The AFFDL-Nielsen Flow-Field Study

DTIC Science & Technology

1976-04-01

76-18 1.0 INTRODUCTION This investigation was conducted in the von K ~ n Gas Dynamics Facility (VKF) Supersonic Wind Tunnel (A) for Nielsen...flow field-surveys, using a cone probe rake to determine the local velocity field; (2) pressure distributions on a store model; and (3) force and...moment data on a store model. In addition, free-stream (interference-free) data were obtained with the probe rake and on the force and pressure store

Folding Free Energy Landscape of the Decapeptide Chignolin

NASA Astrophysics Data System (ADS)

Dou, Xianghua; Wang, Jihua

Chignolin is an artificially designed ten-residue (GYDPETGTWG) folded peptide, which is the smallest protein and provides a good template for protein folding. In this work, we completed four explicit water molecular dynamics simulations of Chignolin folding using GROMOS and OPLS-AA force fields from extended initial states without any experiment informations. The four-folding free energy landscapes of the peptide has been drawn. The folded state of Chignolin has been successfully predicated based on the free energy landscapes. The four independent simulations gave similar results. (i) The four free energy landscapes have common characters. They are fairly smooth, barrierless, funnel-like and downhill without intermediate state, which consists with the experiment. (ii) The different extended initial structures converge at similar folded structures with the lowest free energy under GROMOS and OPLS-AA force fields. In the GROMOS force field, the backbone RMSD of the folded structures from the NMR native structure of Chignolin is only 0.114 nm, which is a stable structure in this force field. In the OPLS-AA force field, the similar results have been obtained. In addition, the smallest RMSD structure is in better agreement with the NMR native structure but unlikely stable in the force field.

Acoustic attraction, repulsion and radiation force cancellation on a pair of rigid particles with arbitrary cross-sections in 2D: Circular cylinders example

NASA Astrophysics Data System (ADS)

Mitri, F. G.

2017-11-01

The acoustic radiation forces arising on a pair of sound impenetrable cylindrical particles of arbitrary cross-sections are derived. Plane progressive, standing or quasi-standing waves with an arbitrary incidence angle are considered. Multiple scattering effects are described using the multipole expansion formalism and the addition theorem of cylindrical wave functions. An effective incident acoustic field on a particular object is determined, and used with the scattered field to derive closed-form analytical expressions for the radiation force vector components. The mathematical expressions for the radiation force components are exact, and have been formulated in partial-wave series expansions in cylindrical coordinates involving the angle of incidence, the reflection coefficient forming the progressive or the (quasi)standing wave field, the addition theorem, and the expansion coefficients. Numerical examples illustrate the analysis for two rigid circular cross-sections immersed in a non-viscous fluid. Computations for the dimensionless radiation force functions are performed with emphasis on varying the angle of incidence, the interparticle distance, the sizes of the particles as well as the characteristics of the incident field. Depending on the interparticle distance and angle of incidence, one of the particles yields neutrality; it experiences no force and becomes unresponsive (i.e., ;invisible;) to the linear momentum transfer of the effective incident field due to multiple scattering cancellation effects. Moreover, attractive or repulsive forces between the two particles may arise depending on the interparticle distance, the angle of incidence and size parameters of the particles. This study provides a complete analytical method and computations for the axial and transverse radiation force components in multiple acoustic scattering encompassing the cases of plane progressive, standing or quasi-standing waves of arbitrary incidence by a pair of scatterers. Potential applications concern the prediction of the forces used in acoustically-engineered metamaterials with reconfigurable periodicities, cloaking devices, and liquid crystals to name a few examples.

Influence of ZnO doping on the properties of single domain YBCO bulks fabricated by RE+011 TSIG process

NASA Astrophysics Data System (ADS)

Yang, W. M.; Yuan, X. C.; Guo, Y. X.

2017-10-01

Single domain YBCO bulk superconductors with different additions of ZnO have been successfully fabricated by RE+011 TSIG process with a new solid phase of [(100-x)(Y2O3 + 1.2BaCuO2)+xZnO] and a new liquid phase of (Y2O3+6CuO+10BaCuO2). The effects of ZnO additions on the growth morphology, microstructure, critical temperature (Tc), the levitation force and trapped field of the YBCO bulks have been investigated. It is found that within the range of ZnO additions x=0-1.0 wt.%, all the samples are of the typical characteristic of single-domain YBCO bulk; the Tc of the samples decreases from 92 K to 80 K when the ZnO addition x increases from x=0 wt.% to x=1.0 wt.%; the levitation force and trapped field of the samples firstly increase and then decrease with increase of ZnO additions after going through a maximum, which is closely related with the ZnO addition and the resulting flux pinning force caused by lattice distortion due to the substitution of Zn2+ for Cu2+ site in the YBCO crystal; the largest levitation force 36.8 N (77 K, 0.5 T) and trapped field 0.416 T (77 K, 0.5 T) of the samples are obtained when x=0.1 wt.%, respectively. This result is significantly important and helpful for us to improve the properties of YBCO bulk superconductors.

On the numerical computation of nonlinear force-free magnetic fields. [from solar photosphere

NASA Technical Reports Server (NTRS)

Wu, S. T.; Sun, M. T.; Chang, H. M.; Hagyard, M. J.; Gary, G. A.

1990-01-01

An algorithm has been developed to extrapolate nonlinear force-free magnetic fields from the photosphere, given the proper boundary conditions. This paper presents the results of this work, describing the mathematical formalism that was developed, the numerical techniques employed, and comments on the stability criteria and accuracy developed for these numerical schemes. An analytical solution is used for a benchmark test; the results show that the computational accuracy for the case of a nonlinear force-free magnetic field was on the order of a few percent (less than 5 percent). This newly developed scheme was applied to analyze a solar vector magnetogram, and the results were compared with the results deduced from the classical potential field method. The comparison shows that additional physical features of the vector magnetogram were revealed in the nonlinear force-free case.

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants

PubMed Central

Ewen, James P.; Gattinoni, Chiara; Thakkar, Foram M.; Morgan, Neal; Spikes, Hugh A.; Dini, Daniele

2016-01-01

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed. PMID:28773773

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants.

PubMed

Ewen, James P; Gattinoni, Chiara; Thakkar, Foram M; Morgan, Neal; Spikes, Hugh A; Dini, Daniele

2016-08-02

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n -hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n -hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n -hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed.

Interactions and reversal-field memory in complex magnetic nanowire arrays

NASA Astrophysics Data System (ADS)

Rotaru, Aurelian; Lim, Jin-Hee; Lenormand, Denny; Diaconu, Andrei; Wiley, John. B.; Postolache, Petronel; Stancu, Alexandru; Spinu, Leonard

2011-10-01

Interactions and magnetization reversal of Ni nanowire arrays have been investigated by the first-order reversal curve (FORC) method. Several series of samples with controlled spatial distribution were considered including simple wires of different lengths and diameters (70 and 110 nm) and complex wires with a single modulated diameter along their length. Subtle features of magnetic interactions are revealed through a quantitative analysis of the local interaction field profile distributions obtained from the FORC method. In addition, the FORC analysis indicates that the nanowire systems with a mean diameter of 70 nm appear to be organized in symmetric clusters indicative of a reversal-field memory effect.

Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface.

PubMed

Sandoval-Perez, Angelica; Pluhackova, Kristyna; Böckmann, Rainer A

2017-05-09

Molecular dynamics (MD) simulations offer the possibility to study biological processes at high spatial and temporal resolution often not reachable by experiments. Corresponding biomolecular force field parameters have been developed for a wide variety of molecules ranging from inorganic ligands and small organic molecules over proteins and lipids to nucleic acids. Force fields have typically been parametrized and validated on thermodynamic observables and structural characteristics of individual compounds, e.g. of soluble proteins or lipid bilayers. Less strictly, due to the added complexity and missing experimental data to compare to, force fields have hardly been tested on the properties of mixed systems, e.g. on protein-lipid systems. Their selection and combination for mixed systems is further complicated by the partially differing parametrization strategies. Additionally, the presence of other compounds in the system may shift the subtle balance of force field parameters. Here, we assessed the protein-lipid interactions as described in the four atomistic force fields GROMOS54a7, CHARMM36 and the two force field combinations Amber14sb/Slipids and Amber14sb/Lipid14. Four observables were compared, focusing on the membrane-water interface: the conservation of the secondary structure of transmembrane proteins, the positioning of transmembrane peptides relative to the lipid bilayer, the insertion depth of side chains of unfolded peptides absorbed at the membrane interface, and the ability to reproduce experimental insertion energies of Wimley-White peptides at the membrane interface. Significant differences between the force fields were observed that affect e.g. membrane insertion depths and tilting of transmembrane peptides.

Force Field Development from Periodic Density Functional Theory Calculations for Gas Separation Applications Using Metal–Organic Frameworks

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

Mercado, Rocio; Vlaisavljevich, Bess; Lin, Li -Chiang

We present accurate force fields developed from density functional theory (DFT) calculations with periodic boundary conditions for use in molecular simulations involving M 2(dobdc) (M-MOF-74; dobdc 4– = 2,5-dioxidobenzenedicarboxylate; M = Mg, Mn, Fe, Co, Ni, Zn) and frameworks of similar topology. In these systems, conventional force fields fail to accurately model gas adsorption due to the strongly binding open-metal sites. The DFT-derived force fields predict the adsorption of CO 2, H 2O, and CH 4 inside these frameworks much more accurately than other common force fields. We show that these force fields can also be used for M 2(dobpdc)more » (dobpdc 4– = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate), an extended version of MOF-74, and thus are a promising alternative to common force fields for studying materials similar to MOF-74 for carbon capture applications. Furthermore, it is anticipated that the approach can be applied to other metal–organic framework topologies to obtain force fields for different systems. We have used this force field to study the effect of contaminants such as H 2O and N 2 upon these materials’ performance for the separation of CO 2 from the emissions of natural gas reservoirs and coal-fired power plants. Specifically, mixture adsorption isotherms calculated with these DFT-derived force fields showed a significant reduction in the uptake of many gas components in the presence of even trace amounts of H 2O vapor. The extent to which the various gases are affected by the concentration of H 2O in the reservoir is quantitatively different for the different frameworks and is related to their heats of adsorption. Additionally, significant increases in CO 2 selectivities over CH 4 and N 2 are observed as the temperature of the systems is lowered.« less

Force Field Development from Periodic Density Functional Theory Calculations for Gas Separation Applications Using Metal–Organic Frameworks

DOE PAGES

Mercado, Rocio; Vlaisavljevich, Bess; Lin, Li -Chiang; ...

2016-05-25

We present accurate force fields developed from density functional theory (DFT) calculations with periodic boundary conditions for use in molecular simulations involving M 2(dobdc) (M-MOF-74; dobdc 4– = 2,5-dioxidobenzenedicarboxylate; M = Mg, Mn, Fe, Co, Ni, Zn) and frameworks of similar topology. In these systems, conventional force fields fail to accurately model gas adsorption due to the strongly binding open-metal sites. The DFT-derived force fields predict the adsorption of CO 2, H 2O, and CH 4 inside these frameworks much more accurately than other common force fields. We show that these force fields can also be used for M 2(dobpdc)more » (dobpdc 4– = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate), an extended version of MOF-74, and thus are a promising alternative to common force fields for studying materials similar to MOF-74 for carbon capture applications. Furthermore, it is anticipated that the approach can be applied to other metal–organic framework topologies to obtain force fields for different systems. We have used this force field to study the effect of contaminants such as H 2O and N 2 upon these materials’ performance for the separation of CO 2 from the emissions of natural gas reservoirs and coal-fired power plants. Specifically, mixture adsorption isotherms calculated with these DFT-derived force fields showed a significant reduction in the uptake of many gas components in the presence of even trace amounts of H 2O vapor. The extent to which the various gases are affected by the concentration of H 2O in the reservoir is quantitatively different for the different frameworks and is related to their heats of adsorption. Additionally, significant increases in CO 2 selectivities over CH 4 and N 2 are observed as the temperature of the systems is lowered.« less

Direct folding simulation of helical proteins using an effective polarizable bond force field.

PubMed

Duan, Lili; Zhu, Tong; Ji, Changge; Zhang, Qinggang; Zhang, John Z H

2017-06-14

We report a direct folding study of seven helical proteins (, Trpcage, , C34, N36, , ) ranging from 17 to 53 amino acids through standard molecular dynamics simulations using a recently developed polarizable force field-Effective Polarizable Bond (EPB) method. The backbone RMSDs, radius of gyrations, native contacts and native helix content are in good agreement with the experimental results. Cluster analysis has also verified that these folded structures with the highest population are in good agreement with their corresponding native structures for these proteins. In addition, the free energy landscape of seven proteins in the two dimensional space comprised of RMSD and radius of gyration proved that these folded structures are indeed of the lowest energy conformations. However, when the corresponding simulations were performed using the standard (nonpolarizable) AMBER force fields, no stable folded structures were observed for these proteins. Comparison of the simulation results based on a polarizable EPB force field and a nonpolarizable AMBER force field clearly demonstrates the importance of polarization in the folding of stable helical structures.

Casimir force in a Lorentz violating theory

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

Frank, Mariana; Turan, Ismail

2006-08-01

We study the effects of the minimal extension of the standard model including Lorentz violation on the Casimir force between two parallel conducting plates in the vacuum. We provide explicit solutions for the electromagnetic field using scalar field analogy, for both the cases in which the Lorentz violating terms come from the CPT-even or CPT-odd terms. We also calculate the effects of the Lorentz violating terms for a fermion field between two parallel conducting plates and analyze the modifications of the Casimir force due to the modifications of the Dirac equation. In all cases under consideration, the standard formulas formore » the Casimir force are modified by either multiplicative or additive correction factors, the latter case exhibiting different dependence on the distance between the plates.« less

Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation.

PubMed

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2007-10-14

We have attempted to improve the PARAM99 force field in conjunction with the generalized Born (GB) solvation model with a surface area correction for more consistent protein folding simulations. For this purpose, using an extended alphabeta training set of five well-studied molecules with various folds (alpha, beta, and betabetaalpha), a previously modified version of PARAM99/GBSA is further refined, such that all native states of the five training species correspond to their lowest free energy minimum states. The resulting modified force field (PARAM99MOD5/GBSA) clearly produces reasonably acceptable conformational free energy surfaces of the training set with correct identifications of their native states in the free energy minimum states. Moreover, due to its well-balanced nature, this new force field is expected to describe secondary structure propensities of diverse folds in a more consistent manner. Remarkably, temperature dependent behaviors simulated with the current force field are in good agreement with the experiment. This agreement is a significant improvement over the existing standard all-atom force fields. In addition, fundamentally important thermodynamic quantities, such as folding enthalpy (DeltaH) and entropy (DeltaS), agree reasonably well with the experimental data.

Influence of Applying Additional Forcing Fans for the Air Distribution in Ventilation Network

NASA Astrophysics Data System (ADS)

Szlązak, Nikodem; Obracaj, Dariusz; Korzec, Marek

2016-09-01

Mining progress in underground mines cause the ongoing movement of working areas. Consequently, it becomes necessary to adapt the ventilation network of a mine to direct airflow into newly-opened districts. For economic reasons, opening new fields is often achieved via underground workings. Length of primary intake and return routes increases and also increases the total resistance of a complex ventilation network. The development of a subsurface structure can make it necessary to change the air distribution in a ventilation network. Increasing airflow into newly-opened districts is necessary. In mines where extraction does not entail gas-related hazards, there is possibility of implementing a push-pull ventilation system in order to supplement airflows to newly developed mining fields. This is achieved by installing subsurface fan stations with forcing fans at the bottom of downcast shaft. In push-pull systems with multiple main fans, it is vital to select forcing fans with characteristic curves matching those of the existing exhaust fans to prevent undesirable mutual interaction. In complex ventilation networks it is necessary to calculate distribution of airflow (especially in networks with a large number of installed fans). In the article the influence of applying additional forcing fans for the air distribution in ventilation network for underground mine were considered. There are also analysed the extent of overpressure caused by the additional forcing fan in branches of the ventilation network (the operating range of additional forcing fan). Possibilities of increasing airflow rate in working areas were conducted.

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

PubMed

Lemkul, Justin A; Roux, Benoît; van der Spoel, David; MacKerell, Alexander D

2015-07-15

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field. © 2015 Wiley Periodicals, Inc.

Detecting the gravitational sensitivity of Paramecium caudatum using magnetic forces

NASA Astrophysics Data System (ADS)

Guevorkian, Karine; Valles, James M., Jr.

2006-03-01

Under normal conditions, Paramecium cells regulate their swimming speed in response to the pN level mechanical force of gravity. This regulation, known as gravikinesis, is more pronounced when the external force is increased by methods such as centrifugation. Here we present a novel technique that simulates gravity fields using the interactions between strong inhomogeneous magnetic fields and cells. We are able to achieve variable gravities spanning from 10xg to -8xg; where g is earth's gravity. Our experiments show that the swimming speed regulation of Paramecium caudatum to magnetically simulated gravity is a true physiological response. In addition, they reveal a maximum propulsion force for paramecia. This advance establishes a general technique for applying continuously variable forces to cells or cell populations suitable for exploring their force transduction mechanisms.

Air Force Institutional Requirements: Opportunities for Improving the Efficiency of Sourcing, Managing, and Manning Corporate Requirements

DTIC Science & Technology

prolonged undermanning. Most career field managers are unable to fully man their associated authorizations and are acutely aware of additional...IRs are valid, funded manpower requirements that do not align with a traditional, functional career field but are needed to support the Air Force...fill an IR position, though there are exceptions for some IR positions with unique educational or experiential requirements.

Fringe Field Effects on Bending Magnets, Derived for TRANSPORT/TURTLE

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

Molloy, Riley; Blitz, Sam

2013-08-05

A realistic magnetic dipole has complex effects on a charged particle near the entrance and exit of the magnet, even with a constant and uniform magnetic field deep within the interior of the magnet. To satisfy Maxwell's equations, the field lines near either end of a realistic magnet are significantly more complicated, yielding non-trivial forces. The effects of this fringe field are calculated to first order, applying both the paraxial and thin lens approximations. We find that, in addition to zeroth order effects, the position of a particle directly impacts the forces in the horizontal and vertical directions.

Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations.

PubMed

Zgarbová, Marie; Otyepka, Michal; Sponer, Jirí; Hobza, Pavel; Jurecka, Petr

2010-09-21

The intermolecular interaction energy components for several molecular complexes were calculated using force fields available in the AMBER suite of programs and compared with Density Functional Theory-Symmetry Adapted Perturbation Theory (DFT-SAPT) values. The extent to which such comparison is meaningful is discussed. The comparability is shown to depend strongly on the intermolecular distance, which means that comparisons made at one distance only are of limited value. At large distances the coulombic and van der Waals 1/r(6) empirical terms correspond fairly well with the DFT-SAPT electrostatics and dispersion terms, respectively. At the onset of electronic overlap the empirical values deviate from the reference values considerably. However, the errors in the force fields tend to cancel out in a systematic manner at equilibrium distances. Thus, the overall performance of the force fields displays errors an order of magnitude smaller than those of the individual interaction energy components. The repulsive 1/r(12) component of the van der Waals expression seems to be responsible for a significant part of the deviation of the force field results from the reference values. We suggest that further improvement of the force fields for intermolecular interactions would require replacement of the nonphysical 1/r(12) term by an exponential function. Dispersion anisotropy and its effects are discussed. Our analysis is intended to show that although comparing the empirical and non-empirical interaction energy components is in general problematic, it might bring insights useful for the construction of new force fields. Our results are relevant to often performed force-field-based interaction energy decompositions.

Effect of field cooling heights on the levitation force of pure and starch/polystyrene/MWCNT added bulk MgB2 superconductors

NASA Astrophysics Data System (ADS)

Tripathi, D.; Dey, T. K.

2014-12-01

A series of MgB2 pellets with and without addition of carbon from different sources (viz. starch, polystyrene and carbon nanotubes) have been synthesized by solid state reaction under argon atmosphere. XRD analysis indicates a decrease in lattice parameters of MgB2 with addition of starch, polystyrene (PS) and MWCNT and confirms substitution of carbon in boron sites. The presence of nanosized carbon inclusions between the grain boundaries in the present set of samples is evident in TEM photographs. Resistivity data confirms a decrease in superconducting transition temperature (Tc0) for MgB2 doped with starch/PS/MWCNT. The effect of different field cooling heights (HIFC) at 20 K on maximum levitation force (FMLF) and maximum attractive force (FMAF) of pure MgB2 and MgB2 doped with starch/PS/MWCNT have been investigated. Except for MWCNT, doping of starch and PS in MgB2 is found to improve FMLF and FMAF and the best result is obtained for MgB2 doped with 1 wt.% PS. Levitation force measured as a function of decreasing initial field cooling height indicates exponential dependence of both maximum levitation force (FMLF) and maximum attractive force (FMAF). However, the gap distance between PM and the sample (H0AF and HMAF) corresponding to maximum attractive force (FMAF) and zero attractive force (F0AF) varies linearly and their difference remains constant. This constancy in (HMAF - H0AF) is understood in terms of constant reduction rate of magnetic flux density between H0AF and HMAF.

Measurements of the Casimir-Lifshitz force in fluids: The effect of electrostatic forces and Debye screening

NASA Astrophysics Data System (ADS)

Munday, J. N.; Capasso, Federico; Parsegian, V. Adrian; Bezrukov, Sergey M.

2008-09-01

We present detailed measurements of the Casimir-Lifshitz force between two gold surfaces (a sphere and a plate) immersed in ethanol and study the effect of residual electrostatic forces, which are dominated by static fields within the apparatus and can be reduced with proper shielding. Electrostatic forces are further reduced by Debye screening through the addition of salt ions to the liquid. Additionally, the salt leads to a reduction of the Casimir-Lifshitz force by screening the zero-frequency contribution to the force; however, the effect is small between gold surfaces at the measured separations and within experimental error. An improved calibration procedure is described and compared with previous methods. Finally, the experimental results are compared with Lifshitz’s theory and found to be consistent for the materials used in the experiment.

ff14IDPs Force Field Improving the Conformation Sampling of Intrinsically Disordered Proteins

PubMed Central

Song, Dong; Wang, Wei; Ye, Wei; Ji, Dingjue; Luo, Ray; Chen, Hai-Feng

2017-01-01

Intrinsically disordered proteins (IDPs) are proteins which lack of specific tertiary structure and unable to fold spontaneously without the partner binding. These IDPs are found to associate with various diseases, such as diabetes, cancer, and neurodegenerative diseases. However, current widely used force fields, such as ff99SB, ff14SB, OPLS/AA, and Charmm27 are insufficient in sampling the conformational characters of IDPs. In this study, the CMAP method was used to correct the φ/ψ distributions of disorder-promoting amino acids. The simulation results show that the force filed parameters (ff14IDPs) can improve the φ/ψ distributions of the disorder-promoting amino acids, with RMSD less than 0.10% relative to the benchmark data of IDPs. Further test suggests that the calculated secondary chemical shifts under ff14IDPs force field are in quantitative agreement with the data of NMR experiment for five tested systems. In addition, the simulation results show that ff14IDPs can still be used to model structural proteins, such as tested lysozyme and ubiquitin, with better performance in coil regions than the original general Amber force field ff14SB. These findings confirm that the newly developed Amber ff14IDPs force field is a robust model for improving the conformation sampling of IDPs. PMID:27484738

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.

PubMed

Kim, Seonghoon; Lee, Jumin; Jo, Sunhwan; Brooks, Charles L; Lee, Hui Sun; Im, Wonpil

2017-06-05

Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files of the corresponding molecules are not available. To address this problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in various forms (using PDB ID, ligand ID, SMILES, MOL/MOL2/SDF file, or PDB/mmCIF file), and the uploaded structure is displayed on a sketchpad for verification and further modification. Based on the displayed structure, Ligand Reader & Modeler generates the ligand force field parameters and necessary structure files by searching for the ligand in the CHARMM force field library or using the CHARMM general force field (CGenFF). In addition, users can define chemical substitution sites and draw substituents in each site on the sketchpad to generate a set of combinatorial structure files and corresponding force field parameters for throughput or alchemical free energy simulations. Finally, the output from Ligand Reader & Modeler can be used in other CHARMM-GUI modules to build a protein-ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Ligand Reader & Modeler is available as a functional module of CHARMM-GUI at http://www.charmm-gui.org/input/ligandrm. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field.

PubMed

García-Pérez, E; Serra-Crespo, P; Hamad, S; Kapteijn, F; Gascon, J

2014-08-14

Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations of gas adsorption and diffusion of carbon dioxide and methane in NH2-MIL-53(Al) are carried out using a linear combination of two crystallographic structures with rigid force fields. Once the interactions of carbon dioxide molecules and the bridging hydroxyls groups of the framework are optimized, an excellent match is found for simulations and experimental data for the adsorption of methane and carbon dioxide, including the stepwise uptake due to the breathing effect. In addition, diffusivities of pure components are calculated. The pore expansion by the breathing effect influences the self-diffusion mechanism and much higher diffusivities are observed at relatively high adsorbate loadings. This work demonstrates that using a rigid force field combined with a minimum number of experiments, reproduces adsorption and simulates diffusion of carbon dioxide and methane in the flexible metal-organic framework NH2-MIL-53(Al).

Nonlinear generation of large-scale magnetic fields in forced spherical shell dynamos

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

Livermore, P. W.; Hughes, D. W.; Tobias, S. M.

2010-03-15

In an earlier paper [P. W. Livermore, D. W. Hughes, and S. M. Tobias, ''The role of helicity and stretching in forced kinematic dynamos in a spherical shell'', Phys. Fluids 19, 057101 (2007)], we considered the kinematic dynamo action resulting from a forced helical flow in a spherical shell. Although mean field electrodynamics suggests that the resulting magnetic field should have a significant mean (axisymmetric) component, we found no evidence for this; the dynamo action was distinctly small scale. Here we extend our investigation into the nonlinear regime in which the magnetic field reacts back on the velocity via themore » Lorentz force. Our main result is somewhat surprising, namely, that nonlinear effects lead to a considerable change in the structure of the magnetic field, its final state having a significant mean component. By investigating the dominant flow-field interactions, we isolate the dynamo mechanism and show schematically how the generation process differs between the kinematic and nonlinear regimes. In addition, we are able to calculate some components of the transport coefficient {alpha} and thus discuss our results within the context of mean field electrodynamics.« less

Mapping the Drude polarizable force field onto a multipole and induced dipole model

NASA Astrophysics Data System (ADS)

Huang, Jing; Simmonett, Andrew C.; Pickard, Frank C.; MacKerell, Alexander D.; Brooks, Bernard R.

2017-10-01

The induced dipole and the classical Drude oscillator represent two major approaches for the explicit inclusion of electronic polarizability into force field-based molecular modeling and simulations. In this work, we explore the equivalency of these two models by comparing condensed phase properties computed using the Drude force field and a multipole and induced dipole (MPID) model. Presented is an approach to map the electrostatic model optimized in the context of the Drude force field onto the MPID model. Condensed phase simulations on water and 15 small model compounds show that without any reparametrization, the MPID model yields properties similar to the Drude force field with both models yielding satisfactory reproduction of a range of experimental values and quantum mechanical data. Our results illustrate that the Drude oscillator model and the point induced dipole model are different representations of essentially the same physical model. However, results indicate the presence of small differences between the use of atomic multipoles and off-center charge sites. Additionally, results on the use of dispersion particle mesh Ewald further support its utility for treating long-range Lennard Jones dispersion contributions in the context of polarizable force fields. The main motivation in demonstrating the transferability of parameters between the Drude and MPID models is that the more than 15 years of development of the Drude polarizable force field can now be used with MPID formalism without the need for dual-thermostat integrators nor self-consistent iterations. This opens up a wide range of new methodological opportunities for polarizable models.

Reconstruction and separation of vibratory field using structural holography

NASA Astrophysics Data System (ADS)

Chesnais, C.; Totaro, N.; Thomas, J.-H.; Guyader, J.-L.

2017-02-01

A method for reconstructing and separating vibratory field on a plate-like structure is presented. The method, called "Structural Holography" is derived from classical Near-field Acoustic Holography (NAH) but in the vibratory domain. In this case, the plate displacement is measured on one-dimensional lines (the holograms) and used to reconstruct the entire two-dimensional displacement field. As a consequence, remote measurements on non directly accessible zones are possible with Structural Holography. Moreover, as it is based on the decomposition of the field into forth and back waves, Structural Holography permits to separate forces in the case of multi-sources excitation. The theoretical background of the Structural Holography method is described first. Then, to illustrate the process and the possibilities of Structural Holography, the academic test case of an infinite plate excited by few point forces is presented. With the principle of vibratory field separation, the displacement fields produced by each point force separately is reconstructed. However, the displacement field is not always meaningful and some additional treatments are mandatory to localize the position of point forces for example. From the simple example of an infinite plate, a post-processing based on the reconstruction of the structural intensity field is thus proposed. Finally, Structural Holography is generalized to finite plates and applied to real experimental measurements

Large pinning forces and matching effects in YBa2Cu3O7-δ thin films with Ba2Y(Nb/Ta)O6 nano-precipitates

NASA Astrophysics Data System (ADS)

Opherden, Lars; Sieger, Max; Pahlke, Patrick; Hühne, Ruben; Schultz, Ludwig; Meledin, Alexander; van Tendeloo, Gustaaf; Nast, Rainer; Holzapfel, Bernhard; Bianchetti, Marco; MacManus-Driscoll, Judith L.; Hänisch, Jens

2016-02-01

The addition of mixed double perovskite Ba2Y(Nb/Ta)O6 (BYNTO) to YBa2Cu3O7-δ (YBCO) thin films leads to a large improvement of the in-field current carrying capability. For low deposition rates, BYNTO grows as well-oriented, densely distributed nanocolumns. We achieved a pinning force density of 25 GN/m3 at 77 K at a matching field of 2.3 T, which is among the highest values reported for YBCO. The anisotropy of the critical current density shows a complex behavior whereby additional maxima are developed at field dependent angles. This is caused by a matching effect of the magnetic fields c-axis component. The exponent N of the current-voltage characteristics (inversely proportional to the creep rate S) allows the depinning mechanism to be determined. It changes from a double-kink excitation below the matching field to pinning-potential-determined creep above it.

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

PubMed Central

2016-01-01

Small metal ions play critical roles in numerous biological processes. Of particular interest is how metalloenzymes are allosterically regulated by the binding of specific ions. Understanding how ion binding affects these biological processes requires atomic models that accurately treat the microscopic interactions with the protein ligands. Theoretical approaches at different levels of sophistication can contribute to a deeper understanding of these systems, although computational models must strike a balance between accuracy and efficiency in order to enable long molecular dynamics simulations. In this study, we present a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions (K+, Na+, Ca2+, and Cl–) and coordinating amino-acid residues for a set of 30 biologically important proteins. By combining ab initio calculations and experimental thermodynamic data, we derive a polarizable force field that is consistent with a wide range of properties, including the geometries and interaction energies of gas-phase ion/protein-like model compound clusters, and the experimental solvation free-energies of the cations in liquids. The resulting models display significant improvements relative to the fixed-atomic-charge additive CHARMM C36 force field, particularly in their ability to reproduce the many-body electrostatic nonadditivity effects estimated from ab initio calculations. The analysis clarifies the fundamental limitations of the pairwise additivity assumption inherent in classical fixed-charge force fields, and shows its dramatic failures in the case of Ca2+ binding sites. These optimized polarizable models, amenable to computationally efficient large-scale MD simulations, set a firm foundation and offer a powerful avenue to study the roles of the ions in soluble and membrane transport proteins. PMID:25578354

Detecting chameleons through Casimir force measurements

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

Brax, Philippe; Bruck, Carsten van de; Davis, Anne-Christine

2007-12-15

The best laboratory constraints on strongly coupled chameleon fields come not from tests of gravity per se but from precision measurements of the Casimir force. The chameleonic force between two nearby bodies is more akin to a Casimir-like force than a gravitational one: The chameleon force behaves as an inverse power of the distance of separation between the surfaces of two bodies, just as the Casimir force does. Additionally, experimental tests of gravity often employ a thin metallic sheet to shield electrostatic forces; however, this sheet masks any detectable signal due to the presence of a strongly coupled chameleon field.more » As a result of this shielding, experiments that are designed to specifically test the behavior of gravity are often unable to place any constraint on chameleon fields with a strong coupling to matter. Casimir force measurements do not employ a physical electrostatic shield and as such are able to put tighter constraints on the properties of chameleons fields with a strong matter coupling than tests of gravity. Motivated by this, we perform a full investigation on the possibility of testing chameleon models with both present and future Casimir experiments. We find that present-day measurements are not able to detect the chameleon. However, future experiments have a strong possibility of detecting or rule out a whole class of chameleon models.« less

Hall devices improve electric motor efficiency

NASA Technical Reports Server (NTRS)

Haeussermann, W.

1979-01-01

Efficiency of electric motors and generators is reduced by radial magnetic forces created by symmetric fields within device. Forces are sensed and counteracted by Hall devices on excitation or control windings. Hall generators directly measure and provide compensating control of anu asymmetry, eliminating additional measurements needed for calibration feedback control loop.

Improved treatment of nucleosides and nucleotides in the OPLS-AA force field

NASA Astrophysics Data System (ADS)

Robertson, Michael J.; Tirado-Rives, Julian; Jorgensen, William L.

2017-09-01

DFT calculations have been used to develop improved descriptions of the torsional energetics for nucleosides and nucleotides in the OPLS-AA force field. Scans of nucleotide dihedral angles (γ, χ, and β) and methyl phosphates provided the bases for the new torsional parameters. In addition, the angle-bending parameters of phosphodiesters and ribose were updated, and adjustments were made to existing carbohydrate torsions to better capture the sugar puckering landscape of ribose. MD simulations of nucleosides with the new parameters demonstrate a significant improvement in the ribose sugar puckering and χ angle distributions. Additionally, energy-minimization of protein-nucleotide crystal structures with the new parameters produced accurate poses.

Force Field for Peptides and Proteins based on the Classical Drude Oscillator

PubMed Central

Lopes, Pedro E.M.; Huang, Jing; Shim, Jihyun; Luo, Yun; Li, Hui; Roux, Benoît; MacKerell, Alexander D.

2013-01-01

Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation studies of peptides and proteins. Building upon parameters for model compounds representative of the functional groups in proteins, the development of the force field focused on the optimization of the parameters for the polypeptide backbone and the connectivity between the backbone and side chains. Optimization of the backbone electrostatic parameters targeted quantum mechanical conformational energies, interactions with water, molecular dipole moments and polarizabilities and experimental condensed phase data for short polypeptides such as (Ala)5. Additional optimization of the backbone φ, ψ conformational preferences included adjustments of the tabulated two-dimensional spline function through the CMAP term. Validation of the model included simulations of a collection of peptides and proteins. This 1st generation polarizable model is shown to maintain the folded state of the studied systems on the 100 ns timescale in explicit solvent MD simulations. The Drude model typically yields larger RMS differences as compared to the additive CHARMM36 force field (C36) and shows additional flexibility as compared to the additive model. Comparison with NMR chemical shift data shows a small degradation of the polarizable model with respect to the additive, though the level of agreement may be considered satisfactory, while for residues shown to have significantly underestimated S2 order parameters in the additive model, improvements are calculated with the polarizable model. Analysis of dipole moments associated with the peptide backbone and tryptophan side chains show the Drude model to have significantly larger values than those present in C36, with the dipole moments of the peptide backbone enhanced to a greater extent in sheets versus helices and the dipoles of individual moieties observed to undergo significant variations during the MD simulations. Although there are still some limitations, the presented model, termed Drude-2013, is anticipated to yield a molecular picture of peptide and protein structure and function that will be of increased physical validity and internal consistency in a computationally accessible fashion. PMID:24459460

Weber electrodynamics, part I. general theory, steady current effects

NASA Astrophysics Data System (ADS)

Wesley, J. P.

1990-10-01

The original Weber action at a distance theory, valid for slowly varying effects, is extended to time-retarded fields, valid for rapidly varying effects including radiation. A new law for the force on a charge moving in this field is derived (replacing the Lorentz force which violates Newton's third law). The limitations of the Maxwell theory are discussed. The Weber theory, in addition to predicting all of the usual electrodynamic results, predicts the following crucial results for slowly varying effects (where Maxwell theory fails): 1) the force on Ampere's bridge in agreement with the measurements of Moyssides and Pappas, 2) the tension required to rupture current carrying wires as observed by Graneau, 3) the force to drive the Graneau-Hering submarine, 4) the force to drive the mercury in Hering's pump, and 5) the force to drive the oscillations in a current carrying mercury wedge as observed by Phipps.

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

PubMed Central

2016-01-01

We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides—all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

Shock Magnetic Field and Origin of the Earth

NASA Technical Reports Server (NTRS)

Tunyi, I.; Timko, M.; Roth, L. E.

2001-01-01

To the effects of impulse magnetic field in protoplanetary nebula (fast melting, cooling and magnetization of chondrules), there is added another possible effect - mechanism associated with the forces of attraction between magnetized planetesimals. Additional information is contained in the original extended abstract.

Application of Enlisted Force Retention Levels and Career Field Stability

DTIC Science & Technology

2017-03-23

a priority. This research focuses on modeling the enlisted force retention behavior. Specifically, this research examines a statistically based ...and must be manually corrected. Air Force Manpower , Personnel and Services (AF/A1PF) supplied the data used in this research . The data was...Stability Jamie T. Zimmerman Follow this and additional works at: https://scholar.afit.edu/etd Part of the Operational Research Commons This Thesis is

Effect of self-consistent magnetic field on plasma sheet penetration to the inner magnetosphere: Rice convection model simulations combined with modified Dungey force-balanced magnetic field solver

NASA Astrophysics Data System (ADS)

Gkioulidou, Matina; Wang, Chih-Ping; Lyons, Larry R.

2011-12-01

Transport of plasma sheet particles into the inner magnetosphere is crucial to the development of the region 2 (R2) field-aligned current system (FAC), which results in the shielding of the penetration electric field and the formation of subauroral polarization streams (SAPS) and the Harang reversal, phenomena closely associated with storms and substorms. In addition to the electric field, this transport is also strongly affected by the magnetic field, which changes with plasma pressure and is distinctly different from the dipole field in the inner plasma sheet. To determine the feedback of force-balanced magnetic field to the transport, we have integrated the Rice convection model (RCM) with a modified Dungey magnetic field solver to obtain the required force balance in the equatorial plane. Comparing our results with those from a RCM run using a T96 magnetic field, we find that transport under a force-balanced magnetic field results in weaker pressure gradients and thus weaker R2 FAC in the near-Earth region and weaker shielding of the penetration electric field. As a result, plasma sheet protons and electrons penetrate farther earthward, and their inner edges become closer together and more azimuthally symmetric than in the T96 case. The Harang reversal extends farther dawnward, and the SAPS become more confined in radial and latitudinal extents. The magnitudes of azimuthal pressure gradient, the inner edges of thermal protons and electrons, the latitudinal range of the Harang reversal, and the radial and latitudinal widths of the SAPS from the force-balanced run are found to be more consistent with observations.

Force Balance and Substorm Effects in the Magnetotail

NASA Technical Reports Server (NTRS)

Kaufmann, Richard L.; Larson, Douglas J.; Kontodinas, Ioannis D.; Ball, Bryan M.

1997-01-01

A model of the quiet time middle magnetotail is developed using a consistent orbit tracing technique. The momentum equation is used to calculate geocentric solar magnetospheric components of the particle and electromagnetic forces throughout the current sheet. Ions generate the dominant x and z force components. Electron and ion forces almost cancel in the y direction because the two species drift earthward at comparable speeds. The force viewpoint is applied to a study of some substorm processes. Generation of the rapid flows seen during substorm injection and bursty bulk flow events implies substantial force imbalances. The formation of a substorm diversion loop is one cause of changes in the magnetic field and therefore in the electromagnetic force. It is found that larger forces are produced when the cross-tail current is diverted to the ionosphere than would be produced if the entire tail current system simply decreased. Plasma is accelerated while the forces are unbalanced resulting in field lines within a diversion loop becoming more dipolar. Field lines become more stretched and the plasma sheet becomes thinner outside a diversion loop. Mechanisms that require thin current sheets to produce current disruption then can create additional diversion loops in the newly thinned regions. This process may be important during multiple expansion substorms and in differentiating pseudoexpansions from full substorms. It is found that the tail field model used here can be generated by a variety of particle distribution functions. However, for a given energy distribution the mixture of particle mirror or reflection points is constrained by the consistency requirement. The study of uniqueness also leads to the development of a technique to select guiding center electrons that will produce charge neutrality all along a flux tube containing nonguiding center ions without the imposition of a parallel electric field.

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy.

PubMed

Balke, Nina; Jesse, Stephen; Carmichael, Ben; Okatan, M Baris; Kravchenko, Ivan I; Kalinin, Sergei V; Tselev, Alexander

2017-01-04

Atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm -1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.

Quantum Field Energy Sensor based on the Casimir Effect

NASA Astrophysics Data System (ADS)

Ludwig, Thorsten

The Casimir effect converts vacuum fluctuations into a measurable force. Some new energy technologies aim to utilize these vacuum fluctuations in commonly used forms of energy like electricity or mechanical motion. In order to study these energy technologies it is helpful to have sensors for the energy density of vacuum fluctuations. In today's scientific instrumentation and scanning microscope technologies there are several common methods to measure sub-nano Newton forces. While the commercial atomic force microscopes (AFM) mostly work with silicon cantilevers, there are a large number of reports on the use of quartz tuning forks to get high-resolution force measurements or to create new force sensors. Both methods have certain advantages and disadvantages over the other. In this report the two methods are described and compared towards their usability for Casimir force measurements. Furthermore a design for a quantum field energy sensor based on the Casimir force measurement will be described. In addition some general considerations on extracting energy from vacuum fluctuations will be given.

Manipulation of dielectric Rayleigh particles using highly focused elliptically polarized vector fields.

PubMed

Gu, Bing; Xu, Danfeng; Rui, Guanghao; Lian, Meng; Cui, Yiping; Zhan, Qiwen

2015-09-20

Generation of vectorial optical fields with arbitrary polarization distribution is of great interest in areas where exotic optical fields are desired. In this work, we experimentally demonstrate the versatile generation of linearly polarized vector fields, elliptically polarized vector fields, and circularly polarized vortex beams through introducing attenuators in a common-path interferometer. By means of Richards-Wolf vectorial diffraction method, the characteristics of the highly focused elliptically polarized vector fields are studied. The optical force and torque on a dielectric Rayleigh particle produced by these tightly focused vector fields are calculated and exploited for the stable trapping of dielectric Rayleigh particles. It is shown that the additional degree of freedom provided by the elliptically polarized vector field allows one to control the spatial structure of polarization, to engineer the focusing field, and to tailor the optical force and torque on a dielectric Rayleigh particle.

Vector electric field measurement via position-modulated Kelvin probe force microscopy

NASA Astrophysics Data System (ADS)

Dwyer, Ryan P.; Smieska, Louisa M.; Tirmzi, Ali Moeed; Marohn, John A.

2017-10-01

High-quality spatially resolved measurements of electric fields are critical to understanding charge injection, charge transport, and charge trapping in semiconducting materials. Here, we report a variation of frequency-modulated Kelvin probe force microscopy that enables spatially resolved measurements of the electric field. We measure electric field components along multiple directions simultaneously by employing position modulation and lock-in detection in addition to numeric differentiation of the surface potential. We demonstrate the technique by recording linescans of the in-plane electric field vector in the vicinity of a patch of trapped charge in a 2,7-diphenyl[1]benzothieno[3,2-b][1]benzothiophene (DPh-BTBT) organic field-effect transistor. This technique is simple to implement and should be especially useful for studying electric fields in spatially inhomogeneous samples like organic transistors and photovoltaic blends.

Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data

PubMed Central

Wickstrom, Lauren; Okur, Asim; Simmerling, Carlos

2009-01-01

Abstract Force-field validation is essential for the identification of weaknesses in current models and the development of more accurate models of biomolecules. NMR coupling and relaxation methods have been used to effectively diagnose the strengths and weaknesses of many existing force fields. Studies using the ff99SB force field have shown excellent agreement between experimental and calculated order parameters and residual dipolar calculations. However, recent studies have suggested that ff99SB demonstrates poor agreement with J-coupling constants for short polyalanines. We performed extensive replica-exchange molecular-dynamics simulations on Ala3 and Ala5 in TIP3P and TIP4P-Ew solvent models. Our results suggest that the performance of ff99SB is among the best of currently available models. In addition, scalar coupling constants derived from simulations in the TIP4P-Ew model show a slight improvement over those obtained using the TIP3P model. Despite the overall excellent agreement, the data suggest areas for possible improvement. PMID:19651043

Transient electrophoretic motion of a charged particle through a converging-diverging microchannel: effect of direct current-dielectrophoretic force.

PubMed

Ai, Ye; Joo, Sang W; Jiang, Yingtao; Xuan, Xiangchun; Qian, Shizhi

2009-07-01

Transient electrophoretic motion of a charged particle through a converging-diverging microchannel is studied by solving the coupled system of the Navier-Stokes equations for fluid flow and the Laplace equation for electrical field with an arbitrary Lagrangian-Eulerian finite-element method. A spatially non-uniform electric field is induced in the converging-diverging section, which gives rise to a direct current dielectrophoretic (DEP) force in addition to the electrostatic force acting on the charged particle. As a sequence, the symmetry of the particle velocity and trajectory with respect to the throat is broken. We demonstrate that the predicted particle trajectory shifts due to DEP show quantitative agreements with the existing experimental data. Although converging-diverging microchannels can be used for super fast electrophoresis due to the enhancement of the local electric field, it is shown that large particles may be blocked due to the induced DEP force, which thus must be taken into account in the study of electrophoresis in microfluidic devices where non-uniform electric fields are present.

Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field.

PubMed

Bradshaw, Richard T; Essex, Jonathan W

2016-08-09

Hydration free energy (HFE) calculations are often used to assess the performance of biomolecular force fields and the quality of assigned parameters. The AMOEBA polarizable force field moves beyond traditional pairwise additive models of electrostatics and may be expected to improve upon predictions of thermodynamic quantities such as HFEs over and above fixed-point-charge models. The recent SAMPL4 challenge evaluated the AMOEBA polarizable force field in this regard but showed substantially worse results than those using the fixed-point-charge GAFF model. Starting with a set of automatically generated AMOEBA parameters for the SAMPL4 data set, we evaluate the cumulative effects of a series of incremental improvements in parametrization protocol, including both solute and solvent model changes. Ultimately, the optimized AMOEBA parameters give a set of results that are not statistically significantly different from those of GAFF in terms of signed and unsigned error metrics. This allows us to propose a number of guidelines for new molecule parameter derivation with AMOEBA, which we expect to have benefits for a range of biomolecular simulation applications such as protein-ligand binding studies.

Scalar Casimir densities and forces for parallel plates in cosmic string spacetime

NASA Astrophysics Data System (ADS)

Bezerra de Mello, E. R.; Saharian, A. A.; Abajyan, S. V.

2018-04-01

We analyze the Green function, the Casimir densities and forces associated with a massive scalar quantum field confined between two parallel plates in a higher dimensional cosmic string spacetime. The plates are placed orthogonal to the string, and the field obeys the Robin boundary conditions on them. The boundary-induced contributions are explicitly extracted in the vacuum expectation values (VEVs) of the field squared and of the energy-momentum tensor for both the single plate and two plates geometries. The VEV of the energy-momentum tensor, in additional to the diagonal components, contains an off diagonal component corresponding to the shear stress. The latter vanishes on the plates in special cases of Dirichlet and Neumann boundary conditions. For points outside the string core the topological contributions in the VEVs are finite on the plates. Near the string the VEVs are dominated by the boundary-free part, whereas at large distances the boundary-induced contributions dominate. Due to the nonzero off diagonal component of the vacuum energy-momentum tensor, in addition to the normal component, the Casimir forces have nonzero component parallel to the boundary (shear force). Unlike the problem on the Minkowski bulk, the normal forces acting on the separate plates, in general, do not coincide if the corresponding Robin coefficients are different. Another difference is that in the presence of the cosmic string the Casimir forces for Dirichlet and Neumann boundary conditions differ. For Dirichlet boundary condition the normal Casimir force does not depend on the curvature coupling parameter. This is not the case for other boundary conditions. A new qualitative feature induced by the cosmic string is the appearance of the shear stress acting on the plates. The corresponding force is directed along the radial coordinate and vanishes for Dirichlet and Neumann boundary conditions. Depending on the parameters of the problem, the radial component of the shear force can be either positive or negative.

A Determination of the Benefits Derived by the Air Force from Providing Air Force Officers in the Logistics Field with Graduate Degrees in the Business Area from Civilian Graduate Institutions.

ERIC Educational Resources Information Center

Chamberlin, Brian; Smith, Richard A.

This thesis is concerned with what benefits the Air Force receives from sending logistics officers to civilian graduate institutions (CID). Additionally, the authors wanted to find how CID graduates fare as compared with graduates of the Graduate Logistics Management (GL). Three samples gathered were for CID graduates, the non-degree group…

Combining configurational energies and forces for molecular force field optimization

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

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

Combining configurational energies and forces for molecular force field optimization

DOE PAGES

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

2017-07-21

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

Magnetohydrodynamics of atmospheric transients. IV - Nonplane two-dimensional analyses of energy conversion and magnetic field evolution. [during corona following solar flare

NASA Technical Reports Server (NTRS)

Wu, S. T.; Nakagawa, Y.; Han, S. M.; Dryer, M.

1982-01-01

The evolution of the magnetic field and the manner of conversion of thermal energy into different forms in the corona following a solar flare are investigated by means of a nonplane magnetohydrodynamic (MHD) analysis. All three components of magnetic field and velocity are treated in a physically self-consistent manner, with all physical variables as functions of time (t) and two spatial coordinates (r, theta). The difference arising from the initial magnetic field, either twisted (force-free) or non-twisted (potential), is demonstrated. Consideration is given to two initial field topologies (open vs. closed). The results demonstrate that the conversion of magnetic energy is faster for the case of the initially twisted (force-free) field than for the initially untwisted (potential) field. In addition, the twisted field is found to produce a complex structure of the density enhancements.

Large pinning forces and matching effects in YBa2Cu3O7-δ thin films with Ba2Y(Nb/Ta)O6 nano-precipitates

PubMed Central

Opherden, Lars; Sieger, Max; Pahlke, Patrick; Hühne, Ruben; Schultz, Ludwig; Meledin, Alexander; Van Tendeloo, Gustaaf; Nast, Rainer; Holzapfel, Bernhard; Bianchetti, Marco; MacManus-Driscoll, Judith L.; Hänisch, Jens

2016-01-01

The addition of mixed double perovskite Ba2Y(Nb/Ta)O6 (BYNTO) to YBa2Cu3O7−δ (YBCO) thin films leads to a large improvement of the in-field current carrying capability. For low deposition rates, BYNTO grows as well-oriented, densely distributed nanocolumns. We achieved a pinning force density of 25 GN/m3 at 77 K at a matching field of 2.3 T, which is among the highest values reported for YBCO. The anisotropy of the critical current density shows a complex behavior whereby additional maxima are developed at field dependent angles. This is caused by a matching effect of the magnetic fields c-axis component. The exponent N of the current-voltage characteristics (inversely proportional to the creep rate S) allows the depinning mechanism to be determined. It changes from a double-kink excitation below the matching field to pinning-potential-determined creep above it. PMID:26887291

Force feedback delay affects perception of stiffness but not action, and the effect depends on the hand used but not on the handedness.

PubMed

Leib, Raz; Rubin, Inbar; Nisky, Ilana

2018-05-16

Interaction with an object often requires the estimation of its mechanical properties. We examined whether the hand that is used to interact with the object and their handedness affected people's estimation of these properties using stiffness estimation as a test case. We recorded participants' responses on a stiffness discrimination of a virtual elastic force field and the grip force applied on the robotic device during the interaction. In half of the trials, the robotic device delayed the participants' force feedback. Consistent with previous studies, delayed force feedback biased the perceived stiffness of the force field. Interestingly, in both left-handed and right-handed participants, for the delayed force field, there was even less perceived stiffness when participants used their left hand than their right hand. This result supports the idea that haptic processing is affected by laterality in the brain, not by handedness. Consistent with previous studies, participants adjusted their applied grip force according to the correct size and timing of the load force regardless of the hand that was used, the handedness, or the delay. This suggests that in all these conditions, participants were able to form an accurate internal representation of the anticipated trajectory of the load force (size and timing) and that this representation was used for accurate control of grip force independently of the perceptual bias. Thus, these results provide additional evidence for the dissociation between action and perception in the processing of delayed information.

Transferable Coarse-Grained Models for Ionic Liquids.

PubMed

Wang, Yanting; Feng, Shulu; Voth, Gregory A

2009-04-14

The effective force coarse-graining (EF-CG) method was applied to the imidazolium-based nitrate ionic liquids with various alkyl side-chain lengths. The nonbonded EF-CG forces for the ionic liquid with a short side chain were extended to generate the nonbonded forces for the ionic liquids with longer side chains. The EF-CG force fields for the ionic liquids exhibit very good transferability between different systems at various temperatures and are suitable for investigating the mesoscopic structural properties of this class of ionic liquids. The good additivity and ease of manipulation of the EF-CG force fields can allow for an inverse design methodology of ionic liquids at the coarse-grained level. With the EF-CG force field, the molecular dynamics (MD) simulation at a very large scale has been performed to check the significance of finite size effects on the structural properties. From these MD simulation results, it can be concluded that the finite size effect on the phenomenon of ionic liquid spatial heterogeneity (Wang, Y.; Voth, G. A. J. Am. Chem. Soc. 2005, 127, 12192) is small and that this phenomenon is indeed a nanostructural behavior which leads to the experimentally observed mesoscopic heterogeneous structure of ionic liquids.

Operation of A Sunpower M87 Cryocooler In A Magnetic Field

NASA Technical Reports Server (NTRS)

Breon, S. R.; Shirey, K. A.; Banks, I. S.; Warner, B. A.; Boyle, R. F.; Mustafi, S.; Krebs,Carolyn A. (Technical Monitor)

2002-01-01

The Alpha Magnetic Spectrometer-02 (AMS-02) is an experiment that will be flown as an attached payload on the International Space Station to detect dark matter and antimatter. It uses large superconducting magnets cooled with superfluid helium to bend the path of cosmic particles through a series of detectors, which then measure the mass, speed, charge, and direction of the particles. Four Sunpower M87N Stirling-cycle cryocoolers are used to extend the mission life by cooling the outer vapor-cooled shield of the dewar. The main magnet coils are separated by a distance of approximately 1 m and the coolers are located approximately 1.5 m from the center line of the magnet, where the field is as high as 925 gauss perpendicular to the cryocooler axis and 400 gauss along the cryocooler axis. Interactions between the applied magnetic field and the linear motor may result in additional forces and torques on the compressor piston. Motion of the compressor arid displacer pistons through the magnetic field spatial gradients will generate eddy currents. Additional eddy currents are created during magnet charge, discharge, and quench by the time-varying magnetic field. The results of tests to determine the magnitude of the forces, torques, and heating effects, as well as the need for additional magnetic shielding, are presented.

Numerical studies on the force characteristic of superconducting linear synchronous motor with HTS bulk magnet

NASA Astrophysics Data System (ADS)

Tang, Junjie; Li, Jing; Li, Xiang; Han, Le

2018-03-01

High temperature superconductor (HTS) bulks have significant potential use in linear motor application act as quasi-permanent magnet to replace traditional magnets. Force characteristic between HTS bulk magnet and traveling magnetic field was investigated with numerical simulation and experimental measurement in this paper. Influences of bulk height and number on the force characteristic were studied by the finite element model considering the nonlinear E-J relationship. Study was also made on addition of a back iron plate to the bulk magnet. Besides, force characteristic of bulk was compared with the permanent magnet results. The small initial decrease of the thrust could be explained by inside superconducting current redistribution. It was found that efficiency of linear motor did not increase by adding more bulk magnets. The bulk magnet will be remagnetized instead of erasing trapped field with the increase of the traveling magnetic field strength. The conclusions are helpful in prediction and design the linear motor with HTS bulk magnet.

Mean-field dynamos: The old concept and some recent developments. Karl Schwarzschild Award Lecture 2013

NASA Astrophysics Data System (ADS)

Rädler, K.-H.

This article elucidates the basic ideas of electrodynamics and magnetohydrodynamics of mean fields in turbulently moving conducting fluids. It is stressed that the connection of the mean electromotive force with the mean magnetic field and its first spatial derivatives is in general neither local nor instantaneous and that quite a few claims concerning pretended failures of the mean-field concept result from ignoring this aspect. In addition to the mean-field dynamo mechanisms of α2 and α Ω type several others are considered. Much progress in mean-field electrodynamics and magnetohydrodynamics results from the test-field method for calculating the coefficients that determine the connection of the mean electromotive force with the mean magnetic field. As an important example the memory effect in homogeneous isotropic turbulence is explained. In magnetohydrodynamic turbulence there is the possibility of a mean electromotive force that is primarily independent of the mean magnetic field and labeled as Yoshizawa effect. Despite of many efforts there is so far no convincing comprehensive theory of α quenching, that is, the reduction of the α effect with growing mean magnetic field, and of the saturation of mean-field dynamos. Steps toward such a theory are explained. Finally, some remarks on laboratory experiments with dynamos are made.

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.

PubMed

He, Yi; Xiao, Yi; Liwo, Adam; Scheraga, Harold A

2009-10-01

We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal alpha-helical and a minimal beta-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with alpha or alpha + beta structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. Copyright 2009 Wiley Periodicals, Inc.

Solvation of magnesium dication: molecular dynamics simulation and vibrational spectroscopic study of magnesium chloride in aqueous solutions.

PubMed

Callahan, Karen M; Casillas-Ituarte, Nadia N; Roeselová, Martina; Allen, Heather C; Tobias, Douglas J

2010-04-22

Magnesium dication plays many significant roles in biochemistry. While it is available to the environment from both ocean waters and mineral salts on land, its roles in environmental and atmospheric chemistry are still relatively unknown. Several pieces of experimental evidence suggest that contact ion pairing may not exist at ambient conditions in solutions of magnesium chloride up to saturation concentrations. This is not typical of most ions. There has been disagreement in the molecular dynamics literature concerning the existence of ion pairing in magnesium chloride solutions. Using a force field developed during this study, we show that contact ion pairing is not energetically favorable. Additionally, we present a concentration-dependent Raman spectroscopic study of the Mg-O(water) hexaaquo stretch that clearly supports the absence of ion pairing in MgCl(2) solutions, although a transition occurring in the spectrum between 0.06x and 0.09x suggests a change in solution structure. Finally, we compare experimental and calculated observables to validate our force field as well as two other commonly used magnesium force fields, and in the process show that ion pairing of magnesium clearly is not observed at higher concentrations in aqueous solutions of magnesium chloride, independent of the choice of magnesium force field, although some force fields give better agreement to experimental results than others.

Single-sided lateral-field and phototransistor-based optoelectronic tweezers

NASA Technical Reports Server (NTRS)

Ohta, Aaron (Inventor); Chiou, Pei-Yu (Inventor); Hsu, Hsan-Yin (Inventor); Jamshidi, Arash (Inventor); Wu, Ming-Chiang (Inventor); Neale, Steven L. (Inventor)

2011-01-01

Described herein are single-sided lateral-field optoelectronic tweezers (LOET) devices which use photosensitive electrode arrays to create optically-induced dielectrophoretic forces in an electric field that is parallel to the plane of the device. In addition, phototransistor-based optoelectronic tweezers (PhOET) devices are described that allow for optoelectronic tweezers (OET) operation in high-conductivity physiological buffer and cell culture media.

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy

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

Balke, Nina Wisinger; Jesse, Stephen; Carmichael, Ben D.

Here, atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. Inmore » combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm –1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.« less

Quantification of In-Contact Probe-Sample Electrostatic Forces with Dynamic Atomic Force Microscopy.

PubMed

Balke, Nina; Jesse, Stephen; Carmichael, Ben; Okatan, M; Kravchenko, Ivan; Kalinin, Sergei; Tselev, Alexander

2016-12-13

Atomic Force Microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V/nm at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids. Copyright 2016 IOP Publishing Ltd.

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy

DOE PAGES

Balke, Nina Wisinger; Jesse, Stephen; Carmichael, Ben D.; ...

2017-01-04

Here, atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. Inmore » combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm –1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.« less

Nonequilibrium forces between atoms and dielectrics mediated by a quantum field

NASA Astrophysics Data System (ADS)

Behunin, Ryan O.; Hu, Bei-Lok

2011-07-01

In this paper we give a first principles microphysics derivation of the nonequilibrium forces between an atom, treated as a three-dimensional harmonic oscillator, and a bulk dielectric medium modeled as a continuous lattice of oscillators coupled to a reservoir. We assume no direct interaction between the atom and the medium but there exist mutual influences transmitted via a common electromagnetic field. By employing concepts and techniques of open quantum systems we introduce coarse-graining to the physical variables—the medium, the quantum field, and the atom’s internal degrees of freedom, in that order—to extract their averaged effects from the lowest tier progressively to the top tier. The first tier of coarse-graining provides the averaged effect of the medium upon the field, quantified by a complex permittivity (in the frequency domain) describing the response of the dielectric to the field in addition to its back action on the field through a stochastic forcing term. The last tier of coarse-graining over the atom’s internal degrees of freedom results in an equation of motion for the atom’s center of mass from which we can derive the force on the atom. Our nonequilibrium formulation provides a fully dynamical description of the atom’s motion including back-action effects from all other relevant variables concerned. In the long-time limit we recover the known results for the atom-dielectric force when the combined system is in equilibrium or in a nonequilibrium stationary state.

A modification of Einstein-Schrödinger theory that contains both general relativity and electrodynamics

NASA Astrophysics Data System (ADS)

Shifflett, J. A.

2008-08-01

We modify the Einstein-Schrödinger theory to include a cosmological constant Λ z which multiplies the symmetric metric, and we show how the theory can be easily coupled to additional fields. The cosmological constant Λ z is assumed to be nearly cancelled by Schrödinger’s cosmological constant Λ b which multiplies the nonsymmetric fundamental tensor, such that the total Λ = Λ z + Λ b matches measurement. The resulting theory becomes exactly Einstein-Maxwell theory in the limit as | Λ z | → ∞. For | Λ z | ~ 1/(Planck length)2 the field equations match the ordinary Einstein and Maxwell equations except for extra terms which are < 10-16 of the usual terms for worst-case field strengths and rates-of-change accessible to measurement. Additional fields can be included in the Lagrangian, and these fields may couple to the symmetric metric and the electromagnetic vector potential, just as in Einstein-Maxwell theory. The ordinary Lorentz force equation is obtained by taking the divergence of the Einstein equations when sources are included. The Einstein-Infeld-Hoffmann (EIH) equations of motion match the equations of motion for Einstein-Maxwell theory to Newtonian/Coulombian order, which proves the existence of a Lorentz force without requiring sources. This fixes a problem of the original Einstein-Schrödinger theory, which failed to predict a Lorentz force. An exact charged solution matches the Reissner-Nordström solution except for additional terms which are ~10-66 of the usual terms for worst-case radii accessible to measurement. An exact electromagnetic plane-wave solution is identical to its counterpart in Einstein-Maxwell theory.

Resonances of an Oscillating Conductive Pipe Driven by an Alternating Magnetic Field in the Presence of a Static Magnetic Field

ERIC Educational Resources Information Center

Ladera, Celso L.; Donoso, Guillermo

2011-01-01

A short conducting pipe that hangs from a weak spring is forced to oscillate by the magnetic field of a surrounding coaxial coil that has been excited by a low-frequency current source in the presence of an additional static magnetic field. Induced oscillating currents appear in the pipe. The pipe motion becomes damped by the dragging forces…

On the extraction of pressure fields from PIV velocity measurements in turbines

NASA Astrophysics Data System (ADS)

Villegas, Arturo; Diez, Fancisco J.

2012-11-01

In this study, the pressure field for a water turbine is derived from particle image velocimetry (PIV) measurements. Measurements are performed in a recirculating water channel facility. The PIV measurements include calculating the tangential and axial forces applied to the turbine by solving the integral momentum equation around the airfoil. The results are compared with the forces obtained from the Blade Element Momentum theory (BEMT). Forces are calculated by using three different methods. In the first method, the pressure fields are obtained from PIV velocity fields by solving the Poisson equation. The boundary conditions are obtained from the Navier-Stokes momentum equations. In the second method, the pressure at the boundaries is determined by spatial integration of the pressure gradients along the boundaries. In the third method, applicable only to incompressible, inviscid, irrotational, and steady flow, the pressure is calculated using the Bernoulli equation. This approximated pressure is known to be accurate far from the airfoil and outside of the wake for steady flows. Additionally, the pressure is used to solve for the force from the integral momentum equation on the blade. From the three methods proposed to solve for pressure and forces from PIV measurements, the first one, which is solved by using the Poisson equation, provides the best match to the BEM theory calculations.

On some Aspects of Gravitomagnetism and Correction for Perihelion Advance

NASA Astrophysics Data System (ADS)

Rocha, F.; Malheiro, M.; Marinho, R., Jr.

2016-04-01

In 1918 Joseph Lense and Hans Thirring, discovered the gravitomagnetic effect when studied solutions to the Einstein field equations using the weak field and slow motion approximation of rotating systems. They noted that when a body falls towards a massive object in rotation it feels a force perpendicular to its movement. The equations that they obtained were similar to Maxwell’s equations of electromagnetism, now known as Maxwell’s equations for gravitomagnetism. Some authors affirm that the gravitomagnetic effect can cause precession then in this paper we calculate the precession that gravitomagnetic effect cause in Mercury’s perihelion advance. To make this we calculate the field between dipoles to measure the influence that the Sun has on Mercury, taking into account the gravitomagnetic field that the Sun and Mercury produces when they rotate around themselves. In addition, we calculate the ratio of the dipole force (of all solar system planet’s) and the Newton’s gravitational force to see how much is smaller.

All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model

PubMed Central

Savelyev, Alexey; MacKerell, Alexander D.

2014-01-01

Presented is a first generation atomistic force field for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting QM data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude force field yields stable DNA duplexes on the 100 ns time scale and satisfactorily reproduces (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII sub-states of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive force field, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978

Simulating the Activation of Voltage Sensing Domain for a Voltage-Gated Sodium Channel Using Polarizable Force Field.

PubMed

Sun, Rui-Ning; Gong, Haipeng

2017-03-02

Voltage-gated sodium (Na V ) channels play vital roles in the signal transduction of excitable cells. Upon activation of a Na V channel, the change of transmembrane voltage triggers conformational change of the voltage sensing domain, which then elicits opening of the pore domain and thus allows an influx of Na + ions. Description of this process with atomistic details is in urgent demand. In this work, we simulated the partial activation process of the voltage sensing domain of a prokaryotic Na V channel using a polarizable force field. We not only observed the conformational change of the voltage sensing domain from resting to preactive state, but also rigorously estimated the free energy profile along the identified reaction pathway. Comparison with the control simulation using an additive force field indicates that voltage-gating thermodynamics of Na V channels may be inaccurately described without considering the electrostatic polarization effect.

Environmental Assessment for Proposed Demolition and Consolidation, Maxwell Air Force Base, Montgomery County, Alabama

DTIC Science & Technology

2013-09-01

leadership, and management responsibilities. In addition, AU is responsible for research in designated fields of aerospace, education, leadership...County, Alabama. Designation : Final Environmental Assessment Abstract: As a result of a memorandum signed by President Obama in June 2010, the...Force Exchange Service) -ANG (Air National Guard) & Reserve facilities -Government-owned, contractor-funded facilities -RDT&E ( Research

Novel System for Bite-Force Sensing and Monitoring Based on Magnetic Near Field Communication

PubMed Central

Lantada, Andres Diaz; Bris, Carlos González; Morgado, Pilar Lafont; Maudes, Jesús Sanz

2012-01-01

Intraoral devices for bite-force sensing have several applications in odontology and maxillofacial surgery, as bite-force measurements provide additional information to help understand the characteristics of bruxism disorders and can also be of help for the evaluation of post-surgical evolution and for comparison of alternative treatments. A new system for measuring human bite forces is proposed in this work. This system has future applications for the monitoring of bruxism events and as a complement for its conventional diagnosis. Bruxism is a pathology consisting of grinding or tight clenching of the upper and lower teeth, which leads to several problems such as lesions to the teeth, headaches, orofacial pain and important disorders of the temporomandibular joint. The prototype uses a magnetic field communication scheme similar to low-frequency radio frequency identification (RFID) technology (NFC). The reader generates a low-frequency magnetic field that is used as the information carrier and powers the sensor. The system is notable because it uses an intra-mouth passive sensor and an external interrogator, which remotely records and processes information regarding a patient's dental activity. This permits a quantitative assessment of bite-force, without requiring intra-mouth batteries, and can provide supplementary information to polysomnographic recordings, current most adequate early diagnostic method, so as to initiate corrective actions before irreversible dental wear appears. In addition to describing the system's operational principles and the manufacture of personalized prototypes, this report will also demonstrate the feasibility of the system and results from the first in vitro and in vivo trials. PMID:23112669

Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4+ Interactions.

PubMed

Khan, Hanif M; Grauffel, Cédric; Broer, Ria; MacKerell, Alexander D; Havenith, Remco W A; Reuter, Nathalie

2016-11-08

Cation-π interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH 3 ) 3 ) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol-tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARMM36 and Drude polarizable force fields in modeling tyrosine-choline interactions. We show that the potential energy surface (PES) obtained using SAPT2+/aug-cc-pVDZ compares well with the large basis-set CCSD(T) PES when TMA approaches the phenol ring perpendicularly. Furthermore, the SAPT energy decomposition reveals comparable contributions from electrostatics and dispersion in phenol-TMA interactions. We then compared the SAPT2+/aug-cc-pVDZ PES obtained along various approach directions to the corresponding PES obtained with CHARMM, and we show that the force field accurately reproduces the minimum distances while the interaction energies are underestimated. The use of the Drude polarizable force field significantly improves the interaction energies but decreases the agreement on distances at energy minima. The best agreement between force field and QM PES is obtained by modifying the Lennard-Jones terms for atom pairs involved in the phenol-TMA cation-π interactions. This is further shown to improve the correlation between the occupancy of tyrosine-choline cation-π interactions obtained from molecular dynamics simulations of a bilayer-bound bacterial phospholipase and experimental affinity data of the wild-type protein and selected mutants.

A mixed pseudospectral/finite difference method for a thermally driven fluid in a nonuniform gravitational field

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1985-01-01

A numerical study of the steady, axisymmetric flow in a heated, rotating spherical shell is conducted to model the Atmospheric General Circulation Experiment (AGCE) proposed to run aboard a later Shuttle mission. The AGCE will consist of concentric rotating spheres confining a dielectric fluid. By imposing a dielectric field across the fluid a radial body force will be created. The numerical solution technique is based on the incompressible Navier-Stokes equations. In the method a pseudospectral technique is used in the latitudinal direction, and a second-order accurate finite difference scheme discretizes time and radial derivatives. This paper discusses the development and performance of this numerical scheme for the AGCE which has been modeled in the past only by pure FD formulations. In addition, previous models have not investigated the effect of using a dielectric force to simulate terrestrial gravity. The effect of this dielectric force on the flow field is investigated as well as a parameter study of varying rotation rates and boundary temperatures. Among the effects noted are the production of larger velocities and enhanced reversals of radial temperature gradients for a body force generated by the electric field.

Alternating phase focused linacs

DOEpatents

Swenson, Donald A.

1980-01-01

A heavy particle linear accelerator employing rf fields for transverse and ongitudinal focusing as well as acceleration. Drift tube length and gap positions in a standing wave drift tube loaded structure are arranged so that particles are subject to acceleration and succession of focusing and defocusing forces which contain the beam without additional magnetic or electric focusing fields.

Radial force on the vacuum chamber wall during thermal quench in tokamaks

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

Pustovitov, V. D., E-mail: pustovitov-vd@nrcki.ru

The radial force balance during a thermal quench in tokamaks is analyzed. As a rule, the duration τ{sub tp} of such events is much shorter than the resistive time τ{sub w} of the vacuum chamber wall. Therefore, the perturbations of the magnetic field B produced by the evolving plasma cannot penetrate the wall, which makes different the magnetic pressures on its inner and outer sides. The goal of this work is the analytical estimation of the resulting integral radial force on the wall. The plasma is considered axially symmetric; for the description of radial forces on the wall, the resultsmore » of V.D. Shafranov’s classical work [J. Nucl. Energy C 5, 251 (1963)] are used. Developed for tokamaks, the standard equilibrium theory considers three interacting systems: plasma, poloidal field coils, and toroidal field coils. Here, the wall is additionally incorporated with currents driven by ∂B/∂t≠0 accompanying the fast loss of the plasma thermal energy. It is shown that they essentially affect the force redistribution, thereby leading to large loads on the wall. The estimates prove that these loads have to be accounted for in the disruptive scenarios in large tokamaks.« less

An exploration in acoustic radiation force experienced by cylindrical shells via resonance scattering theory.

PubMed

Rajabi, Majid; Behzad, Mehdi

2014-04-01

In nonlinear acoustic regime, a body insonified by a sound field is known to experience a steady force that is called the acoustic radiation force (RF). This force is a second-order quantity of the velocity potential function of the ambient medium. Exploiting the sufficiency of linear solution representation of potential function in RF formulation, and following the classical resonance scattering theorem (RST) which suggests the scattered field as a superposition of the resonant field and a background (non-resonant) component, we will show that the radiation force is a composition of three components: background part, resonant part and their interaction. Due to the nonlinearity effects, each part contains the contribution of pure partial waves in addition to their mutual interaction. The numerical results propose the residue component (i.e., subtraction of the background component from the RF) as a good indicator of the contribution of circumferential surface waves in RF. Defining the modal series of radiation force function and its components, it will be shown that within each partial wave, the resonance contribution can be synthesized as the Breit-Wigner form for adequately none-close resonant frequencies. The proposed formulation may be helpful essentially due to its inherent value as a canonical subject in physical acoustics. Furthermore, it may make a tunnel through the circumferential resonance reducing effects on radiation forces. Copyright © 2013 Elsevier B.V. All rights reserved.

Exact Harmonic Metric for a Uniformly Moving Schwarzschild Black Hole

NASA Astrophysics Data System (ADS)

He, Guan-Sheng; Lin, Wen-Bin

2014-02-01

The harmonic metric for Schwarzschild black hole with a uniform velocity is presented. In the limit of weak field and low velocity, this metric reduces to the post-Newtonian approximation for one moving point mass. As an application, we derive the dynamics of particle and photon in the weak-field limit for the moving Schwarzschild black hole with an arbitrary velocity. It is found that the relativistic motion of gravitational source can induce an additional centripetal force on the test particle, which may be comparable to or even larger than the conventional Newtonian gravitational force.

Parametric study of an acoustic levitation system. [for thermophysical properties determination of nonmetal materials

NASA Technical Reports Server (NTRS)

Oran, W. A.; Berge, L. H.; Parker, H. W.

1980-01-01

The performance of an acoustic levitation system designed for the containerless processing of materials and consisting of a St. Clair generator and a reflector arranged in a six-axis configuration, is examined in order to define critical parameters of high-temperature systems and limitations of earth-based devices. The fields and forces along the axis of the system are measured and the forces are plotted versus body volume. It is found that for a range of shapes and sizes the levitation force is roughly proportional to body volume until the characteristic 'diameter' reaches a value of about lambda/2. A significant (i.e., factor of four) enhancement in the levitation force is obtained by curving the faces of the driver and reflector. In addition, the behavior of liquid materials in the acoustic fields is studied, and the radius at which the deformation of a levitated drop occurs is calculated.

Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

USGS Publications Warehouse

Lee, M.W.; Meuwly, M.

2013-01-01

The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

Quenching and anisotropy of hydromagnetic turbulent transport

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

Karak, Bidya Binay; Brandenburg, Axel; Rheinhardt, Matthias

2014-11-01

Hydromagnetic turbulence affects the evolution of large-scale magnetic fields through mean-field effects like turbulent diffusion and the α effect. For stronger fields, these effects are usually suppressed or quenched, and additional anisotropies are introduced. Using different variants of the test-field method, we determine the quenching of the turbulent transport coefficients for the forced Roberts flow, isotropically forced non-helical turbulence, and rotating thermal convection. We see significant quenching only when the mean magnetic field is larger than the equipartition value of the turbulence. Expressing the magnetic field in terms of the equipartition value of the quenched flows, we obtain for themore » quenching exponents of the turbulent magnetic diffusivity about 1.3, 1.1, and 1.3 for Roberts flow, forced turbulence, and convection, respectively. However, when the magnetic field is expressed in terms of the equipartition value of the unquenched flows, these quenching exponents become about 4, 1.5, and 2.3, respectively. For the α effect, the exponent is about 1.3 for the Roberts flow and 2 for convection in the first case, but 4 and 3, respectively, in the second. In convection, the quenching of turbulent pumping follows the same power law as turbulent diffusion, while for the coefficient describing the Ω×J effect nearly the same quenching exponent is obtained as for α. For forced turbulence, turbulent diffusion proportional to the second derivative along the mean magnetic field is quenched much less, especially for larger values of the magnetic Reynolds number. However, we find that in corresponding axisymmetric mean-field dynamos with dominant toroidal field the quenched diffusion coefficients are the same for the poloidal and toroidal field constituents.« less

Friction forces on atoms after acceleration

DOE PAGES

Intravaia, Francesco; Mkrtchian, Vanik E.; Buhmann, Stefan Yoshi; ...

2015-05-12

The aim of this study is to revisit the calculation of atom–surface quantum friction in the quantum field theory formulation put forward by Barton (2010 New J. Phys. 12 113045). We show that the power dissipated into field excitations and the associated friction force depend on how the atom is boosted from being initially at rest to a configuration in which it is moving at constant velocity (v) parallel to the planar interface. In addition, we point out that there is a subtle cancellation between the one-photon and part of the two-photon dissipating power, resulting in a leading order contributionmore » to the frictional power which goes as v 4. These results are also confirmed by an alternative calculation of the average radiation force, which scales as v 3.« less

Pinch dynamics in a low-β plasma

NASA Astrophysics Data System (ADS)

Moffatt, H. K.; Mizerski, K.

2018-02-01

The relaxation of a helical magnetic field {B}({x},t) in a high-conductivity plasma contained in the annulus between two perfectly conducting coaxial cylinders is considered. The plasma is of low density and its pressure is negligible compared with the magnetic pressure; the flow of the plasma is driven by the Lorentz force and energy is dissipated primarily by the viscosity of the medium. The axial and toroidal fluxes of magnetic field are conserved in the perfect-conductivity limit, as is the mass per unit axial length. The magnetic field relaxes during a rapid initial stage to a force-free state, and then decays slowly, due to the effect of weak resistivity η, while constrained to remain approximately force-free. Interest centres on whether the relaxed field may attain a Taylor state; but under the assumed conditions with axial and toroidal flux conserved inside every cylindrical Lagrangian surface, this is not possible. The effect of an additional α-effect associated with instabilities and turbulence in the plasma is therefore investigated in exploratory manner. An assumed pseudo-scalar form of α proportional to q η ({j}\\cdot {B}) is adopted, where {j}={{\

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.

PubMed

Antipov, Sergey V; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2017-11-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H 2 , local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

PubMed Central

Antipov, Sergey V.; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2018-01-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research “Molecular Ultrafast Science and Technology,” are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase. PMID:29376107

A mixed pseudospectral/finite difference method for a thermally driven fluid in a nonuniform gravitational field

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1985-01-01

A numerical study of the steady, axisymmetric flow in a heated, rotating spherical shell is conducted to model the Atmospheric General Circulation Experiment (AGCE) proposed to run aboard a later shuttle mission. The AGCE will consist of concentric rotating spheres confining a dielectric fluid. By imposing a dielectric field across the fluid a radial body force will be created. The numerical solution technique is based on the incompressible Navier-Stokes equations. In the method a pseudospectral technique is based on the incompressible Navier-Stokes equations. In the method a pseudospectral technique is used in the latitudinal direction, and a second-order accurate finite difference scheme discretizes time and radial derivatives. This paper discusses the development and performance of this numerical scheme for the AGCE which has been modelled in the past only by pure FD formulations. In addition, previous models have not investigated the effect of using a dielectric force to simulate terrestrial gravity. The effect of this dielectric force on the flow field is investigated as well as a parameter study of varying rotation rates and boundary temperatures. Among the effects noted are the production of larger velocities and enhanced reversals of radial temperature gradients for a body force generated by the electric field.

First Observation of a Hall Effect in a Dusty Plasma: A Charged Granular Flow with Relevance to Planetary Rings

NASA Astrophysics Data System (ADS)

Eiskowitz, Skylar; Ballew, Nolan; Rojas, Rubén; Lathrop, Daniel

2017-11-01

The particles in Saturn's rings exhibit complex dynamic behavior. They experience solar radiation pressure, electromagnetic forces, and granular collisions. To investigate the possibility of the Hall Effect in the dusty plasma that comprise Saturn's rings, we have built an experiment that demonstrates the Hall Effect in granular matter. We focus on the Hall Effect because the rings' grains become collisionally charged and experience Saturn's dipolar magnetic field and Lorentz forces as they orbit. The experimental setup includes a closed ring-like track where granular matter is forced to circulate driven by compressed air. The structure sits between two electromagnets so that a portion of the track experiences up to a 0.2 T magnetic field. We vary the strength of the field and the speed of the particles. We report the voltage differences between two conducting plates on opposite sides of the track. If Saturn's rings do experience the Hall Effect, the inside and outside of the rings will develop a charge separation that can lead to a radial electric field and various phenomena including orbital effects due to the additional electric forces. Observational evidence from Cassini suggests that Saturn's rings exhibit lighting, supporting the notion that they are electrically charged. TREND REU program sponsored by the National Science Foundation.

A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation

PubMed Central

Gu, Junfeng; Bai, Fang; Li, Honglin; Wang, Xicheng

2012-01-01

Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the Cα root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled. PMID:23203075

Extending the Range for Force Calibration in Magnetic Tweezers

PubMed Central

Daldrop, Peter; Brutzer, Hergen; Huhle, Alexander; Kauert, Dominik J.; Seidel, Ralf

2015-01-01

Magnetic tweezers are a wide-spread tool used to study the mechanics and the function of a large variety of biomolecules and biomolecular machines. This tool uses a magnetic particle and a strong magnetic field gradient to apply defined forces to the molecule of interest. Forces are typically quantified by analyzing the lateral fluctuations of the biomolecule-tethered particle in the direction perpendicular to the applied force. Since the magnetic field pins the anisotropy axis of the particle, the lateral fluctuations follow the geometry of a pendulum with a short pendulum length along and a long pendulum length perpendicular to the field lines. Typically, the short pendulum geometry is used for force calibration by power-spectral-density (PSD) analysis, because the movement of the bead in this direction can be approximated by a simple translational motion. Here, we provide a detailed analysis of the fluctuations according to the long pendulum geometry and show that for this direction, both the translational and the rotational motions of the particle have to be considered. We provide analytical formulas for the PSD of this coupled system that agree well with PSDs obtained in experiments and simulations and that finally allow a faithful quantification of the magnetic force for the long pendulum geometry. We furthermore demonstrate that this methodology allows the calibration of much larger forces than the short pendulum geometry in a tether-length-dependent manner. In addition, the accuracy of determination of the absolute force is improved. Our force calibration based on the long pendulum geometry will facilitate high-resolution magnetic-tweezers experiments that rely on short molecules and large forces, as well as highly parallelized measurements that use low frame rates. PMID:25992733

Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions.

PubMed

Fischer, Nina M; van Maaren, Paul J; Ditz, Jonas C; Yildirim, Ahmet; van der Spoel, David

2015-07-14

In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http://virtualchemistry.org, aimed at facilitating sharing and reuse of input files for molecular simulations.

Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.; ...

2016-06-23

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

NIS, IR and Raman spectra with quantum mechanical calculations for analyzing the force field of hypericin model compounds

NASA Astrophysics Data System (ADS)

Ulicny, Jozef; Leulliot, Nicolas; Grajcar, Lydie; Baron, Marie-Hélène; Jobic, Hervé; Ghomi, Mahmoud

1999-06-01

Geometry optimization as well as harmonic force field calculations at HF and DFT levels of theory have been performed in order to elucidate the ground state properties of anthrone and emodin, two polycyclic conjugated molecules considered as hypericin model compounds. NIS, IR and FT-Raman spectra of these compounds have been recorded to validate the calculated results (geometry and vibrational modes). Calculated NIS spectra using the lowest energy conformers are in agreement with experiment. In addition, the intramolecular H-bonds in emodin predicted by the calculations can be evidenced using IR spectra as a function of temperature.

NIS, IR and Raman spectra with quantum mechanical calculations for analyzing the force field of hypericin model compounds

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

Ulicny, Jozef; Department of Biophysics, Safarik University, Jesenna 5, 04154 Kosice; Leulliot, Nicolas

1999-06-15

Geometry optimization as well as harmonic force field calculations at HF and DFT levels of theory have been performed in order to elucidate the ground state properties of anthrone and emodin, two polycyclic conjugated molecules considered as hypericin model compounds. NIS, IR and FT-Raman spectra of these compounds have been recorded to validate the calculated results (geometry and vibrational modes). Calculated NIS spectra using the lowest energy conformers are in agreement with experiment. In addition, the intramolecular H-bonds in emodin predicted by the calculations can be evidenced using IR spectra as a function of temperature.

Cryogenically enhanced magneto-Archimedes levitation

NASA Astrophysics Data System (ADS)

Catherall, A. T.; López-Alcaraz, P.; Benedict, K. A.; King, P. J.; Eaves, L.

2005-05-01

The application of both a strong magnetic field and magnetic field gradient to a diamagnetic body can produce a vertical force which is sufficient to counteract its weight due to gravity. By immersing the body in a paramagnetic fluid, an additional adjustable magneto-buoyancy force is generated which enhances the levitation effect. Here we show that cryogenic oxygen and oxygen-nitrogen mixtures in both gaseous and liquid form provide sufficient buoyancy to permit the levitation and flotation of a wide range of materials. These fluids may provide an alternative to synthetic ferrofluids for the separation of minerals. We also report the dynamics of corrugation instabilities on the surface of magnetized liquid oxygen.

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate

PubMed Central

2015-01-01

Phosphate groups are commonly observed in biomolecules such as nucleic acids and lipids. Due to their highly charged and polarizable nature, modeling these compounds with classical force fields is challenging. Using quantum mechanical studies and liquid-phase simulations, the AMOEBA force field for dimethyl phosphate (DMP) ion and trimethyl phosphate (TMP) has been developed. On the basis of ab initio calculations, it was found that ion binding and the solution environment significantly impact both the molecular geometry and the energy differences between conformations. Atomic multipole moments are derived from MP2/cc-pVQZ calculations of methyl phosphates at several conformations with their chemical environments taken into account. Many-body polarization is handled via a Thole-style induction model using distributed atomic polarizabilities. van der Waals parameters of phosphate and oxygen atoms are determined by fitting to the quantum mechanical interaction energy curves for water with DMP or TMP. Additional stretch-torsion and angle-torsion coupling terms were introduced in order to capture asymmetry in P–O bond lengths and angles due to the generalized anomeric effect. The resulting force field for DMP and TMP is able to accurately describe both the molecular structure and conformational energy surface, including bond and angle variations with conformation, as well as interaction of both species with water and metal ions. The force field was further validated for TMP in the condensed phase by computing hydration free energy, liquid density, and heat of vaporization. The polarization behavior between liquid TMP and TMP in water is drastically different. PMID:26574325

Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics.

PubMed

Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

2014-02-01

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use (13) C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Copyright © 2013 Wiley Periodicals, Inc.

Manifestations of the rotation and gravity of the Earth in high-energy physics experiments

NASA Astrophysics Data System (ADS)

Obukhov, Yuri N.; Silenko, Alexander J.; Teryaev, Oleg V.

2016-08-01

The inertial (due to rotation) and gravitational fields of the Earth affect the motion of an elementary particle and its spin dynamics. This influence is not negligible and should be taken into account in high-energy physics experiments. Earth's influence is manifest in perturbations in the particle motion, in an additional precession of the spin, and in a change of the constitutive tensor of the Maxwell electrodynamics. Bigger corrections are oscillatory, and their contributions average to zero. Other corrections due to the inhomogeneity of the inertial field are not oscillatory but they are very small and may be important only for the storage ring electric dipole moment experiments. Earth's gravity causes the Newton-like force, the reaction force provided by a focusing system, and additional torques acting on the spin. However, there are no observable indications of the electromagnetic effects due to Earth's gravity.

The Additional Error of Inertial Sensors Induced by Hypersonic Flight Conditions

PubMed Central

Karachun, Volodimir; Mel’nick, Viktorij; Korobiichuk, Igor; Nowicki, Michał; Szewczyk, Roman; Kobzar, Svitlana

2016-01-01

The emergence of hypersonic technology pose a new challenge for inertial navigation sensors, widely used in aerospace industry. The main problems are: extremely high temperatures, vibration of the fuselage, penetrating acoustic radiation and shock N-waves. The nature of the additional errors of the gyroscopic inertial sensor with hydrostatic suspension components under operating conditions generated by forced precession of the movable part of the suspension due to diffraction phenomena in acoustic fields is explained. The cause of the disturbing moments in the form of the Coriolis inertia forces during the transition of the suspension surface into the category of impedance is revealed. The boundaries of occurrence of the features on the resonance wave match are described. The values of the “false” angular velocity as a result of the elastic-stress state of suspension in the acoustic fields are determined. PMID:26927122

Robot Training With Vector Fields Based on Stroke Survivors' Individual Movement Statistics.

PubMed

Wright, Zachary A; Lazzaro, Emily; Thielbar, Kelly O; Patton, James L; Huang, Felix C

2018-02-01

The wide variation in upper extremity motor impairments among stroke survivors necessitates more intelligent methods of customized therapy. However, current strategies for characterizing individual motor impairments are limited by the use of traditional clinical assessments (e.g., Fugl-Meyer) and simple engineering metrics (e.g., goal-directed performance). Our overall approach is to statistically identify the range of volitional movement capabilities, and then apply a robot-applied force vector field intervention that encourages under-expressed movements. We investigated whether explorative training with such customized force fields would improve stroke survivors' (n = 11) movement patterns in comparison to a control group that trained without forces (n = 11). Force and control groups increased Fugl-Meyer UE scores (average of 1.0 and 1.1, respectively), which is not considered clinically meaningful. Interestingly, participants from both groups demonstrated dramatic increases in their range of velocity during exploration following only six days of training (average increase of 166.4% and 153.7% for the Force and Control group, respectively). While both groups showed evidence of improvement, we also found evidence that customized forces affected learning in a systematic way. When customized forces were active, we observed broader distributions of velocity that were not present in the controls. Second, we found that these changes led to specific changes in unassisted motion. In addition, while the shape of movement distributions changed significantly for both groups, detailed analysis of the velocity distributions revealed that customized forces promoted a greater proportion of favorable changes. Taken together, these results provide encouraging evidence that patient-specific force fields based on individuals' movement statistics can be used to create new movement patterns and shape them in a customized manner. To the best of our knowledge, this paper is the first to directly link engineering assessments of stroke survivors' exploration movement behaviors to the design of customized robot therapy.

Management of change through force field analysis.

PubMed

Baulcomb, Jean Sandra

2003-07-01

Today's NHS is rapidly changing, placing more emphasis on the managerial responsibilities of ward managers. Managing change is seen as being skilled at creating, acquiring and transferring knowledge to reflect new knowledge and insights. Defining core concepts is often difficult and requires the drawing on models/theories of change for guidance. Guidance from Lewin's (1951) force field analysis demonstrates the complexities of the change process and how driving and resisting forces were incorporated within the planning and implementation phases. Findings outline the benefits of a small scale change for staff, patients and the organization when successfully used to introduce a change of shift pattern within a progressively busy haematology day unit, in order to meet service demands without additional funding. Conclusions have been drawn in relation to the process and recommendations for practice made to further enhance care delivery within the unit.

Positive and negative effective mass of classical particles in oscillatory and static fields.

PubMed

Dodin, I Y; Fisch, N J

2008-03-01

A classical particle oscillating in an arbitrary high-frequency or static field effectively exhibits a modified rest mass m(eff) derived from the particle averaged Lagrangian. Relativistic ponderomotive and diamagnetic forces, as well as magnetic drifts, are obtained from the m(eff) dependence on the guiding center location and velocity. The effective mass is not necessarily positive and can result in backward acceleration when an additional perturbation force is applied. As an example, adiabatic dynamics with m||>0 and m||<0 is demonstrated for a wave-driven particle along a dc magnetic field, m|| being the effective longitudinal mass derived from m(eff). Multiple energy states are realized in this case, yielding up to three branches of m|| for a given magnetic moment and parallel velocity.

An Atomic Force Microscope with Dual Actuation Capability for Biomolecular Experiments

NASA Astrophysics Data System (ADS)

Sevim, Semih; Shamsudhin, Naveen; Ozer, Sevil; Feng, Luying; Fakhraee, Arielle; Ergeneman, Olgaç; Pané, Salvador; Nelson, Bradley J.; Torun, Hamdi

2016-06-01

We report a modular atomic force microscope (AFM) design for biomolecular experiments. The AFM head uses readily available components and incorporates deflection-based optics and a piezotube-based cantilever actuator. Jetted-polymers have been used in the mechanical assembly, which allows rapid manufacturing. In addition, a FeCo-tipped electromagnet provides high-force cantilever actuation with vertical magnetic fields up to 0.55 T. Magnetic field calibration has been performed with a micro-hall sensor, which corresponds well with results from finite element magnetostatics simulations. An integrated force resolution of 1.82 and 2.98 pN, in air and in DI water, respectively was achieved in 1 kHz bandwidth with commercially available cantilevers made of Silicon Nitride. The controller and user interface are implemented on modular hardware to ensure scalability. The AFM can be operated in different modes, such as molecular pulling or force-clamp, by actuating the cantilever with the available actuators. The electromagnetic and piezoelectric actuation capabilities have been demonstrated in unbinding experiments of the biotin-streptavidin complex.

An Atomic Force Microscope with Dual Actuation Capability for Biomolecular Experiments

PubMed Central

Sevim, Semih; Shamsudhin, Naveen; Ozer, Sevil; Feng, Luying; Fakhraee, Arielle; Ergeneman, Olgaç; Pané, Salvador; Nelson, Bradley J.; Torun, Hamdi

2016-01-01

We report a modular atomic force microscope (AFM) design for biomolecular experiments. The AFM head uses readily available components and incorporates deflection-based optics and a piezotube-based cantilever actuator. Jetted-polymers have been used in the mechanical assembly, which allows rapid manufacturing. In addition, a FeCo-tipped electromagnet provides high-force cantilever actuation with vertical magnetic fields up to 0.55 T. Magnetic field calibration has been performed with a micro-hall sensor, which corresponds well with results from finite element magnetostatics simulations. An integrated force resolution of 1.82 and 2.98 pN, in air and in DI water, respectively was achieved in 1 kHz bandwidth with commercially available cantilevers made of Silicon Nitride. The controller and user interface are implemented on modular hardware to ensure scalability. The AFM can be operated in different modes, such as molecular pulling or force-clamp, by actuating the cantilever with the available actuators. The electromagnetic and piezoelectric actuation capabilities have been demonstrated in unbinding experiments of the biotin-streptavidin complex. PMID:27273214

Large-scale dynamo growth rates from numerical simulations and implications for mean-field theories

NASA Astrophysics Data System (ADS)

Park, Kiwan; Blackman, Eric G.; Subramanian, Kandaswamy

2013-05-01

Understanding large-scale magnetic field growth in turbulent plasmas in the magnetohydrodynamic limit is a goal of magnetic dynamo theory. In particular, assessing how well large-scale helical field growth and saturation in simulations match those predicted by existing theories is important for progress. Using numerical simulations of isotropically forced turbulence without large-scale shear with its implications, we focus on several additional aspects of this comparison: (1) Leading mean-field dynamo theories which break the field into large and small scales predict that large-scale helical field growth rates are determined by the difference between kinetic helicity and current helicity with no dependence on the nonhelical energy in small-scale magnetic fields. Our simulations show that the growth rate of the large-scale field from fully helical forcing is indeed unaffected by the presence or absence of small-scale magnetic fields amplified in a precursor nonhelical dynamo. However, because the precursor nonhelical dynamo in our simulations produced fields that were strongly subequipartition with respect to the kinetic energy, we cannot yet rule out the potential influence of stronger nonhelical small-scale fields. (2) We have identified two features in our simulations which cannot be explained by the most minimalist versions of two-scale mean-field theory: (i) fully helical small-scale forcing produces significant nonhelical large-scale magnetic energy and (ii) the saturation of the large-scale field growth is time delayed with respect to what minimalist theory predicts. We comment on desirable generalizations to the theory in this context and future desired work.

Large-scale dynamo growth rates from numerical simulations and implications for mean-field theories.

PubMed

Park, Kiwan; Blackman, Eric G; Subramanian, Kandaswamy

2013-05-01

Understanding large-scale magnetic field growth in turbulent plasmas in the magnetohydrodynamic limit is a goal of magnetic dynamo theory. In particular, assessing how well large-scale helical field growth and saturation in simulations match those predicted by existing theories is important for progress. Using numerical simulations of isotropically forced turbulence without large-scale shear with its implications, we focus on several additional aspects of this comparison: (1) Leading mean-field dynamo theories which break the field into large and small scales predict that large-scale helical field growth rates are determined by the difference between kinetic helicity and current helicity with no dependence on the nonhelical energy in small-scale magnetic fields. Our simulations show that the growth rate of the large-scale field from fully helical forcing is indeed unaffected by the presence or absence of small-scale magnetic fields amplified in a precursor nonhelical dynamo. However, because the precursor nonhelical dynamo in our simulations produced fields that were strongly subequipartition with respect to the kinetic energy, we cannot yet rule out the potential influence of stronger nonhelical small-scale fields. (2) We have identified two features in our simulations which cannot be explained by the most minimalist versions of two-scale mean-field theory: (i) fully helical small-scale forcing produces significant nonhelical large-scale magnetic energy and (ii) the saturation of the large-scale field growth is time delayed with respect to what minimalist theory predicts. We comment on desirable generalizations to the theory in this context and future desired work.

Performing the Millikan experiment at the molecular scale: Determination of atomic Millikan-Thomson charges by computationally measuring atomic forces.

PubMed

Rogers, T Ryan; Wang, Feng

2017-10-28

An atomic version of the Millikan oil drop experiment is performed computationally. It is shown that for planar molecules, the atomic version of the Millikan experiment can be used to define an atomic partial charge that is free from charge flow contributions. We refer to this charge as the Millikan-Thomson (MT) charge. Since the MT charge is directly proportional to the atomic forces under a uniform electric field, it is the most relevant charge for force field developments. The MT charge shows good stability with respect to different choices of the basis set. In addition, the MT charge can be easily calculated even at post-Hartree-Fock levels of theory. With the MT charge, it is shown that for a planar water dimer, the charge transfer from the proton acceptor to the proton donor is about -0.052 e. While both planar hydrated cations and anions show signs of charge transfer, anions show a much more significant charge transfer to the hydration water than the corresponding cations. It might be important to explicitly model the ion charge transfer to water in a force field at least for the anions.

Magnetic Alignment of γ-Fe2O3 Nanoparticles in Polymer Nanocomposites

NASA Astrophysics Data System (ADS)

Jimenez, Andrew; Kumar, Sanat K.; Jestin, Jacques

Recent work in nanocomposites has been heavily focused on controlling the dispersion state of filler particles. The use of internal self-assembly based on matrix properties provides a limited solution to the desire for specified organizations. By introducing a magnetic field during the casting of a polymer solution it has been shown that particles can be oriented to form anisotropic structures - commonly sought after for improved mechanical properties. Here, magnetic nanoparticles were cast in two different polymer matrices to study the effect of various forces that lead to this highly desired alignment. The addition of the magnetic field as an external trigger was shown to not necessarily force the clustering, but rather orient the agglomerates already available in solution. This demonstrates the importance of other dominant forces introduced into the system by characteristics of the polymers themselves. While this magnetic field provides a direction for the sample, the key forces lie in the interactions between the polymers and nanoparticles (as well as their solvent). The study shows a dependence of anisotropy on the particle loading, matrix, and casting time, from which continued work hopes to quantify the clustering necessary to optimize alignment in the composite.

On the contribution of circumferential resonance modes in acoustic radiation force experienced by cylindrical shells

NASA Astrophysics Data System (ADS)

Rajabi, Majid; Behzad, Mehdi

2014-10-01

A body insonified by a constant (time-varying) intensity sound field is known to experience a steady (oscillatory) force that is called the steady-state (dynamic) acoustic radiation force. Using the classical resonance scattering theorem (RST) which suggests the scattered field as a superposition of a resonance field and a background (non-resonance) component, we show that the radiation force acting on a cylindrical shell may be synthesized as a composition of three components: background part, resonance part and their interaction. The background component reveals the pure geometrical reflection effects and illustrates a regular behavior with respect to frequency, while the others demonstrate a singular behavior near the resonance frequencies. The results illustrate that the resonance effects associated to partial waves can be isolated by the subtraction of the background component from the total (steady-state or dynamic) radiation force function (i.e., residue component). In the case of steady-state radiation force, the components are exerted on the body as static forces. For the case of oscillatory amplitude excitation, the components are exerted at the modulation frequency with frequency-dependant phase shifts. The results demonstrate the dominant contribution of the non-resonance component of dynamic radiation force at high frequencies with respect to the residue component, which offers the potential application of ultrasound stimulated vibro-acoustic spectroscopy technique in low frequency resonance spectroscopy purposes. Furthermore, the proposed formulation may be useful essentially due to its intrinsic value in physical acoustics. In addition, it may unveil the contribution of resonance modes in the dynamic radiation force experienced by the cylindrical objects and its underlying physics.

Force-Mediating Magnetic Nanoparticles to Engineer Neuronal Cell Function

PubMed Central

Gahl, Trevor J.; Kunze, Anja

2018-01-01

Cellular processes like membrane deformation, cell migration, and transport of organelles are sensitive to mechanical forces. Technically, these cellular processes can be manipulated through operating forces at a spatial precision in the range of nanometers up to a few micrometers through chaperoning force-mediating nanoparticles in electrical, magnetic, or optical field gradients. But which force-mediating tool is more suitable to manipulate cell migration, and which, to manipulate cell signaling? We review here the differences in forces sensation to control and engineer cellular processes inside and outside the cell, with a special focus on neuronal cells. In addition, we discuss technical details and limitations of different force-mediating approaches and highlight recent advancements of nanomagnetics in cell organization, communication, signaling, and intracellular trafficking. Finally, we give suggestions about how force-mediating nanoparticles can be used to our advantage in next-generation neurotherapeutic devices. PMID:29867315

Force-Mediating Magnetic Nanoparticles to Engineer Neuronal Cell Function.

PubMed

Gahl, Trevor J; Kunze, Anja

2018-01-01

Cellular processes like membrane deformation, cell migration, and transport of organelles are sensitive to mechanical forces. Technically, these cellular processes can be manipulated through operating forces at a spatial precision in the range of nanometers up to a few micrometers through chaperoning force-mediating nanoparticles in electrical, magnetic, or optical field gradients. But which force-mediating tool is more suitable to manipulate cell migration, and which, to manipulate cell signaling? We review here the differences in forces sensation to control and engineer cellular processes inside and outside the cell, with a special focus on neuronal cells. In addition, we discuss technical details and limitations of different force-mediating approaches and highlight recent advancements of nanomagnetics in cell organization, communication, signaling, and intracellular trafficking. Finally, we give suggestions about how force-mediating nanoparticles can be used to our advantage in next-generation neurotherapeutic devices.

Understrength Air Force Officer Career Fields. A Force Management Approach

DTIC Science & Technology

2005-01-01

LtCol John Crown (DPSA). In addition, we had very helpful interviews with Mr. Vaughan Blackstone (DPAPP) and Mr. Dennis Miller (DPPAO). Also at...econometric impact analysis that was used to determine an optimal bonus amount or target population prior to bonus implementation.15 The success of...problems in managing personnel assignments. First, there is a high " tax " for special-duty jobs that requires them to place personnel officers into

A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces

PubMed Central

Zhou, Y. C.; Holst, Michael; McCammon, J. Andrew

2008-01-01

In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces corresponding to four types of perturbations to an electrostatic potential field, and establish the existance of an equilibrium configuration using a fixed-point argument, under the assumption that the change in the ionic strength and charges due to the additional molecules causing the deformation are sufficiently small. The results are valid for elastic models with arbitrarily complex dielectric interfaces and cavities, and can be generalized to large elastic deformation caused by high ionic strength, large charges, and strong external fields by using continuation methods. PMID:19461946

Path planning for robotic truss assembly

NASA Technical Reports Server (NTRS)

Sanderson, Arthur C.

1993-01-01

A new Potential Fields approach to the robotic path planning problem is proposed and implemented. Our approach, which is based on one originally proposed by Munger, computes an incremental joint vector based upon attraction to a goal and repulsion from obstacles. By repetitively adding and computing these 'steps', it is hoped (but not guaranteed) that the robot will reach its goal. An attractive force exerted by the goal is found by solving for the the minimum norm solution to the linear Jacobian equation. A repulsive force between obstacles and the robot's links is used to avoid collisions. Its magnitude is inversely proportional to the distance. Together, these forces make the goal the global minimum potential point, but local minima can stop the robot from ever reaching that point. Our approach improves on a basic, potential field paradigm developed by Munger by using an active, adaptive field - what we will call a 'flexible' potential field. Active fields are stronger when objects move towards one another and weaker when they move apart. An adaptive field's strength is individually tailored to be just strong enough to avoid any collision. In addition to the local planner, a global planning algorithm helps the planner to avoid local field minima by providing subgoals. These subgoals are based on the obstacles which caused the local planner to fail. A best-first search algorithm A* is used for graph search.

A controllable tactile device for human-like tissue realization using smart magneto-rheological fluids: fabrication and modeling

NASA Astrophysics Data System (ADS)

Cha, Seung-Woo; Kang, Seok-Rae; Hwang, Yong-Hoon; Oh, Jong-Seok; Choi, Seung-Bok

2018-06-01

This paper proposes a new tactile device to realize the force of human-like organs using the viscoelastic property by combing a smart magneto-rheological (MR) fluid with a sponge (MR sponge in short). The effectiveness of the sensor is validated through the comparison of the force obtained through measurement and the proposed prediction model. As the first step, a conventional standard linear solid model is adopted to independently investigate the force characteristics of MR fluid and sponge. Force is measured using a 3-axis robot with a force sensor to obtain certain properties of MR fluid and sponge. In addition, to show that the proposed MR sponge can realize the force of human-like tissues, experiments are performed using three specimens, i.e., porcine heart, lung, and liver. Subsequently, a quasi-static model for predicting the field-dependent force of the MR sponge is formulated using empirical values. It is demonstrated through comparison that the proposed force model can accurately predict the force of the specimens without significant error. In addition, a psychophysical test is carried out by ordinary subjects to validate the effectiveness of the proposed tactile device. Results show that the MR sponge tactile device can easily produce various levels of the force of human-like tissues, such as the liver and lung of the porcine, by controlling input current.

Benefits of an Air Force Contracting Warrant Officer Program

DTIC Science & Technology

2011-12-01

effects of adding the warrant officer track into the contracting career field. The assessment uses personal interviews and surveys covering job...research investigates the perceived benefits and contrasting effects of adding the warrant officer track into the contracting career field. The...centered on cutting costs in the hopes of increasing revenues, which can be disastrous for both the private and public sectors , in addition to the

Levitation forces of a bulk YBCO superconductor in gradient varying magnetic fields

NASA Astrophysics Data System (ADS)

Jiang, J.; Gong, Y. M.; Wang, G.; Zhou, D. J.; Zhao, L. F.; Zhang, Y.; Zhao, Y.

2015-09-01

The levitation forces of a bulk YBCO superconductor in gradient varying high and low magnetic fields generated from a superconducting magnet were investigated. The magnetic field intensity of the superconducting magnet was measured when the exciting current was 90 A. The magnetic field gradient and magnetic force field were both calculated. The YBCO bulk was cooled by liquid nitrogen in field-cooling (FC) and zero-field-cooling (ZFC) condition. The results showed that the levitation forces increased with increasing the magnetic field intensity. Moreover, the levitation forces were more dependent on magnetic field gradient and magnetic force field than magnetic field intensity.

Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.

PubMed

Aliev, Abil E; Courtier-Murias, Denis

2010-09-30

Experimental NMR verification of MD simulations using 12 different force fields (AMBER, CHARMM, GROMOS, and OPLS-AA) and 5 different water models has been undertaken to identify reliable MD protocols for structure and dynamics elucidations of small open chain peptides containing Gly and Pro. A conformationally flexible tetrapeptide Gly-Pro-Gly-Gly was selected for NMR (3)J-coupling, chemical shift, and internuclear distance measurements, followed by their calculations using 2 μs long MD simulations in water. In addition, Ramachandran population maps for Pro-2 and Gly-3 residues of GPGG obtained from MD simulations were used for detailed comparisons with similar maps from the protein data bank (PDB) for large number of Gly and Pro residues in proteins. The MD simulations revealed strong dependence of the populations and geometries of preferred backbone and side chain conformations, as well as the time scales of the peptide torsional transitions on the force field used. On the basis of the analysis of the measured and calculated data, AMBER99SB is identified as the most reliable force field for reproducing NMR measured parameters, which are dependent on the peptide backbone and the Pro side chain geometries and dynamics. Ramachandran maps showing the dependence of conformational populations as a function of backbone ϕ/ψ angles for Pro-2 and Gly-3 residues of GPGG from MD simulations using AMBER99SB, AMBER03, and CHARMM were found to resemble similar maps for Gly and Pro residues from the PDB survey. Three force fields (AMBER99, AMBER99ϕ, and AMBER94) showed the least satisfactory agreement with both the solution NMR and the PDB survey data. The poor performance of these force fields is attributed to their propensity to overstabilize helical peptide backbone conformations at the Pro-2 and Gly-3 residues. On the basis of the similarity of the MD and PDB Ramachandran plots, the following sequence of transitions is suggested for the Gly backbone conformation: α(L) ⇆ β(PR) ⇆ β(S) ⇆ β(P) ⇆ α, where backbone secondary structures α(L) and α are associated with helices and turns, β(P) and β(PR) correspond to the left- and right-handed polyproline II structures and β(S) denotes the fully stretched backbone conformation. Compared to the force field dependence, less significant, but noteworthy, variations in the populations of the peptide backbone conformations were observed. For different solvent models considered, a correlation was noted between the number of torsional transitions in GPGG and the water self-diffusion coefficient on using TIP3P, TIP4P, and TIP5P models. In addition to MD results, we also report DFT derived Karplus relationships for Gly and Pro residues using B972 and B3LYP functionals.

Recent Advances of MEMS Resonators for Lorentz Force Based Magnetic Field Sensors: Design, Applications and Challenges.

PubMed

Herrera-May, Agustín Leobardo; Soler-Balcazar, Juan Carlos; Vázquez-Leal, Héctor; Martínez-Castillo, Jaime; Vigueras-Zuñiga, Marco Osvaldo; Aguilera-Cortés, Luz Antonio

2016-08-24

Microelectromechanical systems (MEMS) resonators have allowed the development of magnetic field sensors with potential applications such as biomedicine, automotive industry, navigation systems, space satellites, telecommunications and non-destructive testing. We present a review of recent magnetic field sensors based on MEMS resonators, which operate with Lorentz force. These sensors have a compact structure, wide measurement range, low energy consumption, high sensitivity and suitable performance. The design methodology, simulation tools, damping sources, sensing techniques and future applications of magnetic field sensors are discussed. The design process is fundamental in achieving correct selection of the operation principle, sensing technique, materials, fabrication process and readout systems of the sensors. In addition, the description of the main sensing systems and challenges of the MEMS sensors are discussed. To develop the best devices, researches of their mechanical reliability, vacuum packaging, design optimization and temperature compensation circuits are needed. Future applications will require multifunctional sensors for monitoring several physical parameters (e.g., magnetic field, acceleration, angular ratio, humidity, temperature and gases).

Recent Advances of MEMS Resonators for Lorentz Force Based Magnetic Field Sensors: Design, Applications and Challenges

PubMed Central

Herrera-May, Agustín Leobardo; Soler-Balcazar, Juan Carlos; Vázquez-Leal, Héctor; Martínez-Castillo, Jaime; Vigueras-Zuñiga, Marco Osvaldo; Aguilera-Cortés, Luz Antonio

2016-01-01

Microelectromechanical systems (MEMS) resonators have allowed the development of magnetic field sensors with potential applications such as biomedicine, automotive industry, navigation systems, space satellites, telecommunications and non-destructive testing. We present a review of recent magnetic field sensors based on MEMS resonators, which operate with Lorentz force. These sensors have a compact structure, wide measurement range, low energy consumption, high sensitivity and suitable performance. The design methodology, simulation tools, damping sources, sensing techniques and future applications of magnetic field sensors are discussed. The design process is fundamental in achieving correct selection of the operation principle, sensing technique, materials, fabrication process and readout systems of the sensors. In addition, the description of the main sensing systems and challenges of the MEMS sensors are discussed. To develop the best devices, researches of their mechanical reliability, vacuum packaging, design optimization and temperature compensation circuits are needed. Future applications will require multifunctional sensors for monitoring several physical parameters (e.g., magnetic field, acceleration, angular ratio, humidity, temperature and gases). PMID:27563912

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

PubMed Central

Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

2010-01-01

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

A force field for 3,3,3-fluoro-1-propenes, including HFO-1234yf.

PubMed

Raabe, Gabriele; Maginn, Edward J

2010-08-12

The European Union (EU) legislation 2006/40/EC bans from January 2011 the cooperative marketing of new car types that use refrigerants in their heating, ventilation, and air conditioning (HVAC) systems with global warming potentials (GWP) higher than 150. Thus, the phase-out of the presently used tetrafluoroethane refrigerant R134a necessitates the adoption of alternative refrigerants. Fluoropropenes such as 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf) are currently regarded as promising low GWP refrigerants, but the lack of experimental data on their thermophysical properties hampers independent studies on their performance in HVAC systems or in other technical applications. In principle, molecular modeling can be used to predict the relevant properties of refrigerants, but adequate intermolecular potential functions ("force fields") are lacking for fluoropropenes. Thus, we developed a transferable force field for fluoropropenes composed of CF(3)-, -CF=, -CH=, CF(2)=, and CH(2)= groups and applied the force field to study 3,3,3 trifluoro-1-propene (HFO-1243zf), 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), and hexafluoro-1-propene (HFO-1216). We performed Gibbs ensemble simulations on these three fluoropropenes to compute the vapor pressure, saturated densities, and heats of vaporization. In addition, molecular dynamics simulations were conducted to provide predictions for the density, thermal expansivity, isobaric heat capacity, and transport properties of liquid HFO-1234yf in the temperature range from 263.15 to 310 K and pressures up to 2 MPa. Agreement between simulation results and experimental data and/or correlations (when available) was good, thereby validating the predictive ability of the force field.

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

PubMed Central

Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

2014-01-01

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use 13C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Proteins 2014; 82:195–215. © 2013 Wiley Periodicals, Inc. PMID:23818175

Conformational analysis of bis(methylthio)methane and diethyl sulfide molecules in the liquid phase: reverse Monte Carlo studies using classical interatomic potential functions.

PubMed

Gereben, Orsolya; Pusztai, László

2013-11-13

Series of flexible molecule reverse Monte Carlo calculations, using bonding and non-bonding interatomic potential functions (FMP-RMC), were performed starting from previous molecular dynamics results that had applied the OPLS-AA and EncadS force fields. During RMC modeling, the experimental x-ray total scattering structure factor was approached. The discrepancy between experimental and calculated structure factors, in comparison with the molecular dynamics results, decreased substantially in each case. The room temperature liquid structure of bis(methylthio)methane is excellently described by the FMP-RMC simulation that applied the EncadS force field parameters. The main conformer was found to be AG with 55.2%, followed by 37.2% of G(+)G(+) (G(-)G(-)) and 7.6% of AA; the stability of the G(+)G(+) (G(-)G(-)) conformer is most probably caused by the anomer effect. The liquid structure of diethyl sulfide can be best described by applying the OPLS-AA force field parameters during FMP-RMC simulation, although in this case the force field parameters were found to be not fully compatible with experimental data. Here, the two main conformers are AG (50.6%) and the AA (40%). In addition to findings on the actual real systems, a fairly detailed comparison between traditional and FMP-RMC methodology is provided.

Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein.

PubMed

Shao, Qiang; Shi, Jiye; Zhu, Weiliang

2012-09-28

The ability of molecular dynamics simulation to capturing the transient states within the folding pathway of protein is important to the understanding of protein folding mechanism. In the present study, the integrated-tempering-sampling molecular dynamics (ITS-MD) simulation was performed to investigate the transient states including intermediate and unfolded ones in the folding pathway of a miniprotein, Trp-cage. Three force fields (FF03, FF99SB, and FF96) were tested, and both intermediate and unfolded states with their characteristics in good agreement with experiments were observed during the simulations, which supports the hypothesis that observable intermediates might present in the folding pathway of small polypeptides. In addition, it was demonstrated that FF03 force field as combined with ITS-MD is in overall a more proper force field than the others in reproducing experimentally recorded properties in UVRS, ECD, and NMR, Photo-CIDNP NMR, and IR T-jump experiments, and the folding∕unfolding thermodynamics parameters, such as ΔG(U), ΔC(p), and ΔH(U) (T(m)). In summary, the present study showed that using suitable force field and energy sampling method, molecular dynamics simulation could capture the transient states within the folding pathway of protein which are consistent with the experimental measurements, and thus provide information of protein folding mechanism and thermodynamics.

Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

PubMed Central

Miller, Mark S.; Lay, Wesley K.

2016-01-01

Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium:carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by re-deriving the partial charges for each peptide. PMID:27052117

Anisotropic particles near surfaces: Propulsion force and friction

NASA Astrophysics Data System (ADS)

Müller, Boris; Krüger, Matthias

2016-03-01

We theoretically study the phenomenon of propulsion through Casimir forces in thermal nonequilibrium. Using fluctuational electrodynamics, we derive a formula for the propulsion force for an arbitrary small object in two scenarios: (i) for the object being isolated, and (ii) for the object being close to a planar surface. In the latter case, the propulsion force (i.e., the force parallel to the surface) increases with decreasing distance, i.e., it couples to the near field. We numerically calculate the lateral force acting on a hot spheroid near a surface and show that it can be as large as the gravitational force, thus being potentially measurable in fly-by experiments. We close by linking our results to well-known relations of linear-response theory in fluctuational electrodynamics: Looking at the friction of the anisotropic object for constant velocity, we identify a correction term that is additional to the typically used approach.

Field-Assisted Contact Line Motion in Thin Films.

PubMed

Ghosh, Udita Uday; DasGupta, Sunando

2018-04-25

The balance of intermolecular and surface forces plays a critical role in the transport phenomena near the contact line region of an extended meniscus in several technologically important processes. Externally applied fields can alter the equilibrium and stability of the meniscus with concomitant effects on its shape and spreading characteristics and may even lead to an oscillation. This feature article provides a detailed account of the present and past efforts in exploring the behavior of curved thin liquid films subjected to mild thermal perturbations, heat input, and electrical and magnetic fields for pure as well as colloidal suspensions, including the effects of particle charge and polarity. The shape-dependent intermolecular force field has been evaluated in situ by a nonobtrusive optical technique utilizing the interference phenomena and subsequent image processing. The critical role of disjoining pressure is identified along with the determination of the Hamaker constant. The spatial and temporal variations of the capillary forces are evaluated for the advancing and receding menisci. The Maxwell-stress-induced enhanced spreading during electrowetting, at relatively low voltages, and that due to the application of a magnetic field are discussed with respect to their distinctly different characteristics and application potentials. The use of the augmented Young-Laplace equation elicited additional insights into the fundamental physics for flow in ultrathin liquid films.

Determination of coronal magnetic fields from vector magnetograms

NASA Technical Reports Server (NTRS)

Mikic, Zoran

1992-01-01

The determination of coronal magnetic fields from vector magnetograms, including the development and application of algorithms to determine force-free coronal fields above selected observations of active regions is studied. Two additional active regions were selected and analyzed. The restriction of periodicity in the 3-D code which is used to determine the coronal field was removed giving the new code variable mesh spacing and is thus able to provide a more realistic description of coronal fields. The NOAA active region AR5747 of 20 Oct. 1989 was studied. A brief account of progress during the research performed is reported.

Computer Applications for Air Force Construction Management.

DTIC Science & Technology

1979-08-01

The addition of a motor in 1920, resulted in the first electrical calculators. Charles Babbage is considered the "father" of the computer. In 1883, he...management applications. Watt (1795), Owen (early 1800’s), and Babbage (1832), made the first real- istic management applications in the field of production...network scheduling by the contractor "if" it is felt that the government can benefit by its use. 2 Captain Charles D. Sprick, Resident Air Force

A Primer on Fire Support for Joint Special Operations

DTIC Science & Technology

1993-04-15

been "a battery commander with the 99th Field Artillery (Pack) at Fort Hoyle , Maryland." 3 7 The addition of the provisional cannon company to the Force...gatherer for special operations.143 ROLE OF THE FIRE SUPPORT OFFICER During a recent interview, Major General Fred F. Marty, Commandant of the Field...143. Ibid., 722-724. 144. Fred F. Marty, Major General, U.S. Army, Commandant of the U.S. Army Field Artillery School, Fort Sill, Oklahoma, interview by

Three-dimensional morphologies of inclined equiaxed dendrites growing under forced convection by phase-field-lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi; Shimokawabe, Takashi; Aoki, Takayuki

2018-02-01

Three-dimensional growth morphologies of equiaxed dendrites growing under forced convection, with their preferred growth direction inclined from the flow direction, were investigated by performing large-scale phase-field lattice Boltzmann simulations on a graphical-processing-unit supercomputer. The tip velocities of the dendrite arms with their preferred growth directions inclined toward the upstream and downstream directions increased and decreased, respectively, as a result of forced convection. In addition, the tip velocities decreased monotonically as the angle between the preferred growth direction and the upstream direction increased. Here, the degree of acceleration of the upstream tips was larger than the degree of deceleration of the downstream tips. The angles between the actual tip growth directions and the preferred growth direction of the dendrite arms exhibited a characteristic change with two local maxima and two local minima.

The evolution and future of minimalism in neurological surgery.

PubMed

Liu, Charles Y; Wang, Michael Y; Apuzzo, Michael L J

2004-11-01

The evolution of the field of neurological surgery has been marked by a progressive minimalism. This has been evident in the development of an entire arsenal of modern neurosurgical enterprises, including microneurosurgery, neuroendoscopy, stereotactic neurosurgery, endovascular techniques, radiosurgical systems, intraoperative and navigational devices, and in the last decade, cellular and molecular adjuvants. In addition to reviewing the major developments and paradigm shifts in the cyclic reinvention of the field as it currently stands, this paper attempts to identify forces and developments that are likely to fuel the irresistible escalation of minimalism into the future. These forces include discoveries in computational science, imaging, molecular science, biomedical engineering, and information processing as they relate to the theme of minimalism. These areas are explained in the light of future possibilities offered by the emerging field of nanotechnology with molecular engineering.

Surface‐wave Green’s tensors in the near field

USGS Publications Warehouse

Haney, Matt; Nakahara, Hisashi

2014-01-01

We demonstrate the connection between theoretical expressions for the correlation of ambient noise Rayleigh and Love waves and the exact surface‐wave Green’s tensors for a point force. The surface‐wave Green’s tensors are well known in the far‐field limit. On the other hand, the imaginary part of the exact Green’s tensors, including near‐field effects, arises in correlation techniques such as the spatial autocorrelation (SPAC) method. Using the imaginary part of the exact Green’s tensors from the SPAC method, we find the associated real part using the Kramers–Kronig relations. The application of the Kramers–Kronig relations is not straightforward, however, because the causality properties of the different tensor components vary. In addition to the Green’s tensors for a point force, we also derive expressions for a general point moment tensor source.

ON ESTIMATING FORCE-FREENESS BASED ON OBSERVED MAGNETOGRAMS

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

Zhang, X. M.; Zhang, M.; Su, J. T., E-mail: xmzhang@nao.cas.cn

It is a common practice in the solar physics community to test whether or not measured photospheric or chromospheric vector magnetograms are force-free, using the Maxwell stress as a measure. Some previous studies have suggested that magnetic fields of active regions in the solar chromosphere are close to being force-free whereas there is no consistency among previous studies on whether magnetic fields of active regions in the solar photosphere are force-free or not. Here we use three kinds of representative magnetic fields (analytical force-free solutions, modeled solar-like force-free fields, and observed non-force-free fields) to discuss how measurement issues such asmore » limited field of view (FOV), instrument sensitivity, and measurement error could affect the estimation of force-freeness based on observed magnetograms. Unlike previous studies that focus on discussing the effect of limited FOV or instrument sensitivity, our calculation shows that just measurement error alone can significantly influence the results of estimates of force-freeness, due to the fact that measurement errors in horizontal magnetic fields are usually ten times larger than those in vertical fields. This property of measurement errors, interacting with the particular form of a formula for estimating force-freeness, would result in wrong judgments of the force-freeness: a truly force-free field may be mistakenly estimated as being non-force-free and a truly non-force-free field may be estimated as being force-free. Our analysis calls for caution when interpreting estimates of force-freeness based on measured magnetograms, and also suggests that the true photospheric magnetic field may be further away from being force-free than it currently appears to be.« less

On the Role of Global Magnetic Field Configuration in Affecting Ring Current Dynamics

NASA Technical Reports Server (NTRS)

Zheng, Y.; Zaharia, S. G.; Fok, M. H.

2010-01-01

Plasma and field interaction is one important aspect of inner magnetospheric physics. The magnetic field controls particle motion through gradient, curvature drifts and E cross B drift. In this presentation, we show how the global magnetic field affects dynamics of the ring current through simulations of two moderate geomagnetic storms (20 November 2007 and 8-9 March 2008). Preliminary results of coupling the Comprehensive Ring Current Model (CRCM) with a three-dimensional plasma force balance code (to achieve self-consistency in both E and B fields) indicate that inclusion of self-consistency in B tends to mitigate the intensification of the ring current as other similar coupling efforts have shown. In our approach, self-consistency in the electric field is already an existing capability of the CRCM. The magnetic self-consistency is achieved by computing the three-dimensional magnetic field in force balance with anisotropic ring current ion distributions. We discuss the coupling methodology and its further improvement. In addition, comparative studies by using various magnetic field models will be shown. Simulation results will be put into a global context by analyzing the morphology of the ring current, its anisotropy and characteristics ofthe interconnected region 2 field-aligned currents.

Permanent magnet system to guide superparamagnetic particles

NASA Astrophysics Data System (ADS)

Baun, Olga; Blümler, Peter

2017-10-01

A new concept of using permanent magnet systems for guiding superparamagnetic nano-particles on arbitrary trajectories over a large volume is proposed. The basic idea is to use one magnet system which provides a strong, homogeneous, dipolar magnetic field to magnetize and orient the particles, and a second constantly graded, quadrupolar field, superimposed on the first, to generate a force on the oriented particles. In this configuration the motion of the particles is driven predominantly by the component of the gradient field which is parallel to the direction of the homogeneous field. As a result, particles are guided with constant force and in a single direction over the entire volume. The direction is simply adjusted by varying the angle between quadrupole and dipole. Since a single gradient is impossible due to Gauß' law, the other gradient component of the quadrupole determines the angular deviation of the force. However, the latter can be neglected if the homogeneous field is stronger than the local contribution of the quadrupole field. A possible realization of this idea is a coaxial arrangement of two Halbach cylinders. A dipole to evenly magnetize and orient the particles, and a quadrupole to generate the force. The local force was calculated analytically for this particular geometry and the directional limits were analyzed and discussed. A simple prototype was constructed to demonstrate the principle in two dimensions on several nano-particles of different size, which were moved along a rough square by manual adjustment of the force angle. The observed velocities of superparamagnetic particles in this prototype were always several orders of magnitude higher than the theoretically expected value. This discrepancy is attributed to the observed formation of long particle chains as a result of their polarization by the homogeneous field. The magnetic moment of such a chain is then the combination of that of its constituents, while its hydrodynamic radius stays low. A complete system will consist of another quadrupole (third cylinder) to additionally enable scaling of the gradient/force strength by another rotation. In this configuration the device could then also be used as a simple MRI machine to image the particles between movement intervals. Finally, a concept is proposed by which superparamagnetic particles can be guided in three-dimensional space.

Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

PubMed Central

Mohamed, Noor Asidah; Bradshaw, Richard T.

2016-01-01

The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise‐additive force field. Although AMOEBA results give mean errors close to “chemical accuracy,” GAFF performs surprisingly well, with statistically significantly more accurate results than AMOEBA in some solvents. However, for both models, free energies calculated in chloroform show worst agreement to experiment and individual solutes are consistently poor performers, suggesting non‐potential‐specific errors also contribute to inaccuracy. Scope for the improvement of both potentials remains limited by the lack of high quality experimental data across multiple solvents, particularly those of high dielectric constant. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27757978

Calculating the sensitivity and robustness of binding free energy calculations to force field parameters

PubMed Central

Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.

2013-01-01

Binding free energy calculations offer a thermodynamically rigorous method to compute protein-ligand binding, and they depend on empirical force fields with hundreds of parameters. We examined the sensitivity of computed binding free energies to the ligand’s electrostatic and van der Waals parameters. Dielectric screening and cancellation of effects between ligand-protein and ligand-solvent interactions reduce the parameter sensitivity of binding affinity by 65%, compared with interaction strengths computed in the gas-phase. However, multiple changes to parameters combine additively on average, which can lead to large changes in overall affinity from many small changes to parameters. Using these results, we estimate that random, uncorrelated errors in force field nonbonded parameters must be smaller than 0.02 e per charge, 0.06 Å per radius, and 0.01 kcal/mol per well depth in order to obtain 68% (one standard deviation) confidence that a computed affinity for a moderately-sized lead compound will fall within 1 kcal/mol of the true affinity, if these are the only sources of error considered. PMID:24015114

Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field

NASA Astrophysics Data System (ADS)

Jing, Zhifeng; Qi, Rui; Liu, Chengwen; Ren, Pengyu

2017-10-01

The interactions between metal ions and proteins are ubiquitous in biology. The selective binding of metal ions has a variety of regulatory functions. Therefore, there is a need to understand the mechanism of protein-ion binding. The interactions involving metal ions are complicated in nature, where short-range charge-penetration, charge transfer, polarization, and many-body effects all contribute significantly, and a quantitative description of all these interactions is lacking. In addition, it is unclear how well current polarizable force fields can capture these energy terms and whether these polarization models are good enough to describe the many-body effects. In this work, two energy decomposition methods, absolutely localized molecular orbitals and symmetry-adapted perturbation theory, were utilized to study the interactions between Mg2+/Ca2+ and model compounds for amino acids. Comparison of individual interaction components revealed that while there are significant charge-penetration and charge-transfer effects in Ca complexes, these effects can be captured by the van der Waals (vdW) term in the AMOEBA force field. The electrostatic interaction in Mg complexes is well described by AMOEBA since the charge penetration is small, but the distance-dependent polarization energy is problematic. Many-body effects were shown to be important for protein-ion binding. In the absence of many-body effects, highly charged binding pockets will be over-stabilized, and the pockets will always favor Mg and thus lose selectivity. Therefore, many-body effects must be incorporated in the force field in order to predict the structure and energetics of metalloproteins. Also, the many-body effects of charge transfer in Ca complexes were found to be non-negligible. The absorption of charge-transfer energy into the additive vdW term was a main source of error for the AMOEBA many-body interaction energies.

Application of advanced sampling and analysis methods to predict the structure of adsorbed protein on a material surface

PubMed Central

Abramyan, Tigran M.; Hyde-Volpe, David L.; Stuart, Steven J.; Latour, Robert A.

2017-01-01

The use of standard molecular dynamics simulation methods to predict the interactions of a protein with a material surface have the inherent limitations of lacking the ability to determine the most likely conformations and orientations of the adsorbed protein on the surface and to determine the level of convergence attained by the simulation. In addition, standard mixing rules are typically applied to combine the nonbonded force field parameters of the solution and solid phases the system to represent interfacial behavior without validation. As a means to circumvent these problems, the authors demonstrate the application of an efficient advanced sampling method (TIGER2A) for the simulation of the adsorption of hen egg-white lysozyme on a crystalline (110) high-density polyethylene surface plane. Simulations are conducted to generate a Boltzmann-weighted ensemble of sampled states using force field parameters that were validated to represent interfacial behavior for this system. The resulting ensembles of sampled states were then analyzed using an in-house-developed cluster analysis method to predict the most probable orientations and conformations of the protein on the surface based on the amount of sampling performed, from which free energy differences between the adsorbed states were able to be calculated. In addition, by conducting two independent sets of TIGER2A simulations combined with cluster analyses, the authors demonstrate a method to estimate the degree of convergence achieved for a given amount of sampling. The results from these simulations demonstrate that these methods enable the most probable orientations and conformations of an adsorbed protein to be predicted and that the use of our validated interfacial force field parameter set provides closer agreement to available experimental results compared to using standard CHARMM force field parameterization to represent molecular behavior at the interface. PMID:28514864

Environmental Impact Analysis Process. Preliminary Draft Environmental Impact Statement Construction and Operation of Space Launch Complex 7. Volume 2. Appendices

DTIC Science & Technology

1988-11-15

3 Sincerely, William H. Ehorn3Suerintenent United States Department of the Interior FISH AND WILDLIFE SERVICE LAGUNA NIGUEL FIELD OFFICE 24000 Avila...Road Laguna Niguel, California 92656 Ma’ 19, 1988 Department of the Air Force Headquarters Space Division (AFSC) Los Angeles Air Force Station P. 0...agricultural supply, and ground water recharge. In addition, all minor streams and tributaries in the central coastal region, including Honda Creek and Jalama

Roller Coaster Science.

ERIC Educational Resources Information Center

Sumners, Carolyn; Jones, Howard L.

1983-01-01

Discusses the science of roller coasters, relating gravity, potential/kinetic energy, inertia, and centripetal force to the various parts of the ride, providing tips on linking classroom discussions to field trips. Includes sample student activity sheet and source for additional units using amusement park rides/playground activities to teach…

Revolution in Military Manpower: The Citizen-Warrior Total Career Continuum Construct

DTIC Science & Technology

2014-02-13

stressed career-fields, professional military education, and other situations to provide additional 12 incentives for desired behaviors and force...authorized telecommuting workload. 33 An example of an accrued service obligation would be required active service for a specified period of time after

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

PubMed

Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

2012-01-01

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

Determining the interparticle force laws in amorphous solids from a visual image.

PubMed

Gendelman, Oleg; Pollack, Yoav G; Procaccia, Itamar

2016-06-01

We consider the problem of how to determine the force laws in an amorphous system of interacting particles. Given the positions of the centers of mass of the constituent particles we propose an algorithm to determine the interparticle force laws. Having n different types of constituents we determine the coefficients in the Laurent polynomials for the n(n+1)/2 possibly different force laws. A visual providing the particle positions in addition to a measurement of the pressure is all that is required. The algorithm proposed includes a part that can correct for experimental errors in the positions of the particles. Such a correction of unavoidable measurement errors is expected to benefit many experiments in the field.

Gravitational matter-antimatter asymmetry and four-dimensional Yang-Mills gauge symmetry

NASA Technical Reports Server (NTRS)

Hsu, J. P.

1981-01-01

A formulation of gravity based on the maximum four-dimensional Yang-Mills gauge symmetry is studied. The theory predicts that the gravitational force inside matter (fermions) is different from that inside antimatter. This difference could lead to the cosmic separation of matter and antimatter in the evolution of the universe. Moreover, a new gravitational long-range spin-force between two fermions is predicted, in addition to the usual Newtonian force. The geometrical foundation of such a gravitational theory is the Riemann-Cartan geometry, in which there is a torsion. The results of the theory for weak fields are consistent with previous experiments.

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

PubMed Central

Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart; MacKerell, Alexander D.

2011-01-01

Here, we present an update of the CHARMM27 all-atom additive force field for nucleic acids that improves the treatment of RNA molecules. The original CHARMM27 force field parameters exhibit enhanced Watson-Crick (WC) base pair opening which is not consistent with experiment while analysis of MD simulations show the 2′-hydroxyl moiety to almost exclusively sample the O3′ orientation. Quantum mechanical studies of RNA related model compounds indicate the energy minimum associated with the O3′ orientation to be too favorable, consistent with the MD results. Optimization of the dihedral parameters dictating the energy of the 2′-hydroxyl proton targeting the QM data yielded several parameter sets, which sample both the base and O3′ orientations of the 2′-hydroxyl to varying degrees. Selection of the final dihedral parameters was based on reproduction of hydration behavior as related to a survey of crystallographic data and better agreement with experimental NMR J-coupling values. Application of the model, designated CHARMM36, to a collection of canonical and non-canonical RNA molecules reveals overall improved agreement with a range of experimental observables as compared to CHARMM27. The results also indicate the sensitivity of the conformational heterogeneity of RNA to the orientation of the 2′-hydroxyl moiety and support a model whereby the 2′-hydroxyl can enhance the probability of conformational transitions in RNA. PMID:21469161

Son of IXION: A Steady State Centrifugally Confined Plasma for Fusion*

NASA Astrophysics Data System (ADS)

Hassam, Adil

1996-11-01

A magnetic confinement scheme in which the inertial, u.grad(u), forces effect parallel confinement is proposed. The basic geometry is mirror-like as far as the poloidal field goes or, more simply, multipole (FM-1) type. The rotation is toroidal in this geometry. A supersonic rotation can effect complete parallel confinement, with the usual magnetic mirror force rendered irrelevant. The rotation shear, in addition, aids in the suppression of the flute mode. This suppression is not complete which indicates the addition of a toroidal field, at maximum of the order of the poloidal field. We show that at rotation in excess of Mach 3, the parallel particle and heat losses can be minimized to below the Lawson breakeven point. The crossfield transport can be expected to be better than tokamaks on account of the large velocity shear. Other advantages of the scheme are that it is steady state and disruption free. An exploratory experiment that tests equilibrium, parallel detachment, and MHD stability is proposed. The concept resembles earlier (Geneva, 1958) experiments on "homopolar generators" and a mirror configuration called IXION. Ixion, Greek mythological king, was forever strapped to a rotating, flaming wheel. *Work supported by DOE

The effect of force feedback delay on stiffness perception and grip force modulation during tool-mediated interaction with elastic force fields

PubMed Central

Karniel, Amir; Nisky, Ilana

2015-01-01

During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain. PMID:25717155

The effect of force feedback delay on stiffness perception and grip force modulation during tool-mediated interaction with elastic force fields.

PubMed

Leib, Raz; Karniel, Amir; Nisky, Ilana

2015-05-01

During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain. Copyright © 2015 the American Physiological Society.

Acoustic radiation force control: Pulsating spherical carriers.

PubMed

Rajabi, Majid; Mojahed, Alireza

2018-02-01

The interaction between harmonic plane progressive acoustic beams and a pulsating spherical radiator is studied. The acoustic radiation force function exerted on the spherical body is derived as a function of the incident wave pressure and the monopole vibration characteristics (i.e., amplitude and phase) of the body. Two distinct strategies are presented in order to alter the radiation force effects (i.e., pushing and pulling states) by changing its magnitude and direction. In the first strategy, an incident wave field with known amplitude and phase is considered. It is analytically shown that the zero- radiation force state (i.e., radiation force function cancellation) is achievable for specific pulsation characteristics belong to a frequency-dependent straight line equation in the plane of real-imaginary components (i.e., Nyquist Plane) of prescribed surface displacement. It is illustrated that these characteristic lines divide the mentioned displacement plane into two regions of positive (i.e., pushing) and negative (i.e., pulling) radiation forces. In the second strategy, the zero, negative and positive states of radiation force are obtained through adjusting the incident wave field characteristics (i.e., amplitude and phase) which insonifies the radiator with prescribed pulsation characteristics. It is proved that zero radiation force state occurs for incident wave pressure characteristics belong to specific frequency-dependent circles in Nyquist plane of incident wave pressure. These characteristic circles divide the Nyquist plane into two distinct regions corresponding to positive (out of circles) and negative (in the circles) values of radiation force function. It is analytically shown that the maximum amplitude of negative radiation force is exactly equal to the amplitude of the (positive) radiation force exerted upon the sphere in the passive state, by the same incident field. The developed concepts are much more deepened by considering the required power supply for distinct cases of zero, negative and positive radiation force states along with the frequency dependent asymmetry index. In addition, considering the effect of phase difference between the incident wave field and the pulsating object, and its possible variation with respect to spatial position of object, some practical points about the spatial average of generated radiation force, the optimal state of operation, the stability of zero radiation force states and the possibly of precise motion control are discussed. This work would extend the novel concept of smart carriers to and may be helpful for robust single-beam acoustic handling techniques. Furthermore, the shown capability of precise motion control may be considered as a new way toward smart acoustic driven micro-mechanisms and micro-machines. Copyright © 2017 Elsevier B.V. All rights reserved.

Kinematics and dynamics of Nubia-Somalia divergence along the East African rift

NASA Astrophysics Data System (ADS)

Stamps, Dorothy Sarah

Continental rifting is fundamental to the theory of plate tectonics, yet the force balance driving Earth's largest continental rift system, the East African Rift (EAR), remains debated. The EAR actively diverges the Nubian and Somalian plates spanning ˜5000 km N-S from the Red Sea to the Southwest Indian Ridge and ˜3000 km NW-SE from eastern Congo to eastern Madagascar. Previous studies suggest either lithospheric buoyancy forces or horizontal tractions dominate the force balance acting to rupture East Africa. In this work, we investigate the large-scale dynamics of Nubia-Somalia divergence along the EAR driving present-day kinematics. Because Africa is largely surrounded by spreading ridges, we assume plate-plate interactions are minimal and that the major driving forces are gradients in gravitational potential energy (GPE), which includes the effect of vertical mantle tractions, and horizontal basal tractions arising from viscous coupling to horizontal mantle flow. We quantify a continuous strain rate and velocity field based on kinematic models, an updated GPS velocity solution, and the style of earthquake focal mechanisms, which we use as an observational constraint on surface deformation. We solve the 3D force balance equations and calculate vertically averaged deviatoric stress for a 100 km thick lithosphere constrained by the CRUST2.0 crustal density and thickness model. By comparing vertically integrated deviatoric stress with integrated lithospheric strength we demonstrate forces arising from gradients in gravitational potential energy are insufficient to rupture strong lithosphere, hence weakening mechanisms are required to initiate continental rupture. The next step involves inverting for a stress field boundary condition that is the long-wavelength minimum energy deviatoric stress field required to best-fit the style of our continuous strain rate field in addition to deviatoric stress from gradients in GPE. We infer the stress field boundary condition is an estimate of basal shear stress from viscous coupling to horizontal mantle flow. The stress field boundary condition is small (˜1.6 MPa) compared to deviatoric stress from GPE gradients (8-20 MPa) and does not improve the fit to surface deformation indicators more than 8% when combined with deviatoric stress from GPE gradients. Hence we suggest the style of deformation across the EAR can be explained by forces derived from gradients in GPE. We then calculate dynamic velocities using two types of forward models to solve the instantaneous momentum equations. One method is regional and requires vertically averaged effective viscosity to define lithospheric structure with velocity boundary conditions and a free-slip basal boundary condition. The second is a global model that accounts for a brittle upper crust and viscous mantle lithosphere with velocity boundary conditions imposed at the base of the lithosphere from 5 mantle flow models. With both methods we find deformation driven by internal lithospheric buoyancy forces provides the best-fit to GPS observations of surface velocities on the Somalian plate. We find that any additional contribution from horizontal tractions results in overpredicting surface velocities. This work indicates horizontal mantle flow plays a minimal role in Nubia-Somalia divergence and the EAR is driven largely by gradients in GPE.

Action-at-a-distance metamaterials: Distributed local actuation through far-field global forces

NASA Astrophysics Data System (ADS)

Hedayati, R.; Mirzaali, M. J.; Vergani, L.; Zadpoor, A. A.

2018-03-01

Mechanical metamaterials are a sub-category of designer materials where the geometry of the material at the small-scale is rationally designed to give rise to unusual properties and functionalities. Here, we propose the concept of "action-at-a-distance" metamaterials where a specific pattern of local deformation is programmed into the fabric of (cellular) materials. The desired pattern of local actuation could then be achieved simply through the application of one single global and far-field force. We proposed graded designs of auxetic and conventional unit cells with changing Poisson's ratios as a way of making "action-at-a-distance" metamaterials. We explored five types of graded designs including linear, two types of radial gradients, checkered, and striped. Specimens were fabricated with indirect additive manufacturing and tested under compression, tension, and shear. Full-field strain maps measured with digital image correlation confirmed different patterns of local actuation under similar far-field strains. These materials have potential applications in soft (wearable) robotics and exosuits.

A stochastically forced time delay solar dynamo model: Self-consistent recovery from a maunder-like grand minimum necessitates a mean-field alpha effect

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

Hazra, Soumitra; Nandy, Dibyendu; Passos, Dário, E-mail: s.hazra@iiserkol.ac.in, E-mail: dariopassos@ist.utl.pt, E-mail: dnandi@iiserkol.ac.in

Fluctuations in the Sun's magnetic activity, including episodes of grand minima such as the Maunder minimum have important consequences for space and planetary environments. However, the underlying dynamics of such extreme fluctuations remain ill-understood. Here, we use a novel mathematical model based on stochastically forced, non-linear delay differential equations to study solar cycle fluctuations in which time delays capture the physics of magnetic flux transport between spatially segregated dynamo source regions in the solar interior. Using this model, we explicitly demonstrate that the Babcock-Leighton poloidal field source based on dispersal of tilted bipolar sunspot flux, alone, cannot recover the sunspotmore » cycle from a grand minimum. We find that an additional poloidal field source effective on weak fields—e.g., the mean-field α effect driven by helical turbulence—is necessary for self-consistent recovery of the sunspot cycle from grand minima episodes.« less

Effective Forces Between Colloidal Particles

NASA Technical Reports Server (NTRS)

Tehver, Riina; Banavar, Jayanth R.; Koplik, Joel

1999-01-01

Colloidal suspensions have proven to be excellent model systems for the study of condensed matter and its phase behavior. Many of the properties of colloidal suspensions can be investigated with a systematic variation of the characteristics of the systems and, in addition, the energy, length and time scales associated with them allow for experimental probing of otherwise inaccessible regimes. The latter property also makes colloidal systems vulnerable to external influences such as gravity. Experiments performed in micro-ravity by Chaikin and Russell have been invaluable in extracting the true behavior of the systems without an external field. Weitz and Pusey intend to use mixtures of colloidal particles with additives such as polymers to induce aggregation and form weak, tenuous, highly disordered fractal structures that would be stable in the absence of gravitational forces. When dispersed in a polarizable medium, colloidal particles can ionize, emitting counterions into the solution. The standard interaction potential in these charged colloidal suspensions was first obtained by Derjaguin, Landau, Verwey and Overbeek. The DLVO potential is obtained in the mean-field linearized Poisson-Boltzmann approximation and thus has limited applicability. For more precise calculations, we have used ab initio density functional theory. In our model, colloidal particles are charged hard spheres, the counterions are described by a continuum density field and the solvent is treated as a homogeneous medium with a specified dielectric constant. We calculate the effective forces between charged colloidal particles by integrating over the solvent and counterion degrees of freedom, taking into account the direct interactions between the particles as well as particle-counterion, counterion-counterion Coulomb, counterion entropic and correlation contributions. We obtain the effective interaction potential between charged colloidal particles in different configurations. We evaluate two- and three-body forces in the bulk as well as study the influence of soft walls. We qualitatively explain the effects of the walls on the forces and demonstrate that many-body effects are negligible in our system. With adjustments in the parameters, the DLVO pair-potential can describe the results quantitatively. Besides electrostatic interactions, entropic depletion effects that arise from (hard-core) exclusion play an important role in determining the behavior of multi-component colloidal suspensions. A standard theory for depletion forces is due to Asakura and Oosawa and is based on the ideal gas approximation. To go beyond this approximation, we have studied entropic forces in molecular dynamics simulations of systems of hard spheres (the effects of the solvent have been ignored). The effective depletion forces for these systems can be found either from equilibrium distribution functions or from direct momentum transfer calculations. Our results obtained by either method show qualitative differences from the Asakura-Oosawa forces, indicating a longer range, higher value at contact and most importantly a more complicated structure, comprising of several maxima and minima. Our calculations include the determination of effective forces between two spheres, a hard sphere and a wall, and the behavior of a hard sphere near a step-edge and a corner. We also demonstrate that such entropic forces do not necessarily satisfy pairwise additivity.

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

S. Chouhan, J. DeKamp, A. Zeller, P. Brindza, S. Lassiter, M. Fowler, E. Sun

A collaboration between NSCL and Jlab has developed the reference design and coil winding for Jlab's Super High Momentum Spectrometer (SHMS) horizontal bend magnet. A warm iron ??C?? type superferric dipole magnet will bend the 12 GeV/c particles horizontally by 3?? to allow the SHMS to reach angles as low as 5.5??. This requires an integral field strength of up to 2.1 T.m. The major challenges are the tight geometry, high and unbalanced forces and a required low fringe field in primary beam path. A coil design based on flattened SSC Rutherford cable that provides a large current margin andmore » commercially available fiberglass prepreg epoxy tape has been developed. A complete test coil has been wound and will be cold tested. This paper present the modified magnet design includes coil forces, coil restraint system and fringe field. In addition, coil properties, quench calculations and the full mechanical details are also presented.« less

Influence of Polarization on Carbohydrate Hydration: A Comparative Study Using Additive and Polarizable Force Fields.

PubMed

Pandey, Poonam; Mallajosyula, Sairam S

2016-07-14

Carbohydrates are known to closely modulate their surrounding solvent structures and influence solvation dynamics. Spectroscopic investigations studying far-IR regions (below 1000 cm(-1)) have observed spectral shifts in the libration band (around 600 cm(-1)) of water in the presence of monosaccharides and polysaccharides. In this paper, we use molecular dynamics simulations to gain atomistic insight into carbohydrate-water interactions and to specifically highlight the differences between additive (nonpolarizable) and polarizable simulations. A total of six monosaccharide systems, α and β anomers of glucose, galactose, and mannose, were studied using additive and polarizable Chemistry at HARvard Macromolecular Mechanics (CHARMM) carbohydrate force fields. Solvents were modeled using three additive water models TIP3P, TIP4P, and TIP5P in additive simulations and polarizable water model SWM4 in polarizable simulations. The presence of carbohydrate has a significant effect on the microscopic water structure, with the effects being pronounced for proximal water molecules. Notably, disruption of the tetrahedral arrangement of proximal water molecules was observed due to the formation of strong carbohydrate-water hydrogen bonds in both additive and polarizable simulations. However, the inclusion of polarization resulted in significant water-bridge occupancies, improved ordered water structures (tetrahedral order parameter), and longer carbohydrate-water H-bond correlations as compared to those for additive simulations. Additionally, polarizable simulations also allowed the calculation of power spectra from the dipole-dipole autocorrelation function, which corresponds to the IR spectra. From the power spectra, we could identify spectral signatures differentiating the proximal and bulk water structures, which could not be captured from additive simulations.

Heat transfer enhancement of Fe3O4 ferrofluids in the presence of magnetic field

NASA Astrophysics Data System (ADS)

Fadaei, Farzad; Shahrokhi, Mohammad; Molaei Dehkordi, Asghar; Abbasi, Zeinab

2017-05-01

In this article, three-dimensional (3D) forced-convection heat transfer of magnetic nanofluids in a pipe subject to constant wall heat flux in the presence of single or double permanent magnet(s) or current-carrying wire has been investigated and compared. In this regard, laminar fluid flow and equilibrium magnetization for the ferrofluid were considered. In addition, variations of magnetic field in different media were taken into account and the assumption of having a linear relationship of magnetization with applied magnetic field intensity was also relaxed. Effects of magnetic field intensity, nanoparticle volume fraction, Reynolds number value, and the type of magnetic field source (i.e., a permanent magnet or current-carrying wire) on the forced-convection heat transfer of magnetic nanofluids were carefully investigated. It was found that by applying the magnetic field, the fluid mixing could be intensified that leads to an increase in the Nusselt number value along the pipe length. Moreover, the obtained simulation results indicate that applying the magnetic field induced by two permanent magnets with a magnetization of 3×105 (A/m) (for each one), the fully developed Nusselt number value can be increased by 196%.

Radiation drag in the field of a non-spherical source

NASA Astrophysics Data System (ADS)

Bini, D.; Geralico, A.; Passamonti, A.

2015-01-01

The motion of a test particle in the gravitational field of a non-spherical source endowed with both mass and mass quadrupole moment is investigated when a test radiation field is also present. The background is described by the Erez-Rosen solution, which is a static space-time belonging to the Weyl class of solutions to the vacuum Einstein's field equations, and reduces to the familiar Schwarzschild solution when the quadrupole parameter vanishes. The radiation flux has a fixed but arbitrary (non-zero) angular momentum. The interaction with the radiation field is assumed to be Thomson-like, i.e. the particles absorb and re-emit radiation, thus suffering for a friction-like drag force. Such an additional force is responsible for the Poynting-Robertson effect, which is well established in the framework of Newtonian gravity and has been recently extended to the general theory of relativity. The balance between gravitational attraction, centrifugal force and radiation drag leads to the occurrence of equilibrium circular orbits which are attractors for the surrounding matter for every fixed value of the interaction strength. The presence of the quadrupolar structure of the source introduces a further degree of freedom: there exists a whole family of equilibrium orbits parametrized by the quadrupole parameter, generalizing previous works. This scenario is expected to play a role in the context of accretion matter around compact objects.

Relating GRACE terrestrial water storage variations to global fields of atmospheric forcing

NASA Astrophysics Data System (ADS)

Humphrey, Vincent; Gudmundsson, Lukas; Isabelle Seneviratne, Sonia

2015-04-01

Synoptic, seasonal and inter-annual fluctuations in atmospheric dynamics all influence terrestrial water storage, with impacts on ecosystems functions, human activities and land-climate interactions. Here we explore to which degree atmospheric variables can explain GRACE estimates of terrestrial water storage on different time scales. Since 2012, the most recent GRACE gravity field solutions (Release 05) can be used to monitor global changes in terrestrial water storage with an unprecedented level of accuracy over more than a decade. In addition, the release of associated gridded and post-processed products facilitates comparisons with other global datasets such as land surface model outputs or satellite observations. We investigate how decadal trends, inter-annual fluctuations as well as monthly anomalies of the seasonal cycle of terrestrial water storage can be related to fields of atmospheric forcing, including e.g. precipitation and temperature as estimated in global reanalysis products using statistical techniques. In the majority of the locations with high signal to noise ratio, both short and long-term fluctuations of total terrestrial water storage can be reconstructed to a large degree based on available atmospheric forcing. However, in some locations atmospheric forcing alone is not sufficient to explain the total change in water storage, suggesting strong influence of other processes. Within that framework, the question of an amplification or attenuation of atmospheric forcing through land-surface feedbacks and changes in long term water storage is discussed, also with respect to uncertainties and potential systematic biases in the results.

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

PubMed

Yildirim, Ilyas; Stern, Harry A; Kennedy, Scott D; Tubbs, Jason D; Turner, Douglas H

2010-05-11

A reparameterization of the torsional parameters for the glycosidic dihedral angle, chi, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99chi. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99chi force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99chi force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) (1)H, steady-state 1D (1)H nuclear Overhauser effect (NOE), and transient 1D (1)H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2'-endo sugar puckering of the pyrimidines, while the AMBER99chi force field's predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310 degrees for the base orientation of purines. The AMBER99chi force field prefers anti conformations around 185 degrees , which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99chi force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures.

Competition among Li+, Na+, K+ and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations using the Additive CHARMM36 and Drude Polarizable Force Fields

PubMed Central

Savelyev, Alexey; MacKerell, Alexander D.

2015-01-01

In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li+, Na+, K+ and Rb+, and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and osmotic pressures of bulk electrolyte solutions of chemically relevant ions. The optimized ionic parameters are validated against counterion condensation theory and buffer exchange-atomic emission spectroscopy measurements providing quantitative data on the competitive association of different monovalent ions with DNA. Comparison between experimental and MD simulation results demonstrates that, compared to the additive CHARMM36 model, the Drude FF provides an improved description of the general features of the ionic atmosphere around DNA and leads to closer agreement with experiment on the ionic competition within the ion atmosphere. Results indicate the importance of extended simulation systems on the order of 25 Å beyond the DNA surface to obtain proper convergence of ion distributions. PMID:25751286

On the Adaptation of Pelvic Motion by Applying 3-dimensional Guidance Forces Using TPAD.

PubMed

Kang, Jiyeon; Vashista, Vineet; Agrawal, Sunil K

2017-09-01

Pelvic movement is important to human locomotion as the center of mass is located near the center of pelvis. Lateral pelvic motion plays a crucial role to shift the center of mass on the stance leg, while swinging the other leg and keeping the body balanced. In addition, vertical pelvic movement helps to reduce metabolic energy expenditure by exchanging potential and kinetic energy during the gait cycle. However, patient groups with cerebral palsy or stroke have excessive pelvic motion that leads to high energy expenditure. In addition, they have higher chances of falls as the center ofmass could deviate outside the base of support. In this paper, a novel control method is suggested using tethered pelvic assist device (TPAD) to teach subjects to walk with a specified target pelvic trajectory while walking on a treadmill. In this method, a force field is applied to the pelvis to guide it to move on a target trajectory and correctional forces are applied, if the pelvis motion has excessive deviations from the target trajectory. Three different experimentswith healthy subjects were conducted to teach them to walk on a new target pelvic trajectory with the presented control method. For all three experiments, the baseline trajectory of the pelvis was experimentally determined for each participating subject. To design a target pelvic trajectory which is different from the baseline, Experiment I scaled up the lateral component of the baseline pelvic trajectory, while Experiment II scaled down the lateral component of the baseline trajectory. For both Experiments I and II, the controller generated a 2-D force field in the transverse plane to provide the guidance force. In this paper, seven subjects were recruited for each experiment who walked on the treadmill with suggested control methods and visual feedback of their pelvic trajectory. The results show that the subjects were able to learn the target pelvic trajectory in each experiment and also retained the training effects after the completion of the experiment. In Experiment III, both lateral and vertical components of the pelvic trajectory were scaled down from the baseline trajectory. The force field was extended to three dimensions in order to correct the vertical pelvic movement as well. Three subgroups (force feedback alone, visual feedback alone, and both force and visual feedback) were recruited to understand the effects of force feedback and visual feedback alone to distinguish the results from Experiments I and II. The results showthat a trainingmethod that combines visual and force feedback is superior to the training methods with visual or force feedback alone. We believe that the present control strategy holds potential in training and correcting abnormal pelvic movements in different patient populations.

Magnetic tweezers for the measurement of twist and torque.

PubMed

Lipfert, Jan; Lee, Mina; Ordu, Orkide; Kerssemakers, Jacob W J; Dekker, Nynke H

2014-05-19

Single-molecule techniques make it possible to investigate the behavior of individual biological molecules in solution in real time. These techniques include so-called force spectroscopy approaches such as atomic force microscopy, optical tweezers, flow stretching, and magnetic tweezers. Amongst these approaches, magnetic tweezers have distinguished themselves by their ability to apply torque while maintaining a constant stretching force. Here, it is illustrated how such a "conventional" magnetic tweezers experimental configuration can, through a straightforward modification of its field configuration to minimize the magnitude of the transverse field, be adapted to measure the degree of twist in a biological molecule. The resulting configuration is termed the freely-orbiting magnetic tweezers. Additionally, it is shown how further modification of the field configuration can yield a transverse field with a magnitude intermediate between that of the "conventional" magnetic tweezers and the freely-orbiting magnetic tweezers, which makes it possible to directly measure the torque stored in a biological molecule. This configuration is termed the magnetic torque tweezers. The accompanying video explains in detail how the conversion of conventional magnetic tweezers into freely-orbiting magnetic tweezers and magnetic torque tweezers can be accomplished, and demonstrates the use of these techniques. These adaptations maintain all the strengths of conventional magnetic tweezers while greatly expanding the versatility of this powerful instrument.

Active electromagnetic invisibility cloaking and radiation force cancellation

NASA Astrophysics Data System (ADS)

Mitri, F. G.

2018-03-01

This investigation shows that an active emitting electromagnetic (EM) Dirichlet source (i.e., with axial polarization of the electric field) in a homogeneous non-dissipative/non-absorptive medium placed near a perfectly conducting boundary can render total invisibility (i.e. zero extinction cross-section or efficiency) in addition to a radiation force cancellation on its surface. Based upon the Poynting theorem, the mathematical expression for the extinction, radiation and amplification cross-sections (or efficiencies) are derived using the partial-wave series expansion method in cylindrical coordinates. Moreover, the analysis is extended to compute the self-induced EM radiation force on the active source, resulting from the waves reflected by the boundary. The numerical results predict the generation of a zero extinction efficiency, achieving total invisibility, in addition to a radiation force cancellation which depend on the source size, the distance from the boundary and the associated EM mode order of the active source. Furthermore, an attractive EM pushing force on the active source directed toward the boundary or a repulsive pulling one pointing away from it can arise accordingly. The numerical predictions and computational results find potential applications in the design and development of EM cloaking devices, invisibility and stealth technologies.

Validating empirical force fields for molecular-level simulation of cellulose dissolution

USDA-ARS?s Scientific Manuscript database

The calculations presented here, which include dynamics simulations using analytical force fields and first principles studies, indicate that the COMPASS force field is preferred over the Dreiding and Universal force fields for studying dissolution of large cellulose structures. The validity of thes...

Hierarchical atom type definitions and extensible all-atom force fields.

PubMed

Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

2016-03-15

The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Pushing, pulling and electromagnetic radiation force cloaking by a pair of conducting cylindrical particles

NASA Astrophysics Data System (ADS)

Mitri, F. G.

2018-02-01

The present analysis shows that two conducting cylindrical particles illuminated by an axially-polarized electric field of plane progressive waves at arbitrary incidence will attract, repel or become totally cloaked (i.e., invisible to the transfer of linear momentum carried by the incident waves), depending on their sizes, the interparticle distance as well as the angle of incidence of the incident field. Based on the rigorous multipole expansion method and the translational addition theorem of cylindrical wave functions, the electromagnetic (EM) radiation forces arising from multiple scattering effects between a pair of perfectly conducting cylindrical particles of circular cross-sections are derived and computed. An effective incident field on a particular particle is determined first, and used subsequently with its corresponding scattered field to derive the closed-form analytical expressions for the radiation force vector components. The mathematical expressions for the EM radiation force components (i.e. longitudinal and transverse) are exact, and have been formulated in partial-wave series expansions in cylindrical coordinates involving the angle of incidence, the interparticle distance and the expansion coefficients. Numerical examples illustrate the analysis for two perfectly conducting circular cylinders in a homogeneous nonmagnetic medium of wave propagation. The computations for the dimensionless radiation force functions are performed with particular emphasis on varying the angle of incidence, the interparticle distance, and the sizes of the particles. Depending on the interparticle distance and angle of incidence, the cylinders yield total neutrality (or invisibility); they experience no force and become unresponsive to the transfer of the EM linear momentum due to multiple scattering cancellation effects. Moreover, pushing or pulling EM forces between the two cylinders arise depending on the interparticle distance, the angle of incidence and their size parameters. This study provides a complete analytical method and computations for the longitudinal and transverse radiation force components in the multiple scattering of EM plane progressive waves with potential applications in particle manipulation, optically-engineered metamaterials with reconfigurable periodicities and cloaking devices to name a few examples.

Numerical and experimental study of the effect of the induced electric potential in Lorentz force velocimetry

NASA Astrophysics Data System (ADS)

Hernández, Daniel; Boeck, Thomas; Karcher, Christian; Wondrak, Thomas

2018-01-01

Lorentz force velocimetry (LFV) is a contactless velocity measurement technique for electrically conducting fluids. When a liquid metal or a molten glass flows through an externally applied magnetic field, eddy currents and a flow-braking force are generated inside the liquid. This force is proportional to the velocity or flow rate of the fluid and, due to Newton’s third law, a force of the same magnitude but in opposite direction acts on the source of the applied magnetic field which in our case are permanent magnets. According to Ohm’s law for moving conductors at low magnetic Reynolds numbers, an electric potential is induced which ensures charge conservation. In this paper, we analyze the contribution of the induced electric potential to the total Lorentz force by considering two different scenarios: conducting walls of finite thickness and aspect ratio variation of the cross-section of the flow. In both the cases, the force component generated by the electric potential is always in the opposite direction to the total Lorentz force. This force component is sensitive to the electric boundary conditions of the flow of which insulating and perfectly conducting walls are the two limiting cases. In the latter case, the overall electric resistance of the system is minimized, resulting in a considerable increase in the measured Lorentz force. Additionally, this force originating from the electric potential also decays when the aspect ratio of the cross-section of the flow is changed. Hence, the sensitivity of the measurement technique is enhanced by either increasing wall conductivity or optimizing the aspect ratio of the cross-section of the flow.

Neural network based architectures for aerospace applications

NASA Technical Reports Server (NTRS)

Ricart, Richard

1987-01-01

A brief history of the field of neural networks research is given and some simple concepts are described. In addition, some neural network based avionics research and development programs are reviewed. The need for the United States Air Force and NASA to assume a leadership role in supporting this technology is stressed.

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

PubMed

Riniker, Sereina

2018-03-26

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

GeoFORCE Texas: An Outreach Program that is Increasing the Number and Diversity of Students Completing STEM Degrees and Entering the Workforce

NASA Astrophysics Data System (ADS)

Snow, E.; Moore, S. L.

2014-12-01

GeoFORCE Texas is an outreach program of the Jackson School of Geosciences, University of Texas at Austin. Established in 2005 with the goal of increasing the number and diversity of students studying geosciences and engineering and entering the high-tech workforce, GeoFORCE has been highly successful. Key elements to that success will be presented here. GeoFORCE targets bright students in rural and inner-city schools where they are generally not academically challenged. Every summer throughout high school we take them on geologic field trips all over the country. In 2014, GeoFORCE led 15 field academies for about 600 students. The program is rigorous and academic. We emphasize college-level thinking skills. Because it is a 4-year program, they have a pretty good grounding in physical geology by the time they graduate. More importantly, they develop confidence in their ability to handle college, and a strong motivation to earn a college degree. GeoFORCE students are mostly minority (85%) and more than half will be the first in their family to graduate from college. GeoFORCE students exceed national averages in rates of going to college (97%), majoring in STEM fields (66%), majoring in geosciences (15%) and engineering (13%), and graduating from college (~85%). GeoFORCE is a public/private partnership and a workforce-focused program. The Jackson School funds staff and operating expenses (37%). Money for student programs comes from private industry (44%), state and federal grants (14%), and foundations and individual donors (5%). Our corporate partners are in the energy sector. In addition to funding, corporate sponsors attend the summer field programs, mentor GeoFORCE students, and provide opportunities for the students to visit the companies. As our students move toward college graduation, our industry and government partners have begun to hire them as interns. GeoFORCE graduates are now entering the workforce. Our first two cohorts are 4 and 5 years past high school graduation. That group of 155 students boasts 70 college graduates and another 60 still pursuing degrees. There are 19 geoscience majors and 9 engineers. They are also contributing to the body of science with a growing list of publications, including at least one at this meeting.

Optical trapping/modification of nano-(micro)particles by gradient and photorefractive forces during laser illumination

NASA Astrophysics Data System (ADS)

Kukhtarev, N.; Kukhtareva, T.; Okafor, F.

2010-08-01

In this paper we describe photo-induced trapping/redistribution of silver nano-(micro) particles near the surface of photorefractive crystal LiNbO3:Fe. This type of optical trapping is due to combined forces of direct gradient-force trapping and asymmetric photorefractive forces of electro-phoresis and dielectro-phoresis. The silver nanoparticles were produced through extracellular biosynthesis on exposure to the fungus, Fusarium oxysporum (FO) and to the plant extracts. Pulsed and CW visible laser radiation lead to significant modification of nanoparticle clusters. This study indicates that extracellular biosynthesis can constitute a possible viable alternative method for the production of nanoparticles. In addition, the theoretical modeling of asymmetric photorefractive electric field grating has been presented and compared with the experimental results.

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

PubMed Central

Lange, Oliver F.; van der Spoel, David; de Groot, Bert L.

2010-01-01

Abstract Protein dynamics on the atomic level and on the microsecond timescale has recently become accessible from both computation and experiment. To validate molecular dynamics (MD) at the submicrosecond timescale against experiment we present microsecond MD simulations in 10 different force-field configurations for two globular proteins, ubiquitin and the gb3 domain of protein G, for which extensive NMR data is available. We find that the reproduction of the measured NMR data strongly depends on the chosen force field and electrostatics treatment. Generally, particle-mesh Ewald outperforms cut-off and reaction-field approaches. A comparison to measured J-couplings across hydrogen bonds suggests that there is room for improvement in the force-field description of hydrogen bonds in most modern force fields. Our results show that with current force fields, simulations beyond hundreds of nanoseconds run an increased risk of undergoing transitions to nonnative conformational states or will persist within states of high free energy for too long, thus skewing the obtained population frequencies. Only for the AMBER99sb force field have such transitions not been observed. Thus, our results have significance for the interpretation of data obtained with long MD simulations, for the selection of force fields for MD studies and for force-field development. We hope that this comprehensive benchmark based on NMR data applied to many popular MD force fields will serve as a useful resource to the MD community. Finally, we find that for gb3, the force-field AMBER99sb reaches comparable accuracy in back-calculated residual dipolar couplings and J-couplings across hydrogen bonds to ensembles obtained by refinement against NMR data. PMID:20643085

Maglev performance of a double-layer bulk high temperature superconductor above a permanent magnet guideway

NASA Astrophysics Data System (ADS)

Deng, Z.; Wang, J.; Zheng, J.; Lin, Q.; Zhang, Y.; Wang, S.

2009-05-01

In order to improve the performance of the present high temperature superconducting (HTS) maglev vehicle system, the maglev performance of single- and double-layer bulk high temperature superconductors (HTSC) was investigated above a permanent magnet guideway (PMG). It is found that the maglev performance of a double-layer bulk HTSC is not a simple addition of each layer's levitation and guidance force. Moreover, the applied magnetic field at the position of the upper layer bulk HTSC is not completely shielded by the lower layer bulk HTSC either. 53.5% of the levitation force and 27.5% of the guidance force of the upper layer bulk HTSC are excited in the double-layer bulk HTSC arrangement in the applied field-cooling condition and working gap, bringing a corresponding improvement of 16.9% and 8.8% to the conventional single-layer bulk HTSC. The present research implies that the cost performance of upper layer bulk HTSC is a little low for the whole HTS maglev system.

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

PubMed

Fenn, Timothy D; Schnieders, Michael J; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S; Brunger, Axel T

2011-04-13

Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

PubMed Central

Fenn, Timothy D.; Schnieders, Michael J.; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S.; Brunger, Axel T.

2011-01-01

Summary Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. PMID:21481775

Dark matter, long-range forces, and large-scale structure

NASA Technical Reports Server (NTRS)

Gradwohl, Ben-Ami; Frieman, Joshua A.

1992-01-01

If the dark matter in galaxies and clusters is nonbaryonic, it can interact with additional long-range fields that are invisible to experimental tests of the equivalence principle. We discuss the astrophysical and cosmological implications of a long-range force coupled only to the dark matter and find rather tight constraints on its strength. If the force is repulsive (attractive), the masses of galaxy groups and clusters (and the mean density of the universe inferred from them) have been systematically underestimated (overestimated). We explore the consequent effects on the two-point correlation function, large-scale velocity flows, and microwave background anisotropies, for models with initial scale-invariant adiabatic perturbations and cold dark matter.

Low-speed wind-tunnel tests of an advanced eight-bladed propeller

NASA Technical Reports Server (NTRS)

Coe, P. L., Jr.; Gentry, G. L., Jr.; Dunham, D. M.

1985-01-01

As part of a research program on advanced turboprop aircraft aerodynamics, a low-speed wind-tunnel investigation was conducted to document the basic performance and force and moment characteristics of an advanced eight-bladed propeller. The results show that in addition to the normal force and pitching moment produced by the propeller/nacelle combination at angle of attack, a significant side force and yawing moment are also produced. Furthermore, it is shown that for test conditions wherein compressibility effects can be ignored, accurate simulation of propeller performance and flow fields can be achieved by matching the nondimensional power loading of the model propeller to that of the full-scale propeller.

Temperature of maximum density and excess thermodynamics of aqueous mixtures of methanol

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

González-Salgado, D.; Zemánková, K.; Noya, E. G.

In this work, we present a study of representative excess thermodynamic properties of aqueous mixtures of methanol over the complete concentration range, based on extensive computer simulation calculations. In addition to test various existing united atom model potentials, we have developed a new force-field which accurately reproduces the excess thermodynamics of this system. Moreover, we have paid particular attention to the behavior of the temperature of maximum density (TMD) in dilute methanol mixtures. The presence of a temperature of maximum density is one of the essential anomalies exhibited by water. This anomalous behavior is modified in a non-monotonous fashion bymore » the presence of fully miscible solutes that partly disrupt the hydrogen bond network of water, such as methanol (and other short chain alcohols). In order to obtain a better insight into the phenomenology of the changes in the TMD of water induced by small amounts of methanol, we have performed a new series of experimental measurements and computer simulations using various force fields. We observe that none of the force-fields tested capture the non-monotonous concentration dependence of the TMD for highly diluted methanol solutions.« less

Traction force and tension fluctuations in growing axons

NASA Astrophysics Data System (ADS)

Urbach, Jeffrey; Polackwich, Jamie; Koch, Daniel; McAllister, Ryan; Geller, Herbert

Actively generated mechanical forces play a central role in axon growth and guidance during nervous system development. We describe the dynamics of traction stresses from growth cones of actively advancing axons from postnatal rat DRG neurons. By tracking the movement of the growth cone and analyzing the traction stresses in a co-moving reference frame, we show that there is a clear and consistent average stress field underlying the complex spatial stresses present at any one time. The average stress field has strong maxima on the sides of the growth cone, directed inward toward the growth cone neck. This pattern represents a Contractile stress contained within the growth cone, and a net force that is balanced by the axon tension. In addition, using high time-resolution measurements, we show that the stress field is composed of fluctuating local stress peaks, with a population of peaks whose lifetime distribution follows an exponential decay, and a small number of very long-lived peaks. We also find that the tension appears to vary randomly over short time scales, roughly consistent with the lifetime of the stress peaks, suggesting that the tension fluctuations originate from stochastic adhesion dynamics.

Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment

PubMed Central

Marzinek, Jan K.; Lakshminarayanan, Rajamani; Goh, Eunice; Huber, Roland G.; Panzade, Sadhana; Verma, Chandra; Bond, Peter J.

2016-01-01

Conformational changes in the envelope proteins of flaviviruses help to expose the highly conserved fusion peptide (FP), a region which is critical to membrane fusion and host cell infection, and which represents a significant target for antiviral drugs and antibodies. In principle, extended timescale atomic-resolution simulations may be used to characterize the dynamics of such peptides. However, the resultant accuracy is critically dependent upon both the underlying force field and sufficient conformational sampling. In the present study, we report a comprehensive comparison of three simulation methods and four force fields comprising a total of more than 40 μs of sampling. Additionally, we describe the conformational landscape of the FP fold across all flavivirus family members. All investigated methods sampled conformations close to available X-ray structures, but exhibited differently populated ensembles. The best force field / sampling combination was sufficiently accurate to predict that the solvated peptide fold is less ordered than in the crystallographic state, which was subsequently confirmed via circular dichroism and spectrofluorometric measurements. Finally, the conformational landscape of a mutant incapable of membrane fusion was significantly shallower than wild-type variants, suggesting that dynamics should be considered when therapeutically targeting FP epitopes. PMID:26785994

Characterization of an induced pressure pumping force for microfluidics

NASA Astrophysics Data System (ADS)

Jiang, Hai; Fan, Na; Peng, Bei; Weng, Xuan

2017-05-01

The electro-osmotic pumping and pressure-driven manipulation of fluids are considered as the most common strategies in microfluidic devices. However, both of them exhibit major disadvantages such as hard integration and high reagent consumption, and they are destructive methods for detection and photo bleaching. In this paper, an electric field-effect flow control approach, combining the electro-osmotic pumping force and the pressure-driven pumping force, was developed to generate the induced pressure-driven flow in a T-shaped microfluidic chip. Electro-osmotic flow between the T-intersection and two reservoirs was demonstrated, and it provided a stable, continuous, and electric field-free flow in the section of the microchannel without the electrodes. The velocity of the induced pressure-driven flow was linearly proportional to the applied voltages. Both numerical and experimental investigations were conducted to prove the concept, and the experimental results showed good agreement with the numerical simulations. In comparison to other induced pressure pumping methods, this approach can induce a high and controllable pressure drop in the electric field-free segment, subsequently causing an induced pressure-driven flow for transporting particles or biological cells. In addition, the generation of bubbles and the blocking of the microchannel are avoided.

Effect of pulsed electric field on the proteolysis of cold boned beef M. Longissimus lumborum and M. Semimembranosus.

PubMed

Suwandy, Via; Carne, Alan; van de Ven, Remy; Bekhit, Alaa El-Din A; Hopkins, David L

2015-02-01

The effects of pulsed electric field (PEF) and ageing (3, 7, 14 and 21 days) on the shear force, protein profile, and post-mortem proteolysis of beef loins (M. Longissimus lumborum, LL) and topsides (M. Semimembranosus, SM) were investigated using a range of pulsed electric field treatments [voltages (5 and 10 kV) and frequencies (20, 50, and 90 Hz)]. PEF treatment decreased the shear force of beef LL and SM muscles by up to 19%. The reduction in the shear force in the LL was not affected by the treatment intensity whereas the reduction in the SM was dependent on PEF frequency. PEF treated beef loins showed increased proteolysis, both early post-mortem and during subsequent post-mortem storage reflected by increased degradation of troponin-T and desmin. The most prominent troponin-T degradation was found in samples treated with 5 kV-90 Hz, 10 kV-20 Hz at day 3 and day 7 post-treatment in addition to 10 kV-50 Hz in subsequent post-treatment times. The degradation of desmin in PEF treated beef loins increased with ageing time.

Fracture analysis for a penny-shaped crack problem of a superconducting cylinder in a parallel magnetic field

NASA Astrophysics Data System (ADS)

Gao, S. W.; Feng, W. J.; Fang, X. Q.; Zhang, G. L.

2014-11-01

In this work, the penny-shaped crack problem is investigated for an infinite long superconducting cylinder under electromagnetic forces. The distributions of magnetic flux density in the superconducting cylinder are obtained analytically for both the zero-field cooling (ZFC) and the field cooling (FC) activation processes, where the magnetically impermeable crack surface condition and the Bean model outside the crack region are adopted. Based on the finite element method (FEM), the stress intensity factor (SIF) and energy release rate (ERR) at the crack tips in the process of field descent are further numerically calculated. Numerical results obtained show that according to the maximal energy release rate criterion, the FC process is generally easier to enhance crack initiation and propagation than the ZFC activation process. On the other hand, for the FC activation process, the larger the maximal applied magnetic field, more likely the crack propagates. Additionally, crack size has important and slightly different effects on the crack extension forces for the ZFC and FC cases. Thus, all of the activation processes, the applied field and the diameter of the penny-shaped crack have significant effects on the intensity analysis and design of superconducting materials.

Nonlinear Bubble Interactions in Acoustic Pressure Fields

NASA Technical Reports Server (NTRS)

Barbat, Tiberiu; Ashgriz, Nasser; Liu, Ching-Shi

1996-01-01

The systems consisting of a two-phase mixture, as clouds of bubbles or drops, have shown many common features in their responses to different external force fields. One of particular interest is the effect of an unsteady pressure field applied to these systems, case in which the coupling of the vibrations induced in two neighboring components (two drops or two bubbles) may result in an interaction force between them. This behavior was explained by Bjerknes by postulating that every body that is moving in an accelerating fluid is subjected to a 'kinetic buoyancy' equal with the product of the acceleration of the fluid multiplied by the mass of the fluid displaced by the body. The external sound wave applied to a system of drops/bubbles triggers secondary sound waves from each component of the system. These secondary pressure fields integrated over the surface of the neighboring drop/bubble may result in a force additional to the effect of the primary sound wave on each component of the system. In certain conditions, the magnitude of these secondary forces may result in significant changes in the dynamics of each component, thus in the behavior of the entire system. In a system containing bubbles, the sound wave radiated by one bubble at the location of a neighboring one is dominated by the volume oscillation mode and its effects can be important for a large range of frequencies. The interaction forces in a system consisting of drops are much smaller than those consisting of bubbles. Therefore, as a first step towards the understanding of the drop-drop interaction subject to external pressure fluctuations, it is more convenient to study the bubble interactions. This paper presents experimental results and theoretical predictions concerning the interaction and the motion of two levitated air bubbles in water in the presence of an acoustic field at high frequencies (22-23 KHz).

Prediction of Mechanical Properties of Polymers With Various Force Fields

NASA Technical Reports Server (NTRS)

Odegard, Gregory M.; Clancy, Thomas C.; Gates, Thomas S.

2005-01-01

The effect of force field type on the predicted elastic properties of a polyimide is examined using a multiscale modeling technique. Molecular Dynamics simulations are used to predict the atomic structure and elastic properties of the polymer by subjecting a representative volume element of the material to bulk and shear finite deformations. The elastic properties of the polyimide are determined using three force fields: AMBER, OPLS-AA, and MM3. The predicted values of Young s modulus and shear modulus of the polyimide are compared with experimental values. The results indicate that the mechanical properties of the polyimide predicted with the OPLS-AA force field most closely matched those from experiment. The results also indicate that while the complexity of the force field does not have a significant effect on the accuracy of predicted properties, small differences in the force constants and the functional form of individual terms in the force fields determine the accuracy of the force field in predicting the elastic properties of the polyimide.

On the glitches in the force transmitted by an electrodynamic exciter to a structure

NASA Technical Reports Server (NTRS)

Rao, Dantam K.

1987-01-01

Around resonance, the force transmitted by an exciter into a structure will be smaller or greater than a reference force generated by its coils due to electromechanical interaction. A simple analysis is presented which reveals how this phenomenon of force drop-off is controlled by three factors. The first factor, called Armature Mass Factor, describes a purely mechanical interaction between the structure and the exciter. The electromechanical energy conversion and its interaction with the structure yields two additional factors, called Electrical Resistance and Electrical Inductance Factors. They describe the effects of coil resistance, inductance and magnetic field strength relative to structural damping and stiffness. Present analysis indicates that, under proper circumstances, more than 90 percent of the force drop-off can be eliminated if armature-to-structure mass ratio is smaller or equal to half of modal loss factor.

Dark matter and the equivalence principle

NASA Technical Reports Server (NTRS)

Frieman, Joshua A.; Gradwohl, Ben-Ami

1991-01-01

If the dark matter in galaxies and clusters is nonbaryonic, it can interact with additional long-range fields that are invisible to experimental tests of the equivalence principle. The astrophysical and cosmological implications of a long-range force coupled only to the dark matter are discussed and rather tight constraints on its strength are found. If the force is repulsive (attractive), the masses of galaxy groups and clusters (and the mean density of the universe inferred from them) have been systematically underestimated (overestimated). Such an interaction also has unusual implications for the growth of large-scale structure.

TPX: Contractor preliminary design review. Volume 3, Design and analysis

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

NONE

1995-06-30

Several models have been formed for investigating the maximum electromagnetic loading and magnetic field levels associated with the Tokamak Physics eXperiment (TPX) superconducting Poloidal Field (PF) coils. The analyses have been performed to support the design of the individual fourteen hoop coils forming the PF system. The coils have been sub-divided into three coil systems consisting of the central solenoid (CS), PF5 coils, and the larger radius PF6 and PF7 coils. Various electromagnetic analyses have been performed to determine the electromagnetic loadings that the coils will experience during normal operating conditions, plasma disruptions, and fault conditions. The loadings are presentedmore » as net body forces acting individual coils, spatial variations throughout the coil cross section, and force variations along the path of the conductor due to interactions with the TF coils. Three refined electromagnetic models of the PF coil system that include a turn-by-turn description of the fields and forces during a worst case event are presented in this report. A global model including both the TF and PF system was formed to obtain the force variations along the path of the PF conductors resulting from interactions with the TF currents. In addition to spatial variations, the loadings are further subdivided into time-varying and steady components so that structural fatigue issues can be addressed by designers and analysts. Other electromagnetic design issues such as the impact of the detailed coil designs on field errors are addressed in this report. Coil features that are analyzed include radial transitions via short jogs vs. spiral type windings and the effects of layer-to-layer rotations (i.e clocking) on the field errors.« less

Force Field for Water Based on Neural Network.

PubMed

Wang, Hao; Yang, Weitao

2018-05-18

We developed a novel neural network based force field for water based on training with high level ab initio theory. The force field was built based on electrostatically embedded many-body expansion method truncated at binary interactions. Many-body expansion method is a common strategy to partition the total Hamiltonian of large systems into a hierarchy of few-body terms. Neural networks were trained to represent electrostatically embedded one-body and two-body interactions, which require as input only one and two water molecule calculations at the level of ab initio electronic structure method CCSD/aug-cc-pVDZ embedded in the molecular mechanics water environment, making it efficient as a general force field construction approach. Structural and dynamic properties of liquid water calculated with our force field show good agreement with experimental results. We constructed two sets of neural network based force fields: non-polarizable and polarizable force fields. Simulation results show that the non-polarizable force field using fixed TIP3P charges has already behaved well, since polarization effects and many-body effects are implicitly included due to the electrostatic embedding scheme. Our results demonstrate that the electrostatically embedded many-body expansion combined with neural network provides a promising and systematic way to build the next generation force fields at high accuracy and low computational costs, especially for large systems.

Vertical motion of a charged colloidal particle near an AC polarized electrode with a nonuniform potential distribution: theory and experimental evidence.

PubMed

Fagan, Jeffrey A; Sides, Paul J; Prieve, Dennis C

2004-06-08

Electroosmotic flow in the vicinity of a colloidal particle suspended over an electrode accounts for observed changes in the average height of the particle when the electrode passes alternating current at 100 Hz. The main findings are (1) electroosmotic flow provides sufficient force to move the particle and (2) a phase shift between the purely electrical force on the particle and the particle's motion provides evidence of an E2 force acting on the particle. The electroosmotic force in this case arises from the boundary condition applied when faradaic reactions occur on the electrode. The presence of a potential-dependent electrode reaction moves the likely distribution of electrical current at the electrode surface toward uniform current density around the particle. In the presence of a particle the uniform current density is associated with a nonuniform potential; thus, the electric field around the particle has a nonzero radial component along the electrode surface, which interacts with unbalanced charge in the diffuse double layer on the electrode to create a flow pattern and impose an electroosmotic-flow-based force on the particle. Numerical solutions are presented for these additional height-dependent forces on the particle as a function of the current distribution on the electrode and for the time-dependent probability density of a charged colloidal particle near a planar electrode with a nonuniform electrical potential boundary condition. The electrical potential distribution on the electrode, combined with a phase difference between the electric field in solution and the electrode potential, can account for the experimentally observed motion of particles in ac electric fields in the frequency range from approximately 10 to 200 Hz.

Different elution modes and field programming in gravitational field-flow fractionation. III. Field programming by flow-rate gradient generated by a programmable pump.

PubMed

Plocková, J; Chmelík, J

2001-05-25

Gravitational field-flow fractionation (GFFF) utilizes the Earth's gravitational field as an external force that causes the settlement of particles towards the channel accumulation wall. Hydrodynamic lift forces oppose this action by elevating particles away from the channel accumulation wall. These two counteracting forces enable modulation of the resulting force field acting on particles in GFFF. In this work, force-field programming based on modulating the magnitude of hydrodynamic lift forces was implemented via changes of flow-rate, which was accomplished by a programmable pump. Several flow-rate gradients (step gradients, linear gradients, parabolic, and combined gradients) were tested and evaluated as tools for optimization of the separation of a silica gel particle mixture. The influence of increasing amount of sample injected on the peak resolution under flow-rate gradient conditions was also investigated. This is the first time that flow-rate gradients have been implemented for programming of the resulting force field acting on particles in GFFF.

Skyrmions Driven by Intrinsic Magnons

NASA Astrophysics Data System (ADS)

Psaroudaki, Christina; Loss, Daniel

2018-06-01

We study the dynamics of a Skyrmion in a magnetic insulating nanowire in the presence of time-dependent oscillating magnetic field gradients. These ac fields act as a net driving force on the Skyrmion via its own intrinsic magnetic excitations. In a microscopic quantum field theory approach, we include the unavoidable coupling of the external field to the magnons, which gives rise to time-dependent dissipation for the Skyrmion. We demonstrate that the magnetic ac field induces a super-Ohmic to Ohmic crossover behavior for the Skyrmion dissipation kernels with time-dependent Ohmic terms. The ac driving of the magnon bath at resonance results in a unidirectional helical propagation of the Skyrmion in addition to the otherwise periodic bounded motion.

Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles.

PubMed

Verbaro, Daniel; Ghosh, Indrajit; Nau, Werner M; Schweitzer-Stenner, Reinhard

2010-12-30

Structural preferences in the unfolded state of peptides determined by molecular dynamics still contradict experimental data. A remedy in this regard has been suggested by MD simulations with an optimized Amber force field ff03* ( Best, R. Hummer, G. J. Phys. Chem. B 2009 , 113 , 9004 - 9015 ). The simulations yielded a statistical coil distribution for alanine which is at variance with recent experimental results. To check the validity of this distribution, we investigated the peptide H-A(5)W-OH, which with the exception of the additional terminal tryptophan is analogous to the peptide used to optimize the force fields ff03*. Electronic circular dichroism, vibrational circular dichroism, and infrared spectroscopy as well as J-coupling constants obtained from NMR experiments were used to derive the peptide's conformational ensemble. Additionally, Förster resonance energy transfer between the terminal chromophores of the fluorescently labeled peptide analogue H-Dbo-A(5)W-OH was used to determine its average length, from which the end-to-end distance of the unlabeled peptide was estimated. Qualitatively, the experimental (3)J(H(N),C(α)), VCD, and ECD indicated a preference of alanine for polyproline II-like conformations. The experimental (3)J(H(N),C(α)) for A(5)W closely resembles the constants obtained for A(5). In order to quantitatively relate the conformational distribution of A(5) obtained with the optimized AMBER ff03* force field to experimental data, the former was used to derive a distribution function which expressed the conformational ensemble as a mixture of polyproline II, β-strand, helical, and turn conformations. This model was found to satisfactorily reproduce all experimental J-coupling constants. We employed the model to calculate the amide I' profiles of the IR and vibrational circular dichroism spectrum of A(5)W, as well as the distance between the two terminal peptide carbonyls. This led to an underestimated negative VCD couplet and an overestimated distance between terminal carbonyl groups. In order to more accurately account for the experimental data, we changed the distribution parameters based on results recently obtained for the alanine-based tripeptides. The final model, which satisfactorily reproduced amide I' profiles, J-coupling constant, and the end-to-end distance of A(5)W, reinforces alanine's high structural preference for polyproline II. Our results suggest that distributions obtained from MD simulations suggesting a statistical coil-like distribution for alanine are still based on insufficiently accurate force fields.

Force field development with GOMC, a fast new Monte Carlo molecular simulation code

NASA Astrophysics Data System (ADS)

Mick, Jason Richard

In this work GOMC (GPU Optimized Monte Carlo) a new fast, flexible, and free molecular Monte Carlo code for the simulation atomistic chemical systems is presented. The results of a large Lennard-Jonesium simulation in the Gibbs ensemble is presented. Force fields developed using the code are also presented. To fit the models a quantitative fitting process is outlined using a scoring function and heat maps. The presented n-6 force fields include force fields for noble gases and branched alkanes. These force fields are shown to be the most accurate LJ or n-6 force fields to date for these compounds, capable of reproducing pure fluid behavior and binary mixture behavior to a high degree of accuracy.

B-spline tight frame based force matching method

NASA Astrophysics Data System (ADS)

Yang, Jianbin; Zhu, Guanhua; Tong, Dudu; Lu, Lanyuan; Shen, Zuowei

2018-06-01

In molecular dynamics simulations, compared with popular all-atom force field approaches, coarse-grained (CG) methods are frequently used for the rapid investigations of long time- and length-scale processes in many important biological and soft matter studies. The typical task in coarse-graining is to derive interaction force functions between different CG site types in terms of their distance, bond angle or dihedral angle. In this paper, an ℓ1-regularized least squares model is applied to form the force functions, which makes additional use of the B-spline wavelet frame transform in order to preserve the important features of force functions. The B-spline tight frames system has a simple explicit expression which is useful for representing our force functions. Moreover, the redundancy of the system offers more resilience to the effects of noise and is useful in the case of lossy data. Numerical results for molecular systems involving pairwise non-bonded, three and four-body bonded interactions are obtained to demonstrate the effectiveness of our approach.

Simulation Protocol for Prediction of a Solid-Electrolyte Interphase on the Silicon-based Anodes of a Lithium-Ion Battery: ReaxFF Reactive Force Field.

PubMed

Yun, Kang-Seop; Pai, Sung Jin; Yeo, Byung Chul; Lee, Kwang-Ryeol; Kim, Sun-Jae; Han, Sang Soo

2017-07-06

We propose the ReaxFF reactive force field as a simulation protocol for predicting the evolution of solid-electrolyte interphase (SEI) components such as gases (C 2 H 4 , CO, CO 2 , CH 4 , and C 2 H 6 ), and inorganic (Li 2 CO 3 , Li 2 O, and LiF) and organic (ROLi and ROCO 2 Li: R = -CH 3 or -C 2 H 5 ) products that are generated by the chemical reactions between the anodes and liquid electrolytes. ReaxFF was developed from ab initio results, and a molecular dynamics simulation with ReaxFF realized the prediction of SEI formation under real experimental conditions and with a reasonable computational cost. We report the effects on SEI formation of different kinds of Si anodes (pristine Si and SiO x ), of the different types and compositions of various carbonate electrolytes, and of the additives. From the results, we expect that ReaxFF will be very useful for the development of novel electrolytes or additives and for further advances in Li-ion battery technology.

Combined targeting of lentiviral vectors and positioning of transduced cells by magnetic nanoparticles.

PubMed

Hofmann, Andreas; Wenzel, Daniela; Becher, Ulrich M; Freitag, Daniel F; Klein, Alexandra M; Eberbeck, Dietmar; Schulte, Maike; Zimmermann, Katrin; Bergemann, Christian; Gleich, Bernhard; Roell, Wilhelm; Weyh, Thomas; Trahms, Lutz; Nickenig, Georg; Fleischmann, Bernd K; Pfeifer, Alexander

2009-01-06

Targeting of viral vectors is a major challenge for in vivo gene delivery, especially after intravascular application. In addition, targeting of the endothelium itself would be of importance for gene-based therapies of vascular disease. Here, we used magnetic nanoparticles (MNPs) to combine cell transduction and positioning in the vascular system under clinically relevant, nonpermissive conditions, including hydrodynamic forces and hypothermia. The use of MNPs enhanced transduction efficiency of endothelial cells and enabled direct endothelial targeting of lentiviral vectors (LVs) by magnetic force, even in perfused vessels. In addition, application of external magnetic fields to mice significantly changed LV/MNP biodistribution in vivo. LV/MNP-transduced cells exhibited superparamagnetic behavior as measured by magnetorelaxometry, and they were efficiently retained by magnetic fields. The magnetic interactions were strong enough to position MNP-containing endothelial cells at the intima of vessels under physiological flow conditions. Importantly, magnetic positioning of MNP-labeled cells was also achieved in vivo in an injury model of the mouse carotid artery. Intravascular gene targeting can be combined with positioning of the transduced cells via nanomagnetic particles, thereby combining gene- and cell-based therapies.

Improved tests of extra-dimensional physics and thermal quantum field theory from new Casimir force measurements

NASA Astrophysics Data System (ADS)

Decca, R. S.; Fischbach, E.; Klimchitskaya, G. L.; Krause, D. E.; López, D.; Mostepanenko, V. M.

2003-12-01

We report new constraints on extra-dimensional models and other physics beyond the standard model based on measurements of the Casimir force between two dissimilar metals for separations in the range 0.2 1.2 μm. The Casimir force between a Au-coated sphere and a Cu-coated plate of a microelectromechanical torsional oscillator was measured statically with an absolute error of 0.3 pN. In addition, the Casimir pressure between two parallel plates was determined dynamically with an absolute error of ≈0.6 mPa. Within the limits of experimental and theoretical errors, the results are in agreement with a theory that takes into account the finite conductivity and roughness of the two metals. The level of agreement between experiment and theory was then used to set limits on the predictions of extra-dimensional physics and thermal quantum field theory. It is shown that two theoretical approaches to the thermal Casimir force which predict effects linear in temperature are ruled out by these experiments. Finally, constraints on Yukawa corrections to Newton’s law of gravity are strengthened by more than an order of magnitude in the range 56 330 nm.

Precise calculation of the local pressure tensor in Cartesian and spherical coordinates in LAMMPS

NASA Astrophysics Data System (ADS)

Nakamura, Takenobu; Kawamoto, Shuhei; Shinoda, Wataru

2015-05-01

An accurate and efficient algorithm for calculating the 3D pressure field has been developed and implemented in the open-source molecular dynamics package, LAMMPS. Additionally, an algorithm to compute the pressure profile along the radial direction in spherical coordinates has also been implemented. The latter is particularly useful for systems showing a spherical symmetry such as micelles and vesicles. These methods yield precise pressure fields based on the Irving-Kirkwood contour integration and are particularly useful for biomolecular force fields. The present methods are applied to several systems including a buckled membrane and a vesicle.

Influence of the ionic liquid/gas surface on ionic liquid chemistry.

PubMed

Lovelock, Kevin R J

2012-04-21

Applications such as gas storage, gas separation, NP synthesis and supported ionic liquid phase catalysis depend upon the interaction of different species with the ionic liquid/gas surface. Consequently, these applications cannot proceed to the full extent of their potential without a profound understanding of the surface structure and properties. As a whole, this perspective contains more questions than answers, which demonstrates the current state of the field. Throughout this perspective, crucial questions are posed and a roadmap is proposed to answer these questions. A critical analysis is made of the field of ionic liquid/gas surface structure and properties, and a number of design rules are mined. The effects of ionic additives on the ionic liquid/gas surface structure are presented. A possible driving force for surface formation is discussed that has, to the best of my knowledge, not been postulated in the literature to date. This driving force suggests that for systems composed solely of ions, the rules for surface formation of dilute electrolytes do not apply. The interaction of neutral additives with the ionic liquid/gas surface is discussed. Particular attention is focussed upon H(2)O and CO(2), vital additives for many applications of ionic liquids. Correlations between ionic liquid/gas surface structure and properties, ionic liquid surfaces plus additives, and ionic liquid applications are given. This journal is © the Owner Societies 2012

Phobos' gravity field and its influence on its orbit and physical librations

NASA Technical Reports Server (NTRS)

Borderies, N.; Yoder, C. F.

1990-01-01

A model describing the physical libration in longitude and latitude for Phobos is derived. The major effect is the well-known longitude variation with the anomalistic orbital period and amplitude. Several additional meter-sized periodic librations in longitude exist. The latitude variation is dominated by the forced precession of Phobos' figure axis with the precession of Phobos' orbital plane. The contribution of Phobos' topography to its gravity field is estimated using the control network model of Duxbury and Callahan (1989).

Maneuvering to Mass Fires: How Interwar Field Artillery Developments Enabled the Allies to Blend Maneuver and Firepower to Defeat the Axis Through Combined Arms Operations

DTIC Science & Technology

2017-03-15

effectiveness with the provision of both operational and tactical level fires. Division artillery reinforced with FAB assets must focus on close support of...the infantry and armored force. In turn, FAB assets must focus on both reinforcing divisional artillery and striking throughout an enemy’s depth...by FABs ) to retain assets for operational level fires. Field artillery firepower must see a qualitative increase in addition to a quantitative

The pedagogical value of the four-dimensional picture: II. Another way of looking at the electromagnetic field

NASA Astrophysics Data System (ADS)

Kosyakov, B. P.

2014-03-01

A definition of the electromagnetic field can be neatly formulated by recognizing that the simplest form of the four-force is indeed feasible. We show that Maxwell’s equations almost entirely stem from the properties of spacetime, notably from the fact that our world has dimension d = 4. Their complete reconstruction requires three additional assumptions that are seemingly divorced from spacetime properties but which may, in fact, have much to do with their geometry.

Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.

PubMed

Matthews, James F; Beckham, Gregg T; Bergenstråhle-Wohlert, Malin; Brady, John W; Himmel, Michael E; Crowley, Michael F

2012-02-14

Molecular dynamics simulations of cellulose have recently become more prevalent due to increased interest in renewable energy applications, and many atomistic and coarse-grained force fields exist that can be applied to cellulose. However, to date no systematic comparison between carbohydrate force fields has been conducted for this important system. To that end, we present a molecular dynamics simulation study of hydrated, 36-chain cellulose Iβ microfibrils at room temperature with three carbohydrate force fields (CHARMM35, GLYCAM06, and Gromos 45a4) up to the near-microsecond time scale. Our results indicate that each of these simulated microfibrils diverge from the cellulose Iβ crystal structure to varying degrees under the conditions tested. The CHARMM35 and GLYCAM06 force fields eventually result in structures similar to those observed at 500 K with the same force fields, which are consistent with the experimentally observed high-temperature behavior of cellulose I. The third force field, Gromos 45a4, produces behavior significantly different from experiment, from the other two force fields, and from previously reported simulations with this force field using shorter simulation times and constrained periodic boundary conditions. For the GLYCAM06 force field, initial hydrogen-bond conformations and choice of electrostatic scaling factors significantly affect the rate of structural divergence. Our results suggest dramatically different time scales for convergence of properties of interest, which is important in the design of computational studies and comparisons to experimental data. This study highlights that further experimental and theoretical work is required to understand the structure of small diameter cellulose microfibrils typical of plant cellulose.

Influence of Short Distance Super-large Diameter Shield Tunneling on Existing Tunnels in Sea Areas

NASA Astrophysics Data System (ADS)

Li, Zhuolin; Liu, Dagang; Wang, Mingnian; Xiao, Shihui; Yuan, Jiawei

2018-03-01

In oder to find out the influence of large diameter shield tunneling on the existing tunnel under the condition of compound strata in the sea area, taking the Maliuzhou traffic tunnel as the research background, numerical simulation and field test were combined to get the regulation of the additional internal force and deformation of the existing tunnel caused by the shield tunneling. Analysis of the data showed that: the shield construction caused the secondary additional internal force; The moment of the vault was most affected by the tunnel excavation; The axial force of the arch bottom was most affected by the excavation of the tunnel. The deformation of arch waist near excavation tunnel was more affected by tunnel excavation than that of the other side. Combined with the construction experience, the influence of the tunnel close-distance construction on the existing tunnel was within the control range, which could ensure the normal construction.

Three Dimensional Distribution of Sensitive Field and Stress Field Inversion of Force Sensitive Materials under Constant Current Excitation.

PubMed

Zhao, Shuanfeng; Liu, Min; Guo, Wei; Zhang, Chuanwei

2018-02-28

Force sensitive conductive composite materials are functional materials which can be used as the sensitive material of force sensors. However, the existing sensors only use one-dimensional electrical properties of force sensitive conductive materials. Even in tactile sensors, the measurement of contact pressure is achieved by large-scale arrays and the units of a large-scale array are also based on the one-dimensional electrical properties of force sensitive materials. The main contribution of this work is to study the three-dimensional electrical properties and the inversion method of three-dimensional stress field of a force sensitive material (conductive rubber), which pushes the application of force sensitive material from one dimensional to three-dimensional. First, the mathematical model of the conductive rubber current field distribution under a constant force is established by the effective medium theory, and the current field distribution model of conductive rubber with different geometry, conductive rubber content and conductive rubber relaxation parameters is deduced. Secondly, the inversion method of the three-dimensional stress field of conductive rubber is established, which provides a theoretical basis for the design of a new tactile sensor, three-dimensional stress field and space force based on force sensitive materials.

Comparison of three empirical force fields for phonon calculations in CdSe quantum dots

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

Kelley, Anne Myers

Three empirical interatomic force fields are parametrized using structural, elastic, and phonon dispersion data for bulk CdSe and their predictions are then compared for the structures and phonons of CdSe quantum dots having average diameters of ~2.8 and ~5.2 nm (~410 and ~2630 atoms, respectively). The three force fields include one that contains only two-body interactions (Lennard-Jones plus Coulomb), a Tersoff-type force field that contains both two-body and three-body interactions but no Coulombic terms, and a Stillinger-Weber type force field that contains Coulombic interactions plus two-body and three-body terms. While all three force fields predict nearly identical peak frequencies formore » the strongly Raman-active “longitudinal optical” phonon in the quantum dots, the predictions for the width of the Raman peak, the peak frequency and width of the infrared absorption peak, and the degree of disorder in the structure are very different. The three force fields also give very different predictions for the variation in phonon frequency with radial position (core versus surface). The Stillinger-Weber plus Coulomb type force field gives the best overall agreement with available experimental data.« less

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.

PubMed

Best, Robert B; Hummer, Gerhard

2009-07-02

Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.

Air Force construction automation/robotics

NASA Technical Reports Server (NTRS)

Nease, AL; Dusseault, Christopher

1994-01-01

The Air Force has several unique requirements that are being met through the development of construction robotic technology. The missions associated with these requirements place construction/repair equipment operators in potentially harmful situations. Additionally, force reductions require that human resources be leveraged to the maximum extent possible and that more stringent construction repair requirements push for increased automation. To solve these problems, the U.S. Air Force is undertaking a research and development effort at Tyndall AFB, FL to develop robotic teleoperation, telerobotics, robotic vehicle communications, automated damage assessment, vehicle navigation, mission/vehicle task control architecture, and associated computing environment. The ultimate goal is the fielding of robotic repair capability operating at the level of supervised autonomy. The authors of this paper will discuss current and planned efforts in construction/repair, explosive ordnance disposal, hazardous waste cleanup, fire fighting, and space construction.

Single-drop reactive extraction/extractive reaction with forced convective diffusion and interphase mass transfer

NASA Technical Reports Server (NTRS)

Kleinman, Leonid S.; Red, X. B., Jr.

1995-01-01

An algorithm has been developed for time-dependent forced convective diffusion-reaction having convection by a recirculating flow field within the drop that is hydrodynamically coupled at the interface with a convective external flow field that at infinity becomes a uniform free-streaming flow. The concentration field inside the droplet is likewise coupled with that outside by boundary conditions at the interface. A chemical reaction can take place either inside or outside the droplet, or reactions can take place in both phases. The algorithm has been implemented, and for comparison results are shown here for the case of no reaction in either phase and for the case of an external first order reaction, both for unsteady behavior. For pure interphase mass transfer, concentration isocontours, local and average Sherwood numbers, and average droplet concentrations have been obtained as a function of the physical properties and external flow field. For mass transfer enhanced by an external reaction, in addition to the above forms of results, we present the enhancement factor, with the results now also depending upon the (dimensionless) rate of reaction.

Single-drop reactive extraction/extractive reaction with forced convective diffusion and interphase mass transfer

NASA Technical Reports Server (NTRS)

Kleinman, Leonid S.; Reed, X. B., Jr.

1995-01-01

An algorithm has been developed for the forced convective diffusion-reaction problem for convection inside and outside a droplet by a recirculating flow field hydrodynamically coupled at the droplet interface with an external flow field that at infinity becomes a uniform streaming flow. The concentration field inside the droplet is likewise coupled with that outside by boundary conditions at the interface. A chemical reaction can take place either inside or outside the droplet or reactions can take place in both phases. The algorithm has been implemented and results are shown here for the case of no reaction and for the case of an external first order reaction, both for unsteady behavior. For pure interphase mass transfer, concentration isocontours, local and average Sherwood numbers, and average droplet concentrations have been obtained as a function of the physical properties and external flow field. For mass transfer enhanced by an external reaction, in addition to the above forms of results, we present the enhancement factor, with the results now also depending upon the (dimensionless) rate of reaction.

A triangular prism solid and shell interactive mapping element for electromagnetic sheet metal forming process

NASA Astrophysics Data System (ADS)

Cui, Xiangyang; Li, She; Feng, Hui; Li, Guangyao

2017-05-01

In this paper, a novel triangular prism solid and shell interactive mapping element is proposed to solve the coupled magnetic-mechanical formulation in electromagnetic sheet metal forming process. A linear six-node "Triprism" element is firstly proposed for transient eddy current analysis in electromagnetic field. In present "Triprism" element, shape functions are given explicitly, and a cell-wise gradient smoothing operation is used to obtain the gradient matrices without evaluating derivatives of shape functions. In mechanical field analysis, a shear locking free triangular shell element is employed in internal force computation, and a data mapping method is developed to transfer the Lorentz force on solid into the external forces suffered by shell structure for dynamic elasto-plasticity deformation analysis. Based on the deformed triangular shell structure, a "Triprism" element generation rule is established for updated electromagnetic analysis, which means inter-transformation of meshes between the coupled fields can be performed automatically. In addition, the dynamic moving mesh is adopted for air mesh updating based on the deformation of sheet metal. A benchmark problem is carried out for confirming the accuracy of the proposed "Triprism" element in predicting flux density in electromagnetic field. Solutions of several EMF problems obtained by present work are compared with experiment results and those of traditional method, which are showing excellent performances of present interactive mapping element.

Cooperative effects between color centers in diamond: applications to optical tweezers and optomechanics

NASA Astrophysics Data System (ADS)

Bradac, Carlo; Prasanna Venkatesh, B.; Besga, Benjamin; Johnsson, Mattias; Brennen, Gavin; Molina-Terriza, Gabriel; Volz, Thomas; Juan, Mathieu L.

2017-08-01

Since the early work by Ashkin in 1970,1 optical trapping has become one of the most powerful tools for manipulating small particles, such as micron sized beads2 or single atoms.3 Interestingly, both an atom and a lump of dielectric material can be manipulated through the same mechanism: the interaction energy of a dipole and the electric field of the laser light. In the case of atom trapping, the dominant contribution typically comes from the allowed optical transition closest to the laser wavelength while it is given by the bulk polarisability for mesoscopic particles. This difference lead to two very different contexts of applications: one being the trapping of small objects mainly in biological settings,4 the other one being dipole traps for individual neutral atoms5 in the field of quantum optics. In this context, solid state artificial atoms present the interesting opportunity to combine these two aspects of optical manipulation. We are particularly interested in nanodiamonds as they constitute a bulk dielectric object by themselves, but also contain artificial atoms such as nitrogen-vacancy (NV) or silicon-vacancy (SiV) colour centers. With this system, both regimes of optical trapping can be observed at the same time even at room temperature. In this work, we demonstrate that the resonant force from the optical transition of NV centres at 637 nm can be measured in a nanodiamond trapped in water. This additional contribution to the total force is significant, reaching up to 10%. In addition, due to the very large density of NV centres in a sub-wavelength crystal, collective effects between centres have an important effect on the magnitude of the resonant force.6 The possibility to observe such cooperatively enhanced optical force at room temperature is also theoretically confirmed.7 This approach may enable the study of cooperativity in various nanoscale solid-state systems and the use of atomic physics techniques in the field of nano-manipulation and opto-mechanics.

Gravity and Nonconservative Force Model Tuning for the GEOSAT Follow-On Spacecraft

NASA Technical Reports Server (NTRS)

Lemoine, Frank G.; Zelensky, Nikita P.; Rowlands, David D.; Luthcke, Scott B.; Chinn, Douglas S.; Marr, Gregory C.; Smith, David E. (Technical Monitor)

2000-01-01

The US Navy's GEOSAT Follow-On spacecraft was launched on February 10, 1998 and the primary objective of the mission was to map the oceans using a radar altimeter. Three radar altimeter calibration campaigns have been conducted in 1999 and 2000. The spacecraft is tracked by satellite laser ranging (SLR) and Doppler beacons and a limited amount of data have been obtained from the Global Positioning Receiver (GPS) on board the satellite. Even with EGM96, the predicted radial orbit error due to gravity field mismodelling (to 70x70) remains high at 2.61 cm (compared to 0.88 cm for TOPEX). We report on the preliminary gravity model tuning for GFO using SLR, and altimeter crossover data. Preliminary solutions using SLR and GFO/GFO crossover data from CalVal campaigns I and II in June-August 1999, and January-February 2000 have reduced the predicted radial orbit error to 1.9 cm and further reduction will be possible when additional data are added to the solutions. The gravity model tuning has improved principally the low order m-daily terms and has reduced significantly the geographically correlated error present in this satellite orbit. In addition to gravity field mismodelling, the largest contributor to the orbit error is the non-conservative force mismodelling. We report on further nonconservative force model tuning results using available data from over one cycle in beta prime.

An assessment of mean-field mixed semiclassical approaches: Equilibrium populations and algorithm stability

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

Bellonzi, Nicole; Jain, Amber; Subotnik, Joseph E.

2016-04-21

We study several recent mean-field semiclassical dynamics methods, focusing on the ability to recover detailed balance for long time (equilibrium) populations. We focus especially on Miller and Cotton’s [J. Phys. Chem. A 117, 7190 (2013)] suggestion to include both zero point electronic energy and windowing on top of Ehrenfest dynamics. We investigate three regimes: harmonic surfaces with weak electronic coupling, harmonic surfaces with strong electronic coupling, and anharmonic surfaces with weak electronic coupling. In most cases, recent additions to Ehrenfest dynamics are a strong improvement upon mean-field theory. However, for methods that include zero point electronic energy, we show thatmore » anharmonic potential energy surfaces often lead to numerical instabilities, as caused by negative populations and forces. We also show that, though the effect of negative forces can appear hidden in harmonic systems, the resulting equilibrium limits do remain dependent on any windowing and zero point energy parameters.« less

Computation of Relative Magnetic Helicity in Spherical Coordinates

NASA Astrophysics Data System (ADS)

Moraitis, Kostas; Pariat, Étienne; Savcheva, Antonia; Valori, Gherardo

2018-06-01

Magnetic helicity is a quantity of great importance in solar studies because it is conserved in ideal magnetohydrodynamics. While many methods for computing magnetic helicity in Cartesian finite volumes exist, in spherical coordinates, the natural coordinate system for solar applications, helicity is only treated approximately. We present here a method for properly computing the relative magnetic helicity in spherical geometry. The volumes considered are finite, of shell or wedge shape, and the three-dimensional magnetic field is considered to be fully known throughout the studied domain. Testing of the method with well-known, semi-analytic, force-free magnetic-field models reveals that it has excellent accuracy. Further application to a set of nonlinear force-free reconstructions of the magnetic field of solar active regions and comparison with an approximate method used in the past indicates that the proposed method can be significantly more accurate, thus making our method a promising tool in helicity studies that employ spherical geometry. Additionally, we determine and discuss the applicability range of the approximate method.

MagnetoSperm: A microrobot that navigates using weak magnetic fields

NASA Astrophysics Data System (ADS)

Khalil, Islam S. M.; Dijkslag, Herman C.; Abelmann, Leon; Misra, Sarthak

2014-06-01

In this work, a propulsion system similar in motion to a sperm-cell is investigated. This system consists of a structure resembling a sperm-cell with a magnetic head and a flexible tail of 42 μm and 280 μm in length, respectively. The thickness, length, and width of this structure are 5.2 μm, 322 μm, and 42 μm, respectively. The magnetic head includes a 200 nm-thick cobalt-nickel layer. The cobalt-nickel layer provides a dipole moment and allows the flexible structure to align along oscillating weak (less than 5 mT) magnetic field lines, and hence generates a propulsion thrust force that overcomes the drag force. The frequency response of this system shows that the propulsion mechanism allows for swimming at an average speed of 158 ± 32 μm/s at alternating weak magnetic field of 45 Hz. In addition, we experimentally demonstrate controlled steering of the flexible structure towards reference positions.

Satellite Remote Sensing of Aerosol Forcing

NASA Technical Reports Server (NTRS)

Remer, Lorraine; Kaufman, Yoram; Ramaprasad, Jaya; Procopio, Aline; Levin, Zev

1999-01-01

The role of aerosol forcing remains one of the largest uncertainties in estimating man's impact on the global climate system. One school of thought suggests that remote sensing by satellite sensors will provide the data necessary to narrow these uncertainties. While satellite measurements of direct aerosol forcing appear to be straightforward, satellite measurements of aerosol indirect forcing will be more complicated. Pioneering studies identified indirect aerosol forcing using AVHRR data in the biomass burning regions of Brazil. We have expanded this analysis with AVHRR to include an additional year of data and assimilated water vapor fields. The results show similar latitudinal dependence as reported by Kaufman and Fraser, but by using water vapor observations we conclude that latitude is not a proxy for water vapor and the strength of the indirect effect is not correlated to water vapor amounts. In addition to the AVHRR study we have identified indirect aerosol forcing in Brazil at much smaller spatial scales using the MODIS Airborne Simulator. The strength of the indirect effect appears to be related to cloud type and cloud dynamics. There is a suggestion that some of the cloud dynamics may be influenced by smoke destabilization of the atmospheric column. Finally, this study attempts to quantify remote sensing limitations due to the accuracy limits of the retrieval algorithms. We use a combination of numerical aerosol transport models, ground-based AERONET data and ISCCP cloud climatology to determine how much of the forcing occurs in regions too clean to determine from satellite retrievals.

Electromechanical response of silk fibroin hydrogel and conductive polycarbazole/silk fibroin hydrogel composites as actuator material.

PubMed

Srisawasdi, Thanida; Petcharoen, Karat; Sirivat, Anuvat; Jamieson, Alexander M

2015-11-01

Pure silk fibroin (SF) hydrogel and polycarbazole/silk fibroin (SF/PCZ) hydrogels were fabricated by solvent casting technique to evaluate electromechanical responses, dielectric properties, and cantilever deflection properties as functions of electric field strength, SF concentration, glutaraldehyde concentration, and PCZ concentration in the blends. Electromechanical properties were characterized in oscillatory shear mode at electric field strengths ranging from 0 to 600V/mm and at a temperature of 27°C. For both the pristine SF and SF/PCZ hydrogels, the storage modulus response (ΔG') and the storage modulus sensitivity (ΔG'/G'0) increased dramatically with increasing electric field strength. The pristine hydrogel possessed the highest storage modulus sensitivity value of 5.87, a relatively high value when compared with other previously studied electroactive polymers. With the addition of conductive PCZ in SF hydrogel, the storage modulus sensitivity and the relative dielectric constant decreased; the conductive polymer thus provided the softening effect under electric field. In the deflection response, the dielectrophoresis force and deflection distance increased monotonically with electric field strength, where the pure SF hydrogel showed the highest deflection distance and dielectrophoresis force. Copyright © 2015 Elsevier B.V. All rights reserved.

Self-organization processes in polysiloxane block copolymers, initiated by modifying fullerene additives

NASA Astrophysics Data System (ADS)

Voznyakovskii, A. P.; Kudoyarova, V. Kh.; Kudoyarov, M. F.; Patrova, M. Ya.

2017-08-01

Thin films of a polyblock polysiloxane copolymer and their composites with a modifying fullerene C60 additive are studied by atomic force microscopy, Rutherford backscattering, and neutron scattering. The data of atomic force microscopy show that with the addition of fullerene to the bulk of the polymer matrix, the initial relief of the film surface is leveled more, the larger the additive. This trend is associated with the processes of self-organization of rigid block sequences, which are initiated by the field effect of the surface of fullerene aggregates and lead to an increase in the number of their domains in the bulk of the polymer matrix. The data of Rutherford backscattering and neutron scattering indicate the formation of additional structures with a radius of 60 nm only in films containing fullerene, and their fraction increases with increasing fullerene concentration. A comparative analysis of the data of these methods has shown that such structures are, namely, the domains of a rigid block and are not formed by individual fullerene aggregates. The interrelation of the structure and mechanical properties of polymer films is considered.

Alternating Field Electronanofluidization

NASA Astrophysics Data System (ADS)

Espin, M. J.; Valverde, J. M.; Quintanilla, M. A. S.; Castellanos, A.

2009-06-01

The use of fluidized beds to remove submicron particles from gases has been investigated since 1949. High efficiency removal was achieved in the 1970's by imposing an electric field on a fluidized bed of semi-insulating granules that were able to collect the charged pollutant entrained in the fluidizing gas. In spite of their extended use nowadays, the collection efficiency of electrofluidized beds (EFB) is still hindered by gas bypassing associated to gas bubbling and the consequent requirement of too high gas flow and pressure drop. In this paper we report on the electromechanical behavior of an EFB of insulating nanoparticles. When fluidized by gas, these nanoparticles form extremely porous light agglomerates of size of the order of hundreds of microns that allow for a highly expanded nonbubbling fluidized state at reduced gas flow. It is found that fluidization uniformity and bed expansion are additionally enhanced by an imposed AC electric field for field oscillation frequencies of several tens of hertzs and field strengths of the order of 1 kV/cm. For oscillation frequencies of the order of hertzs, or smaller, bed expansion is hindered due to electrophoretic deposition of the agglomerates onto the vessel walls, whereas for oscillation frequencies of the order of kilohertzs, or larger, electrophoresis is nullified and bed expansion is not affected. According to a proposed model, the size of nanoparticle agglomerates stems from the balance between shear, which depends on field strength, and van der Waals forces. The optimum field strength for enhancing bed expansion produces an electric force on the agglomerates similar to their weight force, while the oscillation velocity of the agglomerates is similar to the gas velocity.

Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.

PubMed

Watts, Charles R; Gregory, Andrew; Frisbie, Cole; Lovas, Sándor

2018-03-01

The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different. © 2017 Wiley Periodicals, Inc.

Catch trials in force field learning influence adaptation and consolidation of human motor memory

PubMed Central

Stockinger, Christian; Focke, Anne; Stein, Thorsten

2014-01-01

Force field studies are a common tool to investigate motor adaptation and consolidation. Thereby, subjects usually adapt their reaching movements to force field perturbations induced by a robotic device. In this context, so-called catch trials, in which the disturbing forces are randomly turned off, are commonly used to detect after-effects of motor adaptation. However, catch trials also produce sudden large motor errors that might influence the motor adaptation and the consolidation process. Yet, the detailed influence of catch trials is far from clear. Thus, the aim of this study was to investigate the influence of catch trials on motor adaptation and consolidation in force field experiments. Therefore, 105 subjects adapted their reaching movements to robot-generated force fields. The test groups adapted their reaching movements to a force field A followed by learning a second interfering force field B before retest of A (ABA). The control groups were not exposed to force field B (AA). To examine the influence of diverse catch trial ratios, subjects received catch trials during force field adaptation with a probability of either 0, 10, 20, 30, or 40%, depending on the group. First, the results on motor adaptation revealed significant differences between the diverse catch trial ratio groups. With increasing amount of catch trials, the subjects' motor performance decreased and subjects' ability to accurately predict the force field—and therefore internal model formation—was impaired. Second, our results revealed that adapting with catch trials can influence the following consolidation process as indicated by a partial reduction to interference. Here, the optimal catch trial ratio was 30%. However, detection of consolidation seems to be biased by the applied measure of performance. PMID:24795598

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

PubMed Central

Noid, W. G.; Liu, Pu; Wang, Yanting; Chu, Jhih-Wei; Ayton, Gary S.; Izvekov, Sergei; Andersen, Hans C.; Voth, Gregory A.

2008-01-01

The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+∕NO3− ionic liquid are provided to illustrate the method. PMID:18601325

Rapid and label-free separation of Burkitt's lymphoma cells from red blood cells by optically-induced electrokinetics.

PubMed

Liang, Wenfeng; Zhao, Yuliang; Liu, Lianqing; Wang, Yuechao; Dong, Zaili; Li, Wen Jung; Lee, Gwo-Bin; Xiao, Xiubin; Zhang, Weijing

2014-01-01

Early stage detection of lymphoma cells is invaluable for providing reliable prognosis to patients. However, the purity of lymphoma cells in extracted samples from human patients' marrow is typically low. To address this issue, we report here our work on using optically-induced dielectrophoresis (ODEP) force to rapidly purify Raji cells' (a type of Burkitt's lymphoma cell) sample from red blood cells (RBCs) with a label-free process. This method utilizes dynamically moving virtual electrodes to induce negative ODEP force of varying magnitudes on the Raji cells and RBCs in an optically-induced electrokinetics (OEK) chip. Polarization models for the two types of cells that reflect their discriminate electrical properties were established. Then, the cells' differential velocities caused by a specific ODEP force field were obtained by a finite element simulation model, thereby established the theoretical basis that the two types of cells could be separated using an ODEP force field. To ensure that the ODEP force dominated the separation process, a comparison of the ODEP force with other significant electrokinetics forces was conducted using numerical results. Furthermore, the performance of the ODEP-based approach for separating Raji cells from RBCs was experimentally investigated. The results showed that these two types of cells, with different concentration ratios, could be separated rapidly using externally-applied electrical field at a driven frequency of 50 kHz at 20 Vpp. In addition, we have found that in order to facilitate ODEP-based cell separation, Raji cells' adhesion to the OEK chip's substrate should be minimized. This paper also presents our experimental results of finding the appropriate bovine serum albumin concentration in an isotonic solution to reduce cell adhesion, while maintaining suitable medium conductivity for electrokinetics-based cell separation. In short, we have demonstrated that OEK technology could be a promising tool for efficient and effective purification of Raji cells from RBCs.

A new hysteresis model based on force-displacement characteristics of magnetorheological fluid actuators subjected to squeeze mode operation

NASA Astrophysics Data System (ADS)

Chen, Peng; Bai, Xian-Xu; Qian, Li-Jun; Choi, Seung-Bok

2017-06-01

This paper presents a new hysteresis model based on the force-displacement characteristics of magnetorheological (MR) fluid actuators (or devices) subjected to squeeze mode operation. The idea of the proposed model is originated from experimental observation of the field-dependent hysteretic behavior of MR fluids, which shows that from a view of rate-independence of hysteresis, a gap width-dependent hysteresis is occurred in the force-displacement relationship instead of the typical relationship of the force-velocity. To effectively and accurately portray the hysteresis behavior, the gap width-dependent hysteresis elements, the nonlinear viscous effect and the inertial effect are considered for the formulation of the hysteresis model. Then, a model-based feedforward force tracking control scheme is established through an observer which can estimate the virtual displacement. The effectiveness of the proposed hysteresis model is validated through the identification and prediction of the damping force of MR fluids in the squeeze mode. In addition, it is shown that superior force tracking performance of the feedforward control associated with the proposed hysteresis mode is evaluated by adopting several tracking trajectories.

The application of atomic force microscopy in mineral flotation.

PubMed

Xing, Yaowen; Xu, Mengdi; Gui, Xiahui; Cao, Yijun; Babel, Bent; Rudolph, Martin; Weber, Stefan; Kappl, Michael; Butt, Hans-Jürgen

2018-06-01

During the past years, atomic force microscopy (AFM) has matured to an indispensable tool to characterize nanomaterials in colloid and interface science. For imaging, a sharp probe mounted near to the end of a cantilever scans over the sample surface providing a high resolution three-dimensional topographic image. In addition, the AFM tip can be used as a force sensor to detect local properties like adhesion, stiffness, charge etc. After the invention of the colloidal probe technique it has also become a major method to measure surface forces. In this review, we highlight the advances in the application of AFM in the field of mineral flotation, such as mineral morphology imaging, water at mineral surface, reagent adsorption, inter-particle force, and bubble-particle interaction. In the coming years, the complementary characterization of chemical composition such as using infrared spectroscopy and Raman spectroscopy for AFM topography imaging and the synchronous measurement of the force and distance involving deformable bubble as a force sensor will further assist the fundamental understanding of flotation mechanism. Copyright © 2018 Elsevier B.V. All rights reserved.

Euler force actuation mechanism for siphon valving in compact disk-like microfluidic chips.

PubMed

Deng, Yongbo; Fan, Jianhua; Zhou, Song; Zhou, Teng; Wu, Junfeng; Li, Yin; Liu, Zhenyu; Xuan, Ming; Wu, Yihui

2014-03-01

Based on the Euler force induced by the acceleration of compact disk (CD)-like microfluidic chip, this paper presents a novel actuation mechanism for siphon valving. At the preliminary stage of acceleration, the Euler force in the tangential direction of CD-like chip takes the primary place compared with the centrifugal force to function as the actuation of the flow, which fills the siphon and actuates the siphon valving. The Euler force actuation mechanism is demonstrated by the numerical solution of the phase-field based mathematical model for the flow in siphon valve. In addition, experimental validation is implemented in the polymethylmethacrylate-based CD-like microfluidic chip manufactured using CO2 laser engraving technique. To prove the application of the proposed Euler force actuation mechanism, whole blood separation and plasma extraction has been conducted using the Euler force actuated siphon valving. The newly introduced actuation mechanism overcomes the dependence on hydrophilic capillary filling of siphon by avoiding external manipulation or surface treatments of polymeric material. The sacrifice for highly integrated processing in pneumatic pumping technique is also prevented by excluding the volume-occupied compressed air chamber.

Particle force model effects in a shock-driven multiphase instability

NASA Astrophysics Data System (ADS)

Black, W. J.; Denissen, N.; McFarland, J. A.

2018-05-01

This work presents simulations on a shock-driven multiphase instability (SDMI) at an initial particle volume fraction of 1% with the addition of a suite of particle force models applicable in dense flows. These models include pressure-gradient, added-mass, and interparticle force terms in an effort to capture the effects neighboring particles have in non-dilute flow regimes. Two studies are presented here: the first seeks to investigate the individual contributions of the force models, while the second study focuses on examining the effect of these force models on the hydrodynamic evolution of a SDMI with various particle relaxation times (particle sizes). In the force study, it was found that the pressure gradient and interparticle forces have little effect on the instability under the conditions examined, while the added-mass force decreases the vorticity deposition and alters the morphology of the instability. The relaxation-time study likewise showed a decrease in metrics associated with the evolution of the SDMI for all sizes when the particle force models were included. The inclusion of these models showed significant morphological differences in both the particle and carrier species fields, which increased as particle relaxation times increased.

QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input.

PubMed

Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon; Schmid, Rochus; Waroquier, Michel; Van Speybroeck, Veronique

2015-05-15

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

PubMed

Nessler, Ian J; Litman, Jacob M; Schnieders, Michael J

2016-11-09

First principles prediction of the structure, thermodynamics and solubility of organic molecular crystals, which play a central role in chemical, material, pharmaceutical and engineering sciences, challenges both potential energy functions and sampling methodologies. Here we calculate absolute crystal deposition thermodynamics using a novel dual force field approach whose goal is to maintain the accuracy of advanced multipole force fields (e.g. the polarizable AMOEBA model) while performing more than 95% of the sampling in an inexpensive fixed charge (FC) force field (e.g. OPLS-AA). Absolute crystal sublimation/deposition phase transition free energies were determined using an alchemical path that grows the crystalline state from a vapor reference state based on sampling with the OPLS-AA force field, followed by dual force field thermodynamic corrections to change between FC and AMOEBA resolutions at both end states (we denote the three step path as AMOEBA/FC). Importantly, whereas the phase transition requires on the order of 200 ns of sampling per compound, only 5 ns of sampling was needed for the dual force field thermodynamic corrections to reach a mean statistical uncertainty of 0.05 kcal mol -1 . For five organic compounds, the mean unsigned error between direct use of AMOEBA and the AMOEBA/FC dual force field path was only 0.2 kcal mol -1 and not statistically significant. Compared to experimental deposition thermodynamics, the mean unsigned error for AMOEBA/FC (1.4 kcal mol -1 ) was more than a factor of two smaller than uncorrected OPLS-AA (3.2 kcal mol -1 ). Overall, the dual force field thermodynamic corrections reduced condensed phase sampling in the expensive force field by a factor of 40, and may prove useful for protein stability or binding thermodynamics in the future.

The electromagnetic force field, fluid flow field and temperature profiles in levitated metal droplets

NASA Technical Reports Server (NTRS)

El-Kaddah, N.; Szekely, J.

1982-01-01

A mathematical representation was developed for the electromagnetic force field, the flow field, the temperature field (and for transport controlled kinetics), in a levitation melted metal droplet. The technique of mutual inductances was employed for the calculation of the electromagnetic force field, while the turbulent Navier - Stokes equations and the turbulent convective transport equations were used to represent the fluid flow field, the temperature field and the concentration field. The governing differential equations, written in spherical coordinates, were solved numerically. The computed results were in good agreement with measurements, regarding the lifting force, and the average temperature of the specimen and carburization rates, which were transport controlled.

Molecular dynamics simulation of sodium aluminosilicate glass structures and glass surface-water reactions using the reactive force field (ReaxFF)

NASA Astrophysics Data System (ADS)

Dongol, R.; Wang, L.; Cormack, A. N.; Sundaram, S. K.

2018-05-01

Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.

Extracting the potential-well of a near-field optical trap using the Helmholtz-Hodge decomposition

NASA Astrophysics Data System (ADS)

Zaman, Mohammad Asif; Padhy, Punnag; Hansen, Paul C.; Hesselink, Lambertus

2018-02-01

The non-conservative nature of the force field generated by a near-field optical trap is analyzed. A plasmonic C-shaped engraving on a gold film is considered as the trap. The force field is calculated using the Maxwell stress tensor method. The Helmholtz-Hodge decomposition is used to extract the conservative and the non-conservative component of the force. Due to the non-negligible non-conservative component, it is found that the conventional approach of extracting the potential by direct integration of the force is not accurate. Despite the non-conservative nature of the force field, it is found that the statistical properties of a trapped nanoparticle can be estimated from the conservative component of the force field alone. Experimental and numerical results are presented to support the claims.

Current kinematics and dynamics of Africa and the East African Rift System

NASA Astrophysics Data System (ADS)

Stamps, D. S.; Flesch, L. M.; Calais, E.; Ghosh, A.

2014-06-01

Although the East African Rift System (EARS) is an archetype continental rift, the forces driving its evolution remain debated. Some contend buoyancy forces arising from gravitational potential energy (GPE) gradients within the lithosphere drive rifting. Others argue for a major role of the diverging mantle flow associated with the African Superplume. Here we quantify the forces driving present-day continental rifting in East Africa by (1) solving the depth averaged 3-D force balance equations for 3-D deviatoric stress associated with GPE, (2) inverting for a stress field boundary condition that we interpret as originating from large-scale mantle tractions, (3) calculating dynamic velocities due to lithospheric buoyancy forces, lateral viscosity variations, and velocity boundary conditions, and (4) calculating dynamic velocities that result from the stress response of horizontal mantle tractions acting on a viscous lithosphere in Africa and surroundings. We find deviatoric stress associated with lithospheric GPE gradients are ˜8-20 MPa in EARS, and the minimum deviatoric stress resulting from basal shear is ˜1.6 MPa along the EARS. Our dynamic velocity calculations confirm that a force contribution from GPE gradients alone is sufficient to drive Nubia-Somalia divergence and that additional forcing from horizontal mantle tractions overestimates surface kinematics. Stresses from GPE gradients appear sufficient to sustain present-day rifting in East Africa; however, they are lower than the vertically integrated strength of the lithosphere along most of the EARS. This indicates additional processes are required to initiate rupture of continental lithosphere, but once it is initiated, lithospheric buoyancy forces are enough to maintain rifting.

Muscle co-contraction patterns in robot-mediated force field learning to guide specific muscle group training.

PubMed

Pizzamiglio, Sara; Desowska, Adela; Shojaii, Pegah; Taga, Myriam; Turner, Duncan L

2017-01-01

Muscle co-contraction is a strategy of increasing movement accuracy and stability employed in dealing with force perturbation of movement. It is often seen in neuropathological populations. The direction of movement influences the pattern of co-contraction, but not all movements are easily achievable for populations with motor deficits. Manipulating the direction of the force instead, may be a promising rehabilitation protocol to train movement with use of a co-contraction reduction strategy. Force field learning paradigms provide a well described procedure to evoke and test muscle co-contraction. The aim of this study was to test the muscle co-contraction pattern in a wide range of arm muscles in different force-field directions utilising a robot-mediated force field learning paradigm of motor adaptation. Forty-two participants volunteered to participate in a study utilising robot-mediated force field motor adaptation paradigm with a clockwise or counter-clockwise force field. Kinematics and surface electromyography (EMG) of eight arm muscles were measured. Both muscle activation and co-contraction was earlier and stronger in flexors in the clockwise condition and in extensors in the counter-clockwise condition. Manipulating the force field direction leads to changes in the pattern of muscle co-contraction.

A Maximum-Likelihood Approach to Force-Field Calibration.

PubMed

Zaborowski, Bartłomiej; Jagieła, Dawid; Czaplewski, Cezary; Hałabis, Anna; Lewandowska, Agnieszka; Żmudzińska, Wioletta; Ołdziej, Stanisław; Karczyńska, Agnieszka; Omieczynski, Christian; Wirecki, Tomasz; Liwo, Adam

2015-09-28

A new approach to the calibration of the force fields is proposed, in which the force-field parameters are obtained by maximum-likelihood fitting of the calculated conformational ensembles to the experimental ensembles of training system(s). The maximum-likelihood function is composed of logarithms of the Boltzmann probabilities of the experimental conformations, calculated with the current energy function. Because the theoretical distribution is given in the form of the simulated conformations only, the contributions from all of the simulated conformations, with Gaussian weights in the distances from a given experimental conformation, are added to give the contribution to the target function from this conformation. In contrast to earlier methods for force-field calibration, the approach does not suffer from the arbitrariness of dividing the decoy set into native-like and non-native structures; however, if such a division is made instead of using Gaussian weights, application of the maximum-likelihood method results in the well-known energy-gap maximization. The computational procedure consists of cycles of decoy generation and maximum-likelihood-function optimization, which are iterated until convergence is reached. The method was tested with Gaussian distributions and then applied to the physics-based coarse-grained UNRES force field for proteins. The NMR structures of the tryptophan cage, a small α-helical protein, determined at three temperatures (T = 280, 305, and 313 K) by Hałabis et al. ( J. Phys. Chem. B 2012 , 116 , 6898 - 6907 ), were used. Multiplexed replica-exchange molecular dynamics was used to generate the decoys. The iterative procedure exhibited steady convergence. Three variants of optimization were tried: optimization of the energy-term weights alone and use of the experimental ensemble of the folded protein only at T = 280 K (run 1); optimization of the energy-term weights and use of experimental ensembles at all three temperatures (run 2); and optimization of the energy-term weights and the coefficients of the torsional and multibody energy terms and use of experimental ensembles at all three temperatures (run 3). The force fields were subsequently tested with a set of 14 α-helical and two α + β proteins. Optimization run 1 resulted in better agreement with the experimental ensemble at T = 280 K compared with optimization run 2 and in comparable performance on the test set but poorer agreement of the calculated folding temperature with the experimental folding temperature. Optimization run 3 resulted in the best fit of the calculated ensembles to the experimental ones for the tryptophan cage but in much poorer performance on the training set, suggesting that use of a small α-helical protein for extensive force-field calibration resulted in overfitting of the data for this protein at the expense of transferability. The optimized force field resulting from run 2 was found to fold 13 of the 14 tested α-helical proteins and one small α + β protein with the correct topologies; the average structures of 10 of them were predicted with accuracies of about 5 Å C(α) root-mean-square deviation or better. Test simulations with an additional set of 12 α-helical proteins demonstrated that this force field performed better on α-helical proteins than the previous parametrizations of UNRES. The proposed approach is applicable to any problem of maximum-likelihood parameter estimation when the contributions to the maximum-likelihood function cannot be evaluated at the experimental points and the dimension of the configurational space is too high to construct histograms of the experimental distributions.

Nanomaterials for in vivo imaging of mechanical forces and electrical fields

NASA Astrophysics Data System (ADS)

Mehlenbacher, Randy D.; Kolbl, Rea; Lay, Alice; Dionne, Jennifer A.

2018-02-01

Cellular signalling is governed in large part by mechanical forces and electromagnetic fields. Mechanical forces play a critical role in cell differentiation, tissue organization and diseases such as cancer and heart disease; electrical fields are essential for intercellular communication, muscle contraction, neural signalling and sensory perception. Therefore, quantifying a biological system's forces and fields is crucial for understanding physiology and disease pathology and for developing medical tools for repair and recovery. This Review highlights advances in sensing mechanical forces and electrical fields in vivo, focusing on optical probes. The emergence of biocompatible optical probes, such as genetically encoded voltage indicators, molecular rotors, fluorescent dyes, semiconducting nanoparticles, plasmonic nanoparticles and lanthanide-doped upconverting nanoparticles, offers exciting opportunities to push the limits of spatial and temporal resolution, stability, multi-modality and stimuli sensitivity in bioimaging. We further discuss the materials design principles behind these probes and compare them across various metrics to facilitate sensor selection. Finally, we examine which advances are necessary to fully unravel the role of mechanical forces and electrical fields in vivo, such as the ability to probe the vectorial nature of forces, the development of combined force and field sensors, and the design of efficient optical actuators.

Magnetic fields applied to collagen-coated ferric oxide beads induce stretch-activated Ca2+ flux in fibroblasts.

PubMed

Glogauer, M; Ferrier, J; McCulloch, C A

1995-11-01

The ability to apply controlled forces to the cell membrane may enable elucidation of the mechanisms and pathways involved in signal transduction in response to applied physical stimuli. We have developed a magnetic particle-electromagnet model that allows the application of controlled forces to the plasma membrane of substrate-attached fibroblasts. The system allows applied forces to be controlled by the magnitude of the magnetic field and by the surface area of cell membrane covered with collagen-coated ferric beads. Analysis by single-cell ratio fluorimetry of fura 2-loaded cells demonstrated large calcium transients (50-300 nM) in response to the magnetic force applications. Experiments using either the stretch-activated channel blocker gadolinium chloride or ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid to eliminate external calcium ions, or addition of extracellular manganese ions, indicated that there was a calcium influx through putative stretch-activated channels. The probability of a calcium influx in single cells was increased by higher surface bead loading and the degree of cell spreading. Depolymerization of actin filaments by cytochalasin D increased the amplitude of calcium response twofold. The regulation of calcium flux by filamentous actin content and by cell spreading indicates a possible modulatory role for the cytoskeleton in channel sensitivity. Magnetic force application to beads on single cells provides a controlled model to study mechanisms and heterogeneity in physical force stimulation of cation-permeable channels.

KSC-2009-5882

NASA Image and Video Library

2009-10-21

VANDENBERG AIR FORCE BASE, Calif. - At Space Launch Complex 2 at Vandenberg Air Force Base in California, workers receive the first of three solid rocket boosters for the United Launch Alliance Delta II rocket for launch of NASA's Wide-field Infrared Survey Explorer, or WISE, at the pad. WISE will survey the entire sky at infrared wavelengths, creating a cosmic clearinghouse of hundreds of millions of objects which will be catalogued and provide a vast storehouse of knowledge about the solar system, the Milky Way, and the universe. Launch is scheduled for Dec. 7. For additional information, visit http://wise.ssl.berkeley.edu. Photo credit: NASA/VAFB

Numerical Simulation of Ion Transport in a Nano-Electrospray Ion Source at Atmospheric Pressure

NASA Astrophysics Data System (ADS)

Wang, Wei; Bajic, Steve; John, Benzi; Emerson, David R.

2018-03-01

Understanding ion transport properties from the ion source to the mass spectrometer (MS) is essential for optimizing device performance. Numerical simulation helps in understanding of ion transport properties and, furthermore, facilitates instrument design. In contrast to previously reported numerical studies, ion transport simulations in a continuous injection mode whilst considering realistic space-charge effects have been carried out. The flow field was solved using Reynolds-averaged Navier-Stokes (RANS) equations, and a particle-in-cell (PIC) method was applied to solve a time-dependent electric field with local charge density. A series of ion transport simulations were carried out at different cone gas flow rates, ion source currents, and capillary voltages. A force evaluation analysis reveals that the electric force, the drag force, and the Brownian force are the three dominant forces acting on the ions. Both the experimental and simulation results indicate that cone gas flow rates of ≤250 slph (standard liter per hour) are important for high ion transmission efficiency, as higher cone gas flow rates reduce the ion signal significantly. The simulation results also show that the ion transmission efficiency reduces exponentially with an increased ion source current. Additionally, the ion loss due to space-charge effects has been found to be predominant at a higher ion source current, a lower capillary voltage, and a stronger cone gas counterflow. The interaction of the ion driving force, ion opposing force, and ion dispersion is discussed to illustrate ion transport mechanism in the ion source at atmospheric pressure. [Figure not available: see fulltext.

Numerical Simulation of Ion Transport in a Nano-Electrospray Ion Source at Atmospheric Pressure.

PubMed

Wang, Wei; Bajic, Steve; John, Benzi; Emerson, David R

2018-03-01

Understanding ion transport properties from the ion source to the mass spectrometer (MS) is essential for optimizing device performance. Numerical simulation helps in understanding of ion transport properties and, furthermore, facilitates instrument design. In contrast to previously reported numerical studies, ion transport simulations in a continuous injection mode whilst considering realistic space-charge effects have been carried out. The flow field was solved using Reynolds-averaged Navier-Stokes (RANS) equations, and a particle-in-cell (PIC) method was applied to solve a time-dependent electric field with local charge density. A series of ion transport simulations were carried out at different cone gas flow rates, ion source currents, and capillary voltages. A force evaluation analysis reveals that the electric force, the drag force, and the Brownian force are the three dominant forces acting on the ions. Both the experimental and simulation results indicate that cone gas flow rates of ≤250 slph (standard liter per hour) are important for high ion transmission efficiency, as higher cone gas flow rates reduce the ion signal significantly. The simulation results also show that the ion transmission efficiency reduces exponentially with an increased ion source current. Additionally, the ion loss due to space-charge effects has been found to be predominant at a higher ion source current, a lower capillary voltage, and a stronger cone gas counterflow. The interaction of the ion driving force, ion opposing force, and ion dispersion is discussed to illustrate ion transport mechanism in the ion source at atmospheric pressure. Graphical Abstract.

A Guide to Computer Simulations of Three Adaptive Instructional Models for the Advanced Instructional System Phases II and III. Final Report.

ERIC Educational Resources Information Center

Hansen, Duncan N.; And Others

Computer simulations of three individualized adaptive instructional models (AIM) were undertaken to determine if these models function as prescribed in Air Force technical training programs. In addition, the project sought to develop a user's guide for effective understanding of adaptive models during field implementation. Successful simulations…

COMBINED LABORATORY/FIELD STUDY ON THE USE OF NITRATE FOR IN SITU BIOREMEDIATION OF A FUEL-CONTAMINATED AQUIFER

EPA Science Inventory

A pilot demonstration project was conducted at Eglin Air Force Base, FL, to compare the extent of bioremediation of a fuel-contaminated aquifer using sprinkler application with and without nitrate addition on two adjacent 30 m x 30 m cells. Target compound groups included both B...

The Effect of Venue and Wind on the Distance of a Hammer Throw

ERIC Educational Resources Information Center

Hunter, Iain

2005-01-01

In track and field, gravity and air resistance act on the hammer after it has been released. Both of these forces depend on altitude and latitude. In addition, air resistance also depends on wind, temperature, humidity, and barometric pressure. Often, air resistance and varying gravity throughout the earth are not considered when throwing…

Positioning Technology and Engineering Education as a Key Force in STEM Education

ERIC Educational Resources Information Center

Strimel, Greg; Grubbs, Michael E.

2016-01-01

As the presence of engineering content and practices increases in science education, the distinction between the two fields of science and technology education becomes even more vague than previously theorized. Furthermore, the addition of engineering to the title of the profession raises the question of the true aim of technology education. As a…

TET Offensive II Field Force Vietnam After Action Report 31 January - 18 February 1968

DTIC Science & Technology

1968-03-01

and the 5th VC Division. V During this same period of time there were no majur shifts in ARVN forces . However III Corps shifted three...8217-".•: ’ ’SSIFJED U.S. ARMY. VIETNAM. II FIELD FORCE . TET OFFENSIVE II FIELD FORCE VIETNAM AFTER ACTION REPORT, 31 JANUARY-18 FEB- RUARY 1968...H FIELD FORCE VIETNAM AFTER ACTION REPORT 31 January-18 February 1968 RECORD K0- ! FlSjl fi-.-A-,>-•: it tT*\\ : *si h s» -wP Mr-, £< St

Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC

PubMed Central

2017-01-01

We have calculated the excess free energy of mixing of 1053 binary mixtures with the OPLS-AA force field using two different methods: thermodynamic integration (TI) of molecular dynamics simulations and the Pair Configuration to Molecular Activity Coefficient (PAC-MAC) method. PAC-MAC is a force field based quasi-chemical method for predicting miscibility properties of various binary mixtures. The TI calculations yield a root mean squared error (RMSE) compared to experimental data of 0.132 kBT (0.37 kJ/mol). PAC-MAC shows a RMSE of 0.151 kBT with a calculation speed being potentially 1.0 × 104 times greater than TI. OPLS-AA force field parameters are optimized using PAC-MAC based on vapor–liquid equilibrium data, instead of enthalpies of vaporization or densities. The RMSE of PAC-MAC is reduced to 0.099 kBT by optimizing 50 force field parameters. The resulting OPLS-PM force field has a comparable accuracy as the OPLS-AA force field in the calculation of mixing free energies using TI. PMID:28418655

Magnetic moment of solar plasma and the Kelvin force: -The driving force of plasma up-flow -

NASA Astrophysics Data System (ADS)

Shibasaki, Kiyoto

2017-04-01

Thermal plasma in the solar atmosphere is magnetized (diamagnetic). The magnetic moment does not disappear by collisions because complete gyration is not a necessary condition to have magnetic moment. Magnetized fluid is subjected to Kelvin force in non-uniform magnetic field. Generally, magnetic field strength decreases upwards in the solar atmosphere, hence the Kelvin force is directed upwards along the field. This force is not included in the fluid treatment of MHD. By adding the Kelvin force to the MHD equation of motion, we can expect temperature dependent plasma flows along the field which are reported by many observations. The temperature dependence of the flow speed is explained by temperature dependence of magnetic moment. From the observed parameters, we can infer physical parameters in the solar atmosphere such as scale length of the magnetic field strength and the friction force acting on the flowing plasma. In case of closed magnetic field lines, loop-top concentration of hot plasma is expected which is frequently observed.

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

Selvamanickam, V; Chen, Y; Shi, T

The critical current and structural properties of (Gd,Y)BaCuO tapes made by metal organic chemical vapor deposition (MOCVD) with Zr addition levels up to 30 at.% have been investigated. The reduction in critical current beyond the previously optimized Zr addition level of 7.5 at.% was found to be due to structural deterioration of the (Gd,Y)Ba2Cu3Ox film. By a modified MOCVD process,enhanced critical current densities have been achieved with high levels of Zr addition,including 3.83 MA cm(-2) in 15 at.% Zr- added 1.1 mu m thick film at 77 K in zero magnetic field. Critical currents as high as 1072 A/ 12more » mm have been reached in (Gd,Y) BaCuO tapes with 15 at.% Zr addition at 30 K in a field of 3 T applied perpendicular to the tape,corresponding to a pinning force value of 268 GN m(-3). The enhanced critical currents achievable with a high density of nanoscale defects by employing high levels of second- phase additions enable the performance targets needed for the use of HTS tapes in coil applications involving high magnetic fields at temperatures below 50 K to be met.« less

Load estimation from photoelastic fringe patterns under combined normal and shear forces

NASA Astrophysics Data System (ADS)

Dubey, V. N.; Grewal, G. S.

2009-08-01

Recently there has been some spurt of interests to use photoelastic materials for sensing applications. This has been successfully applied for designing a number of signal-based sensors, however, there have been limited efforts to design image-based sensors on photoelasticity which can have wider applications in term of actual loading and visualisation. The main difficulty in achieving this is the infinite loading conditions that may generate same image on the material surface. This, however, can be useful for known loading situations as this can provide dynamic and actual conditions of loading in real time. This is particularly useful for separating components of forces in and out of the loading plane. One such application is the separation of normal and shear forces acting on the plantar surface of foot of diabetic patients for predicting ulceration. In our earlier work we have used neural networks to extract normal force information from the fringe patterns using image intensity. This paper considers geometric and various other statistical parameters in addition to the image intensity to extract normal as well as shear force information from the fringe pattern in a controlled experimental environment. The results of neural network output with the above parameters and their combinations are compared and discussed. The aim is to generalise the technique for a range of loading conditions that can be exploited for whole-field load visualisation and sensing applications in biomedical field.

Polarization: A Key Difference between Man-made and Natural Electromagnetic Fields, in regard to Biological Activity.

PubMed

Panagopoulos, Dimitris J; Johansson, Olle; Carlo, George L

2015-10-12

In the present study we analyze the role of polarization in the biological activity of Electromagnetic Fields (EMFs)/Electromagnetic Radiation (EMR). All types of man-made EMFs/EMR - in contrast to natural EMFs/EMR - are polarized. Polarized EMFs/EMR can have increased biological activity, due to: 1) Ability to produce constructive interference effects and amplify their intensities at many locations. 2) Ability to force all charged/polar molecules and especially free ions within and around all living cells to oscillate on parallel planes and in phase with the applied polarized field. Such ionic forced-oscillations exert additive electrostatic forces on the sensors of cell membrane electro-sensitive ion channels, resulting in their irregular gating and consequent disruption of the cell's electrochemical balance. These features render man-made EMFs/EMR more bioactive than natural non-ionizing EMFs/EMR. This explains the increasing number of biological effects discovered during the past few decades to be induced by man-made EMFs, in contrast to natural EMFs in the terrestrial environment which have always been present throughout evolution, although human exposure to the latter ones is normally of significantly higher intensities/energy and longer durations. Thus, polarization seems to be a trigger that significantly increases the probability for the initiation of biological/health effects.

Polarization: A Key Difference between Man-made and Natural Electromagnetic Fields, in regard to Biological Activity

PubMed Central

Panagopoulos, Dimitris J.; Johansson, Olle; Carlo, George L.

2015-01-01

In the present study we analyze the role of polarization in the biological activity of Electromagnetic Fields (EMFs)/Electromagnetic Radiation (EMR). All types of man-made EMFs/EMR - in contrast to natural EMFs/EMR - are polarized. Polarized EMFs/EMR can have increased biological activity, due to: 1) Ability to produce constructive interference effects and amplify their intensities at many locations. 2) Ability to force all charged/polar molecules and especially free ions within and around all living cells to oscillate on parallel planes and in phase with the applied polarized field. Such ionic forced-oscillations exert additive electrostatic forces on the sensors of cell membrane electro-sensitive ion channels, resulting in their irregular gating and consequent disruption of the cell’s electrochemical balance. These features render man-made EMFs/EMR more bioactive than natural non-ionizing EMFs/EMR. This explains the increasing number of biological effects discovered during the past few decades to be induced by man-made EMFs, in contrast to natural EMFs in the terrestrial environment which have always been present throughout evolution, although human exposure to the latter ones is normally of significantly higher intensities/energy and longer durations. Thus, polarization seems to be a trigger that significantly increases the probability for the initiation of biological/health effects. PMID:26456585

Polarization: A Key Difference between Man-made and Natural Electromagnetic Fields, in regard to Biological Activity

NASA Astrophysics Data System (ADS)

Panagopoulos, Dimitris J.; Johansson, Olle; Carlo, George L.

2015-10-01

In the present study we analyze the role of polarization in the biological activity of Electromagnetic Fields (EMFs)/Electromagnetic Radiation (EMR). All types of man-made EMFs/EMR - in contrast to natural EMFs/EMR - are polarized. Polarized EMFs/EMR can have increased biological activity, due to: 1) Ability to produce constructive interference effects and amplify their intensities at many locations. 2) Ability to force all charged/polar molecules and especially free ions within and around all living cells to oscillate on parallel planes and in phase with the applied polarized field. Such ionic forced-oscillations exert additive electrostatic forces on the sensors of cell membrane electro-sensitive ion channels, resulting in their irregular gating and consequent disruption of the cell’s electrochemical balance. These features render man-made EMFs/EMR more bioactive than natural non-ionizing EMFs/EMR. This explains the increasing number of biological effects discovered during the past few decades to be induced by man-made EMFs, in contrast to natural EMFs in the terrestrial environment which have always been present throughout evolution, although human exposure to the latter ones is normally of significantly higher intensities/energy and longer durations. Thus, polarization seems to be a trigger that significantly increases the probability for the initiation of biological/health effects.

New Force Field Model for Propylene Glycol: Insight to Local Structure and Dynamics.

PubMed

Ferreira, Elisabete S C; Voroshylova, Iuliia V; Koverga, Volodymyr A; Pereira, Carlos M; Cordeiro, M Natália D S

2017-12-07

In this work we developed a new force field model (FFM) for propylene glycol (PG) based on the OPLS all-atom potential. The OPLS potential was refined using quantum chemical calculations, taking into account the densities and self-diffusion coefficients. The validation of this new FFM was carried out based on a wide range of physicochemical properties, such as density, enthalpy of vaporization, self-diffusion coefficients, isothermal compressibility, surface tension, and shear viscosity. The molecular dynamics (MD) simulations were performed over a large range of temperatures (293.15-373.15 K). The comparison with other force field models, such as OPLS, CHARMM27, and GAFF, revealed a large improvement of the results, allowing a better agreement with experimental data. Specific structural properties (radial distribution functions, hydrogen bonding and spatial distribution functions) were then analyzed in order to support the adequacy of the proposed FFM. Pure propylene glycol forms a continuous phase, displaying no microstructures. It is shown that the developed FFM gives rise to suitable results not only for pure propylene glycol but also for mixtures by testing its behavior for a 50 mol % aqueous propylene glycol solution. Furthermore, it is demonstrated that the addition of water to the PG phase produces a homogeneous solution and that the hydration interactions prevail over the propylene glycol self-association interactions.

A Lorentz force actuated magnetic field sensor with capacitive read-out

NASA Astrophysics Data System (ADS)

Stifter, M.; Steiner, H.; Kainz, A.; Keplinger, F.; Hortschitz, W.; Sauter, T.

2013-05-01

We present a novel design of a resonant magnetic field sensor with capacitive read-out permitting wafer level production. The device consists of a single-crystal silicon cantilever manufactured from the device layer of an SOI wafer. Cantilevers represent a very simple structure with respect to manufacturing and function. On the top of the structure, a gold lead carries AC currents that generate alternating Lorentz forces in an external magnetic field. The free end oscillation of the actuated cantilever depends on the eigenfrequencies of the structure. Particularly, the specific design of a U-shaped structure provides a larger force-to-stiffness-ratio than standard cantilevers. The electrodes for detecting cantilever deflections are separately fabricated on a Pyrex glass-wafer. They form the counterpart to the lead on the freely vibrating planar structure. Both wafers are mounted on top of each other. A custom SU-8 bonding process on wafer level creates a gap which defines the equilibrium distance between sensing electrodes and the vibrating structure. Additionally to the capacitive read-out, the cantilever oscillation was simultaneously measured with laser Doppler vibrometry through proper windows in the SOI handle wafer. Advantages and disadvantages of the asynchronous capacitive measurement configuration are discussed quantitatively and presented by a comprehensive experimental characterization of the device under test.

Calculations of the free energy of interaction of the c-Fos-c-Jun coiled coil: effects of the solvation model and the inclusion of polarization effects.

PubMed

Zuo, Zhili; Gandhi, Neha S; Mancera, Ricardo L

2010-12-27

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein-protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson-Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos-c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos-c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Using polarizable POSSIM force field and fuzzy-border continuum solvent model to calculate pK(a) shifts of protein residues.

PubMed

Sharma, Ity; Kaminski, George A

2017-01-15

Our Fuzzy-Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second-order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol. It was then used to compute pK a shifts for carboxylic and basic residues of the turkey ovomucoid third domain (OMTKY3) protein. The average unsigned errors in the acid and base pK a values were 0.37 and 0.4 pH units, respectively, versus 0.58 and 0.7 pH units as calculated with a previous version of polarizable protein force field and Poisson Boltzmann continuum solvent. This POSSIM/FB result is produced with explicit refitting of the hydration parameters to the pK a values of the carboxylic and basic residues of the OMTKY3 protein; thus, the values of the acidity constants can be viewed as additional fitting target data. In addition to calculating pK a shifts for the OMTKY3 residues, we have studied aspartic acid residues of Rnase Sa. This was done without any further refitting of the parameters and agreement with the experimental pK a values is within an average unsigned error of 0.65 pH units. This result included the Asp79 residue that is buried and thus has a high experimental pK a value of 7.37 units. Thus, the presented model is capable or reproducing pK a results for residues in an environment that is significantly different from the solvated protein surface used in the fitting. Therefore, the POSSIM force field and the FB continuum solvent parameters have been demonstrated to be sufficiently robust and transferable. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Modeling the hydration of mono-atomic anions from the gas phase to the bulk phase: the case of the halide ions F-, Cl-, and Br-.

PubMed

Trumm, Michael; Martínez, Yansel Omar Guerrero; Réal, Florent; Masella, Michel; Vallet, Valérie; Schimmelpfennig, Bernd

2012-01-28

In this work, we investigate the hydration of the halide ions fluoride, chloride, and bromide using classical molecular dynamics simulations at the 10 ns scale and based on a polarizable force-field approach, which treats explicitly the cooperative bond character of strong hydrogen bond networks. We have carried out a thorough analysis of the ab initio data at the MP2 or CCSD(T) level concerning anion/water clusters in gas phase to adjust the force-field parameters. In particular, we consider the anion static polarizabilities computed in gas phase using large atomic basis sets including additional diffuse functions. The information extracted from trajectories in solution shows well structured first hydration shells formed of 6.7, 7.0, and 7.6 water molecules at about 2.78 Å, 3.15 Å, and 3.36 Å for fluoride, chloride, and bromide, respectively. These results are in excellent agreement with the latest neutron- and x-ray diffraction studies. In addition, our model reproduces several other properties of halide ions in solution, such as diffusion coefficients, description of hydration processes, and exchange reactions. Moreover, it is also able to reproduce the electrostatic properties of the anions in solution (in terms of anion dipole moment) as reported by recent ab initio quantum simulations. All the results show the ability of the proposed model in predicting data, as well as the need of accounting explicitly for the cooperative character of strong hydrogen bonds to reproduce ab initio potential energy surfaces in a mean square sense and to build up a reliable force field. © 2012 American Institute of Physics

Modeling the benefits of an artificial gravity countermeasure coupled with exercise and vibration

NASA Astrophysics Data System (ADS)

Goel, Rahul; Kaderka, Justin; Newman, Dava

2012-01-01

The current, system-specific countermeasures to space deconditioning have limited success with the musculoskeletal system in long duration missions. Artificial gravity (AG) that is produced by short radius centrifugation has been hypothesized as an effective countermeasure because it reintroduces an acceleration field in space; however, AG alone might not be enough stimuli to preserve the musculoskeletal system. A novel combination of AG coupled with one-legged squats on a vibrating platform may preserve muscle and bone in the lower limbs to a greater extent than the current exercise paradigm. The benefits of the proposed countermeasure have been analyzed through the development of a simulation platform. Ground reaction force data and motion data were collected using a motion capture system while performing one-legged and two-legged squats in 1-G. The motion was modeled in OpenSim, an open-source software, and inverse dynamics were applied in order to determine the muscle and reaction forces of lower limb joints. Vibration stimulus was modeled by adding a 20 Hz sinusoidal force of 0.5 body weight to the force plate data. From the numerical model in a 1-G acceleration field, muscle forces for quadriceps femoris, plantar flexors and glutei increased substantially for one-legged squats with vibration compared to one- or two-legged squats without vibration. Additionally, joint reaction forces for one-legged squats with vibration also increased significantly compared to two-legged squats with or without vibration. Higher muscle forces and joint reaction forces might help to stimulate muscle activation and bone modeling and thus might reduce musculoskeletal deconditioning. These results indicate that the proposed countermeasure might surpass the performance of the current space countermeasures and should be further studied as a method of mitigating musculoskeletal deconditioning.

Enhanced settling of nonheavy inertial particles in homogeneous isotropic turbulence: The role of the pressure gradient and the Basset history force.

PubMed

van Hinsberg, M A T; Clercx, H J H; Toschi, F

2017-02-01

The Stokes drag force and the gravity force are usually sufficient to describe the behavior of sub-Kolmogorov-size (or pointlike) heavy particles in turbulence, in particular when the particle-to-fluid density ratio ρ_{p}/ρ_{f}≳10^{3} (with ρ_{p} and ρ_{f} the particle and fluid density, respectively). This is, in general, not the case for smaller particle-to-fluid density ratios, in particular not for ρ_{p}/ρ_{f}≲10^{2}. In that case the pressure gradient force, added mass effects, and the Basset history force also play important roles. In this study we focus on the understanding of the role of these additional forces, all of hydrodynamic origin, in the settling of particles in turbulence. In order to qualitatively elucidate the complex dynamics of such particles in homogeneous isotropic turbulence, we first focus on the case of settling of such particles in the flow field of a single vortex. After having explored this simplified case we extend our analysis to homogeneous isotropic turbulence. In general, we found that the pressure gradient force leads to a decrease in the settling velocity. This can be qualitatively understood by the fact that this force prevents the particles from sweeping out of vortices, a mechanism known as preferential sweeping which causes enhanced settling. Additionally, we found that the Basset history force can both increase and decrease the enhanced settling, depending on the particle Stokes number. Finally, the role of the nonlinear Stokes drag has been explored, confirming that it affects settling of inertial particles in turbulence, but only in a limited way for the parameter settings used in this investigation.

Communication: Multiple atomistic force fields in a single enhanced sampling simulation

NASA Astrophysics Data System (ADS)

Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H.

2015-07-01

The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

Floating electrode dielectrophoresis.

PubMed

Golan, Saar; Elata, David; Orenstein, Meir; Dinnar, Uri

2006-12-01

In practice, dielectrophoresis (DEP) devices are based on micropatterned electrodes. When subjected to applied voltages, the electrodes generate nonuniform electric fields that are necessary for the DEP manipulation of particles. In this study, electrically floating electrodes are used in DEP devices. It is demonstrated that effective DEP forces can be achieved by using floating electrodes. Additionally, DEP forces generated by floating electrodes are different from DEP forces generated by excited electrodes. The floating electrodes' capabilities are explained theoretically by calculating the electric field gradients and demonstrated experimentally by using test-devices. The test-devices show that floating electrodes can be used to collect erythrocytes (red blood cells). DEP devices which contain many floating electrodes ought to have fewer connections to external signal sources. Therefore, the use of floating electrodes may considerably facilitate the fabrication and operation of DEP devices. It can also reduce device dimensions. However, the key point is that DEP devices can integrate excited electrodes fabricated by microtechnology processes and floating electrodes fabricated by nanotechnology processes. Such integration is expected to promote the use of DEP devices in the manipulation of nanoparticles.

The Maximum Levitation Force of High- T c Superconductors

NASA Astrophysics Data System (ADS)

Zhao, Xian-Feng; Liu, Yuan

2007-11-01

In this paper we present the dependence of the maximum levitation force ( F {/z max }) of a high- T c superconductor (HTS) on the structural factors of high- T c superconducting systems based on the Bean critical state model and Ampère’s law. A transition point of the surface magnetic field ( B s ) of a permanent magnet (PM) is found at which the relation between F {/z max } and B s changes: while the surface magnetic field is less than the transition value the dependence is subject to a nonlinear function, otherwise it is a linear one. The two different relations are estimated to correspond to partial penetration of the shielding currents inside the superconductor below the transition point and complete penetration above it respectively. The influence of geometric properties of superconductors on the dependence is also investigated. In addition, the relation between F {/z max } and the critical current density ( J c ) of the HTS is discussed. The maximum levitation force saturates at high J c . An optimum function of the J c and the B s is presented in order to achieve large F {/z max }.

Mixed convection of magnetohydrodynamic nanofluids inside microtubes at constant wall temperature

NASA Astrophysics Data System (ADS)

Moshizi, S. A.; Zamani, M.; Hosseini, S. J.; Malvandi, A.

2017-05-01

Laminar fully developed mixed convection of magnetohydrodynamic nanofluids inside microtubes at a constant wall temperature (CWT) under the effects of a variable directional magnetic field is investigated numerically. Nanoparticles are assumed to have slip velocities relative to the base fluid owing to thermophoretic diffusion (temperature gradient driven force) and Brownian diffusion (concentration gradient driven force). The no-slip boundary condition is avoided at the fluid-solid mixture to assess the non-equilibrium region at the fluid-solid interface. A scale analysis is performed to estimate the relative significance of the pertaining parameters that should be included in the governing equations. After the effects of pertinent parameters on the pressure loss and heat transfer enhancement were considered, the figure of merit (FoM) is employed to evaluate and optimize the thermal performance of heat exchange equipment. The results indicate the optimum thermal performance is obtained when the thermophoresis overwhelms the Brownian diffusion, which is for larger nanoparticles. This enhancement boosts when the buoyancy force increases. In addition, increasing the magnetic field strength and slippage at the fluid-solid interface enhances the thermal performance.

A detailed analysis of open-field habituation and behavioral and neurochemical antidepressant-like effects in postweaning enriched rats.

PubMed

Brenes, Juan C; Padilla, Michael; Fornaguera, Jaime

2009-01-30

Our previous work has shown that male Sprague-Dawley rats reared in social isolation, standard housing and environmental enrichment differ in their spontaneous open-field activity and in some neurobehavioral depressive-like parameters. Here, we extended this evidence by using a shorter postweaning rearing period (1 month) and including additional evaluations. First, in order to obtain a better characterization of the exploratory strategies among rearing conditions we analyzed in detail the spontaneous activity at the first minute and during the 10-min session. Second, we asked whether the changes in open-field activity were related with basal anxiety levels in the elevated plus-maze. Third, behavior in the forced-swimming test was analyzed and afterward, the tissue levels of hippocampal norepinephrine and serotonin were assessed. The possible relationship between neurotransmitters and forced-swimming behavior were explored through correlation analyses. We found that rearing conditions (i) differed on locomotor habituation and on sensory-motor exploration at the first minute and during the 10-min session without modifying the plus-maze behavior; (ii) affected differentially the grooming time, its sequential components, and the relationship between grooming and locomotor parameters; (iii) modified forced-swimming behavior and the hippocampal concentration of norepinephrine, serotonin, and its turnover; and (iv) produced different correlation patterns between both neurotransmitters and forced-swimming behaviors. Overall, environmental enrichment accelerated open-field habituation and led to behavioral and neurochemical antidepressant-like effects. In contract, isolation rearing strongly impaired habituation and simple information processing, but showed marginal effects on depressive-like behavior and on hippocampal neurochemistry. The current results suggest that differential rearing is not only a useful procedure to study behavioral plasticity or rigidity in response to early experience, but also to modeling some developmental protective or risk factors underlying depressive disorders.

Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations

NASA Astrophysics Data System (ADS)

Yang, Zaixing; Wang, Zhigang; Tian, Xingling; Xiu, Peng; Zhou, Ruhong

2012-01-01

Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

Amino acid analogues bind to carbon nanotube via π-π interactions: comparison of molecular mechanical and quantum mechanical calculations.

PubMed

Yang, Zaixing; Wang, Zhigang; Tian, Xingling; Xiu, Peng; Zhou, Ruhong

2012-01-14

Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

Neutral Atom Diffusion in a Partially Ionized Prominence Plasma

NASA Technical Reports Server (NTRS)

Gilbert, Holly

2010-01-01

The support of solar prominences is normally described in terms of a magnetic force on the prominence plasma that balances the solar gravitational force. Because the prominence plasma is only partially ionized. it is necessary to consider in addition the support of the neutral component of the prominence plasma. This support is accomplished through a frictional interaction between the neutral and ionized components of the plasma, and its efficacy depends strongly on the degree of ionization of the plasma. More specifically, the frictional force is proportional to the relative flow of neutral and ion species, and for a sufficiently weakly ionized plasma, this flow must be relatively large to produce a frictional force that balances gravity. A large relative flow, of course, implies significant draining of neutral particles from the prominence. We evaluate the importance of this draining effect for a hydrogen-helium plasma, and consider the observational evidence for cross-field diffusion of neutral prominence material,

A space-frequency multiplicative regularization for force reconstruction problems

NASA Astrophysics Data System (ADS)

Aucejo, M.; De Smet, O.

2018-05-01

Dynamic forces reconstruction from vibration data is an ill-posed inverse problem. A standard approach to stabilize the reconstruction consists in using some prior information on the quantities to identify. This is generally done by including in the formulation of the inverse problem a regularization term as an additive or a multiplicative constraint. In the present article, a space-frequency multiplicative regularization is developed to identify mechanical forces acting on a structure. The proposed regularization strategy takes advantage of one's prior knowledge of the nature and the location of excitation sources, as well as that of their spectral contents. Furthermore, it has the merit to be free from the preliminary definition of any regularization parameter. The validity of the proposed regularization procedure is assessed numerically and experimentally. It is more particularly pointed out that properly exploiting the space-frequency characteristics of the excitation field to identify can improve the quality of the force reconstruction.

Models And Experiments Of Laminar Diffusion Flames In Non-Uniform Magnetic Fields

NASA Technical Reports Server (NTRS)

Baker, J.; Varagani, R.; Saito, K.

2003-01-01

Non-uniform magnetic fields affect laminar diffusion flames as a result of the paramagnetic and diamagnetic properties of the products and reactants. Paramagnetism is the weak attraction to a magnetic field a material exhibits as a result of permanent magnetic dipole moments in the atoms of the material. Diamagnetism is the weak repulsion to a magnetic field exhibited by a material due to the lack of permanent magnetic dipole moments in the atoms of a material. The forces associated with paramagnetic and diamagnetism are several orders of magnitude less than the forces associated with the more familiar ferromagnetism. A typical example of a paramagnetic gas is oxygen while hydrocarbon fuels and products of combustion are almost always diamagnetic. The fact that magnets can affect flame behavior has been recognized for more than one hundred years. Early speculation was that such behavior was due to the magnetic interaction with the ionized gases associated with a flame. Using a scaling analysis, it was later shown that for laminar diffusion flames the magnetic field/ionized gas interaction was insignificant to the paramagnetic and diamagnetic influences. In this effort, the focus has been on examining laminar diffusion slot flames in the presence of non-uniform upward decreasing magnetic fields produced using permanent magnets. The principal reason for choosing slot flames was mathematical models of such flames show an explicit dependence on gravitational body forces, in the buoyancy-controlled regime, and an applied magnetic field would also impose a body force. In addition, the behavior of such flames was more easily visualized while maintaining the symmetry of the two-dimensional problem whereas it would have been impossible to obtain a symmetric magnetic field around a circular flame and still visually record the flame height and shape along the burner axis. The motivation for choosing permanent magnets to produce the magnetic fields was the assumption that space-related technologies based on the knowledge gained during this investigation would more likely involve permanent magnets as opposed to electromagnets. While no analysis has been done here to quantify the impact that an electric field, associated with an electromagnetic, would have relative to the paramagnetic and diamagnetic interactions, by using permanent magnets this potential effect was completely eliminated and thus paramagnetic and diamagnetic effects were isolated.

Novel strategies in feedforward adaptation to a position-dependent perturbation.

PubMed

Hinder, Mark R; Milner, Theodore E

2005-08-01

To investigate the control mechanisms used in adapting to position-dependent forces, subjects performed 150 horizontal reaching movements over 25 cm in the presence of a position-dependent parabolic force field (PF). The PF acted only over the first 10 cm of the movement. On every fifth trial, a virtual mechanical guide (double wall) constrained subjects to move along a straight-line path between the start and target positions. Its purpose was to register lateral force to track formation of an internal model of the force field, and to look for evidence of possible alternative adaptive strategies. The force field produced a force to the right, which initially caused subjects to deviate in that direction. They reacted by producing deviations to the left, "into" the force field, as early as the second trial. Further adaptation resulted in rapid exponential reduction of kinematic error in the latter portion of the movement, where the greatest perturbation to the handpath was initially observed, whereas there was little modification of the handpath in the region where the PF was active. Significant force directed to counteract the PF was measured on the first guided trial, and was modified during the first half of the learning set. The total force impulse in the region of the PF increased throughout the learning trials, but it always remained less than that produced by the PF. The force profile did not resemble a mirror image of the PF in that it tended to be more trapezoidal than parabolic in shape. As in previous studies of force-field adaptation, we found that changes in muscle activation involved a general increase in the activity of all muscles, which increased arm stiffness, and selectively-greater increases in the activation of muscles which counteracted the PF. With training, activation was exponentially reduced, albeit more slowly than kinematic error. Progressive changes in kinematics and EMG occurred predominantly in the region of the workspace beyond the force field. We suggest that constraints on muscle mechanics limit the ability of the central nervous system to employ an inverse dynamics model to nullify impulse-like forces by generating mirror-image forces. Consequently, subjects adopted a strategy of slightly overcompensating for the first half of the force field, then allowing the force field to push them in the opposite direction. Muscle activity patterns in the region beyond the boundary of the force field were subsequently adjusted because of the relatively-slow response of the second-order mechanics of muscle impedance to the force impulse.

On the theory of the relativistic motion of a charged particle in the field of intense electromagnetic radiation

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

Milant'ev, V. P., E-mail: vmilantiev@sci.pfu.edu.ru; Castillo, A. J., E-mail: vmilant@mail.ru

2013-04-15

Averaged relativistic equations of motion of a charged particle in the field of intense electromagnetic radiation have been obtained in the geometrical optics approximation using the Bogoliubov method. Constraints are determined under which these equations are valid. Oscillating additions to the smoothed dynamical variables of the particle have been found; they are reduced to known expressions in the case of the circularly and linearly polarized plane waves. It has been shown that the expressions for the averaged relativistic force in both cases contain new additional small terms weakening its action. The known difference between the expressions for the ponderomotive forcemore » in the cases of circularly and linearly polarized waves has been confirmed.« less

Imaging the magnetic nanodomains in Nd 2 Fe 14 B

DOE PAGES

Huang, Lunan; Taufour, Valentin; Lamichhane, T. N.; ...

2016-03-08

Here, we study magnetic domains in Nd 2Fe 14B single crystals using high resolution magnetic force microscopy (MFM). Previous MFM studies and small angle neutron scattering experiments suggested the presence of nanoscale domains in addition to optically detected micrometer-scale ones. We find, in addition to the elongated, wavy nanodomains reported by a previous MFM study, that the micrometer-sized, star-shaped fractal pattern is constructed of an elongated network of nanodomains ~20 nm in width, with resolution-limited domain walls thinner than 2 nm. While the microscopic domains exhibit significant resilience to an external magnetic field, some of the nanodomains are sensitive tomore » the magnetic field of the MFM tip.« less

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

PubMed

Lemkul, Justin A; MacKerell, Alexander D

2017-05-09

Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.

How accurately do force fields represent protein side chain ensembles?

PubMed

Petrović, Dušan; Wang, Xue; Strodel, Birgit

2018-05-23

Although the protein backbone is the most fundamental part of the structure, the fine-tuning of side-chain conformations is important for protein function, for example, in protein-protein and protein-ligand interactions, and also in enzyme catalysis. While several benchmarks testing the performance of protein force fields for side chain properties have already been published, they often considered only a few force fields and were not tested against the same experimental observables; hence, they are not directly comparable. In this work, we explore the ability of twelve force fields, which are different flavors of AMBER, CHARMM, OPLS, or GROMOS, to reproduce average rotamer angles and rotamer populations obtained from extensive NMR studies of the 3 J and residual dipolar coupling constants for two small proteins: ubiquitin and GB3. Based on a total of 196 μs sampling time, our results reveal that all force fields identify the correct side chain angles, while the AMBER and CHARMM force fields clearly outperform the OPLS and GROMOS force fields in estimating rotamer populations. The three best force fields for representing the protein side chain dynamics are AMBER 14SB, AMBER 99SB*-ILDN, and CHARMM36. Furthermore, we observe that the side chain ensembles of buried amino acid residues are generally more accurately represented than those of the surface exposed residues. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

PubMed

Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

2011-07-01

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

Nonlinear Force-free Coronal Magnetic Stereoscopy

NASA Astrophysics Data System (ADS)

Chifu, Iulia; Wiegelmann, Thomas; Inhester, Bernd

2017-03-01

Insights into the 3D structure of the solar coronal magnetic field have been obtained in the past by two completely different approaches. The first approach are nonlinear force-free field (NLFFF) extrapolations, which use photospheric vector magnetograms as boundary condition. The second approach uses stereoscopy of coronal magnetic loops observed in EUV coronal images from different vantage points. Both approaches have their strengths and weaknesses. Extrapolation methods are sensitive to noise and inconsistencies in the boundary data, and the accuracy of stereoscopy is affected by the ability of identifying the same structure in different images and by the separation angle between the view directions. As a consequence, for the same observational data, the 3D coronal magnetic fields computed with the two methods do not necessarily coincide. In an earlier work (Paper I) we extended our NLFFF optimization code by including stereoscopic constrains. The method was successfully tested with synthetic data, and within this work, we apply the newly developed code to a combined data set from SDO/HMI, SDO/AIA, and the two STEREO spacecraft. The extended method (called S-NLFFF) contains an additional term that monitors and minimizes the angle between the local magnetic field direction and the orientation of the 3D coronal loops reconstructed by stereoscopy. We find that when we prescribe the shape of the 3D stereoscopically reconstructed loops, the S-NLFFF method leads to a much better agreement between the modeled field and the stereoscopically reconstructed loops. We also find an appreciable decrease by a factor of two in the angle between the current and the magnetic field. This indicates the improved quality of the force-free solution obtained by S-NLFFF.

Magnetic induction constraints on electrical conductivity within Europa

NASA Astrophysics Data System (ADS)

Bills, B. G.; Vance, S.

2017-12-01

We examine the problem of inferring radial variations in electrical conductivity within Europa, from measurements of the magnetic field induced within Europa by its motion through Jupiter's magnetic field. The Europa Clipper mission is expected to make multiple encounters with Europa, sampling several periods at which significant magnetic induction forcing occurs. Most previous analyses have considered a simple 3-layer model of Europa's internal structure, with an insulating core, a uniform conductivity ocean, and an insulating ice shell, and have only examined responses at 2 forcing periods. We attempt to address the broader issues of what level of detail can be inferred from plausible estimates of induced field response at several additional forcing periods. We will present results of an analysis of the periods and amplitudes of magnetic field variations at Europa, and at the Europa Clipper spacecraft. It appears likely that useful information on the induction response will be attained at 6 forcing frequencies, spanning the interval from 1 to just over 15 cycles per orbital period, in Europa's motion about Jupiter. The range of periods is 5.6 to 85 hours. The induced field diffuses into the interior, and signals at longer periods penetrate more deeply. Having measurements at a range of forcing periods thus helps resolve radial structure. Even if the ocean is well mixed and has uniform salinity, there will be some depth-dependent variations in electrical conductivity due to temperature and pressure variations. Much larger variations would be present if the ocean were stably stratified, with a denser brine underlying a fresher upper layer. While vigorous convection within the ocean would likely mix and homogenize the water column, a stratified ocean is at least possible. Could such a feature of the ocean be detected via magnetic induction? Also, the conductivities in the ice shell above, and silicate layer beneath the ocean are expected to be substantially smaller than in a salty ocean. However, they are not zero. We will consider the extent to which these regions might also be interrogated via magnetic induction.

Acute reversible inactivation of the bed nucleus of stria terminalis induces antidepressant-like effect in the rat forced swimming test

PubMed Central

2010-01-01

Background The bed nucleus of stria terminalis (BNST) is a limbic forebrain structure involved in hypothalamo-pituitary-adrenal axis regulation and stress adaptation. Inappropriate adaptation to stress is thought to compromise the organism's coping mechanisms, which have been implicated in the neurobiology of depression. However, the studies aimed at investigating BNST involvement in depression pathophysiology have yielded contradictory results. Therefore, the objective of the present study was to investigate the effects of temporary acute inactivation of synaptic transmission in the BNST by local microinjection of cobalt chloride (CoCl2) in rats subjected to the forced swimming test (FST). Methods Rats implanted with cannulae aimed at the BNST were submitted to 15 min of forced swimming (pretest). Twenty-four hours later immobility time was registered in a new 5 min forced swimming session (test). Independent groups of rats received bilateral microinjections of CoCl2 (1 mM/100 nL) before or immediately after pretest or before the test session. Additional groups received the same treatment and were submitted to the open field test to control for unspecific effects on locomotor behavior. Results CoCl2 injection into the BNST before either the pretest or test sessions reduced immobility in the FST, suggesting an antidepressant-like effect. No significant effect of CoCl2 was observed when it was injected into the BNST immediately after pretest. In addition, no effect of BNST inactivation was observed in the open field test. Conclusion These results suggest that acute reversible inactivation of synaptic transmission in the BNST facilitates adaptation to stress and induces antidepressant-like effects. PMID:20515458

Enhanced critical currents in (Gd,Y)Ba2Cu3Ox superconducting tapes with high levels of Zr addition

NASA Astrophysics Data System (ADS)

Selvamanickam, V.; Chen, Y.; Shi, T.; Liu, Y.; Khatri, N. D.; Liu, J.; Yao, Y.; Xiong, X.; Lei, C.; Soloveichik, S.; Galstyan, E.; Majkic, G.

2013-03-01

The critical current and structural properties of (Gd,Y)BaCuO tapes made by metal organic chemical vapor deposition (MOCVD) with Zr addition levels up to 30 at.% have been investigated. The reduction in critical current beyond the previously optimized Zr addition level of 7.5 at.% was found to be due to structural deterioration of the (Gd,Y)Ba2Cu3Ox film. By a modified MOCVD process, enhanced critical current densities have been achieved with high levels of Zr addition, including 3.83 MA cm-2 in 15 at.% Zr-added 1.1 μm thick film at 77 K in zero magnetic field. Critical currents as high as 1072 A/12 mm have been reached in (Gd,Y)BaCuO tapes with 15 at.% Zr addition at 30 K in a field of 3 T applied perpendicular to the tape, corresponding to a pinning force value of 268 GN m-3. The enhanced critical currents achievable with a high density of nanoscale defects by employing high levels of second-phase additions enable the performance targets needed for the use of HTS tapes in coil applications involving high magnetic fields at temperatures below 50 K to be met.

Modelling the effects of the radiation reaction force on the interaction of thin foils with ultra-intense laser fields

NASA Astrophysics Data System (ADS)

Duff, M. J.; Capdessus, R.; Del Sorbo, D.; Ridgers, C. P.; King, M.; McKenna, P.

2018-06-01

The effects of the radiation reaction (RR) force on thin foils undergoing radiation pressure acceleration (RPA) are investigated. Using QED-particle-in-cell simulations, the influence of the RR force on the collective electron dynamics within the target can be examined. The magnitude of the RR force is found to be strongly dependent on the target thickness, leading to effects which can be observed on a macroscopic scale, such as changes to the distribution of the emitted radiation and the target dynamics. This suggests that such parameters may be controlled in experiments at multi-PW laser facilities. In addition, the effects of the RR force are characterized in terms of an average radiation emission angle. We present an analytical model which, for the first time, describes the effect of the RR force on the collective electron dynamics within the ‘light-sail’ regime of RPA. The predictions of this model can be tested in future experiments with ultra-high intensity lasers interacting with solid targets.

Developing a molecular dynamics force field for both folded and disordered protein states.

PubMed

Robustelli, Paul; Piana, Stefano; Shaw, David E

2018-05-07

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB- disp , should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields. Copyright © 2018 the Author(s). Published by PNAS.

Improved side-chain torsion potentials for the Amber ff99SB protein force field

PubMed Central

Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L; Dror, Ron O; Shaw, David E

2010-01-01

Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data. Proteins 2010. © 2010 Wiley-Liss, Inc. PMID:20408171

All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.

PubMed

Arnautova, Yelena A; Abagyan, Ruben; Totrov, Maxim

2015-05-12

We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N -acetylglucosamine, N -acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran-cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1-12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide-monosaccharide and protein-glycan linkages are derived from the extensive analysis of conformational properties of glycoprotein structures reported in the Protein Data Bank. Use of the BPMC search leads to significant improvements in sampling efficiency for glycan simulations. Moreover, good agreement with the X-ray glycoprotein structures is achieved for all glycan chain lengths. Thus, average/median RMSDs are 0.81/0.68 Å for one-residue glycans and 1.32/1.47 Å for three-residue glycans. RMSD from the native structure for the lowest-energy conformation of the 12-residue glycan chain (PDB ID 3og2) is 1.53 Å. Additionally, results obtained for free short oligosaccharides using the new force field are in line with the available experimental data, i.e., the most populated conformations in solution are predicted to be the lowest energy ones. The newly developed parameters allow for the accurate modeling of linear and branched hexopyranose glycosides in heterogeneous systems.

Electron diamagnetic effect in a magnetic nozzle on a helicon plasma thruster performance

NASA Astrophysics Data System (ADS)

Takahashi, Kazunori; Lafleur, Trevor; Charles, Christine; Alexander, Peter; Boswell, Rod

2012-10-01

The axial force, which is called thrust sometimes, imparted from a magnetically expanding helicon plasma thruster is directly measured and the results are compared with a two-dimensional fluid theory. The force component solely transmitted to the expanding field is directly measured and identified as an axial force produced by the azimuthal current due to an electron diamagnetic drift and the radial component of the applied magnetic field. In this type of configuration, plasma diffusion in magnetic field affects a spatial profile of the plasma density and the resultant axial force onto the magnetic field. It is observed that the force component onto the magnetic field increases with an increase in the magnetic field strength, simultaneously with an increase in the plasma density downstream of the source exit, which could be due to suppression of the cross field diffusion in the magnetic nozzle.

Three-Dimensional Measurement of the Helicity-Dependent Forces on a Mie Particle.

PubMed

Liu, Lulu; Di Donato, Andrea; Ginis, Vincent; Kheifets, Simon; Amirzhan, Arman; Capasso, Federico

2018-06-01

Recently, it was shown that a Mie particle in an evanescent field ought to experience optical forces that depend on the helicity of the totally internally reflected beam. As yet, a direct measurement of such helicity-dependent forces has been elusive, as the widely differing force magnitudes in the three spatial dimensions place stringent demands on a measurement's sensitivity and range. In this study, we report the simultaneous measurement of all components of this polarization-dependent optical force by using a 3D force spectroscopy technique with femtonewton sensitivity. The vector force fields are compared quantitatively with our theoretical calculations as the polarization state of the incident light is varied and show excellent agreement. By plotting the 3D motion of the Mie particle in response to the switched force field, we offer visual evidence of the effect of spin momentum on the Poynting vector of an evanescent optical field.

Three-Dimensional Measurement of the Helicity-Dependent Forces on a Mie Particle

NASA Astrophysics Data System (ADS)

Liu, Lulu; Di Donato, Andrea; Ginis, Vincent; Kheifets, Simon; Amirzhan, Arman; Capasso, Federico

2018-06-01

Recently, it was shown that a Mie particle in an evanescent field ought to experience optical forces that depend on the helicity of the totally internally reflected beam. As yet, a direct measurement of such helicity-dependent forces has been elusive, as the widely differing force magnitudes in the three spatial dimensions place stringent demands on a measurement's sensitivity and range. In this study, we report the simultaneous measurement of all components of this polarization-dependent optical force by using a 3D force spectroscopy technique with femtonewton sensitivity. The vector force fields are compared quantitatively with our theoretical calculations as the polarization state of the incident light is varied and show excellent agreement. By plotting the 3D motion of the Mie particle in response to the switched force field, we offer visual evidence of the effect of spin momentum on the Poynting vector of an evanescent optical field.

Force fields for describing the solution-phase synthesis of shape-selective metal nanoparticles

NASA Astrophysics Data System (ADS)

Zhou, Ya; Al-Saidi, Wissam; Fichthorn, Kristen

2013-03-01

Polyvinylpyrrolidone (PVP) and polyethylene oxide (PEO) are structure-directing agents that exhibit different performance in the polyol synthesis of Ag nanostructures. The success of these structure-directing agents in selective nanostructure synthesis is often attributed to their selective binding to Ag(100) facets. We use first-principles, density-functional theory (DFT) calculations in a vacuum environment to show that PVP has a stronger preference to bind to Ag(100) than to Ag(111), whereas PEO exhibits much weaker selectivity. To understand the role of solvent in the surface-sensitive binding, we develop classical force fields to describe the interactions of the structure-directing (PVP and PEO) and solvent (ethylene glycol) molecules with various Ag substrates. We parameterize the force fields through force-and-energy matching to DFT results using simulated annealing. We validate the force fields by comparisons to DFT and experimental binding energies. Our force fields reproduce the surface-sensitive binding predicted by DFT calculations. Molecular dynamics simulations based on these force fields can be used to reveal the role of solvent, polymer chain length, and polymer concentration in the selective synthesis of Ag nanostructures.

Magnetodynamic stability of a fluid cylinder under the Lundquist force-free magnetic field

NASA Astrophysics Data System (ADS)

Radwan, Ahmed E.; Halawa, Mohamed A.

1990-04-01

The magnetodynamic (in)stability of a conducting fluid cylinder subject to the capillarity and electromagnetic forces has been developed. The cylinder is pervaded by a uniform magnetic field but embedded in the Lundquist force-free varying field that allows for flowing a current surrounding the fluid. A general eigenvalue relation is derived based on a study of the equilibrium and perturbed states. The stability criterion is discussed analytically in general terms. The surface tension is destabilizing for small axisymmetric mode and stable for all others. The principle of the exchange of stability is allowed for the present problem due to the non-uniform behavior of the force-free field. Each of the axial and transverse force-free fields separately exerts a stabilizing influence in the most dangerous mode but the combined contribution of them is strongly destabilizing. Whether the model is acted upon the electromagnetic force (with the Lundquist field) the stability restrictions or/and the capillarity force are identified. Several reported works can be recovered as limiting cases with appropriate simplifications.

Demonstration of a positron beam-driven hollow channel plasma wakefield accelerator

NASA Astrophysics Data System (ADS)

Gessner, Spencer; Adli, Erik; Allen, James M.; An, Weiming; Clarke, Christine I.; Clayton, Chris E.; Corde, Sebastien; Delahaye, J. P.; Frederico, Joel; Green, Selina Z.; Hast, Carsten; Hogan, Mark J.; Joshi, Chan; Lindstrøm, Carl A.; Lipkowitz, Nate; Litos, Michael; Lu, Wei; Marsh, Kenneth A.; Mori, Warren B.; O'Shea, Brendan; Vafaei-Najafabadi, Navid; Walz, Dieter; Yakimenko, Vitaly; Yocky, Gerald

2016-06-01

Plasma wakefield accelerators have been used to accelerate electron and positron particle beams with gradients that are orders of magnitude larger than those achieved in conventional accelerators. In addition to being accelerated by the plasma wakefield, the beam particles also experience strong transverse forces that may disrupt the beam quality. Hollow plasma channels have been proposed as a technique for generating accelerating fields without transverse forces. Here we demonstrate a method for creating an extended hollow plasma channel and measure the wakefields created by an ultrarelativistic positron beam as it propagates through the channel. The plasma channel is created by directing a high-intensity laser pulse with a spatially modulated profile into lithium vapour, which results in an annular region of ionization. A peak decelerating field of 230 MeV m-1 is inferred from changes in the beam energy spectrum, in good agreement with theory and particle-in-cell simulations.

Effects of reaction control system jet simulation on the stability and control characteristics of a 0.015-scale space shuttle orbiter model in the Ames Research Center 3.5-foot hypersonic wind tunnel

NASA Technical Reports Server (NTRS)

Dziubala, T. J.; Marroquin, J.; Cleary, J. W.; Mellenthin, J. A.

1973-01-01

An experimental investigation was performed in the Ames Research Center 3.5-Foot Hypersonic Wind Tunnel to obtain detailed effects which interactions between the RCS jet flow field and the local orbiter flow field have on orbiter hypersonic stability and control characteristics. Six-component force data were obtained through an angle-of-attack range of 15 to 35 deg with 0 deg angle of sideslip. The test was conducted with yaw, pitch and roll jet simulation at a free-stream Mach number of 10.3. These data simulate two SSV reentry flight conditions at Mach numbers of 28.3 and 10.3. Fuselage base pressures and pressures on the nonmetric RCS pods were obtained in addition to the basic force measurements. Model 42-0 was used for these tests.

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

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

Search for Length Dependent Stable Structures of Polyglutamaine Proteins with Replica Exchange Molecular Dynamic

NASA Astrophysics Data System (ADS)

Kluber, Alexander; Hayre, Robert; Cox, Daniel

2012-02-01

Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.

Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields

NASA Astrophysics Data System (ADS)

Steffen, Julien; Hartke, Bernd

2017-10-01

Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections. However, the additional expense at the reference level remains very modest. We demonstrate all this for three arbitrarily chosen example reactions.

Demonstration of a positron beam-driven hollow channel plasma wakefield accelerator

PubMed Central

Gessner, Spencer; Adli, Erik; Allen, James M.; An, Weiming; Clarke, Christine I.; Clayton, Chris E.; Corde, Sebastien; Delahaye, J. P.; Frederico, Joel; Green, Selina Z.; Hast, Carsten; Hogan, Mark J.; Joshi, Chan; Lindstrøm, Carl A.; Lipkowitz, Nate; Litos, Michael; Lu, Wei; Marsh, Kenneth A.; Mori, Warren B.; O'Shea, Brendan; Vafaei-Najafabadi, Navid; Walz, Dieter; Yakimenko, Vitaly; Yocky, Gerald

2016-01-01

Plasma wakefield accelerators have been used to accelerate electron and positron particle beams with gradients that are orders of magnitude larger than those achieved in conventional accelerators. In addition to being accelerated by the plasma wakefield, the beam particles also experience strong transverse forces that may disrupt the beam quality. Hollow plasma channels have been proposed as a technique for generating accelerating fields without transverse forces. Here we demonstrate a method for creating an extended hollow plasma channel and measure the wakefields created by an ultrarelativistic positron beam as it propagates through the channel. The plasma channel is created by directing a high-intensity laser pulse with a spatially modulated profile into lithium vapour, which results in an annular region of ionization. A peak decelerating field of 230 MeV m−1 is inferred from changes in the beam energy spectrum, in good agreement with theory and particle-in-cell simulations. PMID:27250570

Particle motion around magnetized black holes: Preston-Poisson space-time

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

Konoplya, R. A.

We analyze the motion of massless and massive particles around black holes immersed in an asymptotically uniform magnetic field and surrounded by some mechanical structure, which provides the magnetic field. The space-time is described by the Preston-Poisson metric, which is the generalization of the well-known Ernst metric with a new parameter, tidal force, characterizing the surrounding structure. The Hamilton-Jacobi equations allow the separation of variables in the equatorial plane. The presence of a tidal force from the surroundings considerably changes the parameters of the test particle motion: it increases the radius of circular orbits of particles and increases the bindingmore » energy of massive particles going from a given circular orbit to the innermost stable orbit near the black hole. In addition, it increases the distance of the minimal approach, time delay, and bending angle for a ray of light propagating near the black hole.« less

Theoretical and experimental studies of the structure and vibrational spectra of NTO

NASA Astrophysics Data System (ADS)

Sorescu, Dan C.; Sutton, Teressa R. L.; Thompson, Donald L.; Beardall, David; Wight, Charles A.

1996-10-01

The structure and vibrational spectra of the high explosive 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) have been determined by ab initio molecular orbital calculations at the Hartree-Fock and second-order Møller-Plesset levels and by density functional theory (B3LYP). Experimental frequencies for the molecule have been determined from infrared spectra of pure NTO films and NTO molecules isolated in an argon matrix at 21 K. A force field for gas phase NTO has been obtained based on calculated results at the MP2/6-311G∗∗ level. In addition, a force field for solid state NTO has been constructed using the experimental vibrational frequencies for NTO films and scaled ab initio vibrational frequencies. Differences between the solid state and gas phase results indicate that the environment and preparation procedure exert a marked influence on the spectral characteristics of the NTO molecule.

Validation and Application of the ReaxFF Reactive Force Field to Hydrocarbon Oxidation Kinetics

DTIC Science & Technology

2016-06-23

AFRL-AFOSR-VA-TR-2016-0278 Validation and application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics Adrianus Van Duin...application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-14-1-0355 5c.  PROGRAM...Chenoweth Dec14 Validation and application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics DISTRIBUTION A: Distribution approved for

Surface structure and stability of partially hydroxylated silica surfaces

DOE PAGES

Rimsza, J. M.; Jones, R. E.; Criscenti, L. J.

2017-04-04

Surface energies of silicates influence crack propagation during brittle fracture and decrease with surface relaxation caused by annealing and hydroxylation. Molecular-level simulations are particularly suited for the investigation of surface processes. In this work, classical MD simulations of silica surfaces are performed with two force fields (ClayFF and ReaxFF) to investigate the effect of force field reactivity on surface structure and energy as a function of surface hydroxylation. An unhydroxylated fracture surface energy of 5.1 J/m 2 is calculated with the ClayFF force field, and 2.0 J/m 2 is calculated for the ReaxFF force field. The ClayFF surface energies aremore » consistent with the experimental results from double cantilever beam fracture tests (4.5 J/m 2), whereas ReaxFF underestimated these surface energies. Surface relaxation via annealing and hydroxylation was performed by creating a low-energy equilibrium surface. Annealing condensed neighboring siloxane bonds increased the surface connectivity, and decreased the surface energies by 0.2 J/m 2 for ClayFF and 0.8 J/m 2 for ReaxFF. Posthydroxylation surface energies decreased further to 4.6 J/m 2 with the ClayFF force field and to 0.2 J/m 2 with the ReaxFF force field. Experimental equilibrium surface energies are ~0.35 J/m 2, consistent with the ReaxFF force field. Although neither force field was capable of replicating both the fracture and equilibrium surface energies reported from experiment, each was consistent with one of these conditions. Furthermore, future computational investigations that rely on accurate surface energy values should consider the surface state of the system and select the appropriate force field.« less

Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms.

PubMed

Saito, Minoru; Okazaki, Isao

2009-12-01

The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field. (c) 2009 Wiley Periodicals, Inc.

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

Rimsza, J. M.; Jones, R. E.; Criscenti, L. J.

Surface energies of silicates influence crack propagation during brittle fracture and decrease with surface relaxation caused by annealing and hydroxylation. Molecular-level simulations are particularly suited for the investigation of surface processes. In this work, classical MD simulations of silica surfaces are performed with two force fields (ClayFF and ReaxFF) to investigate the effect of force field reactivity on surface structure and energy as a function of surface hydroxylation. An unhydroxylated fracture surface energy of 5.1 J/m 2 is calculated with the ClayFF force field, and 2.0 J/m 2 is calculated for the ReaxFF force field. The ClayFF surface energies aremore » consistent with the experimental results from double cantilever beam fracture tests (4.5 J/m 2), whereas ReaxFF underestimated these surface energies. Surface relaxation via annealing and hydroxylation was performed by creating a low-energy equilibrium surface. Annealing condensed neighboring siloxane bonds increased the surface connectivity, and decreased the surface energies by 0.2 J/m 2 for ClayFF and 0.8 J/m 2 for ReaxFF. Posthydroxylation surface energies decreased further to 4.6 J/m 2 with the ClayFF force field and to 0.2 J/m 2 with the ReaxFF force field. Experimental equilibrium surface energies are ~0.35 J/m 2, consistent with the ReaxFF force field. Although neither force field was capable of replicating both the fracture and equilibrium surface energies reported from experiment, each was consistent with one of these conditions. Furthermore, future computational investigations that rely on accurate surface energy values should consider the surface state of the system and select the appropriate force field.« less

Dissolution study of active pharmaceutical ingredients using molecular dynamics simulations with classical force fields

NASA Astrophysics Data System (ADS)

Greiner, Maximilian; Elts, Ekaterina; Schneider, Julian; Reuter, Karsten; Briesen, Heiko

2014-11-01

The CHARMM, general Amber and OPLS force fields are evaluated for their suitability in simulating the molecular dynamics of the dissolution of the hydrophobic, small-molecule active pharmaceutical ingredients aspirin, ibuprofen, and paracetamol in aqueous media. The force fields are evaluated by comparison with quantum chemical simulations or experimental references on the basis of the following capabilities: accurately representing intra- and intermolecular interactions, appropriately reproducing crystal lattice parameters, adequately describing thermodynamic properties, and the qualitative description of the dissolution behavior. To make this approach easily accessible for evaluating the dissolution properties of novel drug candidates in the early stage of drug development, the force field parameter files are generated using online resources such as the SWISS PARAM servers, and the software packages ACPYPE and Maestro. All force fields are found to reproduce the intermolecular interactions with a reasonable degree of accuracy, with the general Amber and CHARMM force fields showing the best agreement with quantum mechanical calculations. A stable crystal bulk structure is obtained for all model substances, except for ibuprofen, where the reproductions of the lattice parameters and observed crystal stability are considerably poor for all force fields. The heat of solution used to evaluate the solid-to-solution phase transitions is found to be in qualitative agreement with the experimental data for all combinations tested, with the results being quantitatively optimum for the general Amber and CHARMM force fields. For aspirin and paracetamol, stable crystal-water interfaces were obtained. The (100), (110), (011) and (001) interfaces of aspirin or paracetamol and water were simulated for each force field for 30 ns. Although generally expected as a rare event, in some of the simulations, dissolution is observed at 310 K and ambient pressure conditions.

Combined targeting of lentiviral vectors and positioning of transduced cells by magnetic nanoparticles

PubMed Central

Hofmann, Andreas; Wenzel, Daniela; Becher, Ulrich M.; Freitag, Daniel F.; Klein, Alexandra M.; Eberbeck, Dietmar; Schulte, Maike; Zimmermann, Katrin; Bergemann, Christian; Gleich, Bernhard; Roell, Wilhelm; Weyh, Thomas; Trahms, Lutz; Nickenig, Georg; Fleischmann, Bernd K.; Pfeifer, Alexander

2009-01-01

Targeting of viral vectors is a major challenge for in vivo gene delivery, especially after intravascular application. In addition, targeting of the endothelium itself would be of importance for gene-based therapies of vascular disease. Here, we used magnetic nanoparticles (MNPs) to combine cell transduction and positioning in the vascular system under clinically relevant, nonpermissive conditions, including hydrodynamic forces and hypothermia. The use of MNPs enhanced transduction efficiency of endothelial cells and enabled direct endothelial targeting of lentiviral vectors (LVs) by magnetic force, even in perfused vessels. In addition, application of external magnetic fields to mice significantly changed LV/MNP biodistribution in vivo. LV/MNP-transduced cells exhibited superparamagnetic behavior as measured by magnetorelaxometry, and they were efficiently retained by magnetic fields. The magnetic interactions were strong enough to position MNP-containing endothelial cells at the intima of vessels under physiological flow conditions. Importantly, magnetic positioning of MNP-labeled cells was also achieved in vivo in an injury model of the mouse carotid artery. Intravascular gene targeting can be combined with positioning of the transduced cells via nanomagnetic particles, thereby combining gene- and cell-based therapies. PMID:19118196

Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

PubMed Central

2015-01-01

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

The effect of power-law body forces on a thermally driven flow between concentric rotating spheres

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1986-01-01

A numerical study is conducted to determine the effect of power-law body forces on a thermally-driven axisymmetric flow field confined between concentric co-rotating spheres. This study is motivated by Spacelab geophysical fluid-flow experiments, which use an electrostatic force on a dielectric fluid to simulate gravity; this force exhibits a (1/r)sup 5 distribution. Meridional velocity is found to increase when the electrostatic body force is imposed, relative to when the body force is uniform. Correlation among flow fields with uniform, inverse-square, and inverse-quintic force fields is obtained using a modified Grashof number.

The effect of power law body forces on a thermally-driven flow between concentric rotating spheres

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1985-01-01

A numerical study is conducted to determine the effect of power-law body forces on a thermally-driven axisymmetric flow field confined between concentric co-rotating spheres. This study is motivated by Spacelab geophysical fluid-flow experiments, which use an electrostatic force on a dielectric fluid to simulate gravity; this force exhibits a (1/r)sup 5 distribution. Meridional velocity is found to increase when the electrostatic body force is imposed, relative to when the body force is uniform. Correlation among flow fields with uniform, inverse-square, and inverse-quintic force fields is obtained using a modified Grashof number.

Surfzone alongshore advective accelerations: observations and modeling

NASA Astrophysics Data System (ADS)

Hansen, J.; Raubenheimer, B.; Elgar, S.

2014-12-01

The sources, magnitudes, and impacts of non-linear advective accelerations on alongshore surfzone currents are investigated with observations and a numerical model. Previous numerical modeling results have indicated that advective accelerations are an important contribution to the alongshore force balance, and are required to understand spatial variations in alongshore currents (which may result in spatially variable morphological change). However, most prior observational studies have neglected advective accelerations in the alongshore force balance. Using a numerical model (Delft3D) to predict optimal sensor locations, a dense array of 26 colocated current meters and pressure sensors was deployed between the shoreline and 3-m water depth over a 200 by 115 m region near Duck, NC in fall 2013. The array included 7 cross- and 3 alongshore transects. Here, observational and numerical estimates of the dominant forcing terms in the alongshore balance (pressure and radiation-stress gradients) and the advective acceleration terms will be compared with each other. In addition, the numerical model will be used to examine the force balance, including sources of velocity gradients, at a higher spatial resolution than possible with the instrument array. Preliminary numerical results indicate that at O(10-100 m) alongshore scales, bathymetric variations and the ensuing alongshore variations in the wave field and subsequent forcing are the dominant sources of the modeled velocity gradients and advective accelerations. Additional simulations and analysis of the observations will be presented. Funded by NSF and ASDR&E.

The Electromotive Force in Different Reference Frames

NASA Astrophysics Data System (ADS)

Adler, Charles L.

2018-05-01

The electromotive force (EMF) is the work per unit charge around a wire loop caused by a time-varying magnetic flux threading the loop. It is due to a force moving the charges around the loop. This is true whether the change in flux is due to the wire loop being stationary and the field changing in time, or the loop moving through a spatially varying field. In the first case, we say that the time-varying magnetic field induces an electric field that provides the force; in the second, we say that the force is due to the magnetic field acting on the charges in the moving loop. The theory of relativity states that both viewpoints must be equivalent, but it is sometimes difficult to harmonize them.

Distinct findings from the steady-state analysis of a microbial model with time-invariant or seasonal driving forces

NASA Astrophysics Data System (ADS)

Wang, G.; Mayes, M. A.

2017-12-01

Microbially-explicit soil organic matter (SOM) decomposition models are thought to be more biologically realistic than conventional models. Current testing or evaluation of microbial models majorly uses steady-state analysis with time-invariant forces (i.e., soil temperature, moisture and litter input). The findings from such simplified analyses are assumed to be capable of representing the model responses in field soil conditions with seasonal driving forces. Here we show that the steady-state modeling results with seasonal forces may result in distinct findings from the simulations with time-invariant forcing data. We evaluate the response of soil organic C (SOC) to litter addition (L+) in a subtropical pine forest using the calibrated Microbial-ENzyme Decomposition (MEND) model. We implemented two sets of modeling analyses, with each set including two scenarios, i.e., control (CR) vs. litter-addition (L+). The first set (Set1) uses fixed soil temperature and moisture, and constant litter input under Scenario CR vs. increased constant litter input under Scenario L+. The second set (Set2) employs hourly soil temperature and moisture and monthly litter input under Scenario CR. Under Scenario L+ of Set2, A logistic function with an upper plateau represents the increasing trend of litter input to SOM. We conduct long-term simulations to ensure that the models reach steady-states for Set1 or dynamic equilibrium for Set2. Litter addition of Set2 causes an increase of SOC by 29%. However, the steady-state SOC pool sizes of Set1 would not respond to L+ as long as the chemical composition of litter remained the same. Our results indicate the necessity to implement dynamic model simulations with seasonal forcing data, which could lead to modeling results qualitatively different from the steady-state analysis with time-invariant forcing data.

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

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

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.

We developed a new modified embedded-atom method (MEAM) force field for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997)], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquidmore » density, self-diffusivity, viscosity, and vapor-liquid surface tension. We show that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.« less

Optimization of classical nonpolarizable force fields for OH(-) and H3O(+).

PubMed

Bonthuis, Douwe Jan; Mamatkulov, Shavkat I; Netz, Roland R

2016-03-14

We optimize force fields for H3O(+) and OH(-) that reproduce the experimental solvation free energies and the activities of H3O(+) Cl(-) and Na(+) OH(-) solutions up to concentrations of 1.5 mol/l. The force fields are optimized with respect to the partial charge on the hydrogen atoms and the Lennard-Jones parameters of the oxygen atoms. Remarkably, the partial charge on the hydrogen atom of the optimized H3O(+) force field is 0.8 ± 0.1|e|--significantly higher than the value typically used for nonpolarizable water models and H3O(+) force fields. In contrast, the optimal partial charge on the hydrogen atom of OH(-) turns out to be zero. Standard combination rules can be used for H3O(+) Cl(-) solutions, while for Na(+) OH(-) solutions, we need to significantly increase the effective anion-cation Lennard-Jones radius. While highlighting the importance of intramolecular electrostatics, our results show that it is possible to generate thermodynamically consistent force fields without using atomic polarizability.

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

NASA Astrophysics Data System (ADS)

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.; Carter, Emily A.; Debenedetti, Pablo G.; Panagiotopoulos, Athanassios Z.

2017-02-01

A new modified embedded-atom method (MEAM) force field is developed for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997), 10.1103/PhysRevLett.79.2482], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquid density, self-diffusivity, viscosity, and vapor-liquid surface tension. It is shown that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.

Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field

NASA Astrophysics Data System (ADS)

Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa

2015-07-01

Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

DOE PAGES

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.; ...

2017-02-01

We developed a new modified embedded-atom method (MEAM) force field for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997)], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquidmore » density, self-diffusivity, viscosity, and vapor-liquid surface tension. We show that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.« less

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

PubMed Central

Reddy, Swarnalatha Y.; Leclerc, Fabrice; Karplus, Martin

2003-01-01

The improvements of the force fields and the more accurate treatment of long-range interactions are providing more reliable molecular dynamics simulations of nucleic acids. The abilities of certain nucleic acid force fields to represent the structural and conformational properties of nucleic acids in solution are compared. The force fields are AMBER 4.1, BMS, CHARMM22, and CHARMM27; the comparison of the latter two is the primary focus of this paper. The performance of each force field is evaluated first on its ability to reproduce the B-DNA decamer d(CGATTAATCG)2 in solution with simulations in which the long-range electrostatics were treated by the particle mesh Ewald method; the crystal structure determined by Quintana et al. (1992) is used as the starting point for all simulations. A detailed analysis of the structural and solvation properties shows how well the different force fields can reproduce sequence-specific features. The results are compared with data from experimental and previous theoretical studies. PMID:12609851

Lipid14: The Amber Lipid Force Field

PubMed Central

2015-01-01

The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package. The modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. The Lennard-Jones and torsion parameters of both the head and tail groups have been revised and updated partial charges calculated. The force field has been validated by simulating bilayers of six different lipid types for a total of 0.5 μs each without applying a surface tension; with favorable comparison to experiment for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. As the derivation of this force field is consistent with the AMBER development philosophy, Lipid14 is compatible with the AMBER protein, nucleic acid, carbohydrate, and small molecule force fields. PMID:24803855

Mechanical reinforcement for RACC cables in high magnetic background fields

NASA Astrophysics Data System (ADS)

Bayer, C. M.; Gade, P. V.; Barth, C.; Preuß, A.; Jung, A.; Weiß, K. P.

2016-02-01

Operable in liquid helium, liquid hydrogen or liquid nitrogen, high temperature superconductor (HTS) cables are investigated as future alternatives to low temperature superconductor (LTS) cables in magnet applications. Different high current HTS cable concepts have been developed and optimized in the last years—each coming with its own benefits and challenges. As the Roebel assembled coated conductor (RACC) is the only fully transposed HTS cable investigated so far, it is attractive for large scale magnet and accelerator magnet applications when field quality and alternating current (AC) losses are of highest importance. However, due to its filamentary character, the RACC is very sensitive to Lorentz forces. In order to increase the mechanical strength of the RACC, each of the HTS strands was covered by an additional copper tape. After investigating the maximum applicable transverse pressure on the strand composition, the cable was clamped into a stainless steel structure to reinforce it against Lorentz forces. A comprehensive test has been carried out in the FBI facility at 4.2 K in a magnetic field of up to 12 T. This publication discusses the maximum applicable pressure as well as the behaviour of the RACC cable as a function of an external magnetic field.

Lorentz Body Force Induced by Traveling Magnetic Fields

NASA Technical Reports Server (NTRS)

Volz, M. P.; Mazuruk, K.

2003-01-01

The Lorentz force induced by a traveling magnetic field (TMF) in a cylindrical container has been calculated. The force can be used to control flow in dectrically conducting melts and the direction of the magnetic field and resulting flow can be reversed. A TMF can be used to partially cancel flow driven by buoyancy. The penetration of the field into the cylinder decreases as the frequency increases, and there exists an optimal value of frequency for which the resulting force is a maximum. Expressions for the Lorentz force in the limiting cases of low frequency and infinite cylinder are also given and compared to the numerical calculations.

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

PubMed Central

2015-01-01

We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard–Jones combining rules. The force field gives strong performance on α-helical and β-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields. PMID:25328495

Thermodynamic properties for applications in chemical industry via classical force fields.

PubMed

Guevara-Carrion, Gabriela; Hasse, Hans; Vrabec, Jadran

2012-01-01

Thermodynamic properties of fluids are of key importance for the chemical industry. Presently, the fluid property models used in process design and optimization are mostly equations of state or G (E) models, which are parameterized using experimental data. Molecular modeling and simulation based on classical force fields is a promising alternative route, which in many cases reasonably complements the well established methods. This chapter gives an introduction to the state-of-the-art in this field regarding molecular models, simulation methods, and tools. Attention is given to the way modeling and simulation on the scale of molecular force fields interact with other scales, which is mainly by parameter inheritance. Parameters for molecular force fields are determined both bottom-up from quantum chemistry and top-down from experimental data. Commonly used functional forms for describing the intra- and intermolecular interactions are presented. Several approaches for ab initio to empirical force field parameterization are discussed. Some transferable force field families, which are frequently used in chemical engineering applications, are described. Furthermore, some examples of force fields that were parameterized for specific molecules are given. Molecular dynamics and Monte Carlo methods for the calculation of transport properties and vapor-liquid equilibria are introduced. Two case studies are presented. First, using liquid ammonia as an example, the capabilities of semi-empirical force fields, parameterized on the basis of quantum chemical information and experimental data, are discussed with respect to thermodynamic properties that are relevant for the chemical industry. Second, the ability of molecular simulation methods to describe accurately vapor-liquid equilibrium properties of binary mixtures containing CO(2) is shown.

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

NASA Astrophysics Data System (ADS)

Small, Meagan C.; Aytenfisu, Asaminew H.; Lin, Fang-Yu; He, Xibing; MacKerell, Alexander D.

2017-04-01

The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars ( d-allose and d-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars d-allose and d-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.

PubMed

Small, Meagan C; Aytenfisu, Asaminew H; Lin, Fang-Yu; He, Xibing; MacKerell, Alexander D

2017-04-01

The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (D-allose and D-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars D-allose and D-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

Drude Polarizable Force Field for Aliphatic Ketones and Aldehydes, and their Associated Acyclic Carbohydrates

PubMed Central

Small, Meagan C.; Aytenfisu, Asaminew H.; Lin, Fang-Yu; He, Xibing; MacKerell, Alexander D.

2017-01-01

The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (D-allose and D-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars D-allose and D-psicose, thereby extending the available biomolecules in the Drude polarizable FF. PMID:28190218

The influence of inhomogeneous magnetic field over a NdFeB guideway on levitation force of the HTS bulk maglev system

NASA Astrophysics Data System (ADS)

Zhao, Lifeng; Deng, Jiangtao; Li, Linbo; Feng, Ning; Wei, Pu; Lei, Wei; Jiang, Jing; Wang, Xiqin; Zhang, Yong; Zhao, Yong

2018-04-01

Dynamic responses of high temperature superconducting bulk to inhomogeneous magnetic field distribution of permanent magnet guideway, as well as enlarged amplitude of magnetic field obtained by partially covering the permanent magnet guideway (PMG) with iron sheets in different thickness, are investigated. Experiments show that the instantaneous levitation force increases with the increase of the variation rate of magnetic field (dB/dt). Meanwhile, inhomogeneous magnetic field from PMG causes the decay of levitation force. The decay of levitation force almost increases linearly with the increase of alternating magnetic field amplitude. It should be very important for the application of high-speed maglev system.

Modeling of wind-initiated liberation of fungal propagules from host plant leaves

NASA Astrophysics Data System (ADS)

Gonzalinajec, Trevor

2014-11-01

Successful airborne propagule dispersal must begin with liberation into the air. The physical shedding mechanism of airborne propagules in the 100--250 μm size range are not well understood. Many fungal plant pathogens have propagules in this size range that are shed from the bottom of infected leaves. If turbulent air flow is sufficient to liberate the sporocarps of fungi from leaves then the aerodynamic forces exerted must be sufficient to overcome adhesive forces. In this study I have sought to quantify the magnitude and direction of these aerodynamic forces and their causal flow fields with dynamically scaled physical models. I chose a genus of powdery mildew because maturation of the sporocarp entails morphological changes that lever the sporocarp further away from the leaf surface and out of the viscous boundary layer. Consequently I varied the sporocarp morphology, the boundary layer thickness, and the flow velocity as forces on models were measured with a transducer. Additionally I analyzed the fluid velocity around the models using PIV, which allowed for quantification of the relative importance of shear forces and pressure-gradient forces. The results suggest that forces from steady and unsteady wind alike are insufficient to explain liberation.

Euler force actuation mechanism for siphon valving in compact disk-like microfluidic chips

PubMed Central

Deng, Yongbo; Fan, Jianhua; Zhou, Song; Zhou, Teng; Wu, Junfeng; Li, Yin; Liu, Zhenyu; Xuan, Ming; Wu, Yihui

2014-01-01

Based on the Euler force induced by the acceleration of compact disk (CD)-like microfluidic chip, this paper presents a novel actuation mechanism for siphon valving. At the preliminary stage of acceleration, the Euler force in the tangential direction of CD-like chip takes the primary place compared with the centrifugal force to function as the actuation of the flow, which fills the siphon and actuates the siphon valving. The Euler force actuation mechanism is demonstrated by the numerical solution of the phase-field based mathematical model for the flow in siphon valve. In addition, experimental validation is implemented in the polymethylmethacrylate-based CD-like microfluidic chip manufactured using CO2 laser engraving technique. To prove the application of the proposed Euler force actuation mechanism, whole blood separation and plasma extraction has been conducted using the Euler force actuated siphon valving. The newly introduced actuation mechanism overcomes the dependence on hydrophilic capillary filling of siphon by avoiding external manipulation or surface treatments of polymeric material. The sacrifice for highly integrated processing in pneumatic pumping technique is also prevented by excluding the volume-occupied compressed air chamber. PMID:24753736

U.S. Field Artillery after World War I: Modernizing the Force While Downsizing

DTIC Science & Technology

2014-06-13

weapons, and tactics. It convened several boards to assess the requirements for an effective field artillery force, studying the materiel and......weapons, and tactics. It convened several boards to assess the requirements for an effective field artillery force, studying the materiel and

The Energetics of Motivated Cognition: A Force-Field Analysis

ERIC Educational Resources Information Center

Kruglanski, Arie W.; Belanger, Jocelyn J.; Chen, Xiaoyan; Kopetz, Catalina; Pierro, Antonio; Mannetti, Lucia

2012-01-01

A force-field theory of motivated cognition is presented and applied to a broad variety of phenomena in social judgment and self-regulation. Purposeful cognitive activity is assumed to be propelled by a "driving force" and opposed by a "restraining force". "Potential" driving force represents the maximal amount of energy an individual is prepared…

The Ehrenfest force field: Topology and consequences for the definition of an atom in a molecule.

PubMed

Martín Pendás, A; Hernández-Trujillo, J

2012-10-07

The Ehrenfest force is the force acting on the electrons in a molecule due to the presence of the other electrons and the nuclei. There is an associated force field in three-dimensional space that is obtained by the integration of the corresponding Hermitian quantum force operator over the spin coordinates of all of the electrons and the space coordinates of all of the electrons but one. This paper analyzes the topology induced by this vector field and its consequences for the definition of molecular structure and of an atom in a molecule. Its phase portrait reveals: that the nuclei are attractors of the Ehrenfest force, the existence of separatrices yielding a dense partitioning of three-dimensional space into disjoint regions, and field lines connecting the attractors through these separatrices. From the numerical point of view, when the Ehrenfest force field is obtained as minus the divergence of the kinetic stress tensor, the induced topology was found to be highly sensitive to choice of gaussian basis sets at long range. Even the use of large split valence and highly uncontracted basis sets can yield spurious critical points that may alter the number of attraction basins. Nevertheless, at short distances from the nuclei, in general, the partitioning of three-dimensional space with the Ehrenfest force field coincides with that induced by the gradient field of the electron density. However, exceptions are found in molecules where the electron density yields results in conflict with chemical intuition. In these cases, the molecular graphs of the Ehrenfest force field reveal the expected atomic connectivities. This discrepancy between the definition of an atom in a molecule between the two vector fields casts some doubts on the physical meaning of the integration of Ehrenfest forces over the basins of the electron density.

Levitation and guidance force relaxations of the single-seeded and multi-seeded YBCO superconductors

NASA Astrophysics Data System (ADS)

Abdioglu, M.; Ozturk, K.; Kabaer, M.; Ekici, M.

2018-01-01

The stable levitation and guidance forces at higher force levels are important parameters for technological applicability of high temperature superconductors (HTSs) in Maglev and Flywheel energy storage systems. In this study, we have investigated the levitation and guidance force relaxation of both the single-seeded and multi-seeded YBCOs for different (HTS)-permanent magnetic guideway (PMG) arrangements in different cooling heights (CH). The measured saturated force values of Halbach PMG arrangements are bigger than the maximum force values of other PMGs. It is determined that the normalized magnetic levitation force (MLF) and normalized guidance force (GF) relaxation rate values decrease while the relaxation rates increase with increasing magnetic pole number and the effective external magnetic field area for both the single-seeded and multi-seeded YBCO. Also it can be said that the force stability at the higher force value of Halbach PMG arrangement indicates that the relaxation quality of Halbach PMG is better than that of the others. Additionally, it can be said that both the MLF and GF relaxation qualities of the multi-seeded YBCOs are better than that of the single-seeded ones. This magnetic force and relaxation results of the single-seeded and multi-seeded YBCOs are useful to optimize the loading capacity and lateral reliability of HTS Maglev and similar magnetic bearing systems.

Bubble Dynamics, Two-Phase Flow, and Boiling Heat Transfer in Microgravity

NASA Technical Reports Server (NTRS)

Chung, Jacob N.

1996-01-01

The objective of the research is to study the feasibility of employing an external force to replace the buoyancy force in order to maintain nucleate boiling in microgravity. We have found that a bulk velocity field, an electric field and an acoustic field could each play the role of the gravity field in microgravity. Nucleate boiling could be maintained by any one of the three external force fields in space.

KSC-2009-5874

NASA Image and Video Library

2009-10-19

VANDENBERG AIR FORCE BASE, Calif. - At Space Launch Complex 2 at Vandenberg Air Force Base in California, workers supervise the first stage of the United Launch Alliance Delta II rocket for launch of NASA's Wide-field Infrared Survey Explorer, or WISE, as it is lowered onto pedestal's in the pad's mobile service tower. WISE will survey the entire sky at infrared wavelengths, creating a cosmic clearinghouse of hundreds of millions of objects which will be catalogued and provide a vast storehouse of knowledge about the solar system, the Milky Way, and the universe. Launch is scheduled for Dec. 7. For additional information, visit http://wise.ssl.berkeley.edu. Photo credit: NASA/Roy Allison, VAFB

Cosmic matter-antimatter asymmetry and gravitational force

NASA Technical Reports Server (NTRS)

Hsu, J. P.

1980-01-01

Cosmic matter-antimatter asymmetry due to the gravitational interaction alone is discussed, considering the gravitational coupling of fermion matter related to the Yang-Mills (1954) gauge symmetry with the unique generalization of the four-dimensional Poincare group. Attention is given to the case of weak static fields which determines the space-time metric where only large source terms are retained. In addition, considering lowest-order Feynman diagrams, there are presented gravitational potential energies between fermions, between antifermions, and between a fermion and an antifermion. It is concluded that the gravitational force between matter is different from that between antimatter; implications from this concerning the evolution of the universe are discussed.

Field emission microplasma actuation for microchannel flows

NASA Astrophysics Data System (ADS)

Sashank Tholeti, Siva; Shivkumar, Gayathri; Alexeenko, Alina A.

2016-06-01

Microplasmas offer attractive flow control methodology for gas transport in microsystems where large viscous losses make conventional pumping methods highly inefficient. We study microscale flow actuation by dielectric-barrier discharge (DBD) with field emission (FE) of electrons, which allows lowering the operational voltage from kV to a few hundred volts and below. A feasibility study of FE-DBD for flow actuation is performed using 2D particle-in-cell method with Monte Carlo collisions (PIC/MCC) at 10 MHz in nitrogen at atmospheric pressure. The free diffusion dominated, high velocity field emission electrons create a large positive space charge and a body force on the order of 106 N m-3. The body force and Joule heat decrease with increase in dielectric thickness and electrode thickness. The body force also decreases at lower pressures. The plasma body force distribution along with the Joule heating is then used in the Navier-Stokes simulations to quantify the flow actuation in a microchannel. Theoretical analysis and simulations for plasma actuated planar Poiseuille flow show that the gain in flow rate is inversely proportional to Reynolds number. This theoretical analysis is in good agreement with the simulations for a microchannel with closely placed actuators under incompressible conditions. Flow rate of FE-DBD driven 2D microchannel is around 100 ml min-1 mm-1 for an input power of 64 μW mm-1. The gas temperature rises by 1500 K due to the Joule heating, indicating FE-DBD’s potential for microcombustion, micropropulsion and chemical sensing in addition to microscale pumping and mixing applications.

Casimir effect for parallel plates in a Friedmann-Robertson-Walker universe

NASA Astrophysics Data System (ADS)

Bezerra de Mello, E. R.; Saharian, A. A.; Setare, M. R.

2017-03-01

We evaluate the Hadamard function, the vacuum expectation values (VEVs) of the field squared and the energy-momentum tensor for a massive scalar field with a general curvature coupling parameter in the geometry of two parallel plates on a spatially flat Friedmann-Robertson-Walker background with a general scale factor. On the plates, the field operator obeys the Robin boundary conditions with the coefficients depending on the scale factor. In all the spatial regions, the VEVs are decomposed into the boundary-free and boundary-induced contributions. Unlike the problem with the Minkowski bulk, in the region between the plates, the normal stress is not homogeneous and does not vanish in the geometry of a single plate. Near the plates, it has different signs for accelerated and decelerated expansions of the Universe. The VEV of the energy-momentum tensor, in addition to the diagonal components, has a nonzero off-diagonal component describing an energy flux along the direction normal to the boundaries. Expressions are derived for the Casimir forces acting on the plates. Depending on the Robin coefficients and on the vacuum state, these forces can be either attractive or repulsive. An important difference from the corresponding result in the Minkowski bulk is that the forces on the separate plates, in general, are different if the corresponding Robin coefficients differ. We give the applications of general results for the class of α vacua in the de Sitter bulk. It is shown that, compared with the Bunch-Davies vacuum state, the Casimir forces for a given α vacuum may change the sign.

Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance

PubMed Central

Noel, Martin; Fortin, Karine; Bouyer, Laurent J

2009-01-01

Background Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Methods Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; ~10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. Results When initially exposed to a mid-stance force field (FF20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over ~50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF50% catch strides were not simply due to a large ankle impedance. Conclusion Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle during locomotion. Our data suggest that, for short duration exposure, a feedforward modification in torque output occurs during mid-stance but not during push-off. These findings are important for the design of novel rehabilitation methods, as they suggest that the ability to use resistive force fields for training may depend on targeted gait phases. PMID:19493356

Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance.

PubMed

Noel, Martin; Fortin, Karine; Bouyer, Laurent J

2009-06-03

Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; approximately 10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. When initially exposed to a mid-stance force field (FF 20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF 20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over approximately 50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF 50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF 50% catch strides were not simply due to a large ankle impedance. Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle during locomotion. Our data suggest that, for short duration exposure, a feedforward modification in torque output occurs during mid-stance but not during push-off. These findings are important for the design of novel rehabilitation methods, as they suggest that the ability to use resistive force fields for training may depend on targeted gait phases.

Tuning Bacterial Hydrodynamics with Magnetic Fields: A Path to Bacterial Robotics

NASA Astrophysics Data System (ADS)

Pierce, Christopher; Mumper, Eric; Brangham, Jack; Wijesinghe, Hiran; Lower, Stephen; Lower, Brian; Yang, Fengyuan; Sooryakumar, Ratnasingham

Magnetotactic Bacteria (MTB) are a group of motile prokaryotes that synthesize chains of lipid-bound, magnetic nano-particles. In this study, the innate magnetism of these flagellated swimmers is exploited to explore their hydrodynamics near confining surfaces, using the magnetic field as a tuning parameter. With weak (Gauss), uniform, external, magnetic ?elds and the field gradients arising from micro-magnetic surface patterns, the relative strength of hydrodynamic, magnetic and ?agellar force components is tuned through magnetic control of the bacteria's orientation and position. In addition to direct measurement of several hydrodynamic quantities related to the motility of individual cells, their tunable dynamics reveal a number of novel, highly controllable swimming behaviors with potential value in micro-robotics applications. Specifically, the experiments permit the MTB cells to be directed along parallel or divergent trajectories, suppress their flagellar forces through magnetic means, and induce transitions between planar, circulating trajectories and drifting, vertically oriented ``top-like'' motion. The implications of the work for fundamental hydrodynamics research as well as bacterially driven robotics applications will be discussed.

Radiation Forces and Torques without Stress (Tensors)

ERIC Educational Resources Information Center

Bohren, Craig F.

2011-01-01

To understand radiation forces and torques or to calculate them does not require invoking photon or electromagnetic field momentum transfer or stress tensors. According to continuum electromagnetic theory, forces and torques exerted by radiation are a consequence of electric and magnetic fields acting on charges and currents that the fields induce…

Force-Field Prediction of Materials Properties in Metal-Organic Frameworks

PubMed Central

2016-01-01

In this work, MOF bulk properties are evaluated and compared using several force fields on several well-studied MOFs, including IRMOF-1 (MOF-5), IRMOF-10, HKUST-1, and UiO-66. It is found that, surprisingly, UFF and DREIDING provide good values for the bulk modulus and linear thermal expansion coefficients for these materials, excluding those that they are not parametrized for. Force fields developed specifically for MOFs including UFF4MOF, BTW-FF, and the DWES force field are also found to provide accurate values for these materials’ properties. While we find that each force field offers a moderately good picture of these properties, noticeable deviations can be observed when looking at properties sensitive to framework vibrational modes. This observation is more pronounced upon the introduction of framework charges. PMID:28008758

Deep eutectic solvent formation: a structural view using molecular dynamics simulations with classical force fields

NASA Astrophysics Data System (ADS)

Mainberger, Sebastian; Kindlein, Moritz; Bezold, Franziska; Elts, Ekaterina; Minceva, Mirjana; Briesen, Heiko

2017-06-01

Deep eutectic solvents (DES) have gained a reputation as inexpensive and easy to handle ionic liquid analogues. This work employs molecular dynamics (MD) to simulate a variety of DES. The hydrogen bond acceptor (HBA) choline chloride was paired with the hydrogen bond donors (HBD) glycerol, 1,4-butanediol, and levulinic acid. Levulinic acid was also paired with the zwitterionic HBA betaine. In order to evaluate the reliability of data MD simulations can provide for DES, two force fields were compared: the Merck Molecular Force Field and the General Amber Force Field with two different sets of partial charges for the latter. The force fields were evaluated by comparing available experimental thermodynamic and transport properties against simulated values. Structural analysis was performed on the eutectic systems and compared to non-eutectic compositions. All force fields could be validated against certain experimental properties, but performance varied depending on the system and property in question. While extensive hydrogen bonding was found for all systems, details about the contribution of individual groups strongly varied among force fields. Interaction potentials revealed that HBA-HBA interactions weaken linearly with increasing HBD ratio, while HBD-HBD interactions grew disproportionally in magnitude, which might hint at the eutectic composition of a system.

Commensurability effects in the critical forces of a superconducting film with Kagomé pinning array at submatching fields

NASA Astrophysics Data System (ADS)

Vizarim, Nicolas P.; Carlone, Maicon; Verga, Lucas G.; Venegas, Pablo A.

2017-09-01

Using molecular dynamics simulations, we find the commensurability force peaks in a two-dimensional superconducting thin-film with a Kagomé pinning array. A transport force is applied in two mutually perpendicular directions, and the magnetic field is increased up to the first matching field. Usually the condition to have pronounced force peaks in systems with periodic pinning is associated to the rate between the applied magnetic field and the first matching field, it must be an integer or a rational fraction. Here, we show that another condition must be satisfied, the vortex ground state must be ordered. Our calculations show that the pinning size and strength may dramatically change the vortex ground state. Small pinning radius and high values of pinning strength may lead to disordered vortex configurations, which fade the critical force peaks. The critical forces show anisotropic behavior, but the same dependence on pinning strength and radius is observed for both driven force directions. Different to cases where the applied magnetic field is higher than the first matching field, here the depinning process begins with vortices weakly trapped on top of a pinning site and not with interstitial vortices. Our results are in good agreement with recent experimental results.

Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ-ψ) Space.

PubMed

Liu, Zhiwei; Ensing, Bernd; Moore, Preston B

2011-02-08

The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (ϕ-ψ) conformational space. The FES is obtained from metadynamics simulations with five commonly used force fields and from ab initio density functional theory calculations in both gas phase and aqueous solution. The FESs obtained at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d,p) level of theory are validated by comparison with previously reported MP2 and LMP2 results as well as with experimentally obtained probability distribution between the C5-β (or β-PPII) and αR states. A quantitative assessment is made for each force field in three conformational basins, LeRI (C5-β-C7eq), LeRII (β2-αR), and LeRIII(αL-C7ax-αD) as well as three transition-state regions linking the above conformational basins. The performance of each force field is evaluated in terms of the average free energy of each region in comparison with that of the ab initio results. We quantify how well a force field FES matches the ab initio FES through the calculation of the standard deviation of a free energy difference map between the two FESs. The results indicate that the performance varies largely from region to region or from force field to force field. Although not one force field is able to outperform all others in all conformational areas, the OPLSAA/L force field gives the best performance overall, followed by OPLSAA and AMBER03. For the three top performers, the average free energies differ from the corresponding ab initio values from within the error range (<0.4 kcal/mol) to ∼1.5 kcal/mol for the low-energy regions and up to ∼2.0 kcal/mol for the transition-state regions. The strategy presented and the results obtained here should be useful for improving the parametrization of force fields targeting both accuracy in the energies of conformers and the transition-state barriers.

The influence of centrifugal forces on the B field structure of an axially symmetric equilibrium magnetosphere

NASA Technical Reports Server (NTRS)

Ye, Gang; Voigt, Gerd-Hannes

1989-01-01

A model is presented of an axially symmetric pole-on magnetosphere in MHD force balance, in which both plasma thermal pressure gradients and centrifugal force are taken into account. Assuming that planetary rotation leads to differentially rotating magnetotail field lines, the deformation of magnetotail field lines under the influence of both thermal plasma pressure and centrifugal forces was calculated. Analytic solutions to the Grad-Shafranov equation are presented, which include the centrifugal force term. It is shown that the nonrotational magnetosphere with hot thermal plasma leads to a field configuration without a toroidal B(phi) component and without field-aligned Birkeland currents. The other extreme, a rapidly rotating magnetosphere with cold plasma, leads to a configuration in which plasma must be confined within a thin disk in a plane where the radial magnetic field component B(r) vanishes locally.

Particles with nonlinear electric response: Suppressing van der Waals forces by an external field.

PubMed

Soo, Heino; Dean, David S; Krüger, Matthias

2017-01-01

We study the classical thermal component of Casimir, or van der Waals, forces between point particles with highly anharmonic dipole Hamiltonians when they are subjected to an external electric field. Using a model for which the individual dipole moments saturate in a strong field (a model that mimics the charges in a neutral, perfectly conducting sphere), we find that the resulting Casimir force depends strongly on the strength of the field, as demonstrated by analytical results. For a certain angle between the external field and center-to-center axis, the fluctuation force can be tuned and suppressed to arbitrarily small values. We compare the forces between these particles with those between particles with harmonic Hamiltonians and also provide a simple formula for asymptotically large external fields, which we expect to be generally valid for the case of saturating dipole moments.

Preface: Special Topic: From Quantum Mechanics to Force Fields.

PubMed

Piquemal, Jean-Philip; Jordan, Kenneth D

2017-10-28

This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

Preface: Special Topic: From Quantum Mechanics to Force Fields

NASA Astrophysics Data System (ADS)

Piquemal, Jean-Philip; Jordan, Kenneth D.

2017-10-01

This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

It's Rather like Learning a Language: Development of talk and conceptual understanding in mechanics lessons

NASA Astrophysics Data System (ADS)

Rincke, Karsten

2011-01-01

Although a broad literature exists concerning the development of conceptual understanding of force and other topics within mechanics, little is known about the role and development of students' talk about the subject. The paper presents an in-depth investigation of students' talk whilst being introduced to the concept of force. The main research goal was to investigate and understand how students develop an understanding of the concept of force and how they use and understand the term 'force'. Therefore, we make relation to the research field of students' preconceptions and the field of second language learning. Two classes of students (N = 47) were videotaped during a time period of nine lessons, each transcribed and analysed using a category system. Additional data were obtained via written tasks, logs kept by the students, and tests. The detailed analysis of the talk and the results of the tests indicate that students face difficulties in using the term 'force' scientifically similar to those in a foreign language instruction. Vygotsky already recognised a relationship between learning in science and learning a language. In this paper, important aspects of this relationship are discussed based upon empirical data. We conclude that in some respects it might be useful to make reference to the research related to language learning when thinking about improving science education. In particular, according to Selinker's concept of interlanguage describing language-learning processes within language instruction, the language used by the students during physics lessons can be viewed as a 'scientific interlanguage'.

Revisiting imidazolium based ionic liquids: Effect of the conformation bias of the [NTf2] anion studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Neumann, Jan; Golub, Benjamin; Odebrecht, Lisa-Marie; Ludwig, Ralf; Paschek, Dietmar

2018-05-01

We study ionic liquids composed of 1-alkyl-3-methylimidazolium cations and bis(trifluoromethyl-sulfonyl)imide anions ([CnMIm][NTf2]) with varying chain-length n = 2, 4, 6, 8 by using molecular dynamics simulations. We show that a reparametrization of the dihedral potentials as well as charges of the [NTf2] anion leads to an improvement of the force field model introduced by Köddermann, Paschek, and Ludwig [ChemPhysChem 8, 2464 (2007)] (KPL-force field). A crucial advantage of the new parameter set is that the minimum energy conformations of the anion (trans and gauche), as deduced from ab initio calculations and Raman experiments, are now both well represented by our model. In addition, the results for [CnMIm][NTf2] show that this modification leads to an even better agreement between experiment and molecular dynamics simulation as demonstrated for densities, diffusion coefficients, vaporization enthalpies, reorientational correlation times, and viscosities. Even though we focused on a better representation of the anion conformation, also the alkyl chain-length dependence of the cation behaves closer to the experiment. We strongly encourage to use the new NGOLP (Neumann, Golub, Odebrecht, Ludwig, Paschek) force field for the [NTf2] anion instead of the earlier KPL parameter set for computer simulations aiming to describe the thermodynamics, dynamics, and also structure of imidazolium-based ionic liquids.

Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension

PubMed Central

Sonne, Jacob; Jensen, Morten Ø.; Hansen, Flemming Y.; Hemmingsen, Lars; Peters, Günther H.

2007-01-01

Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of ∼48 Å2. To obtain fluid (Lα) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2. In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field. PMID:17400696

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility.

PubMed

Drake, Justin A; Harris, Robert C; Pettitt, B Montgomery

2016-08-23

Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Effect of molecular environment on the vibrational dynamics of pyrimidine bases as analysed by NIS, optical spectroscopy and quantum mechanical force fields

NASA Astrophysics Data System (ADS)

Ghomi, M.; Aamouche, A.; Cadioli, B.; Berthier, G.; Grajcar, L.; Baron, M. H.

1997-06-01

A complete set of vibrational spectra, obtained from several spectroscopic techniques, i.e. neutron inelastic scattering (NIS), Raman scattering and infrared absorption (IR), has been used in order to assign the vibrational modes of pyrimidine bases (uracil, thymine, cytosine) and their N-deuterated species. The spectra of solid and aqueous samples allowed us to analyse the effects of hydrogen bonding in crystal and in solution. In a first step, to assign the observed vibrational modes, we have resorted to harmonic quantum mechanical force field, calculated at SCF + MP2 level using double-zeta 6-31G and D95V basis sets with non-standard exponents for d-orbital polarisation functions. In order to improve the agreement between the experimental results obtained in condensed phases and the calculated ones based on isolated molecules, the molecular force field has been scaled. In a second step, to estimate the effect of intermolecular interactions on the vibrational dynamics of pyrimidine bases, we have undertaken additional calculations with the density functional theory (DFT) method using B3LYP functionals and polarised 6-31G basis sets. Two theoretical models have been considered: 1. a uracil embedded in a dielectric continuum ( ɛ = 78), and 2. a uracil H-bonded to two water molecules (through N1 and N3 atoms).

Error analysis regarding the calculation of nonlinear force-free field

NASA Astrophysics Data System (ADS)

Liu, S.; Zhang, H. Q.; Su, J. T.

2012-02-01

Magnetic field extrapolation is an alternative method to study chromospheric and coronal magnetic fields. In this paper, two semi-analytical solutions of force-free fields (Low and Lou in Astrophys. J. 352:343, 1990) have been used to study the errors of nonlinear force-free (NLFF) fields based on force-free factor α. Three NLFF fields are extrapolated by approximate vertical integration (AVI) Song et al. (Astrophys. J. 649:1084, 2006), boundary integral equation (BIE) Yan and Sakurai (Sol. Phys. 195:89, 2000) and optimization (Opt.) Wiegelmann (Sol. Phys. 219:87, 2004) methods. Compared with the first semi-analytical field, it is found that the mean values of absolute relative standard deviations (RSD) of α along field lines are about 0.96-1.19, 0.63-1.07 and 0.43-0.72 for AVI, BIE and Opt. fields, respectively. While for the second semi-analytical field, they are about 0.80-1.02, 0.67-1.34 and 0.33-0.55 for AVI, BIE and Opt. fields, respectively. As for the analytical field, the calculation error of <| RSD|> is about 0.1˜0.2. It is also found that RSD does not apparently depend on the length of field line. These provide the basic estimation on the deviation of extrapolated field obtained by proposed methods from the real force-free field.

Sonoluminescence and sonochemiluminescence study of cavitation field in a 1.2MHz focused ultrasound

NASA Astrophysics Data System (ADS)

Yin, Hui; Qiao, Yangzi; Cao, Hua; Wan, Mingxi

2017-03-01

An intensified CCD (ICCD) and an electron-multiplying CCD (EMCCD) were employed to observe the spatial distribution of sonoluminescence (SL) and sonochemiluminescence (SCL) generated by cavitation bubbles in a 1.2MHz HIFU field. Various sonication conditions, which are free field and focal region near a water-parenchyma interface, were studied. In addition, the differences of two shells coated UCAs were also investigated. In this study, an acoustic radiation force (ARF) counterbalance appliance was added to reduce bubble displacement. Cavitation mapping in this situation was also operated through SCL recording. SCL was also employed to measure cavitation does and map the spatial distribution of cavitation near a boundary of parenchyma.

Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures

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

Hölzl, Christoph; Horinek, Dominik, E-mail: dominik.horinek@ur.de; Kibies, Patrick

Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatmentmore » of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.« less

Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures.

PubMed

Hölzl, Christoph; Kibies, Patrick; Imoto, Sho; Frach, Roland; Suladze, Saba; Winter, Roland; Marx, Dominik; Horinek, Dominik; Kast, Stefan M

2016-04-14

Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures--while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

Spinmotive force due to domain wall motion in high field regime

NASA Astrophysics Data System (ADS)

Ieda, Jun'ichi; Yamane, Yuta; Maekawa, Sadamichi

2012-02-01

Spinmotive force associated with a moving vortex domain wall is investigated numerically. Dynamics of magnetization textures such as a domain wall exerts a non-conservative spin-force on conduction electrons [1], offering a new concept of magnetic devices [2]. This spinmotive force in permalloy nanowires has been detected by voltage measurement [3] where magnitude of the signal is limited less than 500 nV. Theoretically it is suggested that the spinmotive force signal increases as a function of external magnetic fields. At higher magnetic fields, however, the wall propagation mode becomes rather chaotic involving transformations of the wall structure and it remains to be seen how the spinmotive force appears. Numerical simulations show that the spinmotive force scales with the field even in a field range where the wall motion is no longer associated coherent precession. This feature has been tested in a recent experiment [4]. Further enhancement of the spinmotive force is explored by designing ferromagnetic nanostructures [5] and materials. [1] S. Barnes and S. Maekawa, PRL (2007). [2] S. Barnes, J. Ieda, and S. Maekawa, APL (2006). [3] S. A. Yang et al., PRL (2009). [4] M. Hayashi, J. Ieda et al., submitted. [5] Y. Yamane, J. Ieda et al., APEX (2011).

Telemicrobiology for Mission Support in the Field of Infectious Diseases

DTIC Science & Technology

2010-04-01

bacterial meningitis so that important additional verification was lacking. Microscopic diagnoses in the expert laboratory also rarely yield a...With bacterial infections, depending on the country of deployment, also unusual resistance behavior of the pathogens will occur because numerous...missions of the US Forces in the recent years, well-documented with respect to epidemiology , the weekly incidence of infectious diseases was always

Classifying Particles By Acoustic Levitation

NASA Technical Reports Server (NTRS)

Barmatz, Martin B.; Stoneburner, James D.

1983-01-01

Separation technique well suited to material processing. Apparatus with rectangular-cross-section chamber used to measure equilibrium positions of low-density spheres in gravitational field. Vertical acoustic forces generated by two opposing compression drivers exciting fundamental plane-wave mode at 1.2 kHz. Additional horizontal drivers centered samples along vertical axis. Applications in fusion-target separation, biological separation, and manufacturing processes in liquid or gas media.

Brief: Field measurements of casing tension forces

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

Quigley, M.S.; Lewis, D.B.; Boswell, R.S.

1995-02-01

Tension forces acting on individual casing joints were accurately measured during installation of 10,158 ft of 9 5/8-in. {times} 47-lbm/ft casing and 11,960 ft of 11 7/8-in. {times} 71.8-lbm/ft casing. A unique casing load table (CLT) weighed the casing string after the addition of each casing joint. Strain gauges attached inside the pin ends of instrumented casing joints (ICJ`s) directly measured tension force on those joints. A high-speed computer data-acquisition system (DAS) automatically recorded data from all the sensors. Several casing joints were intentionally subjected to extreme deceleration to determine upper limits for dynamic tension forces. Data from these testsmore » clearly show effects of wellbore friction and casing handling conditions. In every case, tension forces in the casing during maximum deceleration were considerably less than expected. In some cases, the highest tension forces occurred when the casing lifted out of the slips. Peak tension forces caused by setting the casing slips were typically no more than 5% greater than tension forces in the casing at rest. This dynamic amplification was far less than the 60% value used in the previous casing design method. Reducing the safety factor for installation loads has permitted use of lighter, less-expensive casing than dictated by older design criteria.« less

Systematic Validation of Protein Force Fields against Experimental Data

PubMed Central

Eastwood, Michael P.; Dror, Ron O.; Shaw, David E.

2012-01-01

Molecular dynamics simulations provide a vehicle for capturing the structures, motions, and interactions of biological macromolecules in full atomic detail. The accuracy of such simulations, however, is critically dependent on the force field—the mathematical model used to approximate the atomic-level forces acting on the simulated molecular system. Here we present a systematic and extensive evaluation of eight different protein force fields based on comparisons of experimental data with molecular dynamics simulations that reach a previously inaccessible timescale. First, through extensive comparisons with experimental NMR data, we examined the force fields' abilities to describe the structure and fluctuations of folded proteins. Second, we quantified potential biases towards different secondary structure types by comparing experimental and simulation data for small peptides that preferentially populate either helical or sheet-like structures. Third, we tested the force fields' abilities to fold two small proteins—one α-helical, the other with β-sheet structure. The results suggest that force fields have improved over time, and that the most recent versions, while not perfect, provide an accurate description of many structural and dynamical properties of proteins. PMID:22384157

77 FR 14006 - Record of Decision for the Military Housing Privatization Initiative Hurlburt Field and Eglin Air...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-08

... DEPARTMENT OF DEFENSE Department of the Air Force Record of Decision for the Military Housing Privatization Initiative Hurlburt Field and Eglin Air Force Base, Florida, Final Environmental Impact Statement... Field and Eglin Air Force Base, Florida, Final Environmental Impact Statement (FEIS). The MHPI ROD...

High-Frequency Intermuscular Coherence between Arm Muscles during Robot-Mediated Motor Adaptation

PubMed Central

Pizzamiglio, Sara; De Lillo, Martina; Naeem, Usman; Abdalla, Hassan; Turner, Duncan L.

2017-01-01

Adaptation of arm reaching in a novel force field involves co-contraction of upper limb muscles, but it is not known how the co-ordination of multiple muscle activation is orchestrated. We have used intermuscular coherence (IMC) to test whether a coherent intermuscular coupling between muscle pairs is responsible for novel patterns of activation during adaptation of reaching in a force field. Subjects (N = 16) performed reaching trials during a null force field, then during a velocity-dependent force field and then again during a null force field. Reaching trajectory error increased during early adaptation to the force-field and subsequently decreased during later adaptation. Co-contraction in the majority of all possible muscle pairs also increased during early adaptation and decreased during later adaptation. In contrast, IMC increased during later adaptation and only in a subset of muscle pairs. IMC consistently occurred in frequencies between ~40–100 Hz and during the period of arm movement, suggesting that a coherent intermuscular coupling between those muscles contributing to adaptation enable a reduction in wasteful co-contraction and energetic cost during reaching. PMID:28119620

Magnetic field exposure stiffens regenerating plant protoplast cell walls.

PubMed

Haneda, Toshihiko; Fujimura, Yuu; Iino, Masaaki

2006-02-01

Single suspension-cultured plant cells (Catharanthus roseus) and their protoplasts were anchored to a glass plate and exposed to a magnetic field of 302 +/- 8 mT for several hours. Compression forces required to produce constant cell deformation were measured parallel to the magnetic field by means of a cantilever-type force sensor. Exposure of intact cells to the magnetic field did not result in any changes within experimental error, while exposure of regenerating protoplasts significantly increased the measured forces and stiffened regenerating protoplasts. The diameters of intact cells or regenerating protoplasts were not changed after exposure to the magnetic field. Measured forces for regenerating protoplasts with and without exposure to the magnetic field increased linearly with incubation time, with these forces being divided into components based on the elasticity of synthesized cell walls and cytoplasm. Cell wall synthesis was also measured using a cell wall-specific fluorescent dye, and no changes were noted after exposure to the magnetic field. Analysis suggested that exposure to the magnetic field roughly tripled the Young's modulus of the newly synthesized cell wall without any lag.

Structural learning in feedforward and feedback control.

PubMed

Yousif, Nada; Diedrichsen, Jörn

2012-11-01

For smooth and efficient motor control, the brain needs to make fast corrections during the movement to resist possible perturbations. It also needs to adapt subsequent movements to improve future performance. It is important that both feedback corrections and feedforward adaptation need to be made based on noisy and often ambiguous sensory data. Therefore, the initial response of the motor system, both for online corrections and adaptive responses, is guided by prior assumptions about the likely structure of perturbations. In the context of correcting and adapting movements perturbed by a force field, we asked whether these priors are hard wired or whether they can be modified through repeated exposure to differently shaped force fields. We found that both feedback corrections to unexpected perturbations and feedforward adaptation to a new force field changed, such that they were appropriate to counteract the type of force field that participants had experienced previously. We then investigated whether these changes were driven by a common mechanism or by two separate mechanisms. Participants experienced force fields that were either temporally consistent, causing sustained adaptation, or temporally inconsistent, causing little overall adaptation. We found that the consistent force fields modified both feedback and feedforward responses. In contrast, the inconsistent force field modified the temporal shape of feedback corrections but not of the feedforward adaptive response. These results indicate that responses to force perturbations can be modified in a structural manner and that these modifications are at least partly dissociable for feedback and feedforward control.

Structural learning in feedforward and feedback control

PubMed Central

Diedrichsen, Jörn

2012-01-01

For smooth and efficient motor control, the brain needs to make fast corrections during the movement to resist possible perturbations. It also needs to adapt subsequent movements to improve future performance. It is important that both feedback corrections and feedforward adaptation need to be made based on noisy and often ambiguous sensory data. Therefore, the initial response of the motor system, both for online corrections and adaptive responses, is guided by prior assumptions about the likely structure of perturbations. In the context of correcting and adapting movements perturbed by a force field, we asked whether these priors are hard wired or whether they can be modified through repeated exposure to differently shaped force fields. We found that both feedback corrections to unexpected perturbations and feedforward adaptation to a new force field changed, such that they were appropriate to counteract the type of force field that participants had experienced previously. We then investigated whether these changes were driven by a common mechanism or by two separate mechanisms. Participants experienced force fields that were either temporally consistent, causing sustained adaptation, or temporally inconsistent, causing little overall adaptation. We found that the consistent force fields modified both feedback and feedforward responses. In contrast, the inconsistent force field modified the temporal shape of feedback corrections but not of the feedforward adaptive response. These results indicate that responses to force perturbations can be modified in a structural manner and that these modifications are at least partly dissociable for feedback and feedforward control. PMID:22896725

Determination of structure and properties of molecular crystals from first principles.

PubMed

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods.

Force-field prediction of materials properties in metal-organic frameworks

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

Boyd, Peter G.; Moosavi, Seyed Mohamad; Witman, Matthew

In this work, MOF bulk properties are evaluated and compared using several force fields on several well-studied MOFs, including IRMOF-1 (MOF-5), IRMOF-10, HKUST-1, and UiO-66. It is found that, surprisingly, UFF and DREIDING provide good values for the bulk modulus and linear thermal expansion coefficients for these materials, excluding those that they are not parametrized for. Force fields developed specifically for MOFs including UFF4MOF, BTW-FF, and the DWES force field are also found to provide accurate values for these materials’ properties. While we find that each force field offers a moderately good picture of these properties, noticeable deviations can bemore » observed when looking at properties sensitive to framework vibrational modes. As a result, this observation is more pronounced upon the introduction of framework charges.« less

Flexible Force Field Parameterization through Fitting on the Ab Initio-Derived Elastic Tensor

PubMed Central

2017-01-01

Constructing functional forms and their corresponding force field parameters for the metal–linker interface of metal–organic frameworks is challenging. We propose fitting these parameters on the elastic tensor, computed from ab initio density functional theory calculations. The advantage of this top-down approach is that it becomes evident if functional forms are missing when components of the elastic tensor are off. As a proof-of-concept, a new flexible force field for MIL-47(V) is derived. Negative thermal expansion is observed and framework flexibility has a negligible effect on adsorption and transport properties for small guest molecules. We believe that this force field parametrization approach can serve as a useful tool for developing accurate flexible force field models that capture the correct mechanical behavior of the full periodic structure. PMID:28661672

Force-field prediction of materials properties in metal-organic frameworks

DOE PAGES

Boyd, Peter G.; Moosavi, Seyed Mohamad; Witman, Matthew; ...

2016-12-23

In this work, MOF bulk properties are evaluated and compared using several force fields on several well-studied MOFs, including IRMOF-1 (MOF-5), IRMOF-10, HKUST-1, and UiO-66. It is found that, surprisingly, UFF and DREIDING provide good values for the bulk modulus and linear thermal expansion coefficients for these materials, excluding those that they are not parametrized for. Force fields developed specifically for MOFs including UFF4MOF, BTW-FF, and the DWES force field are also found to provide accurate values for these materials’ properties. While we find that each force field offers a moderately good picture of these properties, noticeable deviations can bemore » observed when looking at properties sensitive to framework vibrational modes. As a result, this observation is more pronounced upon the introduction of framework charges.« less

Driving reconnection in sheared magnetic configurations with forced fluctuations

NASA Astrophysics Data System (ADS)

Pongkitiwanichakul, Peera; Makwana, Kirit D.; Ruffolo, David

2018-02-01

We investigate reconnection of magnetic field lines in sheared magnetic field configurations due to fluctuations driven by random forcing by means of numerical simulations. The simulations are performed with an incompressible, pseudo-spectral magnetohydrodynamics code in 2D where we take thick, resistively decaying, current-sheet like sheared magnetic configurations which do not reconnect spontaneously. We describe and test the forcing that is introduced in the momentum equation to drive fluctuations. It is found that the forcing does not change the rate of decay; however, it adds and removes energy faster in the presence of the magnetic shear structure compared to when it has decayed away. We observe that such a forcing can induce magnetic reconnection due to field line wandering leading to the formation of magnetic islands and O-points. These reconnecting field lines spread out as the current sheet decays with time. A semi-empirical formula is derived which reasonably explains the formation and spread of O-points. We find that reconnection spreads faster with stronger forcing and longer correlation time of forcing, while the wavenumber of forcing does not have a significant effect. When the field line wandering becomes large enough, the neighboring current sheets with opposite polarity start interacting, and then the magnetic field is rapidly annihilated. This work is useful to understand how forced fluctuations can drive reconnection in large scale current structures in space and astrophysical plasmas that are not susceptible to reconnection.

Magnetically adjustable intraocular lens.

PubMed

Matthews, Michael Wayne; Eggleston, Harry Conrad; Pekarek, Steven D; Hilmas, Greg Eugene

2003-11-01

To provide a noninvasive, magnetic adjustment mechanism to the repeatedly and reversibly adjustable, variable-focus intraocular lens (IOL). University of Missouri-Rolla, Rolla, and Eggleston Adjustable Lens, St. Louis, Missouri, USA. Mechanically adjustable IOLs have been fabricated and tested. Samarium and cobalt rare-earth magnets have been incorporated into the poly(methyl methacrylate) (PMMA) optic of these adjustable lenses. The stability of samarium and cobalt in the PMMA matrix was examined with leaching studies. Operational force testing of the magnetic optics with emphasis on the rotational forces of adjustment was done. Prototype optics incorporating rare-earth magnetic inserts were consistently produced. After 32 days in solution, samarium and cobalt concentration reached a maximum of 5 ppm. Operational force measurements indicate that successful adjustments of this lens can be made using external magnetic fields with rotational torques in excess of 0.6 ounce inch produced. Actual lenses were remotely adjusted using magnetic fields. The magnetically adjustable version of this IOL is a viable and promising means of handling the common issues of postoperative refractive errors without the requirement of additional surgery. The repeatedly adjustable mechanism of this lens also holds promise for the developing eyes of pediatric patients and the changing needs of all patients.

Insole optical fiber Bragg grating sensors network for dynamic vertical force monitoring

NASA Astrophysics Data System (ADS)

Domingues, Maria Fátima; Tavares, Cátia; Leitão, Cátia; Frizera-Neto, Anselmo; Alberto, Nélia; Marques, Carlos; Radwan, Ayman; Rodriguez, Jonathan; Postolache, Octavian; Rocon, Eduardo; André, Paulo; Antunes, Paulo

2017-09-01

In an era of unprecedented progress in technology and increase in population age, continuous and close monitoring of elder citizens and patients is becoming more of a necessity than a luxury. Contributing toward this field and enhancing the life quality of elder citizens and patients with disabilities, this work presents the design and implementation of a noninvasive platform and insole fiber Bragg grating sensors network to monitor the vertical ground reaction forces distribution induced in the foot plantar surface during gait and body center of mass displacements. The acquired measurements are a reliable indication of the accuracy and consistency of the proposed solution in monitoring and mapping the vertical forces active on the foot plantar sole, with a sensitivity up to 11.06 pm/N. The acquired measurements can be used to infer the foot structure and health condition, in addition to anomalies related to spine function and other pathologies (e.g., related to diabetes); also its application in rehabilitation robotics field can dramatically reduce the computational burden of exoskeletons' control strategy. The proposed technology has the advantages of optical fiber sensing (robustness, noninvasiveness, accuracy, and electromagnetic insensitivity) to surpass all drawbacks verified in traditionally used sensing systems (fragility, instability, and inconsistent feedback).

Insole optical fiber Bragg grating sensors network for dynamic vertical force monitoring.

PubMed

Domingues, Maria Fátima; Tavares, Cátia; Leitão, Cátia; Frizera-Neto, Anselmo; Alberto, Nélia; Marques, Carlos; Radwan, Ayman; Rodriguez, Jonathan; Postolache, Octavian; Rocon, Eduardo; André, Paulo; Antunes, Paulo

2017-09-01

In an era of unprecedented progress in technology and increase in population age, continuous and close monitoring of elder citizens and patients is becoming more of a necessity than a luxury. Contributing toward this field and enhancing the life quality of elder citizens and patients with disabilities, this work presents the design and implementation of a noninvasive platform and insole fiber Bragg grating sensors network to monitor the vertical ground reaction forces distribution induced in the foot plantar surface during gait and body center of mass displacements. The acquired measurements are a reliable indication of the accuracy and consistency of the proposed solution in monitoring and mapping the vertical forces active on the foot plantar sole, with a sensitivity up to 11.06 ?? pm / N . The acquired measurements can be used to infer the foot structure and health condition, in addition to anomalies related to spine function and other pathologies (e.g., related to diabetes); also its application in rehabilitation robotics field can dramatically reduce the computational burden of exoskeletons’ control strategy. The proposed technology has the advantages of optical fiber sensing (robustness, noninvasiveness, accuracy, and electromagnetic insensitivity) to surpass all drawbacks verified in traditionally used sensing systems (fragility, instability, and inconsistent feedback).

Entropy generation minimization (EGM) of nanofluid flow by a thin moving needle with nonlinear thermal radiation

NASA Astrophysics Data System (ADS)

Waleed Ahmed Khan, M.; Ijaz Khan, M.; Hayat, T.; Alsaedi, A.

2018-04-01

Entropy generation minimization (EGM) and heat transport in nonlinear radiative flow of nanomaterials over a thin moving needle has been discussed. Nonlinear thermal radiation and viscous dissipation terms are merged in the energy expression. Water is treated as ordinary fluid while nanomaterials comprise titanium dioxide, copper and aluminum oxide. The nonlinear governing expressions of flow problems are transferred to ordinary ones and then tackled for numerical results by Built-in-shooting technique. In first section of this investigation, the entropy expression is derived as a function of temperature and velocity gradients. Geometrical and physical flow field variables are utilized to make it nondimensionalized. An entropy generation analysis is utilized through second law of thermodynamics. The results of temperature, velocity, concentration, surface drag force and heat transfer rate are explored. Our outcomes reveal that surface drag force and Nusselt number (heat transfer) enhanced linearly for higher nanoparticle volume fraction. Furthermore drag force decays for aluminum oxide and it enhances for copper nanoparticles. In addition, the lowest heat transfer rate is achieved for higher radiative parameter. Temperature field is enhanced with increase in temperature ratio parameter.

Mechanical testing and development of the helical field coil joint for the Advanced Toroidal Facility

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

Nelson, B.E.; Bryan, W.E.; Goranson, P.L.

1985-01-01

The helical field (HF) coil set for the Advanced Toroidal Facility (ATF) is an M = 12, l = 2, constant-ratio torsatron winding consisting of 2 coils, each with 14 turns of heavy copper conductor. The coils are divided into 24 identical segments to facilitate fabrication and minimize the assembly schedule. The segments are connected across through-bolted lap joints that must carry up to 124,000 A per turn for 5 s or 62,500 A steady-state. In addition, the joints must carry the high magnetic and thermal loads induced in the conductor and still fit within the basic 140- by 30-mmmore » copper envelope. Extensive testing and development were undertaken to verify and refine the basic joint design. Tests included assembly force and clamping force for various types of misalignment; joint resistance as a function of clamping force; clamp bolt relaxation due to thermal cycling; fatigue testing of full-size, multiturn joint prototypes; and low-cycle fatigue and tensile tests of annealed CDA102 copper. The required performance parameters and actual test results, as well as the final joint configuration, are presented. 2 refs., 9 figs., 4 tabs.« less

Molecular Mechanics

PubMed Central

Vanommeslaeghe, Kenno; Guvench, Olgun; MacKerell, Alexander D.

2014-01-01

Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This section introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments such as polarizable force fields are discussed. The section ends with a brief overview of common force fields in CSBDD. PMID:23947650

The edge of supersymmetry: Stability walls in heterotic theory

DOE PAGES

Anderson, Lara B.; Gray, James; Lukas, Andre; ...

2009-05-15

We explicitly describe, in the language of four-dimensional N = 1 supersymmetric field theory, what happens when the moduli of a heterotic Calabi-Yau compactification change so as to make the internal non-Abelian gauge fields non-supersymmetric. At the edge of the region in Kähler moduli space where supersymmetry can be preserved, an additional anomalous U(1) gauge symmetry appears in the four-dimensional theory. The D-term contribution to the scalar potential associated to this U(1) attempts to force the system back into a supersymmetric configuration and provides a consistent low-energy description of gauge bundle stability.

Vehicle Charging And Potential (VCAP)

NASA Astrophysics Data System (ADS)

Roberts, B.

1986-01-01

The vehicle charging and potential (VCAP) payload includes a small electron accelerator capable of operating in a pulsed mode with firing pulses ranging from 600 nanoseconds to 107 seconds (100 milliamps at 1000 volts), a spherical retarding potential analyzer - Langmuir probe, and charge current probes. This instrumentation will support studies of beam plasma interactions and the electrical charging of the spacecraft. Active experiments may also be performed to investigate the fundamental processes of artificial aurora and ionospheric perturbations. In addition, by firing the beam up the geomagnetic field lines of force (away from the Earth) investigations of parallel electric field may be performed.

Vehicle Charging And Potential (VCAP)

NASA Astrophysics Data System (ADS)

Roberts, W. T.

The vehicle charging and potential (VCAP) payload includes a small electron accelerator capable of operating in a pulsed mode with firing pulses ranging from 600 nanoseconds to 107 seconds (100 milliamps at 1000 volts), a spherical retarding potential analyzer - Langmuir probe, and charge current probes. This instrumentation will support studies of beam plasma interactions and the electrical charging of the spacecraft. Active experiments may also be performed to investigate the fundamental processes of artificial aurora and ionospheric perturbations. In addition, by firing the beam up the geomagnetic field lines of force (away from the Earth) investigations of parallel electric field may be performed.

Experimental measurements of rf breakdowns and deflecting gradients in mm-wave metallic accelerating structures

DOE PAGES

Dal Forno, Massimo; Dolgashev, Valery; Bowden, Gordon; ...

2016-05-03

We present an experimental study of a high-gradient metallic accelerating structure at sub-THz frequencies, where we investigated the physics of rf breakdowns. Wakefields in the structure were excited by an ultrarelativistic electron beam. We present the first quantitative measurements of gradients and metal vacuum rf breakdowns in sub-THz accelerating cavities. When the beam travels off axis, a deflecting field is induced in addition to the longitudinal field. We measured the deflecting forces by observing the displacement and changes in the shape of the electron bunch. This behavior can be exploited for subfemtosecond beam diagnostics.

A data-driven decomposition approach to model aerodynamic forces on flapping airfoils

NASA Astrophysics Data System (ADS)

Raiola, Marco; Discetti, Stefano; Ianiro, Andrea

2017-11-01

In this work, we exploit a data-driven decomposition of experimental data from a flapping airfoil experiment with the aim of isolating the main contributions to the aerodynamic force and obtaining a phenomenological model. Experiments are carried out on a NACA 0012 airfoil in forward flight with both heaving and pitching motion. Velocity measurements of the near field are carried out with Planar PIV while force measurements are performed with a load cell. The phase-averaged velocity fields are transformed into the wing-fixed reference frame, allowing for a description of the field in a domain with fixed boundaries. The decomposition of the flow field is performed by means of the POD applied on the velocity fluctuations and then extended to the phase-averaged force data by means of the Extended POD approach. This choice is justified by the simple consideration that aerodynamic forces determine the largest contributions to the energetic balance in the flow field. Only the first 6 modes have a relevant contribution to the force. A clear relationship can be drawn between the force and the flow field modes. Moreover, the force modes are closely related (yet slightly different) to the contributions of the classic potential models in literature, allowing for their correction. This work has been supported by the Spanish MINECO under Grant TRA2013-41103-P.

Force, torque, linear momentum, and angular momentum in classical electr odynamics

NASA Astrophysics Data System (ADS)

Mansuripur, Masud

2017-10-01

The classical theory of electrodynamics is built upon Maxwell's equations and the concepts of electromagnetic (EM) field, force, energy, and momentum, which are intimately tied together by Poynting's theorem and by the Lorentz force law. Whereas Maxwell's equations relate the fields to their material sources, Poynting's theorem governs the flow of EM energy and its exchange between fields and material media, while the Lorentz law regulates the back-and-forth transfer of momentum between the media and the fields. An alternative force law, first proposed by Einstein and Laub, exists that is consistent with Maxwell's equations and complies with the conservation laws as well as with the requirements of special relativity. While the Lorentz law requires the introduction of hidden energy and hidden momentum in situations where an electric field acts on a magnetized medium, the Einstein-Laub (E-L) formulation of EM force and torque does not invoke hidden entities under such circumstances. Moreover, total force/torque exerted by EM fields on any given object turns out to be independent of whether the density of force/torque is evaluated using the law of Lorentz or that of Einstein and Laub. Hidden entities aside, the two formulations differ only in their predicted force and torque distributions inside matter. Such differences in distribution are occasionally measurable, and could serve as a guide in deciding which formulation, if either, corresponds to physical reality.

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

PubMed

Beauchamp, Kyle A; Behr, Julie M; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

2015-10-08

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.

A transferable force field for CdS-CdSe-PbS-PbSe solid systems

NASA Astrophysics Data System (ADS)

Fan, Zhaochuan; Koster, Rik S.; Wang, Shuaiwei; Fang, Changming; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; van Huis, Marijn A.; Vlugt, Thijs J. H.

2014-12-01

A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., "Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth," Nano Lett. 14, 3661-3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and CdS, and provide detailed information on the validation of this force field. The parameterization combines Bader charge analysis, empirical fitting, and ab initio energy surface fitting. When compared with experimental data and density functional theory calculations, it is shown that a wide range of physical properties of bulk PbS, PbSe, CdS, CdSe, and their mixed phases can be accurately reproduced using this force field. The choice of functional forms and parameterization strategy is demonstrated to be rational and effective. This transferable force field can be used in various studies on II-VI and IV-VI semiconductor materials consisting of CdS, CdSe, PbS, and PbSe. Here, we demonstrate the applicability of the force field model by molecular dynamics simulations whereby transformations are initiated by cation exchange.

Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35-56) in aqueous environment.

PubMed

Kundu, Sangeeta

2018-02-01

The hallmark of Parkinson's disease (PD) is the intracellular protein aggregation forming Lewy Bodies (LB) and Lewy neuritis which comprise mostly of a protein, alpha synuclein (α-syn). Molecular dynamics (MD) simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution. The quality of MD simulations for proteins and peptides depends greatly on the accuracy of empirical force fields. The aim of this work is to investigate the effects of different force fields on the structural character of β hairpin fragment of α-syn (residues 35-56) peptide in aqueous solution. Six independent MD simulations are done in explicit solvent using, AMBER03, AMBER99SB, GROMOS96 43A1, GROMOS96 53A6, OPLS-AA, and CHARMM27 force fields with CMAP corrections. The performance of each force field is assessed from several structural parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), formation of β-turn, the stability of folded β-hairpin structure, and the favourable conformations obtained for different force fields. In this study, CMAP correction of CHARMM27 force field is found to overestimate the helical conformation, while GROMOS96 53A6 is found to most successfully capture the conformational dynamics of α-syn β-hairpin fragment as elicited from NMR.

Dynamo Induced by Time-periodic Force

NASA Astrophysics Data System (ADS)

Wei, Xing

2018-03-01

To understand the dynamo driven by time-dependent flow, e.g., turbulence, we investigate numerically the dynamo induced by time-periodic force in rotating magnetohydrodynamic flow and focus on the effect of force frequency on the dynamo action. It is found that the dynamo action depends on the force frequency. When the force frequency is near resonance the force can drive dynamo, but when it is far away from resonance dynamo fails. In the frequency range near resonance to support dynamo, the force frequency at resonance induces a weak magnetic field and magnetic energy increases as the force frequency deviates from the resonant frequency. This is opposite to the intuition that a strong flow at resonance will induce a strong field. It is because magnetic field nonlinearly couples with fluid flow in the self-sustained dynamo and changes the resonance of driving force and inertial wave.

In Situ Measurement of Aerosol Extinction

NASA Technical Reports Server (NTRS)

Strawa, Anthony W.; Castaneda, R.; Owano, T. G.; Bear, D.; Gore, Warren J. (Technical Monitor)

2001-01-01

Aerosols are important contributors to the radiative forcing in the atmosphere. Much of the uncertainty in our knowledge of climate forcing is due to uncertainties in the radiative forcing due to aerosols as illustrated in the IPCC reports of the last ten years. Improved measurement of aerosol optical properties, therefore, is critical to an improved understanding of atmospheric radiative forcing. Additionally, attempts to reconcile in situ and remote measurements of aerosol radiative properties have generally not been successful. This is due in part to the fact that it has been impossible to measure aerosol extinction in situ in the past. In this presentation we introduce a new instrument that employs the techniques used in cavity ringdown spectroscopy to measure the aerosol extinction and scattering coefficients in situ. A prototype instrument has been designed and tested in the lab and the field. It is capable of measuring aerosol extinction coefficient to 2x10(exp -6) per meter. This prototype instrument is described and results are presented.

Relaxation of microparticles exposed to hydrodynamic forces in microfluidic conduits.

PubMed

Janča, Josef; Halabalová, Věra; Polášek, Vladimír; Vašina, Martin; Menshikova, Anastasia Yu

2011-02-01

The behavior of microparticles exposed to gravitational and lift forces and to the velocity gradient in flow velocity profile formed in microfluidic conduits is studied from the viewpoint of the transient period (the relaxation) between the moment at which a particle starts to be transported by the hydrodynamic flow and the time at which it reaches an equilibrium position, characterized by a balance of all active forces. The theoretical model allowing the calculation of the relaxation time is proposed. The numerical calculus based on the proposed model is compared with the experimental data obtained under different experimental conditions, namely, for different lengths of microfluidic channels, different average linear velocities of the carrier liquid, and different sizes and densities of the particles used in the study. The results are important for the optimization of microfluidic separation units such as microthermal field-flow fractionation channels in which the separation or manipulation of the microparticles of various origin, synthetic, natural, biological, etc., is performed under similar experimental conditions but by applying an additional thermodynamic force.

Air Force construction automation/robotics

NASA Technical Reports Server (NTRS)

Nease, A. D.; Alexander, E. F.

1993-01-01

The Air Force has several missions which generate unique requirements that are being met through the development of construction robotic technology. One especially important mission will be the conduct of Department of Defense (DOD) space activities. Space operations and other missions place construction/repair equipment operators in dangerous environments and potentially harmful situations. Additionally, force reductions require that human resources be leveraged to the maximum extent possible, and more stringent construction repair requirements push for increased automation. To solve these problems, the U.S. Air Force is undertaking a research and development effort at Tyndall AFB, FL, to develop robotic construction/repair equipment. This development effort involves the following technologies: teleoperation, telerobotics, construction operations (excavation, grading, leveling, tool change), robotic vehicle communications, vehicle navigation, mission/vehicle task control architecture, and associated computing environment. The ultimate goal is the fielding of a robotic repair capability operating at the level of supervised autonomy. This paper will discuss current and planned efforts in space construction/repair, explosive ordnance disposal, hazardous waste cleanup, and fire fighting.

Finger-Shaped GelForce: Sensor for Measuring Surface Traction Fields for Robotic Hand.

PubMed

Sato, K; Kamiyama, K; Kawakami, N; Tachi, S

2010-01-01

It is believed that the use of haptic sensors to measure the magnitude, direction, and distribution of a force will enable a robotic hand to perform dexterous operations. Therefore, we develop a new type of finger-shaped haptic sensor using GelForce technology. GelForce is a vision-based sensor that can be used to measure the distribution of force vectors, or surface traction fields. The simple structure of the GelForce enables us to develop a compact finger-shaped GelForce for the robotic hand. GelForce that is developed on the basis of an elastic theory can be used to calculate surface traction fields using a conversion equation. However, this conversion equation cannot be analytically solved when the elastic body of the sensor has a complicated shape such as the shape of a finger. Therefore, we propose an observational method and construct a prototype of the finger-shaped GelForce. By using this prototype, we evaluate the basic performance of the finger-shaped GelForce. Then, we conduct a field test by performing grasping operations using a robotic hand. The results of this test show that using the observational method, the finger-shaped GelForce can be successfully used in a robotic hand.

Evaluation of reactive force fields for prediction of the thermo-mechanical properties of cellulose Iâ

Treesearch

Fernando L. Dri; Xiawa Wu; Robert J. Moon; Ashlie Martini; Pablo D. Zavattieri

2015-01-01

Molecular dynamics simulation is commonly used to study the properties of nanocellulose-based materials at the atomic scale. It is well known that the accuracy of these simulations strongly depends on the force field that describes energetic interactions. However, since there is no force field developed specifically for cellulose, researchers utilize models...

The calculation of transport phenomena in electromagnetically levitated metal droplets

NASA Technical Reports Server (NTRS)

El-Kaddah, N.; Szekely, J.

1982-01-01

A mathematical representation has been developed for the electromagnetic force field, fluid flow field, and solute concentration field of levitation-melted metal specimens. The governing equations consist of the conventional transport equations combined with the appropriate expressions for the electromagnetic force field. The predictions obtained by solving the governing equations numerically on a digital computer are in good agreement with lifting force and average temperature measurements reported in the literature.

Comparison of gimbal approaches to decrease drag force and radar cross sectional area in missile application

NASA Astrophysics Data System (ADS)

Sakarya, Doǧan Uǧur

2017-05-01

Drag force effect is an important aspect of range performance in missile applications especially for long flight time. However, old fashioned gimbal approaches force to increase missile diameter. This increase has negative aspect of rising in both drag force and radar cross sectional area. A new gimbal approach was proposed recently. It uses a beam steering optical arrangement. Therefore, it needs less volume envelope for same field of regard and same optomechanical assembly than the old fashioned gimbal approaches. In addition to longer range performance achieved with same fuel in the new gimbal approach, this method provides smaller cross sectional area which can be more invisible in enemies' radar. In this paper, the two gimbal approaches - the old fashioned one and the new one- are compared in order to decrease drag force and radar cross sectional area in missile application. In this study; missile parameters are assumed to generate gimbal and optical design parameters. Optical design is performed according to these missile criteria. Two gimbal configurations are designed with respect to modeled missile parameters. Also analyzes are performed to show decreased drag force and radar cross sectional area in the new approach for comparison.

Perspective: Ab initio force field methods derived from quantum mechanics

NASA Astrophysics Data System (ADS)

Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

2018-03-01

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

Comparing Molecular Dynamics Force Fields in the Essential Subspace

PubMed Central

Gomez-Puertas, Paulino; Boomsma, Wouter; Lindorff-Larsen, Kresten

2015-01-01

The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship between force-field parameterization, the resulting ensemble of conformations and the agreement with experiments. In particular, our results show that, at a coarse level, many of the motional properties are preserved across several, though not all, force fields. At a finer level of detail, however, there are distinct differences in both the structure and dynamics of the two proteins, which can, together with comparison with experimental data, help to select force fields for simulations of proteins. A noteworthy observation is that force fields that have been reparameterized and improved to provide a more accurate energetic description of the balance between helical and coil structures are difficult to distinguish from their “unbalanced” counterparts in these simulations. This observation implies that simulations of stable, folded proteins, even those reaching 10 microseconds in length, may provide relatively little information that can be used to modify torsion parameters to achieve an accurate balance between different secondary structural elements. PMID:25811178

Acoustic forcing of a liquid drop

NASA Technical Reports Server (NTRS)

Lyell, M. J.

1992-01-01

The development of systems such as acoustic levitation chambers will allow for the positioning and manipulation of material samples (drops) in a microgravity environment. This provides the capability for fundamental studies in droplet dynamics as well as containerless processing work. Such systems use acoustic radiation pressure forces to position or to further manipulate (e.g., oscillate) the sample. The primary objective was to determine the effect of a viscous acoustic field/tangential radiation pressure forcing on drop oscillations. To this end, the viscous acoustic field is determined. Modified (forced) hydrodynamic field equations which result from a consistent perturbation expansion scheme are solved. This is done in the separate cases of an unmodulated and a modulated acoustic field. The effect of the tangential radiation stress on the hydrodynamic field (drop oscillations) is found to manifest as a correction to the velocity field in a sublayer region near the drop/host interface. Moreover, the forcing due to the radiation pressure vector at the interface is modified by inclusion of tangential stresses.

Dielectrophoretic immobilization of proteins: Quantification by atomic force microscopy.

PubMed

Laux, Eva-Maria; Knigge, Xenia; Bier, Frank F; Wenger, Christian; Hölzel, Ralph

2015-09-01

The combination of alternating electric fields with nanometer-sized electrodes allows the permanent immobilization of proteins by dielectrophoretic force. Here, atomic force microscopy is introduced as a quantification method, and results are compared with fluorescence microscopy. Experimental parameters, for example the applied voltage and duration of field application, are varied systematically, and the influence on the amount of immobilized proteins is investigated. A linear correlation to the duration of field application was found by atomic force microscopy, and both microscopical methods yield a square dependence of the amount of immobilized proteins on the applied voltage. While fluorescence microscopy allows real-time imaging, atomic force microscopy reveals immobilized proteins obscured in fluorescence images due to low S/N. Furthermore, the higher spatial resolution of the atomic force microscope enables the visualization of the protein distribution on single nanoelectrodes. The electric field distribution is calculated and compared to experimental results with very good agreement to atomic force microscopy measurements. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular dynamics simulations of methane hydrate using polarizable force fields

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

Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

2007-06-14

Molecular dynamics simulations of methane hydrate have been carried out using the polarizable AMOEBA and COS/G2 force fields. Properties calculated include the temperature dependence of the lattice constant, the OC and OO radial distribution functions, and the vibrational spectra. Both the AMOEBA and COS/G2 force fields are found to successfully account for the available experimental data, with overall somewhat better agreement with experiment being found for the AMOEBA model. Comparison is made with previous results obtained using TIP4P and SPC/E effective two-body force fields and the polarizable TIP4P-FQ force field, which allows for in-plane polarization only. Significant differences are foundmore » between the properties calculated using the TIP4P-FQ model and those obtained using the other models, indicating an inadequacy of restricting explicit polarization to in-plane onl« less

The Alexandria library, a quantum-chemical database of molecular properties for force field development.

PubMed

Ghahremanpour, Mohammad M; van Maaren, Paul J; van der Spoel, David

2018-04-10

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

The Alexandria library, a quantum-chemical database of molecular properties for force field development

NASA Astrophysics Data System (ADS)

Ghahremanpour, Mohammad M.; van Maaren, Paul J.; van der Spoel, David

2018-04-01

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

Molecular dynamics simulations of polarizable DNA in crystal environment

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Baucom, Jason; Darden, Thomas A.; Sagui, Celeste

We have investigated the role of the electrostatic description and cell environment in molecular dynamics (MD) simulations of DNA. Multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2 have been carried out using two different force fields: a traditional description based on atomic point charges and a polarizable force field. For the time scales probed, and given the ?right? distribution of divalent ions, the latter performs better than the nonpolarizable force field. In particular, by imposing the experimental unit cell environment, an initial configuration with ideal B-DNA duplexes in the unit cell acquires sequence-dependent features that very closely resemble the crystallographic ones. Simultaneously, the all-atom root-mean-square coordinates deviation (RMSD) with respect to the crystallographic structure is seen to decay. At later times, the polarizable force field is able to maintain this lower RMSD, while the nonpolarizable force field starts to drift away.

An Engineer's Physics Lab -- using a Large Force Frame

NASA Astrophysics Data System (ADS)

Heid, Christy; Rampolla, Donald

2009-03-01

We have constructed very economical, easy to assemble force frames that are used by students in our general physics laboratory at Chatham University. The force frame is used at the beginning of the semester to study vector properties of forces. The force frame can be used as a horizontal or vertical force table. Angles of forces are measured using a large movable (rotation and translation) Cartesian coordinate board attached to the frame with large binder clips. The force frame is a versatile device which is used for a number of other experiments, including beam bending and torsion, mechanical resonance, projectile trajectories, torque, mechanical equilibrium, an isolated non-magnetic support for magnetic field experiments, easily adjustable support for inclined plane experiments, support for traveling wave experiments with heavy rope, and support for large scale fluid flow experiments. One advantage to a wood frame is that things can be easily stapled, nailed, screwed or glued just about anywhere on the frame, and damaged frame members can be replaced easily. As one of the few remaining women's undergraduate institutions, we have found the use of these frames to provide an additional advantage in helping women overcome their fear of simple power tools and assembly of mechanical parts as they become comfortable with these through working with the force frames throughout the semester. We intend to describe and model these applications during the session.

Dynamic Stall of Finite Span Blades and its Control

NASA Astrophysics Data System (ADS)

Taylor, Keith; Leong, Chia; Amitay, Michael

2013-11-01

An experimental investigational study into a dynamically pitching s809 airfoil at a Reynolds number of 220,000 was conducted. Particle Image Velocimetry was employed to visualize and quantify the flow field around the airfoil. This investigation compares a 2-D configuration with 3-D configuration (i.e., a finite span blade). The difference in the flow field between these two configurations is explored, as the vibrations present in the 3-D configuration (due to the dynamic stall) may contribute to a different apparent flow field than classical results would suggest. In addition, a comparison between lift and drag coefficients, measured on the 2-D and 3-D configurations, is explored, demonstrating how time varying lift and drag forces oscillate at characteristic frequencies associated with the primary vibrational modes of the model. In addition, flow control is applied through the actuation of an array of synthetic jets located near the leading edge of the model, in order to effect changes in the flow field around the model, demonstrating how dynamic stall can be delayed or eliminated during dynamic conditions.

The force-free configuration of flux ropes in geomagnetotail: Cluster observations

NASA Astrophysics Data System (ADS)

Yang, Y. Y.; Shen, C.; Zhang, Y. C.; Rong, Z. J.; Li, X.; Dunlop, M.; Ma, Y. H.; Liu, Z. X.; Carr, C. M.; Rème, H.

2014-08-01

Unambiguous knowledge of magnetic field structure and the electric current distribution is critical for understanding the origin, evolution, and related dynamic properties of magnetic flux ropes (MFRs). In this paper, a survey of 13 MFRs in the Earth's magnetotail are conducted by Cluster multipoint analysis, so that their force-free feature, i.e., the kind of magnetic field structure satisfying J × B = 0, can be probed directly. It is showed that the selected flux ropes with the bipolar signature of the south-north magnetic field component generally lie near the equatorial plane, as expected, and that the magnetic field gradient is rather weak near the axis center, where the curvature radius is large. The current density (up to several tens of nA/m2) reaches their maximum values as the center is approached. It is found that the stronger the current density, the smaller the angles between the magnetic field and current in MFRs. The direct observations show that only quasi force-free structure is observed, and it tends to appear in the low plasma beta regime (in agreement with the theoretic results). The quasi force-free region is generally found to be embedded in the central portion of the MFRs, where the current is approximately field aligned and proportional to the strength of core field. It is shown that ~60% of surveyed MFRs can be globally approximated as force free. The force-free factor α is found to be nonconstantly varied through the quasi force-free MFR, suggesting that the force-free structure is nonlinear.

Tailor-made force fields for crystal-structure prediction.

PubMed

Neumann, Marcus A

2008-08-14

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

Evaluation of the attractive force of different types of new-generation magnetic attachment systems.

PubMed

Akin, Hakan; Coskun, M Emre; Akin, E Gulsah; Ozdemir, A Kemal

2011-03-01

Rare earth magnets have been used in prosthodontics, but their tendency for corrosion in the oral cavity and insufficient attractive forces limit long-term clinical application. The purpose of this study was to evaluate the attractive force of different types of new-generation magnetic attachment systems. The attractive force of the neodymium-iron-boron (Nd-Fe-B) and samarium-cobalt (Sm-Co) magnetic attachment systems, including closed-field (Hilop and Hicorex) and open-field (Dyna and Steco) systems, was measured in a universal testing machine (n=5). The data were statistically evaluated with 1-way ANOVA and post hoc Tukey-Kramer multiple comparison test (α=.05). The closed-field systems exhibited greater (P<.001) attractive force than the open-field systems. Moreover, there was a statistically significant difference in attractive force between Nd-Fe-B and Sm-Co magnets (P<.001). The strongest attractive force was found with the Hilop system (9.2 N), and the lowest force was found with the Steco system (2.3 N). The new generation of Nd-Fe-B closed-field magnets, along with improved technology, provides sufficient denture retention for clinical application. Copyright © 2011 The Editorial Council of the Journal of Prosthetic Dentistry. Published by Mosby, Inc. All rights reserved.

Dynamics of a rigid body in an inhomogenous force field

NASA Astrophysics Data System (ADS)

Resch, Andreas; Laemmerzahl, Claus; Lorek, Dennis; Schaffer, Isabell

Extended rigid bodies do not move on geodesics but couple to the space-time curvature. We discuss this effect at the Newtonian level where the deviation from the ordinary Keplerian orbits occurs in two ways: we obtain an additional force in the equation of motion for the center-of-mass and a torque acting on the rotational degrees of freedom. We give a survey of the dynamics for various initial conditions. We discuss whether these modifications of the equations of motion can explain the so-called flyby anomaly. In particular, the behavior of satellites during a flyby is studied and a comparison with the flyby anomaly of Galileo, NEAR, Cassini and Rosetta is made.

Topological constraints and the existence of force-free fields

NASA Technical Reports Server (NTRS)

Antiochos, S. K.

1986-01-01

A fundamental problem in plasma theory is the question of the existence of MHD equilibria. The issue of topological constraints is of crucial importance for the problem of the existence of equilibria. Heuristic methods are used to discuss the coronal wrapping pattern. It is concluded that for a given set of footpoint positions the wrapping pattern in the corona is completely fixed. The topological constraints are included in the boundary conditions on the Euler potentials and impost no additional restrictions on possible equilibria. Although this does not prove that equilibria always exist, it does show that the force-free problem is not overdetermined and that existence of equilibria is still an open question.

KSC-2009-6550

NASA Image and Video Library

2009-10-19

VANDENBERG AIR FORCE BASE, Calif. - At the Astrotech payload processing facility at Vandenberg Air Force Base in California, spacecraft technicians supervise the lift of a transportation canister containing NASA's Wide-field Infrared Survey Explorer, or WISE, from a work stand for its move to Space Launch Complex 2. WISE will survey the entire sky at infrared wavelengths, creating a cosmic clearinghouse of hundreds of millions of objects which will be catalogued and provide a vast storehouse of knowledge about the solar system, the Milky Way, and the universe. Launch aboard a United Launch Alliance Delta II rocket is scheduled for Dec. 9. For additional information, visit http://www.nasa.gov/wise. Photo credit: NASA/Daniel Liberotti, VAFB

KSC-2009-6543

NASA Image and Video Library

2009-10-18

VANDENBERG AIR FORCE BASE, Calif. - At the Astrotech payload processing facility at Vandenberg Air Force Base in California, spacecraft technicians inspect the direct mate adapter, a transport fixture on which NASA's Wide-field Infrared Survey Explorer, or WISE, enclosed in an environmental covering, will be moved to Space Launch Complex 2. WISE will survey the entire sky at infrared wavelengths, creating a cosmic clearinghouse of hundreds of millions of objects which will be catalogued and provide a vast storehouse of knowledge about the solar system, the Milky Way, and the universe. Launch aboard a United Launch Alliance Delta II rocket is scheduled for Dec. 9. For additional information, visit http://www.nasa.gov/wise. Photo credit: NASA

KSC-2009-6547

NASA Image and Video Library

2009-10-19

VANDENBERG AIR FORCE BASE, Calif. - At the Astrotech payload processing facility at Vandenberg Air Force Base in California, spacecraft technicians secure the transportation canister, in which NASA's Wide-field Infrared Survey Explorer, or WISE, is enclosed, to the direct mate adapter, a transport fixture, for the spacecraft's move to Space Launch Complex 2. WISE will survey the entire sky at infrared wavelengths, creating a cosmic clearinghouse of hundreds of millions of objects which will be catalogued and provide a vast storehouse of knowledge about the solar system, the Milky Way, and the universe. Launch aboard a United Launch Alliance Delta II rocket is scheduled for Dec. 9. For additional information, visit http://www.nasa.gov/wise. Photo credit: NASA/Daniel Liberotti, VAFB

Numerical Simulations of Plasma Based Flow Control Applications

NASA Technical Reports Server (NTRS)

Suzen, Y. B.; Huang, P. G.; Jacob, J. D.; Ashpis, D. E.

2005-01-01

A mathematical model was developed to simulate flow control applications using plasma actuators. The effects of the plasma actuators on the external flow are incorporated into Navier Stokes computations as a body force vector. In order to compute this body force vector, the model solves two additional equations: one for the electric field due to the applied AC voltage at the electrodes and the other for the charge density representing the ionized air. The model is calibrated against an experiment having plasma-driven flow in a quiescent environment and is then applied to simulate a low pressure turbine flow with large flow separation. The effects of the plasma actuator on control of flow separation are demonstrated numerically.

Axisymmetric analysis of a tube-type acoustic levitator by a finite element method.

PubMed

Hatano, H

1994-01-01

A finite element approach was taken for the study of the sound field and positioning force in a tube-type acoustic levitator. An axisymmetric model, where a rigid sphere is suspended on the tube axis, was introduced to model a cylindrical chamber of a levitation tube furnace. Distributions of velocity potential, magnitudes of positioning force, and resonance frequency shifts of the chamber due to the presence of the sphere were numerically estimated in relation to the sphere's position and diameter. Experiments were additionally made to compare with the simulation. The finite element method proved to be a useful tool for analyzing and designing the tube-type levitator.

NONLINEAR FORCE-FREE FIELD MODELING OF A SOLAR ACTIVE REGION USING SDO/HMI AND SOLIS/VSM DATA

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

Thalmann, J. K.; Wiegelmann, T.; Pietarila, A.

2012-08-15

We use SDO/HMI and SOLIS/VSM photospheric magnetic field measurements to model the force-free coronal field above a solar active region, assuming magnetic forces dominate. We take measurement uncertainties caused by, e.g., noise and the particular inversion technique, into account. After searching for the optimum modeling parameters for the particular data sets, we compare the resulting nonlinear force-free model fields. We show the degree of agreement of the coronal field reconstructions from the different data sources by comparing the relative free energy content, the vertical distribution of the magnetic pressure, and the vertically integrated current density. Though the longitudinal and transversemore » magnetic flux measured by the VSM and HMI is clearly different, we find considerable similarities in the modeled fields. This indicates the robustness of the algorithm we use to calculate the nonlinear force-free fields against differences and deficiencies of the photospheric vector maps used as an input. We also depict how much the absolute values of the total force-free, virial, and the free magnetic energy differ and how the orientation of the longitudinal and transverse components of the HMI- and VSM-based model volumes compare to each other.« less

The harmonic force field of benzene. A local density functional study

NASA Astrophysics Data System (ADS)

Bérces, Attila; Ziegler, Tom

1993-03-01

The harmonic force field of benzene has been calculated by a method based on local density functional theory (LDF). The calculations were carried out employing a triple zeta basis set with triple polarization on hydrogen and double polarization on carbon. The LDF force field was compared to the empirical field due to Ozkabak, Goodman, and Thakur [A. G. Ozkabak, L. Goodman, and S. N. Thakur, J. Phys. Chem. 95, 9044 (1991)], which has served as a benchmark for theoretical calculations as well as the theoretical field based on scaled Hartree-Fock ab initio calculation due to Pulay, Fogarasi, and Boggs [P. Pulay, G. Fogarasi, and J. E. Boggs, J. Chem. Phys. 74, 3999 (1981)]. The calculated LDF force field is in excellent qualitative and very good quantitative agreement with the theoretical field proposed by Pulay, Fogarasi, and Boggs as well as the empirical field due to Ozkabak, Goodman, and Thakur. The LDF field is closest to the values of Pulay and co-workers in those cases where the force constants due to Pulay, Fogarasi, and Boggs and to Ozkabak, Goodman, and Thakur differ in sign or magnitude. The accuracy of the LDF force field was investigated by evaluating a number of eigenvalue and eigenfunction dependent quantities from the the LDF force constants. The quantities under investigation include vibrational frequencies of seven isotopomers, isotopic shifts, as well as absorption intensities. The calculations were performed at both theoretical optimized and approximate equilibrium reference geometries. The predicted frequencies are usually within 1%-2% compared to the empirical harmonic frequencies. The least accurate frequency deviates by 5% from the experimental value. The average deviations from the empirical harmonic frequencies of C6H6 and C6D6 are 16.7 cm-1 (1.5%) and 15.2 cm-1 (1.7%), respectively, not including CH stretching frequencies, in the case where a theoretical reference geometry was used. The accuracy of the out-of-plane force field is especially remarkable; the average deviations for the C6H6 and C6D6 frequencies, based on the LDF force field, are 9.4 cm-1 (1.2%) and 7.3 cm-1 (1.2%), respectively. The absorption intensities were not predicted as accurately as it was expected based on the size of the basis set applied. An analysis is provided to ensure that the force constants are not significantly affected by numerical errors due to the numerical integration scheme employed.

Spectroscopically determined force field for water dimer: physically enhanced treatment of hydrogen bonding in molecular mechanics energy functions.

PubMed

Mannfors, Berit; Palmo, Kim; Krimm, Samuel

2008-12-11

Our ab initio transformed spectroscopically determined force field (SDFF) methodology emphasizes, in addition to accurate structure and energy performance, comparable prediction of vibrational properties in order to improve reproduction of interaction forces. It is now applied to the determination of a molecular mechanics (MM) force field for the water monomer and dimer as an initial step in developing a more physically based treatment of the hydrogen bonding that not only underlies condensed-phase water but also must be important in molecular-level protein-water interactions. Essential electrical components of the SDFF for monomer water are found to be the following: an off-plane charge distribution, this distribution consisting of four off-atom charge sites in traditional lone pair (LP) but also in inverted lone pair (ILP) positions; allowance for a diffuse size to these off-atom sites; and the incorporation of charge fluxes (i.e., the change in charge with change in internal coordinate). Parametrization of such an LP/ILP model together with the SDFF analytically transformed valence force field results in essentially exact agreement with ab initio (in this case MP2/6-31++G(d,p)) structure, electrical, and vibrational properties. Although we demonstrate that the properties of this monomer electrical model together with its van der Waals and polarization interactions are transferable to the dimer, this is not sufficient in reproducing comparable dimer properties, most notably the huge increase in infrared intensity of a donor OH stretch mode. This deficiency, which can be eliminated by a large dipole-derivative-determined change in the effective charge flux of the donor hydrogen-bonded OH bond, is not accounted for by the charge flux change in this bond due to the induction effects of the acceptor electric field alone, and can only be fully removed by an added bond flux associated with the extent of overlap of the wave functions of the two molecules. We show that this overlap charge flux (OCF) emulates an actual O-H...LP-O intermolecular dipole flux, reflecting the unitary nature of the hydrogen-bonded system in the context of MM-separable molecules. The effectiveness of incorporating the OCF noncanonical character demonstrates that a distinctively QM-unique property can be substantively represented in MM energy functions.

3D-QSAR based on quantum-chemical molecular fields: toward an improved description of halogen interactions.

PubMed

Güssregen, Stefan; Matter, Hans; Hessler, Gerhard; Müller, Marco; Schmidt, Friedemann; Clark, Timothy

2012-09-24

Current 3D-QSAR methods such as CoMFA or CoMSIA make use of classical force-field approaches for calculating molecular fields. Thus, they can not adequately account for noncovalent interactions involving halogen atoms like halogen bonds or halogen-π interactions. These deficiencies in the underlying force fields result from the lack of treatment of the anisotropy of the electron density distribution of those atoms, known as the "σ-hole", although recent developments have begun to take specific interactions such as halogen bonding into account. We have now replaced classical force field derived molecular fields by local properties such as the local ionization energy, local electron affinity, or local polarizability, calculated using quantum-mechanical (QM) techniques that do not suffer from the above limitation for 3D-QSAR. We first investigate the characteristics of QM-based local property fields to show that they are suitable for statistical analyses after suitable pretreatment. We then analyze these property fields with partial least-squares (PLS) regression to predict biological affinities of two data sets comprising factor Xa and GABA-A/benzodiazepine receptor ligands. While the resulting models perform equally well or even slightly better in terms of consistency and predictivity than the classical CoMFA fields, the most important aspect of these augmented field-types is that the chemical interpretation of resulting QM-based property field models reveals unique SAR trends driven by electrostatic and polarizability effects, which cannot be extracted directly from CoMFA electrostatic maps. Within the factor Xa set, the interaction of chlorine and bromine atoms with a tyrosine side chain in the protease S1 pocket are correctly predicted. Within the GABA-A/benzodiazepine ligand data set, PLS models of high predictivity resulted for our QM-based property fields, providing novel insights into key features of the SAR for two receptor subtypes and cross-receptor selectivity of the ligands. The detailed interpretation of regression models derived using improved QM-derived property fields thus provides a significant advantage by revealing chemically meaningful correlations with biological activity and helps in understanding novel structure-activity relationship features. This will allow such knowledge to be used to design novel molecules on the basis of interactions additional to steric and hydrogen-bonding features.

Multiloop atom interferometer measurements of chameleon dark energy in microgravity

NASA Astrophysics Data System (ADS)

Chiow, Sheng-wey; Yu, Nan

2018-02-01

Chameleon field is one of the promising candidates of dark energy scalar fields. As in all viable candidate field theories, a screening mechanism is implemented to be consistent with all existing tests of general relativity. The screening effect in the chameleon theory manifests its influence limited only to the thin outer layer of a bulk object, thus producing extra forces orders of magnitude weaker than that of the gravitational force of the bulk. For pointlike particles such as atoms, the depth of screening is larger than the size of the particle, such that the screening mechanism is ineffective and the chameleon force is fully expressed on the atomic test particles. Extra force measurements using atom interferometry are thus much more sensitive than bulk mass based measurements, and indeed have placed the most stringent constraints on the parameters characterizing chameleon field. In this paper, we present a conceptual measurement approach for chameleon force detection using atom interferometry in microgravity, in which multiloop atom interferometers exploit specially designed periodic modulation of chameleon fields. We show that major systematics of the dark energy force measurements, i.e., effects of gravitational forces and their gradients, can be suppressed below all hypothetical chameleon signals in the parameter space of interest.

Force field dependent solution properties of glycine oligomers

PubMed Central

Drake, Justin A.

2015-01-01

Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly3 and Gly10 in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g. end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

PubMed Central

Petrov, Drazen; Zagrovic, Bojan

2014-01-01

The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the picture of protein behavior in biologically relevant crowded environments. PMID:24854339

Magnetically actuated tissue engineered scaffold: insights into mechanism of physical stimulation

NASA Astrophysics Data System (ADS)

Sapir-Lekhovitser, Yulia; Rotenberg, Menahem Y.; Jopp, Juergen; Friedman, Gary; Polyak, Boris; Cohen, Smadar

2016-02-01

Providing the right stimulatory conditions resulting in efficient tissue promoting microenvironment in vitro and in vivo is one of the ultimate goals in tissue development for regenerative medicine. It has been shown that in addition to molecular signals (e.g. growth factors) physical cues are also required for generation of functional cell constructs. These cues are particularly relevant to engineering of biological tissues, within which mechanical stress activates mechano-sensitive receptors, initiating biochemical pathways which lead to the production of functionally mature tissue. Uniform magnetic fields coupled with magnetizable nanoparticles embedded within three dimensional (3D) scaffold structures remotely create transient physical forces that can be transferrable to cells present in close proximity to the nanoparticles. This study investigated the hypothesis that magnetically responsive alginate scaffold can undergo reversible shape deformation due to alignment of scaffold's walls in a uniform magnetic field. Using custom made Helmholtz coil setup adapted to an Atomic Force Microscope we monitored changes in matrix dimensions in situ as a function of applied magnetic field, concentration of magnetic particles within the scaffold wall structure and rigidity of the matrix. Our results show that magnetically responsive scaffolds exposed to an externally applied time-varying uniform magnetic field undergo a reversible shape deformation. This indicates on possibility of generating bending/stretching forces that may exert a mechanical effect on cells due to alternating pattern of scaffold wall alignment and relaxation. We suggest that the matrix structure deformation is produced by immobilized magnetic nanoparticles within the matrix walls resulting in a collective alignment of scaffold walls upon magnetization. The estimated mechanical force that can be imparted on cells grown on the scaffold wall at experimental conditions is in the order of 1 pN, which correlates well with reported threshold to induce mechanotransduction effects on cellular level. This work is our next step in understanding of how to accurately create proper stimulatory microenvironment for promotion of cellular organization to form mature tissue engineered constructs.

Magnetically actuated tissue engineered scaffold: insights into mechanism of physical stimulation

PubMed Central

Sapir-Lekhovitser, Yulia; Rotenberg, Menahem Y.; Jopp, Juergen; Friedman, Gary; Polyak, Boris; Cohen, Smadar

2016-01-01

Providing the right stimulatory conditions resulting in efficient tissue promoting microenvironment in vitro and in vivo is one of the ultimate goals in tissue development for regenerative medicine. It has been shown that in addition to molecular signals (e.g. growth factors) physical cues are also required for generation of functional cell constructs. These cues are particularly relevant to engineering of biological tissues, within which mechanical stress activates mechano-sensitive receptors, initiating biochemical pathways which lead to the production of functionally mature tissue. Uniform magnetic fields coupled with magnetizable nanoparticles embedded within three dimensional (3D) scaffold structures remotely create transient physical forces that can be transferrable to cells present in close proximity to the nanoparticles. This study investigated the hypothesis that magnetically responsive alginate scaffold can undergo reversible shape deformation due to alignment of scaffold’s walls in a uniform magnetic field. Using custom made Helmholtz coil setup adapted to an Atomic Force Microscope we monitored changes in matrix dimensions in situ as a function of applied magnetic field, concentration of magnetic particles within the scaffold wall structure and rigidity of the matrix. Our results show that magnetically responsive scaffolds exposed to an externally applied time-varying uniform magnetic field undergo a reversible shape deformation. This indicates on possibility of generating bending/stretching forces that may exert a mechanical effect on cells due to alternating pattern of scaffold wall alignment and relaxation. We suggest that the matrix structure deformation is produced by immobilized magnetic nanoparticles within the matrix walls resulting in a collective alignment of scaffold walls upon magnetization. The estimated mechanical force that can be imparted on cells grown on the scaffold wall at experimental conditions is in the order of 1 pN, which correlates well with reported threshold to induce mechanotransduction effects on cellular level. This work is our next step in understanding of how to accurately create proper stimulatory microenvironment for promotion of cellular organization to form mature tissue engineered constructs. PMID:26790538

Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers.

PubMed

Bennett, W F Drew; Hong, Chun Kit; Wang, Yi; Tieleman, D Peter

2016-09-13

Due to antimicrobial resistance, the development of new drugs to combat bacterial and fungal infections is an important area of research. Nature uses short, charged, and amphipathic peptides for antimicrobial defense, many of which disrupt the lipid membrane in addition to other possible targets inside the cell. Computer simulations have revealed atomistic details for the interactions of antimicrobial peptides and cell-penetrating peptides with lipid bilayers. Strong interactions between the polar interface and the charged peptides can induce bilayer deformations - including membrane rupture and peptide stabilization of a hydrophilic pore. Here, we performed microsecond-long simulations of the antimicrobial peptide CM15 in a POPC bilayer expecting to observe pore formation (based on previous molecular dynamics simulations). We show that caution is needed when interpreting results of equilibrium peptide-membrane simulations, given the length of time single trajectories can dwell in local energy minima for 100's of ns to microseconds. While we did record significant membrane perturbations from the CM15 peptide, pores were not observed. We explain this discrepancy by computing the free energy for pore formation with different force fields. Our results show a large difference in the free energy barrier (ca. 40 kJ/mol) against pore formation predicted by the different force fields that would result in orders of magnitude differences in the simulation time required to observe spontaneous pore formation. This explains why previous simulations using the Berger lipid parameters reported pores induced by charged peptides, while with CHARMM based models pores were not observed in our long time-scale simulations. We reconcile some of the differences in the distance dependent free energies by shifting the free energy profiles to account for thickness differences between force fields. The shifted curves show that all the models describe small defects in lipid bilayers in a consistent manner, suggesting a common physical basis.

Acquisition Logistics Guidelines for Improving the Argentine Air Force Weapon System Acquisition Process

DTIC Science & Technology

1999-03-01

these kinds of sources: Industry standards Other commercial or military customers LMI specification summaries Contractor’s in-house data Section...government and industry managers to achieve program objectives. • Putting in place for fielded systems additional incentives to reduce operating and...meaning clarifications; an explanation of the roles of Congress, the Executive Branch, and Industry in defense acquisition; and an overview on the

Surface-Micromachined Microfluidic Devices

DOEpatents

Galambos, Paul C.; Okandan, Murat; Montague, Stephen; Smith, James H.; Paul, Phillip H.; Krygowski, Thomas W.; Allen, James J.; Nichols, Christopher A.; Jakubczak, II, Jerome F.

2004-09-28

Microfluidic devices are disclosed which can be manufactured using surface-micromachining. These devices utilize an electroosmotic force or an electromagnetic field to generate a flow of a fluid in a microchannel that is lined, at least in part, with silicon nitride. Additional electrodes can be provided within or about the microchannel for separating particular constituents in the fluid during the flow based on charge state or magnetic moment. The fluid can also be pressurized in the channel. The present invention has many different applications including electrokinetic pumping, chemical and biochemical analysis (e.g. based on electrophoresis or chromatography), conducting chemical reactions on a microscopic scale, and forming hydraulic actuators. Microfluidic devices are disclosed which can be manufactured using surface-micromachining. These devices utilize an electroosmotic force or an electromagnetic field to generate a flow of a fluid in a microchannel that is lined, at least in part, with silicon nitride. Additional electrodes can be provided within or about the microchannel for separating particular constituents in the fluid during the flow based on charge state or magnetic moment. The fluid can also be pressurized in the channel. The present invention has many different applications including electrokinetic pumping, chemical and biochemical analysis (e.g. based on electrophoresis or chromatography), conducting chemical reactions on a microscopic scale, and forming hydraulic actuators.

Concurrent use of magnetic bearings for rotor support and force sensing for the nondestructive evaluation of manufacturing processes

NASA Astrophysics Data System (ADS)

Kasarda, Mary; Imlach, Joseph; Balaji, P. A.; Marshall, Jeremy T.

2000-06-01

Active magnetic bearings are a proven technology in turbomachinery applications and they offer considerable promise for improving the performance of manufacturing processes. The Active Magnetic Bearing (AMB) is a feedback mechanism that supports a spinning shaft by levitating it in a magnetic field. AMBs have significantly higher surface speed capability than rolling element bearings and they eliminate the potential for product contamination by eliminating the requirement for bearing lubrication. In addition, one of the most promising capabilities for manufacturing applications is the ability of the AMB to act concurrently as both a support bearing and non-invasive force sensor. The feedback nature of the AMB allows for its use as a load cell to continuously measure shaft forces necessary for levitation based on information about the magnetic flux density in the air gaps. This measurement capability may be exploited to improve the process control of such products as textile fibers and photographic films where changes in shaft loads may indicate changes in product quality. This paper discusses the operation of AMBs and their potential benefits in manufacturing equipment along with results from research addressing accurate AMB force sensing performance in field applications. Specifically, results from the development of enhanced AMB measurement algorithms to better account for magnetic fringing and leakage effects to improve the accuracy of this technique are presented. Results from the development of a new on-line calibration procedure for robust in-situ calibration of AMBs in a field application such as a manufacturing plant scenario are also presented including results of Magnetic Finite Element Analysis (MFEA) verification of the procedure.

Adaptation of multijoint coordination during standing balance in healthy young and healthy old individuals

PubMed Central

Pasma, J. H.; Schouten, A. C.; Aarts, R. G. K. M.; Meskers, C. G. M.; Maier, A. B.; van der Kooij, H.

2015-01-01

Standing balance requires multijoint coordination between the ankles and hips. We investigated how humans adapt their multijoint coordination to adjust to various conditions and whether the adaptation differed between healthy young participants and healthy elderly. Balance was disturbed by push/pull rods, applying two continuous and independent force disturbances at the level of the hip and between the shoulder blades. In addition, external force fields were applied, represented by an external stiffness at the hip, either stabilizing or destabilizing the participants' balance. Multivariate closed-loop system-identification techniques were used to describe the neuromuscular control mechanisms by quantifying the corrective joint torques as a response to body sway, represented by frequency response functions (FRFs). Model fits on the FRFs resulted in an estimation of time delays, intrinsic stiffness, reflexive stiffness, and reflexive damping of both the ankle and hip joint. The elderly generated similar corrective joint torques but had reduced body sway compared with the young participants, corresponding to the increased FRF magnitude with age. When a stabilizing or destabilizing external force field was applied at the hip, both young and elderly participants adapted their multijoint coordination by lowering or respectively increasing their neuromuscular control actions around the ankles, expressed in a change of FRF magnitude. However, the elderly adapted less compared with the young participants. Model fits on the FRFs showed that elderly had higher intrinsic and reflexive stiffness of the ankle, together with higher time delays of the hip. Furthermore, the elderly adapted their reflexive stiffness around the ankle joint less compared with young participants. These results imply that elderly were stiffer and were less able to adapt to external force fields. PMID:26719084

Charge/spin supercurrent and the Fulde-Ferrell state induced by crystal deformation in Weyl/Dirac superconductors

NASA Astrophysics Data System (ADS)

Matsushita, Taiki; Liu, Tianyu; Mizushima, Takeshi; Fujimoto, Satoshi

2018-04-01

It has been predicted that emergent chiral magnetic fields can be generated by crystal deformation in Weyl/Dirac metals and superconductors. The emergent fields give rise to chiral anomaly phenomena as in the case of Weyl semimetals with usual electromagnetic fields. Here, we clarify effects of the chiral magnetic field on Cooper pairs in Weyl/Dirac superconductors on the basis of the Ginzburg-Landau equation microscopically derived from the quasiclassical Eilenberger formalism. It is found that Cooper pairs are affected by the emergent chiral magnetic field in a dramatic way, and the pseudo-Lorentz force due to the chiral magnetic field stabilizes the Fulde-Ferrell state and causes a charge/spin supercurrent, which flows parallel to the chiral magnetic field in the case of Weyl/Dirac superconductors. This effect is in analogy with the chiral magnetic effect of Weyl semimetals. In addition, we elucidate that neither Meissner effect nor vortex state due to chiral magnetic fields occurs.

The Introduction of Fields in Relation to Force

ERIC Educational Resources Information Center

Brunt, Marjorie; Brunt, Geoff

2012-01-01

The introduction of force at age 14-16 years is considered, starting with elementary student experiments using magnetic force fields. The meaningless use of terms such as "action" and "reaction", or "agent" and "receiver" is discussed. (Contains 6 figures.)

A Tapered Aluminium Microelectrode Array for Improvement of Dielectrophoresis-Based Particle Manipulation

PubMed Central

Buyong, Muhamad Ramdzan; Larki, Farhad; Faiz, Mohd Syafiq; Hamzah, Azrul Azlan; Yunas, Jumrail; Majlis, Burhanuddin Yeop

2015-01-01

In this work, the dielectrophoretic force (FDEP) response of Aluminium Microelectrode Arrays with tapered profile is investigated through experimental measurements and numerical simulations. A standard CMOS processing technique with a step for the formation of a tapered profile resist is implemented in the fabrication of Tapered Aluminium Microelectrode Arrays (TAMA). The FDEP is investigated through analysis of the Clausius-Mossotti factor (CMF) and cross-over frequency (fxo). The performance of TAMA with various side wall angles is compared to that of microelectrodes with a straight cut sidewall profile over a wide range of frequencies through FEM numerical simulations. Additionally, electric field measurement (EFM) is performed through scanning probe microscopy (SPM) in order to obtain the region of force focus in both platforms. Results showed that the tapered profile microelectrodes with angles between 60° and 70° produce the highest electric field gradient on the particles. Also, the region of the strongest electric field in TAMA is located at the bottom and top edge of microelectrode while the strongest electric field in microelectrodes with straight cut profile is found at the top corner of the microelectrode. The latter property of microelectrodes improves the probability of capturing/repelling the particles at the microelectrode’s side wall. PMID:25970255

A tapered aluminium microelectrode array for improvement of dielectrophoresis-based particle manipulation.

PubMed

Buyong, Muhamad Ramdzan; Larki, Farhad; Faiz, Mohd Syafiq; Hamzah, Azrul Azlan; Yunas, Jumrail; Majlis, Burhanuddin Yeop

2015-05-11

In this work, the dielectrophoretic force (F(DEP)) response of Aluminium Microelectrode Arrays with tapered profile is investigated through experimental measurements and numerical simulations. A standard CMOS processing technique with a step for the formation of a tapered profile resist is implemented in the fabrication of Tapered Aluminium Microelectrode Arrays (TAMA). The F(DEP) is investigated through analysis of the Clausius-Mossotti factor (CMF) and cross-over frequency (f(xo)). The performance of TAMA with various side wall angles is compared to that of microelectrodes with a straight cut sidewall profile over a wide range of frequencies through FEM numerical simulations. Additionally, electric field measurement (EFM) is performed through scanning probe microscopy (SPM) in order to obtain the region of force focus in both platforms. Results showed that the tapered profile microelectrodes with angles between 60° and 70° produce the highest electric field gradient on the particles. Also, the region of the strongest electric field in TAMA is located at the bottom and top edge of microelectrode while the strongest electric field in microelectrodes with straight cut profile is found at the top corner of the microelectrode. The latter property of microelectrodes improves the probability of capturing/repelling the particles at the microelectrode's side wall.

Improved characterization of heterogeneous permeability in saline aquifers from transient pressure data during freshwater injection

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

Kang, Peter K.; Lee, Jonghyun; Fu, Xiaojing

Managing recharge of freshwater into saline aquifers requires accurate estimation of the heterogeneous permeability field for maximizing injection and recovery efficiency. Here we present a methodology for subsurface characterization in saline aquifers that takes advantage of the density difference between the injected freshwater and the ambient saline groundwater. We combine high-resolution forward modeling of density-driven flow with an efficient Bayesian geostatistical inversion algorithm. In the presence of a density difference between the injected and ambient fluids due to differences in salinity, the pressure field is coupled to the spatial distribution of salinity. This coupling renders the pressure field transient: themore » time evolution of the salinity distribution controls the density distribution which then leads to a time-evolving pressure distribution. We exploit this coupling between pressure and salinity to obtain an improved characterization of the permeability field without multiple pumping tests or additional salinity measurements. We show that the inversion performance improves with an increase in the mixed convection ratio—the relative importance between viscous forces from injection and buoyancy forces from density difference. Thus, our work shows that measuring transient pressure data at multiple sampling points during freshwater injection into saline aquifers can be an effective strategy for aquifer characterization, key to the successful management of aquifer recharge.« less

Field-driven chiral bubble dynamics analysed by a semi-analytical approach

NASA Astrophysics Data System (ADS)

Vandermeulen, J.; Leliaert, J.; Dupré, L.; Van Waeyenberge, B.

2017-12-01

Nowadays, field-driven chiral bubble dynamics in the presence of the Dzyaloshinskii-Moriya interaction are a topic of thorough investigation. In this paper, a semi-analytical approach is used to derive equations of motion that express the bubble wall (BW) velocity and the change in in-plane magnetization angle as function of the micromagnetic parameters of the involved interactions, thereby taking into account the two-dimensional nature of the bubble wall. It is demonstrated that the equations of motion enable an accurate description of the expanding and shrinking convex bubble dynamics and an expression for the transition field between shrinkage and expansion is derived. In addition, these equations of motion show that the BW velocity is not only dependent on the driving force, but also on the BW curvature. The absolute BW velocity increases for both a shrinking and an expanding bubble, but for different reasons: for expanding bubbles, it is due to the increasing importance of the driving force, while for shrinking bubbles, it is due to the increasing importance of contributions related to the BW curvature. Finally, using this approach we show how the recently proposed magnetic bubblecade memory can operate in the flow regime in the presence of a tilted sinusoidal magnetic field and at greatly reduced bubble sizes compared to the original device prototype.

Improved characterization of heterogeneous permeability in saline aquifers from transient pressure data during freshwater injection

DOE PAGES

Kang, Peter K.; Lee, Jonghyun; Fu, Xiaojing; ...

2017-05-31

Managing recharge of freshwater into saline aquifers requires accurate estimation of the heterogeneous permeability field for maximizing injection and recovery efficiency. Here we present a methodology for subsurface characterization in saline aquifers that takes advantage of the density difference between the injected freshwater and the ambient saline groundwater. We combine high-resolution forward modeling of density-driven flow with an efficient Bayesian geostatistical inversion algorithm. In the presence of a density difference between the injected and ambient fluids due to differences in salinity, the pressure field is coupled to the spatial distribution of salinity. This coupling renders the pressure field transient: themore » time evolution of the salinity distribution controls the density distribution which then leads to a time-evolving pressure distribution. We exploit this coupling between pressure and salinity to obtain an improved characterization of the permeability field without multiple pumping tests or additional salinity measurements. We show that the inversion performance improves with an increase in the mixed convection ratio—the relative importance between viscous forces from injection and buoyancy forces from density difference. Thus, our work shows that measuring transient pressure data at multiple sampling points during freshwater injection into saline aquifers can be an effective strategy for aquifer characterization, key to the successful management of aquifer recharge.« less

Particle-in-cell simulations of Hall plasma thrusters

NASA Astrophysics Data System (ADS)

Miranda, Rodrigo; Ferreira, Jose Leonardo; Martins, Alexandre

2016-07-01

Hall plasma thrusters can be modelled using particle-in-cell (PIC) simulations. In these simulations, the plasma is described by a set of equations which represent a coupled system of charged particles and electromagnetic fields. The fields are computed using a spatial grid (i.e., a discretization in space), whereas the particles can move continuously in space. Briefly, the particle and fields dynamics are computed as follows. First, forces due to electric and magnetic fields are employed to calculate the velocities and positions of particles. Next, the velocities and positions of particles are used to compute the charge and current densities at discrete positions in space. Finally, these densities are used to solve the electromagnetic field equations in the grid, which are interpolated at the position of the particles to obtain the acting forces, and restart this cycle. We will present numerical simulations using software for PIC simulations to study turbulence, wave and instabilities that arise in Hall plasma thrusters. We have sucessfully reproduced a numerical simulation of a SPT-100 Hall thruster using a two-dimensional (2D) model. In addition, we are developing a 2D model of a cylindrical Hall thruster. The results of these simulations will contribute to improve the performance of plasma thrusters to be used in Cubesats satellites currenty in development at the Plasma Laboratory at University of Brasília.

Memory effects for a stochastic fractional oscillator in a magnetic field

NASA Astrophysics Data System (ADS)

Mankin, Romi; Laas, Katrin; Laas, Tõnu; Paekivi, Sander

2018-01-01

The problem of random motion of harmonically trapped charged particles in a constant external magnetic field is studied. A generalized three-dimensional Langevin equation with a power-law memory kernel is used to model the interaction of Brownian particles with the complex structure of viscoelastic media (e.g., dusty plasmas). The influence of a fluctuating environment is modeled by an additive fractional Gaussian noise. In the long-time limit the exact expressions of the first-order and second-order moments of the fluctuating position for the Brownian particle subjected to an external periodic force in the plane perpendicular to the magnetic field have been calculated. Also, the particle's angular momentum is found. It is shown that an interplay of external periodic forcing, memory, and colored noise can generate a variety of cooperation effects, such as memory-induced sign reversals of the angular momentum, multiresonance versus Larmor frequency, and memory-induced particle confinement in the absence of an external trapping field. Particularly in the case without external trapping, if the memory exponent is lower than a critical value, we find a resonancelike behavior of the anisotropy in the particle position distribution versus the driving frequency, implying that it can be efficiently excited by an oscillating electric field. Similarities and differences between the behaviors of the models with internal and external noises are also discussed.

On radiation forces acting on a transparent nanoparticle in the field of a focused laser beam

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

Afanas'ev, A A; Rubinov, A N; Gaida, L S

2015-10-31

Radiation forces acting on a transparent spherical nanoparticle in the field of a focused Gaussian laser beam are studied theoretically in the Rayleigh scattering regime. Expressions are derived for the scattering force and Cartesian components of the gradient force. The resultant force acting on a nanoparticle located in the centre of a laser beam is found. The parameters of the focused beam and optical properties of the nanoparticle for which the longitudinal component of the gradient force exceeds the scattering force are determined. Characteristics of the transverse gradient force are discussed. (nanophotonics)

The Tai Chi in Star Formation

NASA Astrophysics Data System (ADS)

Li, Hua-bai

2017-10-01

Tai Chi, a Chinese martial art developed based on the laws of nature, emphasises how 'to conquer the unyielding with the yielding'. The recent observation of star formation shows that stars result from the interaction between gravity, turbulence and magnetic fields. This interaction again follows the nature rules that inspired Tai Chi. For example, if self-gravity is the force that dominates, the molecular cloud will collapse isotropically, which compresses magnetic field lines. The density of the yielding field lines increases until magnetic pressure reaches the critical value to support the cloud against the gravitational force in directions perpendicular to the field lines (Lorentz force). Then gravity gives way to Lorentz force, accumulating gas only along the field lines till the gas density achieves the critical value to again compress the field lines. The Tai Chi goes on in a self-similar way.

Driving Force of Plasma Bullet in Atmospheric-Pressure Plasma

NASA Astrophysics Data System (ADS)

Yambe, Kiyoyuki; Masuda, Seiya; Kondo, Shoma

2018-06-01

When plasma is generated by applying high-voltage alternating current (AC), the driving force of the temporally and spatially varying electric field is applied to the plasma. The strength of the driving force of the plasma at each spatial position is different because the electrons constituting the atmospheric-pressure nonequilibrium (cold) plasma move at a high speed in space. If the force applied to the plasma is accelerated only by the driving force, the plasma will be accelerated infinitely. The equilibrium between the driving force and the restricting force due to the collision between the plasma and neutral particles determines the inertial force and the drift velocity of the plasma. Consequently, the drift velocity depends on the strength of the time-averaged AC electric field. The pressure applied by the AC electric field equilibrates with the plasma pressure. From the law of conservation of energy, the pressure equilibrium is maintained by varying the drift velocity of the plasma.

Introducing a new and rapid microextraction approach based on magnetic ionic liquids: Stir bar dispersive liquid microextraction.

PubMed

Chisvert, Alberto; Benedé, Juan L; Anderson, Jared L; Pierson, Stephen A; Salvador, Amparo

2017-08-29

With the aim of contributing to the development and improvement of microextraction techniques, a novel approach combining the principles and advantages of stir bar sorptive extraction (SBSE) and dispersive liquid-liquid microextraction (DLLME) is presented. This new approach, termed stir bar dispersive liquid microextraction (SBDLME), involves the addition of a magnetic ionic liquid (MIL) and a neodymium-core magnetic stir bar into the sample allowing the MIL coat the stir bar due to physical forces (i.e., magnetism). As long as the stirring rate is maintained at low speed, the MIL resists rotational (centrifugal) forces and remains on the stir bar surface in a manner closely resembling SBSE. By increasing the stirring rate, the rotational forces surpass the magnetic field and the MIL disperses into the sample solution in a similar manner to DLLME. After extraction, the stirring is stopped and the MIL returns to the stir bar without the requirement of an additional external magnetic field. The MIL-coated stir bar containing the preconcentrated analytes is thermally desorbed directly into a gas chromatographic system coupled to a mass spectrometric detector (TD-GC-MS). This novel approach opens new insights into the microextraction field, by using the benefits provided by SBSE and DLLME simultaneously, such as automated thermal desorption and high surface contact area, respectively, but most importantly, it enables the use of tailor-made solvents (i.e., MILs). To prove its utility, SBDLME has been used in the extraction of lipophilic organic UV filters from environmental water samples as model analytical application with excellent analytical features in terms of linearity, enrichment factors (67-791), limits of detection (low ng L -1 ), intra- and inter-day repeatability (RSD<15%) and relative recoveries (87-113%, 91-117% and 89-115% for river, sea and swimming pool water samples, respectively). Copyright © 2017 Elsevier B.V. All rights reserved.

Repetitively Pulsed Nonequilibrium Plasmas for Plasma-Assisted Combustion, Flow Control, and Molecular Lasers

NASA Astrophysics Data System (ADS)

Adamovich, Igor

2006-10-01

The paper presents results of three experiments using high voltage, short pulse duration, high repetition rate discharge plasmas. High electric field during the pulse (E/N˜500-1000 Td) allows efficient ionization and molecular dissociation. Between the pulses, additional energy can be coupled to the decaying plasma using a DC field set below the breakdown threshold. While the DC sustainer discharge adds 90-95% of all the power to the flow, it does not produce any additional ionization. The pulser and the sustainer discharges are fully overlapped in space. Low duty cycle of the pulsed ionizer, ˜1/1000, allows sustaining diffuse and uniform pulser-sustainer plasmas at high pressures and power loadings. The first experiment using the pulsed discharge is ignition of premixed hydrocarbon-air flows, which occurs at low pulsed discharge powers, ˜100 W, and very low plasma temperatures, 100-200^0 C. The second experiment is Lorentz force acceleration of low-temperature supersonic flows. The pulsed discharge was used to generate electrical conductivity in M=3 nitrogen and air flows, while the sustainer discharge produced transverse current in the presence of magnetic field of B=1.5 T. Retarding Lorentz force applied to the flow produced a static pressure increase of up to 15-20%, while accelerating force of the same magnitude resulted in static pressure rise of up to 7-8%, i.e. a factor of two smaller. The third experiment is singlet delta oxygen (SDO) generation in a high-pressure pulser-sustainer discharge. SDO yield was inferred from the integrated intensity of SDO infrared emission spectra calibrated using a blackbody source. The measured yield exceeds the laser threshold yield by about a factor of three, which makes possible achieving positive gain in the laser cavity. The highest gain measured so far is 0.03%/cm.

Flows, Fields, and Forces in the Mars-Solar Wind Interaction

NASA Astrophysics Data System (ADS)

Halekas, J. S.; Brain, D. A.; Luhmann, J. G.; DiBraccio, G. A.; Ruhunusiri, S.; Harada, Y.; Fowler, C. M.; Mitchell, D. L.; Connerney, J. E. P.; Espley, J. R.; Mazelle, C.; Jakosky, B. M.

2017-11-01

We utilize suprathermal ion and magnetic field measurements from the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission, organized by the upstream magnetic field, to investigate the morphology and variability of flows, fields, and forces in the Mars-solar wind interaction. We employ a combination of case studies and statistical investigations to characterize the interaction in both quasi-parallel and quasi-perpendicular regions and under high and low solar wind Mach number conditions. For the first time, we include a detailed investigation of suprathermal ion temperature and anisotropy. We find that the observed magnetic fields and suprathermal ion moments in the magnetosheath, bow shock, and upstream regions have observable asymmetries controlled by the interplanetary magnetic field, with particularly large asymmetries found in the ion parallel temperature and anisotropy. The greatest temperature anisotropies occur in quasi-perpendicular regions of the magnetosheath and under low Mach number conditions. These results have implications for the growth and evolution of wave-particle instabilities and their role in energy transport and dissipation. We utilize the measured parameters to estimate the average ion pressure gradient, J × B, and v × B macroscopic force terms. The pressure gradient force maintains nearly cylindrical symmetry, while the J × B force has larger asymmetries and varies in magnitude in comparison to the pressure gradient force. The v × B force felt by newly produced planetary ions exceeds the other forces in magnitude in the magnetosheath and upstream regions for all solar wind conditions.

Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials

NASA Astrophysics Data System (ADS)

Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D.

2017-08-01

Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.

Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins

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

Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie

2015-08-06

Studies on light-harvesting (LH) systems have attracted much attention after the finding of long-lived quantum coherences in the exciton dynamics of the Fenna–Matthews–Olson (FMO) complex. In this complex, excitation energy transfer occurs between the bacteriochlorophyll a (BChl a) pigments. Two quantum mechanics/molecular mechanics (QM/MM) studies, each with a different force-field and quantum chemistry approach, reported different excitation energy distributions for the FMO complex. To understand the reasons for these differences in the predicted excitation energies, we have carried out a comparative study between the simulations using the CHARMM and AMBER force field and the Zerner intermediate neglect of differential orbitalmore » (ZINDO)/S and time-dependent density functional theory (TDDFT) quantum chemistry methods. The calculations using the CHARMM force field together with ZINDO/S or TDDFT always show a wider spread in the energy distribution compared to those using the AMBER force field. High- or low-energy tails in these energy distributions result in larger values for the spectral density at low frequencies. A detailed study on individual BChl a molecules in solution shows that without the environment, the density of states is the same for both force field sets. Including the environmental point charges, however, the excitation energy distribution gets broader and, depending on the applied methods, also asymmetric. The excitation energy distribution predicted using TDDFT together with the AMBER force field shows a symmetric, Gaussian-like distribution.« less

Method and apparatus for removal of gaseous, liquid and particulate contaminants from molten metals

DOEpatents

Hobson, D.O.; Alexeff, I.; Sikka, V.K.

1987-08-10

Method and apparatus for removal of nonelectrically-conducting gaseous, liquid, and particulate contaminants from molten metal compositions by applying a force thereto. The force (commonly referred to as the Lorentz Force) exerted by simultaneous application of an electric field and a magnetic field on a molten conductor causes an increase, in the same direction as the force, in the apparent specific gravity thereof, but does not affect the nonconducting materials. This difference in apparent densities cause the nonconducting materials to ''float'' in the opposite direction from the Lorentz Force at a rapid rate. Means are further provided for removal of the contaminants and prevention of stirring due to rotational forces generated by the applied fields. 6 figs.

Method and apparatus for removal of gaseous, liquid and particulate contaminants from molten metals

DOEpatents

Hobson, David O.; Alexeff, Igor; Sikka, Vinod K.

1988-01-01

Method and apparatus for removal of nonelectrically-conducting gaseous, liquid, and particulate contaminants from molten metal compositions by applying a force thereto. The force (commonly referred to as the Lorentz Force) exerted by simultaneous application of an electric field and a magnetic field on a molten conductor causes an increase, in the same direction as the force, in the apparent specific gravity thereof, but does not affect the nonconducting materials. This difference in apparent densities cause the nonconducting materials to "float" in the opposite direction from the Lorentz Force at a rapid rate. Means are further provided for removal of the contaminants and prevention of stirring due to rotational forces generated by the applied fields.

Machine-Thermal Coupling Stresses Analysis of the Fin-Type Structural Thermoelectric Generator

NASA Astrophysics Data System (ADS)

Zhang, Zheng; Yue, Hao; Chen, Dongbo; Qin, Delei; Chen, Zijian

2017-05-01

The design structure and heat-transfer mechanism of a thermoelectric generator (TEG) determine its body temperature state. Thermal stress and thermal deformation generated by the temperature variation directly affect the stress state of thermoelectric modules (TEMs). Therefore, the rated temperature and pressing force of TEMs are important parameters in TEG design. Here, the relationships between structural of a fin-type TEG (FTEG) and these parameters are studied by modeling and "machine-thermal" coupling simulation. An indirect calculation method is adopted in the coupling simulation. First, numerical heat transfer calculations of a three-dimensional FTEG model are conducted according to an orthogonal simulation table. The influences of structural parameters for heat transfer in the channel and outer fin temperature distribution are analyzed. The optimal structural parameters are obtained and used to simulate temperature field of the outer fins. Second, taking the thermal calculation results as the initial condition, the thermal-solid coupling calculation is adopted. The thermal stresses of outer fin, mechanical force of spring-angle pressing mechanism, and clamping force on a TEM are analyzed. The simulation results show that the heat transfer area of the inner fin and the physical parameters of the metal materials are the keys to determining the FTEG temperature field. The pressing mechanism's mechanical force can be reduced by reducing the outer fin angle. In addition, a corrugated cooling water pipe, which has cooling and spring functionality, is conducive to establishing an adaptable clamping force to avoid the TEMs being crushed by the thermal stresses in the body.

A Generalization of the Einstein-Maxwell Equations

NASA Astrophysics Data System (ADS)

Cotton, Fredrick

2016-03-01

The proposed modifications of the Einstein-Maxwell equations include: (1) the addition of a scalar term to the electromagnetic side of the equation rather than to the gravitational side, (2) the introduction of a 4-dimensional, nonlinear electromagnetic constitutive tensor and (3) the addition of curvature terms arising from the non-metric components of a general symmetric connection. The scalar term is defined by the condition that a spherically symmetric particle be force-free and mathematically well-behaved everywhere. The constitutive tensor introduces two auxiliary fields which describe the particle structure. The additional curvature terms couple both to particle solutions and to electromagnetic and gravitational wave solutions. http://sites.google.com/site/fwcotton/em-30.pdf

Molecular dynamics study of response of liquid N,N-dimethylformamide to externally applied electric field using a polarizable force field

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

Gao, Weimin; Niu, Haitao; Lin, Tong

2014-01-28

The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform externalmore » electric fields of higher than 0.01 V/nm have a significant effect on the structure of the liquid, which exhibits a variation in numerous properties, including molecular polarization, local cluster structure, rotation, alignment, energetics, and bulk thermodynamic and structural properties.« less

Demonstration of a positron beam-driven hollow channel plasma wakefield accelerator

DOE PAGES

Gessner, Spencer; Adli, Erik; Allen, James M.; ...

2016-06-02

Plasma wakefield accelerators have been used to accelerate electron and positron particle beams with gradients that are orders of magnitude larger than those achieved in conventional accelerators. In addition to being accelerated by the plasma wakefield, the beam particles also experience strong transverse forces that may disrupt the beam quality. Hollow plasma channels have been proposed as a technique for generating accelerating fields without transverse forces. In this study, we demonstrate a method for creating an extended hollow plasma channel and measure the wakefields created by an ultrarelativistic positron beam as it propagates through the channel. The plasma channel ismore » created by directing a high-intensity laser pulse with a spatially modulated profile into lithium vapour, which results in an annular region of ionization. A peak decelerating field of 230 MeV m -1 is inferred from changes in the beam energy spectrum, in good agreement with theory and particle-in-cell simulations.« less

Force-field and quantum-mechanical binding study of selected SAMPL3 host-guest complexes

NASA Astrophysics Data System (ADS)

Hamaguchi, Nobuko; Fusti-Molnar, Laszlo; Wlodek, Stanislaw

2012-05-01

A Merck molecular force field classical potential combined with Poisson-Boltzmann electrostatics (MMFF/PB) has been used to estimate the binding free energy of seven guest molecules (six tertiary amines and one primary amine) into a synthetic receptor (acyclic cucurbit[4]uril congener) and two benzimidazoles into cyclic cucurbit[7]uril (CB[7]) and cucurbit[8]uril (CB[8]) hosts. In addition, binding enthalpies for the benzimidazoles were calculated with density functional theory (DFT) using the B3LYP functional and a polarizable continuum model (PCM). Although in most cases the MMFF/PB approach returned reasonable agreements with the experiment (±2 kcal/mol), significant, much larger deviations were reported in the case of three host-guest pairs. All four binding enthalpy predictions with the DFT/PCM method suffered 70% or larger deviations from the calorimetry data. Results are discussed in terms of the molecular models used for guest-host complexation and the quality of the intermolecular potentials.

Interaction and dynamics of ionic liquids based on choline and amino acid anions

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

Campetella, M.; Bodo, E., E-mail: enrico.bodo@uniroma1.it; Caminiti, R., E-mail: ruggero.caminiti@uniroma1.it

2015-06-21

The combination of amino acid anions with the choline cation gives origin to a new and potentially important class of organic ionic liquids that might represent a viable and bio-compatible alternative with respect to the traditional ones. We present here a detailed study of the bulk phase of the prototype system composed of the simplest amino acid (alanine) anion and the choline cation, based on ab initio and classical molecular dynamics. Theoretical findings have been validated by comparing with accurate experimental X-ray diffraction data and infrared spectra. We find that hydrogen bonding (HB) features in these systems are crucial inmore » establishing their local geometric structure. We have also found that these HBs once formed are persistent and that the proton resides exclusively on the choline cation. In addition, we show that a classical force field description for this particular ionic liquid can be accurately performed by using a slightly modified version of the generalized AMBER force field.« less

Interaction and dynamics of ionic liquids based on choline and amino acid anions

NASA Astrophysics Data System (ADS)

Campetella, M.; Bodo, E.; Caminiti, R.; Martino, A.; D'Apuzzo, F.; Lupi, S.; Gontrani, L.

2015-06-01

The combination of amino acid anions with the choline cation gives origin to a new and potentially important class of organic ionic liquids that might represent a viable and bio-compatible alternative with respect to the traditional ones. We present here a detailed study of the bulk phase of the prototype system composed of the simplest amino acid (alanine) anion and the choline cation, based on ab initio and classical molecular dynamics. Theoretical findings have been validated by comparing with accurate experimental X-ray diffraction data and infrared spectra. We find that hydrogen bonding (HB) features in these systems are crucial in establishing their local geometric structure. We have also found that these HBs once formed are persistent and that the proton resides exclusively on the choline cation. In addition, we show that a classical force field description for this particular ionic liquid can be accurately performed by using a slightly modified version of the generalized AMBER force field.

Biological applications of near-field scanning optical microscopy

NASA Astrophysics Data System (ADS)

Moers, Marco H. P.; Ruiter, A. G. T.; Jalocha, Alain; van Hulst, Niko F.; Kalle, W. H. J.; Wiegant, J. C. A. G.; Raap, A. K.

1995-09-01

Near-field Scanning Optical Microscopy (NSOM) is a true optical microscopic technique allowing fluorescence, absorption, reflection and polarization contrast with the additional advantage of nanometer lateral resolution, unlimited by diffraction and operation at ambient conditions. NSOM based on metal coated adiabatically tapered fibers, combined with shear force feedback and operated in illumination mode, has proven to be the most powerful NSOM arrangement, because of its true localization of the optical interaction, its various optical contrast possibilities and its sensitivity down to the single molecular level. In this paper applications of `aperture' NSOM to Fluorescence In Situ Hybridization of human metaphase chromosomes are presented, where the localized fluorescence allows to identify specific DNA sequences. All images are accompanied by the simultaneously acquired force image, enabling direct comparison of the optical contrast with the sample topography on nanometer scale, far beyond the diffraction limit. Thus the unique combination of high resolution, specific optical contrast and ambient operation offers many new direction possibilities in biological studies.

About improving efficiency of the P3 M algorithms when computing the inter-particle forces in beam dynamics

NASA Astrophysics Data System (ADS)

Kozynchenko, Alexander I.; Kozynchenko, Sergey A.

2017-03-01

In the paper, a problem of improving efficiency of the particle-particle- particle-mesh (P3M) algorithm in computing the inter-particle electrostatic forces is considered. The particle-mesh (PM) part of the algorithm is modified in such a way that the space field equation is solved by the direct method of summation of potentials over the ensemble of particles lying not too close to a reference particle. For this purpose, a specific matrix "pattern" is introduced to describe the spatial field distribution of a single point charge, so the "pattern" contains pre-calculated potential values. This approach allows to reduce a set of arithmetic operations performed at the innermost of nested loops down to an addition and assignment operators and, therefore, to decrease the running time substantially. The simulation model developed in C++ substantiates this view, showing the descent accuracy acceptable in particle beam calculations together with the improved speed performance.

Penetration Barrier of Water through Graphynes' Pores: First-Principles Predictions and Force Field Optimization.

PubMed

Bartolomei, Massimiliano; Carmona-Novillo, Estela; Hernández, Marta I; Campos-Martínez, José; Pirani, Fernando; Giorgi, Giacomo; Yamashita, Koichi

2014-02-20

Graphynes are novel two-dimensional carbon-based materials that have been proposed as molecular filters, especially for water purification technologies. We carry out first-principles electronic structure calculations at the MP2C level of theory to assess the interaction between water and graphyne, graphdiyne, and graphtriyne pores. The computed penetration barriers suggest that water transport is unfeasible through graphyne while being unimpeded for graphtriyne. For graphdiyne, with a pore size almost matching that of water, a low barrier is found that in turn disappears if an active hydrogen bond with an additional water molecule on the opposite side of the opening is considered. Thus, in contrast with previous determinations, our results do not exclude graphdiyne as a promising membrane for water filtration. In fact, present calculations lead to water permeation probabilities that are 2 orders of magnitude larger than estimations based on common force fields. A new pair potential for the water-carbon noncovalent component of the interaction is proposed for molecular dynamics simulations involving graphdiyne and water.

Trapped atomic ions for quantum-limited metrology

NASA Astrophysics Data System (ADS)

Wineland, David

2017-04-01

Laser-beam-manipulated trapped ions are a candidate for large-scale quantum information processing and quantum simulation but the basic techniques used can also be applied to quantum-limited metrology and sensing. Some examples being explored at NIST are: 1) As charged harmonic oscillators, trapped ions can be used to sense electric fields; this can be used to characterize the electrode-surface-based noisy electric fields that compromise logic-gate fidelities and may eventually be used as a tool in surface science. 2) Since typical qubit logic gates depend on state-dependent forces, we can adapt the gate dynamics to sensitively detect additional forces. 3) We can use extensions of Bell inequality measurements to further restrict the degree of local realism possessed by Bell states. 4) We also briefly describe experiments for creation of Bell states using Hilbert space engineering. This work is a joint effort including the Ion-Storage group, the Quantum processing group, and the Computing and Communications Theory group at NIST, Boulder. Supported by IARPA, ONR, and the NIST Quantum Information Program.

Smoking and deployment: perspectives of junior-enlisted U.S. Air Force and U.S. Army personnel and their supervisors.

PubMed

Poston, Walker S C; Taylor, Jennifer E; Hoffman, Kevin M; Peterson, Alan L; Lando, Harry A; Shelton, Suzanne; Haddock, C Keith

2008-05-01

Smoking during deployments is a growing problem, particularly among junior-enlisted personnel, who have the highest smoking rates in the military. Few studies have examined reasons for smoking initiation among never smokers, relapse among former smokers, or increased smoking frequency among current smokers. We conducted 24 focus groups at four Air Force and two Army installations (N = 189) to examine the extent of smoking during deployment and to elucidate factors thought to contribute to new initiation, relapse, and increased smoking in a sample of junior-enlisted personnel and their supervisors. Important reasons for smoking included: (1) managing stress, boredom, anxiety, and sleep deprivation; (2) lack of alternate activities and privileges; (3) the perception that dangers in the field trumps the health impact of smoking; and (4) the role of the military environment in encouraging smoking. In addition, the phenomenon of new initiation and relapse to smoking in the field was discussed.

Study of a magnetorheological fluid submitted to a uniform magnetic field

NASA Astrophysics Data System (ADS)

Fonseca, H. A.; Gonzalez, E.; Restrepo, J.

2017-12-01

In this work, the rheological and hyperfine properties of a magnetorheological fluid (MRF) under the action of a uniform external magnetic field are analysed. Powders of native mineral magnetite of micrometric particle size, after a pulverization process, form the solute of these fluids. The sizes of these samples are selected by sieving in order to obtain sizes of around 20µm and 45µm. The powders are characterized by means of Mössbauer spectroscopy to analyse their stoichiometry giving rise to a non-stoichiometric magnetite Fe2.96O4 in addition to a hematite component. Result of viscosity and shear stress in the low-speed regime were analysed using the Hershel Buckley method. In particular, the case of surface tension it decreases with the application of a uniform magnetic flux density, which is understood in terms of a phase separation due to the formation of mesoscopic structures, thus decreasing the cohesion force and increasing the adhesion force.

Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

PubMed

Mazack, Michael J M; Gao, Jiali

2014-05-28

The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping

PubMed Central

2015-01-01

Base flipping in DNA is an important process involved in genomic repair and epigenetic control of gene expression. The driving forces for these processes are not fully understood, especially in the context of the underlying dynamics of the DNA and solvent effects. We studied double-stranded DNA oligomers that have been previously characterized by imino proton exchange NMR using both additive and polarizable force fields. Our results highlight the importance of induced polarization on the base flipping process, yielding near-quantitative agreement with experimental measurements of the equilibrium between the base-paired and flipped states. Further, these simulations allow us to quantify for the first time the energetic implications of polarization on the flipping pathway. Free energy barriers to base flipping are reduced by changes in dipole moments of both the flipped bases that favor solvation of the bases in the open state and water molecules adjacent to the flipping base. PMID:24976900

Improved short-term variability in the thermosphere-ionosphere-mesosphere-electrodynamics general circulation model

NASA Astrophysics Data System (ADS)

Häusler, K.; Hagan, M. E.; Baumgaertner, A. J. G.; Maute, A.; Lu, G.; Doornbos, E.; Bruinsma, S.; Forbes, J. M.; Gasperini, F.

2014-08-01

We report on a new source of tidal variability in the National Center for Atmospheric Research thermosphere-ionosphere-mesosphere-electrodynamics general circulation model (TIME-GCM). Lower boundary forcing of the TIME-GCM for a simulation of November-December 2009 based on 3-hourly Modern-Era Retrospective Analysis for Research and Application (MERRA) reanalysis data includes day-to-day variations in both diurnal and semidiurnal tides of tropospheric origin. Comparison with TIME-GCM results from a heretofore standard simulation that includes climatological tropospheric tides from the global-scale wave model reveal evidence of the impacts of MERRA forcing throughout the model domain, including measurable tidal variability in the TIME-GCM upper thermosphere. Additional comparisons with measurements made by the Gravity field and steady-state Ocean Circulation Explorer satellite show improved TIME-GCM capability to capture day-to-day variations in thermospheric density for the November-December 2009 period with the new MERRA lower boundary forcing.

Energy distributions of an ion in a radio-frequency trap immersed in a buffer gas under the influence of additional external forces

NASA Astrophysics Data System (ADS)

Rouse, I.; Willitsch, S.

2018-04-01

An ion held in a radio-frequency trap interacting with a uniform buffer gas of neutral atoms develops a steady-state energy distribution characterized by a power-law tail at high energies instead of the exponential decay characteristic of thermal equilibrium. We have previously shown that the Tsallis statistics frequently used as an empirical model for this distribution is a good approximation when the ion is heated due to a combination of micromotion interruption and exchange of kinetic energy with the buffer gas [Rouse and Willitsch, Phys. Rev. Lett. 118, 143401 (2017), 10.1103/PhysRevLett.118.143401]. Here, we extend our treatment to include the heating due to additional motion of the ion caused by external forces, including the "excess micromotion" induced by uniform electric fields and rf phase offsets. We show that this also leads to a Tsallis distribution with a potentially different power-law exponent from that observed in the absence of this additional forced motion, with the difference increasing as the ratio of the mass of the neutral atoms to that of the ion decreases. Our results indicate that unless the excess micromotion is minimized to a very high degree, then even a system with very light neutrals and a heavy ion does not exhibit a thermal distribution.

Enhanced cell trapping throughput using DC-biased AC electric field in a dielectrophoresis-based fluidic device with densely packed silica beads.

PubMed

Lewpiriyawong, Nuttawut; Xu, Guolin; Yang, Chun

2018-03-01

This paper presents the use of DC-biased AC electric field for enhancing cell trapping throughput in an insulator-based dielectrophoretic (iDEP) fluidic device with densely packed silica beads. Cell suspension is carried through the iDEP device by a pressure-driven flow. Under an applied DC-biased AC electric field, DEP trapping force is produced as a result of non-uniform electric field induced by the gap of electrically insulating silica beads packed between two mesh electrodes that allow both fluid and cells to pass through. While the AC component is mainly to control the magnitude of DEP trapping force, the DC component generates local electroosmotic (EO) flow in the cavity between the beads and the EO flow can be set to move along or against the main pressure-driven flow. Our experimental and simulation results show that desirable trapping is achieved when the EO flow direction is along (not against) the main flow direction. Using our proposed DC-biased AC field, the device can enhance the trapping throughput (in terms of the flowrate of cell suspension) up to five times while yielding almost the same cell capture rates as compared to the pure AC field case. Additionally, the device was demonstrated to selectively trap dead yeast cells from a mixture of flowing live and dead yeast cells. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Air Force Officer Accession Planning: Addressing Key Gaps in Meeting Career Field Academic Degree Requirements for Nonrated Officers

DTIC Science & Technology

2016-06-09

C O R P O R A T I O N Research Report Air Force Officer Accession Planning Addressing Key Gaps in Meeting Career Field Academic Degree Requirements...various Air Force missions in particular career fields. Key to this goal for nonrated officers is establishing and enforcing academic degree...35 Developing Accession Targets by Academic Degree Type

Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.

PubMed

Miller, Mark S; Lay, Wesley K; Li, Shuxiang; Hacker, William C; An, Jiadi; Ren, Jianlan; Elcock, Adrian H

2017-04-11

There is a small, but growing, body of literature describing the use of osmotic coefficient measurements to validate and reparametrize simulation force fields. Here we have investigated the ability of five very commonly used force field and water model combinations to reproduce the osmotic coefficients of seven neutral amino acids and five small molecules. The force fields tested include AMBER ff99SB-ILDN, CHARMM36, GROMOS54a7, and OPLS-AA, with the first of these tested in conjunction with the TIP3P and TIP4P-Ew water models. In general, for both the amino acids and the small molecules, the tested force fields produce computed osmotic coefficients that are lower than experiment; this is indicative of excessively favorable solute-solute interactions. The sole exception to this general trend is provided by GROMOS54a7 when applied to amino acids: in this case, the computed osmotic coefficients are consistently too high. Importantly, we show that all of the force fields tested can be made to accurately reproduce the experimental osmotic coefficients of the amino acids when minor modifications-some previously reported by others and some that are new to this study-are made to the van der Waals interactions of the charged terminal groups. Special care is required, however, when simulating Proline with a number of the force fields, and a hydroxyl-group specific modification is required in order to correct Serine and Threonine when simulated with AMBER ff99SB-ILDN. Interestingly, an alternative parametrization of the van der Waals interactions in the latter force field, proposed by the Nerenberg and Head-Gordon groups, is shown to immediately produce osmotic coefficients that are in excellent agreement with experiment. Overall, this study reinforces the idea that osmotic coefficient measurements can be used to identify general shortcomings in commonly used force fields' descriptions of solute-solute interactions and further demonstrates that modifications to van der Waals parameters provide a simple route to optimizing agreement with experiment.

Geophysical variables and behavior: LIII. Epidemiological considerations for incidence of cancer and depression in areas of frequent UFO reports.

PubMed

Persinger, M A

1988-12-01

Luminous phenomena and anomalous physical forces have been hypothesized to be generated by focal tectonic strain fields that precede earthquakes. If these geophysical processes exist, then their spatial and temporal density should be greatest during periods of protracted, localized UFO reports; they might be used as dosimetric indicators. Contemporary epidemiological data concerning the health risks of power frequency electromagnetic fields and radon gas levels (expected correlates of certain tectonic strain fields), suggest that increased incidence (odds ratios greater 1:3) of brain tumors and leukemia should be evident within "flap" areas. In addition the frequency of variants of temporal lobe lability, psychological depression and posttraumatic stress should be significantly elevated. UFO field investigators, because they have repeated, intermittent close proximity to these fields, are considered to be a particularly high risk population for these disorders.

Observation of nanoscale magnetic fields using twisted electron beams

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

Grillo, Vincenzo; Harvey, Tyler R.; Venturi, Federico

Electron waves give an unprecedented enhancement to the field of microscopy by providing higher resolving power compared to their optical counterpart. Further information about a specimen, such as electric and magnetic features, can be revealed in electron microscopy because electrons possess both a magnetic moment and charge. In-plane magnetic structures in materials can be studied experimentally using the effect of the Lorentz force. On the other hand, full mapping of the magnetic field has hitherto remained challenging. Here we measure a nanoscale out-of-plane magnetic field by interfering a highly twisted electron vortex beam with a reference wave. We implement amore » recently developed holographic technique to manipulate the electron wavefunction, which gives free electrons an additional unbounded quantized magnetic moment along their propagation direction. Our finding demonstrates that full reconstruction of all three components of nanoscale magnetic fields is possible without tilting the specimen.« less

Geophysical variables and behavior: LIII. Epidemiological considerations for incidence of cancer and depression in areas of frequent UFO reports

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

Persinger, M.A.

Luminous phenomena and anomalous physical forces have been hypothesized to be generated by focal tectonic strain fields that precede earthquakes. If these geophysical processes exist, then their spatial and temporal density should be greatest during periods of protracted, localized UFO reports; they might be used as dosimetric indicators. Contemporary epidemiological data concerning the health risks of power frequency electromagnetic fields and radon gas levels (expected correlates of certain tectonic strain fields), suggest that increased incidence (odds ratios greater 1:3) of brain tumors and leukemia should be evident within flap areas. In addition the frequency of variants of temporal lobe lability,more » psychological depression and posttraumatic stress should be significantly elevated. UFO field investigators, because they have repeated, intermittent close proximity to these fields, are considered to be a particularly high risk population for these disorders. 22 references.« less

Determination of coronal magnetic fields from vector magnetograms

NASA Technical Reports Server (NTRS)

Mikic, Zoran

1993-01-01

This report covers technical progress during the second year of the contract entitled 'Determination of Coronal Magnetic Fields from Vector Magnetograms,' NASW-4728, between NASA and Science Applications International Corporation, and covers the period January 1, 1993 to December 31, 1993. Under this contract SAIC has conducted research into the determination of coronal magnetic fields from vector magnetograms, including the development and application of algorithms to determine force-free coronal fields above selected observations of active regions. The contract began on June 30, 1992 and has a completion date of December 31, 1994. This contract is a continuation of work started in a previous contract, NASW-4571, which covered the period November 15, 1990 to December 14, 1991. During this second year we have concentrated on studying additional active regions and in using the estimated coronal magnetic fields to compare to coronal features inferred from observations.

Permanent-magnet multipole with adjustable strength

DOEpatents

Halbach, K.

1982-09-20

Two or more magnetically soft pole pieces are symmetrically positioned along a longitudinal axis to provide a magnetic field within a space defined by the pole pieces. Two or more permanent magnets are mounted to an external magnetically-soft cylindrical sleeve which rotates to bring the permanent magnets into closer coupling with the pole pieces and thereby adjustably control the field strength of the magnetic field produced in the space defined by the pole pieces. The permanent magnets are preferably formed of rare earth cobalt (REC) material which has a high remanent magnetic field and a strong coercive force. The pole pieces and the permanent magnets have corresponding cylindrical surfaces which are positionable with respect to each other to vary the coupling there between. Auxiliary permanent magnets are provided between the pole pieces to provide additional magnetic flux to the magnetic field without saturating the pole pieces.

Permanent magnet multipole with adjustable strength

DOEpatents

Halbach, Klaus

1985-01-01

Two or more magnetically soft pole pieces are symmetrically positioned along a longitudinal axis to provide a magnetic field within a space defined by the pole pieces. Two or more permanent magnets are mounted to an external magnetically-soft cylindrical sleeve which rotates to bring the permanent magnets into closer coupling with the pole pieces and thereby adjustably control the field strength of the magnetic field produced in the space defined by the pole pieces. The permanent magnets are preferably formed of rare earth cobalt (REC) material which has a high remanent magnetic field and a strong coercive force. The pole pieces and the permanent magnets have corresponding cylindrical surfaces which are positionable with respect to each other to vary the coupling therebetween. Auxiliary permanent magnets are provided between the pole pieces to provide additional magnetic flux to the magnetic field without saturating the pole pieces.

Observation of nanoscale magnetic fields using twisted electron beams

DOE PAGES

Grillo, Vincenzo; Harvey, Tyler R.; Venturi, Federico; ...

2017-09-25

Electron waves give an unprecedented enhancement to the field of microscopy by providing higher resolving power compared to their optical counterpart. Further information about a specimen, such as electric and magnetic features, can be revealed in electron microscopy because electrons possess both a magnetic moment and charge. In-plane magnetic structures in materials can be studied experimentally using the effect of the Lorentz force. On the other hand, full mapping of the magnetic field has hitherto remained challenging. Here we measure a nanoscale out-of-plane magnetic field by interfering a highly twisted electron vortex beam with a reference wave. We implement amore » recently developed holographic technique to manipulate the electron wavefunction, which gives free electrons an additional unbounded quantized magnetic moment along their propagation direction. Our finding demonstrates that full reconstruction of all three components of nanoscale magnetic fields is possible without tilting the specimen.« less

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.

PubMed

Caleman, Carl; van Maaren, Paul J; Hong, Minyan; Hub, Jochen S; Costa, Luciano T; van der Spoel, David

2012-01-10

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

PubMed Central

2011-01-01

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields. PMID:22241968