2015-11-15

NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

Molecular dynamics simulations

International Nuclear Information System (INIS)

Alder, B.J.

1985-07-01

The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs

A new algorithm for extended nonequilibrium molecular dynamics simulations of mixed flow

NARCIS (Netherlands)

Hunt, T.A.; Hunt, Thomas A.; Bernardi, Stefano; Todd, B.D.

2010-01-01

In this work, we develop a new algorithm for nonequilibrium molecular dynamics of fluids under planar mixed flow, a linear combination of planar elongational flow and planar Couette flow. To date, the only way of simulating mixed flow using nonequilibrium molecular dynamics techniques was to impose

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

NARCIS (Netherlands)

van Dijk, Marc; Wassenaar, Tsjerk A; Bonvin, Alexandre M J J

2012-01-01

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations

NARCIS (Netherlands)

van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.

2012-01-01

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

Reaction dynamics in polyatomic molecular systems

Energy Technology Data Exchange (ETDEWEB)

Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

1993-12-01

The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

Energy conservation in molecular dynamics simulations of classical systems

DEFF Research Database (Denmark)

Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

2012-01-01

Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

Implementation of surface hopping molecular dynamics using semiempirical methods

International Nuclear Information System (INIS)

Fabiano, E.; Keal, T.W.; Thiel, W.

2008-01-01

A molecular dynamics driver and surface hopping algorithm for nonadiabatic dynamics has been implemented in a development version of the MNDO semiempirical electronic structure package. The required energies, gradients and nonadiabatic couplings are efficiently evaluated on the fly using semiempirical configuration interaction methods. The choice of algorithms for the time evolution of the nuclear motion and quantum amplitudes is discussed, and different schemes for the computation of nonadiabatic couplings are analysed. The importance of molecular orbital tracking and electronic state following is underlined in the context of configuration interaction calculations. The method is applied to three case studies (ethylene, methaniminium ion, and methanimine) using the orthogonalization corrected OM2 Hamiltonian. In all three cases decay times and dynamics paths similar to high-level ab initio results are obtained

Polar bear population dynamics in the southern Beaufort Sea during a period of sea ice decline

Science.gov (United States)

Bromaghin, Jeffrey F.; McDonald, Trent L.; Stirling, Ian; Derocher, Andrew E.; Richardson, Evan S.; Regehr, Eric V.; Douglas, David C.; Durner, George M.; Atwood, Todd C.; Amstrup, Steven C.

2015-01-01

In the southern Beaufort Sea of the United States and Canada, prior investigations have linked declines in summer sea ice to reduced physical condition, growth, and survival of polar bears (Ursus maritimus). Combined with projections of population decline due to continued climate warming and the ensuing loss of sea ice habitat, those findings contributed to the 2008 decision to list the species as threatened under the U.S. Endangered Species Act. Here, we used mark–recapture models to investigate the population dynamics of polar bears in the southern Beaufort Sea from 2001 to 2010, years during which the spatial and temporal extent of summer sea ice generally declined. Low survival from 2004 through 2006 led to a 25–50% decline in abundance. We hypothesize that low survival during this period resulted from (1) unfavorable ice conditions that limited access to prey during multiple seasons; and possibly, (2) low prey abundance. For reasons that are not clear, survival of adults and cubs began to improve in 2007 and abundance was comparatively stable from 2008 to 2010, with ~900 bears in 2010 (90% CI 606–1212). However, survival of subadult bears declined throughout the entire period. Reduced spatial and temporal availability of sea ice is expected to increasingly force population dynamics of polar bears as the climate continues to warm. However, in the short term, our findings suggest that factors other than sea ice can influence survival. A refined understanding of the ecological mechanisms underlying polar bear population dynamics is necessary to improve projections of their future status and facilitate development of management strategies.

Ab Initio molecular dynamics with excited electrons

NARCIS (Netherlands)

Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

1994-01-01

A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

Conformation Analysis of T1 Lipase on Alcohols Solvent using Molecular Dynamics Simulation

Science.gov (United States)

Putri, A. M.; Sumaryada, T.; Wahyudi, S. T.

2017-07-01

Biodiesel usually is produced commercially via a transesterification reaction of vegetable oil with alcohol and alkali catalyst. The alkali catalyst has some drawbacks, such as the soap formation during the reaction. T1 Lipase enzyme had been known as a thermostable biocatalyst which is able to produce biodiesel through a cleaner process. In this paper the performance of T1 lipase enzyme as catalyst for transesterification reaction in pure ethanol, methanol, and water solvents were studied using a Molecular Dynamics (MD) Simulation at temperature of 300 K for 10 nanoseconds. The results have shown that in general the conformation of T1 lipase enzyme in methanol is more dynamics as shown by the value of root mean square deviation (RMSD), root mean squared fluctuation (RMSF), and radius of gyration. The highest solvent accessible surface area (SASA) total was also found in methanol due to the contribution of non-polar amino acid in the interior of the protein. Analysis of MD simulation has also revealed that the enzyme structure tend to be more rigid in ethanol environment. The analysis of electrostatic interactions have shown that Glu359-Arg270 salt-bridge pair might hold the key of thermostability of T1 lipase enzyme as shown by its strong and stable binding in all three solvents.

Molecular dynamics coupled with a virtual system for effective conformational sampling.

Science.gov (United States)

Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

2018-07-15

An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation

DEFF Research Database (Denmark)

Pedersen, U.R.; Peters, Günther H.j.; Westh, P.

2007-01-01

The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...

Polarized infrared reflectance study of free standing cubic GaN grown by molecular beam epitaxy

International Nuclear Information System (INIS)

Lee, S.C.; Ng, S.S.; Hassan, H. Abu; Hassan, Z.; Zainal, N.; Novikov, S.V.; Foxon, C.T.; Kent, A.J.

2014-01-01

Optical properties of free standing cubic gallium nitride grown by molecular beam epitaxy system are investigated by a polarized infrared (IR) reflectance technique. A strong reststrahlen band, which reveals the bulk-like optical phonon frequencies, is observed. Meanwhile, continuous oscillation fringes, which indicate the sample consists of two homogeneous layers with different dielectric constants, are observed in the non-reststrahlen region. By obtaining the first derivative of polarized IR reflectance spectra measured at higher angles of incidence, extra phonon resonances are identified at the edges of the reststrahlen band. The observations are verified with the theoretical results simulated based on a multi-oscillator model. - Highlights: • First time experimental studies of IR optical phonons in bulk like, cubic GaN layer. • Detection of extra phonon modes of cubic GaN by polarized IR reflectance technique. • Revelation of IR multiphonon modes of cubic GaN by first derivative numerical method. • Observation of multiphonon modes requires very high angle of incidence. • Resonance splitting effect induced by third phonon mode is a qualitative indicator

Molecular dynamics simulations of the helical antimicrobial peptide ovispirin-1 in a zwitterionic dodecylphosphocholine micelle

DEFF Research Database (Denmark)

Khandelia, Himanshu; Kaznessis, Yiannis N

2005-01-01

We have carried out a 40-ns all-atom molecular dynamics simulation of the helical antimicrobial peptide ovispirin-1 (OVIS) in a zwitterionic diphosphocholine (DPC) micelle. The DPC micelle serves as an economical and effective model for a cellular membrane owing to the presence of a choline...... headgroup, which resembles those of membrane phospholipids. OVIS, which was initially placed along a micelle diameter, diffuses out to the water-DPC interface, and the simulation stabilizes to an interface-bound steady state in 40 ns. The helical content of the peptide marginally increases in the process...... in the micellar core and the polar side chains protruding into the aqueous phase. There is overwhelming evidence that points to the significant and indispensable participation of hydrophobic residues in binding to the zwitterionic interface. The simulation starts with a conformation that is unbiased toward...

Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

Science.gov (United States)

Shekhar, Adarsh

Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu H. G.; Muckerman, J.T.

2012-05-29

The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

Molecular dynamics simulation of self-diffusion coefficients for liquid metals

International Nuclear Information System (INIS)

Ju Yuan-Yuan; Zhang Qing-Ming; Gong Zi-Zheng; Ji Guang-Fu

2013-01-01

The temperature-dependent coefficients of self-diffusion for liquid metals are simulated by molecular dynamics methods based on the embedded-atom-method (EAM) potential function. The simulated results show that a good inverse linear relation exists between the natural logarithm of self-diffusion coefficients and temperature, though the results in the literature vary somewhat, due to the employment of different potential functions. The estimated activation energy of liquid metals obtained by fitting the Arrhenius formula is close to the experimental data. The temperature-dependent shear-viscosities obtained from the Stokes—Einstein relation in conjunction with the results of molecular dynamics simulation are generally consistent with other values in the literature. (atomic and molecular physics)

Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Federica Chiappori

Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.

Solid state nuclear magnetic resonance studies of cross polarization from quadrupolar nuclei

Energy Technology Data Exchange (ETDEWEB)

De Paul, Susan M. [Univ. of California, Berkeley, CA (United States)

1997-08-01

The development of solid-state Nuclear Magnetic Resonance (NMR) has, to a large extent, focused on using spin-1/2 nuclei as probes to investigate molecular structure and dynamics. For such nuclei, the technique of cross polarization is well-established as a method for sensitivity enhancement. However, over two-thirds of the nuclei in the periodic table have a spin-quantum number greater than one-half and are known as quadrupolar nuclei. Such nuclei are fundamental constituents of many inorganic materials including minerals, zeolites, glasses, and gels. It is, therefore, of interest to explore the extent to which polarization can be transferred from quadrupolar nuclei. In this dissertation, solid-state NMR experiments involving cross polarization from quadrupolar nuclei to spin-1/2 nuclei under magic-angle spinning (MAS) conditions are investigated in detail.

Catalysis and communication in dynamic molecular networks

NARCIS (Netherlands)

Fanlo Virgos, Hugo

2015-01-01

The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity

Molecular dynamics study of atomic displacements in disordered solid alloys

Science.gov (United States)

Puzyrev, Yevgeniy S.

The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.

Bridging the gap between molecular dynamics simulations and phase-field modelling: dynamics of a [NixZr1-x]liquid-Zrcrystal solidification front

International Nuclear Information System (INIS)

Danilov, Denis; Nestler, Britta; Guerdane, Mohammed; Teichler, Helmar

2009-01-01

Results are presented from phase-field modelling and molecular dynamics simulations concerning the relaxation dynamics in a finite-temperature two-phase crystal-liquid sample subjected to an abrupt temperature drop. Relaxation takes place by propagation of the solidification front under formation of a spatially varying concentration profile in the melt. The molecular dynamics simulations are carried out with an interatomic model appropriate for the NiZr alloy system and provide the thermophysical data required for setting up the phase-field simulations. Regarding the concentration profile and velocity of the solidification front, best agreement between the phase-field model and molecular dynamics simulation is obtained when increasing the apparent diffusion coefficients in the phase-field treatment by a factor of four against their molecular dynamics estimates.

Visualizing functional motions of membrane transporters with molecular dynamics simulations.

Science.gov (United States)

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

Polarized particle levitation in hexapole field

International Nuclear Information System (INIS)

Jones, T.B.; Kallio, G.A.; Robinson, K.S.

1976-06-01

Proposed here is a novel electrostatic levitation scheme which uses the force exerted by a non-uniform electric field on a polarized particle. The scheme differs from conventional quadrupole levitation devices principally in that the levitated particle is uncharged. In order to provide the proper force required to achieve dynamic stabilization, a very intense non-uniform time-varying electric field produced by a three-dimensional hexapole electrode structure is utilized. The primary advantage of this levitation scheme might accrue in target fabrication operations where particle charge is undesirable or where reproducible charging of the particles themselves is difficult, due to high resistivity. The disadvantages of this scheme, as compared to charged particle levitation, are (i) a more complex electrode structure and (ii) significantly higher voltages. The scheme has possible application to molecular mass spectrometry, in situations where un-ionized but strongly polar or polarizable molecules are to be trapped or confined for analysis

Laser Controlled Molecular Orientation Dynamics

International Nuclear Information System (INIS)

Atabek, O.

2004-01-01

Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation

Dynamic exposure model analysis of continuous laser direct writing in Polar-coordinate

Science.gov (United States)

Zhang, Shan; Lv, Yingjun; Mao, Wenjie

2018-01-01

In order to exactly predict the continuous laser direct writing quality in Polar-coordinate, we take into consideration the effect of the photoresist absorbing beam energy, the Gaussian attribute of the writing beam and the dynamic exposure process, and establish a dynamic exposure model to describe the influence of the tangential velocity of the normal incident facular center and laser power on the line width and sidewall angle. Numerical simulation results indicate that while writing velocity remains unchanged, the line width and sidewall angle are all increased as the laser power increases; while laser power remains unchanged, the line width and sidewall angle are all decreased as the writing velocity increases; at the same time the line profile in the exposure section is asymmetry and the center of the line has tiny excursion toward the Polar-coordinate origin compared with the facular center. Then it is necessary to choose the right writing velocity and laser power to obtain the ideal line profile. The model makes up the shortcomings of traditional models that can only predict line width or estimate the profile of the writing line in the absence of photoresist absorption, and can be considered as an effect analysis method for optimizing the parameters of fabrication technique of laser direct writing.

Resonance-inclined optical nuclear spin polarization of liquids in diamond structures

Science.gov (United States)

Chen, Q.; Schwarz, I.; Jelezko, F.; Retzker, A.; Plenio, M. B.

2016-02-01

Dynamic nuclear polarization (DNP) of molecules in a solution at room temperature has the potential to revolutionize nuclear magnetic resonance spectroscopy and imaging. The prevalent methods for achieving DNP in solutions are typically most effective in the regime of small interaction correlation times between the electron and nuclear spins, limiting the size of accessible molecules. To solve this limitation, we design a mechanism for DNP in the liquid phase that is applicable for large interaction correlation times. Importantly, while this mechanism makes use of a resonance condition similar to solid-state DNP, the polarization transfer is robust to a relatively large detuning from the resonance due to molecular motion. We combine this scheme with optically polarized nitrogen-vacancy (NV) center spins in nanodiamonds to design a setup that employs optical pumping and is therefore not limited by room temperature electron thermal polarization. We illustrate numerically the effectiveness of the model in a flow cell containing nanodiamonds immobilized in a hydrogel, polarizing flowing water molecules 4700-fold above thermal polarization in a magnetic field of 0.35 T, in volumes detectable by current NMR scanners.

Molecular dynamics simulations of solutions at constant chemical potential

Science.gov (United States)

Perego, C.; Salvalaglio, M.; Parrinello, M.

2015-04-01

Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

The 2011 Dynamics of Molecular Collisions Conference

Energy Technology Data Exchange (ETDEWEB)

Nesbitt, David J. [JILA, NIST

2011-07-11

The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

Dynamic nuclear polarization of membrane proteins: covalently bound spin-labels at protein–protein interfaces

International Nuclear Information System (INIS)

Wylie, Benjamin J.; Dzikovski, Boris G.; Pawsey, Shane; Caporini, Marc; Rosay, Melanie; Freed, Jack H.; McDermott, Ann E.

2015-01-01

We demonstrate that dynamic nuclear polarization of membrane proteins in lipid bilayers may be achieved using a novel polarizing agent: pairs of spin labels covalently bound to a protein of interest interacting at an intermolecular interaction surface. For gramicidin A, nitroxide tags attached to the N-terminal intermolecular interface region become proximal only when bimolecular channels forms in the membrane. We obtained signal enhancements of sixfold for the dimeric protein. The enhancement effect was comparable to that of a doubly tagged sample of gramicidin C, with intramolecular spin pairs. This approach could be a powerful and selective means for signal enhancement in membrane proteins, and for recognizing intermolecular interfaces

A review of molecular effects in gas-phase KL X-ray emission

Energy Technology Data Exchange (ETDEWEB)

Guillemin, Renaud; Carniato, Stéphane; Journel, Loïc [UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); Stolte, Wayne C. [Department of Chemistry, University of Nevada, Las Vegas, NV 89154-4003 (United States); Marchenko, Tatiana; Khoury, Lara El; Kawerk, Elie; Piancastelli, Maria Novella [UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); Hudson, Amanda C.; Lindle, Dennis W. [Department of Chemistry, University of Nevada, Las Vegas, NV 89154-4003 (United States); Simon, Marc, E-mail: marc.simon@upmc.fr [UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France)

2013-06-15

The unique capabilities of resonant inelastic X-ray scattering (RIXS) to provide a deep insight into molecular dynamics following core excitation are reviewed here. Characteristic features of molecular X-ray emission are experimentally observed and theoretically interpreted. Some of our most significant results on molecular dynamics following deep core excitation are presented. In particular, we provide several examples of nuclear dynamics on the femtosecond or subfemtosecond time scale; line-narrowing effects related to the quenching of vibrational structure due to parallelism of intermediate and final state curves; anomalous line dispersion across a resonance, which is due to core-hole lifetime effects; spin–orbit-state populations derived from polarized RIXS experiments. We also show how to connect the RIXS results to the general chemical properties of the investigated systems.

A review of molecular effects in gas-phase KL X-ray emission

International Nuclear Information System (INIS)

Guillemin, Renaud; Carniato, Stéphane; Journel, Loïc; Stolte, Wayne C.; Marchenko, Tatiana; Khoury, Lara El; Kawerk, Elie; Piancastelli, Maria Novella; Hudson, Amanda C.; Lindle, Dennis W.; Simon, Marc

2013-01-01

The unique capabilities of resonant inelastic X-ray scattering (RIXS) to provide a deep insight into molecular dynamics following core excitation are reviewed here. Characteristic features of molecular X-ray emission are experimentally observed and theoretically interpreted. Some of our most significant results on molecular dynamics following deep core excitation are presented. In particular, we provide several examples of nuclear dynamics on the femtosecond or subfemtosecond time scale; line-narrowing effects related to the quenching of vibrational structure due to parallelism of intermediate and final state curves; anomalous line dispersion across a resonance, which is due to core-hole lifetime effects; spin–orbit-state populations derived from polarized RIXS experiments. We also show how to connect the RIXS results to the general chemical properties of the investigated systems

Fluorescence and NMR spectroscopy together with molecular simulations reveal amphiphilic characteristics of a Burkholderia biofilm exopolysaccharide.

Science.gov (United States)

Kuttel, Michelle M; Cescutti, Paola; Distefano, Marco; Rizzo, Roberto

2017-06-30

Biofilms are a collective mode of bacterial life in which a self-produced matrix confines cells in close proximity to each other. Biofilms confer many advantages, including protection from chemicals (including antibiotics), entrapment of useful extracellular enzymes and nutrients, as well as opportunities for efficient recycling of molecules from dead cells. Biofilm matrices are aqueous gel-like structures composed of polysaccharides, proteins, and DNA stabilized by intermolecular interactions that may include non-polar connections. Recently, polysaccharides extracted from biofilms produced by species of the Burkholderia cepacia complex were shown to possess clusters of rhamnose, a 6-deoxy sugar with non-polar characteristics. Molecular dynamics simulations are well suited to characterizing the structure and dynamics of polysaccharides, but only relatively few such studies exist of their interaction with non-polar molecules. Here we report an investigation into the hydrophobic properties of the exopolysaccharide produced by Burkholderia multivorans strain C1576. Fluorescence experiments with two hydrophobic fluorescent probes established that this polysaccharide complexes hydrophobic species, and NMR experiments confirmed these interactions. Molecular simulations to model the hydrodynamics of the polysaccharide and the interaction with guest species revealed a very flexible, amphiphilic carbohydrate chain that has frequent dynamic interactions with apolar molecules; both hexane and a long-chain fatty acid belonging to the quorum-sensing system of B. multivorans were tested. A possible role of the non-polar domains of the exopolysaccharide in facilitating the diffusion of aliphatic species toward specific targets within the biofilm aqueous matrix is proposed. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Towards the molecular bases of polymerase dynamics

International Nuclear Information System (INIS)

Chela Flores, J.

1991-03-01

One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs

Dynamical quenching of tunneling in molecular magnets

International Nuclear Information System (INIS)

José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.

2015-01-01

It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation

Dynamical quenching of tunneling in molecular magnets

Energy Technology Data Exchange (ETDEWEB)

José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)

2015-12-15

It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.

A stochastic phase-field model determined from molecular dynamics

KAUST Repository

von Schwerin, Erik

2010-03-17

The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

A stochastic phase-field model determined from molecular dynamics

KAUST Repository

von Schwerin, Erik; Szepessy, Anders

2010-01-01

The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

Nuclear magnetic resonance in pulse radiolysis. Chemically induced dynamic nuclear polarization

International Nuclear Information System (INIS)

Trifunac, A.D.; Johnson, K.W.; Lowers, R.H.

1976-01-01

Nuclear magnetic resonance and chemically induced dynamic nuclear polarization (CIDNP) were applied to the study of pulse radiolysis. Samples were irradiated with a 3-MeV electron beam from the Argonne Van de Graaff accelerator in an EPR magnet (approximately 4000 G) which had axial holes for beam access. A fast flow system transferred the irradiated solution to the rotating 5-mm NMR sample tube. The NMR spectra of mixtures of sodium acetate and methanol were presented to demonstrate the features of the CIDNP in pulse radiolysis

A new and unifying approach to spin dynamics and beam polarization in storage rings

International Nuclear Information System (INIS)

Heinemann, K.; Ellison, J.A.

2014-09-01

With this paper we extend our studies on polarized beams by distilling tools from the theory of principal bundles. Four major theorems are presented, one which ties invariant fields with the notion of normal form, one which allows one to compare different invariant fields, and two that relate the existence of invariant fields to the existence of certain invariant sets and relations between them. We then apply the theory to the dynamics of spin-1/2 and spin-1 particles and their density matrices describing statistically the particle-spin content of bunches. Our approach thus unifies the spin-vector dynamics from the T-BMT equation with the spin-tensor dynamics and other dynamics. This unifying aspect of our approach relates the examples elegantly and uncovers relations between the various underlying dynamical systems in a transparent way.

Nanopore wall-liquid interaction under scope of molecular dynamics study: Review

Science.gov (United States)

Tsukanov, A. A.; Psakhie, S. G.

2017-12-01

The present review is devoted to the analysis of recent molecular dynamics based on the numerical studies of molecular aspects of solid-fluid interaction in nanoscale channels. Nanopore wall-liquid interaction plays the crucial role in such processes as gas separation, water desalination, liquids decontamination, hydrocarbons and water transport in nano-fractured geological formations. Molecular dynamics simulation is one of the most suitable tools to study molecular level effects occurred in such multicomponent systems. The nanopores are classified by their geometry to four groups: nanopore in nanosheet, nanotube-like pore, slit-shaped nanopore and soft-matter nanopore. The review is focused on the functionalized nanopores in boron nitride nanosheets as novel selective membranes and on the slit-shaped nanopores formed by minerals.

Dynamic deuteron polarization measurements performed in a new type of horizontal dilution cryostat

International Nuclear Information System (INIS)

Meyer, W.; Althoff, K.H.; Kaul, O.; Riechert, H.; Schilling, E.

1982-05-01

We have reached 31% deuteron polarization in D- ammonia (ND 3 ) and 27% in D- butanol (C 4 D 10 O). The dynamic polarization experiments were performed at a magnetic field of 2.5 T in a new type of horizontal dilution cryostat. This dilution cryostat, built for target asymmetry measurements with a photon beam, was developed with special regard to fast cool-down and easy loading of the target material. The cooling power is 5 mW at 0.2 K, 20 mW at 0.3 K and 34 mW at 0.4 K. Starting from room temperature the lowest temperature of 165 mK is reached in about 2 h including the loading of the target material. (orig.)

Inter-cage dynamics in structure I, II, and H fluoromethane hydrates as studied by NMR and molecular dynamics simulations

International Nuclear Information System (INIS)

Trueba, Alondra Torres; Kroon, Maaike C.; Peters, Cor J.; Moudrakovski, Igor L.; Ratcliffe, Christopher I.; Ripmeester, John A.; Alavi, Saman

2014-01-01

Prospective industrial applications of clathrate hydrates as materials for gas separation require further knowledge of cavity distortion, cavity selectivity, and defects induction by guest-host interactions. The results presented in this contribution show that under certain temperature conditions the guest combination of CH 3 F and a large polar molecule induces defects on the clathrate hydrate framework that allow intercage guest dynamics. 13 C NMR chemical shifts of a CH 3 F/CH 4 /TBME sH hydrate and a temperature analysis of the 2 H NMR powder lineshapes of a CD 3 F/THF sII and CD 3 F/TBME sH hydrate, displayed evidence that the populations of CH 4 and CH 3 F in the D and D ′ cages were in a state of rapid exchange. A hydrogen bonding analysis using molecular dynamics simulations on the TBME/CH 3 F and TBME/CH 4 sH hydrates showed that the presence of CH 3 F enhances the hydrogen bonding probability of the TBME molecule with the water molecules of the cavity. Similar results were obtained for THF/CH 3 F and THF/CH 4 sII hydrates. The enhanced hydrogen bond formation leads to the formation of defects in the water hydrogen bonding lattice and this can enhance the migration of CH 3 F molecules between adjacent small cages

Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics

International Nuclear Information System (INIS)

Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.

2004-01-01

Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the 'Wannier gauge'. An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches

Ferroelectric glass of spheroidal dipoles with impurities: polar nanoregions, response to applied electric field, and ergodicity breakdown

International Nuclear Information System (INIS)

Takae, Kyohei; Onuki, Akira

2017-01-01

Using molecular dynamics simulation, we study dipolar glass in crystals composed of slightly spheroidal, polar particles and spherical, apolar impurities between metal walls. We present physical pictures of ferroelectric glass, which have been observed in relaxors, mixed crystals (such as KCN x KBr 1−x ), and polymers. Our systems undergo a diffuse transition in a wide temperature range, where we visualize polar nanoregions (PNRs) surrounded by impurities. In our simulation, the impurities form clusters and their space distribution is heterogeneous. The polarization fluctuations are enhanced at relatively high T depending on the size of the dipole moment. They then form frozen PNRs as T is further lowered into the nonergodic regime. As a result, the dielectric permittivity exhibits the characteristic features of relaxor ferroelectrics. We also examine nonlinear response to cyclic applied electric field and nonergodic response to cyclic temperature changes (ZFC/FC), where the polarization and the strain change collectively and heterogeneously. We also study antiferroelectric glass arising from molecular shape asymmetry. We use an Ewald scheme of calculating the dipolar interaction in applied electric field. (paper)

The use of molecular dynamics for the thermodynamic properties of simple and transition metals

International Nuclear Information System (INIS)

Straub, G.K.

1987-04-01

The technique of computer simulation of the molecular dynamics in metallic systems to calculate thermodynamic properties is discussed. The nature of a metal as determined by its electronic structure is used to determine the total adiabatic potential. The effective screened ion-ion interaction can then be used in a molecular dynamics simulation. The method for the construction of a molecular dynamics ensemble, its relation to the canonical ensemble, and the definition of thermodynamic functions from the Helmholtz free energy is given. The method for the analysis of the molecular dynamics results from quasiharmonic lattice dynamics and the decomposition in terms of harmonic and anharmonic contributions is given for solids. For fluid phase metals, procedures for calculating the thermodynamics and determining the constant of entropy are presented. The solid-fluid phase boundary as a function of pressure and temperature is determined using the results of molecular dynamics. Throughout, examples and results for metallic sodium are used. The treatment of the transition metal electronic d-states in terms of an effective pair-wise interaction is also discussed and the phonon dispersion curves of Al, Ni, and Cu are calculated

Molecular dynamic simulation of the self-assembly of DAP12-NKG2C activating immunoreceptor complex.

Directory of Open Access Journals (Sweden)

Peng Wei

Full Text Available The DAP12-NKG2C activating immunoreceptor complex is one of the multisubunit transmembrane protein complexes in which ligand-binding receptor chains assemble with dimeric signal-transducing modules through non-covalent associations in their transmembrane (TM domains. In this work, both coarse grained and atomistic molecular dynamic simulation methods were applied to investigate the self-assembly dynamics of the transmembrane domains of the DAP12-NKG2C activating immunoreceptor complex. Through simulating the dynamics of DAP12-NKG2C TM heterotrimer and point mutations, we demonstrated that a five-polar-residue motif including: 2 Asps and 2 Thrs in DAP12 dimer, as well as 1 Lys in NKG2C TM plays an important role in the assembly structure of the DAP12-NKG2C TM heterotrimer. Furthermore, we provided clear evidences to exclude the possibility that another NKG2C could stably associate with the DAP12-NKG2C heterotrimer. Based on the simulation results, we proposed a revised model for the self-assembly of DAP12-NKG2C activating immunoreceptor complex, along with a plausible explanation for the association of only one NKG2C with a DAP12 dimer.

Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene

Energy Technology Data Exchange (ETDEWEB)

Cawkwell, M. J., E-mail: cawkwell@lanl.gov; Niklasson, Anders M. N. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Dattelbaum, Dana M. [Weapons Experiments Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2015-02-14

The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene.

Science.gov (United States)

Cawkwell, M J; Niklasson, Anders M N; Dattelbaum, Dana M

2015-02-14

The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS

NARCIS (Netherlands)

AHLSTROM, P; BERENDSEN, HJC

1993-01-01

Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)

Photophysics of Curcumin excited state in toluene-polar solvent mixtures: Role of H-bonding properties of the polar solvent

Energy Technology Data Exchange (ETDEWEB)

Saini, R.K.; Das, K., E-mail: kaustuv@rrcat.gov.in

2014-01-15

Excited state dynamics of Curcumin in binary solvent mixtures of toluene and polar H-bonding solvents were compared by using an instrument endowed with 40 ps time resolution. The solvation time constant of Curcumin increases significantly (and can therefore be measured) in polar solvents which have, either, both H-bond donating and accepting ability, or, only H-bond donating ability. These results suggest that the rate limiting step in the excited state dynamics of the pigment might be the formation and reorganization of the intermolecular H-bonding between the keto group of the pigment and the H-bond donating moieties of the polar solvent. -- Highlights: • Excited state dynamics of Curcumin in a binary solvent mixture of toluene and three polar H-bonding solvents were compared. • The solvation time constant increases significantly with polar solvents having, H-bond donating and accepting, or, H-bond donating ability. • Observed results suggest that H-bonding property of polar solvent plays an important role in the excited state dynamics. • Intermolecular H-bonding between the keto group of the pigment and polar solvent may be the rate limiting step.

Photophysics of Curcumin excited state in toluene-polar solvent mixtures: Role of H-bonding properties of the polar solvent

International Nuclear Information System (INIS)

Saini, R.K.; Das, K.

2014-01-01

Excited state dynamics of Curcumin in binary solvent mixtures of toluene and polar H-bonding solvents were compared by using an instrument endowed with 40 ps time resolution. The solvation time constant of Curcumin increases significantly (and can therefore be measured) in polar solvents which have, either, both H-bond donating and accepting ability, or, only H-bond donating ability. These results suggest that the rate limiting step in the excited state dynamics of the pigment might be the formation and reorganization of the intermolecular H-bonding between the keto group of the pigment and the H-bond donating moieties of the polar solvent. -- Highlights: • Excited state dynamics of Curcumin in a binary solvent mixture of toluene and three polar H-bonding solvents were compared. • The solvation time constant increases significantly with polar solvents having, H-bond donating and accepting, or, H-bond donating ability. • Observed results suggest that H-bonding property of polar solvent plays an important role in the excited state dynamics. • Intermolecular H-bonding between the keto group of the pigment and polar solvent may be the rate limiting step

Correlations and symmetry of interactions influence collective dynamics of molecular motors

International Nuclear Information System (INIS)

Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B

2015-01-01

Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)

Molecular dynamics simulation of impact test

International Nuclear Information System (INIS)

Akahoshi, Y.; Schmauder, S.; Ludwig, M.

1998-01-01

This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

Molecular dynamics simulation of impact test

Energy Technology Data Exchange (ETDEWEB)

Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

1998-11-01

This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

Pulsed Electrical Spin Injection into InGaAs Quantum Dots: Studies of the Electroluminescence Polarization Dynamics

International Nuclear Information System (INIS)

Asshoff, P.; Loeffler, W.; Fluegge, H.; Zimmer, J.; Mueller, J.; Westenfelder, B.; Hu, D. Z.; Schaadt, D. M.; Kalt, H.; Hetterich, M.

2010-01-01

We present time-resolved studies of the spin polarization dynamics during and after initialization through pulsed electrical spin injection into InGaAs quantum dots embedded in a p-i-n-type spin-injection light-emitting diode. Experiments are performed with pulse widths in the nanosecond range and a time-resolved single photon counting setup is used to detect the subsequent electroluminescence. We find evidence that the achieved spin polarization shows an unexpected temporal behavior, attributed mainly to many-carrier and non-equilibrium effects in the device.

Carrier and polarization dynamics in monolayer MoS2: temperature and power dependence

Science.gov (United States)

Urbaszek, Bernhard; Lagarde, D.; Bouet, L.; Amand, T.; Marie, X.; Zhu, C. R.; Liu, B. L.; Tan, P. H.

2014-03-01

In monolayer (ML) MoS2 optical transitions across the direct bandgap are governed by chiral selection rules, allowing optical k-valley initialization. Here we present the first time resolved photoluminescence (PL) polarization measurements in MoS2 MLs, providing vital information on the electron valley dynamics. Using quasi-resonant excitation of the A-exciton transitions, we can infer that the PL decays within τ ~= 4ps. The PL polarization of Pc ~ 60 % remains nearly constant in time for experiments from 4K - 300K, a necessary condition for the success of future Valley Hall experiments. τ does not vary significantly over this temperature range. This is surprising when considering the decrease of Pc in continuous wave experiments when going from 4K to 300K reported in the literature. By tuning the laser following the shift of the A-exciton resonance with temperature we are able to recover at 300K ~ 80 % of the polarization observed at 4K. For pulsed laser excitation, we observe a decrease of Pc with increasing laser power at all temperatures.

Collapse dynamics of a vector vortex optical field with inhomogeneous states of polarization

International Nuclear Information System (INIS)

Chen, Rui-Pin; Zhao, Ting-Yu; Zhang, Xiaobo; Zhong, Li-Xin; Chew, Khian-Hooi

2015-01-01

Based on a pair of coupled 2D nonlinear Schrödinger equations, the collapse dynamics of a vector field with hybrid states of polarization (SoP) in a Kerr medium is demonstrated. The critical power for an optical field to collapse is present, and the full vectorial numerical simulations provide detailed information about the evolution and partial collapse of the vector field in a Kerr medium. Our results reveal that the optical field prefers to collapse in linearly-polarization, as a result of the self-focusing effect difference in linearly, elliptically and circularly polarized components. The SoP in the field cross-section changes and propagates with a spiral trajectory when the vector beams are imposed with a vortex. The vectorial effect on the collapse of a vector optical field can prevail over the noise even though it reaches 10% amplitude of the optical field. The unique feature of these structured collapses of a vector optical field may lead to new phenomena in the interaction of light with matter. (paper)

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Science.gov (United States)

Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

2017-02-14

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

Dopamine and Caffeine Encapsulation within Boron Nitride (14,0) Nanotubes: Classical Molecular Dynamics and First Principles Calculations.

Science.gov (United States)

García-Toral, Dolores; González-Melchor, Minerva; Rivas-Silva, Juan F; Meneses-Juárez, Efraín; Cano-Ordaz, José; H Cocoletzi, Gregorio

2018-06-07

Classical molecular dynamics (MD) and density functional theory (DFT) calculations are developed to investigate the dopamine and caffeine encapsulation within boron nitride (BN) nanotubes (NT) with (14,0) chirality. Classical MD studies are done at canonical and isobaric-isothermal conditions at 298 K and 1 bar in explicit water. Results reveal that both molecules are attracted by the nanotube; however, only dopamine is able to enter the nanotube, whereas caffeine moves in its vicinity, suggesting that both species can be transported: the first by encapsulation and the second by drag. Findings are analyzed using the dielectric behavior, pair correlation functions, diffusion of the species, and energy contributions. The DFT calculations are performed according to the BLYP approach and applying the atomic base of the divided valence 6-31g(d) orbitals. The geometry optimization uses the minimum-energy criterion, accounting for the total charge neutrality and multiplicity of 1. Adsorption energies in the dopamine encapsulation indicate physisorption, which induces the highly occupied molecular orbital-lower unoccupied molecular orbital gap reduction yielding a semiconductor behavior. The charge redistribution polarizes the BNNT/dopamine and BNNT/caffeine structures. The work function decrease and the chemical potential values suggest the proper transport properties in these systems, which may allow their use in nanobiomedicine.

Molecular Dynamics Simulations of a Linear Nanomotor Driven by Thermophoretic Forces

DEFF Research Database (Denmark)

Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

Molecular Dynamics of a Linear Nanomotor Driven by Thermophoresis Harvey A. Zambrano1, Jens H. Walther1,2 and Richard L. Jaffe3 1Department of Mechanical Engineering, Fluid Mechanics, Technical University of Denmark, DK-2800 Lyngby, Denmark; 2Computational Science and Engineering Laboratory, ETH...... future molecular machines a complete understanding of the friction forces involved on the transport process at the molecular level have to be addressed.18 In this work we perform Molecular Dynamics (MD) simulations using the MD package FASTTUBE19 to study a molecular linear motor consisting of coaxial...... the valence forces within the CNT using Morse, harmonic angle and torsion potentials.19We include a nonbonded carbon-carbon Lennard-Jones potential to describe the vdW interaction between the carbon atoms within the double wall portion of the system. We equilibrate the system at 300K for 0.1 ns, by coupling...

Dynamics of the quiet polar cap

International Nuclear Information System (INIS)

Carlson, H.C. Jr.

1990-01-01

Work in the past has established that a few percent of the time, under northward interplanetary magnetic field and thus magnetically quiet conditions, sun aligned arcs are found in the polar cap with intensities greater than the order of a kilo Rayleigh in the visible. Here we extend this view. We first note that imaging systems with sensitivity down to tens of Rayleighs in the visible find sun aligned arcs in the polar cap far more often, closer to half the time than a few percent. Furthermore, these sun aligned arcs have simple electrodynamics. They mark boundaries between rapid antisunward flow of ionospheric plasma on their dawn side and significantly slower flow, or even sunward flow, on their dusk side. Since the sun aligned arcs are typically the order of 1000 km to transpolar in the sun-earth direction, and the order of 100 km or less in the dawn-dusk direction, they demarcate lines of strongly anisotropic ionospheric flow shears or convection cells. The very quiet polar cap (strongly northward IMF) is in fact characterized by the presence of sun aligned arcs and multiple highly anisotropic ionospheric flow shears. Sensitive optical images are a valuable diagnostic with which to study polar ionospheric convection under these poorly understood conditions. (author)

Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

Science.gov (United States)

Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

2017-08-22

A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

Molecular dynamics simulation of a phospholipid membrane

NARCIS (Netherlands)

Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.

We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)

2013-12-21

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

International Nuclear Information System (INIS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-01-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

Science.gov (United States)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Dynamical polarizability of graphene irradiated by circularly polarized ac electric fields

DEFF Research Database (Denmark)

Busl, Maria; Platero, Gloria; Jauho, Antti-Pekka

2012-01-01

We examine the low-energy physics of graphene in the presence of a circularly polarized electric field in the terahertz regime. Specifically, we derive a general expression for the dynamical polarizability of graphene irradiated by an ac electric field. Several approximations are developed...... that allow one to develop a semianalytical theory for the weak-field regime. The ac field changes qualitatively the single- and many-electron excitations of graphene: Undoped samples may exhibit collective excitations (in contrast to the equilibrium situation), and the properties of the excitations in doped...

Thermosetting polymer for dynamic nuclear polarization: Solidification of an epoxy resin mixture including TEMPO

Energy Technology Data Exchange (ETDEWEB)

Noda, Yohei, E-mail: noda.yohei@jaea.go.jp [Quantum Beam Science Centre, Sector of Nuclear Science Research, Japan Atomic Energy Agency, Shirakata-Shirane, Tokai, Ibaraki 319-1195 (Japan); Kumada, Takayuki [Quantum Beam Science Centre, Sector of Nuclear Science Research, Kansai Photon Science Institute, Japan Atomic Energy Agency, Kizugawa, Kyoto 619-0215 (Japan); Yamaguchi, Daisuke; Shamoto, Shin-ichi [Quantum Beam Science Centre, Sector of Nuclear Science Research, Japan Atomic Energy Agency, Shirakata-Shirane, Tokai, Ibaraki 319-1195 (Japan)

2015-03-11

We investigated the dynamic nuclear polarization (DNP) of typical thermosetting polymers (two-component type epoxy resins; Araldite{sup ®} Standard or Araldite{sup ®} Rapid) doped with a (2,2,6,6-tetramethylpiperidine-1-yl)oxy (TEMPO) radical. The doping process was developed by carefully considering the decomposition of TEMPO during the solidification of the epoxy resin. The TEMPO electron spin in each two-component paste decayed slowly, which was favorable for our study. Furthermore, despite the dissolved TEMPO, the mixture of the two-component paste successfully solidified. With the resulting TEMPO-doped epoxy-resin samples, DNP experiments at 1.2 K and 3.35 T indicated a magnitude of a proton-spin polarization up to 39%. This polarization is similar to that (35%) obtained for TEMPO-doped polystyrene (PS), which is often used as a standard sample for DNP. To combine this solidification of TEMPO-including mixture with a resin-casting technique enables a creation of polymeric target materials with a precise and complex structure.

Scattering with polarized neutrons

International Nuclear Information System (INIS)

Schweizer, J.

2007-01-01

In the history of neutron scattering, it was shown very soon that the use of polarized neutron beams brings much more information than usual scattering with unpolarized neutrons. We shall develop here the different scattering methods that imply polarized neutrons: 1) polarized beams without polarization analysis, the flipping ratio method; 2) polarized beams with a uniaxial polarization analysis; 3) polarized beams with a spherical polarization analysis. For all these scattering methods, we shall give examples of the physical problems which can been solved by these methods, particularly in the field of magnetism: investigation of complex magnetic structures, investigation of spin or magnetization densities in metals, insulators and molecular compounds, separation of magnetic and nuclear scattering, investigation of magnetic properties of liquids and amorphous materials and even, for non magnetic material, separation between coherent and incoherent scattering. (author)

Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

DEFF Research Database (Denmark)

Solov'yov, Ilia A.; Korol, Andrei V.; Solov'yov, Andrey V.

-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science...... of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational...... practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational...

Extended Lagrangian formulation of charge-constrained tight-binding molecular dynamics.

Science.gov (United States)

Cawkwell, M J; Coe, J D; Yadav, S K; Liu, X-Y; Niklasson, A M N

2015-06-09

The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [Niklasson, Phys. Rev. Lett., 2008, 100, 123004] has been applied to a tight-binding model under the constraint of local charge neutrality to yield microcanonical trajectories with both precise, long-term energy conservation and a reduced number of self-consistent field optimizations at each time step. The extended Lagrangian molecular dynamics formalism restores time reversal symmetry in the propagation of the electronic degrees of freedom, and it enables the efficient and accurate self-consistent optimization of the chemical potential and atomwise potential energy shifts in the on-site elements of the tight-binding Hamiltonian that are required when enforcing local charge neutrality. These capabilities are illustrated with microcanonical molecular dynamics simulations of a small metallic cluster using an sd-valent tight-binding model for titanium. The effects of weak dissipation on the propagation of the auxiliary degrees of freedom for the chemical potential and on-site Hamiltonian matrix elements that is used to counteract the accumulation of numerical noise during trajectories was also investigated.

Electron-nuclear corellations for photoinduced dynamics in molecular dimers

Science.gov (United States)

Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

2003-03-01

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

Vectorization, parallelization and implementation of Quantum molecular dynamics codes (QQQF, MONTEV)

Energy Technology Data Exchange (ETDEWEB)

Kato, Kaori [High Energy Accelerator Research Organization, Tsukuba, Ibaraki (Japan); Kunugi, Tomoaki; Kotake, Susumu; Shibahara, Masahiko

1998-03-01

This report describes parallelization, vectorization and implementation for two simulation codes, Quantum molecular dynamics simulation code QQQF and Photon montecalro molecular dynamics simulation code MONTEV, that have been developed for the analysis of the thermalization of photon energies in the molecule or materials. QQQF has been vectorized and parallelized on Fujitsu VPP and has been implemented from VPP to Intel Paragon XP/S and parallelized. MONTEV has been implemented from VPP to Paragon and parallelized. (author)

Dynamic Nuclear Polarization at low temperature and high magnetic eld for biomedical applications in Magnetic Resonance Spectroscopic Imaging

International Nuclear Information System (INIS)

Goutailler, Florent

2011-01-01

The aim of this thesis work was to design, build and optimize a large volume multi-samples DNP (Dynamic Nuclear Polarization) polarizer dedicated to Magnetic Resonance Spectroscopic Imaging applications. The experimental system is made up of a high magnetic field magnet (3,35 T) in which takes place a cryogenic system with a pumped bath of liquid helium ("4He) allowing temperatures lower than 1,2 K. A set of inserts is used for the different steps of DNP: irradiation of the sample by a microwave field (f=94 GHz and P=50 mW), polarization measurement by Nuclear Magnetic Resonance... With this system, up to three samples of 1 mL volume can be polarized to a rate of few per-cents. The system has a long autonomy of four hours, so it can be used for polarizing molecules with a long time constant of polarization. Finally, the possibility to get quasi-simultaneously, after dissolution, several samples with a high rate of polarization opens the way of new applications in biomedical imaging. (author) [fr

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

Science.gov (United States)

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS

NARCIS (Netherlands)

JUFFER, AH; BERENDSEN, HJC

1993-01-01

A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the

Molecular dynamics simulations and quantum chemical calculations ...

African Journals Online (AJOL)

Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...

Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain

NARCIS (Netherlands)

Periole, Xavier; Vendruscolo, Michele; Mark, Alan E.

2007-01-01

A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al. (Nat Struct Mol Biol 2004;11:443-449) using molecular dynamics simulations in which

Droplet spreading driven by van der Waals force: a molecular dynamics study

KAUST Repository

Wu, Congmin

2010-07-07

The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t) ∼ √t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid. © 2010 IOP Publishing Ltd.

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.

Science.gov (United States)

Sodt, Alexander J; Mei, Ye; König, Gerhard; Tao, Peng; Steele, Ryan P; Brooks, Bernard R; Shao, Yihan

2015-03-05

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton-Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin-luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.

Magnetic switching of a single molecular magnet due to spin-polarized current

Science.gov (United States)

Misiorny, Maciej; Barnaś, Józef

2007-04-01

Magnetic switching of a single molecular magnet (SMM) due to spin-polarized current flowing between ferromagnetic metallic leads (electrodes) is investigated theoretically. Magnetic moments of the leads are assumed to be collinear and parallel to the magnetic easy axis of the molecule. Electrons tunneling through the barrier between magnetic leads are coupled to the SMM via exchange interaction. The current flowing through the system, as well as the spin relaxation times of the SMM, are calculated from the Fermi golden rule. It is shown that spin of the SMM can be reversed by applying a certain voltage between the two magnetic electrodes. Moreover, the switching may be visible in the corresponding current-voltage characteristics.

Cis-to- Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics.

Science.gov (United States)

Muždalo, Anja; Saalfrank, Peter; Vreede, Jocelyne; Santer, Mark

2018-04-10

Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomerization mechanisms and rates, especially the thermally activated relaxation. For small azo derivatives considered in the gas phase or simple solvents, Eyring's classical transition state theory (TST) approach yields useful predictions for trends in activation energies or corresponding half-life times of the cis isomer. However, TST or improved theories cannot easily be applied when the azo moiety is part of a larger molecular complex or embedded into a heterogeneous environment, where a multitude of possible reaction pathways may exist. In these cases, only the sampling of an ensemble of dynamic reactive trajectories (transition path sampling, TPS) with explicit models of the environment may reveal the nature of the processes involved. In the present work we show how a TPS approach can conveniently be implemented for the phenomenon of relaxation-isomerization of azobenzenes starting with the simple examples of pure azobenzene and a push-pull derivative immersed in a polar (DMSO) and apolar (toluene) solvent. The latter are represented explicitly at a molecular mechanical (MM) and the azo moiety at a quantum mechanical (QM) level. We demonstrate for the push-pull azobenzene that path sampling in combination with the chosen QM/MM scheme produces the expected change in isomerization pathway from inversion to rotation in going from a low to a high permittivity (explicit) solvent model. We discuss the potential of the simulation procedure presented for comparative calculation of

Molecular dynamics simulations of melting behavior of alkane as phase change materials slurry

International Nuclear Information System (INIS)

Rao Zhonghao; Wang Shuangfeng; Wu Maochun; Zhang Yanlai; Li Fuhuo

2012-01-01

Highlights: ► The melting behavior of phase change materials slurry was investigated by molecular dynamics simulation method. ► Four different PCM slurry systems including pure water and water/n-nonadecane composite were constructed. ► Amorphous structure and periodic boundary conditions were used in the molecular dynamics simulations. ► The simulated melting temperatures are very close to the published experimental values. - Abstract: The alkane based phase change materials slurry, with high latent heat storage capacity, is effective to enhance the heat transfer rate of traditional fluid. In this paper, the melting behavior of composite phase change materials slurry which consists of n-nonadecane and water was investigated by using molecular dynamics simulation. Four different systems including pure water and water/n-nonadecane composite were constructed with amorphous structure and periodic boundary conditions. The results showed that the simulated density and melting temperature were very close to the published experimental values. Mixing the n-nonadecane into water decreased the mobility but increased the energy storage capacity of composite systems. To describe the melting behavior of alkane based phase change materials slurry on molecular or atomic scale, molecular dynamics simulation is an effective method.

Polarization experiments

International Nuclear Information System (INIS)

Halzen, F.

1977-02-01

In a theoretical review of polarization experiments two important points are emphasized: (a) their versatility and their relevance to a large variety of aspects of hadron physics (tests of basic symmetries; a probe of strong interaction dynamics; a tool for hadron spectroscopy); (b) the wealth of experimental data on polarization parameters in pp and np scattering in the Regge language and in the diffraction language. (author)

Magnetic nanoparticles in fluid environment: combining molecular dynamics and Lattice-Boltzmann

Energy Technology Data Exchange (ETDEWEB)

Melenev, Petr, E-mail: melenev@icmm.ru [Ural Federal University, 4, Turgeneva str., 620000 Ekaterinburg (Russian Federation); Institute of Continuous Media Mechanics, 1, Koroleva str., 614013 Perm (Russian Federation)

2017-06-01

Hydrodynamic interactions between magnetic nanoparticles suspended in the Newtonian liquid are accounted for using a combination of the lattice Boltzmann method and molecular dynamics simulations. Nanoparticle is modelled by the system of molecular dynamics material points (which form structure resembles raspberry) coupled to the lattice Boltzmann fluid. The hydrodynamic coupling between the colloids is studied by simulations of the thermo-induced rotational diffusion of two raspberry objects. It was found that for the considered range of model parameters the approaching of the raspberries leads to slight retard of the relaxation process. The presence of the weak magnetic dipolar interaction between the objects leads to modest decrease of the relaxation time and the extent of the acceleration of the diffusion is intensified along with magnetic forces. - Highlights: • The combination of molecular dynamics and lattice Boltzmann method is utilized for the reveal of the role of hydrodynamic interaction in rotational dynamics of colloid particles. • The verification of the model parameters is done based on the comparison with the results of Langevin dynamics. • For the task of free rotational diffusion of the pair of colloid particles the influence of the hydrodynamic interactions on the relaxation time is examined in the case of nonmagnetic particles and at the presence of weak dipolar interaction.

Development and performance of a 129-GHz dynamic nuclear polarizer in an ultra-wide bore superconducting magnet.

Science.gov (United States)

Lumata, Lloyd L; Martin, Richard; Jindal, Ashish K; Kovacs, Zoltan; Conradi, Mark S; Merritt, Matthew E

2015-04-01

We sought to build a dynamic nuclear polarization system for operation at 4.6 T (129 GHz) and evaluate its efficiency in terms of (13)C polarization levels using free radicals that span a range of ESR linewidths. A liquid helium cryostat was placed in a 4.6 T superconducting magnet with a 150-mm warm bore diameter. A 129-GHz microwave source was used to irradiate (13)C enriched samples. Temperatures close to 1 K were achieved using a vacuum pump with a 453-m(3)/h roots blower. A hyperpolarized (13)C nuclear magnetic resonance (NMR) signal was detected using a saddle coil and a Varian VNMRS console operating at 49.208 MHz. Samples doped with free radicals BDPA (1,3-bisdiphenylene-2-phenylallyl), trityl OX063 (tris{8-carboxyl-2,2,6,6-benzo(1,2-d:4,5-d)-bis(1,3)dithiole-4-yl}methyl sodium salt), galvinoxyl ((2,6-di-tert-butyl-α-(3,5-di-tert-butyl-4-oxo-2,5-cyclohexadien-1-ylidene)-p-tolyloxy), 2,2-diphenylpicrylhydrazyl (DPPH) and 4-oxo-TEMPO (4-Oxo-2,2,6,6-tetramethyl-1-piperidinyloxy) were assayed. Microwave dynamic nuclear polarization (DNP) spectra and solid-state (13)C polarization levels for these samples were determined. (13)C polarization levels close to 50 % were achieved for [1-(13)C]pyruvic acid at 1.15 K using the narrow electron spin resonance (ESR) linewidth free radicals trityl OX063 and BDPA, while 10-20 % (13)C polarizations were achieved using galvinoxyl, DPPH and 4-oxo-TEMPO. At this field strength free radicals with smaller ESR linewidths are still superior for DNP of (13)C as opposed to those with linewidths that exceed that of the (1)H Larmor frequency.

Low-temperature dynamic nuclear polarization at 9.4 T with a 30 mW microwave source.

Science.gov (United States)

Thurber, Kent R; Yau, Wai-Ming; Tycko, Robert

2010-06-01

Dynamic nuclear polarization (DNP) can provide large signal enhancements in nuclear magnetic resonance (NMR) by transfer of polarization from electron spins to nuclear spins. We discuss several aspects of DNP experiments at 9.4 T (400 MHz resonant frequency for (1)H, 264 GHz for electron spins in organic radicals) in the 7-80K temperature range, using a 30 mW, frequency-tunable microwave source and a quasi-optical microwave bridge for polarization control and low-loss microwave transmission. In experiments on frozen glycerol/water doped with nitroxide radicals, DNP signal enhancements up to a factor of 80 are observed (relative to (1)H NMR signals with thermal equilibrium spin polarization). The largest sensitivity enhancements are observed with a new triradical dopant, DOTOPA-TEMPO. Field modulation with a 10 G root-mean-squared amplitude during DNP increases the nuclear spin polarizations by up to 135%. Dependencies of (1)H NMR signal amplitudes, nuclear spin relaxation times, and DNP build-up times on the dopant and its concentration, temperature, microwave power, and modulation frequency are reported and discussed. The benefits of low-temperature DNP can be dramatic: the (1)H spin polarization is increased approximately 1000-fold at 7 K with DNP, relative to thermal polarization at 80K. (c) 2010 Elsevier Inc. All rights reserved.

Microsecond atomic-scale molecular dynamics simulations of polyimides

NARCIS (Netherlands)

Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.

2013-01-01

We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long

Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

Directory of Open Access Journals (Sweden)

Dirk-Sören Lühmann

2015-08-01

Full Text Available In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.

Dynamic polarization potentials in heavy ion scattering

International Nuclear Information System (INIS)

Wolf, R.

1984-01-01

In this thesis the polarization potential is calculated which is caused by several collective, strongly coupled states. In the framework of the considered model space the calculation of the polarization potential was exact, i.e. no approximations were made. For this purpose the Green function of the system had to be calculated. This led to a nonlocal polarization potential. For the better interpretation possibility and for the easier use in coupled-channel or optical-model calculations from the nonlocal potentials also equivalent potentials were constructed. The properties of the local and nonlocal potentials as shape, angular momentum, and energy dependence were discussed. Furthermore parametrizations were given, how polarization effects can be regarded in a simple way in optical-model or coupled-channel calculations. The calculations were performed for the systems 12 C+ 12 C and 16 O+ 16 O. To meet as realistic results as possible, parameters for the unperturbed potential were looked for which describe as many data as possible, like angular distributions, excitation functions, and alignment of the main channels. As unperturbed potential both folding potentials and phenomenological potentials were applied in order to study the differences in the polarization potential in the application of deep and flat potentials. (orig./HSI) [de

Moving contact lines: linking molecular dynamics and continuum-scale modelling.

Science.gov (United States)

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

2018-05-04

Despite decades of research, the modelling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily-life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide the link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which govern the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modelling, and highlight the opportunities for future developments in this area.

Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

Science.gov (United States)

Li, Jianwei; Nowak, Piotr; Otto, Sijbren

2013-06-26

Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

Subfemtosecond electron dynamics of H{sub 2} in strong fields or the quest for the molecular clock

Energy Technology Data Exchange (ETDEWEB)

Staudte, A.

2005-07-01

In this work we have studied experimentally and theoretically hydrogen and deuterium molecules in strong laser fields. We wanted to demonstrate that control of dynamical processes on the time scale below a single laser cycle (2.7 fs) can be achieved even without using attosecond pulses just by employing the advanced experimental technique COLTRIMS. In order to do this, we have pursued two goals: 1. To examine, whether laser steered electron wavepackets can be used for laser induced electron diffraction (LIED) on molecules. 2. To demonstrate, that the double ionization of H{sub 2} can be followed with sub laser cycle temporal resolution (the molecular clock). Laser induced electron diffraction needs linearly polarized light since its mechanism relies on rescattering of the ionized electron in the molecular potential. With rescattering occurring within a few hundred attoseconds, LIED is really a process of attosecond physics. In principle, two extreme scattering geometries are possible for a homonuclear diatomic molecule like H{sub 2}: the perpendicular geometry, which corresponds to the classical double slit experiment where the electron microbunch is steered transversely to the molecular axis, and the tangential geometry with the electron moving parallel to the molecular axis. Experimental restrictions prevented us to investigate the perpendicular geometry. The molecular clock, on the other hand, employs circularly polarized light to map the absolute phase of the laser electric field onto the spatial direction of the electron momentum. Thereby, a full laser cycle is mapped onto 360 in momentum space. Thus, different electron ejection angles in the laboratory frame correspond to different ejection times. Together with the correlated kinetic energy release of the Coulomb exploding molecules an unambiguous clock running from 0-8 fs with a few 100 as resolution can be envisioned. In direct relation to this experiment, we studied the influence of the long range

Relativistic classical and quantum dynamics in intense crossed laser beams of various polarizations

Directory of Open Access Journals (Sweden)

M. Verschl

2007-02-01

Full Text Available The dynamics of an electron in crossed laser fields is investigated analytically. Two different standing wave configurations are compared. The counterpropagating laser waves are either linearly or circularly polarized. Both configurations have in common that there are one-dimensional trajectories on which the electron can oscillate with vanishing Lorentz force. The dynamics is analyzed for the situations when the electron moves in the vicinity of these ideal axes. If the laser intensities imply nonrelativistic electron dynamics, the system is described quantum mechanically. A semiclassical treatment renders the strongly relativistic regime accessible as well. To describe relativistic wave packets, the results of the classical analysis are employed for a Monte Carlo ensemble. This allows for a comparison of the wave packet dynamics for both configurations in the strongly relativistic regime. It is found for certain cases that relativity slows down the dynamics, i.e., for higher laser intensities, wave packet spreading and the drift away from the ideal axis of vanishing Lorentz force are shown to be increasingly suppressed.

Microphase separation and the formation of ion conductivity channels in poly(ionic liquid)s: A coarse-grained molecular dynamics study

Science.gov (United States)

Weyman, Alexander; Bier, Markus; Holm, Christian; Smiatek, Jens

2018-05-01

We study generic properties of poly(ionic liquid)s (PILs) via coarse-grained molecular dynamics simulations in bulk solution and under confinement. The influence of different side chain lengths on the spatial properties of the PIL systems and on the ionic transport mechanism is investigated in detail. Our results reveal the formation of apolar and polar nanodomains with increasing side chain length in good agreement with previous results for molecular ionic liquids. The ion transport numbers are unaffected by the occurrence of these domains, and the corresponding values highlight the potential role of PILs as single-ion conductors in electrochemical devices. In contrast to bulk behavior, a pronounced formation of ion conductivity channels in confined systems is initiated in close vicinity to the boundaries. We observe higher ion conductivities in these channels for increasing PIL side chain lengths in comparison with bulk values and provide an explanation for this effect. The appearance of these domains points to an improved application of PILs in modern polymer electrolyte batteries.

Estimation of flow stress of radiation induced F/M steels using molecular dynamics and discrete dislocation dynamics approach

International Nuclear Information System (INIS)

More, Ameya; Dutta, B.K.; Durgaprasad, P.V.; Arya, A.K.

2012-01-01

Fe-Cr based Ferritic/Martensitic (F/M) steels are the candidate structural materials for future fusion reactors. In this work, a multi-scale approach comprising atomistic Molecular Dynamics (MD) simulations and Discrete Dislocation Dynamics (DDD) simulations are used to model the effect of irradiation dose on the flow stress of F/M steels. At the atomic scale, molecular dynamics simulations are used to study the dislocation interaction with irradiation induced defects, i.e. voids and He bubbles. Whereas, the DDD simulations are used to estimate the change in flow stress of the material as a result of irradiation hardening. (author)

Molecular dynamics studies of superionic conductors

International Nuclear Information System (INIS)

Rahman, A.; Vashishta, P.

1983-01-01

Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables

Generation of nanoclusters by ultrafast laser ablation of Al: Molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Miloshevsky, Alexander; Phillips, Mark C.; Harilal, Sivanandan S.; Dressman, Phillip; Miloshevsky, Gennady

2017-11-01

The laser ablation of materials induced by an ultrashort femtosecond pulse is a complex phenomenon, which depends on both the material properties and the properties of the laser pulse. The unique capability of a combination of molecular dynamics (MD) and Momentum Scaling Model (MSM) methods is developed and applied to a large atomic system for studying the process of ultrafast laser-material interactions, behavior of matter in a highly non-equilibrium state, material disintegration, and formation of nanoparticles (NPs). Laser pulses with several fluences in the range from 500 J/m2 to 5000 J/m2 interacting with a large system of aluminum atoms are simulated. The response of Al material to the laser energy deposition is investigated within the finite-size laser spot. It is found that the shape of the plasma plume is dynamically changing during an expansion process. At several tens of picoseconds it can be characterized as a long hollow ellipsoid surrounded by atomized and nano-clustered particles. The time evolution of NP clusters in the plume is investigated. The collisions between the single Al atoms and generated NPs and fragmentation of large NPs determine the fractions of different-size NP clusters in the plume. The MD-MSM simulations show that laser fluence greatly affects the size distribution of NPs, their polar angles, magnitude and direction vectors of NP velocities. These results and predictions are supported by the experimental data and previous MD simulations.

Nonequilibrium molecular dynamics theory, algorithms and applications

CERN Document Server

Todd, Billy D

2017-01-01

Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...

Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles

NARCIS (Netherlands)

Marrink, SJ; Mark, AE

2003-01-01

Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at

Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations

NARCIS (Netherlands)

Baoukina, Svetlana; Monticelli, Luca; Marrink, Siewert J.; Tieleman, D. Peter

2007-01-01

We calculated the pressure-area isotherm of a dipalmitoyl-phosphatidylcholine (DPPC) lipid monolayer from molecular dynamics simulations using a coarse-grained molecular model. We characterized the monolayer structure, geometry, and phases directly from the simulations and compared the calculated

Quantum molecular dynamics study of the Su-Schrieffer-Heeger model

NARCIS (Netherlands)

Michielsen, Kristel; Raedt, Hans De

A quantum molecular dynamics technique is presented to compute the static and dynamic properties of a system of fermions coupled to classical degrees of freedom. The method is employed to investigate the properties of the Su-Schrieffer-Heeger model, an electron-phonon model which is often used to

A comparative molecular dynamics study of diffusion of n-decane ...

Indian Academy of Sciences (India)

Administrator

Abstract. Molecular dynamics simulations are reported on the structure and dynamics of n-decane and. 3-methylpentane in zeolite NaY. We have calculated several properties such as the center of mass-center of mass rdf, the end-end distance distribution, bond angle distribution and dihedral angle distribution. We.

Molecular Interactions and Reaction Dynamics in Supercritical Water Oxidation

National Research Council Canada - National Science Library

Johnston, K

1998-01-01

.... From UV-vis spectroscopic measurements and molecular dynamics simulation of chemical equilibria, we have shown that density effects on broad classes of reactions may be explained in terms of changes...

Friction in Carborane-Based Molecular Rotors Driven by Gas Flow or Electric Field: Classical Molecular Dynamics

Czech Academy of Sciences Publication Activity Database

Prokop, Alexandr; Vacek, Jaroslav; Michl, Josef

2012-01-01

Roč. 6, č. 3 (2012), s. 1901-1914 ISSN 1936-0851 R&D Projects: GA ČR GA203/09/1802; GA MŠk ME09020 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular rotors * molecular dynamics * potential energy barriers * friction * intramolecular vibrational redistribution Subject RIV: CC - Organic Chemistry Impact factor: 12.062, year: 2012

Dynamic elections and ideological polarization