Direct computation of parameters for accurate polarizable force fields
Verstraelen, Toon Vandenbrande, Steven; Ayers, Paul W.
2014-11-21
We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields.
Developing accurate molecular mechanics force fields for conjugated molecular systems.
Do, Hainam; Troisi, Alessandro
2015-10-14
A rapid method to parameterize the intramolecular component of classical force fields for complex conjugated molecules is proposed. The method is based on a procedure of force matching with a reference electronic structure calculation. It is particularly suitable for those applications where molecular dynamics simulations are used to generate structures that are therefore analysed by electronic structure methods, because it is possible to build force fields that are consistent with electronic structure calculations that follow classical simulations. Such applications are commonly encountered in organic electronics, spectroscopy of complex systems and photobiology (e.g. photosynthetic systems). We illustrate the method by parameterizing the force fields of a molecule used in molecular semiconductors (2,2-dicyanovinyl-capped S,N-heteropentacene or DCV-SN5), a polymeric semiconductor (thieno[3,2-b]thiophene-diketopyrrolopyrrole TT-DPP) and a chromophore embedded in a protein environment (15,16-dihydrobiliverdin or DBV) where several hundreds of parameters need to be optimized in parallel.
An accurate ab initio quartic force field for ammonia
NASA Technical Reports Server (NTRS)
Martin, J. M. L.; Lee, Timothy J.; Taylor, Peter R.
1992-01-01
The quartic force field of ammonia is computed using basis sets of spdf/spd and spdfg/spdf quality and an augmented coupled cluster method. After correcting for Fermi resonance, the computed fundamentals and nu 4 overtones agree on average to better than 3/cm with the experimental ones except for nu 2. The discrepancy for nu 2 is principally due to higher-order anharmonicity effects. The computed omega 1, omega 3, and omega 4 confirm the recent experimental determination by Lehmann and Coy (1988) but are associated with smaller error bars. The discrepancy between the computed and experimental omega 2 is far outside the expected error range, which is also attributed to higher-order anharmonicity effects not accounted for in the experimental determination. Spectroscopic constants are predicted for a number of symmetric and asymmetric top isotopomers of NH3.
Accurate force fields and methods for modelling organic molecular crystals at finite temperatures.
Nyman, Jonas; Pundyke, Orla Sheehan; Day, Graeme M
2016-06-21
We present an assessment of the performance of several force fields for modelling intermolecular interactions in organic molecular crystals using the X23 benchmark set. The performance of the force fields is compared to several popular dispersion corrected density functional methods. In addition, we present our implementation of lattice vibrational free energy calculations in the quasi-harmonic approximation, using several methods to account for phonon dispersion. This allows us to also benchmark the force fields' reproduction of finite temperature crystal structures. The results demonstrate that anisotropic atom-atom multipole-based force fields can be as accurate as several popular DFT-D methods, but have errors 2-3 times larger than the current best DFT-D methods. The largest error in the examined force fields is a systematic underestimation of the (absolute) lattice energy.
An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.
1995-01-01
A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.
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.
An Accurate Quartic Force Field and Vibrational Frequencies for HNO and DNO
NASA Technical Reports Server (NTRS)
Dateo, Christopher E.; Lee, Timothy J.; Schwenke, David W.
1994-01-01
An accurate ab initio quartic force field for HNO has been determined using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, CCSD(T), in conjunction with the correlation consistent polarized valence triple zeta (cc-pVTZ) basis set. Improved harmonic frequencies were determined with the cc-pVQZ basis set. Fundamental vibrational frequencies were determined using a second-order perturbation theory analysis and also using variational calculations. The N-0 stretch and bending fundamentals are determined well from both vibrational analyses. The H-N stretch, however, is shown to have an unusually large anharmonic correction, and is not well determined using second-order perturbation theory. The H-N fundamental is well determined from the variational calculations, demonstrating the quality of the ab initio quartic force field. The zero-point energy of HNO that should be used in isodesmic reactions is also discussed.
Accurate ab initio quartic force fields for the ions HCO(+) and HOC(+)
NASA Technical Reports Server (NTRS)
Martin, J. M. L.; Taylor, Peter R.; Lee, Timothy J.
1993-01-01
The quartic force fields of HCO(+) and HOC(+) have been computed using augmented coupled cluster methods and basis sets of spdf and spdfg quality. Calculations on HCN, CO, and N2 have been performed to assist in calibrating the computed results. Going from an spdf to an spdfg basis shortens triple bonds by about 0.004 A, and increases the corresponding harmonic frequency by 10-20/cm, leaving bond distances about 0.003 A too long and triple bond stretching frequencies about 5/cm too low. Accurate estimates for the bond distances, fundamental frequencies, and thermochemical quantities are given. HOC(+) lies 37.8 +/- 0.5 kcal/mol (0 K) above HCO(+); the classical barrier height for proton exchange is 76.7 +/- 1.0 kcal/mol.
Accurate Quartic Force Fields and Vibrational Frequencies for HCN and HNC
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Dateo, Christopher E.; Gazdy, Bela; Bowman, Joel M.
1993-01-01
The quartic force fields of HCN and HNC are determined using atomic natural orbital one-particle basis sets of spdf/spd and spdfg/spdf quality in conjunction with the CCSD(T) electron correlation method (singles and doubles coupled-cluster theory plus a perturbation estimate of the effects of connected triple excitations). The HCN force field is in good agreement with a recent experimentally derived force field and also with the force field recently computed by Wong and Bacskay. On the basis of the good agreement obtained for HCN, it is argued that the ab initio quartic force field for HNC is superior to a prior force field derived from experiment. The harmonic frequencies of HNC are predicted to be 3822 +/- 10, 472 +/- 5, and 2051 +/- 10 cm(exp -1) for omega(sub 1), omega(sub 2), and omega(sub 3), respectively; the experimentally derived values are above these values and fall outside the estimated uncertainties. Using the quartic force field, spectroscopic constants are predicted for HNC based on a vibrational second-order perturbation theory analysis. It is also asserted that the gas-phase fundamental nu(sub 3) for HNC is slightly lower than the matrix isolation value. The range of validity of the quartic force fields is investigated by comparison of variational vibrational energies computed with the quartic force fields to those obtained from our recently reported global HCN/HNC potential energy surface and also to experimental data.
Accurate Quartic Force Fields and Vibrational Frequencies for HCN and HNC
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Dateo, Christopher E.; Gazdy, Bela; Bowman, Joel M.
1993-01-01
The quartic force fields of HCN and HNC are determined using atomic natural orbital one-particle basis sets of spdf/spd and spdfg/spdf quality in conjunction with the CCSD(T) electron correlation method (singles and doubles coupled-cluster theory plus a perturbational estimate of the effects of connected triple excitations). The HCN force field is in good agreement with a recent experimentally derived force field and also with the force field recently computed by Wong and Bacskay. On the basis of the good agreement obtained for HCN, it is argued that the ab initio quartic force field for HNC is superior to a prior force field derived from experiment. The harmonic frequencies of HNC are predicted to be 3822 +/- 10,472 +/- 5, and 2051 +/-10/cm for omega1, omega2, and omega3, respectively; the experimentally derived values are above these values and fall outside the estimated uncertainties. Using the quartic force field, spectroscopic constants are predicted for HNC based on a vibrational second-order perturbation theory analysis. It is also asserted that the gas-phase fundamental v(sub 3) for HNC is slightly lower than the matrix isolation value. The range of validity of the quartic force fields is investigated by comparison of variational vibrational energies computed with the quartic force fields to those obtained from our recently reported global HCN/HNC potential energy surface and also to experimental data.
Accurate ab initio Quartic Force Fields of Cyclic and Bent HC2N Isomers
NASA Technical Reports Server (NTRS)
Inostroza, Natalia; Huang, Xinchuan; Lee, Timothy J.
2012-01-01
Highly correlated ab initio quartic force field (QFFs) are used to calculate the equilibrium structures and predict the spectroscopic parameters of three HC2N isomers. Specifically, the ground state quasilinear triplet and the lowest cyclic and bent singlet isomers are included in the present study. Extensive treatment of correlation effects were included using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T). Dunning s correlation-consistent basis sets cc-pVXZ, X=3,4,5, were used, and a three-point formula for extrapolation to the one-particle basis set limit was used. Core-correlation and scalar relativistic corrections were also included to yield highly accurate QFFs. The QFFs were used together with second-order perturbation theory (with proper treatment of Fermi resonances) and variational methods to solve the nuclear Schr dinger equation. The quasilinear nature of the triplet isomer is problematic, and it is concluded that a QFF is not adequate to describe properly all of the fundamental vibrational frequencies and spectroscopic constants (though some constants not dependent on the bending motion are well reproduced by perturbation theory). On the other hand, this procedure (a QFF together with either perturbation theory or variational methods) leads to highly accurate fundamental vibrational frequencies and spectroscopic constants for the cyclic and bent singlet isomers of HC2N. All three isomers possess significant dipole moments, 3.05D, 3.06D, and 1.71D, for the quasilinear triplet, the cyclic singlet, and the bent singlet isomers, respectively. It is concluded that the spectroscopic constants determined for the cyclic and bent singlet isomers are the most accurate available, and it is hoped that these will be useful in the interpretation of high-resolution astronomical observations or laboratory experiments.
Are current atomistic force fields accurate enough to study proteins in crowded environments?
Petrov, Drazen; Zagrovic, Bojan
2014-05-01
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
Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
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
Are current atomistic force fields accurate enough to study proteins in crowded environments?
Petrov, Drazen; Zagrovic, Bojan
2014-05-01
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
Accurate ab initio quartic force fields for borane and BeH2
NASA Technical Reports Server (NTRS)
Martin, J. M. L.; Lee, Timothy J.
1992-01-01
The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.
NASA Astrophysics Data System (ADS)
Martin, Jan M. L.
The quartic force fields of a number of small polyatomic molecules (specifically, rm H _2O, NH_2, NH_3, CH_4, BH_3, BeH_2, H_2CO, N_2O, CO_2, CS_2, OCS, H_2S, FNO, ClNO, and H_2CS) have been computed ab initio using large basis sets and augmented coupled cluster methods. It has been established throughout that harmonic and fundamental frequencies can consistently be reproduced to within about 10 cm^{ -1} of experimental using spdf basis sets, except in such inherently problematic cases as the umbrella motion in NH_3; such problems are solved by recomputing the harmonic frequencies with an spdf g basis set. Coupled cluster frequencies using small basis sets of spd quality agree surprisingly well with experiment (mean absolute error of 26 cm^ {-1}), but bond distances are generally seriously overestimated. Using spdf basis sets, they are consistently overestimated by 0.002 and 0.006-7 A for single and multiple bonds, respectively; for spdf g basis sets this drops to 0.001 and 0.003-4 A, respectively. Geometries and harmonic frequencies for highly polar fluorine compounds such as HF and FNO are qualitatively wrong unless special anion functions are added to the fluorine basis set. Anharmonicity, rovibrational coupling, and centrifugal distortion constants are consistently predicted well; the anharmonic portions of the computed force fields are probably more reliable than their experimental counterparts in many cases. Remaining errors in the computed geometries and harmonic frequencies are shown to be almost entirely due to a combination of core correlation and residual deficiencies in the electron correlation treatment. A 3-term correction for remaining basis set incompleteness to computed total atomization energies is proposed by the author, and is shown to result in mean absolute errors of as little as 0.5 kcal/mol for spdf g basis sets. Example applications on rm HCO^+, HOC^+, B_2C, BCN, and BNC testify to the predictive power of the methods used in this work.
NASA Astrophysics Data System (ADS)
Liu, Qianlong; Reifsnider, Kenneth
2012-11-01
The basis of dielectrophoresis (DEP) is the prediction of the force and torque on particles. The classical approach to the prediction is based on the effective moment method, which, however, is an approximate approach, assumes infinitesimal particles. Therefore, it is well-known that for finite-sized particles, the DEP approximation is inaccurate as the mutual field, particle, wall interactions become strong, a situation presently attracting extensive research for practical significant applications. In the present talk, we provide accurate calculations of the force and torque on the particles from first principles, by directly resolving the local geometry and properties and accurately accounting for the mutual interactions for finite-sized particles with both dielectric polarization and conduction in a sinusoidally steady-state electric field. Since the approach has a significant advantage, compared to other numerical methods, to efficiently simulate many closely packed particles, it provides an important, unique, and accurate technique to investigate complex DEP phenomena, for example heterogeneous mixtures containing particle chains, nanoparticle assembly, biological cells, non-spherical effects, etc. This study was supported by the Department of Energy under funding for an EFRC (the HeteroFoaM Center), grant no. DE-SC0001061.
Romanov, V N; Cygan, R T; Myshakin, E M
2012-06-21
Naturally occurring clay minerals provide a distinctive material for carbon capture and carbon dioxide sequestration. Swelling clay minerals, such as the smectite variety, possess an aluminosilicate structure that is controlled by low-charge layers that readily expand to accommodate water molecules and, potentially, CO2. Recent experimental studies have demonstrated the efficacy of intercalating CO2 in the interlayer of layered clays, but little is known about the molecular mechanisms of the process and the extent of carbon capture as a function of clay charge and structure. A series of molecular dynamics simulations and vibrational analyses have been completed to assess the molecular interactions associated with incorporation of CO2 and H2O in the interlayer of montmorillonite clay and to help validate the models with experimental observation. An accurate and fully flexible set of interatomic potentials for CO2 is developed and combined with Clayff potentials to help evaluate the intercalation mechanism and examine the effect of molecular flexibility onthe diffusion rate of CO2 in water.
NASA Astrophysics Data System (ADS)
Sagui, Celeste; Pedersen, Lee G.; Darden, Thomas A.
2004-01-01
The accurate simulation of biologically active macromolecules faces serious limitations that originate in the treatment of electrostatics in the empirical force fields. The current use of "partial charges" is a significant source of errors, since these vary widely with different conformations. By contrast, the molecular electrostatic potential (MEP) obtained through the use of a distributed multipole moment description, has been shown to converge to the quantum MEP outside the van der Waals surface, when higher order multipoles are used. However, in spite of the considerable improvement to the representation of the electronic cloud, higher order multipoles are not part of current classical biomolecular force fields due to the excessive computational cost. In this paper we present an efficient formalism for the treatment of higher order multipoles in Cartesian tensor formalism. The Ewald "direct sum" is evaluated through a McMurchie-Davidson formalism [L. McMurchie and E. Davidson, J. Comput. Phys. 26, 218 (1978)]. The "reciprocal sum" has been implemented in three different ways: using an Ewald scheme, a particle mesh Ewald (PME) method, and a multigrid-based approach. We find that even though the use of the McMurchie-Davidson formalism considerably reduces the cost of the calculation with respect to the standard matrix implementation of multipole interactions, the calculation in direct space remains expensive. When most of the calculation is moved to reciprocal space via the PME method, the cost of a calculation where all multipolar interactions (up to hexadecapole-hexadecapole) are included is only about 8.5 times more expensive than a regular AMBER 7 [D. A. Pearlman et al., Comput. Phys. Commun. 91, 1 (1995)] implementation with only charge-charge interactions. The multigrid implementation is slower but shows very promising results for parallelization. It provides a natural way to interface with continuous, Gaussian-based electrostatics in the future. It is
Sagui, Celeste; Pedersen, Lee G; Darden, Thomas A
2004-01-01
The accurate simulation of biologically active macromolecules faces serious limitations that originate in the treatment of electrostatics in the empirical force fields. The current use of "partial charges" is a significant source of errors, since these vary widely with different conformations. By contrast, the molecular electrostatic potential (MEP) obtained through the use of a distributed multipole moment description, has been shown to converge to the quantum MEP outside the van der Waals surface, when higher order multipoles are used. However, in spite of the considerable improvement to the representation of the electronic cloud, higher order multipoles are not part of current classical biomolecular force fields due to the excessive computational cost. In this paper we present an efficient formalism for the treatment of higher order multipoles in Cartesian tensor formalism. The Ewald "direct sum" is evaluated through a McMurchie-Davidson formalism [L. McMurchie and E. Davidson, J. Comput. Phys. 26, 218 (1978)]. The "reciprocal sum" has been implemented in three different ways: using an Ewald scheme, a particle mesh Ewald (PME) method, and a multigrid-based approach. We find that even though the use of the McMurchie-Davidson formalism considerably reduces the cost of the calculation with respect to the standard matrix implementation of multipole interactions, the calculation in direct space remains expensive. When most of the calculation is moved to reciprocal space via the PME method, the cost of a calculation where all multipolar interactions (up to hexadecapole-hexadecapole) are included is only about 8.5 times more expensive than a regular AMBER 7 [D. A. Pearlman et al., Comput. Phys. Commun. 91, 1 (1995)] implementation with only charge-charge interactions. The multigrid implementation is slower but shows very promising results for parallelization. It provides a natural way to interface with continuous, Gaussian-based electrostatics in the future. It is
Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Yan; Zhang, Dinglin; Cao, Liaoran; Li, Guohui
2016-06-14
Classical molecular dynamic (MD) simulation of membrane proteins faces significant challenges in accurately reproducing and predicting experimental observables such as ion conductance and permeability due to its incapability of precisely describing the electronic interactions in heterogeneous systems. In this work, the free energy profiles of K(+) and Na(+) permeating through the gramicidin A channel are characterized by using the AMOEBA polarizable force field with a total sampling time of 1 μs. Our results indicated that by explicitly introducing the multipole terms and polarization into the electrostatic potentials, the permeation free energy barrier of K(+) through the gA channel is considerably reduced compared to the overestimated results obtained from the fixed-charge model. Moreover, the estimated maximum conductance, without any corrections, for both K(+) and Na(+) passing through the gA channel are much closer to the experimental results than any classical MD simulations, demonstrating the power of AMOEBA in investigating the membrane proteins. PMID:27171823
Fortenberry, Ryan C; Huang, Xinchuan; Schwenke, David W; Lee, Timothy J
2014-02-01
In this work, computational procedures are employed to compute the rotational and rovibrational spectra and line lists for H2O, CO2, and SO2. Building on the established use of quartic force fields, MP2 and CCSD(T) Dipole Moment Surfaces (DMSs) are computed for each system of study in order to produce line intensities as well as the transition energies. The computed results exhibit a clear correlation to reference data available in the HITRAN database. Additionally, even though CCSD(T) DMSs produce more accurate intensities as compared to experiment, the use of MP2 DMSs results in reliable line lists that are still comparable to experiment. The use of the less computationally costly MP2 method is beneficial in the study of larger systems where use of CCSD(T) would be more costly. PMID:23692860
NASA Technical Reports Server (NTRS)
Huang, Xinchuan; Taylor, Peter R.; Lee, Timothy J.
2011-01-01
High levels of theory have been used to compute quartic force fields (QFFs) for the cyclic and linear forms of the C H + molecular cation, referred to as c-C H + and I-C H +. Specifically the 33 3333 singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations, CCSD(T), has been used in conjunction with extrapolation to the one-particle basis set limit and corrections for scalar relativity and core correlation have been included. The QFFs have been used to compute highly accurate fundamental vibrational frequencies and other spectroscopic constants using both vibrational 2nd-order perturbation theory and variational methods to solve the nuclear Schroedinger equation. Agreement between our best computed fundamental vibrational frequencies and recent infrared photodissociation experiments is reasonable for most bands, but there are a few exceptions. Possible sources for the discrepancies are discussed. We determine the energy difference between the cyclic and linear forms of C H +, 33 obtaining 27.9 kcal/mol at 0 K, which should be the most reliable available. It is expected that the fundamental vibrational frequencies and spectroscopic constants presented here for c-C H + 33 and I-C H + are the most reliable available for the free gas-phase species and it is hoped that 33 these will be useful in the assignment of future high-resolution laboratory experiments or astronomical observations.
Huang, Xinchuan; Taylor, Peter R; Lee, Timothy J
2011-05-19
High levels of theory have been used to compute quartic force fields (QFFs) for the cyclic and linear forms of the C(3)H(3)(+) molecular cation, referred to as c-C(3)H(3)(+) and l-C(3)H(3)(+). Specifically, the singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations, CCSD(T), has been used in conjunction with extrapolation to the one-particle basis set limit, and corrections for scalar relativity and core correlation have been included. The QFFs have been used to compute highly accurate fundamental vibrational frequencies and other spectroscopic constants by use of both vibrational second-order perturbation theory and variational methods to solve the nuclear Schrödinger equation. Agreement between our best computed fundamental vibrational frequencies and recent infrared photodissociation experiments is reasonable for most bands, but there are a few exceptions. Possible sources for the discrepancies are discussed. We determine the energy difference between the cyclic and linear forms of C(3)H(3)(+), obtaining 27.9 kcal/mol at 0 K, which should be the most reliable available. It is expected that the fundamental vibrational frequencies and spectroscopic constants presented here for c-C(3)H(3)(+) and l-C(3)H(3)(+) are the most reliable available for the free gas-phase species, and it is hoped that these will be useful in the assignment of future high-resolution laboratory experiments or astronomical observations. PMID:21510653
Abramyan, Tigran M; Snyder, James A; Yancey, Jeremy A; Thyparambil, Aby A; Wei, Yang; Stuart, Steven J; Latour, Robert A
2015-01-01
Interfacial force field (IFF) parameters for use with the CHARMM force field have been developed for interactions between peptides and high-density polyethylene (HDPE). Parameterization of the IFF was performed to achieve agreement between experimental and calculated adsorption free energies of small TGTG-X-GTGT host-guest peptides (T = threonine, G = glycine, and X = variable amino-acid residue) on HDPE, with ±0.5 kcal/mol agreement. This IFF parameter set consists of tuned nonbonded parameters (i.e., partial charges and Lennard-Jones parameters) for use with an in-house-modified CHARMM molecular dynamic program that enables the use of an independent set of force field parameters to control molecular behavior at a solid-liquid interface. The R correlation coefficient between the simulated and experimental peptide adsorption free energies increased from 0.00 for the standard CHARMM force field parameters to 0.88 for the tuned IFF parameters. Subsequent studies are planned to apply the tuned IFF parameter set for the simulation of protein adsorption behavior on an HDPE surface for comparison with experimental values of adsorbed protein orientation and conformation. PMID:25818122
Abramyan, Tigran M.; Snyder, James A.; Yancey, Jeremy A.; Thyparambil, Aby A.; Wei, Yang; Stuart, Steven J.; Latour, Robert A.
2015-01-01
Interfacial force field (IFF) parameters for use with the CHARMM force field have been developed for interactions between peptides and high-density polyethylene (HDPE). Parameterization of the IFF was performed to achieve agreement between experimental and calculated adsorption free energies of small TGTG–X–GTGT host–guest peptides (T = threonine, G = glycine, and X = variable amino-acid residue) on HDPE, with ±0.5 kcal/mol agreement. This IFF parameter set consists of tuned nonbonded parameters (i.e., partial charges and Lennard–Jones parameters) for use with an in-house-modified CHARMM molecular dynamic program that enables the use of an independent set of force field parameters to control molecular behavior at a solid–liquid interface. The R correlation coefficient between the simulated and experimental peptide adsorption free energies increased from 0.00 for the standard CHARMM force field parameters to 0.88 for the tuned IFF parameters. Subsequent studies are planned to apply the tuned IFF parameter set for the simulation of protein adsorption behavior on an HDPE surface for comparison with experimental values of adsorbed protein orientation and conformation. PMID:25818122
Piquemal, Jean-Philip; Perera, Lalith; Cisneros, G Andrés; Ren, Pengyu; Pedersen, Lee G; Darden, Thomas A
2006-08-01
Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Thole polarization damping model parametrization was modified based on the ab initio polarization energy computed by a constrained space orbital variation energy decomposition scheme. Excellent agreement has been found with condensed phase experimental results using parameters derived from gas phase ab initio calculations. Additionally, we have observed that the coordination of the calcium cation is influenced by the size of the periodic water box, a recurrent issue in first principles molecular dynamics studies.
Hermosilla, Laura; Prampolini, Giacomo; Calle, Paloma; García de la Vega, José Manuel; Brancato, Giuseppe; Barone, Vincenzo
2015-01-01
A computational strategy that combines both time-dependent and time-independent approaches is exploited to accurately model molecular dynamics and solvent effects on the isotropic hyperfine coupling constants of the DMPO-H nitroxide. Our recent general force field for nitroxides derived from AMBER ff99SB is further extended to systems involving hydrogen atoms in β-positions with respect to NO. The resulting force-field has been employed in a series of classical molecular dynamics simulations, comparing the computed EPR parameters from selected molecular configurations to the corresponding experimental data in different solvents. The effect of vibrational averaging on the spectroscopic parameters is also taken into account, by second order vibrational perturbation theory involving semi-diagonal third energy derivatives together first and second property derivatives. PMID:26584116
The Anharmonic Force Field of Ethylene, C2H4, by Means of Accurate Ab Initio Calculations
NASA Technical Reports Server (NTRS)
Martin, Jan M. L.; Lee, Timothy J.; Taylor, Peter R.; Francois, Jean-Pierre; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
The quartic force field of ethylene, C2H4, has been calculated ab initio using augmented coupled cluster, CCSD(T), methods and correlation consistent basis sets of spdf quality. For the C-12 isotopomers C2H4, C2H3D, H2CCD2, cis-C2H2D2, trans-C2H2D2, C2HD3, and C2D4, all fundamentals could be reproduced to better than 10 per centimeter, except for three cases of severe Fermi type 1 resonance. The problem with these three bands is identified as a systematic overestimate of the Kiij Fermi resonance constants by a factor of two or more; if this is corrected for, the predicted fundamentals come into excellent agreement with experiment. No such systematic overestimate is seen for Fermi type 2 resonances. Our computed harmonic frequencies suggest a thorough revision of the accepted experimentally derived values. Our computed and empirically corrected re geometry differs substantially from experimentally derived values: both the predicted rz geometry and the ground-state rotational constants are, however, in excellent agreement with experiment, suggesting revision of the older values. Anharmonicity constants agree well with experiment for stretches, but differ substantially for stretch-bend interaction constants, due to equality constraints in the experimental analysis that do not hold. Improved criteria for detecting Fermi and Coriolis resonances are proposed and found to work well, contrary to the established method based on harmonic frequency differences that fails to detect several important resonances for C2H4 and its isotopomers. Surprisingly good results are obtained with a small spd basis at the CCSD(T) level. The well-documented strong basis set effect on the v8 out-of-plane motion is present to a much lesser extent when correlation-optimized polarization functions are used. Complete sets of anharmonic, rovibrational coupling, and centrifugal distortion constants for the isotopomers are available as supplementary material to the paper.
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Martin, Jan M. L.; Kwak, Dochan (Technical Monitor)
2002-01-01
The CCSD(T) method has been used to compute a highly accurate quartic force field and fundamental frequencies for all N-14 and N-15 isotopomers of the high energy density material T(sub d)N(sub 4). The computed fundamental frequencies show beyond doubt that the bands observed in a matrix isolation experiment by Radziszewski and coworkers are not due to different isotopomers of T(sub d)N(sub 4). The most sophisticated thermochemical calculations to date yield a N(sub 4) -> 2N(sub 2) heat of reaction of 182.22 +/- 0.5 kcal/mol at 0 K (180.64 +/- 0.5 at 298 K). It is hoped that the data reported herein will aid in the ultimate detection of T(sub d)N(sub 4).
Antila, Hanne S; Salonen, Emppu
2013-01-01
This chapter provides an overview of the most common methods for including an explicit description of electronic polarization in molecular mechanics force fields: the induced point dipole, shell, and fluctuating charge models. The importance of including polarization effects in biomolecular simulations is discussed, and some of the most important achievements in the development of polarizable biomolecular force fields to date are highlighted.
Control Strategies for Accurate Force Generation and Relaxation.
Ohtaka, Chiaki; Fujiwara, Motoko
2016-10-01
Characteristics and motor strategies for force generation and force relaxation were examined using graded tasks during isometric force control. Ten female college students (M age = 20.2 yr., SD = 1.1) were instructed to accurately control the force of isometric elbow flexion using their right arm to match a target force level as quickly as possible. They performed: (1) a generation task, wherein they increased their force from 0% maximum voluntary force to 20% maximum voluntary force (0%-20%), 40% maximum voluntary force (0%-40%), or 60% maximum voluntary force (0%-60%) and (2) and a relaxation task, in which they decreased their force from 60% maximum voluntary force to 40% maximum voluntary force (60%-40%), 20% maximum voluntary force (60%-20%), or to 0% maximum voluntary force (60%-0%). Produced force parameters of point of accuracy (force level, error), quickness (reaction time, adjustment time, rate of force development), and strategy (force wave, rate of force development) were analyzed. Errors of force relaxation were all greater, and reaction times shorter, than those of force generation. Adjustment time depended on the magnitude of force and peak rates of force development and force relaxation differed. Controlled relaxation of force is more difficult with low magnitude of force control.
Control Strategies for Accurate Force Generation and Relaxation.
Ohtaka, Chiaki; Fujiwara, Motoko
2016-10-01
Characteristics and motor strategies for force generation and force relaxation were examined using graded tasks during isometric force control. Ten female college students (M age = 20.2 yr., SD = 1.1) were instructed to accurately control the force of isometric elbow flexion using their right arm to match a target force level as quickly as possible. They performed: (1) a generation task, wherein they increased their force from 0% maximum voluntary force to 20% maximum voluntary force (0%-20%), 40% maximum voluntary force (0%-40%), or 60% maximum voluntary force (0%-60%) and (2) and a relaxation task, in which they decreased their force from 60% maximum voluntary force to 40% maximum voluntary force (60%-40%), 20% maximum voluntary force (60%-20%), or to 0% maximum voluntary force (60%-0%). Produced force parameters of point of accuracy (force level, error), quickness (reaction time, adjustment time, rate of force development), and strategy (force wave, rate of force development) were analyzed. Errors of force relaxation were all greater, and reaction times shorter, than those of force generation. Adjustment time depended on the magnitude of force and peak rates of force development and force relaxation differed. Controlled relaxation of force is more difficult with low magnitude of force control. PMID:27555365
Foley, B. Lachele; Tessier, Matthew B.; Woods, Robert J.
2014-01-01
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion. PMID:25530813
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Martin, Jan M. L.; Dateo, Christopher E.; Taylor, Peter R.
1995-01-01
The XCN and XNC (X = F, Cl) isomers have been investigated using the CCSD(T) method in conjunction with correlation consistent basis sets. Equilibrium geometries, harmonic frequencies, anharmonic constants, fundamental frequencies, and heats of formation have been evaluated. Agreement with experiment for the fundamental frequencies is very good, even for nu(sub 2), for CICN, which is subject to a strong Fermi resonance with 2nu(sub 3). It is also shown that a second-order perturbation theory approach to solving the nuclear Schroedinger equation gives results in excellent agreement with essentially exact variational calculations. This is true even for nu(sub 2) of ClCN, provided that near-singular terms are eliminated from the perturbation theory formulas and the appropriate Fermi interaction energy matrix is then diagonalized. A band at 615/cm, tentatively assigned as the Cl-N stretch in ClNC in matrix isolation experiments, is shown not to be due to ClNC. Accurate atomization energies are determined and are used to evaluate accurate heats of formation (3.1 +/- 1.5, 33.2 +/- 1.5, 72.6 +/- 1.5, and 75.9 +/- 1.5 kcal/mol for FCN, ClCN, FNC, and ClNC, respectively). It is expected that the theoretical heats of formation for FCN, FNC, and ClNC are the most accurate available.
Practical Schemes for Accurate Forces in Quantum Monte Carlo.
Moroni, S; Saccani, S; Filippi, C
2014-11-11
While the computation of interatomic forces has become a well-established practice within variational Monte Carlo (VMC), the use of the more accurate Fixed-Node Diffusion Monte Carlo (DMC) method is still largely limited to the computation of total energies on structures obtained at a lower level of theory. Algorithms to compute exact DMC forces have been proposed in the past, and one such scheme is also put forward in this work, but remain rather impractical due to their high computational cost. As a practical route to DMC forces, we therefore revisit here an approximate method, originally developed in the context of correlated sampling and named here the Variational Drift-Diffusion (VD) approach. We thoroughly investigate its accuracy by checking the consistency between the approximate VD force and the derivative of the DMC potential energy surface for the SiH and C2 molecules and employ a wide range of wave functions optimized in VMC to assess its robustness against the choice of trial function. We find that, for all but the poorest wave function, the discrepancy between force and energy is very small over all interatomic distances, affecting the equilibrium bond length obtained with the VD forces by less than 0.004 au. Furthermore, when the VMC forces are approximate due to the use of a partially optimized wave function, the DMC forces have smaller errors and always lead to an equilibrium distance in better agreement with the experimental value. We also show that the cost of computing the VD forces is only slightly larger than the cost of calculating the DMC energy. Therefore, the VD approximation represents a robust and efficient approach to compute accurate DMC forces, superior to the VMC counterparts.
Polarization effects in molecular mechanical force fields
Cieplak, Piotr; Dupradeau, François-Yves; Duan, Yong; Wang, Junmei
2014-01-01
The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component—polarization energy—and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. PMID:21828594
2015-05-27
ParFit is a flexible and extendable framework and library of classes for fitting force-field parameters to data from high-level ab-initio calculations on the basis of deterministic and stochastic algorithms. Currently, the code is fitting MM3 and Merck force-field parameters but could easily extend to other force-field types.
Motor equivalence during multi-finger accurate force production
Mattos, Daniela; Schöner, Gregor; Zatsiorsky, Vladimir M.; Latash, Mark L.
2014-01-01
We explored stability of multi-finger cyclical accurate force production action by analysis of responses to small perturbations applied to one of the fingers and inter-cycle analysis of variance. Healthy subjects performed two versions of the cyclical task, with and without an explicit target. The “inverse piano” apparatus was used to lift/lower a finger by 1 cm over 0.5 s; the subjects were always instructed to perform the task as accurate as they could at all times. Deviations in the spaces of finger forces and modes (hypothetical commands to individual fingers) were quantified in directions that did not change total force (motor equivalent) and in directions that changed the total force (non-motor equivalent). Motor equivalent deviations started immediately with the perturbation and increased progressively with time. After a sequence of lifting-lowering perturbations leading to the initial conditions, motor equivalent deviations were dominating. These phenomena were less pronounced for analysis performed with respect to the total moment of force with respect to an axis parallel to the forearm/hand. Analysis of inter-cycle variance showed consistently higher variance in a subspace that did not change the total force as compared to the variance that affected total force. We interpret the results as reflections of task-specific stability of the redundant multi-finger system. Large motor equivalent deviations suggest that reactions of the neuromotor system to a perturbation involve large changes of neural commands that do not affect salient performance variables, even during actions with the purpose to correct those salient variables. Consistency of the analyses of motor equivalence and variance analysis provides additional support for the idea of task-specific stability ensured at a neural level. PMID:25344311
Motor equivalence during multi-finger accurate force production.
Mattos, Daniela; Schöner, Gregor; Zatsiorsky, Vladimir M; Latash, Mark L
2015-02-01
We explored stability of multi-finger cyclical accurate force production action by analysis of responses to small perturbations applied to one of the fingers and inter-cycle analysis of variance. Healthy subjects performed two versions of the cyclical task, with and without an explicit target. The "inverse piano" apparatus was used to lift/lower a finger by 1 cm over 0.5 s; the subjects were always instructed to perform the task as accurate as they could at all times. Deviations in the spaces of finger forces and modes (hypothetical commands to individual fingers) were quantified in directions that did not change total force (motor equivalent) and in directions that changed the total force (non-motor equivalent). Motor equivalent deviations started immediately with the perturbation and increased progressively with time. After a sequence of lifting-lowering perturbations leading to the initial conditions, motor equivalent deviations were dominating. These phenomena were less pronounced for analysis performed with respect to the total moment of force with respect to an axis parallel to the forearm/hand. Analysis of inter-cycle variance showed consistently higher variance in a subspace that did not change the total force as compared to the variance that affected total force. We interpret the results as reflections of task-specific stability of the redundant multi-finger system. Large motor equivalent deviations suggest that reactions of the neuromotor system to a perturbation involve large changes in neural commands that do not affect salient performance variables, even during actions with the purpose to correct those salient variables. Consistency of the analyses of motor equivalence and variance analysis provides additional support for the idea of task-specific stability ensured at a neural level. PMID:25344311
Accurate Satellite-Derived Estimates of Tropospheric Ozone Radiative Forcing
NASA Technical Reports Server (NTRS)
Joiner, Joanna; Schoeberl, Mark R.; Vasilkov, Alexander P.; Oreopoulos, Lazaros; Platnick, Steven; Livesey, Nathaniel J.; Levelt, Pieternel F.
2008-01-01
Estimates of the radiative forcing due to anthropogenically-produced tropospheric O3 are derived primarily from models. Here, we use tropospheric ozone and cloud data from several instruments in the A-train constellation of satellites as well as information from the GEOS-5 Data Assimilation System to accurately estimate the instantaneous radiative forcing from tropospheric O3 for January and July 2005. We improve upon previous estimates of tropospheric ozone mixing ratios from a residual approach using the NASA Earth Observing System (EOS) Aura Ozone Monitoring Instrument (OMI) and Microwave Limb Sounder (MLS) by incorporating cloud pressure information from OMI. Since we cannot distinguish between natural and anthropogenic sources with the satellite data, our estimates reflect the total forcing due to tropospheric O3. We focus specifically on the magnitude and spatial structure of the cloud effect on both the shortand long-wave radiative forcing. The estimates presented here can be used to validate present day O3 radiative forcing produced by models.
Huang, Xinchuan; Valeev, Edward F; Lee, Timothy J
2010-12-28
One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H(2)O, N(2)H(+), NO(2)(+), and C(2)H(2) molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N(2)H(+) where it is concluded that basis set extrapolation is still preferred. The differences for H(2)O and NO(2)(+) are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C(2)H(2), however, a known one-particle basis set deficiency for C-C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)(R12), incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N(2)H(+) and NO(2)(+) were computed, including basis set extrapolation, core-correlation, scalar
Accurate force spectroscopy in tapping mode atomic force microscopy in liquids
NASA Astrophysics Data System (ADS)
Xu, Xin; Melcher, John; Raman, Arvind
2010-01-01
Existing force spectroscopy methods in tapping mode atomic force microscopy (AFM) such as higher harmonic inversion [M. Stark, R. W. Stark, W. M. Heckl, and R. Guckenberger, Proc. Natl. Acad. Sci. U.S.A. 99, 8473 (2002)] or scanning probe acceleration microscopy [J. Legleiter, M. Park, B. Cusick, and T. Kowalewski, Proc. Natl. Acad. Sci. U.S.A. 103, 4813 (2006)] or integral relations [M. Lee and W. Jhe, Phys. Rev. Lett. 97, 036104 (2006); S. Hu and A. Raman, Nanotechnology 19, 375704 (2008); H. Hölscher, Appl. Phys. Lett. 89, 123109 (2006); A. J. Katan, Nanotechnology 20, 165703 (2009)] require and assume as an observable the tip dynamics in a single eigenmode of the oscillating microcantilever. We demonstrate that this assumption can distort significantly the extracted tip-sample interaction forces when applied to tapping mode AFM with soft cantilevers in liquid environments. This exception is due to the fact that under these conditions the second eigenmode is momentarily excited and the observed tip dynamics clearly contains contributions from the fundamental and second eigenmodes. To alleviate this problem, a simple experimental method is proposed to screen the second eigenmode contributions in the observed tip deflection signal to allow accurate tip-sample force reconstruction in liquids. The method is implemented experimentally to reconstruct interaction forces on polymer, bacteriorhodopsin membrane, and mica samples in buffer solutions.
Dynamic properties of force fields.
Vitalini, F; Mey, A S J S; Noé, F; Keller, B G
2015-02-28
Molecular-dynamics simulations are increasingly used to study dynamic properties of biological systems. With this development, the ability of force fields to successfully predict relaxation timescales and the associated conformational exchange processes moves into focus. We assess to what extent the dynamic properties of model peptides (Ac-A-NHMe, Ac-V-NHMe, AVAVA, A10) differ when simulated with different force fields (AMBER ff99SB-ILDN, AMBER ff03, OPLS-AA/L, CHARMM27, and GROMOS43a1). The dynamic properties are extracted using Markov state models. For single-residue models (Ac-A-NHMe, Ac-V-NHMe), the slow conformational exchange processes are similar in all force fields, but the associated relaxation timescales differ by up to an order of magnitude. For the peptide systems, not only the relaxation timescales, but also the conformational exchange processes differ considerably across force fields. This finding calls the significance of dynamic interpretations of molecular-dynamics simulations into question.
NASA Astrophysics Data System (ADS)
Inami, Eiichi; Sugimoto, Yoshiaki
2016-08-01
We propose a new method of extracting electrostatic force. The technique is based on frequency modulation atomic force microscopy (FM-AFM) combined with a voltage pulse. In this method, the work that the electrostatic field does on the oscillating tip is measured through the cantilever energy dissipation. This allows us to directly extract capacitive forces including the longer range part, to which the conventional FM-AFM is insensitive. The distance-dependent contact potential difference, which is modulated by local charges distributed on the surfaces of the tip and/or sample, could also be correctly obtained. In the absence of local charges, our method can perfectly reproduce the electrostatic force as a function of the distance and the bias voltage. Furthermore, we demonstrate that the system serves as a sensitive sensor enabling us to check the existence of the local charges such as trapped charges and patch charges.
Garrido, Nuno M; Jorge, Miguel; Queimada, António J; Gomes, José R B; Economou, Ioannis G; Macedo, Eugénia A
2011-10-14
The Gibbs energy of hydration is an important quantity to understand the molecular behavior in aqueous systems at constant temperature and pressure. In this work we review the performance of some popular force fields, namely TraPPE, OPLS-AA and Gromos, in reproducing the experimental Gibbs energies of hydration of several alkyl-aromatic compounds--benzene, mono-, di- and tri-substituted alkylbenzenes--using molecular simulation techniques. In the second part of the paper, we report a new model that is able to improve such hydration energy predictions, based on Lennard Jones parameters from the recent TraPPE-EH force field and atomic partial charges obtained from natural population analysis of density functional theory calculations. We apply a scaling factor determined by fitting the experimental hydration energy of only two solutes, and then present a simple rule to generate atomic partial charges for different substituted alkyl-aromatics. This rule has the added advantages of eliminating the unnecessary assumption of fixed charge on every substituted carbon atom and providing a simple guideline for extrapolating the charge assignment to any multi-substituted alkyl-aromatic molecule. The point charges derived here yield excellent predictions of experimental Gibbs energies of hydration, with an overall absolute average deviation of less than 0.6 kJ mol(-1). This new parameter set can also give good predictive performance for other thermodynamic properties and liquid structural information.
Accurate computation of surface stresses and forces with immersed boundary methods
NASA Astrophysics Data System (ADS)
Goza, Andres; Liska, Sebastian; Morley, Benjamin; Colonius, Tim
2016-09-01
Many immersed boundary methods solve for surface stresses that impose the velocity boundary conditions on an immersed body. These surface stresses may contain spurious oscillations that make them ill-suited for representing the physical surface stresses on the body. Moreover, these inaccurate stresses often lead to unphysical oscillations in the history of integrated surface forces such as the coefficient of lift. While the errors in the surface stresses and forces do not necessarily affect the convergence of the velocity field, it is desirable, especially in fluid-structure interaction problems, to obtain smooth and convergent stress distributions on the surface. To this end, we show that the equation for the surface stresses is an integral equation of the first kind whose ill-posedness is the source of spurious oscillations in the stresses. We also demonstrate that for sufficiently smooth delta functions, the oscillations may be filtered out to obtain physically accurate surface stresses. The filtering is applied as a post-processing procedure, so that the convergence of the velocity field is unaffected. We demonstrate the efficacy of the method by computing stresses and forces that converge to the physical stresses and forces for several test problems.
Light Field Imaging Based Accurate Image Specular Highlight Removal.
Wang, Haoqian; Xu, Chenxue; Wang, Xingzheng; Zhang, Yongbing; Peng, Bo
2016-01-01
Specular reflection removal is indispensable to many computer vision tasks. However, most existing methods fail or degrade in complex real scenarios for their individual drawbacks. Benefiting from the light field imaging technology, this paper proposes a novel and accurate approach to remove specularity and improve image quality. We first capture images with specularity by the light field camera (Lytro ILLUM). After accurately estimating the image depth, a simple and concise threshold strategy is adopted to cluster the specular pixels into "unsaturated" and "saturated" category. Finally, a color variance analysis of multiple views and a local color refinement are individually conducted on the two categories to recover diffuse color information. Experimental evaluation by comparison with existed methods based on our light field dataset together with Stanford light field archive verifies the effectiveness of our proposed algorithm. PMID:27253083
Light Field Imaging Based Accurate Image Specular Highlight Removal
Wang, Haoqian; Xu, Chenxue; Wang, Xingzheng; Zhang, Yongbing; Peng, Bo
2016-01-01
Specular reflection removal is indispensable to many computer vision tasks. However, most existing methods fail or degrade in complex real scenarios for their individual drawbacks. Benefiting from the light field imaging technology, this paper proposes a novel and accurate approach to remove specularity and improve image quality. We first capture images with specularity by the light field camera (Lytro ILLUM). After accurately estimating the image depth, a simple and concise threshold strategy is adopted to cluster the specular pixels into “unsaturated” and “saturated” category. Finally, a color variance analysis of multiple views and a local color refinement are individually conducted on the two categories to recover diffuse color information. Experimental evaluation by comparison with existed methods based on our light field dataset together with Stanford light field archive verifies the effectiveness of our proposed algorithm. PMID:27253083
Performance of different force fields in force probe simulations.
Schlesier, Thomas; Diezemann, Gregor
2013-02-14
We present detailed force probe molecular dynamic simulations of mechanically interlocked dimeric calix[4]arene-catenanes, comparing the results obtained using three different commonly used force fields (GROMOS G53a5, OPLS-AA, and AMBER GAFF). The model system is well characterized as a two-state system consisting of a closed compact and an elongated structure. Both states are stabilized by a different hydrogen-bond network, and complete separation of the dimer is prevented by the mechanical lock of the entangled aliphatic loops. The system shows fully reversible rebinding meaning that after bond rupture the system rejoins when the external force is relaxed. We present a detailed study of quantities determined in simulations using a force ramp, like the rupture force and rejoin force distributions. Additionally, we analyze the dynamics of the hydrogen-bond network. We find that the results obtained from using the different force fields qualitatively agree in the sense that always the fully reversible behavior is found. The details, like the mean rupture forces, however, do depend on the particular force field. Some of the differences observed can be traced back to differences in the strength of the hydrogen-bond networks.
Accurate noncontact calibration of colloidal probe sensitivities in atomic force microscopy.
Chung, Koo-Hyun; Shaw, Gordon A; Pratt, Jon R
2009-06-01
The absolute force sensitivities of colloidal probes comprised of atomic force microscope, or AFM, cantilevers with microspheres attached to their distal ends are measured. The force sensitivities are calibrated through reference to accurate electrostatic forces, the realizations of which are described in detail. Furthermore, the absolute accuracy of a common AFM force calibration scheme, known as the thermal noise method, is evaluated. It is demonstrated that the thermal noise method can be applied with great success to colloidal probe calibration in air and in liquid to yield force measurements with relative standard uncertainties below 5%. Techniques to combine the electrostatics-based determination of the AFM force sensitivity with measurements of the colloidal probe's thermal noise spectrum to compute noncontact estimates of the displacement sensitivity and spring constant are also developed.
Accurate noncontact calibration of colloidal probe sensitivities in atomic force microscopy
Chung, Koo-Hyun; Shaw, Gordon A.; Pratt, Jon R.
2009-06-15
The absolute force sensitivities of colloidal probes comprised of atomic force microscope, or AFM, cantilevers with microspheres attached to their distal ends are measured. The force sensitivities are calibrated through reference to accurate electrostatic forces, the realizations of which are described in detail. Furthermore, the absolute accuracy of a common AFM force calibration scheme, known as the thermal noise method, is evaluated. It is demonstrated that the thermal noise method can be applied with great success to colloidal probe calibration in air and in liquid to yield force measurements with relative standard uncertainties below 5%. Techniques to combine the electrostatics-based determination of the AFM force sensitivity with measurements of the colloidal probe's thermal noise spectrum to compute noncontact estimates of the displacement sensitivity and spring constant are also developed.
Transferability of anharmonic force fields in simulations of molecular vibrations.
Parchanský, Václav; Bour, Petr
2010-07-28
Accurate simulations of vibrational molecular spectra require precise molecular force fields, at least with cubic and quartic anharmonic corrections beyond the harmonic limits. Generation of such force field terms becomes computationally prohibitive for larger molecules. In this work, an alternate possibility is explored, where approximate anharmonic force field components are obtained from molecular fragments. Transferability properties of the cubic and incomplete quartic fields are discussed and tested on model oligoproline molecules. Automatic transfer schemes including cubic, two and three atomic quartic force constants are developed and implemented. The results indicate that the main vibrational interactions in molecules are local and the anharmonic constants are mostly well amendable to the transfer. Exact anharmonic normal mode force fields of larger molecules compared very well to those obtained from smaller molecular parts. The most important changes in vibrational spectra caused by the anharmonic interactions could be reproduced with two and three atomic force field terms. The transfer scheme thus provides molecular anharmonic force fields without a significant loss of accuracy and brings significant savings of computer time and memory needed to generate molecular vibrational energies and spectra.
Are current molecular dynamics force fields too helical?
Best, Robert B; Buchete, Nicolae-Viorel; Hummer, Gerhard
2008-07-01
Accurate force fields are essential for the success of molecular dynamics simulations. In apparent contrast to the conformational preferences of most force fields, recent NMR experiments suggest that short polyalanine peptides in water populate the polyproline II structure almost exclusively. To investigate this apparent contradiction, with its ramifications for the assessment of molecular force fields and the structure of unfolded proteins, we performed extensive simulations of Ala(5) in water ( approximately 5 micros total time), using twelve different force fields and three different peptide terminal groups. Using either empirical or density-functional-based Karplus relations for the J-couplings, we find that most current force fields do overpopulate the alpha-region, with quantitative results depending on the choice of Karplus relation and on the peptide termini. Even after reweighting to match experiment, we find that Ala(5) retains significant alpha- and beta-populations. In fact, several force fields match the experimental data well before reweighting and have a significant helical population. We conclude that radical changes to the best current force fields are not necessary, based on the NMR data. Nevertheless, experiments on short peptides open the way toward the systematic improvement of current simulation models.
Meyer, Andrew J.; D'Lima, Darryl D.; Besier, Thor F.; Lloyd, David G.; Colwell, Clifford W.; Fregly, Benjamin J.
2013-01-01
Mechanical loading is believed to be a critical factor in the development and treatment of knee osteoarthritis. However, the contact forces to which the knee articular surfaces are subjected during daily activities cannot be measured clinically. Thus, the ability to predict internal knee contact forces accurately using external measures (i.e., external knee loads and muscle EMG signals) would be clinically valuable. This study quantifies how well external knee load and EMG measures predict internal knee contact forces during gait. A single subject with a force-measuring tibial prosthesis and post-operative valgus alignment performed four gait patterns (normal, medial thrust, walking pole, and trunk sway) to induce a wide range of external and internal knee joint loads. Linear regression analyses were performed to assess how much of the variability in internal contact forces was accounted for by variability in the external measures. Though the different gait patterns successfully induced significant changes in the external and internal quantities, changes in external measures were generally weak indicators of changes in total, medial, and lateral contact force. Our results suggest that when total contact force may be changing, caution should be exercised when inferring changes in knee contact forces based on observed changes in external knee load and EMG measures. Advances in musculoskeletal modeling methods may be needed for accurate estimation of in vivo knee contact forces. PMID:23280647
Lipid14: The Amber Lipid Force Field.
Dickson, Callum J; Madej, Benjamin D; Skjevik, Age A; Betz, Robin M; Teigen, Knut; Gould, Ian R; Walker, Ross C
2014-02-11
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.
Motor adaptation to a small force field superimposed on a large background force.
Liu, Jiayin; Reinkensmeyer, David J
2007-04-01
The human motor system adapts to novel force field perturbations during reaching by forming an internal model of the external dynamics and by modulating arm impedance. We studied whether it uses similar strategies when the perturbation is superimposed on a much larger background force. Consistent with the Weber-Fechner law for force perception, subjects had greater difficulty consciously perceiving the force field perturbation when it was superimposed on the large background force. However, they still adapted to the perturbation, decreasing trajectory distortion with repeated reaching and demonstrating kinematic after effects when the perturbation was unexpectedly removed. They also adapted by increasing their arm impedance when the background force was not present, but did not vary the arm impedance when the background force was present. The identified parameters of a previously proposed mathematical model of motor adaptation changed significantly with the presence of the background force. These results indicate that the motor system maintains its sensitivity for internal model formation even when there are large background forces that mask perception. Further, the motor system modulates arm impedance differently in response to the same perturbation depending on the background force onto which that perturbation is superimposed. Finally, these results suggest that computational models of motor adaptation will likely need to include force-dependent parameters to accurately predict errors.
Static and dynamical Meissner force fields
NASA Technical Reports Server (NTRS)
Weinberger, B. R.; Lynds, L.; Hull, J. R.; Mulcahy, T. M.
1991-01-01
The coupling between copper-based high temperature superconductors (HTS) and magnets is represented by a force field. Zero-field cooled experiments were performed with several forms of superconductors: 1) cold-pressed sintered cylindrical disks; 2) small particles fixed in epoxy polymers; and 3) small particles suspended in hydrocarbon waxes. Using magnets with axial field symmetries, direct spatial force measurements in the range of 0.1 to 10(exp 4) dynes were performed with an analytical balance and force constants were obtained from mechanical vibrational resonances. Force constants increase dramatically with decreasing spatial displacement. The force field displays a strong temperature dependence between 20 and 90 K and decreases exponentially with increasing distance of separation. Distinct slope changes suggest the presence of B-field and temperature-activated processes that define the forces. Hysteresis measurements indicated that the magnitude of force scales roughly with the volume fraction of HTS in composite structures. Thus, the net force resulting from the field interaction appears to arise from regions as small or smaller than the grain size and does not depend on contiguous electron transport over large areas. Results of these experiments are discussed.
Alternating magnetic field forces for satellite formation flying
NASA Astrophysics Data System (ADS)
Youngquist, Robert C.; Nurge, Mark A.; Starr, Stanley O.
2013-03-01
Selected future space missions, such as large aperture telescopes and multi-component interferometers, will require the precise positioning of a number of isolated satellites, yet many of the suggested approaches for providing satellite positioning forces have serious limitations. In this paper we propose a new approach, capable of providing both position and orientation forces, that resolves or alleviates many of these problems. We show that by using alternating fields and currents that finely-controlled forces can be induced on the satellites, which can be individually selected through frequency allocation. We also show, through analysis and experiment, that near field operation is feasible and can provide sufficient force and the necessary degrees of freedom to accurately position and orient small satellites relative to one another. In particular, the case of a telescope with a large number of free mirrors is developed to provide an example of the concept. We also discuss the far field extension of this concept.
Alternating Magnetic Field Forces for Satellite Formation Flying
NASA Technical Reports Server (NTRS)
Youngquist, Robert C.; Nurge, Mark A.; Starr, Stnaley O.
2012-01-01
Selected future space missions, such as large aperture telescopes and multi-component interferometers, will require the precise positioning of a number of isolated satellites, yet many of the suggested approaches for providing satellites positioning forces have serious limitations. In this paper we propose a new approach, capable of providing both position and orientation forces, that resolves or alleviates many of these problems. We show that by using alternating fields and currents that finely-controlled forces can be induced on the satellites, which can be individually selected through frequency allocation. We also show, through analysis and experiment, that near field operation is feasible and can provide sufficient force and the necessary degrees of freedom to accurately position and orient small satellites relative to one another. In particular, the case of a telescope with a large number of free mirrors is developed to provide an example of the concept. We. also discuss the far field extension of this concept.
Accurate calculation of field and carrier distributions in doped semiconductors
NASA Astrophysics Data System (ADS)
Yang, Wenji; Tang, Jianping; Yu, Hongchun; Wang, Yanguo
2012-06-01
We use the numerical squeezing algorithm(NSA) combined with the shooting method to accurately calculate the built-in fields and carrier distributions in doped silicon films (SFs) in the micron and sub-micron thickness range and results are presented in graphical form for variety of doping profiles under different boundary conditions. As a complementary approach, we also present the methods and the results of the inverse problem (IVP) - finding out the doping profile in the SFs for given field distribution. The solution of the IVP provides us the approach to arbitrarily design field distribution in SFs - which is very important for low dimensional (LD) systems and device designing. Further more, the solution of the IVP is both direct and much easy for all the one-, two-, and three-dimensional semiconductor systems. With current efforts focused on the LD physics, knowing of the field and carrier distribution details in the LD systems will facilitate further researches on other aspects and hence the current work provides a platform for those researches.
Comparing molecular dynamics force fields in the essential subspace.
Martín-García, Fernando; Papaleo, Elena; 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.
Comparing molecular dynamics force fields in the essential subspace.
Martín-García, Fernando; Papaleo, Elena; 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
NASA Astrophysics Data System (ADS)
Mead, A. J.; Heymans, C.; Lombriser, L.; Peacock, J. A.; Steele, O. I.; Winther, H. A.
2016-06-01
We present an accurate non-linear matter power spectrum prediction scheme for a variety of extensions to the standard cosmological paradigm, which uses the tuned halo model previously developed in Mead et al. We consider dark energy models that are both minimally and non-minimally coupled, massive neutrinos and modified gravitational forces with chameleon and Vainshtein screening mechanisms. In all cases, we compare halo-model power spectra to measurements from high-resolution simulations. We show that the tuned halo-model method can predict the non-linear matter power spectrum measured from simulations of parametrized w(a) dark energy models at the few per cent level for k < 10 h Mpc-1, and we present theoretically motivated extensions to cover non-minimally coupled scalar fields, massive neutrinos and Vainshtein screened modified gravity models that result in few per cent accurate power spectra for k < 10 h Mpc-1. For chameleon screened models, we achieve only 10 per cent accuracy for the same range of scales. Finally, we use our halo model to investigate degeneracies between different extensions to the standard cosmological model, finding that the impact of baryonic feedback on the non-linear matter power spectrum can be considered independently of modified gravity or massive neutrino extensions. In contrast, considering the impact of modified gravity and massive neutrinos independently results in biased estimates of power at the level of 5 per cent at scales k > 0.5 h Mpc-1. An updated version of our publicly available HMCODE can be found at https://github.com/alexander-mead/hmcode.
Equifinality and its violations in a redundant system: multifinger accurate force production
Wilhelm, Luke; Zatsiorsky, Vladimir M.
2013-01-01
We explored a hypothesis that transient perturbations applied to a redundant system result in equifinality in the space of task-related performance variables but not in the space of elemental variables. The subjects pressed with four fingers and produced an accurate constant total force level. The “inverse piano” device was used to lift and lower one of the fingers smoothly. The subjects were instructed “not to intervene voluntarily” with possible force changes. Analysis was performed in spaces of finger forces and finger modes (hypothetical neural commands to fingers) as elemental variables. Lifting a finger led to an increase in its force and a decrease in the forces of the other three fingers; the total force increased. Lowering the finger back led to a drop in the force of the perturbed finger. At the final state, the sum of the variances of finger forces/modes computed across repetitive trials was significantly higher than the variance of the total force/mode. Most variance of the individual finger force/mode changes between the preperturbation and postperturbation states was compatible with constant total force. We conclude that a transient perturbation applied to a redundant system leads to relatively small variance in the task-related performance variable (equifinality), whereas in the space of elemental variables much more variance occurs that does not lead to total force changes. We interpret the results within a general theoretical scheme that incorporates the ideas of hierarchically organized control, control with referent configurations, synergic control, and the uncontrolled manifold hypothesis. PMID:23904497
Equifinality and its violations in a redundant system: multifinger accurate force production.
Wilhelm, Luke; Zatsiorsky, Vladimir M; Latash, Mark L
2013-10-01
We explored a hypothesis that transient perturbations applied to a redundant system result in equifinality in the space of task-related performance variables but not in the space of elemental variables. The subjects pressed with four fingers and produced an accurate constant total force level. The "inverse piano" device was used to lift and lower one of the fingers smoothly. The subjects were instructed "not to intervene voluntarily" with possible force changes. Analysis was performed in spaces of finger forces and finger modes (hypothetical neural commands to fingers) as elemental variables. Lifting a finger led to an increase in its force and a decrease in the forces of the other three fingers; the total force increased. Lowering the finger back led to a drop in the force of the perturbed finger. At the final state, the sum of the variances of finger forces/modes computed across repetitive trials was significantly higher than the variance of the total force/mode. Most variance of the individual finger force/mode changes between the preperturbation and postperturbation states was compatible with constant total force. We conclude that a transient perturbation applied to a redundant system leads to relatively small variance in the task-related performance variable (equifinality), whereas in the space of elemental variables much more variance occurs that does not lead to total force changes. We interpret the results within a general theoretical scheme that incorporates the ideas of hierarchically organized control, control with referent configurations, synergic control, and the uncontrolled manifold hypothesis. PMID:23904497
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
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.
MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields
Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.
2011-01-01
We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689
Systematic validation of protein force fields against experimental data.
Lindorff-Larsen, Kresten; Maragakis, Paul; Piana, Stefano; 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.
Additive empirical force field for hexopyranose monosaccharides
Guvench, Olgun; Greene, Shannon N.; Kamath, Ganesh; Brady, John W.; Venable, Richard M.; Pastor, Richard W.; MacKerell, Alexander D.
2010-01-01
We present an all-atom additive empirical force field for the hexopyranose monosaccharide form of glucose and its diastereomers allose, altrose, galactose, gulose, idose, mannose, and talose. The model is developed to be consistent with the CHARMM all-atom biomolecular force fields, and the same parameters are used for all diastereomers, including both the α- and β-anomers of each monosaccharide. The force field is developed in a hierarchical manner and reproduces the gas-phase and condensed-phase properties of small-molecule model compounds corresponding to fragments of pyranose monosaccharides. The resultant parameters are transferred to the full pyranose monosaccharides and additional parameter development is done to achieve a complete hexopyranose monosaccharide force field. Parametrization target data include vibrational frequencies, crystal geometries, solute – water interaction energies, molecular volumes, heats of vaporization, and conformational energies, including those for over 1800 monosaccharide conformations at the MP2/cc-pVTZ//MP2/6-31G(d) level of theory. Though not targeted during parametrization, free energies of aqueous solvation for the model compounds compare favorably with experimental values. Also well-reproduced are monosaccharide crystal unit cell dimensions and ring pucker, densities of concentrated aqueous glucose systems, and the thermodynamic and dynamic properties of the exocyclic torsion in dilute aqueous systems. The new parameter set expands the CHARMM additive force field to allow for simulation of heterogeneous systems that include hexopyranose monosaccharides in addition to proteins, nucleic acids, and lipids. PMID:18470966
Lipid14: The Amber Lipid Force Field.
Dickson, Callum J; Madej, Benjamin D; Skjevik, Age A; Betz, Robin M; Teigen, Knut; Gould, Ian R; Walker, Ross C
2014-02-11
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
Controlling Casimir force via coherent driving field
NASA Astrophysics Data System (ADS)
Ahmad, Rashid; Abbas, Muqaddar; Ahmad, Iftikhar; Qamar, Sajid
2016-04-01
A four level atom-field configuration is used to investigate the coherent control of Casimir force between two identical plates made up of chiral atomic media and separated by vacuum of width d. The electromagnetic chirality-induced negative refraction is obtained via atomic coherence. The behavior of Casimir force is investigated using Casimir-Lifshitz formula. It is noticed that Casimir force can be switched from repulsive to attractive and vice versa via coherent control of the driving field. This switching feature provides new possibilities of using the repulsive Casimir force in the development of new emerging technologies, such as, micro-electro-mechanical and nano-electro-mechanical systems, i.e., MEMS and NEMS, respectively.
Valence force field analysis of tetracyanoethylene
NASA Astrophysics Data System (ADS)
Michaelian, K. H.; Rieckhoff, K. E.; Voigt, E. M.
1982-09-01
A valence force field calculation for the out-of-plane modes of tetracyanoethylene is reported, which makes possible a straightforward assignment of the low-frequency vibrations, including several in-plane modes which previously could not be assigned with certainty. The present set of assignments is consistent with observed vibrational spectra, both for uncomplexed and for complexed tetracyanoethylene, and, for the planar vibrations, is supported by recently published force constant calculations.
Passeri, D; Rossi, M; Vlassak, J J
2013-05-01
Accurate quantitative elastic modulus measurements using contact resonance atomic force microscopy require the calibration of geometrical and mechanical properties of the tip as well as the choice of a suitable model for describing the cantilever-tip-sample system. In this work, we demonstrate with both simulations and experiments that the choice of the model influences the results of the calibration. Neglecting lateral force results in the underestimation of the tip indentation modulus and in the overestimation of the tip-sample contact radius. We propose a new approach to the calibration and data analysis, where lateral forces and cantilever inclination are neglected (which simplifies the calculations) and the tip parameters are assumed as fictitious.
Current Status of Protein Force Fields for Molecular Dynamics
Lopes, Pedro E.M.; Guvench, Olgun
2015-01-01
Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958
Current status of protein force fields for molecular dynamics simulations.
Lopes, Pedro E M; Guvench, Olgun; MacKerell, Alexander D
2015-01-01
The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields.
Tailor-made force fields for crystal-structure prediction.
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.
Tailor-made force fields for crystal-structure prediction.
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. PMID:18642947
Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang
2015-10-29
Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.
Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang
2015-01-01
Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson’s ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers. PMID:26510769
Accurate formula for dissipative interaction in frequency modulation atomic force microscopy
NASA Astrophysics Data System (ADS)
Suzuki, Kazuhiro; Kobayashi, Kei; Labuda, Aleksander; Matsushige, Kazumi; Yamada, Hirofumi
2014-12-01
Much interest has recently focused on the viscosity of nano-confined liquids. Frequency modulation atomic force microscopy (FM-AFM) is a powerful technique that can detect variations in the conservative and dissipative forces between a nanometer-scale tip and a sample surface. We now present an accurate formula to convert the dissipation power of the cantilever measured during the experiment to damping of the tip-sample system. We demonstrated the conversion of the dissipation power versus tip-sample separation curve measured using a colloidal probe cantilever on a mica surface in water to the damping curve, which showed a good agreement with the theoretical curve. Moreover, we obtained the damping curve from the dissipation power curve measured on the hydration layers on the mica surface using a nanometer-scale tip, demonstrating that the formula allows us to quantitatively measure the viscosity of a nano-confined liquid using FM-AFM.
Accurate formula for dissipative interaction in frequency modulation atomic force microscopy
Suzuki, Kazuhiro; Matsushige, Kazumi; Yamada, Hirofumi; Kobayashi, Kei; Labuda, Aleksander
2014-12-08
Much interest has recently focused on the viscosity of nano-confined liquids. Frequency modulation atomic force microscopy (FM-AFM) is a powerful technique that can detect variations in the conservative and dissipative forces between a nanometer-scale tip and a sample surface. We now present an accurate formula to convert the dissipation power of the cantilever measured during the experiment to damping of the tip-sample system. We demonstrated the conversion of the dissipation power versus tip-sample separation curve measured using a colloidal probe cantilever on a mica surface in water to the damping curve, which showed a good agreement with the theoretical curve. Moreover, we obtained the damping curve from the dissipation power curve measured on the hydration layers on the mica surface using a nanometer-scale tip, demonstrating that the formula allows us to quantitatively measure the viscosity of a nano-confined liquid using FM-AFM.
Combination of the CHARMM27 force field with united-atom lipid force fields.
Sapay, Nicolas; Tieleman, D Peter
2011-05-01
Computer simulations offer a valuable way to study membrane systems, from simple lipid bilayers to large transmembrane protein complexes and lipid-nucleic acid complexes for drug delivery. Their accuracy depends on the quality of the force field parameters used to describe the components of a particular system. We have implemented the widely used CHARMM22 and CHARMM27 force fields in the GROMACS simulation package to (i) combine the CHARMM22 protein force field with two sets of united-atom lipids parameters; (ii) allow comparisons of the lipid CHARMM27 force field with other lipid force fields or lipid-protein force field combinations. Our tests do not show any particular issue with the combination of the all-atom CHARMM22 force field with united-atoms lipid parameters, although pertinent experimental data are lacking to assess the quality of the lipid-protein interactions. The conversion utilities allow automatic generation of GROMACS simulation files with CHARMM nucleic acids and protein parameters and topologies, starting from pdb files using the standard GROMACS pdb2gmx method. CMAP is currently not implemented.
Jaramillo-Botero, Andres; Naserifar, Saber; Goddard, William A
2014-04-01
First-principles-based force fields prepared from large quantum mechanical data sets are now the norm in predictive molecular dynamics simulations for complex chemical processes, as opposed to force fields fitted solely from phenomenological data. In principle, the former allow improved accuracy and transferability over a wider range of molecular compositions, interactions, and environmental conditions unexplored by experiments. That is, assuming they have been optimally prepared from a diverse training set. The trade-off has been force field engines that are functionally complex, with a large number of nonbonded and bonded analytical forms that give rise to rather large parameter search spaces. To address this problem, we have developed GARFfield (genetic algorithm-based reactive force field optimizer method), a hybrid multiobjective Pareto-optimal parameter development scheme based on genetic algorithms, hill-climbing routines and conjugate-gradient minimization. To demonstrate the capabilities of GARFfield we use it to develop two very different force fields: (1) the ReaxFF reactive force field for modeling the adiabatic reactive dynamics of silicon carbide growth from an methyltrichlorosilane precursor and (2) the SiC electron force field with effective core pseudopotentials for modeling nonadiabatic dynamic phenomena with highly excited electronic states. The flexible and open architecture of GARFfield enables efficient and fast parallel optimization of parameters from quantum mechanical data sets for demanding applications like ReaxFF, electronic fast forward (or electron force field), and others including atomistic reactive charge-optimized many-body interatomic potentials, Morse, and coarse-grain force fields.
Jaramillo-Botero, Andres; Naserifar, Saber; Goddard, William A
2014-04-01
First-principles-based force fields prepared from large quantum mechanical data sets are now the norm in predictive molecular dynamics simulations for complex chemical processes, as opposed to force fields fitted solely from phenomenological data. In principle, the former allow improved accuracy and transferability over a wider range of molecular compositions, interactions, and environmental conditions unexplored by experiments. That is, assuming they have been optimally prepared from a diverse training set. The trade-off has been force field engines that are functionally complex, with a large number of nonbonded and bonded analytical forms that give rise to rather large parameter search spaces. To address this problem, we have developed GARFfield (genetic algorithm-based reactive force field optimizer method), a hybrid multiobjective Pareto-optimal parameter development scheme based on genetic algorithms, hill-climbing routines and conjugate-gradient minimization. To demonstrate the capabilities of GARFfield we use it to develop two very different force fields: (1) the ReaxFF reactive force field for modeling the adiabatic reactive dynamics of silicon carbide growth from an methyltrichlorosilane precursor and (2) the SiC electron force field with effective core pseudopotentials for modeling nonadiabatic dynamic phenomena with highly excited electronic states. The flexible and open architecture of GARFfield enables efficient and fast parallel optimization of parameters from quantum mechanical data sets for demanding applications like ReaxFF, electronic fast forward (or electron force field), and others including atomistic reactive charge-optimized many-body interatomic potentials, Morse, and coarse-grain force fields. PMID:26580361
A high order accurate difference scheme for complex flow fields
Dexun Fu; Yanwen Ma
1997-06-01
A high order accurate finite difference method for direct numerical simulation of coherent structure in the mixing layers is presented. The reason for oscillation production in numerical solutions is analyzed. It is caused by a nonuniform group velocity of wavepackets. A method of group velocity control for the improvement of the shock resolution is presented. In numerical simulation the fifth-order accurate upwind compact difference relation is used to approximate the derivatives in the convection terms of the compressible N-S equations, a sixth-order accurate symmetric compact difference relation is used to approximate the viscous terms, and a three-stage R-K method is used to advance in time. In order to improve the shock resolution the scheme is reconstructed with the method of diffusion analogy which is used to control the group velocity of wavepackets. 18 refs., 12 figs., 1 tab.
Sultan - forced flow, high field test facility
Horvath, I.; Vecsey, G.; Weymuth, P.; Zellweger, J.
1981-09-01
Three European laboratories: CNEN (Frascati, I) ECN (Petten, NL) and SIN (Villigen, CH) decided to coordinate their development efforts and to install a common high field forced flow test facility at Villigen Switzerland. The test facility SULTAN (Supraleiter Testanlage) is presently under construction. As a first step, an 8T/1m bore solenoid with cryogenic periphery will be ready in 1981. The cryogenic system, data acquisition system and power supplies which are contributed by SIN are described. Experimental feasibilities, including cooling, and instrumentation are reviewed. Progress of components and facility construction is described. Planned extension of the background field up to 12T by insert coils is outlined. 5 refs.
The importance of accurate experimental data to marginal field development
Overa, S.J.; Lingelem, M.N.
1997-12-31
Since exploration started in the Norwegian North Sea in 1965 a total of 196 fields have been discovered. Less than one-third of these fields have been developed. The marginal fields can not be developed economically with current technology even though some of those fields have significant reserves. The total cost to develop one of those large installations is estimated to be 2--5 billion US dollars. Therefore new technology is needed to lower the designed and installed costs of each unit. The need for new physical property data is shown. The value of valid operating data from present units is also pointed out.
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design
Vanommeslaeghe, K.
2014-01-01
Background Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. Scope of Review As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular bimolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields’ parametrization philosophy and methodology. Major Conclusions Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1 microsecond on proteins, DNA, lipids and carbohydrates. General Significance Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers a model that is an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. PMID:25149274
Magnetic field models of nine CP stars from "accurate" measurements
NASA Astrophysics Data System (ADS)
Glagolevskij, Yu. V.
2013-01-01
The dipole models of magnetic fields in nine CP stars are constructed based on the measurements of metal lines taken from the literature, and performed by the LSD method with an accuracy of 10-80 G. The model parameters are compared with the parameters obtained for the same stars from the hydrogen line measurements. For six out of nine stars the same type of structure was obtained. Some parameters, such as the field strength at the poles B p and the average surface magnetic field B s differ considerably in some stars due to differences in the amplitudes of phase dependences B e (Φ) and B s (Φ), obtained by different authors. It is noted that a significant increase in the measurement accuracy has little effect on the modelling of the large-scale structures of the field. By contrast, it is more important to construct the shape of the phase dependence based on a fairly large number of field measurements, evenly distributed by the rotation period phases. It is concluded that the Zeeman component measurement methods have a strong effect on the shape of the phase dependence, and that the measurements of the magnetic field based on the lines of hydrogen are more preferable for modelling the large-scale structures of the field.
Self-forces from generalized Killing fields
NASA Astrophysics Data System (ADS)
Harte, Abraham I.
2008-12-01
A non-perturbative formalism is developed that simplifies the understanding of self-forces and self-torques acting on extended scalar charges in curved spacetimes. Laws of motion are locally derived using momenta generated by a set of generalized Killing fields. Self-interactions that may be interpreted as arising from the details of a body's internal structure are shown to have very simple geometric and physical interpretations. Certain modifications to the usual definition for a center-of-mass are identified that significantly simplify the motions of charges with strong self-fields. A derivation is also provided for a generalized form of the Detweiler Whiting axiom that pointlike charges should react only to the so-called regular component of their self-field. Standard results are shown to be recovered for sufficiently small charge distributions.
The variance needed to accurately describe jump height from vertical ground reaction force data.
Richter, Chris; McGuinness, Kevin; O'Connor, Noel E; Moran, Kieran
2014-12-01
In functional principal component analysis (fPCA) a threshold is chosen to define the number of retained principal components, which corresponds to the amount of preserved information. A variety of thresholds have been used in previous studies and the chosen threshold is often not evaluated. The aim of this study is to identify the optimal threshold that preserves the information needed to describe a jump height accurately utilizing vertical ground reaction force (vGRF) curves. To find an optimal threshold, a neural network was used to predict jump height from vGRF curve measures generated using different fPCA thresholds. The findings indicate that a threshold from 99% to 99.9% (6-11 principal components) is optimal for describing jump height, as these thresholds generated significantly lower jump height prediction errors than other thresholds.
A compact high field magnetic force microscope.
Zhou, Haibiao; Wang, Ze; Hou, Yubin; Lu, Qingyou
2014-12-01
We present the design and performance of a simple and compact magnetic force microscope (MFM), whose tip-sample coarse approach is implemented by the piezoelectric tube scanner (PTS) itself. In brief, a square rod shaft is axially spring-clamped on the inner wall of a metal tube which is glued inside the free end of the PTS. The shaft can thus be driven by the PTS to realize image scan and inertial stepping coarse approach. To enhance the inertial force, each of the four outer electrodes of the PTS is driven by an independent port of the controller. The MFM scan head is so compact that it can easily fit into the 52mm low temperature bore of a 20T superconducting magnet. The performance of the MFM is demonstrated by imaging a manganite thin film at low temperature and in magnetic fields up to 15T. PMID:25189114
Management of change through force field analysis.
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. PMID:12801382
Nonlinear Force-Free Field Extrapolation of NOAA AR 0696
NASA Astrophysics Data System (ADS)
Thalmann, J. K.; Wiegelmann, T.
2007-12-01
We investigate the 3D coronal magnetic field structure of NOAA AR 0696 in the period of November 09-11, 2004, before and after an X2.5 flare (occurring around 02:13 UT on November 10, 2004). The coronal magnetic field dominates the structure of the solar corona and consequently plays a key role for the understanding of the initiation of flares. The most accurate presently available method to derive the coronal magnetic field is currently the nonlinear force-free field extrapolation from measurements of the photospheric magnetic field vector. These vector-magnetograms were processed from stokes I, Q, U, and V measurements of the Big Bear Solar Observatory and extrapolated into the corona with the nonlinear force-free optimization code developed by Wiegelmann (2004). We analyze the corresponding time series of coronal equilibria regarding topology changes of the 3D coronal magnetic field during the flare. Furthermore, quantities such as the temporal evolution of the magnetic energy and helicity are computed.
Modeling of Non-Gravitational Forces for Precise and Accurate Orbit Determination
NASA Astrophysics Data System (ADS)
Hackel, Stefan; Gisinger, Christoph; Steigenberger, Peter; Balss, Ulrich; Montenbruck, Oliver; Eineder, Michael
2014-05-01
Remote sensing satellites support a broad range of scientific and commercial applications. The two radar imaging satellites TerraSAR-X and TanDEM-X provide spaceborne Synthetic Aperture Radar (SAR) and interferometric SAR data with a very high accuracy. The precise reconstruction of the satellite's trajectory is based on the Global Positioning System (GPS) measurements from a geodetic-grade dual-frequency Integrated Geodetic and Occultation Receiver (IGOR) onboard the spacecraft. The increasing demand for precise radar products relies on validation methods, which require precise and accurate orbit products. An analysis of the orbit quality by means of internal and external validation methods on long and short timescales shows systematics, which reflect deficits in the employed force models. Following the proper analysis of this deficits, possible solution strategies are highlighted in the presentation. The employed Reduced Dynamic Orbit Determination (RDOD) approach utilizes models for gravitational and non-gravitational forces. A detailed satellite macro model is introduced to describe the geometry and the optical surface properties of the satellite. Two major non-gravitational forces are the direct and the indirect Solar Radiation Pressure (SRP). The satellite TerraSAR-X flies on a dusk-dawn orbit with an altitude of approximately 510 km above ground. Due to this constellation, the Sun almost constantly illuminates the satellite, which causes strong across-track accelerations on the plane rectangular to the solar rays. The indirect effect of the solar radiation is called Earth Radiation Pressure (ERP). This force depends on the sunlight, which is reflected by the illuminated Earth surface (visible spectra) and the emission of the Earth body in the infrared spectra. Both components of ERP require Earth models to describe the optical properties of the Earth surface. Therefore, the influence of different Earth models on the orbit quality is assessed. The scope of
A quantum mechanical polarizable force field for biomolecular interactions.
Donchev, A G; Ozrin, V D; Subbotin, M V; Tarasov, O V; Tarasov, V I
2005-05-31
We introduce a quantum mechanical polarizable force field (QMPFF) fitted solely to QM data at the MP2/aTZ(-hp) level. Atomic charge density is modeled by point-charge nuclei and floating exponentially shaped electron clouds. The functional form of interaction energy parallels quantum mechanics by including electrostatic, exchange, induction, and dispersion terms. Separate fitting of each term to the counterpart calculated from high-quality QM data ensures high transferability of QMPFF parameters to different molecular environments, as well as accurate fit to a broad range of experimental data in both gas and liquid phases. QMPFF, which is much more efficient than ab initio QM, is optimized for the accurate simulation of biomolecular systems and the design of drugs.
Rigorous force field optimization principles based on statistical distance minimization.
Vlcek, Lukas; Chialvo, Ariel A
2015-10-14
We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model's static measurable properties to those of the target. We exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of the approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length. PMID:26472366
Rigorous force field optimization principles based on statistical distance minimization
Vlcek, Lukas; Chialvo, Ariel A.
2015-10-14
We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model’s static measurable properties to those of the target. We exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of the approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length.
Conformal field theory of critical Casimir forces
NASA Astrophysics Data System (ADS)
Emig, Thorsten; Bimonte, Giuseppe; Kardar, Mehran
2015-03-01
Thermal fluctuations of a critical system induce long-ranged Casimir forces between objects that couple to the underlying field. For two dimensional conformal field theories (CFT) we derive exact results for the Casimir interaction for a deformed strip and for two compact objects of arbitrary shape in terms of the free energy of a standard region (circular ring or flat strip) whose dimension is determined by the mutual capacitance of two conductors with the objects' shape; and a purely geometric energy that is proportional to conformal charge of the CFT, but otherwise super-universal in that it depends only on the shapes and is independent of boundary conditions and other details. The effect of inhomogenous boundary conditions is also discussed.
Bauer, Sebastian; Mathias, Gerald; Tavan, Paul
2014-03-14
We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ε(r) is close to one everywhere inside the protein. The Gaussian widths σ{sub i} of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σ{sub i}. A summarizing discussion highlights the achievements of the new theory and of its approximate solution
Bauer, Sebastian; Mathias, Gerald; Tavan, Paul
2014-03-14
We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ε(r) is close to one everywhere inside the protein. The Gaussian widths σ(i) of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σ(i). A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by
Cosmic Ray Acceleration in Force Free Fields
NASA Astrophysics Data System (ADS)
Colgate, Stirling; Li, Hui; Kronberg, Philipp
2002-11-01
Galactic, extragalactic, and cluster magnetic fields are in apparent pressure equilibrium with the in-fall pressure of matter from the external medium, IGM, onto the Galaxies and clusters, and from the voids onto the galaxy sheets, (walls), implying fields of 5 , 0.5, & 20 μG respectively. Equipartition or minimum energy, implies β_CR=n_CRm_pc^2/(B^2/8π)˜= 1. The total energy in field and CRs is then ˜= 10^55 ergs Galactic and ˜= 4 ot 10^60 ergs per galaxy in the IGM and less within clusters, e.g., radio lobes, synchrotron "glow" in the IGM (Kronberg), and the UHECRs spectrum, Γ =-2.6. CRs escape from the Galaxy to the IGM, τ˜=10^7y, and similarly from the walls to the voids, ˜=10^8y, less than the GZK cut-off time provided B_galaxy>B_IGM>B_voids. The free energy of black hole formation, The Los Alamos model, is just sufficient. The lack of shocks at the boundaries of over pressured radio lobes and the need for high acceleration efficiency suggests eE_allel˜= eη_reconJ_allel, acceleration by reconnection of these force-free fields.
Weber's gravitational force as static weak field approximation
NASA Astrophysics Data System (ADS)
Tiandho, Yuant
2016-02-01
Weber's gravitational force (WGF) is one of gravitational model that can accommodate a non-static system because it depends not only on the distance but also on the velocity and the acceleration. Unlike Newton's law of gravitation, WGF can predict the anomalous of Mercury and gravitational bending of light near massive object very well. Then, some researchers use WGF as an alternative model of gravitation and propose a new mechanics theory namely the relational mechanics theory. However, currently we have known that the theory of general relativity which proposed by Einstein can explain gravity with very accurate. Through the static weak field approximation for the non-relativistic object, we also have known that the theory of general relativity will reduce to Newton's law of gravity. In this work, we expand the static weak field approximation that compatible with relativistic object and we obtain a force equation which correspond to WGF. Therefore, WGF is more precise than Newton's gravitational law. The static-weak gravitational field that we used is a solution of the Einstein's equation in the vacuum that satisfy the linear field approximation. The expression of WGF with ξ = 1 and satisfy the requirement of energy conservation are obtained after resolving the geodesic equation. By this result, we can conclude that WGF can be derived from the general relativity.
Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; MacKerell, A. D.
2010-01-01
The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids and carbohydrates. In the present paper an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present paper in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform “all-CHARMM” simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems. PMID:19575467
Recent Developments and Applications of the CHARMM force fields.
Zhu, Xiao; Lopes, Pedro E M; Mackerell, Alexander D
2012-01-01
Empirical force fields commonly used to describe the condensed phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical (QM) methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds and new theoretical developments (eg. polarizable methods) make force-field development a dynamic domain of research. Accordingly, a number of improvements and extensions of the CHARMM force fields have occurred over the years. The objective of the present review is to provide an up-to-date overview of the CHARMM force fields. A limited presentation on the historical aspects of force fields will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable force fields, including examples of recent applications of those force fields.
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…
Force-Field Analysis: Incorporating Critical Thinking in Goal Setting.
ERIC Educational Resources Information Center
Hustedde, Ron; Score, Michael
1995-01-01
Force field analysis encourages members to examine the probability of reaching agreed-upon goals. It can help groups avoid working toward goals that are unlikely to be reached. In every situation are three forces: forces that encourage maintenance of the status quo or change; driving or helping forces that push toward change; and restraining…
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.)
Dislocation core fields and forces in FCC metals
Henager, Charles H.; Hoagland, Richard G.
2004-04-01
Atomistic models were used to obtain dislocation core fields for edge, screw, and mixed dislocations in Al and Cu using EAM. Core fields are analyzed using a line force dipole representation, with dilatant and dipole terms. The core field contribution to the force between dislocations is shown to be significant for interactions within 50b.
Kostov, M K; Cheng, H; Cooper, A C; Pez, G P
2002-09-30
A general force field methodology is developed for description of molecular interactions in carbon-based materials. The method makes use of existing parameters of potential functions developed for sp(2) and sp(3) carbons and allows accurate representation of molecular forces in curved carbon environment. The potential parameters are explicitly curvature and site dependent. The proposed force field approach was used in molecular dynamics (MD) simulations for hydrogen adsorption in single-walled carbon nanotubes (SWNTs). The results reveal significant nanotube deformations and the calculated energies of adsorption are comparable to the reported experimental heat of adsorption for H2 in SWNTs. PMID:12366059
Fang, Hanjun; Kamakoti, Preeti; Ravikovitch, Peter I; Aronson, Matthew; Paur, Charanjit; Sholl, David S
2013-08-21
The development of accurate force fields is vital for predicting adsorption in porous materials. Previously, we introduced a first principles-based transferable force field for CO2 adsorption in siliceous zeolites (Fang et al., J. Phys. Chem. C, 2012, 116, 10692). In this study, we extend our approach to CO2 adsorption in cationic zeolites which possess more complex structures. Na-exchanged zeolites are chosen for demonstrating the approach. These methods account for several structural complexities including Al distribution, cation positions and cation mobility, all of which are important for predicting adsorption. The simulation results are validated with high-resolution experimental measurements of isotherms and microcalorimetric heats of adsorption on well-characterized materials. The choice of first-principles method has a significant influence on the ability of force fields to accurately describe CO2-zeolite interactions. The PBE-D2 derived force field, which performed well for CO2 adsorption in siliceous zeolites, does not do so for Na-exchanged zeolites; the PBE-D2 method overestimates CO2 adsorption energies on multi-cation sites that are common in cationic zeolites with low Si/Al ratios. In contrast, a force field derived from the DFT/CC method performed well. Agreement was obtained between simulation and experiment not only for LTA-4A on which the force field fitting is based, but for other two common adsorbents, NaX and NaY.
Accurate spring constant calibration for very stiff atomic force microscopy cantilevers.
Grutzik, Scott J; Gates, Richard S; Gerbig, Yvonne B; Smith, Douglas T; Cook, Robert F; Zehnder, Alan T
2013-11-01
There are many atomic force microscopy (AFM) applications that rely on quantifying the force between the AFM cantilever tip and the sample. The AFM does not explicitly measure force, however, so in such cases knowledge of the cantilever stiffness is required. In most cases, the forces of interest are very small, thus compliant cantilevers are used. A number of methods have been developed that are well suited to measuring low stiffness values. However, in some cases a cantilever with much greater stiffness is required. Thus, a direct, traceable method for calibrating very stiff (approximately 200 N/m) cantilevers is presented here. The method uses an instrumented and calibrated nanoindenter to determine the stiffness of a reference cantilever. This reference cantilever is then used to measure the stiffness of a number of AFM test cantilevers. This method is shown to have much smaller uncertainty than previously proposed methods. An example application to fracture testing of nanoscale silicon beam specimens is included.
Accurate spring constant calibration for very stiff atomic force microscopy cantilevers
Grutzik, Scott J.; Zehnder, Alan T.; Gates, Richard S.; Gerbig, Yvonne B.; Smith, Douglas T.; Cook, Robert F.
2013-11-15
There are many atomic force microscopy (AFM) applications that rely on quantifying the force between the AFM cantilever tip and the sample. The AFM does not explicitly measure force, however, so in such cases knowledge of the cantilever stiffness is required. In most cases, the forces of interest are very small, thus compliant cantilevers are used. A number of methods have been developed that are well suited to measuring low stiffness values. However, in some cases a cantilever with much greater stiffness is required. Thus, a direct, traceable method for calibrating very stiff (approximately 200 N/m) cantilevers is presented here. The method uses an instrumented and calibrated nanoindenter to determine the stiffness of a reference cantilever. This reference cantilever is then used to measure the stiffness of a number of AFM test cantilevers. This method is shown to have much smaller uncertainty than previously proposed methods. An example application to fracture testing of nanoscale silicon beam specimens is included.
Towards a force field based on density fitting.
Piquemal, Jean-Philip; Cisneros, G Andrés; Reinhardt, Peter; Gresh, Nohad; Darden, Thomas A
2006-03-14
Total intermolecular interaction energies are determined with a first version of the Gaussian electrostatic model (GEM-0), a force field based on a density fitting approach using s-type Gaussian functions. The total interaction energy is computed in the spirit of the sum of interacting fragment ab initio (SIBFA) force field by separately evaluating each one of its components: electrostatic (Coulomb), exchange repulsion, polarization, and charge transfer intermolecular interaction energies, in order to reproduce reference constrained space orbital variation (CSOV) energy decomposition calculations at the B3LYP/aug-cc-pVTZ level. The use of an auxiliary basis set restricted to spherical Gaussian functions facilitates the rotation of the fitted densities of rigid fragments and enables a fast and accurate density fitting evaluation of Coulomb and exchange-repulsion energy, the latter using the overlap model introduced by Wheatley and Price [Mol. Phys. 69, 50718 (1990)]. The SIBFA energy scheme for polarization and charge transfer has been implemented using the electric fields and electrostatic potentials generated by the fitted densities. GEM-0 has been tested on ten stationary points of the water dimer potential energy surface and on three water clusters (n = 16,20,64). The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interaction energies with errors below kBT at room temperature. Preliminary results for Coulomb and exchange-repulsion energies of metal cation complexes and coupled cluster singles doubles electron densities are discussed.
Yin, Jian; Fenley, Andrew T; Henriksen, Niel M; Gilson, Michael K
2015-08-13
Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by nonoptimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery.
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.
Donchev, A. G.; Galkin, N. G.; Illarionov, A. A.; Khoruzhii, O. V.; Olevanov, M. A.; Ozrin, V. D.; Subbotin, M. V.; Tarasov, V. I.
2006-01-01
We have recently introduced a quantum mechanical polarizable force field (QMPFF) fitted solely to high-level quantum mechanical data for simulations of biomolecular systems. Here, we present an improved form of the force field, QMPFF2, and apply it to simulations of liquid water. The results of the simulations show excellent agreement with a variety of experimental thermodynamic and structural data, as good or better than that provided by specialized water potentials. In particular, QMPFF2 is the only ab initio force field to accurately reproduce the anomalous temperature dependence of water density to our knowledge. The ability of the same force field to successfully simulate the properties of both organic molecules and water suggests it will be useful for simulations of proteins and protein–ligand interactions in the aqueous environment. PMID:16723394
Assessing the Current State of Amber Force Field Modifications for DNA.
Galindo-Murillo, Rodrigo; Robertson, James C; Zgarbová, Marie; Šponer, Jiří; Otyepka, Michal; Jurečka, Petr; Cheatham, Thomas E
2016-08-01
The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling, toward being able to generate accurate and stable structures of biopolymers. The Amber force field for nucleic acids has been used extensively since the 1990s, and multiple artifacts have been discovered, corrected, and reassessed by different research groups. We present a direct comparison of two of the most recent and state-of-the-art Amber force field modifications, bsc1 and OL15, that focus on accurate modeling of double-stranded DNA. After extensive MD simulations with five test cases and two different water models, we conclude that both modifications are a remarkable improvement over the previous bsc0 force field. Both force field modifications show better agreement when compared to experimental structures. To ensure convergence, the Drew-Dickerson dodecamer (DDD) system was simulated using 100 independent MD simulations, each extended to at least 10 μs, and the independent MD simulations were concatenated into a single 1 ms long trajectory for each combination of force field and water model. This is significantly beyond the time scale needed to converge the conformational ensemble of the internal portions of a DNA helix absent internal base pair opening. Considering all of the simulations discussed in the current work, the MD simulations performed to
Assessing the Current State of Amber Force Field Modifications for DNA.
Galindo-Murillo, Rodrigo; Robertson, James C; Zgarbová, Marie; Šponer, Jiří; Otyepka, Michal; Jurečka, Petr; Cheatham, Thomas E
2016-08-01
The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling, toward being able to generate accurate and stable structures of biopolymers. The Amber force field for nucleic acids has been used extensively since the 1990s, and multiple artifacts have been discovered, corrected, and reassessed by different research groups. We present a direct comparison of two of the most recent and state-of-the-art Amber force field modifications, bsc1 and OL15, that focus on accurate modeling of double-stranded DNA. After extensive MD simulations with five test cases and two different water models, we conclude that both modifications are a remarkable improvement over the previous bsc0 force field. Both force field modifications show better agreement when compared to experimental structures. To ensure convergence, the Drew-Dickerson dodecamer (DDD) system was simulated using 100 independent MD simulations, each extended to at least 10 μs, and the independent MD simulations were concatenated into a single 1 ms long trajectory for each combination of force field and water model. This is significantly beyond the time scale needed to converge the conformational ensemble of the internal portions of a DNA helix absent internal base pair opening. Considering all of the simulations discussed in the current work, the MD simulations performed to
Assessing the Current State of Amber Force Field Modifications for DNA
2016-01-01
The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling, toward being able to generate accurate and stable structures of biopolymers. The Amber force field for nucleic acids has been used extensively since the 1990s, and multiple artifacts have been discovered, corrected, and reassessed by different research groups. We present a direct comparison of two of the most recent and state-of-the-art Amber force field modifications, bsc1 and OL15, that focus on accurate modeling of double-stranded DNA. After extensive MD simulations with five test cases and two different water models, we conclude that both modifications are a remarkable improvement over the previous bsc0 force field. Both force field modifications show better agreement when compared to experimental structures. To ensure convergence, the Drew–Dickerson dodecamer (DDD) system was simulated using 100 independent MD simulations, each extended to at least 10 μs, and the independent MD simulations were concatenated into a single 1 ms long trajectory for each combination of force field and water model. This is significantly beyond the time scale needed to converge the conformational ensemble of the internal portions of a DNA helix absent internal base pair opening. Considering all of the simulations discussed in the current work, the MD simulations performed to
Subgrid resolution of flow and force fields.
NASA Technical Reports Server (NTRS)
Buneman, O.
1973-01-01
By means of spline fitting, both while converting a Lagrangian distribution of field sources onto an Eulerian grid, and while interpolating the field from its Eulerian grid to the Lagrangian positions of the responding elements, one achieves effective resolution down to about one-eight of a grid mesh unit. One also avoids discontinuities and noise due to cell boundary crossings.
Novel concepts in near-field optics: from magnetic near-field to optical forces
NASA Astrophysics Data System (ADS)
Yang, Honghua
Driven by the progress in nanotechnology, imaging and spectroscopy tools with nanometer spatial resolution are needed for in situ material characterizations. Near-field optics provides a unique way to selectively excite and detect elementary electronic and vibrational interactions at the nanometer scale, through interactions of light with matter in the near-field region. This dissertation discusses the development and applications of near-field optical imaging techniques, including plasmonic material characterization, optical spectral nano-imaging and magnetic field detection using scattering-type scanning near-field optical microscopy (s-SNOM), and exploring new modalities of optical spectroscopy based on optical gradient force detection. Firstly, the optical dielectric functions of one of the most common plasmonic materials---silver is measured with ellipsometry, and analyzed with the Drude model over a broad spectral range from visible to mid-infrared. This work was motivated by the conflicting results of previous measurements, and the need for accurate values for a wide range of applications of silver in plasmonics, optical antennas, and metamaterials. This measurement provides a reference for dielectric functions of silver used in metamaterials, plasmonics, and nanophotonics. Secondly, I implemented an infrared s-SNOM instrument for spectroscopic nano-imaging at both room temperature and low temperature. As one of the first cryogenic s-SNOM instruments, the novel design concept and key specifications are discussed. Initial low-temperature and high-temperature performances of the instrument are examined by imaging of optical conductivity of vanadium oxides (VO2 and V2O 3) across their phase transitions. The spectroscopic imaging capability is demonstrated on chemical vibrational resonances of Poly(methyl methacrylate) (PMMA) and other samples. The third part of this dissertation explores imaging of optical magnetic fields. As a proof-of-principle, the magnetic
Ponderomotive Force in the Presence of Electric Fields
NASA Technical Reports Server (NTRS)
Khazanov, G. V.; Krivorutsky, E. N.
2013-01-01
This paper presents averaged equations of particle motion in an electromagnetic wave of arbitrary frequency with its wave vector directed along the ambient magnetic field. The particle is also subjected to an E cross B drift and a background electric field slowly changing in space and acting along the magnetic field line. The fields, wave amplitude, and the wave vector depend on the coordinate along the magnetic field line. The derivations of the ponderomotive forces are done by assuming that the drift velocity in the ambient magnetic field is comparable to the particle velocity. Such a scenario leads to new ponderomotive forces, dependent on the wave magnetic field intensity, and, as a result, to the additional energy exchange between the wave and the plasma particles. It is found that the parallel electric field can lead to the change of the particle-wave energy exchange rate comparable to that produced by the previously discussed ponderomotive forces.
Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields.
de Jong, Djurre H; Periole, Xavier; Marrink, Siewert J
2012-03-13
The interactions between amino acid side chains govern protein secondary, tertiary, and quaternary structure formation. For molecular modeling approaches to be able to realistically describe these phenomena, the underlying force fields have to represent these interactions as accurately as possible. Here, we compare the side chain-side chain interactions for a number of commonly used force fields, namely the all-atom OPLS, the united-atom GROMOS, and the coarse-grain MARTINI force field. We do so by calculating the dimerization free energies between selected pairs of side chains and structural characterization of their binding modes. To mimic both polar and nonpolar environments, the simulations are performed in water, n-octanol, and decane. In general, reasonable correlations are found between all three force fields, with deviations on the order of 1 kT in aqueous solvent. In apolar solvent, however, significantly larger differences are found, especially for charged amino acid pairs between the OPLS and GROMOS force fields, and for polar interactions in the MARTINI force field in comparison to the higher resolution models. Interestingly, even in cases where the dimerization free energies are similar, the binding mode may differ substantially between the force fields. This was found to be especially the case for aromatic residues. In addition to the inter-force-field comparison, we compared the various force fields to a knowledge-based potential. The two independent approaches show good correlation in aqueous solvent with an exception of aromatic residues for which the interaction strength is lower in the knowledge-based potentials.
Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.
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.
Comparison of Cellulose Ib Simulations with Three Carbohydrate Force Fields
Matthews, J. F.; Beckham, G. T.; Bergenstrahle, M.; Brady, J. W.; Himmel, M. E.; Crowley, M. 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 I{beta} 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 I{beta} 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.
Using force fields methods for locating transition structures
NASA Astrophysics Data System (ADS)
Jensen, Frank
2003-11-01
A previously proposed strategy of using force field methods for generating approximations to the geometry of transition structures is extended to also estimating an approximate Hessian matrix. These two components allow an automated method for locating first order saddle points, which is an essential requisite for studying chemical reactions of systems with many degrees of freedom. The efficiency of using an approximate force field Hessian matrix for initiating the geometry optimization is compared with the use of an exact Hessian. The force field Hessian in general requires more geometry steps to converge, but the additional computational cost is offset by the savings from not calculating the exact Hessian at the initial geometry.
PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS
Ivani, Ivan; Dans, Pablo D.; Noy, Agnes; Pérez, Alberto; Faustino, Ignacio; Hospital, Adam; Walther, Jürgen; Andrio, Pau; Goñi, Ramon; Balaceanu, Alexandra; Portella, Guillem; Battistini, Federica; Gelpí, Josep Lluis; González, Carlos; Vendruscolo, Michele; Laughton, Charles A.; Harris, Sarah A.; Case, David A.; Orozco, Modesto
2015-01-01
We present parmbsc1, a new force-field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (~140 μs) covering most of the DNA structural space. Parmbsc1 provides high quality results in diverse systems, solving problems of previous force-fields. Parmbsc1 aims to be a reference force-field for the study of DNA in the next decade. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/. PMID:26569599
On the resistive diffusion of force-free magnetic fields
NASA Technical Reports Server (NTRS)
Low, B. C.
1980-01-01
Reid and Laing (1979) conjectured on the general behavior of resistive force-free magnetic fields in a slab model following a numerical study. However, the basic properties of resistive force-free magnetic fields had been established previously. Some results from the previous work are extended to show that the conjecture of Reid and Laing is incorrect. A general analytic treatment of the problem provides the correct physical properties that Reid and Laing were unable to deduce from their numerical solutions. A criticism is also given of the results presented in another numerical study treating cylindrical resistive force-free magnetic fields, by the same authors.
Approximate photochemical dynamics of azobenzene with reactive force fields
Li, Yan; Hartke, Bernd
2013-12-14
We have fitted reactive force fields of the ReaxFF type to the ground and first excited electronic states of azobenzene, using global parameter optimization by genetic algorithms. Upon coupling with a simple energy-gap transition probability model, this setup allows for completely force-field-based simulations of photochemical cis→trans- and trans→cis-isomerizations of azobenzene, with qualitatively acceptable quantum yields. This paves the way towards large-scale dynamics simulations of molecular machines, including bond breaking and formation (via the reactive force field) as well as photochemical engines (presented in this work)
New-generation amber united-atom force field.
Yang, Lijiang; Tan, Chun-Hu; Hsieh, Meng-Juei; Wang, Junmei; Duan, Yong; Cieplak, Piotr; Caldwell, James; Kollman, Peter A; Luo, Ray
2006-07-01
We have developed a new-generation Amber united-atom force field for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. In the new united-atom force field, all hydrogens on aliphatic carbons in all amino acids are united with carbons except those on Calpha. Our choice of explicit representation of all protein backbone atoms aims at minimizing perturbation to protein backbone conformational distributions and to simplify development of backbone torsion terms. Tests with dipeptides and solvated proteins show that our goal is achieved quite successfully. The new united-atom force field uses the same new RESP charging scheme based on B3LYP/cc-pVTZ//HF/6-31g** quantum mechanical calculations in the PCM continuum solvent as that in the Duan et al. force field. van der Waals parameters are empirically refitted starting from published values with respect to experimental solvation free energies of amino acid side-chain analogues. The suitability of mixing new point charges and van der Waals parameters with existing Amber covalent terms is tested on alanine dipeptide and is found to be reasonable. Parameters for all new torsion terms are refitted based on the new point charges and the van der Waals parameters. Molecular dynamics simulations of three small globular proteins in the explicit TIP3P solvent are performed to test the overall stability and accuracy of the new united-atom force field. Good agreements between the united-atom force field and the Duan et al. all-atom force field for both backbone and side-chain conformations are observed. In addition, the per-step efficiency of the new united-atom force field is demonstrated for simulations in the implicit generalized Born solvent. A speedup around two is observed over the Duan et al. all-atom force field for the three tested small proteins. Finally, the efficiency gain of the new united-atom force field in conformational sampling is further demonstrated
Accurate near-field calculation in the rigorous coupled-wave analysis method
NASA Astrophysics Data System (ADS)
Weismann, Martin; Gallagher, Dominic F. G.; Panoiu, Nicolae C.
2015-12-01
The rigorous coupled-wave analysis (RCWA) is one of the most successful and widely used methods for modeling periodic optical structures. It yields fast convergence of the electromagnetic far-field and has been adapted to model various optical devices and wave configurations. In this article, we investigate the accuracy with which the electromagnetic near-field can be calculated by using RCWA and explain the observed slow convergence and numerical artifacts from which it suffers, namely unphysical oscillations at material boundaries due to the Gibbs phenomenon. In order to alleviate these shortcomings, we also introduce a mathematical formulation for accurate near-field calculation in RCWA, for one- and two-dimensional straight and slanted diffraction gratings. This accurate near-field computational approach is tested and evaluated for several representative test-structures and configurations in order to illustrate the advantages provided by the proposed modified formulation of the RCWA.
The interoperability force in the ERP field
NASA Astrophysics Data System (ADS)
Boza, Andrés; Cuenca, Llanos; Poler, Raúl; Michaelides, Zenon
2015-04-01
Enterprise resource planning (ERP) systems participate in interoperability projects and this participation sometimes leads to new proposals for the ERP field. The aim of this paper is to identify the role that interoperability plays in the evolution of ERP systems. To go about this, ERP systems have been first identified within interoperability frameworks. Second, the initiatives in the ERP field driven by interoperability requirements have been identified from two perspectives: technological and business. The ERP field is evolving from classical ERP as information system integrators to a new generation of fully interoperable ERP. Interoperability is changing the way of running business, and ERP systems are changing to adapt to the current stream of interoperability.
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.
Comparison of the simulations of cellulosic crystals with three carbohydrate force fields.
Miyamoto, Hitomi; Schnupf, Udo; Crowley, Michael F; Brady, John W
2016-03-01
Three independently developed molecular mechanics force fields for carbohydrates have been used to simulate a suite of small molecule analogs of cellulose for which crystal structures have been reported, as a test to determine which might be best for simulations of cellulose itself. Such evaluation is necessary since the reported cellulose crystal structure is not stable in molecular dynamics simulations with any available force field. The present simulations found that all three resulted in small deviations from the reported crystal structures, but that all were reasonably accurate and none was clearly superior to the others for the entire suite of structures examined.
Refining classical force fields for ionic liquids: theory and application to [MMIM][Cl].
Dommert, Florian; Holm, Christian
2013-02-14
Most of the force fields for ionic liquids cannot properly describe statics and dynamics. In this context, we propose an efficient method to adapt force fields, the basis of any classical molecular dynamics simulation. In the parameterisation process, a target function is minimized by a conjugate gradient based approach that vastly accelerates the tuning of the force field parameters through parallelization. As the description of the dynamics is captured in the parameterisation of the partial charges, we fit the short range parameters using only static properties, thus avoiding long simulations for the force field refinement. In the validation of the final parameterisation, the force field gives a good description of the dynamics in terms of the conductivity, especially in the temperature regime where the reference properties are matched very accurately. This method is sufficiently general and easily altered to fit an arbitrary set of reference properties, such that it can be considered for the construction of a versatile, transferable force field for ionic liquids.
A transferable force field for CdS-CdSe-PbS-PbSe solid systems
Fan, Zhaochuan; Vlugt, Thijs J. H.; Koster, Rik S.; Fang, Changming; Huis, Marijn A. van; Wang, Shuaiwei; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.
2014-12-28
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.
Force Field Model of Periodic Trends in Biomolecular Halogen Bonds.
Scholfield, Matthew R; Ford, Melissa Coates; Vander Zanden, Crystal M; Billman, M Marie; Ho, P Shing; Rappé, Anthony K
2015-07-23
The study of the noncovalent interaction now defined as a halogen bond (X-bond) has become one of the fastest growing areas in experimental and theoretical chemistry--its applications as a design tool are highly extensive. The significance of the interaction in biology has only recently been recognized, but has now become important in medicinal chemistry. We had previously derived a set of empirical potential energy functions to model the structure-energy relationships for bromines in biomolecular X-bonds (BXBs). Here, we have extended this force field for BXBs (ffBXB) to the halogens (Cl, Br, and I) that are commonly seen to form stable X-bonds. The ffBXB calculated energies show a remarkable one-to-one linear relationship to explicit BXB energies determined from an experimental DNA junction system, thereby validating the approach and the model. The resulting parameters allow us to interpret the stabilizing effects of BXBs in terms of well-defined physical properties of the halogen atoms, including their size, shape, and charge, showing periodic trends that are predictable along the Group VII column of elements. Consequently, we have established the ffBXB as an accurate computational tool that can be applied, for example, for the design of new therapeutic compounds against clinically important targets and new biomolecular-based materials.
Force Field Model of Periodic Trends in Biomolecular Halogen Bonds
Scholfield, Matthew R.; Ford, Melissa Coates; Vander Zanden, Crystal M.; Billman, M. Marie; Ho, P. Shing; Rappé, Anthony K.
2016-01-01
The study of the noncovalent interaction now defined as a halogen bond (X-bond) has become one of the fastest growing areas in experimental and theoretical chemistry—its applications as a design tool are highly extensive. The significance of the interaction in biology has only recently been recognized, but has now become important in medicinal chemistry. We had previously derived a set of empirical potential energy functions to model the structure-energy relationships for bromines in biomolecular X-bonds (BXBs). Here, we have extended this force field for BXBs (ffBXB) to the halogens (Cl, Br, and I) that are commonly seen to form stable X-bonds. The ffBXB calculated energies show a remarkable one-to-one linear relationship to explicit BXB energies determined from an experimental DNA junction system, thereby validating the approach and the model. The resulting parameters allow us to interpret the stabilizing effects of BXBs in terms of well-defined physical properties of the halogen atoms, including their size, shape, and charge, showing periodic trends that are predictable along the Group VII column of elements. Consequently, we have established the ffBXB as accurate computational tool that can be applied to, for example, for the design of new therapeutic compounds against clinically important targets and new biomolecular based materials. PMID:25338128
Science in a Box. Magnets III: Force Fields.
ERIC Educational Resources Information Center
Learning, 1992
1992-01-01
Presents ideas to help elementary school educators teach their students about magnetic force fields by observing how iron filings line up around magnets. The article lists materials needed and offers a student page with suggested student activities. (SM)
Molecular dynamics simulations of methane hydrate using polarizable force fields
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 found 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
Wallace, W C; Ghafur, O; Khurmi, C; Sainadh U, Satya; Calvert, J E; Laban, D E; Pullen, M G; Bartschat, K; Grum-Grzhimailo, A N; Wells, D; Quiney, H M; Tong, X M; Litvinyuk, I V; Sang, R T; Kielpinski, D
2016-07-29
Ionization of atoms and molecules in strong laser fields is a fundamental process in many fields of research, especially in the emerging field of attosecond science. So far, demonstrably accurate data have only been acquired for atomic hydrogen (H), a species that is accessible to few investigators. Here, we present measurements of the ionization yield for argon, krypton, and xenon with percent-level accuracy, calibrated using H, in a laser regime widely used in attosecond science. We derive a transferable calibration standard for laser peak intensity, accurate to 1.3%, that is based on a simple reference curve. In addition, our measurements provide a much needed benchmark for testing models of ionization in noble-gas atoms, such as the widely employed single-active electron approximation.
Wallace, W C; Ghafur, O; Khurmi, C; Sainadh U, Satya; Calvert, J E; Laban, D E; Pullen, M G; Bartschat, K; Grum-Grzhimailo, A N; Wells, D; Quiney, H M; Tong, X M; Litvinyuk, I V; Sang, R T; Kielpinski, D
2016-07-29
Ionization of atoms and molecules in strong laser fields is a fundamental process in many fields of research, especially in the emerging field of attosecond science. So far, demonstrably accurate data have only been acquired for atomic hydrogen (H), a species that is accessible to few investigators. Here, we present measurements of the ionization yield for argon, krypton, and xenon with percent-level accuracy, calibrated using H, in a laser regime widely used in attosecond science. We derive a transferable calibration standard for laser peak intensity, accurate to 1.3%, that is based on a simple reference curve. In addition, our measurements provide a much needed benchmark for testing models of ionization in noble-gas atoms, such as the widely employed single-active electron approximation. PMID:27517769
NASA Astrophysics Data System (ADS)
Wallace, W. C.; Ghafur, O.; Khurmi, C.; Sainadh U, Satya; Calvert, J. E.; Laban, D. E.; Pullen, M. G.; Bartschat, K.; Grum-Grzhimailo, A. N.; Wells, D.; Quiney, H. M.; Tong, X. M.; Litvinyuk, I. V.; Sang, R. T.; Kielpinski, D.
2016-07-01
Ionization of atoms and molecules in strong laser fields is a fundamental process in many fields of research, especially in the emerging field of attosecond science. So far, demonstrably accurate data have only been acquired for atomic hydrogen (H), a species that is accessible to few investigators. Here, we present measurements of the ionization yield for argon, krypton, and xenon with percent-level accuracy, calibrated using H, in a laser regime widely used in attosecond science. We derive a transferable calibration standard for laser peak intensity, accurate to 1.3%, that is based on a simple reference curve. In addition, our measurements provide a much needed benchmark for testing models of ionization in noble-gas atoms, such as the widely employed single-active electron approximation.
Critical Assessment of Current Force Fields. Short Peptide Test Case.
Vymětal, Jiří; Vondrášek, Jiří
2013-01-01
The applicability of molecular dynamics simulations for studies of protein folding or intrinsically disordered proteins critically depends on quality of energetic functions-force fields. The four popular force fields for biomolecular simulations, CHARMM22/CMAP, AMBER FF03, AMBER FF99SB, and OPLS-AA/L, were compared in prediction of conformational propensities of all common proteinogenic amino acids. The minimalistic model of terminally block amino acids (dipeptides) was chosen for assessment of side chain effects on backbone propensities. The precise metadynamics simulations revealed striking inconsistency of trends in conformational preferences as manifested by investigated force fields for both backbone and side chains. To trace this disapproval between force fields, the two related AMBER force fields were studied more closely. In the cases of FF99SB and FF03, we uncovered that the distinct tends were driven by different charge models. Additionally, the effects of recent correction for side chain torsion (FF99SB-ILDN) were examined on affected amino acids and exposed significant coupling between free energy profiles and propensities of backbone and side chain conformers. These findings have important consequences for further force field development.
Mitigated-force carriage for high magnetic field environments
Ludtka, Gerard M.; Ludtka, Gail M.; Wilgen, John B.; Murphy, Bart L.
2015-05-19
A carriage for high magnetic field environments includes a plurality of work-piece separators disposed in an operable relationship with a work-piece processing magnet having a magnetic field strength of at least 1 Tesla for supporting and separating a plurality of work-pieces by a preselected, essentially equal spacing, so that, as a first work-piece is inserted into the magnetic field, a second work-piece is simultaneously withdrawn from the magnetic field, so that an attractive magnetic force imparted on the first work-piece offsets a resistive magnetic force imparted on the second work-piece.
Molecular dynamics simulation of hydrated Nafion with a reactive force field for water.
Hofmann, Detlef W M; Kuleshova, Liudmila; D'Aguanno, Bruno
2008-03-01
We apply a newly parameterized central force field to highlight the problem of proton transport in fuel cell membranes and show that central force fields are potential candidates to describe chemical reactions on a classical level. After a short sketch of the parameterization of the force field, we validate the obtained force field for several properties of water. The experimental and simulated radial distribution functions are reproduced very accurately as a consequence of the applied parameterization procedure. Further properties, geometry, coordination, diffusion coefficient and density, are simulated adequately for our purposes. Afterwards we use the new force field for the molecular dynamics simulation of a swollen polyelectrolyte membrane similar to the widespread Nafion 117. We investigate the equilibrated structures, proton transfer, lifetimes of hydronium ions, the diffusion coefficients, and the conductivity in dependence of water content. In a short movie we demonstrate the ability of the obtained force field to describe the bond breaking/formation, and conclude that this force field can be considered as a kind of a reactive force field. The investigations of the lifetimes of hydronium ions give us the information about the kinetics of the proton transfer in a membrane with low water content. We found the evidence for the second order reaction. Finally, we demonstrate that the model is simple enough to handle the large systems sufficient to calculate the conductivity from molecular dynamics simulations. The detailed analysis of the conductivity reveals the importance of the collective moving of hydronium ions in membrane, which might give an interesting encouragement for further development of membranes.
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.
Transferable next-generation force fields from simple liquids to complex materials.
Schmidt, J R; Yu, Kuang; McDaniel, Jesse G
2015-03-17
Molecular simulations have had a transformative impact on chemists' understanding of the structure and dynamics of molecular systems. Simulations can both explain and predict chemical phenomena, and they provide a unique bridge between the microscopic and macroscopic regimes. The input for such simulations is the intermolecular interactions, which then determine the forces on the constituent atoms and therefore the time evolution and equilibrium properties of the system. However, in practice, accuracy and reliability are often limited by the fidelity of the description of those very same interactions, most typically embodied approximately in mathematical form in what are known as force fields. Force fields most often utilize conceptually simple functional forms that have been parametrized to reproduce existing experimental gas phase or bulk data. Yet, reliance on empirical parametrization can sometimes introduce limitations with respect to novel chemical systems or uncontrolled errors when moving to temperatures, pressures, or environments that differ from those for which they were developed. Alternatively, it is possible to develop force fields entirely from first principles, using accurate electronic structure calculations to determine the intermolecular interactions. This introduces a new set of challenges, including the transferability of the resulting force field to related chemical systems. In response, we recently developed an alternative approach to develop force fields entirely from first-principles electronic structure calculations based on intermolecular perturbation theory. Making use of an energy decomposition analysis ensures, by construction, that the resulting force fields contain the correct balance of the various components of intermolecular interaction (exchange repulsion, electrostatics, induction, and dispersion), each treated by a functional form that reflects the underlying physics. We therefore refer to the resulting force fields as
Transferable next-generation force fields from simple liquids to complex materials.
Schmidt, J R; Yu, Kuang; McDaniel, Jesse G
2015-03-17
Molecular simulations have had a transformative impact on chemists' understanding of the structure and dynamics of molecular systems. Simulations can both explain and predict chemical phenomena, and they provide a unique bridge between the microscopic and macroscopic regimes. The input for such simulations is the intermolecular interactions, which then determine the forces on the constituent atoms and therefore the time evolution and equilibrium properties of the system. However, in practice, accuracy and reliability are often limited by the fidelity of the description of those very same interactions, most typically embodied approximately in mathematical form in what are known as force fields. Force fields most often utilize conceptually simple functional forms that have been parametrized to reproduce existing experimental gas phase or bulk data. Yet, reliance on empirical parametrization can sometimes introduce limitations with respect to novel chemical systems or uncontrolled errors when moving to temperatures, pressures, or environments that differ from those for which they were developed. Alternatively, it is possible to develop force fields entirely from first principles, using accurate electronic structure calculations to determine the intermolecular interactions. This introduces a new set of challenges, including the transferability of the resulting force field to related chemical systems. In response, we recently developed an alternative approach to develop force fields entirely from first-principles electronic structure calculations based on intermolecular perturbation theory. Making use of an energy decomposition analysis ensures, by construction, that the resulting force fields contain the correct balance of the various components of intermolecular interaction (exchange repulsion, electrostatics, induction, and dispersion), each treated by a functional form that reflects the underlying physics. We therefore refer to the resulting force fields as
The energetics of motivated cognition: a force-field analysis.
Kruglanski, Arie W; Bélanger, Jocelyn J; Chen, Xiaoyan; Köpetz, 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 to invest in a cognitive activity. Effective driving force corresponds to the amount of energy he or she actually invests in attempt to match the restraining force. Magnitude of the potential driving force derives from a combination of goal importance and the pool of available mental resources, whereas magnitude of the restraining force derives from an individual's inclination to conserve resources, current task demands, and competing goals. The present analysis has implications for choice of means to achieve one's cognitive goals as well as for successful goal attainment under specific force-field constellations. Empirical evidence for these effects is considered, and the underlying theory's integrative potential is highlighted. (PsycINFO Database Record (c) 2012 APA, all rights reserved). PMID:21967165
Apparatus having reduced mechanical forces for supporting high magnetic fields
Prueitt, Melvin L.; Mueller, Fred M.; Smith, James L.
1991-01-01
The present invention identifies several configurations of conducting elements capable of supporting extremely high magnetic fields suitable for plasma confinement, wherein forces experienced by the conducting elements are significantly reduced over those which are present as a result of the generation of such high fields by conventional techniques. It is anticipated that the use of superconducting materials will both permit the attainment of such high fields and further permit such fields to be generated with vastly improved efficiency.
Contrasting students' understanding of electric field and electric force
NASA Astrophysics Data System (ADS)
Garza, Alejandro; Zavala, Genaro
2013-01-01
Students may have greater difficulties in understanding electric interactions because they have less day to day experience with them than with mechanics. There may also be differences in understanding of different electric concepts like electric force and field. This study presents the results of students' responses to two sequences of superposition principle isomorphic questions in which the only difference was that in one of the sequences, the electric force was used and in the other, the electric field. We administered one of the sequences to 249 students at a large private Mexican university after covering electrostatics in an Electricity and Magnetism class. The students' answers, reasoning and drawings were analyzed. We found that students who took the force sequence were better able to correctly answer the questions using the superposition principle than those students with the field sequence. The analysis of the students' reasoning and drawings helped us to examine their understanding of electric field and the use of electric field lines.
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.
Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field
2015-01-01
Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and subtler conformational properties, including the conformational equilibrium between the BI and BII states, and the A and B forms of DNA. The parametrization efforts were simultaneously guided by gas-phase quantum mechanics (QM) data on small model compounds and condensed-phase experimental data on the hydration and osmotic properties of biologically relevant ions and their solutions, as well as theoretical predictions for ionic distribution around DNA oligomer. In addition, fine-tuning of the internal base parameters was performed to obtain the final DNA model. Notably, the Drude model is shown to more accurately reproduce counterion condensation theory predictions of DNA charge neutralization by the condensed ions as compared to the CHARMM36 additive DNA force field, indicating an improved physical description of the forces dictating the ionic solvation of DNA due to the explicit treatment of electronic polarizability. In combination with the polarizable DNA force field, the availability of Drude polarizable parameters for proteins, lipids, and carbohydrates will allow for simulation studies of heterogeneous biological systems. PMID:24874104
Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.
Savelyev, Alexey; MacKerell, Alexander D
2014-06-19
Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and subtler conformational properties, including the conformational equilibrium between the BI and BII states, and the A and B forms of DNA. The parametrization efforts were simultaneously guided by gas-phase quantum mechanics (QM) data on small model compounds and condensed-phase experimental data on the hydration and osmotic properties of biologically relevant ions and their solutions, as well as theoretical predictions for ionic distribution around DNA oligomer. In addition, fine-tuning of the internal base parameters was performed to obtain the final DNA model. Notably, the Drude model is shown to more accurately reproduce counterion condensation theory predictions of DNA charge neutralization by the condensed ions as compared to the CHARMM36 additive DNA force field, indicating an improved physical description of the forces dictating the ionic solvation of DNA due to the explicit treatment of electronic polarizability. In combination with the polarizable DNA force field, the availability of Drude polarizable parameters for proteins, lipids, and carbohydrates will allow for simulation studies of heterogeneous biological systems. PMID:24874104
Force Field Parameter Estimation of Functional Perfluoropolyether Lubricants
Smith, R; Chung, P S; Steckel, J A; Jhon, M S; Biegler, L T
2011-01-01
The head disk interface in hard disk drive can be considered one of the hierarchical multiscale systems, which require the hybridization of multiscale modeling methods with coarse-graining procedure. However, the fundamental force field parameters are required to enable the coarse-graining procedure from atomistic/molecular scale to mesoscale models .In this paper, we investigate beyond molecular level and perform ab-initio calculations to obtain the force field parameters. Intramolecular force field parameters for the Zdol and Ztetraolwere evaluated with truncated PFPE molecules to allow for feasible quantum calculations while still maintaining the characteristic chemical structure of the end groups. Using the harmonic approximation to the bond and angle potentials, the parameters were derived from the Hessian matrix, and the dihedral force constants are fit to the torsional energy profiles generated by a series of constrained molecular geometry optimization.
Force Field Parameter Estimation of Functional Perfluoropolyether Lubricants
Smith, R.; Chung, P.S.; Steckel, J; Jhon, M.S.; Biegler, L.T.
2011-01-01
The head disk interface in a hard disk drive can be considered to be one of the hierarchical multiscale systems, which require the hybridization of multiscale modeling methods with coarse-graining procedure. However, the fundamental force field parameters are required to enable the coarse-graining procedure from atomistic/molecular scale to mesoscale models. In this paper, we investigate beyond molecular level and perform ab initio calculations to obtain the force field parameters. Intramolecular force field parameters for Zdol and Ztetraol were evaluated with truncated PFPE molecules to allow for feasible quantum calculations while still maintaining the characteristic chemical structure of the end groups. Using the harmonic approximation to the bond and angle potentials, the parameters were derived from the Hessian matrix, and the dihedral force constants are fit to the torsional energy profiles generated by a series of constrained molecular geometry optimization.
Force Field Parameter Estimation of Functional Perfluoropolyether Lubricants
Smith, R.; Chung, P.S.; Steckel, J; Jhon, M.S.; Biegler, L.T.
2011-01-01
The head disk interface in hard disk drive can be considered one of the hierarchical multiscale systems, which require the hybridization of multiscale modeling methods with coarse-graining procedure. However, the fundamental force field parameters are required to enable the coarse-graining procedure from atomistic/molecular scale to mesoscale models .In this paper, we investigate beyond molecular level and perform ab-initio calculations to obtain the force field parameters. Intramolecular force field parameters for the Zdol and Ztetraol were evaluated with truncated PFPE molecules to allow for feasible quantum calculations while still maintaining the characteristic chemical structure of the end groups. Using the harmonic approximation to the bond and angle potentials, the parameters were derived from the Hessian matrix, and the dihedral force constants are fit to the torsional energy profiles generated by a series of constrained molecular geometry optimization.
Force field parameter estimation of functional perfluoropolyether lubricants
Smith, Robert; Seung Chung, Pil; Steckel, Janice A.; Jhon, Myung S.; Biegler, Lorenz T.
2011-01-01
The head disk interface in hard disk drive can be considered one of the hierarchical multiscale systems, which require the hybridization of multiscale modeling methods with coarse-graining procedure. However, the fundamental force field parameters are required to enable the coarse-graining procedure from atomistic/molecular scale to mesoscale models .In this paper, we investigate beyond molecular level and perform ab-initio calculations to obtain the force field parameters. Intramolecular force field parameters for the Zdol and Ztetraol were evaluated with truncated PFPE molecules to allow for feasible quantum calculations while still maintaining the characteristic chemical structure of the end groups. Using the harmonic approximation to the bond and angle potentials, the parameters were derived from the Hessian matrix, and the dihedral force constants are fit to the torsional energy profiles generated by a series of constrained molecular geometry optimization.
Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.
Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui
2016-03-01
The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc.
Validating lipid force fields against experimental data: Progress, challenges and perspectives.
Poger, David; Caron, Bertrand; Mark, Alan E
2016-07-01
Biological membranes display a great diversity in lipid composition and lateral structure that is crucial in a variety of cellular functions. Simulations of membranes have contributed significantly to the understanding of the properties, functions and behaviour of membranes and membrane-protein assemblies. This success relies on the ability of the force field used to describe lipid-lipid and lipid-environment interactions accurately, reproducibly and realistically. In this review, we present some recent progress in lipid force-field development and validation strategies. In particular, we highlight how a range of properties obtained from various experimental techniques on lipid bilayers and membranes, can be used to assess the quality of a force field. We discuss the limitations and assumptions that are inherent to both computational and experimental approaches and how these can influence the comparison between simulations and experimental data. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Development of a True Transition State Force Field from Quantum Mechanical Calculations.
Madarász, Ádám; Berta, Dénes; Paton, Robert S
2016-04-12
Transition state force fields (TSFF) treated the TS structure as an artificial minimum on the potential energy surface in the past decades. The necessary parameters were developed either manually or by the Quantum-to-molecular mechanics method (Q2MM). In contrast with these approaches, here we propose to model the TS structures as genuine saddle points at the molecular mechanics level. Different methods were tested on small model systems of general chemical reactions such as protonation, nucleophilic attack, and substitution, and the new procedure led to more accurate models than the Q2MM-type parametrization. To demonstrate the practicality of our approach, transferrable parameters have been developed for Mo-catalyzed olefin metathesis using quantum mechanical properties as reference data. Based on the proposed strategy, any force field can be extended with true transition state force field (TTSFF) parameters, and they can be readily applied in several molecular mechanics programs as well. PMID:26925858
Reactive Force Field for Liquid Hydrazoic Acid with Applications to Detonation Chemistry
NASA Astrophysics Data System (ADS)
Furman, David; Dubnikova, Faina; van Duin, Adri; Zeiri, Yehuda; Kosloff, Ronnie
The development of a reactive force field (ReaxFF formalism) for Hydrazoic acid (HN3), a highly sensitive liquid energetic material, is reported. The force field accurately reproduces results of density functional theory (DFT) calculations. The quality and performance of the force field are examined by detailed comparison with DFT calculations related to uni, bi and trimolecular thermal decomposition routes. Reactive molecular dynamics (RMD) simulations are performed to reveal the initial chemical events governing the detonation chemistry of liquid HN3. The outcome of these simulations compares very well with recent results of tight-binding DFT molecular dynamics and thermodynamic calculations. Based on our RMD simulations, predictions were made for the activation energies and volumes in a broad range of temperatures and initial material compressions. Work Supported by The Center of Excellence for Explosives Detection, Mitigation and Response, Department of Homeland Security.
NASA Astrophysics Data System (ADS)
Hackel, Stefan; Montenbruck, Oliver; Steigenberger, -Peter; Eineder, Michael; Gisinger, Christoph
Remote sensing satellites support a broad range of scientific and commercial applications. The two radar imaging satellites TerraSAR-X and TanDEM-X provide spaceborne Synthetic Aperture Radar (SAR) and interferometric SAR data with a very high accuracy. The increasing demand for precise radar products relies on sophisticated validation methods, which require precise and accurate orbit products. Basically, the precise reconstruction of the satellite’s trajectory is based on the Global Positioning System (GPS) measurements from a geodetic-grade dual-frequency receiver onboard the spacecraft. The Reduced Dynamic Orbit Determination (RDOD) approach utilizes models for the gravitational and non-gravitational forces. Following a proper analysis of the orbit quality, systematics in the orbit products have been identified, which reflect deficits in the non-gravitational force models. A detailed satellite macro model is introduced to describe the geometry and the optical surface properties of the satellite. Two major non-gravitational forces are the direct and the indirect Solar Radiation Pressure (SRP). Due to the dusk-dawn orbit configuration of TerraSAR-X, the satellite is almost constantly illuminated by the Sun. Therefore, the direct SRP has an effect on the lateral stability of the determined orbit. The indirect effect of the solar radiation principally contributes to the Earth Radiation Pressure (ERP). The resulting force depends on the sunlight, which is reflected by the illuminated Earth surface in the visible, and the emission of the Earth body in the infrared spectra. Both components of ERP require Earth models to describe the optical properties of the Earth surface. Therefore, the influence of different Earth models on the orbit quality is assessed within the presentation. The presentation highlights the influence of non-gravitational force and satellite macro models on the orbit quality of TerraSAR-X.
NASA Astrophysics Data System (ADS)
Williams, Paul; Simonds, Brian; Sowards, Jeffrey; Hadler, Joshua
2016-03-01
In laser manufacturing operations, accurate measurement of laser power is important for product quality, operational repeatability, and process validation. Accurate real-time measurement of high-power lasers, however, is difficult. Typical thermal power meters must absorb all the laser power in order to measure it. This constrains power meters to be large, slow and exclusive (that is, the laser cannot be used for its intended purpose during the measurement). To address these limitations, we have developed a different paradigm in laser power measurement where the power is not measured according to its thermal equivalent but rather by measuring the laser beam's momentum (radiation pressure). Very simply, light reflecting from a mirror imparts a small force perpendicular to the mirror which is proportional to the optical power. By mounting a high-reflectivity mirror on a high-sensitivity force transducer (scale), we are able to measure laser power in the range of tens of watts up to ~ 100 kW. The critical parameters for such a device are mirror reflectivity, angle of incidence, and scale sensitivity and accuracy. We will describe our experimental characterization of a radiation-pressure-based optical power meter. We have tested it for modulated and CW laser powers up to 92 kW in the laboratory and up to 20 kW in an experimental laser welding booth. We will describe present accuracy, temporal response, sources of measurement uncertainty, and hurdles which must be overcome to have an accurate power meter capable of routine operation as a turning mirror within a laser delivery head.
Force fields and scoring functions for carbohydrate simulation.
Xiong, Xiuming; Chen, Zhaoqiang; Cossins, Benjamin P; Xu, Zhijian; Shao, Qiang; Ding, Kai; Zhu, Weiliang; Shi, Jiye
2015-01-12
Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design.
Sefcik, Jan; Demiralp, Ersan; Cagin, Tahir; Goddard, William A
2002-12-01
We present the Dynamic Charge Equilibration (DQEq) method for a self-consistent treatment of charge transfer in force field modeling, where atomic charges are designed to reproduce electrostatic potentials calculated quantum mechanically. Force fields coupled with DQEq allow charges to readjust as geometry changes in classical simulations, using appropriate algorithms for periodic boundary conditions. The full electrostatic energy functional is used to derive the corresponding forces and the second derivatives (hessian) for vibrational calculations. Using DQEq electrostatics, we develop a simple nonbond force field for simulation of silica molecular sieves, where nonelectrostatic interactions are described by two-body Morse stretch terms. Energy minimization calculations with the new force field yield accurate unit cell geometries for siliceous zeolites. Relative enthalpies with respect to quartz and third-law entropies calculated from harmonic vibrational analysis agree very well with available calorimetric data: calculated SiO(2) enthalpies relative to alpha-quartz are within 2 kJ/mol and entropies at 298 K are within 3 J/mol K of the respective experimental values. Contributions from the zero point energy and vibrational degrees of freedom were found to be only about 1 kJ/mol for the free energy of mutual transformations between microporous silica polymorphs. The approach presented here can be applied to interfaces and other oxides as well and it is suitable for development of force fields for accurate modeling of geometry and energetics of microporous and mesoporous materials, while providing a realistic description of electrostatic fields near surfaces and inside pores of adsorbents and catalysts.
Highly accurate analytical energy of a two-dimensional exciton in a constant magnetic field
NASA Astrophysics Data System (ADS)
Hoang, Ngoc-Tram D.; Nguyen, Duy-Anh P.; Hoang, Van-Hung; Le, Van-Hoang
2016-08-01
Explicit expressions are given for analytically describing the dependence of the energy of a two-dimensional exciton on magnetic field intensity. These expressions are highly accurate with the precision of up to three decimal places for the whole range of the magnetic field intensity. The results are shown for the ground state and some excited states; moreover, we have all formulae to obtain similar expressions of any excited state. Analysis of numerical results shows that the precision of three decimal places is maintained for the excited states with the principal quantum number of up to n=100.
Thermodynamic properties for applications in chemical industry via classical force fields.
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.
Qiu, Wentao; Ndao, Abdoulaye; Lu, Huihui; Bernal, Maria-Pilar; Baida, Fadi Issam
2016-09-01
We present a theoretical study of guided resonances (GR) on a thin film lithium niobate rectangular lattice photonic crystal by band diagram calculations and 3D Finite Difference Time Domain (FDTD) transmission investigations which cover a broad range of parameters. A photonic crystal with an active zone as small as 13μm×13μm×0.7μm can be easily designed to obtain a resonance Q value in the order of 1000. These resonances are then employed in electric field (E-field) sensing applications exploiting the electro optic (EO) effect of lithium niobate. A local field factor that is calculated locally for each FDTD cell is proposed to accurately estimate the sensitivity of GR based E-field sensor. The local field factor allows well agreement between simulations and reported experimental data therefore providing a valuable method in optimizing the GR structure to obtain high sensitivities. When these resonances are associated with sub-picometer optical spectrum analyzer and high field enhancement antenna design, an E-field probe with a sensitivity of 50 μV/m could be achieved. The results of our simulations could be also exploited in other EO based applications such as EEG (Electroencephalography) or ECG (Electrocardiography) probe and E-field frequency detector with an 'invisible' probe to the field being detected etc. PMID:27607627
A new force field of formamide and the effect of the dielectric constant on miscibility.
de la Luz, Alexander Pérez; Méndez-Maldonado, G Arlette; Núñez-Rojas, Edgar; Bresme, Fernando; Alejandre, José
2015-06-01
Current force fields underestimate significantly the dielectric constant of formamide at standard conditions. We present a derivation of an accurate potential for formamide, with a functional form based on the OPLS/AA force field. Our procedure follows the approach introduced by Salas et al. ( J. Chem. Theory Comput. 2015 , 11 , 683 - 693 ) that relies on ab initio calculations and molecular dynamics simulations. We consider several strategies to derive the atomic charges of formamide. We find that the inclusion of polarization effects in the quantum mechanical computations is essential to obtain reliable force fields. By varying the atomic charges and the Lennard-Jones parameters describing the dispersion interactions in the OPLS/AA force field, we derive an optimum set of parameters that provides accurate results for the dielectric constant, surface tension, and bulk density of liquid formamide in a wide range of thermodynamic states. We test the transferability of our parameters to investigate liquid/liquid mixtures. We have chosen as case study an equimolar mixture of formamide and hexan-2-one. This mixture involves two fluids with very different polar characteristics, namely, large differences in their dielectric constants and their performance as solvents. The new potential predicts a liquid/liquid phase separation, in good agreement with experimental data, and highlights the importance of the correct parametrization of the pure liquid phases to investigate liquid mixtures. Finally, we examine the microscopic origin of the observed inmiscibility between formamide and hexa-2-one.
Benchmarking of Force Fields for Molecule-Membrane Interactions.
Paloncýová, Markéta; Fabre, Gabin; DeVane, Russell H; Trouillas, Patrick; Berka, Karel; Otyepka, Michal
2014-09-01
Studies of drug-membrane interactions witness an ever-growing interest, as penetration, accumulation, and positioning of drugs play a crucial role in drug delivery and metabolism in human body. Molecular dynamics simulations complement nicely experimental measurements and provide us with new insight into drug-membrane interactions; however, the quality of the theoretical data dramatically depends on the quality of the force field used. We calculated the free energy profiles of 11 molecules through a model dimyristoylphosphatidylcholine (DMPC) membrane bilayer using five force fields, namely Berger, Slipids, CHARMM36, GAFFlipids, and GROMOS 43A1-S3. For the sake of comparison, we also employed the semicontinuous tool COSMOmic. High correlation was observed between theoretical and experimental partition coefficients (log K). Partition coefficients calculated by all-atomic force fields (Slipids, CHARMM36, and GAFFlipids) and COSMOmic differed by less than 0.75 log units from the experiment and Slipids emerged as the best performing force field. This work provides the following recommendations (i) for a global, systematic and high throughput thermodynamic evaluations (e.g., log K) of drugs COSMOmic is a tool of choice due to low computational costs; (ii) for studies of the hydrophilic molecules CHARMM36 should be considered; and (iii) for studies of more complex systems, taking into account all pros and cons, Slipids is the force field of choice.
Linear force-free fields in the lower corona
NASA Technical Reports Server (NTRS)
Barbosa, D. D.
1978-01-01
Boundary conditions are imposed on the normal component of B on two parallel planes which delineate the force-free volume of linear magnetic fields in low coronal levels of the solar atmosphere. Green's function is employed to ensure that equations for the magnetic field energy remain bounded and smooth. Field line tracings of a simple bipolar source distribution are developed and compared with empirical data obtained from visual observations in H(alpha), EUV, and X-rays.
Average Lorentz self-force from electric field lines
NASA Astrophysics Data System (ADS)
Aashish, Sandeep; Haque, Asrarul
2015-09-01
We generalize the derivation of electromagnetic fields of a charged particle moving with a constant acceleration Singal (2011 Am. J. Phys. 79 1036) to a variable acceleration (piecewise constants) over a small finite time interval using Coulomb's law, relativistic transformations of electromagnetic fields and Thomson's construction Thomson (1904 Electricity and Matter (New York: Charles Scribners) ch 3). We derive the average Lorentz self-force for a charged particle in arbitrary non-relativistic motion via averaging the fields at retarded time.
Force-free magnetic fields - The magneto-frictional method
NASA Technical Reports Server (NTRS)
Yang, W. H.; Sturrock, P. A.; Antiochos, S. K.
1986-01-01
The problem under discussion is that of calculating magnetic field configurations in which the Lorentz force j x B is everywhere zero, subject to specified boundary conditions. We choose to represent the magnetic field in terms of Clebsch variables in the form B = grad alpha x grad beta. These variables are constant on any field line so that each field line is labeled by the corresponding values of alpha and beta. When the field is described in this way, the most appropriate choice of boundary conditions is to specify the values of alpha and beta on the bounding surface. We show that such field configurations may be calculated by a magneto-frictional method. We imagine that the field lines move through a stationary medium, and that each element of magnetic field is subject to a frictional force parallel to and opposing the velocity of the field line. This concept leads to an iteration procedure for modifying the variables alpha and beta, that tends asymptotically towards the force-free state. We apply the method first to a simple problem in two rectangular dimensions, and then to a problem of cylindrical symmetry that was previously discussed by Barnes and Sturrock (1972). In one important respect, our new results differ from the earlier results of Barnes and Sturrock, and we conclude that the earlier article was in error.
Physical Limitations of Empirical Field Models: Force Balance and Plasma Pressure
Sorin Zaharia; C.Z. Cheng
2002-06-18
In this paper, we study whether the magnetic field of the T96 empirical model can be in force balance with an isotropic plasma pressure distribution. Using the field of T96, we obtain values for the pressure P by solving a Poisson-type equation {del}{sup 2}P = {del} {center_dot} (J x B) in the equatorial plane, and 1-D profiles on the Sun-Earth axis by integrating {del}P = J x B. We work in a flux coordinate system in which the magnetic field is expressed in terms of Euler potentials. Our results lead to the conclusion that the T96 model field cannot be in equilibrium with an isotropic pressure. We also analyze in detail the computation of Birkeland currents using the Vasyliunas relation and the T96 field, which yields unphysical results, again indicating the lack of force balance in the empirical model. The underlying reason for the force imbalance is likely the fact that the derivatives of the least-square fitted model B are not accurate predictions of the actual magnetospheric field derivatives. Finally, we discuss a possible solution to the problem of lack of force balance in empirical field models.
Polarizable Force Field with a σ-Hole for Liquid and Aqueous Bromomethane.
Adluri, Archita N S; Murphy, Jennifer N; Tozer, Tiffany; Rowley, Christopher N
2015-10-22
Bromomethane (CH3Br) is an acutely toxic environmental pollutant that contributes to ozone depletion. Molecular simulation could be a valuable tool for studying its partitioning and transport in the environment if an accurate molecular model was available. The generalized Amber force field (GAFF), OPLS (optimized potentials for liquid simulations) force field, and CHARMM general force field (CGenFF) were tested for their ability to model the physical properties of liquid bromomethane. The OPLS force field was in fairly good agreement with experiment, while CGenFF and GAFF were significantly in error. The Br Lennard-Jones parameters of the GAFF and CGenFF models were reparameterized, but their radial distribution functions still have significant deviations from those calculated by ab initio molecular dynamics (AIMD). A Drude polarizable force field for bromomethane was parametrized with an off-center positively charged site to represent the C-Br σ-hole. This model is in good agreement with the bulk physical properties and the AIMD RDFs. The modest solubility of bromomethane was reproduced by this model, with dispersion interactions being the dominant water-solute interaction. The water-solute electrostatic interactions are a smaller factor in solubility. This model predicts bromomethane to have a 13 kJ mol(-1) surface excess potential at the water-vapor interface. PMID:26419599
Parameterization and optimization of the menthol force field for molecular dynamics simulations.
Jasik, Mateusz; Szefczyk, Borys
2016-10-01
Menthol's various biological properties render it a useful component for medical and cosmetological applications, while its three centers of asymmetry mean that it can be used in a range of organic reactions. Menthol-substituted ionic liquids (ILs) have been found to exhibit promising antimicrobial and antielectrostatic properties, as well as being useful in organic catalysis and biochemical studies. However, so far, a force field designed and validated specifically for the menthol molecule has not been constructed. In the present work, the validation and optimization of force field parameters with regard to the ability to reproduce the macroscopic properties of menthol is presented. The set of optimized potentials for liquid simulations all atom (OPLS-AA) compatible parameters was tested and carefully tuned. The refinement of parameters included fitting of partial atomic charges, optimization of Lennard-Jones parameters, and recalculation of the dihedral angle parameters needed to reproduce quantum energy profiles. To validate the force field, a variety of physicochemical properties were calculated for liquid menthol. Both thermodynamic and kinetic properties were taken into account, including density, surface tension, enthalpy of vaporization, and shear viscosity. The obtained force field was proven to accurately reproduce the properties of the investigated compound while being fully compatible with the OPLS-AA force field. PMID:27604277
Parameterization and optimization of the menthol force field for molecular dynamics simulations.
Jasik, Mateusz; Szefczyk, Borys
2016-10-01
Menthol's various biological properties render it a useful component for medical and cosmetological applications, while its three centers of asymmetry mean that it can be used in a range of organic reactions. Menthol-substituted ionic liquids (ILs) have been found to exhibit promising antimicrobial and antielectrostatic properties, as well as being useful in organic catalysis and biochemical studies. However, so far, a force field designed and validated specifically for the menthol molecule has not been constructed. In the present work, the validation and optimization of force field parameters with regard to the ability to reproduce the macroscopic properties of menthol is presented. The set of optimized potentials for liquid simulations all atom (OPLS-AA) compatible parameters was tested and carefully tuned. The refinement of parameters included fitting of partial atomic charges, optimization of Lennard-Jones parameters, and recalculation of the dihedral angle parameters needed to reproduce quantum energy profiles. To validate the force field, a variety of physicochemical properties were calculated for liquid menthol. Both thermodynamic and kinetic properties were taken into account, including density, surface tension, enthalpy of vaporization, and shear viscosity. The obtained force field was proven to accurately reproduce the properties of the investigated compound while being fully compatible with the OPLS-AA force field.
Imaging Nanoscale Electromagnetic Near-Field Distributions Using Optical Forces.
Huang, Fei; Tamma, Venkata Ananth; Mardy, Zahra; Burdett, Jonathan; Wickramasinghe, H Kumar
2015-01-01
We demonstrate the application of Atomic Force Microscopy (AFM) for mapping optical near-fields with nanometer resolution, limited only by the AFM probe geometry. By detecting the optical force between a gold coated AFM probe and its image dipole on a glass substrate, we profile the electric field distributions of tightly focused laser beams with different polarizations. The experimentally recorded focal force maps agree well with theoretical predictions based on a dipole-dipole interaction model. We experimentally estimate the aspect ratio of the apex of gold coated AFM probe using only optical forces. We also show that the optical force between a sharp gold coated AFM probe and a spherical gold nanoparticle of radius 15 nm, is indicative of the electric field distribution between the two interacting particles. Photo Induced Force Microscopy (PIFM) allows for background free, thermal noise limited mechanical imaging of optical phenomenon over wide range of wavelengths from Visible to RF with detection sensitivity limited only by AFM performance. PMID:26073331
Nonequilibrium forces between neutral atoms mediated by a quantum field
Behunin, Ryan O.; Hu, Bei-Lok
2010-08-15
We study forces between two neutral atoms, modeled as three-dimensional harmonic oscillators, arising from mutual influences mediated by an electromagnetic field but not from their direct interactions. We allow as dynamical variables the center-of-mass motion of the atom, its internal degrees of freedom, and the quantum field treated relativistically. We adopt the method of nonequilibrium quantum field theory which can provide a first-principles, systematic, and unified description including the intrinsic and induced dipole fluctuations. The inclusion of self-consistent back-actions makes possible a fully dynamical description of these forces valid for general atom motion. In thermal equilibrium we recover the known forces--London, van der Waals, and Casimir-Polder--between neutral atoms in the long-time limit. We also reproduce a recently reported force between atoms when the system is out of thermal equilibrium at late times. More noteworthy is the discovery of the existence of a type of (or identification of the source of some known) interatomic force which we call the ''entanglement force,'' originating from the quantum correlations of the internal degrees of freedom of entangled atoms.
NASA Astrophysics Data System (ADS)
Hölzl, Christoph; Kibies, Patrick; Imoto, Sho; Frach, Roland; Suladze, Saba; Winter, Roland; Marx, Dominik; Horinek, Dominik; Kast, Stefan M.
2016-04-01
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.
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.
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. PMID:27083705
Additive CHARMM force field for naturally occurring modified ribonucleotides
Xu, You; Vanommeslaeghe, Kenno; Aleksandrov, Alexey; MacKerell, Alexander D.
2016-01-01
More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all‐atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26841080
Parametrization of macrolide antibiotics using the Force Field Toolkit
Pavlova, Anna; Gumbart, James C
2015-01-01
Macrolides are an important class of antibiotics that target the bacterial ribosome. Computer simulations of macrolides are limited since specific force field parameters have not been previously developed for them. Here we determine CHARMM-compatible force field parameters for erythromycin, azithromycin and telithromycin, using the Force Field Toolkit plugin in VMD. Because of their large size, novel approaches for parametrizing them had to be developed. Two methods for determining partial atomic charges, from interactions with TIP3P water and from the electrostatic potential, as well as several approaches for fitting the dihedral parameters were tested. The performance of the different parameter sets was evaluated by molecular dynamics simulations of the macrolides in ribosome, with a distinct improvement in maintenance of key interactions observed after refinement of the initial parameters. Based on the results of the macrolide tests, recommended procedures for parametrizing very large molecules using ffTK are given. PMID:26280362
An implicit divalent counterion force field for RNA molecular dynamics
NASA Astrophysics Data System (ADS)
Henke, Paul S.; Mak, Chi H.
2016-03-01
How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg2+ screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.
Ab Initio Force Fields for Imidazolium-Based Ionic Liquids.
McDaniel, Jesse G; Choi, Eunsong; Son, Chang Yun; Schmidt, J R; Yethiraj, Arun
2016-07-21
We develop ab initio force fields for alkylimidazolium-based ionic liquids (ILs) that predict the density, heats of vaporization, diffusion, and conductivity that are in semiquantitative agreement with experimental data. These predictions are useful in light of the scarcity of and sometimes inconsistency in experimental heats of vaporization and diffusion coefficients. We illuminate physical trends in the liquid cohesive energy with cation chain length and anion. These trends are different than those based on the experimental heats of vaporization. Molecular dynamics prediction of the room temperature dynamics of such ILs is more difficult than is generally realized in the literature due to large statistical uncertainties and sensitivity to subtle force field details. We believe that our developed force fields will be useful for correctly determining the physics responsible for the structure/property relationships in neat ILs.
Additive CHARMM force field for naturally occurring modified ribonucleotides.
Xu, You; Vanommeslaeghe, Kenno; Aleksandrov, Alexey; MacKerell, Alexander D; Nilsson, Lennart
2016-04-15
More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. PMID:26841080
Interaction Forces Between Multiple Bodies in a Magnetic Field
NASA Technical Reports Server (NTRS)
Joffe, Benjamin
1996-01-01
Some of the results from experiments to determine the interaction forces between multiple bodies in a magnetic field are presented in this paper. It is shown how the force values and the force directions depend on the configuration of the bodies, their relative positions to each other, and the vector of the primary magnetic field. A number of efficient new automatic loading and assembly machines, as well as manipulators and robots, have been created based on the relationship between bodies and magnetic fields. A few of these patented magnetic devices are presented. The concepts involved open a new way to design universal grippers for robot and other kinds of mechanisms for the manipulation of objects. Some of these concepts can be used for space applications.
Additive CHARMM force field for naturally occurring modified ribonucleotides.
Xu, You; Vanommeslaeghe, Kenno; Aleksandrov, Alexey; MacKerell, Alexander D; Nilsson, Lennart
2016-04-15
More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs.
PRIMO: A Transferable Coarse-grained Force Field for Proteins.
Kar, Parimal; Gopal, Srinivasa Murthy; Cheng, Yi-Ming; Predeus, Alexander; Feig, Michael
2013-08-13
We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born model. The bonded interactions are either harmonic or distance-based spline interpolated potentials. These potentials are defined on the basis of all-atom molecular dynamics (MD) simulations of dipeptides with the CHARMM22/CMAP force field. The non-bonded parameters are tuned by matching conformational free energies of diverse set of conformations with that of CHARMM all-atom results. PRIMO is designed to provide a correct description of conformational distribution of the backbone (ϕ/ψ) and side chains (χ1) for all amino acids with a CMAP correction term. The CMAP potential in PRIMO is optimized based on the new CHARMM C36 CMAP. The resulting optimized force field has been applied in MD simulations of several proteins of 36-155 amino acids and shown that the root-mean-squared-deviation of the average structure from the corresponding crystallographic structure varies between 1.80 and 4.03 Å. PRIMO is shown to fold several small peptides to their native-like structures from extended conformations. These results suggest the applicability of the PRIMO force field in the study of protein structures in aqueous solution, structure predictions as well as ab initio folding of small peptides.
Acoustic Force Density Acting on Inhomogeneous Fluids in Acoustic Fields.
Karlsen, Jonas T; Augustsson, Per; Bruus, Henrik
2016-09-01
We present a theory for the acoustic force density acting on inhomogeneous fluids in acoustic fields on time scales that are slow compared to the acoustic oscillation period. The acoustic force density depends on gradients in the density and compressibility of the fluid. For microfluidic systems, the theory predicts a relocation of the inhomogeneities into stable field-dependent configurations, which are qualitatively different from the horizontally layered configurations due to gravity. Experimental validation is obtained by confocal imaging of aqueous solutions in a glass-silicon microchip. PMID:27661695
Acoustic Force Density Acting on Inhomogeneous Fluids in Acoustic Fields.
Karlsen, Jonas T; Augustsson, Per; Bruus, Henrik
2016-09-01
We present a theory for the acoustic force density acting on inhomogeneous fluids in acoustic fields on time scales that are slow compared to the acoustic oscillation period. The acoustic force density depends on gradients in the density and compressibility of the fluid. For microfluidic systems, the theory predicts a relocation of the inhomogeneities into stable field-dependent configurations, which are qualitatively different from the horizontally layered configurations due to gravity. Experimental validation is obtained by confocal imaging of aqueous solutions in a glass-silicon microchip.
A New Force-Matched Reactive Force Field for Bulk Water Under Extreme Thermodynamic Conditions
NASA Astrophysics Data System (ADS)
Fried, Laurence; Koziol, Lucas
2015-06-01
A many-body classical force field is presented for water under dissociative thermodynamic conditions. The force field is optimized by force-matching to ab initio molecular dynamics (AIMD) simulations calculated with Density Functional Theory (DFT). The force field contains short-ranged central and many-body over-coordination terms, and long-range Ewald electrostatics. It is optimized and tested on water at density 1.5 g/mL and 2000 K, which is approximately 10% dissociated according to DFT. Molecular dynamics simulations closely reproduce DFT radial distribution functions, as well as the distribution of wat and dissociation products. The calculated atomic self-diffusion constants appear about 50% lower than in DFT, although precise comparison is impossible due to the short timescale accessible to AIMD (about 20 ps). The force field is also compared to ReaxFF using the CHO parameter set of Chenowith et al. ReaxFF structural and dynamical properties are in overall fair agreement with DFT, although ReaxFF water is not dissociative at these conditions. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field.
Katritch, Vsevolod; Totrov, Maxim; Abagyan, Ruben
2003-01-30
We introduce a new method to accurately "project" a Cartesian force field onto an internal coordinate molecular model with fixed-bond geometry. The algorithm automatically generates the Internal Coordinate Force Field (ICFF), which is a close approximation of the "source" Cartesian force field. The ICFF method reduces the number of free variables in a model by at least 10-fold and facilitates the fast convergence of geometry optimizations, an advantage that is critical for many applications such as the docking of flexible ligands or conformational modeling of macromolecules. Although covalent geometry is fixed in an ICFF model, implicit flexibility is incorporated into the force field parameters in the following two ways. First, we formulate an empirical torsion energy term in ICFF as a sixfold Fourier series and develop a procedure to calculate the Fourier coefficients from the conformational energy profiles of the fully flexible Cartesian model. The ICFF torsion parameters thus represent not only torsion component of the source force field, but also bond bending, bond stretching, and "1-4" van der Waals interactions. Second, we use a soft polynomial repulsion function for "1-5" and "1-6" interactions to mimic the flexibility of bonds, connecting these atoms. Also, we suggest a way to use a local part of the Cartesian force field to automatically generate fixed covalent geometries, compatible with the ICFF energy function. Here, we present an implementation of the ICFF algorithm, which employs the MMFF94s Cartesian force field as a "source." Extensive benchmarking of ICFF with a representative set of organic molecules demonstrates that the implicit flexibility model accurately reproduces MMFF94s equilibrium conformational energy differences (RMSD approximately 0.64 kcal) and, most importantly, detailed torsion energy profiles (RMSD approximately 0.37 kcal). This accuracy is characteristic of the method, because all the ICFF parameters (except one scaling factor in
Magnetic clouds and force-free fields with constant alpha
NASA Technical Reports Server (NTRS)
Burlaga, L. F.
1988-01-01
Magnetic clouds observed at 1 AU are modeled as cylindrically symmetric, constant alpha force-free magnetic fields. The model satisfactorily explains the types of variations of the magnetic field direction that are observed as a magnetic cloud moves past a spacecraft in terms of the possible orientations of the axis of a magnetic cloud. The model also explains why the magnetic field strength is observed to be higher inside a magnetic cloud than near its boundaries. However, the model predicts that the magnetic field strength profile should be symmetric with respect to the axis of the magnetic cloud, whereas observations show that this is not generally the case.
Mitigated-force carriage for high magnetic field environments
Ludtka, Gerard M; Ludtka, Gail M; Wilgen, John B; Murphy, Bart L
2014-05-20
A carriage for high magnetic field environments includes a first work-piece holding means for holding a first work-piece, the first work-piece holding means being disposed in an operable relationship with a work-piece processing magnet having a magnetic field strength of at least 1 Tesla. The first work-piece holding means is further disposed in operable connection with a second work-piece holding means for holding a second work-piece so that, as the first work-piece is inserted into the magnetic field, the second work-piece is simultaneously withdrawn from the magnetic field, so that an attractive magnetic force imparted on the first work-piece offsets a resistive magnetic force imparted on the second work-piece.
Einstein's osmotic equilibrium of colloidal suspensions in conservative force fields
NASA Astrophysics Data System (ADS)
Fu, Jinxin; Ou-Yang, H. Daniel
2014-09-01
Predicted by Einstein in his 1905 paper on Brownian motion, colloidal particles in suspension reach osmotic equilibrium under gravity. The idea was demonstrated by J.B. Perrin to win Nobel Prize in Physics in 1926. We show Einstein's equation for osmotic equilibrium can be applied to colloids in a conservative force field generated by optical gradient forces. We measure the osmotic equation of state of 100nm Polystyrene latex particles in the presence of KCl salt and PEG polymer. We also obtain the osmotic compressibility, which is important for determining colloidal stability and the internal chemical potential, which is useful for predicting the phase transition of colloidal systems. This generalization allows for the use of any conservative force fields for systems ranging from colloidal systems to macromolecular solutions.
Energy buildup in sheared force-free magnetic fields
NASA Technical Reports Server (NTRS)
Wolfson, Richard; Low, Boon C.
1992-01-01
Photospheric displacement of the footpoints of solar magnetic field lines results in shearing and twisting of the field, and consequently in the buildup of electric currents and magnetic free energy in the corona. The sudden release of this free energy may be the origin of eruptive events like coronal mass ejections, prominence eruptions, and flares. An important question is whether such an energy release may be accompanied by the opening of magnetic field lines that were previously closed, for such open field lines can provide a route for matter frozen into the field to escape the sun altogether. This paper presents the results of numerical calculations showing that opening of the magnetic field is permitted energetically, in that it is possible to build up more free energy in a sheared, closed, force-free magnetic field than is in a related magnetic configuration having both closed and open field lines. Whether or not the closed force-free field attains enough energy to become partially open depends on the form of the shear profile; the results presented compare the energy buildup for different shear profiles. Implications for solar activity are discussed briefly.
Comparison of different force fields for the study of disaccharides
Technology Transfer Automated Retrieval System (TEKTRAN)
Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying ß-cellobiose, a-maltose, and a-galabiose [a-D-Galp-(1'4)-a-D-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl and glycosidic linkage orientatio...
Frequency-dependent force fields for QMMM calculations.
Harczuk, Ignat; Vahtras, Olav; Ågren, Hans
2015-03-28
We outline the construction of frequency-dependent polarizable force fields. The force fields are derived from analytic response theory for different frequencies using a generalization of the LoProp algorithm giving a decomposition of a molecular dynamical polarizability to localized atomic dynamical polarizabilities. These force fields can enter in a variety of applications - we focus on two such applications in this work: firstly, they can be incorporated in a physical, straightforward, way for current existing methods that use polarizable embeddings, and we can show, for the first time, the effect of the frequency dispersion within the classical environment of a quantum mechanics-molecular mechanics (QMMM) method. Our methodology is here evaluated for some test cases comprising water clusters and organic residues. Secondly, together with a modified Silberstein-Applequist procedure for interacting inducible point-dipoles, these frequency-dependent polarizable force fields can be used for a classical determination of frequency-dependent cluster polarizabilities. We evaluate this methodology by comparing with the corresponding results obtained from quantum mechanics or QMMM where the absolute mean [small alpha, Greek, macron] is determined with respect to the size of the QM and MM parts of the total system.
Force-Field Analysis: A Functional Management System
ERIC Educational Resources Information Center
Sanders, Stanley G.
1977-01-01
Force field analysis combines the advantages of the basic organization, objectivity, and science of systems theory and systems methods, with a simplicity and clarity that allows its mastery by policy-makers and administrators who are not specialists in engineering, data processing, or programming. (Author/IRT)
A polarizable ellipsoidal force field for halogen bonds.
Du, Likai; Gao, Jun; Bi, Fuzhen; Wang, Lili; Liu, Chengbu
2013-09-01
The anisotropic effects and short-range quantum effects are essential characters in the formation of halogen bonds. Since there are an array of applications of halogen bonds and much difficulty in modeling them in classical force fields, the current research reports solely the polarizable ellipsoidal force field (PEff) for halogen bonds. The anisotropic charge distribution was represented with the combination of a negative charged sphere and a positively charged ellipsoid. The polarization energy was incorporated by the induced dipole model. The resulting force field is "physically motivated," which includes separate, explicit terms to account for the electrostatic, repulsion/dispersion, and polarization interaction. Furthermore, it is largely compatible with existing, standard simulation packages. The fitted parameters are transferable and compatible with the general AMBER force field. This PEff model could correctly reproduces the potential energy surface of halogen bonds at MP2 level. Finally, the prediction of the halogen bond properties of human Cathepsin L (hcatL) has been found to be in excellent qualitative agreement with the cocrystal structures.
Symmetrization of the AMBER and CHARMM force fields.
Małolepsza, Edyta; Strodel, Birgit; Khalili, Mey; Trygubenko, Semen; Fejer, Szilard N; Wales, David J
2010-05-01
The AMBER and CHARMM force fields are analyzed from the viewpoint of the permutational symmetry of the potential for feasible exchanges of identical atoms and chemical groups in amino and nucleic acids. In each case, we propose schemes for symmetrizing the potentials, which greatly facilitate the bookkeeping associated with constructing kinetic transition networks via geometry optimization. PMID:20082393
Frequency-dependent force fields for QMMM calculations.
Harczuk, Ignat; Vahtras, Olav; Ågren, Hans
2015-03-28
We outline the construction of frequency-dependent polarizable force fields. The force fields are derived from analytic response theory for different frequencies using a generalization of the LoProp algorithm giving a decomposition of a molecular dynamical polarizability to localized atomic dynamical polarizabilities. These force fields can enter in a variety of applications - we focus on two such applications in this work: firstly, they can be incorporated in a physical, straightforward, way for current existing methods that use polarizable embeddings, and we can show, for the first time, the effect of the frequency dispersion within the classical environment of a quantum mechanics-molecular mechanics (QMMM) method. Our methodology is here evaluated for some test cases comprising water clusters and organic residues. Secondly, together with a modified Silberstein-Applequist procedure for interacting inducible point-dipoles, these frequency-dependent polarizable force fields can be used for a classical determination of frequency-dependent cluster polarizabilities. We evaluate this methodology by comparing with the corresponding results obtained from quantum mechanics or QMMM where the absolute mean [small alpha, Greek, macron] is determined with respect to the size of the QM and MM parts of the total system. PMID:25714984
ON THE FORCE-FREE NATURE OF PHOTOSPHERIC SUNSPOT MAGNETIC FIELDS AS OBSERVED FROM HINODE (SOT/SP)
Tiwari, Sanjiv Kumar
2012-01-01
A magnetic field is force-free if there is no interaction between it and the plasma in the surrounding atmosphere, i.e., electric currents are aligned with the magnetic field, giving rise to zero Lorentz force. The computation of various magnetic parameters, such as magnetic energy (using the virial theorem), gradient of twist of sunspot magnetic fields (computed from the force-free parameter {alpha}), and any kind of extrapolation, heavily hinges on the force-free approximation of the photospheric sunspot magnetic fields. Thus, it is of vital importance to inspect the force-free behavior of sunspot magnetic fields. The force-free nature of sunspot magnetic fields has been examined earlier by some researchers, ending with incoherent results. Accurate photospheric vector field measurements with high spatial resolution are required to inspect the force-free nature of sunspots. For this purpose, we use several vector magnetograms of high spatial resolution obtained from the Solar Optical Telescope/Spectro-Polarimeter on board Hinode. Both the necessary and sufficient conditions for force-free nature are examined by checking the global and local nature of equilibrium magnetic forces over sunspots. We find that sunspot magnetic fields are not very far from the force-free configuration, although they are not completely force-free on the photosphere. The umbral and inner penumbral fields are more force-free than the middle and outer penumbral fields. During their evolution, sunspot magnetic fields are found to maintain their proximity to force-free field behavior. Although a dependence of net Lorentz force components is seen on the evolutionary stages of the sunspots, we do not find a systematic relationship between the nature of sunspot magnetic fields and the associated flare activity. Further, we examine whether the fields at the photosphere follow linear or nonlinear force-free conditions. After examining this in various complex and simple sunspots, we conclude that
Generation of accurate integral surfaces in time-dependent vector fields.
Garth, Christoph; Krishnan, Han; Tricoche, Xavier; Bobach, Tom; Joy, Kenneth I
2008-01-01
We present a novel approach for the direct computation of integral surfaces in time-dependent vector fields. As opposed to previous work, which we analyze in detail, our approach is based on a separation of integral surface computation into two stages: surface approximation and generation of a graphical representation. This allows us to overcome several limitations of existing techniques. We first describe an algorithm for surface integration that approximates a series of time lines using iterative refinement and computes a skeleton of the integral surface. In a second step, we generate a well-conditioned triangulation. Our approach allows a highly accurate treatment of very large time-varying vector fields in an efficient, streaming fashion. We examine the properties of the presented methods on several example datasets and perform a numerical study of its correctness and accuracy. Finally, we investigate some visualization aspects of integral surfaces. PMID:18988990
NASA Astrophysics Data System (ADS)
Zacharias, Panagiotis P.; Chatzineofytou, Elpida G.; Spantideas, Sotirios T.; Capsalis, Christos N.
2016-07-01
In the present work, the determination of the magnetic behavior of localized magnetic sources from near-field measurements is examined. The distance power law of the magnetic field fall-off is used in various cases to accurately predict the magnetic signature of an equipment under test (EUT) consisting of multiple alternating current (AC) magnetic sources. Therefore, parameters concerning the location of the observation points (magnetometers) are studied towards this scope. The results clearly show that these parameters are independent of the EUT's size and layout. Additionally, the techniques developed in the present study enable the placing of the magnetometers close to the EUT, thus achieving high signal-to-noise ratio (SNR). Finally, the proposed method is verified by real measurements, using a mobile phone as an EUT.
Nonlinear force-free magnetic fields. [quasi-steady state evolution of astrophysical fields
NASA Technical Reports Server (NTRS)
Low, B. C.
1982-01-01
The nonlinear properties of force-free magnetic fields are reviewed with particular reference to the mechanisms for the sudden release of stored energy in flares during the quasi-steady evolution of solar fields. It is shown that in the solar atmosphere, force-free fields with a nonconstant scalar function in the field equations are more likely to occur than those with a constant scalar function, and the nonlinear properties of these fields may give rise to many interesting physical effects. Consideration is then given to two possible mechanisms of field evolution: a model in which a force-free field in a medium of infinite electrical conductivity evolves in response to slowly changing boundary conditions brought about by photospheric motions in the solar active region, and a model in which a field in a medium of small finite electrical conductivity evolves in response to the slow Ohmic dissipation of the electric current.
METHODOLOGICAL NOTES: Force on matter in an electromagnetic field
NASA Astrophysics Data System (ADS)
Makarov, Vyacheslav P.; Rukhadze, Anri A.
2009-09-01
This article, in essence, is a continuation of the work by V L Ginzburg and V A Ugarov (Usp. Fiz. Nauk 118 175 (1976) [Sov. Phys. Usp. 19 94 (1976)]). It is shown that the results given in § 75 of the book Electrodynamics of Continuous Media by L D Landau and E M Lifshitz (Moscow: Nauka, 1982, in Russian) and in § 105 of the book Fundamentals of the Theory of Electricity by I E Tamm (Moscow: Nauka, 1989, in Russian) unambiguously follow only from the Maxwell equations of macroscopic electrodynamics, the corresponding constitutive equations, and the equations of motion of a substance (the hydrodynamic equations). These results are as follows: (1) the force acting on a unit volume of a motionless substance is given by the sum of the Helmholtz force and the Abraham force; (2) the momentum density of an electromagnetic field is the Umov-Poynting vector divided by c2, and (3) the stress tensor related to the field coincides in its form with the sum of the stress tensor of the electrostatic field and the stress tensor of the magnetostatic field. Thus, it is proved that the symmetric form of the Abraham tensor stands for the energy-momentum tensor of an electromagnetic field in a motionless medium.
Direct measurement of optical force induced by near-field plasmonic cavity using dynamic mode AFM
Guan, Dongshi; Hang, Zhi Hong; Marset, Zsolt; Liu, Hui; Kravchenko, Ivan I.; Chan, Ho Bun; Chan, C. T.; Tong, Penger
2015-11-20
Plasmonic nanostructures have attracted much attention in recent years because of their potential applications in optical manipulation through near-field enhancement. Continuing experimental efforts have been made to develop accurate techniques to directly measure the near-field optical force induced by the plasmonic nanostructures in the visible frequency range. In this work, we report a new application of dynamic mode atomic force microscopy (DM-AFM) in the measurement of the enhanced optical force acting on a nano-structured plasmonic resonant cavity. The plasmonic cavity is made of an upper gold-coated glass sphere and a lower quartz substrate patterned with an array of subwavelength goldmore » disks. In the near-field when the sphere is positioned close to the disk array, plasmonic resonance is excited in the cavity and the induced force by a 1550 nm infrared laser is found to be increased by an order of magnitude compared with the photon pressure generated by the same laser light. Lastly, the experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures.« less
Direct measurement of optical force induced by near-field plasmonic cavity using dynamic mode AFM
Guan, Dongshi; Hang, Zhi Hong; Marset, Zsolt; Liu, Hui; Kravchenko, Ivan I.; Chan, Ho Bun; Chan, C. T.; Tong, Penger
2015-11-20
Plasmonic nanostructures have attracted much attention in recent years because of their potential applications in optical manipulation through near-field enhancement. Continuing experimental efforts have been made to develop accurate techniques to directly measure the near-field optical force induced by the plasmonic nanostructures in the visible frequency range. In this work, we report a new application of dynamic mode atomic force microscopy (DM-AFM) in the measurement of the enhanced optical force acting on a nano-structured plasmonic resonant cavity. The plasmonic cavity is made of an upper gold-coated glass sphere and a lower quartz substrate patterned with an array of subwavelength gold disks. In the near-field when the sphere is positioned close to the disk array, plasmonic resonance is excited in the cavity and the induced force by a 1550 nm infrared laser is found to be increased by an order of magnitude compared with the photon pressure generated by the same laser light. Lastly, the experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures.
Direct Measurement of Optical Force Induced by Near-Field Plasmonic Cavity Using Dynamic Mode AFM
Guan, Dongshi; Hang, Zhi Hong; Marcet, Zsolt; Liu, Hui; Kravchenko, I. I.; Chan, C. T.; Chan, H. B.; Tong, Penger
2015-01-01
Plasmonic nanostructures have attracted much attention in recent years because of their potential applications in optical manipulation through near-field enhancement. Continuing experimental efforts have been made to develop accurate techniques to directly measure the near-field optical force induced by the plasmonic nanostructures in the visible frequency range. In this work, we report a new application of dynamic mode atomic force microscopy (DM-AFM) in the measurement of the enhanced optical force acting on a nano-structured plasmonic resonant cavity. The plasmonic cavity is made of an upper gold-coated glass sphere and a lower quartz substrate patterned with an array of subwavelength gold disks. In the near-field when the sphere is positioned close to the disk array, plasmonic resonance is excited in the cavity and the induced force by a 1550 nm infrared laser is found to be increased by an order of magnitude compared with the photon pressure generated by the same laser light. The experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures. PMID:26586455
Automatic molecular structure perception for the universal force field.
Artemova, Svetlana; Jaillet, Léonard; Redon, Stephane
2016-05-15
The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well-adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self-contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience (http://www.samson-connect.net). We validate both the automatic perception method and the UFF implementation on a series of benchmarks. PMID:26927616
Atomistic force field for alumina fit to density functional theory
Sarsam, Joanne; Finnis, Michael W.; Tangney, Paul
2013-11-28
We present a force field for bulk alumina (Al{sub 2}O{sub 3}), which has been parametrized by fitting the energies, forces, and stresses of a large database of reference configurations to those calculated with density functional theory (DFT). We use a functional form that is simpler and computationally more efficient than some existing models of alumina parametrized by a similar technique. Nevertheless, we demonstrate an accuracy of our potential that is comparable to those existing models and to DFT. We present calculations of crystal structures and energies, elastic constants, phonon spectra, thermal expansion, and point defect formation energies.
Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions
2015-01-01
We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein–ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O–O radial distribution functions similar to TIP4P-EW. PMID:24803856
Exploring Adsorption of Water and Ions on Carbon Surfaces using a Polarizable Force Field.
Schyman, Patric; Jorgensen, William L
2013-02-01
Graphene, carbon nanotubes, and fullerenes are of great interest due to their unique properties and diverse applications in biology, molecular electronics, and materials science. Therefore, there is demand for methods that can accurately model the interface between carbon surfaces and their environment. In this letter we compare results for complexes of water, potassium ion, and chloride ion with graphene, carbon nanotube, and fullerene surfaces using a standard non-polarizable force field (OPLS-AA), a polarizable force field (OPLS-AAP), DFT, and ab initio theory. For interactions with water, OPLS-AA with the TIP3P or TIP4P water models describes the interactions with benzene (C(6)H(6)) and coronene (C(24)H(12)) well; however, for acenes larger than circumcoronene (C(54)H(18)) and especially for C(60), the interaction energies are somewhat too weak and polarization is needed. For ions interacting with carbon surfaces, inclusion of polarization is essential, and OPLS-AAP is found to perform well in comparison to the highest-level quantum mechanical methods. Overall, OPLS-AAP provides an accurate and computationally efficient force field for modeling condensed-phase systems featuring carbon surfaces.
Field measurement of basal forces generated by erosive debris flows
McCoy, S.W.; Tucker, G.E.; Kean, J.W.; Coe, J.A.
2013-01-01
It has been proposed that debris flows cut bedrock valleys in steeplands worldwide, but field measurements needed to constrain mechanistic models of this process remain sparse due to the difficulty of instrumenting natural flows. Here we present and analyze measurements made using an automated sensor network, erosion bolts, and a 15.24 cm by 15.24 cm force plate installed in the bedrock channel floor of a steep catchment. These measurements allow us to quantify the distribution of basal forces from natural debris‒flow events that incised bedrock. Over the 4 year monitoring period, 11 debris‒flow events scoured the bedrock channel floor. No clear water flows were observed. Measurements of erosion bolts at the beginning and end of the study indicated that the bedrock channel floor was lowered by 36 to 64 mm. The basal force during these erosive debris‒flow events had a large‒magnitude (up to 21 kN, which was approximately 50 times larger than the concurrent time‒averaged mean force), high‒frequency (greater than 1 Hz) fluctuating component. We interpret these fluctuations as flow particles impacting the bed. The resulting variability in force magnitude increased linearly with the time‒averaged mean basal force. Probability density functions of basal normal forces were consistent with a generalized Pareto distribution, rather than the exponential distribution that is commonly found in experimental and simulated monodispersed granular flows and which has a lower probability of large forces. When the bed sediment thickness covering the force plate was greater than ~ 20 times the median bed sediment grain size, no significant fluctuations about the time‒averaged mean force were measured, indicating that a thin layer of sediment (~ 5 cm in the monitored cases) can effectively shield the subjacent bed from erosive impacts. Coarse‒grained granular surges and water‒rich, intersurge flow had very similar basal force distributions despite
Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew
2013-11-12
The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling.
Non-force-free solar magnetic fields in magnetohydrostatic equilibrium
NASA Technical Reports Server (NTRS)
Comfort, R. H.; Tandberg-Hanssen, E.; Wu, S. T.
1979-01-01
The objective of the paper is to examine a class of non-force-free fields analytically. Specifically, magnetic fields in magnetohydrostatic equilibrium with a plasma in a gravitational field are treated in an approximation of two independent variables but three vector components. Spherical coordinates are emphasized, although the formal results for cylindrical and Cartesian coordinates are presented in the appendices. Formal solutions for the magnetic-field components are obtained in terms of the plasma variables, and field line equations are derived. A final equation governing the plasma variables is then obtained. Procedures are developed for analyzing this equation and obtaining sets of self-consistent particular solutions to the governing equations; a number of such sets of solutions are presented. As an example, one solution set is examined, illustrating the application of the results to the analysis of solar observational data.
A coarse-grain force field for RDX: Density dependent and energy conserving
NASA Astrophysics Data System (ADS)
Moore, Joshua D.; Barnes, Brian C.; Izvekov, Sergei; Lísal, Martin; Sellers, Michael S.; Taylor, DeCarlos E.; Brennan, John K.
2016-03-01
We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions.
Development of Field Excavator with Embedded Force Measurement
NASA Technical Reports Server (NTRS)
Johnson, K.; Creager, C.; Izadnegahdar, A.; Bauman, S.; Gallo, C.; Abel, P.
2012-01-01
A semi-intelligent excavation mechanism was developed for use with the NASA-built Centaur 2 rover prototype. The excavator features a continuously rotatable large bucket supported between two parallel arms, both of which share a single pivot axis near the excavator base attached to the rover. The excavator is designed to simulate the collection of regolith, such as on the Moon, and to dump the collected soil into a hopper up to one meter tall for processing to extract oxygen. Because the vehicle can be autonomous and the terrain is generally unknown, there is risk of damaging equipment or using excessive power when attempting to extract soil from dense or rocky terrain. To minimize these risks, it is critical for the rover to sense the digging forces and adjust accordingly. It is also important to understand the digging capabilities and limitations of the excavator. This paper discusses the implementation of multiple strain gages as an embedded force measurement system in the excavator's arms. These strain gages can accurately measure and resolve multi-axial forces on the excavator. In order to validate these sensors and characterize the load capabilities, a series of controlled excavation tests were performed at Glenn Research Center with the excavator at various depths and cut angles while supported by a six axis load cell. The results of these tests are both compared to a force estimation model and used for calibration of the embedded strain gages. In addition, excavation forces generated using two different types of bucket edge (straight vs. with teeth) were compared.
Force-free fields in thin coronal loops
NASA Technical Reports Server (NTRS)
Emslie, A. Gordon; Wilkinson, L. K.
1994-01-01
We solve the force-free equation J x B = 0 for fields which are toroidally symmetric. The technique utilizes an expansion about a cylindrical field and is therefore valid or tori with a large aspect ratio such as long, thin, coronal loops. The calculation is performed in spatial toroidal coordinates, rather than in the flux coordinates used by previous authors; this allows direct calculation of the loci of flux surfaces and of surfaces of constant magnetic pressure. Our solutions differ significantly from toroidal fields in laboratories, which are in general not force-free. They are characterized by field lines whose projections in the poloidal planes are circles with centers displaced by varying distances from the axis of the torus. In general, flux surfaces do not correspond to surfaces of constant magnetic pressure. We have examined solutions corresponding to simple analytic zero-order cylindrical fields. For moderate twists in the zero-order (cylindrical) field, the magnetic pressure is larger on the inner toroidal radius. However, this effect diminishes with twist angle and in fact, for extreme initial twists, the magnetic pressure can be larger on the outer radius. We compare our results with previous work utilizing flux coordinates.
Non-Markovian Brownian motion in a magnetic field and time-dependent force fields
NASA Astrophysics Data System (ADS)
Hidalgo-Gonzalez, J. C.; Jiménez-Aquino, J. I.; Romero-Bastida, M.
2016-11-01
This work focuses on the derivation of the velocity and phase-space generalized Fokker-Planck equations for a Brownian charged particle embedded in a memory thermal bath and under the action of force fields: a constant magnetic field and arbitrary time-dependent force fields. To achieve the aforementioned goal we use a Gaussian but non-Markovian generalized Langevin equation with an arbitrary friction memory kernel. In a similar way, the generalized diffusion equation in the zero inertia limit is also derived. Additionally we show, in the absence of the time-dependent external forces, that, if the fluctuation-dissipation relation of the second kind is valid, then the generalized Langevin dynamics associated with the charged particle reaches a stationary state in the large-time limit. The consistency of our theoretical results is also verified when they are compared with those derived in the absence of the force fields and in the Markovian case.
Force-field parameters for beryllium complexes in amorphous layers.
Emelyanova, Svetlana; Chashchikhin, Vladimir; Bagaturyants, Alexander
2016-09-01
Unknown force-field parameters for metal organic beryllium complexes used in emitting and electron transporting layers of OLED structures are determined. These parameters can be used for the predictive atomistic simulations of the structure and properties of amorphous organic layers containing beryllium complexes. The parameters are found for the AMBER force field using a relaxed scan procedure and quantum-mechanical DFT calculations of potential energy curves for specific internal (angular) coordinates in a series of three Be complexes (Bebq2; Be(4-mpp)2; Bepp2). The obtained parameters are verified in calculations of some molecular and crystal structures available from either quantum-mechanical DFT calculations or experimental data. Graphical Abstract Beryllium complexes in amorphous layersᅟ. PMID:27550375
A Transferable Force Field for Primary, Secondary, and Tertiary Alkanolamines.
Orozco, Gustavo A; Lachet, Véronique; Nieto-Draghi, Carlos; Mackie, Allan D
2013-04-01
Due to the importance of alkanolamines as solvents in several industrial processes and the absence of a dedicated transferable force field for them, we have developed an anisotropic united-atom (AUA4) force field for primary, secondary, and tertiary alkanolamines. In addition to correctly reproducing the experimental densities, additional properties for six different molecules have been verified at different temperatures including vaporization enthalpies, vapor pressures, normal boiling points, critical temperatures, and critical densities. A qualitative analysis of the radial distribution function of pure monoethanolamine has also been carried out. Furthermore, the viscosity coefficients were also calculated as a function of temperature and found to be in good agreement with experimental data. Finally, and perhaps most strikingly, the prediction of the excess enthalpies of alkanolamines in aqueous solutions has been found to be in excellent qualitative agreement with experimental data. PMID:26583556
Efficient parametrization of complex molecule-surface force fields.
Gao, David Z; Federici Canova, Filippo; Watkins, Matthew B; Shluger, Alexander L
2015-06-15
We present an efficient scheme for parametrizing complex molecule-surface force fields from ab initio data. The cost of producing a sufficient fitting library is mitigated using a 2D periodic embedded slab model made possible by the quantum mechanics/molecular mechanics scheme in CP2K. These results were then used in conjunction with genetic algorithm (GA) methods to optimize the large parameter sets needed to describe such systems. The derived potentials are able to well reproduce adsorption geometries and adsorption energies calculated using density functional theory. Finally, we discuss the challenges in creating a sufficient fitting library, determining whether or not the GA optimization has completed, and the transferability of such force fields to similar molecules.
A Maximum-Likelihood Approach to Force-Field Calibration.
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
Correlated continuous-time random walks in external force fields
NASA Astrophysics Data System (ADS)
Magdziarz, Marcin; Metzler, Ralf; Szczotka, Wladyslaw; Zebrowski, Piotr
2012-05-01
We study the anomalous diffusion of a particle in an external force field whose motion is governed by nonrenewal continuous time random walks with correlated waiting times. In this model the current waiting time Ti is equal to the previous waiting time Ti-1 plus a small increment. Based on the associated coupled Langevin equations the force field is systematically introduced. We show that in a confining potential the relaxation dynamics follows power-law or stretched exponential pattern, depending on the model parameters. The process obeys a generalized Einstein-Stokes-Smoluchowski relation and observes the second Einstein relation. The stationary solution is of Boltzmann-Gibbs form. The case of an harmonic potential is discussed in some detail. We also show that the process exhibits aging and ergodicity breaking.
Force-field parameters for beryllium complexes in amorphous layers.
Emelyanova, Svetlana; Chashchikhin, Vladimir; Bagaturyants, Alexander
2016-09-01
Unknown force-field parameters for metal organic beryllium complexes used in emitting and electron transporting layers of OLED structures are determined. These parameters can be used for the predictive atomistic simulations of the structure and properties of amorphous organic layers containing beryllium complexes. The parameters are found for the AMBER force field using a relaxed scan procedure and quantum-mechanical DFT calculations of potential energy curves for specific internal (angular) coordinates in a series of three Be complexes (Bebq2; Be(4-mpp)2; Bepp2). The obtained parameters are verified in calculations of some molecular and crystal structures available from either quantum-mechanical DFT calculations or experimental data. Graphical Abstract Beryllium complexes in amorphous layersᅟ.
Efficient parametrization of complex molecule-surface force fields.
Gao, David Z; Federici Canova, Filippo; Watkins, Matthew B; Shluger, Alexander L
2015-06-15
We present an efficient scheme for parametrizing complex molecule-surface force fields from ab initio data. The cost of producing a sufficient fitting library is mitigated using a 2D periodic embedded slab model made possible by the quantum mechanics/molecular mechanics scheme in CP2K. These results were then used in conjunction with genetic algorithm (GA) methods to optimize the large parameter sets needed to describe such systems. The derived potentials are able to well reproduce adsorption geometries and adsorption energies calculated using density functional theory. Finally, we discuss the challenges in creating a sufficient fitting library, determining whether or not the GA optimization has completed, and the transferability of such force fields to similar molecules. PMID:25891018
Four-nucleon force in chiral effective field theory
Evgeny Epelbaum
2005-10-25
We derive the leading contribution to the four--nucleon force within the framework of chiral effective field theory. It is governed by the exchange of pions and the lowest--order nucleon--nucleon contact interaction and includes effects due to the nonlinear pion--nucleon couplings and the pion self interactions constrained by the chiral symmetry of QCD. The resulting 4NF does not contain any unknown parameters and can be tested in future few--and many--nucleon studies.
Quantum mechanical force field for water with explicit electronic polarization
Han, Jaebeom; Mazack, Michael J. M.; Zhang, Peng; Truhlar, Donald G.; Gao, Jiali
2013-01-01
A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 106 self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across
Quantum mechanical force field for water with explicit electronic polarization.
Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali
2013-08-01
A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across
Force-free magnetic fields - Generating functions and footpoint displacements
NASA Technical Reports Server (NTRS)
Wolfson, Richard; Verma, Ritu
1991-01-01
This paper presents analytic and numerical calculations that explore equilibrium sequences of bipolar force-free magnetic fields in relation to displacments of their magnetic footpoints. It is shown that the appearance of magnetic islands - sometimes interpreted as marking the loss of equilibrium in models of the solar atmosphere - is likely associated only with physically unrealistic footpoint displacements such as infinite separation or 'tearing' of the model photosphere. The work suggests that the loss of equilibrium in bipolar configurations, sometimes proposed as a mechanism for eruptive solar events, probably requires either fully three-dimensional field configurations or nonzero plasma pressure. The results apply only to fields that are strictly bipolar, and do not rule out equilibrium loss in more complex structures such as quadrupolar fields.
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.
Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field
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
Zhu, Xiao; MacKerell, Alexander D
2010-09-01
Condensed-phase computational studies of molecules using molecular mechanics approaches require the use of force fields to describe the energetics of the systems as a function of structure. The advantage of polarizable force fields over nonpolarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Toward development of a polarizable force field for biological molecules, parameters for a series of sulfur-containing molecules are presented. Parameter optimization was performed to reproduce quantum mechanical and experimental data for gas phase properties including geometries, conformational energies, vibrational spectra, and dipole moments as well as for condensed phase properties such as heats of vaporization, molecular volumes, and free energies of hydration. Compounds in the training set include methanethiol, ethanethiol, propanethiol, ethyl methyl sulfide, and dimethyl disulfide. The molecular volumes and heats of vaporization are in good accordance with experimental values, with the polarizable model performing better than the CHARMM22 nonpolarizable force field. Improvements with the polarizable model were also obtained for molecular dipole moments and in the treatment of intermolecular interactions as a function of orientation, in part due to the presence of lone pairs and anisotropic atomic polarizability on the sulfur atoms. Significant advantage of the polarizable model was reflected in calculation of the dielectric constants, a property that CHARMM22 systematically underestimates. The ability of this polarizable model to accurately describe a range of gas and condensed phase properties paves the way for more accurate simulation studies of sulfur-containing molecules including cysteine and methionine residues in proteins. PMID:20575015
Secondary Structure of Rat and Human Amylin across Force Fields.
Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-Cheng; de Pablo, Juan J
2015-01-01
The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable
Secondary Structure of Rat and Human Amylin across Force Fields.
Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-Cheng; de Pablo, Juan J
2015-01-01
The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable
Secondary Structure of Rat and Human Amylin across Force Fields
Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-cheng; de Pablo, Juan J.
2015-01-01
The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable
Secondary structure of rat and human amylin across force fields
Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi -cheng; de Pablo, Juan J.; Paci, Emanuele
2015-07-29
The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin wasmore » determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states
Secondary structure of rat and human amylin across force fields
Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi -cheng; de Pablo, Juan J.; Paci, Emanuele
2015-07-29
The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable
Force field measurements within the exclusion zone of water.
Chen, Chi-Shuo; Chung, Wei-Ju; Hsu, Ian C; Wu, Chien-Ming; Chin, Wei-Chun
2012-01-01
Water molecules play critical roles in many biological functions, such as protein dynamics, enzymatic activities, and cellular responses. Previous nuclear magnetic resonance and neutron scattering studies have shown that water molecules bind to specific sites on surfaces and form localized clusters. However, most current experimental techniques cannot measure dynamic behaviors of ordered water molecules on cell-size (10 μm) scale. Recently, the long-distance effect of structured water has been demonstrated by Pollack and his colleagues. Namely, there is a structured water layer near the hydrophilic surface that can exclude solutes (Zheng et al, Adv Colloid Interface Sci 127:19-27, 2006; Pollack 2006, Adv Colloid Interface Sci 103:173-196, 2003). The repelling forces of water clusters inside this exclusion region are investigated in this study. With a laser tweezers system, we found the existence of an unexpected force fields inside the solute-free exclusion zone near a Nafion surface. Our results suggest that the water clusters could transduce mechanical signals on the micrometer range within the exclusion zone. This unexpected inhomogeneous force field near the hydrophilic surface would provide a new insight into cellular activities, leading to a potential new physical chemistry mechanism for cell biology. PMID:23277674
Interfacial Force Field Characterization in a Constrained Vapor Bubble Thermosyphon
NASA Technical Reports Server (NTRS)
DasGupta, Sunando; Plawsky, Joel L.; Wayner, Peter C., Jr.
1995-01-01
Isothermal profiles of the extended meniscus in a quartz cuvette were measured in the earth's gravitational field using an image-analyzing interferometer that is based on computer-enhanced video microscopy of the naturally occurring interference fringes. These profiles are a function of the stress field. Experimentally, the augmented Young-Laplace equation is an excellent model for the force field at the solid-liquid-vapor interfaces for heptane and pentane menisci on quartz and tetradecane on SFL6. The effects of refractive indices of the solid and liquid on the measurement techniques were demonstrated. Experimentally obtained values of the disjoining pressure and dispersion constants were compared to those predicted from the Dzyaloshinskii - Lifshitz - Pilaevskii theory for an ideal surface and reasonable agreements were obtained. A parameter introduced gives a quantitative measurement of the closeness of the system to equilibrium. The nonequilibrium behavior of this parameter is also presented
Interfacial force field characterization in a constrained vapor bubble thermosyphon
DasGupta, S.; Plawsky, J.L.; Wayner, P.C. Jr.
1995-09-01
isothermal profiles of the extended meniscus in a quartz cuvette were measured in the earth`s gravitational field using an image analyzing interferometer that is based on computer-enhanced video microscopy of the naturally occurring interference fringes. These profiles are a function of the stress field. Experimentally, the augmented Young-Laplace equation is an excellent model for the force field at the solid-liquid-vapor interfaces for heptane and pentane menisci on quartz and tetradecane on SFL6. Effects of refractive indices of the solid and liquid on the measurement techniques were demonstrated. Experimentally obtained values of the disjoining pressure and dispersion constants were compared to those predicted from the Dzyaloshinskii-Lifshitz-Pitaevskii theory for an ideal surface and reasonable agreements were obtained. A parameter introduced gives a quantitative measurement of the closeness of the system to equilibrium. The nonequilibrium behavior of this parameter is also presented.
Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9.
Guerra, Federico; Adam, Suliman; Bondar, Ana-Nicoleta
2015-05-01
Biological photosynthetic machineries, such as photosystem I, photosystem II, or the bacterial reaction center, use cofactor molecules that absorb light or directly participate in chemical reactions. Accurate description of the structure of the cofactors, and of their interactions with protein groups, is an important step toward understanding how photosynthetic machineries work. Here we revisit the classical force field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9. We present systematic quantum mechanical and classical mechanical computations that lead to a good description of the structure and non-bonded interactions of these cofactors.
Deformation field of the soft substrate induced by capillary force
NASA Astrophysics Data System (ADS)
Liu, J. L.; Nie, Z. X.; Jiang, W. G.
2009-05-01
Prediction on the deformation of a soft substrate induced by capillary force has been widely paid attention in the broad range of applications, such as metallurgy, material science, astronavigation, micro/nano-technology, etc., which is also a supplementary result to the classical Young's equation. We quantitatively analyzed the deformation of an elastic substrate under capillary force by means of the energy principle and the continuum mechanics method. The actual drop's morphology was investigated and was compared with that calculated based on the classical spherical shape assumption of the droplet. The displacement field of the substrate was obtained, especially, its singularity at the droplet edge was also discussed. The results are beneficial to engineering application and micro/nano-measurement.
A polarizable force field for computing the infrared spectra of the polypeptide backbone.
Schultheis, Verena; Reichold, Rudolf; Schropp, Bernhard; Tavan, Paul
2008-10-01
The shapes of the amide bands in the infrared (IR) spectra of proteins and peptides are caused by electrostatically coupled vibrations within the polypeptide backbone and code the structures of these biopolymers. A structural decoding of the amide bands has to resort to simplified models because the huge size of these macromolecules prevents the application of accurate quantum mechanical methods such as density functional theory (DFT). Previous models employed transition-dipole coupling methods that are of limited accuracy. Here we propose a concept for the computation of protein IR spectra, which describes the molecular mechanics (MM) of polypeptide backbones by a polarizable force field of "type II". By extending the concepts of conventional polarizable MM force fields, such a PMM/II approach employs field-dependent parameters not only for the electrostatic signatures of the molecular components but also for the local potentials modeling the stiffness of chemical bonds with respect to elongations, angle deformations, and torsions. Using a PMM/II force field, the IR spectra of the polypeptide backbone can be efficiently calculated from the time dependence of the backbone's dipole moment during a short (e.g., 100 ps) MD simulation by Fourier transformation. PMM/II parameters are derived for harmonic bonding potentials of amide groups in polypeptides from a series of DFT calculations on the model molecule N-methylacetamide (NMA) exposed to homogeneous external electric fields. The amide force constants are shown to vary by as much as 20% for relevant field strengths. As a proof of principle, it is shown that the large solvatochromic effects observed in the IR spectra of NMA upon transfer from the gas phase into aqueous solution are not only excellently reproduced by DFT/MM simulations but are also nicely modeled by the PMM/II approach. The tasks remaining for a proof of practice are specified.
A new cation-exchange method for accurate field speciation of hexavalent chromium
Ball, J.W.; McCleskey, R.B.
2003-01-01
A new method for field speciation of Cr(VI) has been developed to meet present stringent regulatory standards and to overcome the limitations of existing methods. The method consists of passing a water sample through strong acid cation-exchange resin at the field site, where Cr(III) is retained while Cr(VI) passes into the effluent and is preserved for later determination. The method is simple, rapid, portable, and accurate, and makes use of readily available, inexpensive materials. Cr(VI) concentrations are determined later in the laboratory using any elemental analysis instrument sufficiently sensitive to measure the Cr(VI) concentrations of interest. The new method allows measurement of Cr(VI) concentrations as low as 0.05 ??g 1-1, storage of samples for at least several weeks prior to analysis, and use of readily available analytical instrumentation. Cr(VI) can be separated from Cr(III) between pH 2 and 11 at Cr(III)/Cr(VI) concentration ratios as high as 1000. The new method has demonstrated excellent comparability with two commonly used methods, the Hach Company direct colorimetric method and USEPA method 218.6. The new method is superior to the Hach direct colorimetric method owing to its relative sensitivity and simplicity. The new method is superior to USEPA method 218.6 in the presence of Fe(II) concentrations up to 1 mg 1-1 and Fe(III) concentrations up to 10 mg 1-1. Time stability of preserved samples is a significant advantage over the 24-h time constraint specified for USEPA method 218.6.
Wan, Xiaoke; Wang, Ji; Ge, Jian
2010-10-10
Interferometers are key elements in radial velocity (RV) experiments in astronomy observations, and accurate calibration of the group delay of an interferometer is required for high precision measurements. A novel field-compensated white light scanning Michelson interferometer is introduced as an interferometer calibration tool. The optical path difference (OPD) scanning was achieved by translating a compensation prism, such that even if the light source were in low spatial coherence, the interference stays spatially phase coherent over a large interferometer scanning range. In the wavelength region of 500-560 nm, a multimode fiber-coupled LED was used as the light source, and high optical efficiency was essential in elevating the signal-to-noise ratio of the interferogram signal. The achromatic OPD scanning required a one-time calibration, and two methods using dual-laser wavelength references and an iodine absorption spectrum reference were employed and cross-verified. In an experiment measuring the group delay of a fixed Michelson interferometer, Fourier analysis was employed to process the interferogram data. The group delay was determined at an accuracy of 1×10(-5), and the phase angle precision was typically 2.5×10(-6) over the wide wavelength region.
Beekhuizen, Johan; Kromhout, Hans; Bürgi, Alfred; Huss, Anke; Vermeulen, Roel
2015-01-01
The increase in mobile communication technology has led to concern about potential health effects of radio frequency electromagnetic fields (RF-EMFs) from mobile phone base stations. Different RF-EMF prediction models have been applied to assess population exposure to RF-EMF. Our study examines what input data are needed to accurately model RF-EMF, as detailed data are not always available for epidemiological studies. We used NISMap, a 3D radio wave propagation model, to test models with various levels of detail in building and antenna input data. The model outcomes were compared with outdoor measurements taken in Amsterdam, the Netherlands. Results showed good agreement between modelled and measured RF-EMF when 3D building data and basic antenna information (location, height, frequency and direction) were used: Spearman correlations were >0.6. Model performance was not sensitive to changes in building damping parameters. Antenna-specific information about down-tilt, type and output power did not significantly improve model performance compared with using average down-tilt and power values, or assuming one standard antenna type. We conclude that 3D radio wave propagation modelling is a feasible approach to predict outdoor RF-EMF levels for ranking exposure levels in epidemiological studies, when 3D building data and information on the antenna height, frequency, location and direction are available.
Beekhuizen, Johan; Kromhout, Hans; Bürgi, Alfred; Huss, Anke; Vermeulen, Roel
2015-01-01
The increase in mobile communication technology has led to concern about potential health effects of radio frequency electromagnetic fields (RF-EMFs) from mobile phone base stations. Different RF-EMF prediction models have been applied to assess population exposure to RF-EMF. Our study examines what input data are needed to accurately model RF-EMF, as detailed data are not always available for epidemiological studies. We used NISMap, a 3D radio wave propagation model, to test models with various levels of detail in building and antenna input data. The model outcomes were compared with outdoor measurements taken in Amsterdam, the Netherlands. Results showed good agreement between modelled and measured RF-EMF when 3D building data and basic antenna information (location, height, frequency and direction) were used: Spearman correlations were >0.6. Model performance was not sensitive to changes in building damping parameters. Antenna-specific information about down-tilt, type and output power did not significantly improve model performance compared with using average down-tilt and power values, or assuming one standard antenna type. We conclude that 3D radio wave propagation modelling is a feasible approach to predict outdoor RF-EMF levels for ranking exposure levels in epidemiological studies, when 3D building data and information on the antenna height, frequency, location and direction are available. PMID:24472756
Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Limborg, C.; Ng, C.; Prudencio, E.; Schussman, G.; Uplenchwar, R.; Ko, K.; /SLAC
2009-06-19
Over the past years, SLAC's Advanced Computations Department (ACD), under SciDAC sponsorship, has developed a suite of 3D (2D) parallel higher-order finite element (FE) codes, T3P (T2P) and Pic3P (Pic2P), aimed at accurate, large-scale simulation of wakefields and particle-field interactions in radio-frequency (RF) cavities of complex shape. The codes are built on the FE infrastructure that supports SLAC's frequency domain codes, Omega3P and S3P, to utilize conformal tetrahedral (triangular)meshes, higher-order basis functions and quadratic geometry approximation. For time integration, they adopt an unconditionally stable implicit scheme. Pic3P (Pic2P) extends T3P (T2P) to treat charged-particle dynamics self-consistently using the PIC (particle-in-cell) approach, the first such implementation on a conformal, unstructured grid using Whitney basis functions. Examples from applications to the International Linear Collider (ILC), Positron Electron Project-II (PEP-II), Linac Coherent Light Source (LCLS) and other accelerators will be presented to compare the accuracy and computational efficiency of these codes versus their counterparts using structured grids.
Micro-gravity: current distributions creating a uniform force field
NASA Astrophysics Data System (ADS)
Vincent-Viry, O.; Mailfert, A.; Colteu, A.; Dael, A.; Gourdin, C.; Quettier, L.
2001-02-01
This paper presents two structures of superconducting coils able to give satisfactory solutions to the problem of generation of uniform field of high magnetic forces. The first structure is modeled by the use of purely surface current densities, whereas the second one can be described with volume current densities. Both of these structures proceed from the study of a particular expression of the complex magnetic potential introduced for structures with two-dimensional geometry. This work is carried out in a research collaboration between the GREEN and the DSM-DAPNIA department of the CEA Saclay.
On the use of quartic force fields in variational calculations
NASA Astrophysics Data System (ADS)
Fortenberry, Ryan C.; Huang, Xinchuan; Yachmenev, Andrey; Thiel, Walter; Lee, Timothy J.
2013-06-01
Quartic force fields (QFFs) have been shown to be one of the most effective ways to efficiently compute vibrational frequencies for small molecules. In this letter we discuss how the simple-internal or bond-length bond-angle (BLBA) coordinates can be transformed into Morse-cosine (-sine) coordinates which produce potential energy surfaces from QFFs that possess proper limiting behavior and can describe the vibrational (or rovibrational) energy levels of an arbitrary molecular system to 5 cm-1 or better compared to experiment. We investigate parameter scaling in the Morse coordinate, symmetry considerations, and examples of transformed QFFs making use of the MULTIMODE, TROVE, and VTET variational vibrational methods.
The Anharmonic Force Field of BeH2 Revisited
NASA Technical Reports Server (NTRS)
Martin, Jan M. L.; Lee, Timothy J.
2003-01-01
The anharmonic force field of BeH2 has been calculated near the basis set and n-particle space limits. The computed antisymmetric stretch frequencies of BeH2 and BeD2 are in excellent agreement with recent high-resolution gas-phase measurements. The agreement between theory and experiment for the other spectroscopic constants is also excellent, except for omega(sub 3) and X(sub 33) for BeH2 and G(sub 22) for BeD2. It is concluded that further experimental work is needed in order to resolve these discrepancies.
A Polarizable Multipole-based Force Field for Dimethyl and Trimethyl Phosphate
Zhang, Changsheng; Lu, Chao; Wang, Qiantao; Ponder, Jay W.; Ren, Pengyu
2016-01-01
Using quantum mechanical studies and liquid phase simulations, the AMOEBA force field for dimethylphosphate (DMP) ion and trimethylphosphate (TMP) has been developed. Based on 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 accounting of chemical environments. 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 liquid TMP by comparing simulated density and heat of vaporization values with experimental data. Structural insight obtained from MD simulations indicates liquid TMP is stabilized by both nonpolar-nonpolar contacts and hydrogen bonding. The current study is an important step towards developing the AMOEBA model for nucleic acids. PMID:26574325
Nonlinear Force-Free Magnetic Field Modeling of AR 10953: A Critical Assessment
NASA Astrophysics Data System (ADS)
De Rosa, Marc L.; Schrijver, C. J.; Barnes, G.; Leka, K. D.; Lites, B. W.; Aschwanden, M. J.; Amari, T.; Canou, A.; McTiernan, J. M.; Régnier, S.; Thalmann, J. K.; Valori, G.; Wheatland, M. S.; Wiegelmann, T.; Cheung, M. C. M.; Conlon, P. A.; Fuhrmann, M.; Inhester, B.; Tadesse, T.
2009-05-01
Nonlinear force-free field (NLFFF) modeling seeks to provide accurate representations of the structure of the magnetic field above solar active regions, from which estimates of physical quantities of interest (e.g., free energy and helicity) can be made. However, the suite of NLFFF algorithms have failed to arrive at consistent solutions when applied to (thus far, two) cases using the highest-available-resolution vector magnetogram data from Hinode/SOT-SP (in the region of the modeling area of interest) and line-of-sight magnetograms from SOHO/MDI (where vector data were not available). One issue is that NLFFF models require consistent, force-free vector magnetic boundary data, and vector magnetogram data sampling the photosphere do not satisfy this requirement. Consequently, several problems have arisen that are believed to affect such modeling efforts. We use AR 10953 to illustrate these problems, namely: (1) some of the far-reaching, current-carrying connections are exterior to the observational field of view, (2) the solution algorithms do not (yet) incorporate the measurement uncertainties in the vector magnetogram data, and/or (3) a better way is needed to account for the Lorentz forces within the layer between the photosphere and coronal base. In light of these issues, we conclude that it remains difficult to derive useful and significant estimates of physical quantities from NLFFF models.
Optimization of the OPLS-AA Force Field for Long Hydrocarbons.
Siu, Shirley W I; Pluhackova, Kristyna; Böckmann, Rainer A
2012-04-10
The all-atom optimized potentials for liquid simulations (OPLS-AA) force field is a popular force field for simulating biomolecules. However, the current OPLS parameters for hydrocarbons developed using short alkanes cannot reproduce the liquid properties of long alkanes in molecular dynamics simulations. Therefore, the extension of OPLS-AA to (phospho)lipid molecules required for the study of biological membranes was hampered in the past. Here, we optimized the OPLS-AA force field for both short and long hydrocarbons. Following the framework of the OPLS-AA parametrization, we refined the torsional parameters for hydrocarbons by fitting to the gas-phase ab initio energy profiles calculated at the accurate MP2/aug-cc-pVTZ theory level. Additionally, the depth of the Lennard-Jones potential for methylene hydrogen atoms was adjusted to reproduce the densities and the heats of vaporization of alkanes and alkenes of different lengths. Optimization of partial charges finally allowed to reproduce the gel-to-liquid-phase transition temperature for pentadecane and solvation free energies. It is shown that the optimized parameter set (L-OPLS) yields improved hydrocarbon diffusion coefficients, viscosities, and gauche-trans ratios. Moreover, its applicability for lipid bilayer simulations is shown for a GMO bilayer in its liquid-crystalline phase.
Modeling enzymatic transition states by force field methods
NASA Astrophysics Data System (ADS)
Hansen, M. B.; Jensen, H. J. A.; Jensen, F.
The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5prime-monophosphate decarboxylase enzyme. The dependence of the TS geometry on the flexibility of the system has been probed by fixing layers of atoms around the active site and using increasingly larger nonbonded cutoffs. The variability over the 20 structures is found to decrease as the system is made more flexible. Relative energies have been calculated by various electronic structure methods, where part of the enzyme is represented by a force field description and the effects of the solvent are represented by a continuum model. The relative energies vary by several hundreds of kJ/mol between the transition structures, and tests showed that a large part of this variation is due to changes in the enzyme structure at distances more than 5 Å from the active site. There are significant differences between the results obtained by pure quantum methods and those from mixed quantum and molecular mechanics methods.
Coarse graining of force fields for metal-organic frameworks.
Dürholt, Johannes P; Galvelis, Raimondas; Schmid, Rochus
2016-03-14
We have adapted our genetic algorithm based optimization approach, originally developed to generate force field parameters from quantum mechanic reference data, to derive a first coarse grained force field for a MOF, taking the atomistic MOF-FF as a reference. On the example of the copper paddle-wheel based HKUST-1, a maximally coarse grained model, using a single bead for each three and four coordinated vertex, was developed as a proof of concept. By adding non-bonded interactions with a modified Buckingham potential, the resulting MOF-FF-CGNB is able to predict local deformation energies of the building blocks as well as bulk properties like the tbovs.pto energy difference or elastic constants in a semi-quantitative way. As expected, the negative thermal expansion of HKUST-1 is not reproduced by the maximally coarse grained model. At the expense of atomic resolution, substantially larger systems (up to tens of nanometers in size) can be simulated with respect to structural and mechanical properties, bridging the gap to the mesoscale. As an example the deformation of the [111] surface of HKUST-1 by a "tip" could be computed without artifacts from periodic images. PMID:26732756
Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations.
Perez, Alberto; MacCallum, Justin L; Brini, Emiliano; Simmerling, Carlos; Dill, Ken A
2015-10-13
Force fields, such as Amber's ff12SB, can be fairly accurate models of the physical forces in proteins and other biomolecules. When coupled with accurate solvation models, force fields are able to bring insight into the conformational preferences, transitions, pathways, and free energies for these biomolecules. When computational speed/cost matters, implicit solvent is often used but at the cost of accuracy. We present an empirical grid-like correction term, in the spirit of cMAPs, to the combination of the ff12SB protein force field and the GBneck2 implicit-solvent model. Ff12SB-cMAP is parametrized on experimental helicity data. We provide validation on a set of peptides and proteins. Ff12SB-cMAP successfully improves the secondary structure biases observed in ff12SB + Gbneck2. Ff12SB-cMAP can be downloaded ( https://github.com/laufercenter/Amap.git ) and used within the Amber package. It can improve the agreement of force fields + implicit solvent with experiments. PMID:26574266
Wildman, Jack; Repiščák, Peter; Paterson, Martin J; Galbraith, Ian
2016-08-01
We describe a general scheme to obtain force-field parameters for classical molecular dynamics simulations of conjugated polymers. We identify a computationally inexpensive methodology for calculation of accurate intermonomer dihedral potentials and partial charges. Our findings indicate that the use of a two-step methodology of geometry optimization and single-point energy calculations using DFT methods produces potentials which compare favorably to high level theory calculation. We also report the effects of varying the conjugated backbone length and alkyl side-chain lengths on the dihedral profiles and partial charge distributions and determine the existence of converged lengths above which convergence is achieved in the force-field parameter sets. We thus determine which calculations are required for accurate parametrization and the scope of a given parameter set for variations to a given molecule. We perform simulations of long oligomers of dioctylfluorene and hexylthiophene in explicit solvent and find peristence lengths and end-length distributions consistent with experimental values. PMID:27397762
Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields.
Van Vleet, Mary J; Misquitta, Alston J; Stone, Anthony J; Schmidt, J R
2016-08-01
Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (A/r(12)) or Born-Mayer (A exp(-Br)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular 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, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, 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. PMID:27337546
2016-01-01
We describe a general scheme to obtain force-field parameters for classical molecular dynamics simulations of conjugated polymers. We identify a computationally inexpensive methodology for calculation of accurate intermonomer dihedral potentials and partial charges. Our findings indicate that the use of a two-step methodology of geometry optimization and single-point energy calculations using DFT methods produces potentials which compare favorably to high level theory calculation. We also report the effects of varying the conjugated backbone length and alkyl side-chain lengths on the dihedral profiles and partial charge distributions and determine the existence of converged lengths above which convergence is achieved in the force-field parameter sets. We thus determine which calculations are required for accurate parametrization and the scope of a given parameter set for variations to a given molecule. We perform simulations of long oligomers of dioctylfluorene and hexylthiophene in explicit solvent and find peristence lengths and end-length distributions consistent with experimental values. PMID:27397762
Zgarbová, Marie; Rosnik, Andreana M; Luque, F Javier; Curutchet, Carles; Jurečka, Petr
2015-09-30
Recent advances in polarizable force fields have revealed that major reparameterization is necessary when the polarization energy is treated explicitly. This study is focused on the torsional parameters, which are crucial for the accurate description of conformational equilibria in biomolecules. In particular, attention is paid to the influence of polarization on the (i) transferability of dihedral terms between molecules, (ii) transferability between different environments, and (iii) additivity of dihedral energies. To this end, three polarizable force fields based on the induced point dipole model designed for use in AMBER are tested, including two recent ff02 reparameterizations. Attention is paid to the contributions due to short range interactions (1-2, 1-3, and 1-4) within the four atoms defining the dihedral angle. The results show that when short range 1-2 and 1-3 polarization interactions are omitted, as for instance in ff02, the 1-4 polarization contribution is rather small and unlikely to improve the description of the torsional energy. Conversely, when screened 1-2 and 1-3 interactions are included, the polarization contribution is sizeable and shows potential to improve the transferability of parameters between different molecules and environments as well as the additivity of dihedral terms. However, to reproduce intramolecular polarization effects accurately, further fine-tuning of the short range damping of polarization is necessary.
Zgarbová, Marie; Rosnik, Andreana M; Luque, F Javier; Curutchet, Carles; Jurečka, Petr
2015-09-30
Recent advances in polarizable force fields have revealed that major reparameterization is necessary when the polarization energy is treated explicitly. This study is focused on the torsional parameters, which are crucial for the accurate description of conformational equilibria in biomolecules. In particular, attention is paid to the influence of polarization on the (i) transferability of dihedral terms between molecules, (ii) transferability between different environments, and (iii) additivity of dihedral energies. To this end, three polarizable force fields based on the induced point dipole model designed for use in AMBER are tested, including two recent ff02 reparameterizations. Attention is paid to the contributions due to short range interactions (1-2, 1-3, and 1-4) within the four atoms defining the dihedral angle. The results show that when short range 1-2 and 1-3 polarization interactions are omitted, as for instance in ff02, the 1-4 polarization contribution is rather small and unlikely to improve the description of the torsional energy. Conversely, when screened 1-2 and 1-3 interactions are included, the polarization contribution is sizeable and shows potential to improve the transferability of parameters between different molecules and environments as well as the additivity of dihedral terms. However, to reproduce intramolecular polarization effects accurately, further fine-tuning of the short range damping of polarization is necessary. PMID:26224547
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.
Planetary Magnetic Fields and Solar Forcing: Implications for Atmospheric Evolution
NASA Astrophysics Data System (ADS)
Lundin, Rickard; Lammer, Helmut; Ribas, Ignasi
2007-03-01
The solar wind and the solar XUV/EUV radiation constitute a permanent forcing of the upper atmosphere of the planets in our solar system, thereby affecting the habitability and chances for life to emerge on a planet. The forcing is essentially inversely proportional to the square of the distance to the Sun and, therefore, is most important for the innermost planets in our solar system—the Earth-like planets. The effect of these two forcing terms is to ionize, heat, chemically modify, and slowly erode the upper atmosphere throughout the lifetime of a planet. The closer to the Sun, the more efficient are these process. Atmospheric erosion is due to thermal and non-thermal escape. Gravity constitutes the major protection mechanism for thermal escape, while the non-thermal escape caused by the ionizing X-rays and EUV radiation and the solar wind require other means of protection. Ionospheric plasma energization and ion pickup represent two categories of non-thermal escape processes that may bring matter up to high velocities, well beyond escape velocity. These energization processes have now been studied by a number of plasma instruments orbiting Earth, Mars, and Venus for decades. Plasma measurement results therefore constitute the most useful empirical data basis for the subject under discussion. This does not imply that ionospheric plasma energization and ion pickup are the main processes for the atmospheric escape, but they remain processes that can be most easily tested against empirical data. Shielding the upper atmosphere of a planet against solar XUV, EUV, and solar wind forcing requires strong gravity and a strong intrinsic dipole magnetic field. For instance, the strong dipole magnetic field of the Earth provides a “magnetic umbrella”, fending of the solar wind at a distance of 10 Earth radii. Conversely, the lack of a strong intrinsic magnetic field at Mars and Venus means that the solar wind has more direct access to their topside atmosphere, the
NASA Technical Reports Server (NTRS)
Sheeley, N. R., Jr.; Harvey, J. W.
1975-01-01
This paper presents particularly simple mathematical formulas for the calculation of force-free fields of constant alpha from the distribution of discrete sources on a flat surface. The advantage of these formulas lies in their physical simplicity and the fact that they can be easily used in practice to calculate the fields. The disadvantage is that they are limited to fields of 'sufficiently small alpha'. These formulas may be useful in the study of chromospheric magnetic fields by the comparison of high-resolution H-alpha photographs and photospheric magnetograms.
Muddana, Hari S; Gilson, Michael K
2012-05-01
We used the second-generation mining minima method (M2) to compute the binding affinities of the novel host-guest complexes in the SAMPL3 blind prediction challenge. The predictions were in poor agreement with experiment, and we conjectured that much of the error might derive from the force field, CHARMm with Vcharge charges. Repeating the calculations with other generalized force-fields led to no significant improvement, and we observed that the predicted affinities were highly sensitive to the choice of force-field. We therefore embarked on a systematic evaluation of a set of generalized force fields, based upon comparisons with PM6-DH2, a fast yet accurate semi-empirical quantum mechanics method. In particular, we compared gas-phase interaction energies and entropies for the host-guest complexes themselves, as well as for smaller chemical fragments derived from the same molecules. The mean deviations of the force field interaction energies from the quantum results were greater than 3 kcal/mol and 9 kcal/mol, for the fragments and host-guest systems respectively. We further evaluated the accuracy of force-fields for computing the vibrational entropies and found the mean errors to be greater than 4 kcal/mol. Given these errors in energy and entropy, it is not surprising in retrospect that the predicted binding affinities deviated from the experiment by several kcal/mol. These results emphasize the need for improvements in generalized force-fields and also highlight the importance of systematic evaluation of force-field parameters prior to evaluating different free-energy methods.
Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate.
Zhang, Changsheng; Lu, Chao; Wang, Qiantao; Ponder, Jay W; Ren, Pengyu
2015-11-10
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
Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate
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
Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate.
Zhang, Changsheng; Lu, Chao; Wang, Qiantao; Ponder, Jay W; Ren, Pengyu
2015-11-10
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.
A novel force field parameter optimization method based on LSSVR for ECEPP.
Liu, Yunling; Tao, Lan; Lu, Jianjun; Xu, Shuo; Ma, Qin; Duan, Qingling
2011-03-23
In this paper, we propose a novel force field parameter optimization method based on LSSVR and optimize the torsion energy parameters of ECEPP force field. In this method force field parameter optimization problem is turned into a support vector regression problem. Protein samples for regression model training are chosen from Protein Data Bank. The experiments show that the optimized force-field parameters make both α-helix and β-hairpin structures more consistent with the experimental implications than the original parameters.
The exterior source surface for force-free fields. [solar atmosphere magnetic field model
NASA Technical Reports Server (NTRS)
Barbosa, D. D.
1978-01-01
Consideration is given to the exterior source surface for force-free fields. The spherical harmonic expansion is presented for boundary values on two concentric spheres. An upper limit on a constant which measures the strength of coronal currents is found to be a function of the lowest multipole moment of the prescribed boundary values. The solar atmosphere is in the class of magnetic fields for which the study is applicable.
Validating empirical force fields for molecular-level simulation of cellulose dissolution
Technology Transfer Automated Retrieval System (TEKTRAN)
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...
Fu, Haohao; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng
2016-08-01
Proper use of the adaptive biasing force (ABF) algorithm in free-energy calculations needs certain prerequisites to be met, namely, that the Jacobian for the metric transformation and its first derivative be available and the coarse variables be independent and fully decoupled from any holonomic constraint or geometric restraint, thereby limiting singularly the field of application of the approach. The extended ABF (eABF) algorithm circumvents these intrinsic limitations by applying the time-dependent bias onto a fictitious particle coupled to the coarse variable of interest by means of a stiff spring. However, with the current implementation of eABF in the popular molecular dynamics engine NAMD, a trajectory-based post-treatment is necessary to derive the underlying free-energy change. Usually, such a posthoc analysis leads to a decrease in the reliability of the free-energy estimates due to the inevitable loss of information, as well as to a drop in efficiency, which stems from substantial read-write accesses to file systems. We have developed a user-friendly, on-the-fly code for performing eABF simulations within NAMD. In the present contribution, this code is probed in eight illustrative examples. The performance of the algorithm is compared with traditional ABF, on the one hand, and the original eABF implementation combined with a posthoc analysis, on the other hand. Our results indicate that the on-the-fly eABF algorithm (i) supplies the correct free-energy landscape in those critical cases where the coarse variables at play are coupled to either each other or to geometric restraints or holonomic constraints, (ii) greatly improves the reliability of the free-energy change, compared to the outcome of a posthoc analysis, and (iii) represents a negligible additional computational effort compared to regular ABF. Moreover, in the proposed implementation, guidelines for choosing two parameters of the eABF algorithm, namely the stiffness of the spring and the mass
Fu, Haohao; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng
2016-08-01
Proper use of the adaptive biasing force (ABF) algorithm in free-energy calculations needs certain prerequisites to be met, namely, that the Jacobian for the metric transformation and its first derivative be available and the coarse variables be independent and fully decoupled from any holonomic constraint or geometric restraint, thereby limiting singularly the field of application of the approach. The extended ABF (eABF) algorithm circumvents these intrinsic limitations by applying the time-dependent bias onto a fictitious particle coupled to the coarse variable of interest by means of a stiff spring. However, with the current implementation of eABF in the popular molecular dynamics engine NAMD, a trajectory-based post-treatment is necessary to derive the underlying free-energy change. Usually, such a posthoc analysis leads to a decrease in the reliability of the free-energy estimates due to the inevitable loss of information, as well as to a drop in efficiency, which stems from substantial read-write accesses to file systems. We have developed a user-friendly, on-the-fly code for performing eABF simulations within NAMD. In the present contribution, this code is probed in eight illustrative examples. The performance of the algorithm is compared with traditional ABF, on the one hand, and the original eABF implementation combined with a posthoc analysis, on the other hand. Our results indicate that the on-the-fly eABF algorithm (i) supplies the correct free-energy landscape in those critical cases where the coarse variables at play are coupled to either each other or to geometric restraints or holonomic constraints, (ii) greatly improves the reliability of the free-energy change, compared to the outcome of a posthoc analysis, and (iii) represents a negligible additional computational effort compared to regular ABF. Moreover, in the proposed implementation, guidelines for choosing two parameters of the eABF algorithm, namely the stiffness of the spring and the mass
Application of polarizable ellipsoidal force field model to pnicogen bonds.
Liu, Fang; Du, Likai; Gao, Jun; Wang, Lili; Song, Bo; Liu, Chengbu
2015-03-15
Noncovalent interactions, such as hydrogen bonds and halogen bonds, are frequently used in drug designing and crystal engineering. Recently, a novel noncovalent pnicogen bonds have been identified as an important driving force in crystal structures with similar bonding mechanisms as hydrogen bond and halogen bond. Although the pnicogen bond is highly anisotropic, the pnicogen bond angles range from 160° to 180° due to the complicated substituent effects. To understand the anisotropic characters of pnicogen bond, a modification of the polarizable ellipsoidal force field (PEff) model previously used to define halogen bonds was proposed in this work. The potential energy surfaces (PESs) of mono- and polysubstituted PH3 -NH3 complexes were calculated at CCSD(T), MP2, and density functional theory levels and were used to examine the modified PEff model. The results indicate that the modified PEff model can precisely characterize pnicogen bond. The root mean squared error of PES obtained with PEff model is less than 0.5 kcal/mol, compared with MP2 results. In addition, the modified PEff model may be applied to other noncovalent bond interactions, which is important to understand the role of intermolecular interactions in the self-assembly structures.
Molecular dynamics simulations of methane hydrate using polarizable force fields
Jiang, H.N.; Jordan, K.D.; Taylor, C.E.
2007-03-01
Molecular dynamics simulations of methane hydrate have been carried out using the AMOEBA and COS/G2 polarizable force fields. Properties examined 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 models are found to successfully account for the available experimental data, with overall slightly better agreement with experiment being found for the AMOEBA model. Several properties calculated using the AMOEBA and COS/G2 models differ appreciable from the corresponding results obtained previously using the polarizable TIP4P-FQ model. This appears to be due to the inadequacy of the treatment of polarization, especially, the restriction of polarization to in-plane only, in the TIP4P-FQ model.
Systematic procedure to parametrize force fields for molecular fluids.
Salas, Frank José; Méndez-Maldonado, G Arlette; Núñez-Rojas, Edgar; Aguilar-Pineda, Gabriel Eloy; Domínguez, Hector; Alejandre, José
2015-02-10
A new strategy to develop force fields for molecular fluids is presented. The intermolecular parameters are fitted to reproduce experimental values of target properties at ambient conditions and also the critical temperature. The partial charges are chosen to match the dielectric constant. The Lennard-Jones parameters, εii and σii, are fitted to reproduce the surface tension at the vapor-liquid interface and the liquid density, respectively. The choice of those properties allows obtaining systematically the final parameters using a small number of simulations. It is shown that the use of surface tension as a target property is better than the choice of heat of vaporization. The method is applied to molecules, from all atoms to a coarse-grained level, such as pyridine, dichloromethane, methanol, and 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF4) at different temperatures and pressures. The heat of vaporization, radial distribution functions, and self-diffusion coeficient are also calculated.
Derivation of a Molecular Mechanics Force Field for Cholesterol
Cournia, Zoe; Vaiana, Andrea C.; Smith, Jeremy C.; Ullmann, G. Matthias M.
2004-01-01
As a necessary step toward realistic cholesterol:biomembrane simulations, we have derived CHARMM molecular mechanics force-field parameters for cholesterol. For the parametrization we use an automated method that involves fitting the molecular mechanics potential to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. Results for another polycyclic molecule, rhodamine 6G, are also given. The usefulness of the method is thus demonstrated by the use of reference data from two molecules at different levels of theory. The frequency-matching plots for both cholesterol and rhodamine 6G show overall agreement between the CHARMM and quantum chemical normal modes, with frequency matching for both molecules within the error range found in previous benchmark studies.
On the Use of Quartic Force Fields in Variational Calculations
NASA Technical Reports Server (NTRS)
Fortenberry, Ryan C.; Huang, Xinchuan; Yachmenev, Andrey; Thiel, Walter; Lee, Timothy J.
2013-01-01
The use of quartic force fields (QFFs) has been shown to be one of the most effective ways to efficiently compute vibrational frequencies for small molecules. In this paper we outline and discuss how the simple-internal or bond-length bond-angle (BLBA) coordinates can be transformed into Morse-cosine(-sine) coordinates which produce potential energy surfaces from QFFs that possess proper limiting behavior and can effectively describe the vibrational (or rovibrational) energy levels of an arbitrary molecular system. We investigate parameter scaling in the Morse coordinate, symmetry considerations, and examples of transformed QFFs making use of the MULTIMODE, TROVE, and VTET variational vibrational methods. Cases are referenced where variational computations coupled with transformed QFFs produce accuracies compared to experiment for fundamental frequencies on the order of 5 cm(exp -1) and often as good as 1 cm(exp -1).
Accounting for electronic polarization in non-polarizable force fields.
Leontyev, Igor; Stuchebrukhov, Alexei
2011-02-21
The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER, GROMOS, etc should be scaled by a factor about 0.7. Our model explains why a neglect of electronic solvation energy, which typically amounts to about a half of total solvation energy, in non-polarizable simulations with un-scaled charges can produce a correct result; however, the correct solvation energy of ions does not guarantee the correctness of ion-ion pair interactions in many non-polarizable simulations. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force field simulations. The model also explains the striking difference between the value of water dipole μ∼ 3D reported in recent ab initio and experimental studies with the value μ(eff)∼ 2.3D typically used in the empirical potentials, such as TIP3P or SPC/E. It is shown that the effective dipole of water can be understood as a scaled value μ(eff) = μ/√ε(el), where ε(el) = 1.78 is the electronic (high-frequency) dielectric constant of water. This simple theoretical framework provides important insights into the nature of the effective parameters, which is crucial when the computational models of liquid water are used for simulations in different environments, such as proteins, or for interaction with solutes.
ForceFit: a code to fit classical force fields to ab-initio potential energy surfaces
Henson, Neil Jon; Waldher, Benjamin; Kuta, Jadwiga; Clark, Aurora; Clark, Aurora E
2009-01-01
The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under Unix and is written in C++, is an easy to use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program.
Lorentz force electrical impedance tomography using magnetic field measurements
NASA Astrophysics Data System (ADS)
Zengin, Reyhan; Güneri Gençer, Nevzat
2016-08-01
In this study, magnetic field measurement technique is investigated to image the electrical conductivity properties of biological tissues using Lorentz forces. This technique is based on electrical current induction using ultrasound together with an applied static magnetic field. The magnetic field intensity generated due to induced currents is measured using two coil configurations, namely, a rectangular loop coil and a novel xy coil pair. A time-varying voltage is picked-up and recorded while the acoustic wave propagates along its path. The forward problem of this imaging modality is defined as calculation of the pick-up voltages due to a given acoustic excitation and known body properties. Firstly, the feasibility of the proposed technique is investigated analytically. The basic field equations governing the behaviour of time-varying electromagnetic fields are presented. Secondly, the general formulation of the partial differential equations for the scalar and magnetic vector potentials are derived. To investigate the feasibility of this technique, numerical studies are conducted using a finite element method based software. To sense the pick-up voltages a novel coil configuration (xy coil pairs) is proposed. Two-dimensional numerical geometry with a 16-element linear phased array (LPA) ultrasonic transducer (1 MHz) and a conductive body (breast fat) with five tumorous tissues is modeled. The static magnetic field is assumed to be 4 Tesla. To understand the performance of the imaging system, the sensitivity matrix is analyzed. The sensitivity matrix is obtained for two different locations of LPA transducer with eleven steering angles from -{{25}\\circ} to {{25}\\circ} at intervals of {{5}\\circ} . The characteristics of the imaging system are shown with the singular value decomposition (SVD) of the sensitivity matrix. The images are reconstructed with the truncated SVD algorithm. The signal-to-noise ratio in measurements is assumed 80 dB. Simulation studies
Lorentz force electrical impedance tomography using magnetic field measurements.
Zengin, Reyhan; Gençer, Nevzat Güneri
2016-08-21
In this study, magnetic field measurement technique is investigated to image the electrical conductivity properties of biological tissues using Lorentz forces. This technique is based on electrical current induction using ultrasound together with an applied static magnetic field. The magnetic field intensity generated due to induced currents is measured using two coil configurations, namely, a rectangular loop coil and a novel xy coil pair. A time-varying voltage is picked-up and recorded while the acoustic wave propagates along its path. The forward problem of this imaging modality is defined as calculation of the pick-up voltages due to a given acoustic excitation and known body properties. Firstly, the feasibility of the proposed technique is investigated analytically. The basic field equations governing the behaviour of time-varying electromagnetic fields are presented. Secondly, the general formulation of the partial differential equations for the scalar and magnetic vector potentials are derived. To investigate the feasibility of this technique, numerical studies are conducted using a finite element method based software. To sense the pick-up voltages a novel coil configuration (xy coil pairs) is proposed. Two-dimensional numerical geometry with a 16-element linear phased array (LPA) ultrasonic transducer (1 MHz) and a conductive body (breast fat) with five tumorous tissues is modeled. The static magnetic field is assumed to be 4 Tesla. To understand the performance of the imaging system, the sensitivity matrix is analyzed. The sensitivity matrix is obtained for two different locations of LPA transducer with eleven steering angles from [Formula: see text] to [Formula: see text] at intervals of [Formula: see text]. The characteristics of the imaging system are shown with the singular value decomposition (SVD) of the sensitivity matrix. The images are reconstructed with the truncated SVD algorithm. The signal-to-noise ratio in measurements is assumed 80 d
Lorentz force electrical impedance tomography using magnetic field measurements.
Zengin, Reyhan; Gençer, Nevzat Güneri
2016-08-21
In this study, magnetic field measurement technique is investigated to image the electrical conductivity properties of biological tissues using Lorentz forces. This technique is based on electrical current induction using ultrasound together with an applied static magnetic field. The magnetic field intensity generated due to induced currents is measured using two coil configurations, namely, a rectangular loop coil and a novel xy coil pair. A time-varying voltage is picked-up and recorded while the acoustic wave propagates along its path. The forward problem of this imaging modality is defined as calculation of the pick-up voltages due to a given acoustic excitation and known body properties. Firstly, the feasibility of the proposed technique is investigated analytically. The basic field equations governing the behaviour of time-varying electromagnetic fields are presented. Secondly, the general formulation of the partial differential equations for the scalar and magnetic vector potentials are derived. To investigate the feasibility of this technique, numerical studies are conducted using a finite element method based software. To sense the pick-up voltages a novel coil configuration (xy coil pairs) is proposed. Two-dimensional numerical geometry with a 16-element linear phased array (LPA) ultrasonic transducer (1 MHz) and a conductive body (breast fat) with five tumorous tissues is modeled. The static magnetic field is assumed to be 4 Tesla. To understand the performance of the imaging system, the sensitivity matrix is analyzed. The sensitivity matrix is obtained for two different locations of LPA transducer with eleven steering angles from [Formula: see text] to [Formula: see text] at intervals of [Formula: see text]. The characteristics of the imaging system are shown with the singular value decomposition (SVD) of the sensitivity matrix. The images are reconstructed with the truncated SVD algorithm. The signal-to-noise ratio in measurements is assumed 80 d
Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding.
Huang, Wei; Lin, Zhixiong; van Gunsteren, Wilfred F
2011-05-10
The recently developed GROMOS 54A7 force field, a modification of the 53A6 force field, is validated by simulating the folding equilibrium of two β-peptides which show different dominant folds, i.e., a 314-helix and a hairpin, using three different force fields, i.e., GROMOS 45A3, 53A6, and 54A7. The 54A7 force field stabilizes both folds, and the agreement of the simulated NOE atom-atom distances with the experimental NMR data is slightly improved when using the 54A7 force field, while the agreement of the (3)J couplings with experimental results remains essentially unchanged when varying the force field. The 54A7 force field developed to improve the stability of α-helical structures in proteins can thus be safely used in simulations of β-peptides. PMID:26610119
Perspectives on the simulation of protein–surface interactions using empirical force field methods
Latour, Robert A.
2014-01-01
Protein–surface interactions are of fundamental importance for a broad range of applications in the fields of biomaterials and biotechnology. Present experimental methods are limited in their ability to provide a comprehensive depiction of these interactions at the atomistic level. In contrast, empirical force field based simulation methods inherently provide the ability to predict and visualize protein–surface interactions with full atomistic detail. These methods, however, must be carefully developed, validated, and properly applied before confidence can be placed in results from the simulations. In this perspectives paper, I provide an overview of the critical aspects that I consider being of greatest importance for the development of these methods, with a focus on the research that my combined experimental and molecular simulation groups have conducted over the past decade to address these issues. These critical issues include the tuning of interfacial force field parameters to accurately represent the thermodynamics of interfacial behavior, adequate sampling of these types of complex molecular systems to generate results that can be comparable with experimental data, and the generation of experimental data that can be used for simulation results evaluation and validation. PMID:25028242
Nonlinear Force-Free Magnetic Field Modeling of the Solar Corona: A Critical Assessment
NASA Astrophysics Data System (ADS)
De Rosa, M. L.; Schrijver, C. J.; Barnes, G.; Leka, K. D.; Lites, B. W.; Aschwanden, M. J.; McTiernan, J. M.; Régnier, S.; Thalmann, J.; Valori, G.; Wheatland, M. S.; Wiegelmann, T.; Cheung, M.; Conlon, P. A.; Fuhrmann, M.; Inhester, B.; Tadesse, T.
2008-12-01
Nonlinear force-free field (NLFFF) modeling promises to provide accurate representations of the structure of the magnetic field above solar active regions, from which estimates of physical quantities of interest (e.g., free energy and helicity) can be made. However, the suite of NLFFF algorithms have so far failed to arrive at consistent solutions when applied to cases using the highest-available-resolution vector magnetogram data from Hinode/SOT-SP (in the region of the modeling area of interest) and line-of-sight magnetograms from SOHO/MDI (where vector data were not been available). It is our view that the lack of robust results indicates an endemic problem with the NLFFF modeling process, and that this process will likely continue to fail until (1) more of the far-reaching, current-carrying connections are within the observational field of view, (2) the solution algorithms incorporate the measurement uncertainties in the vector magnetogram data, and/or (3) a better way is found to account for the Lorentz forces within the layer between the photosphere and coronal base. In light of these issues, we conclude that it remains difficult to derive useful and significant estimates of physical quantities from NLFFF models.
Clinical use of diodes and micro-chambers to obtain accurate small field output factor measurements.
Kairn, T; Charles, P H; Cranmer-Sargison, G; Crowe, S B; Langton, C M; Thwaites, D I; Trapp, J V
2015-06-01
There have been substantial advances in small field dosimetry techniques and technologies, over the last decade, which have dramatically improved the achievable accuracy of small field dose measurements. This educational note aims to help radiation oncology medical physicists to apply some of these advances in clinical practice. The evaluation of a set of small field output factors (total scatter factors) is used to exemplify a detailed measurement and simulation procedure and as a basis for discussing the possible effects of simplifying that procedure. Field output factors were measured with an unshielded diode and a micro-ionisation chamber, at the centre of a set of square fields defined by a micro-multileaf collimator. Nominal field sizes investigated ranged from 6 × 6 to 98 × 98 mm(2). Diode measurements in fields smaller than 30 mm across were corrected using response factors calculated using Monte Carlo simulations of the diode geometry and daisy-chained to match micro-chamber measurements at intermediate field sizes. Diode measurements in fields smaller than 15 mm across were repeated twelve times over three separate measurement sessions, to evaluate the reproducibility of the radiation field size and its correspondence with the nominal field size. The five readings that contributed to each measurement on each day varied by up to 0.26 %, for the "very small" fields smaller than 15 mm, and 0.18 % for the fields larger than 15 mm. The diode response factors calculated for the unshielded diode agreed with previously published results, within uncertainties. The measured dimensions of the very small fields differed by up to 0.3 mm, across the different measurement sessions, contributing an uncertainty of up to 1.2 % to the very small field output factors. The overall uncertainties in the field output factors were 1.8 % for the very small fields and 1.1 % for the fields larger than 15 mm across. Recommended steps for acquiring small field output
NASA Astrophysics Data System (ADS)
Yao, B. A.; Zhang, C. S.; Sheng, C. J.; Peng, Y. L.
2005-07-01
This paper is the continuation of paper [1]. In this paper we further show that the difference between twilight flat field and night sky exposure is mainly due to the existence of scattered light. Like Grundahl and Sorensen, we also made the pinhole images of the 1.56m at the Shanghai Observatory and the 63cm of the Nanjing University to show the existence of scattered light intuitively. Both the 1.56m and the 63cm reflectors have normal designed baffles. Therefore it is the common weakness of all standard designed reflectors having only two baffles mounted in front of the primary and secondary mirrors which are not enough to protect the CCD cameras from scattered light in getting accurate flat fields. It is of great importance to modify the primary mirror baffle of all similar reflectors in order to get more accurate flat fielding.
Addou, Touria; Krouchev, Nedialko I; Kalaska, John F
2015-01-15
To elucidate how primary motor cortex (M1) neurons contribute to the performance of a broad range of different and even incompatible motor skills, we trained two monkeys to perform single-degree-of-freedom elbow flexion/extension movements that could be perturbed by a variety of externally generated force fields. Fields were presented in a pseudorandom sequence of trial blocks. Different computer monitor background colors signaled the nature of the force field throughout each block. There were five different force fields: null field without perturbing torque, assistive and resistive viscous fields proportional to velocity, a resistive elastic force field proportional to position and a resistive viscoelastic field that was the linear combination of the resistive viscous and elastic force fields. After the monkeys were extensively trained in the five field conditions, neural recordings were subsequently made in M1 contralateral to the trained arm. Many caudal M1 neurons altered their activity systematically across most or all of the force fields in a manner that was appropriate to contribute to the compensation for each of the fields. The net activity of the entire sample population likewise provided a predictive signal about the differences in the time course of the external forces encountered during the movements across all force conditions. The neurons showed a broad range of sensitivities to the different fields, and there was little evidence of a modular structure by which subsets of M1 neurons were preferentially activated during movements in specific fields or combinations of fields.
Linear force-free magnetic fields for solar extrapolation and interpretation
NASA Technical Reports Server (NTRS)
Gary, G. Allen
1989-01-01
This paper discusses the interconnection of the various linear force-free magnetic field formulations, the specific phenomenological and topological parameters of these formulations, and their usefulness. Particularly, the limitations and usefulness of linear force-free fields are discussed. Specific field configurations are related to magnetographic interpretation. The relationship of the integral and Fourier procedures is shown explicitly. The physical interpretation of linear force-free fields is shown by analytic models and from the Marshall Space Flight Center solar vector magnetograms.
A coarse-grain force field for RDX: Density dependent and energy conserving.
Moore, Joshua D; Barnes, Brian C; Izvekov, Sergei; Lísal, Martin; Sellers, Michael S; Taylor, DeCarlos E; Brennan, John K
2016-03-14
We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions. PMID:26979691
Force Field Independent Metal Parameters Using a Nonbonded Dummy Model
2014-01-01
The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce both M2+–O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase I as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers. PMID:24670003
A reactive force field for aqueous-calcium carbonate systems.
Gale, Julian D; Raiteri, Paolo; van Duin, Adri C T
2011-10-01
A new reactive force field has been derived that allows the modelling of speciation in the aqueous-calcium carbonate system. Using the ReaxFF methodology, which has now been implemented in the program GULP, calcium has been simulated as a fixed charge di-cation species in both crystalline phases, such as calcite and aragonite, as well as in the solution phase. Excluding calcium from the charge equilibration process appears to have no adverse effects for the simulation of species relevant to the aqueous environment. Based on this model, the speciation of carbonic acid, bicarbonate and carbonate have been examined in microsolvated conditions, as well as bulk water. When immersed in a droplet of 98 water molecules and two hydronium ions, the carbonate ion is rapidly converted to bicarbonate, and ultimately carbonic acid, which is formed as the metastable cis-trans isomer under kinetic control. Both first principles and ReaxFF calculations exhibit the same behaviour, but the longer timescale accessible to the latter allows the diffusion of the carbonic acid to the surface of the water to be observed, where it is more stable at the interface. Calcium carbonate is also examined as ion pairs in solution for both CaCO(3)(0)((aq)) and CaHCO(3)(+)((aq)), in addition to the (1014) surface in contact with water. PMID:21850319
Force Fields for Carbohydrate-Divalent Cation Interactions.
Chen, Hsieh; Cox, Jason R; Panagiotopoulos, Athanassios Z
2016-06-16
We report molecular dynamics simulations to study intermolecular interactions for carbohydrate-divalent cation complexes. We observed that common force fields from literature with standard Lorentz-Berthelot combining rules are unable to reproduce the experimental stability constants for model carbohydrate monomer (α-d-Allopyranose) and alkali earth metal cation (Mg(2+), Ca(2+), Sr(2+), or Ba(2+)) complexes. A modified combining rule with rescaled effective cross-interaction radius between cations and the hydroxyl oxygens on the carbohydrates was introduced to reproduce the experimental stability constants, which the preferential carbohydrate-cation complexing structures through the ax-eq-ax sequence of O-1, O-2, and O-3 on α-d-Allopyranose were also observed. The effective radius scaling factor obtained from (α-d-Allopyranose)-Ca(2+) complexes was directly transferrable to the similar six-membered ring (α-d-Ribopyranose)-Ca(2+) complexes; however, reparameterization for the scaling factor may be necessary for the five-membered ring (α-d-Ribofuranose)-Ca(2+) complexes. PMID:27210229
The stability properties of cylindrical force-free fields - Effect of an external potential field
NASA Technical Reports Server (NTRS)
Chiuderi, C.; Einaudi, G.; Ma, S. S.; Van Hoven, G.
1980-01-01
A large-scale potential field with an embedded smaller-scale force-free structure gradient x B equals alpha B is studied in cylindrical geometry. Cases in which alpha goes continuously from a constant value alpha 0 on the axis to zero at large r are considered. Such a choice of alpha (r) produces fields which are realistic (few field reversals) but not completely stable. The MHD-unstable wavenumber regime is found. Since the considered equilibrium field exhibits a certain amount of magnetic shear, resistive instabilities can arise. The growth rates of the tearing mode in the limited MHD-stable region of k space are calculated, showing time-scales much shorter than the resistive decay time.
An accurate magnetic field solution for medical electromagnetic tracking coils at close range
NASA Astrophysics Data System (ADS)
Schroeder, Tobias
2015-06-01
Electromagnetic tracking uses transmitter field models to determine position and orientation of an object. An important application of this technology is surgical navigation, where instruments are frequently tracked at short distances from the transmitter. At short distances, conventional and widely used dipole field models can lead to errors in tracked position and orientation. To increase tracking accuracy in this scenario, this work describes a novel transmitter field model and compares its performance against the dipole model. Demonstrated tracking accuracy improvements could have far-reaching benefits for medical navigation applications.
Theis, Riley A; Fortenberry, Ryan C
2015-05-21
The argonium cation, ArH(+), has been previously detected in nature for the first time. This cation is believed to form through the gas-phase reaction of Ar(+) and H2. In this work, quantum chemical techniques show that the reaction of Ar and H3(+) may be a viable alternative or contributor to the creation of ArH(+) corroborating previous analysis. In order to further evaluate this claim, highly accurate quartic force field computations are used to produce spectroscopic data and anharmonic vibrational frequencies for ArH3(+) in its 18 isotopologues. NeH3(+) is also analyzed but has a low Ne-H3(+) dissociation barrier. Therefore, it less likely to be observed. Consequently, NeH(+) is also unlikely to be formed from NeH3(+) as it was also not from NeH2(+). PMID:25923978
Theis, Riley A; Fortenberry, Ryan C
2015-05-21
The argonium cation, ArH(+), has been previously detected in nature for the first time. This cation is believed to form through the gas-phase reaction of Ar(+) and H2. In this work, quantum chemical techniques show that the reaction of Ar and H3(+) may be a viable alternative or contributor to the creation of ArH(+) corroborating previous analysis. In order to further evaluate this claim, highly accurate quartic force field computations are used to produce spectroscopic data and anharmonic vibrational frequencies for ArH3(+) in its 18 isotopologues. NeH3(+) is also analyzed but has a low Ne-H3(+) dissociation barrier. Therefore, it less likely to be observed. Consequently, NeH(+) is also unlikely to be formed from NeH3(+) as it was also not from NeH2(+).
Evaluation of Representations and Response Models for Polarizable Force Fields
2016-01-01
For classical simulations of condensed-phase systems, such as organic liquids and biomolecules, to achieve high accuracy, they will probably need to incorporate an accurate, efficient model of conformation-dependent electronic polarization. Thus, it is of interest to understand what determines the accuracy of a polarizable electrostatics model. This study approaches this problem by breaking polarization models down into two main components: the representation of electronic polarization and the response model used for mapping from an inducing field to the polarization within the chosen representation. Among the most common polarization representations are redistribution of atom-centered charges, such as those used in the fluctuating charge model, and atom-centered point dipoles, such as those used in a number of different polarization models. Each of these representations has been combined with one or more response models. The response model of fluctuating charge, for example, is based on the idea of electronegativity equalization in the context of changing electrostatic potentials (ESPs), whereas point-dipole representations typically use a response model based on point polarizabilities whose induced dipoles are computed based on interaction with other charges and dipoles. Here, we decouple polarization representations from their typical response models to analyze the strengths and weaknesses of various polarization approximations. First, we compare the maximal possible accuracies achievable by the charge redistribution and point-dipole model representations, by testing their ability to replicate quantum mechanical (QM) ESPs around small molecules polarized by external inducing charges. Perhaps not surprisingly, the atom-centered dipole model can yield higher accuracy. Next, we test two of the most commonly used response functions used for the point-dipole representations, self-consistent and direct (or first-order) inducible point polarizabilities, where the
NONLINEAR FORCE-FREE MAGNETIC FIELD FITTING TO CORONAL LOOPS WITH AND WITHOUT STEREOSCOPY
Aschwanden, Markus J.
2013-02-15
We developed a new nonlinear force-free magnetic field (NLFFF) forward-fitting algorithm based on an analytical approximation of force-free and divergence-free NLFFF solutions, which requires as input a line-of-sight magnetogram and traced two-dimensional (2D) loop coordinates of coronal loops only, in contrast to stereoscopically triangulated three-dimensional loop coordinates used in previous studies. Test results of simulated magnetic configurations and from four active regions observed with STEREO demonstrate that NLFFF solutions can be fitted with equal accuracy with or without stereoscopy, which relinquishes the necessity of STEREO data for magnetic modeling of active regions (on the solar disk). The 2D loop tracing method achieves a 2D misalignment of {mu}{sub 2} = 2. Degree-Sign 7 {+-} 1. Degree-Sign 3 between the model field lines and observed loops, and an accuracy of Almost-Equal-To 1.0% for the magnetic energy or free magnetic energy ratio. The three times higher spatial resolution of TRACE or SDO/AIA (compared with STEREO) also yields a proportionally smaller misalignment angle between model fit and observations. Visual/manual loop tracings are found to produce more accurate magnetic model fits than automated tracing algorithms. The computation time of the new forward-fitting code amounts to a few minutes per active region.
Performance of Protein-Ligand Force Fields for the Flavodoxin-Flavin Mononucleotide System.
Robertson, Michael J; Tirado-Rives, Julian; Jorgensen, William L
2016-08-01
The ability to accurately perform molecular dynamics and free energy perturbation calculations for protein-ligand systems is of broad interest to the biophysical and pharmaceutical sciences. In this work, several popular force fields are evaluated for reproducing experimental properties of the flavodoxin/flavin mononucleotide system. Calculated (3)J couplings from molecular dynamics simulations probing φ and χ1 dihedral angles are compared to over 1000 experimental measurements. Free energy perturbation calculations were also executed between different protein mutants for comparison with experimental data for relative free energies of binding. Newer versions of popular protein force fields reproduced (3)J backbone and side chain couplings with good accuracy, with RMSD values near or below one hertz in most cases. OPLS-AA/M paired with CM5 charges for the ligand performed particularly well, both for the (3)J couplings and FEP results, with a mean unsigned error for relative free energies of binding of 0.36 kcal/mol. PMID:27441982
Forced Field Extrapolation of the Magnetic Structure of the Hα fibrils in the Solar Chromosphere
NASA Astrophysics Data System (ADS)
Xiaoshuai, Zhu; Huaning, Wang; Zhanle, Du; Han, He
2016-07-01
We present a careful assessment of forced field extrapolation using the Solar Dynamics Observatory/Helioseismic and Magnetic Imager magnetogram. We use several metrics to check the convergence property. The extrapolated field lines below 3600 km appear to be aligned with most of the Hα fibrils observed by the New Vacuum Solar Telescope. In the region where magnetic energy is far larger than potential energy, the field lines computed by forced field extrapolation are still consistent with the patterns of Hα fibrils while the nonlinear force-free field results show a large misalignment. The horizontal average of the lorentz force ratio shows that the forced region where the force-free assumption fails can reach heights of 1400-1800 km. The non-force-free state of the chromosphere is also confirmed based on recent radiation magnetohydrodynamics simulations.
Forced Field Extrapolation of the Magnetic Structure of the Hα fibrils in the Solar Chromosphere
NASA Astrophysics Data System (ADS)
Xiaoshuai, Zhu; Huaning, Wang; Zhanle, Du; Han, He
2016-07-01
We present a careful assessment of forced field extrapolation using the Solar Dynamics Observatory/Helioseismic and Magnetic Imager magnetogram. We use several metrics to check the convergence property. The extrapolated field lines below 3600 km appear to be aligned with most of the Hα fibrils observed by the New Vacuum Solar Telescope. In the region where magnetic energy is far larger than potential energy, the field lines computed by forced field extrapolation are still consistent with the patterns of Hα fibrils while the nonlinear force-free field results show a large misalignment. The horizontal average of the lorentz force ratio shows that the forced region where the force-free assumption fails can reach heights of 1400–1800 km. The non-force-free state of the chromosphere is also confirmed based on recent radiation magnetohydrodynamics simulations.
Comparison of Methods to Obtain Force-Field Parameters for Metal Sites.
Hu, LiHong; Ryde, Ulf
2011-08-01
We have critically examined and compared various ways to obtain standard harmonic molecular mechanics (MM) force-field parameters for metal sites in proteins, using the 12 most common Zn(2+) sites as test cases. We show that the parametrization of metal sites is hard to treat with automatic methods. The choice of method is a compromise between speed and accuracy and therefore depends on the intended use of the parameters. If the metal site is not of central interest in the investigation, for example, a structural metal far from the active site, a simple and fast parametrization is normally enough, using either a nonbonded model with restraints or a bonded parametrization based on the method of Seminario. On the other hand, if the metal site is of central interest in the investigation, a more accurate method is needed to give quantitative results, for example, the method by Norrby and Liljefors. The former methods are semiautomatic and can be performed in seconds, once a quantum mechanical (QM) geometry optimization and frequency calculation has been performed, whereas the latter method typically takes several days and requires significant human intervention. All approaches require a careful selection of the atom types used. For a nonbonded model, standard atom types can be used, whereas for a bonded model, it is normally wise to use special atom types for each metal ligand. For accurate results, new atom types for all atoms in the metal site can be used. Atomic charges should also be considered. Typically, QM restrained electrostatic potential charges are accurate and easy to obtain once the QM calculation is performed, and they allow for charge transfer within the complex. For negatively charged complexes, it should be checked that hydrogen atoms of the ligands get proper charges. Finally, water ligands pose severe problems for bonded models in force fields that ignore nonbonded interactions for atoms separated by two bonds. Complexes with a single water ligand
Time-accurate Navier-Stokes computations of classical two-dimensional edge tone flow fields
NASA Technical Reports Server (NTRS)
Liu, B. L.; O'Farrell, J. M.; Jones, Jess H.
1990-01-01
Time-accurate Navier-Stokes computations were performed to study a Class II (acoustic) whistle, the edge tone, and gain knowledge of the vortex-acoustic coupling mechanisms driving production of these tones. Results were obtained by solving the full Navier-Stokes equations for laminar compressible air flow of a two-dimensional jet issuing from a slit interacting with a wedge. Cases considered were determined by varying the distance from the slit to the edge. Flow speed was kept constant at 1750 cm/sec as was the slit thickness of 0.1 cm, corresponding to conditions in the experiments of Brown. Excellent agreement was obtained in all four edge tone stage cases between the present computational results and the experimentally obtained results of Brown. Specific edge tone generated phenomena and further confirmation of certain theories concerning these phenomena were brought to light in this analytical simulation of edge tones.
NASA Astrophysics Data System (ADS)
Chen, Jingyi; Zebker, Howard A.; Knight, Rosemary
2015-11-01
Interferometric synthetic aperture radar (InSAR) is a radar remote sensing technique for measuring surface deformation to millimeter-level accuracy at meter-scale resolution. Obtaining accurate deformation measurements in agricultural regions is difficult because the signal is often decorrelated due to vegetation growth. We present here a new algorithm for retrieving InSAR deformation measurements over areas with severe vegetation decorrelation using adaptive phase interpolation between persistent scatterer (PS) pixels, those points at which surface scattering properties do not change much over time and thus decorrelation artifacts are minimal. We apply this algorithm to L-band ALOS interferograms acquired over the San Luis Valley, Colorado, and the Tulare Basin, California. In both areas, the pumping of groundwater for irrigation results in deformation of the land that can be detected using InSAR. We show that the PS-based algorithm can significantly reduce the artifacts due to vegetation decorrelation while preserving the deformation signature.
Power counting for nuclear forces in chiral effective field theory
NASA Astrophysics Data System (ADS)
Long, Bingwei
2016-02-01
The present note summarizes the discourse on power counting issues of chiral nuclear forces, with an emphasis on renormalization-group invariance. Given its introductory nature, I will lean toward narrating a coherent point of view on the concepts, rather than covering comprehensively the development of chiral nuclear forces in different approaches.
ERIC Educational Resources Information Center
Gamble, Reed
1989-01-01
Discusses pupil misconceptions concerning forces. Summarizes some of Assessment of Performance Unit's findings on meaning of (1) force, (2) force and motion in one dimension and two dimensions, and (3) Newton's second law. (YP)
An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution
Fluitt, Aaron M.; de Pablo, Juan J.
2015-09-01
Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.
An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution
Fluitt, Aaron M.; de Pablo, Juan J.
2015-01-01
Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB∗, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation. PMID:26331258
Skelton, Adam; Fenter, Paul; Kubicki, James D.; Wesolowski, David J; Cummings, Peter T
2011-01-01
Classical molecular dynamics (CMD) simulations of the (1011) surface of quartz interacting with bulk liquid water are performed using three different classical force fields, Lopes et al., ClayFF, and CHARMM water contact angle (CWCA), and compared to ab initio molecular dynamics (AIMD) and X-ray reflectivity (XR) results. The axial densities of the water and surface atoms normal to the surface are calculated and compared to previous XR experiments. Favorable agreement is shown for all the force fields with respect to the position of the water atoms. Analyses such as the radial distribution functions between water and hydroxyl atoms and the average cosine of the angle between the water dipole vector and the normal of the surface are also calculated for each force field. Significant differences are found between the different force fields from such analyses, indicating differing descriptions of the structured water in the near vicinity of the surface. AIMD simulations are also performed to obtain the water and hydroxyl structure for comparison among the predictions of the three classical force fields to better understand which force field is most accurate. It is shown that ClayFF exhibits the best agreement with the AIMD simulations for water hydroxyl radial distribution functions, suggesting that ClayFF treats the hydrogen bonding more accurately.
Kutateladze, Andrei G; Mukhina, Olga A
2014-09-01
Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min.
Kutateladze, Andrei G; Mukhina, Olga A
2014-09-01
Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min. PMID:25158224
AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins.
Santos-Martins, Diogo; Forli, Stefano; Ramos, Maria João; Olson, Arthur J
2014-08-25
Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer's disease. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc ion. Thus, accurate prediction of the interaction of ligands with zinc is an important aspect of computational docking and virtual screening against zinc containing proteins. We have extended the AutoDock force field to include a specialized potential describing the interactions of zinc-coordinating ligands. This potential describes both the energetic and geometric components of the interaction. The new force field, named AutoDock4Zn, was calibrated on a data set of 292 crystal complexes containing zinc. Redocking experiments show that the force field provides significant improvement in performance in both free energy of binding estimation as well as in root-mean-square deviation from the crystal structure pose. The new force field has been implemented in AutoDock without modification to the source code.
NASA Astrophysics Data System (ADS)
Moučka, Filip; Nezbeda, Ivo; Smith, William R.
2013-04-01
Thirteen of the most common aqueous NaCl solution force fields based on the SPC/E water solvent are examined with respect to their prediction at ambient conditions of the concentration dependence of the total electrolyte chemical potential and the solution density. We also calculate the salt solubility and the chemical potential and density of the NaCl crystalline solid. We obtain the solution chemical potential in a computationally efficient manner using our recently developed Osmotic Ensemble Monte Carlo method [F. Moučka, M. Lísal, and W. R. Smith, J. Phys. Chem. B 116, 5468 (2012), 10.1021/jp301447z]. We find that the results of the force fields considered are scattered over a wide range of values, and none is capable of producing quantitatively accurate results over the entire concentration range, with only two of them deemed to be acceptable. Our results indicate that several force fields exhibit precipitation at concentrations below the experimental solubility limit, thus limiting their usefulness. This has important implications, both in general and for their use in biomolecular simulations carried out in the presence of counter-ions. We conclude that either different parameter fitting techniques taking high-concentration properties into account must be used when determining force field model parameters, or that the class of models considered here is intrinsically incapable of the task and more sophisticated mathematical forms must be used.
Huang, Lei; Roux, Benoît
2013-08-13
Classical molecular dynamics (MD) simulations based on atomistic models are increasingly used to study a wide range of biological systems. A prerequisite for meaningful results from such simulations is an accurate molecular mechanical force field. Most biomolecular simulations are currently based on the widely used AMBER and CHARMM force fields, which were parameterized and optimized to cover a small set of basic compounds corresponding to the natural amino acids and nucleic acid bases. Atomic models of additional compounds are commonly generated by analogy to the parameter set of a given force field. While this procedure yields models that are internally consistent, the accuracy of the resulting models can be limited. In this work, we propose a method, General Automated Atomic Model Parameterization (GAAMP), for generating automatically the parameters of atomic models of small molecules using the results from ab initio quantum mechanical (QM) calculations as target data. Force fields that were previously developed for a wide range of model compounds serve as initial guess, although any of the final parameter can be optimized. The electrostatic parameters (partial charges, polarizabilities and shielding) are optimized on the basis of QM electrostatic potential (ESP) and, if applicable, the interaction energies between the compound and water molecules. The soft dihedrals are automatically identified and parameterized by targeting QM dihedral scans as well as the energies of stable conformers. To validate the approach, the solvation free energy is calculated for more than 200 small molecules and MD simulations of 3 different proteins are carried out.
Moučka, Filip; Nezbeda, Ivo; Smith, William R
2013-04-21
Thirteen of the most common aqueous NaCl solution force fields based on the SPC/E water solvent are examined with respect to their prediction at ambient conditions of the concentration dependence of the total electrolyte chemical potential and the solution density. We also calculate the salt solubility and the chemical potential and density of the NaCl crystalline solid. We obtain the solution chemical potential in a computationally efficient manner using our recently developed Osmotic Ensemble Monte Carlo method [F. Moučka, M. Lísal, and W. R. Smith, J. Phys. Chem. B 116, 5468 (2012)]. We find that the results of the force fields considered are scattered over a wide range of values, and none is capable of producing quantitatively accurate results over the entire concentration range, with only two of them deemed to be acceptable. Our results indicate that several force fields exhibit precipitation at concentrations below the experimental solubility limit, thus limiting their usefulness. This has important implications, both in general and for their use in biomolecular simulations carried out in the presence of counter-ions. We conclude that either different parameter fitting techniques taking high-concentration properties into account must be used when determining force field model parameters, or that the class of models considered here is intrinsically incapable of the task and more sophisticated mathematical forms must be used.
Accurate field mapping in the presence of B0 inhomogeneities, applied to MR thermometry
Mei, Chang-Sheng; Chu, Renxin; Hoge, W. Scott; Panych, Lawrence P.; Madore, Bruno
2014-01-01
Purpose To describe how B0 inhomogeneities can cause errors in proton resonance frequency (PRF) shift thermometry, and to correct for these errors. Methods With PRF thermometry, measured phase shifts are converted into temperature measurements through the use of a scaling factor proportional to the echo time, TE. However, B0 inhomogeneities can deform, spread, and translate MR echoes, potentially making the ‘true’ echo time vary spatially within the imaged object and take on values that differ from the prescribed TE value. Acquisition and reconstruction methods able to avoid or correct for such errors are presented. Results Tests were performed in a gel phantom during sonication, and temperature measurements were made with proper shimming as well as with intentionally-introduced B0 inhomogeneities. Errors caused by B0 inhomogeneities were observed, described, and corrected by the proposed methods. No statistical difference was found between the corrected results and the reference results obtained with proper shimming, while errors by more than 10% in temperature elevation were corrected for. The approach was also applied to an abdominal in vivo dataset. Conclusion Field variations induce errors in measured field values, which can be detected and corrected. The approach was validated for a PRF thermometry application. PMID:24975329
De Hatten, Xavier; Cournia, Zoe; Smith, Jeremy C; Metzler-Nolte, Nils
2007-08-01
The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1{prime}-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1{micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline{prime}-1-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.
De Hatten, Xavier; Cournia, Zoe; Smith, Jeremy C; Huc, I; Metzler-Nolte, Nils
2007-08-01
The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C{sub 2}-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 {micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 {micro}s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.
Shim, Jihyun; MacKerell, Alexander D.
2011-01-01
A significant number of drug discovery efforts are based on natural products or high throughput screens from which compounds showing potential therapeutic effects are identified without knowledge of the target molecule or its 3D structure. In such cases computational ligand-based drug design (LBDD) can accelerate the drug discovery processes. LBDD is a general approach to elucidate the relationship of a compound's structure and physicochemical attributes to its biological activity. The resulting structure-activity relationship (SAR) may then act as the basis for the prediction of compounds with improved biological attributes. LBDD methods range from pharmacophore models identifying essential features of ligands responsible for their activity, quantitative structure-activity relationships (QSAR) yielding quantitative estimates of activities based on physiochemical properties, and to similarity searching, which explores compounds with similar properties as well as various combinations of the above. A number of recent LBDD approaches involve the use of multiple conformations of the ligands being studied. One of the basic components to generate multiple conformations in LBDD is molecular mechanics (MM), which apply an empirical energy function to relate conformation to energies and forces. The collection of conformations for ligands is then combined with functional data using methods ranging from regression analysis to neural networks, from which the SAR is determined. Accordingly, for effective application of LBDD for SAR determinations it is important that the compounds be accurately modelled such that the appropriate range of conformations accessible to the ligands is identified. Such accurate modelling is largely based on use of the appropriate empirical force field for the molecules being investigated and the approaches used to generate the conformations. The present chapter includes a brief overview of currently used SAR methods in LBDD followed by a more
Grimme, Stefan
2014-10-14
A black-box type procedure is presented for the generation of molecule-specific, classical potential energy functions (force-field, FF) solely from quantum mechanically (QM) computed input data. The approach can treat covalently bound molecules and noncovalent complexes with almost arbitrary structure. The necessary QM information consists of the equilibrium structure and the corresponding Hessian matrix, atomic partial charges, and covalent bond orders. The FF fit is performed automatically without any further input and yields a specific (nontransferable) potential which very closely resembles the QM reference potential near the equilibrium. The resulting atomistic, fully flexible FF is anharmonic and allows smooth dissociation of covalent bonds into atoms. A newly proposed force-constant-bond-energy relation with little empiricism provides reasonably accurate (about 5-10% error) atomization energies for almost arbitrary diatomic and polyatomic molecules. Intra- and intermolecular noncovalent interactions are treated by using well established and accurate D3 dispersion coefficients, CM5 charges from small basis set QM calculations, and a new interatomic repulsion potential. Particular attention has been paid to the construction of the torsion potentials which are partially obtained from automatic QM-tight-binding calculations for model systems. Detailed benchmarks are presented for conformational energies, atomization energies, vibrational frequencies, gas phase structures of organic molecules, and transition metal complexes. Comparisons to results from standard FF or semiempirical methods reveal very good accuracy of the new potential. While further studies are necessary to validate the approach, the initial results suggest QMDFF as a routine tool for the computation of a wide range of properties and systems (e.g., for molecular dynamics of isolated molecules, explicit solvation, self-solvation (melting) or even for molecular crystals) in particular when standard
Grimme, Stefan
2014-10-14
A black-box type procedure is presented for the generation of molecule-specific, classical potential energy functions (force-field, FF) solely from quantum mechanically (QM) computed input data. The approach can treat covalently bound molecules and noncovalent complexes with almost arbitrary structure. The necessary QM information consists of the equilibrium structure and the corresponding Hessian matrix, atomic partial charges, and covalent bond orders. The FF fit is performed automatically without any further input and yields a specific (nontransferable) potential which very closely resembles the QM reference potential near the equilibrium. The resulting atomistic, fully flexible FF is anharmonic and allows smooth dissociation of covalent bonds into atoms. A newly proposed force-constant-bond-energy relation with little empiricism provides reasonably accurate (about 5-10% error) atomization energies for almost arbitrary diatomic and polyatomic molecules. Intra- and intermolecular noncovalent interactions are treated by using well established and accurate D3 dispersion coefficients, CM5 charges from small basis set QM calculations, and a new interatomic repulsion potential. Particular attention has been paid to the construction of the torsion potentials which are partially obtained from automatic QM-tight-binding calculations for model systems. Detailed benchmarks are presented for conformational energies, atomization energies, vibrational frequencies, gas phase structures of organic molecules, and transition metal complexes. Comparisons to results from standard FF or semiempirical methods reveal very good accuracy of the new potential. While further studies are necessary to validate the approach, the initial results suggest QMDFF as a routine tool for the computation of a wide range of properties and systems (e.g., for molecular dynamics of isolated molecules, explicit solvation, self-solvation (melting) or even for molecular crystals) in particular when standard
A New Cation-Exchange Method for Accurate Field Speciation of Hexavalent Chromium
Ball, James W.; McCleskey, R. Blaine
2003-01-01
A new cation-exchange method for field speciation of Cr(VI) has been developed to meet present stringent regulatory standards and to overcome the limitations of existing methods. The new method allows measurement of Cr(VI) concentrations as low as 0.05 micrograms per liter, storage of samples for at least several weeks prior to analysis, and use of readily available analytical instrumentation. The sensitivity, accuracy, and precision of the determination in waters over the pH range of 2 to 11 and Fe concentrations up to 1 milligram per liter are equal to or better than existing methods such as USEPA method 218.6. Time stability of preserved samples is a significant advantage over the 24-hour time constraint specified for USEPA method 218.6.
A very accurate filter wheel for a large field IR imager
NASA Astrophysics Data System (ADS)
Lizon, J. L.
2010-07-01
HAWK-I is a near-infrared imager with a relatively large field of view. Two filter wheels with 6 positions each offer a choice of 10 filters. The filters are directly in front of the detector, a mosaic of 2 × 2HAWAII 2RG 2048×2048 pixels detectors. A rather high positioning reproducibility (< 6 arc sec) is required in order to avoid any disagreement caused by subtraction of eventual fix pattern on the filters. The document describes various drive systems which have been tested in order to reach the specified positioning reproducibility. This includes an interesting dissipation free locking system combining electro magnet and permanent magnet. Every solution is discussed and the performances measured in the laboratory during a long campaign of test are exposed. We also address the choice of other critical components like the ball bearings, mounting of the filters and cooling of the wheels.
Santiago, Régis Tadeu; Haiduke, Roberto Luiz Andrade
2015-10-30
This research provides a performance investigation of density functional theory and also proposes new functional parameterizations to deal with electric field gradient (EFG) calculations at nuclear positions. The entire procedure is conducted within the four-component formalism. First, we noticed that traditional hybrid and long-range corrected functionals are more efficient in the description of EFG variations for a set of elements (indium, antimony, iodine, lutetium, and hafnium) among linear molecules. Thus, we selected the PBE0, B3LYP, and CAM-B3LYP functionals and promoted a reoptimization of their parameters for a better description of these EFG changes. The PBE0q variant developed here showed an overall promising performance in a validation test conducted with potassium, iodine, copper, and gold. In general, the correlation coefficients found in linear regressions between experimental nuclear quadrupole coupling constants and calculated EFGs are improved while the systematic EFG errors also decrease as a result of this reparameterization. PMID:26284820
Cell Separation by Non-Inertial Force Fields in Microfluidic Systems
Tsutsui, Hideaki; Ho, Chih-Ming
2009-01-01
Cell and microparticle separation in microfluidic systems has recently gained significant attention in sample preparations for biological and chemical studies. Microfluidic separation is typically achieved by applying differential forces on the target particles to guide them into different paths. This paper reviews basic concepts and novel designs of such microfluidic separators with emphasis on the use of non-inertial force fields, including dielectrophoretic force, optical gradient force, magnetic force, and acoustic primary radiation force. Comparisons of separation performances with discussions on physiological effects and instrumentation issues toward point-of-care devices are provided as references for choosing appropriate separation methods for various applications. PMID:20046897
Evaluation of force fields for molecular simulation of polyhedral oligomeric silsesquioxanes.
Ionescu, Tudor C; Qi, Feng; McCabe, Clare; Striolo, Alberto; Kieffer, John; Cummings, Peter T
2006-02-16
Polyhedral oligomeric silsesquioxanes (POSS) are nanometer-size molecules suitable for the production of organic-inorganic nanocomposite materials. These organic-inorganic nano-building blocks show promise for enabling the production of polymeric materials of exceptional mechanical properties as well as novel composite materials. While the experimental studies of these materials have rapidly evolved in the past decade, their theoretical investigation is still in its infancy. Toward the validation of force fields for the molecular simulation of POSS-containing systems, we present the charge-transfer reactive (CTR) force field for the molecular simulation of polyhedral oligomeric silsesquioxane (POSS) molecules and compare the ability of this, and several force fields taken from the literature, to predict the thermophysical properties of POSS-containing systems. The literature force fields compared include the universal force field (UFF) and the COMPASS and Hybrid-COMPASS force fields. Predictions from molecular dynamics simulations of the structural parameters (unit cell vectors), melting temperature, and FT-IR spectra of crystals of POSS monomers are presented. The POSS monomers investigated are octahydride, octamethyl, and octapropyl POSS. Predicted quantities are compared to experimental results where available and provide molecular-level physical insight into several aspects of the behavior of POSS molecules. While all the force fields tested perform reasonably well, our results indicate that the Hybrid-COMPASS and CTR force fields predict structural properties that are in good agreement with experimental data.
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.
Beauchamp, Kyle A; Lin, Yu-Shan; Das, Rhiju; Pande, Vijay S
2012-04-10
Recent hardware and software advances have enabled simulation studies of protein systems on biophysically-relevant timescales, often revealing the need for improved force fields. Although early force field development was limited by the lack of direct comparisons between simulation and experiment, recent work from several labs has demonstrated direct calculation of NMR observables from protein simulations. Here we quantitatively evaluate recent molecular dynamics force fields against a suite of 524 chemical shift and J coupling ((3)JH(N)H(α), (3)JH(N)C(β), (3)JH(α)C', (3)JH(N)C', and (3)JH(α)N) measurements on dipeptides, tripeptides, tetra-alanine, and ubiquitin. Of the force fields examined (ff96, ff99, ff03, ff03*, ff03w, ff99sb*, ff99sb-ildn, ff99sb-ildn-phi, ff99sb-ildn-nmr, CHARMM27, OPLS-AA), two force fields (ff99sb-ildn-phi, ff99sb-ildn-nmr) combining recent side chain and backbone torsion modifications achieve high accuracy in our benchmark. For the two optimal force fields, the calculation error is comparable to the uncertainty in the experimental comparison. This observation suggests that extracting additional force field improvements from NMR data may require increased accuracy in J coupling and chemical shift prediction. To further investigate the limitations of current force fields, we also consider conformational populations of dipeptides, which were recently estimated using vibrational spectroscopy.
Force Field Analysis: A Bridge Between Diagnostic Data and Operational Prescriptions.
ERIC Educational Resources Information Center
Wiener, William K.
The technique of force field analysis represents a method for bridging the gap between diagnostic data and learning prescriptions and objectives. Through the use of this technique the teacher is able to delineate the strengths and weaknesses of the individual and to generate strategies for meeting specific objectives. A force field refers to a…
The lift forces acting on a submarine composite pipeline in a wave-current coexisting field
Li, Y.C.; Zhang, N.C.
1994-12-31
The composite pipeline is defined as a main big pipe composed with one or several small pipes. The flow behavior around a submarine composite pipeline is more complicated than that around a single submarine pipeline. A series model test of composite pipelines in a wave-current coexisting field was conducted by the authors. Both in-line and lift forces were measured, and the resultant forces are also analyzed. The results of lift forces and resultant forces are reported in this paper. It is found that the lift force coefficients for composite pipelines are well related to the KC number. The lift force coefficients in an irregular wave-current coexisting field are smaller than those in regular wave-current coexisting field. The frequency of lift force is usually the twice or higher than the wave frequency. It is indicated by the authors` test that the resultant forces are larger than in-line forces (horizontal forces) about 10 to 20 percent. The effect of water depth was analyzed. Finally, the relationship between lift force coefficient C{sub l} and KC number, the statistical characteristics of lift and resultant forces, are given in this paper, which may be useful for practical engineering application.
Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data.
Lange, Oliver F; van der Spoel, David; de Groot, Bert L
2010-07-21
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.
Axial acoustic radiation force on a sphere in Gaussian field
Wu, Rongrong; Liu, Xiaozhou Gong, Xiufen
2015-10-28
Based on the finite series method, the acoustical radiation force resulting from a Gaussian beam incident on a spherical object is investigated analytically. When the position of the particles deviating from the center of the beam, the Gaussian beam is expanded as a spherical function at the center of the particles and the expanded coefficients of the Gaussian beam is calculated. The analytical expression of the acoustic radiation force on spherical particles deviating from the Gaussian beam center is deduced. The acoustic radiation force affected by the acoustic frequency and the offset distance from the Gaussian beam center is investigated. Results have been presented for Gaussian beams with different wavelengths and it has been shown that the interaction of a Gaussian beam with a sphere can result in attractive axial force under specific operational conditions. Results indicate the capability of manipulating and separating spherical spheres based on their mechanical and acoustical properties, the results provided here may provide a theoretical basis for development of single-beam acoustical tweezers.
Next-Generation Force Fields from Symmetry-Adapted Perturbation Theory
NASA Astrophysics Data System (ADS)
McDaniel, Jesse G.; Schmidt, J. R.
2016-05-01
Symmetry-adapted perturbation theory (SAPT) provides a unique set of advantages for parameterizing next-generation force fields from first principles. SAPT provides a direct, basis-set superposition error free estimate of molecular interaction energies, a physically intuitive energy decomposition, and a seamless transition to an asymptotic picture of intermolecular interactions. These properties have been exploited throughout the literature to develop next-generation force fields for a variety of applications, including classical molecular dynamics simulations, crystal structure prediction, and quantum dynamics/spectroscopy. This review provides a brief overview of the formalism and theory of SAPT, along with a practical discussion of the various methodologies utilized to parameterize force fields from SAPT calculations. It also highlights a number of applications of SAPT-based force fields for chemical systems of particular interest. Finally, the review ends with a brief outlook on the future opportunities and challenges that remain for next-generation force fields based on SAPT.
Communication: Multiple atomistic force fields in a single enhanced sampling simulation
Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H.
2015-07-14
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.
Lucas, Timothy R.; Bauer, Brad A.; Patel, Sandeep
2014-01-01
With the continuing advances in computational hardware and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has demonstrated the utility of polarizable force fields, those based on the charge equilibration formalism, for a broad range of physical and biophysical systems. We have constructed and applied polarizable force fields for lipids and lipid bilayers. In this review of our recent work, we discuss the formalism we have adopted for implementing the charge equilibration (CHEQ) method for lipid molecules. We discuss the methodology, related issues, and briefly discuss results from recent applications of such force fields. Application areas include DPPC-water monolayers, potassium ion permeation free energetics in the gramicidin A bacterial channel, and free energetics of permeation of charged amino acid analogues across the water-bilayer interface. PMID:21967961
Next-Generation Force Fields from Symmetry-Adapted Perturbation Theory.
McDaniel, Jesse G; Schmidt, J R
2016-05-27
Symmetry-adapted perturbation theory (SAPT) provides a unique set of advantages for parameterizing next-generation force fields from first principles. SAPT provides a direct, basis-set superposition error free estimate of molecular interaction energies, a physically intuitive energy decomposition, and a seamless transition to an asymptotic picture of intermolecular interactions. These properties have been exploited throughout the literature to develop next-generation force fields for a variety of applications, including classical molecular dynamics simulations, crystal structure prediction, and quantum dynamics/spectroscopy. This review provides a brief overview of the formalism and theory of SAPT, along with a practical discussion of the various methodologies utilized to parameterize force fields from SAPT calculations. It also highlights a number of applications of SAPT-based force fields for chemical systems of particular interest. Finally, the review ends with a brief outlook on the future opportunities and challenges that remain for next-generation force fields based on SAPT.
Lucas, Timothy R; Bauer, Brad A; Patel, Sandeep
2012-02-01
With the continuing advances in computational hardware and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has demonstrated the utility of polarizable force fields, those based on the charge equilibration formalism, for a broad range of physical and biophysical systems. We have constructed and applied polarizable force fields for lipids and lipid bilayers. In this review of our recent work, we discuss the formalism we have adopted for implementing the charge equilibration (CHEQ) method for lipid molecules. We discuss the methodology, related issues, and briefly discuss results from recent applications of such force fields. Application areas include DPPC-water monolayers, potassium ion permeation free energetics in the gramicidin A bacterial channel, and free energetics of permeation of charged amino acid analogs across the water-bilayer interface. This article is part of a Special Issue entitled: Membrane protein structure and function.
Communication: Multiple atomistic force fields in a single enhanced sampling simulation.
Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H
2015-07-14
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.
DFT-Derived Force Fields for Modeling Hydrocarbon Adsorption in MIL-47(V).
Kulkarni, Ambarish R; Sholl, David S
2015-08-01
Generic force fields such as UFF and DREIDING are widely used for predicting molecular adsorption and diffusion in metal-organic frameworks (MOFs), but the accuracy of these force fields is unclear. We describe a general framework for developing transferable force fields for modeling the adsorption of alkanes in a nonflexible MIL-47(V) MOF using periodic density functional theory (DFT) calculations. By calculating the interaction energies for a large number of energetically favorable adsorbate configurations using DFT, we obtain a force field that gives good predictions of adsorption isotherms, heats of adsorption, and diffusion properties for a wide range of alkanes and alkenes in MIL-47(V). The force field is shown to be transferable to related materials such as MIL-53(Cr) and is used to calculate the free-energy differences for the experimentally observed phases of MIL-53(Fe).
Pascal, Tod A; Karasawa, Naoki; Goddard, William A
2010-10-01
As assemblies of graphene sheets, carbon nanotubes, and fullerenes become components of new nanotechnologies, it is important to be able to predict the structures and properties of these systems. A problem has been that the level of quantum mechanics practical for such systems (density functional theory at the PBE level) cannot describe the London dispersion forces responsible for interaction of the graphene planes (thus graphite falls apart into graphene sheets). To provide a basis for describing these London interactions, we derive the quantum mechanics based force field for carbon (QMFF-Cx) by fitting to results from density functional theory calculations at the M06-2X level, which demonstrates accuracies for a broad class of molecules at short and medium range intermolecular distances. We carried out calculations on the dehydrogenated coronene (C24) dimer, emphasizing two geometries: parallel-displaced X (close to the observed structure in graphite crystal) and PD-Y (the lowest energy transition state for sliding graphene sheets with respect to each other). A third, eclipsed geometry is calculated to be much higher in energy. The QMFF-Cx force field leads to accurate predictions of available experimental mechanical and thermodynamics data of graphite (lattice vibrations, elastic constants, Poisson ratios, lattice modes, phonon dispersion curves, specific heat, and thermal expansion). This validates the use of M06-2X as a practical method for development of new first principles based generations of QMFF force fields.
Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins.
Li, Da-Wei; Brüschweiler, Rafael
2011-06-14
High quality molecular mechanics force fields of proteins are key for the quantitative interpretation of experimental data and the predictive understanding of protein function based on computer simulations. A strategy is presented for the optimization of protein force fields based on full-length proteins in their native environment that is guided by experimental NMR chemical shifts and residual dipolar couplings (RDCs). An energy-based reweighting approach is applied to a long molecular dynamics trajectory, performed with a parent force field, to efficiently screen a large number of trial force fields. The force field that yields the best agreement with the experimental data is then used as the new parent force field, and the procedure is repeated until no further improvement is obtained. This method is demonstrated for the optimization of the backbone φ,ψ dihedral angle potential of the Amber ff99SB force field using six trial proteins and another 17 proteins for cross-validation using (13)C chemical shifts with and without backbone RDCs. The φ,ψ dihedral angle potential is systematically improved by the inclusion of correlation effects through the addition of up to 24 bivariate Gaussian functions of variable height, width, and tilt angle. The resulting force fields, termed ff99SB_φψ(g24;CS) and ff99SB_φψ(g8;CS,RDC), perform significantly better than their parent force field in terms of both NMR data reproduction and Cartesian coordinate root-mean-square deviations between the MD trajectories and the X-ray crystal structures. The strategy introduced here represents a powerful addition to force field optimization approaches by overcoming shortcomings of methods that are solely based on quantum-chemical calculations of small molecules and protein fragments in the gas phase.
Knight, Chris; Maupin, C Mark; Izvekov, Sergei; Voth, Gregory A
2010-10-12
In this report, a general methodology is presented for the parametrization of a reactive force field using data from a condensed phase ab initio molecular dynamics (AIMD) simulation. This algorithm allows for the creation of an empirical reactive force field that accurately reproduces the underlying ab initio reactive surface while providing the ability to achieve long-time statistical sampling for large systems not possible with AIMD alone. In this work, a model for the hydrated excess proton is constructed where the hydronium cation and proton hopping portions of the model are statistically force-matched to the results of Car-Parrinello Molecular Dynamics (CPMD) simulations. The flexible nature of the algorithm also allows for the use of the more accurate classical simple point-charge flexible water (SPC/Fw) model to describe the water-water interactions while utilizing the ab initio data to create an overall multistate molecular dynamics (MS-MD) reactive model of the hydrated excess proton in water. The resulting empirical model for the system qualitatively reproduces thermodynamic and dynamic properties calculated from the ab initio simulation while being in good agreement with experimental results and previously developed multistate empirical valence bond (MS-EVB) models. The present methodology, therefore, bridges the AIMD technique with the MS-MD modeling of reactive events, while incorporating key strengths of both. PMID:26616784
Multipolar Ewald Methods, 2: Applications Using a Quantum Mechanical Force Field
2015-01-01
A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pKa. Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework. PMID:25691830
Multipolar Ewald methods, 2: applications using a quantum mechanical force field.
Giese, Timothy J; Panteva, Maria T; Chen, Haoyuan; York, Darrin M
2015-02-10
A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pKa. Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework.
Introducing dielectrophoresis as a new force field for field-flow fractionation.
Huang, Y; Wang, X B; Becker, F F; Gascoyne, P R
1997-01-01
We present the principle of cell characterization and separation by dielectrophoretic field-flow fractionation and show preliminary experimental results. The operational device takes the form of a thin chamber in which the bottom wall supports an array of microelectrodes. By applying appropriate AC voltage signals to these electrodes, dielectrophoretic forces are generated to levitate cells suspended in the chamber and to affect their equilibrium heights. A laminar flow profile is established in the chamber so that fluid flows faster with increasing distance from the chamber walls. A cell carried in the flow stream will attain an equilibrium height, and a corresponding velocity, based on the balance of dielectrophoretic, gravitational, and hydrodynamic lift forces it experiences. We describe a theoretical model for this system and show that the cell velocity is a function of the mean fluid velocity, the voltage and frequency of the signals applied to the electrodes, and, most significantly, the cell dielectric properties. The validity of the model is demonstrated with human leukemia (HL-60) cells subjected to a parallel electrode array, and application of the device to separating HL-60 cells from peripheral blood mononuclear cells is shown. PMID:9251828
A multidimensional pendulum in a nonconservative force field under the presence of linear damping
NASA Astrophysics Data System (ADS)
Shamolin, M. V.
2016-09-01
A nonconservative force field in the dynamics of a multidimensional solid is constructed according to the results from the dynamics of real solids occurring in the force field of the action of the medium. In this case, it becomes possible to generalize the equations of motion of a multidimensional solid in a similarly constructed field of forces and to obtain a complete list of, generally speaking, transcendental first integrals expressed through a finite combination of elementary functions. In the study, the integrability in elementary functions is shown for the simultaneous equations of motion of a dynamically symmetric fixed multidimensional solid under the action of a nonconservative pair of forces in the presence of the linear damping moment (the additional dependence of the force field on the tensor of angular velocity of the solid).
NASA Technical Reports Server (NTRS)
Voorhies, Coerte V.; Conrad, Joy
1996-01-01
The geomagnetic spatial power spectrum R(sub n)(r) is the mean square magnetic induction represented by degree n spherical harmonic coefficients of the internal scalar potential averaged over the geocentric sphere of radius r. McLeod's Rule for the magnetic field generated by Earth's core geodynamo says that the expected core surface power spectrum (R(sub nc)(c)) is inversely proportional to (2n + 1) for 1 less than n less than or equal to N(sub E). McLeod's Rule is verified by locating Earth's core with main field models of Magsat data; the estimated core radius of 3485 kn is close to the seismologic value for c of 3480 km. McLeod's Rule and similar forms are then calibrated with the model values of R(sub n) for 3 less than or = n less than or = 12. Extrapolation to the degree 1 dipole predicts the expectation value of Earth's dipole moment to be about 5.89 x 10(exp 22) Am(exp 2)rms (74.5% of the 1980 value) and the expected geomagnetic intensity to be about 35.6 (mu)T rms at Earth's surface. Archeo- and paleomagnetic field intensity data show these and related predictions to be reasonably accurate. The probability distribution chi(exp 2) with 2n+1 degrees of freedom is assigned to (2n + 1)R(sub nc)/(R(sub nc). Extending this to the dipole implies that an exceptionally weak absolute dipole moment (less than or = 20% of the 1980 value) will exist during 2.5% of geologic time. The mean duration for such major geomagnetic dipole power excursions, one quarter of which feature durable axial dipole reversal, is estimated from the modern dipole power time-scale and the statistical model of excursions. The resulting mean excursion duration of 2767 years forces us to predict an average of 9.04 excursions per million years, 2.26 axial dipole reversals per million years, and a mean reversal duration of 5533 years. Paleomagnetic data show these predictions to be quite accurate. McLeod's Rule led to accurate predictions of Earth's core radius, mean paleomagnetic field
Kelly, Aaron; Markland, Thomas E.; Brackbill, Nora
2015-03-07
In this article, we show how Ehrenfest mean field theory can be made both a more accurate and efficient method to treat nonadiabatic quantum dynamics by combining it with the generalized quantum master equation framework. The resulting mean field generalized quantum master equation (MF-GQME) approach is a non-perturbative and non-Markovian theory to treat open quantum systems without any restrictions on the form of the Hamiltonian that it can be applied to. By studying relaxation dynamics in a wide range of dynamical regimes, typical of charge and energy transfer, we show that MF-GQME provides a much higher accuracy than a direct application of mean field theory. In addition, these increases in accuracy are accompanied by computational speed-ups of between one and two orders of magnitude that become larger as the system becomes more nonadiabatic. This combination of quantum-classical theory and master equation techniques thus makes it possible to obtain the accuracy of much more computationally expensive approaches at a cost lower than even mean field dynamics, providing the ability to treat the quantum dynamics of atomistic condensed phase systems for long times.
Kelly, Aaron; Brackbill, Nora; Markland, Thomas E
2015-03-01
In this article, we show how Ehrenfest mean field theory can be made both a more accurate and efficient method to treat nonadiabatic quantum dynamics by combining it with the generalized quantum master equation framework. The resulting mean field generalized quantum master equation (MF-GQME) approach is a non-perturbative and non-Markovian theory to treat open quantum systems without any restrictions on the form of the Hamiltonian that it can be applied to. By studying relaxation dynamics in a wide range of dynamical regimes, typical of charge and energy transfer, we show that MF-GQME provides a much higher accuracy than a direct application of mean field theory. In addition, these increases in accuracy are accompanied by computational speed-ups of between one and two orders of magnitude that become larger as the system becomes more nonadiabatic. This combination of quantum-classical theory and master equation techniques thus makes it possible to obtain the accuracy of much more computationally expensive approaches at a cost lower than even mean field dynamics, providing the ability to treat the quantum dynamics of atomistic condensed phase systems for long times.
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.
Evaluating the strength of salt bridges: a comparison of current biomolecular force fields.
Debiec, Karl T; Gronenborn, Angela M; Chong, Lillian T
2014-06-19
Recent advances in computer hardware and software have made rigorous evaluation of current biomolecular force fields using microsecond-scale simulations possible. Force fields differ in their treatment of electrostatic interactions, including the formation of salt bridges in proteins. Here we conducted an extensive evaluation of salt bridge interactions in the latest AMBER, CHARMM, and OPLS force fields, using microsecond-scale molecular dynamics simulations of amino acid analogues in explicit solvent. We focused on salt bridges between three different pairs of oppositely charged amino acids: Arg/Asp, Lys/Asp, and His(+)/Asp. Our results reveal considerable variability in the predicted KA values of the salt bridges for these force fields, as well as differences from experimental data: almost all of the force fields overestimate the strengths of the salt bridges. When amino acids are represented by side-chain analogues, the AMBER ff03 force field overestimates the KA values the least, while for complete amino acids, the AMBER ff13α force field yields the lowest KA value, most likely caused by an altered balance of side-chain/side-chain and side-chain/backbone contacts. These findings confirm the notion that the implicit incorporation of solvent polarization improves the accuracy of modeling salt bridge interactions.
A test on reactive force fields for the study of silica dimerization reactions
Moqadam, Mahmoud; Riccardi, Enrico; Trinh, Thuat T.; Åstrand, Per-Olof; Erp, Titus S. van
2015-11-14
We studied silica dimerization reactions in the gas and aqueous phase by density functional theory (DFT) and reactive force fields based on two parameterizations of ReaxFF. For each method (both ReaxFF force fields and DFT), we performed constrained geometry optimizations, which were subsequently evaluated in single point energy calculations using the other two methods. Standard fitting procedures typically compare the force field energies and geometries with those from quantum mechanical data after a geometry optimization. The initial configurations for the force field optimization are usually the minimum energy structures of the ab initio database. Hence, the ab initio method dictates which structures are being examined and force field parameters are being adjusted in order to minimize the differences with the ab initio data. As a result, this approach will not exclude the possibility that the force field predicts stable geometries or low transition states which are realistically very high in energy and, therefore, never considered by the ab initio method. Our analysis reveals the existence of such unphysical geometries even at unreactive conditions where the distance between the reactants is large. To test the effect of these discrepancies, we launched molecular dynamics simulations using DFT and ReaxFF and observed spurious reactions for both ReaxFF force fields. Our results suggest that the standard procedures for parameter fitting need to be improved by a mutual comparative method.
A test on reactive force fields for the study of silica dimerization reactions.
Moqadam, Mahmoud; Riccardi, Enrico; Trinh, Thuat T; Åstrand, Per-Olof; van Erp, Titus S
2015-11-14
We studied silica dimerization reactions in the gas and aqueous phase by density functional theory (DFT) and reactive force fields based on two parameterizations of ReaxFF. For each method (both ReaxFF force fields and DFT), we performed constrained geometry optimizations, which were subsequently evaluated in single point energy calculations using the other two methods. Standard fitting procedures typically compare the force field energies and geometries with those from quantum mechanical data after a geometry optimization. The initial configurations for the force field optimization are usually the minimum energy structures of the ab initio database. Hence, the ab initio method dictates which structures are being examined and force field parameters are being adjusted in order to minimize the differences with the ab initio data. As a result, this approach will not exclude the possibility that the force field predicts stable geometries or low transition states which are realistically very high in energy and, therefore, never considered by the ab initio method. Our analysis reveals the existence of such unphysical geometries even at unreactive conditions where the distance between the reactants is large. To test the effect of these discrepancies, we launched molecular dynamics simulations using DFT and ReaxFF and observed spurious reactions for both ReaxFF force fields. Our results suggest that the standard procedures for parameter fitting need to be improved by a mutual comparative method.
Hierarchical atom type definitions and extensible all-atom force fields.
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.
Comparison of three empirical force fields for phonon calculations in CdSe quantum dots.
Kelley, Anne Myers
2016-06-01
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 for 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.
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.
Best, Robert B; Hummer, Gerhard
2009-07-01
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.
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.
NASA Astrophysics Data System (ADS)
Luo, Yuan; Yobas, Levent
2014-09-01
We report a force field on a particle in a concentration (conductivity) gradient under an externally applied oscillating electric field. The conductivity gradient was established through integrated microcapillaries bridging high- and low-conductivity streams in dedicated microchannels. Particles in low-conductivity electrolyte were observed to experience a strong force with the application of an oscillating field and pulled to the microcapillary openings where they were held against the flow. Particle trapping was accompanied by a concurrent electrolyte injection from high- to low-conductivity channel, triggered with the externally applied field and further contributed to the conductivity gradient near the trapping sites. We experimentally evaluated the force dependence on the magnitude and frequency of the excitation field for 10 μm polystyrene particles immersed at various conductivity levels. The experiments suggest that the observed force cannot be simply explained by dielectrophoresis or diffusiophoresis alone and further requires the consideration of a so-called concentration polarization force. This force has been rather recently postulated based on a theoretical treatment and yet to be experimentally validated. Using the theoretical treatment of this force, together with fluidic drag and diffusiophoresis, we correctly predicted trapping trajectories of particles based on a simultaneous solution of Poisson-Nernst-Planck and Stokes equations. The predicted and measured trapping velocities were found in reasonable agreement (within a factor of <1.6), suggesting that the consideration of the concentration polarization force is necessary for describing the observed particle behavior.
Free-molecule heat transfer in a conservative force field between parallel surfaces
NASA Astrophysics Data System (ADS)
Hardt, Steffen
2016-05-01
The heat flux between parallel surfaces is computed analytically assuming that heat is transferred by particles moving ballistically under the influence of a conservative force field. Particle reflection at the surfaces is governed by a Maxwell-type boundary condition. It is found that the force field can give rise to a substantial reduction, but also to an enhancement of the heat flux, depending on the ratio of the temperatures at the two surfaces. The influence of the accommodation coefficients is studied. An asymmetry introduced by the force field and/or the boundary conditions at the two surfaces causes a significant heat-flux rectification, characteristic for a thermal diode.
An all-atom force field developed for Zn₄O(RCO₂)₆ metal organic frameworks.
Sun, Yingxin; Sun, Huai
2014-03-01
An all-atom force field is developed for metal organic frameworks Zn₄O(RCO₂)₆ by fitting to quantum mechanics data. Molecular simulations are conducted to validate the force field by calculating thermal expansion coefficients, crystal bulk and Young's moduli, power spectra, self-diffusion coefficients, and activation energies of self-diffusions for benzene and n-hexane. The calculated results are in good agreement with available experimental data. The proposed force field is suitable for simulations of adsorption or diffusion of organic molecules with flexible frameworks. PMID:24562858
Numerical derivation of forces on particles and agglomerates in a resonant acoustic field
NASA Astrophysics Data System (ADS)
Knoop, Claas; Fritsching, Udo
2013-10-01
Particles and agglomerates are investigated in gaseous acoustic flow fields. Acoustic fields exert forces on solid objects, which can influence the shape of the exposed bodies, even to the point of breakage of the structures. Motivated by experimentally observed breakage of agglomerates in an acoustic levitator (f = 20 kHz), a numerical study is presented that derives the acoustic forces on a complex model agglomerate from the pressure and velocity fields of a resonant standing ultrasound wave, calculated by computational fluid dynamics (CFD). It is distinguished between the drag and lift/lateral forces on the overall agglomerate and on the different primary particles of the model.
Force field analysis: a model for promoting adolescents' involvement in their own health care.
MacDuffie, Heather; DePoy, Elizabeth
2004-07-01
This article advances a three-step model for engaging adolescents in shaping their own health care supports and services through systems and social change that rely on principles of force field analysis. Consistent with health promotion values and trends for evidence-based practice, force field analysis provides a systematic and multilevel approach to problem assessment, resolution, and social change that is particularly appropriate for adolescents. The article reviews relevant literature, proposes the model, and concludes with a comparative illustration and critical analysis of the use of force field analysis to promote adolescent health. PMID:15228786
Nonlinear force-free magnetic fields: Calculation and applicatin to astrophysics. Ph.D. Thesis
NASA Technical Reports Server (NTRS)
Yang, Wei-Hong
1987-01-01
The problem concerned in this work is that of calculating magnetic field configurations in which the Lorentz force (vector)j x (vector)B is everywhere zero, subject to specified boundary conditions. The magnetic field is represented in terms of Clebsch variables in the form (vector)B = del alpha x del beta. These variables are constant on any field line. The most appropriate choice of boundary conditions is to specify the values of alpha and beta on the bounding surface. It is proposed that the field lines move in the direction of local Lorentz force and relax towards a force-free field configuration. This concept leads to an iteration procedure for modifying the variables alpha and beta that tends asymptotically towards the force-free state. This method is first applied to a simple problem in two rectangular dimensions; the calculation shows that the convergence of magnetic field energy to a minimum state (force-free) is close to exponential. This method is then applied to study some astrophysical force-free magnetic fields, such as the structures and evolution of magnetic fields of rotating sunspots and accretion disks. The implication of the results, as related to the mechanisms of solar flares, extragalactic radio sources and radio jets, are discussed.
Global constant-alpha force-free magnetic fields and coronal structures
NASA Technical Reports Server (NTRS)
Nakagawa, Y.; Wu, S. T.; Tandberg-Hanssen, E.
1978-01-01
Nakagawa's (1973) general formulation of constant-alpha global force-free magnetic fields is used to examine the topological characteristics of axisymmetric constant-alpha fields with specific reference to solar EUV, XUV, and X-ray structures observed from Skylab. The theoretical formulation is briefly summarized, and topological characteristics of the field lines are analyzed. The results are compared with X-ray observations of a large coronal arch and white-light observations of a coronal transient. It is concluded that global-scale force-free magnetic fields are present in the solar atmosphere and that their topological characteristics differ significantly from those of potential fields.
Grassi, Lorenzo; Väänänen, Sami P; Ristinmaa, Matti; Jurvelin, Jukka S; Isaksson, Hanna
2016-03-21
Subject-specific finite element models have been proposed as a tool to improve fracture risk assessment in individuals. A thorough laboratory validation against experimental data is required before introducing such models in clinical practice. Results from digital image correlation can provide full-field strain distribution over the specimen surface during in vitro test, instead of at a few pre-defined locations as with strain gauges. The aim of this study was to validate finite element models of human femora against experimental data from three cadaver femora, both in terms of femoral strength and of the full-field strain distribution collected with digital image correlation. The results showed a high accuracy between predicted and measured principal strains (R(2)=0.93, RMSE=10%, 1600 validated data points per specimen). Femoral strength was predicted using a rate dependent material model with specific strain limit values for yield and failure. This provided an accurate prediction (<2% error) for two out of three specimens. In the third specimen, an accidental change in the boundary conditions occurred during the experiment, which compromised the femoral strength validation. The achieved strain accuracy was comparable to that obtained in state-of-the-art studies which validated their prediction accuracy against 10-16 strain gauge measurements. Fracture force was accurately predicted, with the predicted failure location being very close to the experimental fracture rim. Despite the low sample size and the single loading condition tested, the present combined numerical-experimental method showed that finite element models can predict femoral strength by providing a thorough description of the local bone mechanical response. PMID:26944687
Forced MHD turbulence in a uniform external magnetic field
NASA Technical Reports Server (NTRS)
Hossain, M.; Vahala, G.; Montgomery, D.
1985-01-01
Two-dimensional dissipative MHD turbulence is randomly driven at small spatial scales and is studied by numerical simulation in the presence of a strong uniform external magnetic field. A behavior is observed which is apparently distinct from the inverse cascade which prevails in the absence of an external magnetic field. The magnetic spectrum becomes dominated by the three longest wavelength Alfven waves in the system allowed by the boundary conditions: those which, in a box size of edge 2 pi, have wave numbers (kx' ky) = (1, 1), and (1, -1), where the external magnetic field is in the x direction. At any given instant, one of these three modes dominates the vector potential spectrum, but they do not constitute a resonantly coupled triad. Rather, they are apparently coupled by the smaller-scale turbulence.
The Ehrenfest force field: Topology and consequences for the definition of an atom in a molecule.
Martín Pendás, A; Hernández-Trujillo, J
2012-10-01
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.
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.
Valence force field analysis on nitrogen in silicon
NASA Astrophysics Data System (ADS)
Harada, H.; Ohkubo, I.; Mikayama, T.; Yamanaka, Y.; Inoue, N.
2001-12-01
Nitrogen doping attracts attention because it reduces void defects drastically. But the mechanism has not been clarified yet. Various configurations of nitrogen have been proposed by using the first principles calculation but there is no description how the stress plays a role in determining these nitrogen configurations. We reveal normal vibration modes corresponding to well-known infrared absorption peaks at 766 and 963 cm -1 of nitrogen split interstitial (N-N) and derive force constants for bond stretching and bond bending. Local strain energy near nitrogen is calculated for the optimized structures of N-N, nitrogen-vacancy complex, substitutional N and interstitial N. As a result, it is found that in structures of N-N and N 2-V 2 with filled electron orbitals, strain energy plays an important role in the determination of the stable structure.
Anharmonic force fields from analytic second derivatives: Method and application to methyl bromide
NASA Astrophysics Data System (ADS)
Schneider, Winfried; Thiel, Walter
1989-05-01
An efficient finite difference procedure is described for calculating anharmonic normal-coordinate force constants from quantum-chemical analytic second derivatives. Displacements along normal coordinates are used to generate those cubic and quartic force constants which are needed in a second-order perturbation treatment of anharmonicity. The anharmonic force field of methyl bromide is predicted, and the calculated spectroscopic constants compared with experimental data.
BIOREMEDIATION FIELD EVALUATION - HILL AIR FORCE BASE, UTAH
In 1990, the U.S. Environmental Protection Agency (EPA) established the Bioremediation Field Initiative as part of its overall strategy to increase the use of bioremediation to treat hazardous wastes at Comprehensive Environmental Response, Compensation, and Liabil- ity Act (C...
Steele, Mark A; Forrester, Graham E
2005-09-20
Field experiments provide rigorous tests of ecological hypotheses but are usually limited to small spatial scales. It is thus unclear whether these findings extrapolate to larger scales relevant to conservation and management. We show that the results of experiments detecting density-dependent mortality of reef fish on small habitat patches scale up to have similar effects on much larger entire reefs that are the size of small marine reserves and approach the scale at which some reef fisheries operate. We suggest that accurate scaling is due to the type of species interaction causing local density dependence and the fact that localized events can be aggregated to describe larger-scale interactions with minimal distortion. Careful extrapolation from small-scale experiments identifying species interactions and their effects should improve our ability to predict the outcomes of alternative management strategies for coral reef fishes and their habitats.
Reactive Force Fields Based on Quantum Mechanics for Applications to Materials at Extreme Conditions
NASA Astrophysics Data System (ADS)
van Duin, Adri C. T.; Zybin, Sergey V.; Chenoweth, Kimberley; Zhang, Luzheng; Han, Si-Ping; Strachan, Alejandro; Goddard, William A.
2006-07-01
Understanding the response of energetic materials (EM) to thermal or shock loading at the atomistic level demands a highly accurate description of the reaction dynamics of multimillion-atom systems to capture the complex chemical and mechanical behavior involved: nonequilibrium energy/mass transfer, molecule excitation and decomposition under high strain/heat rates, formation of defects, plastic flow, and phase transitions. To enable such simulations, we developed the ReaxFF reactive force fields based on quantum mechanics (QM) calculations of reactants, products, high-energy intermediates and transition states, but using functional forms suitable for large-scale molecular dynamics simulations of chemical reactions under extreme conditions. The elements of ReaxFF are: - charge distributions change instantaneously as atomic coordinates change, - all valence interactions use bond orders derived uniquely from the bond distances which in turn describe uniquely the energies and forces, - three body (angle) and four body (torsion and inversion) terms are allowed but not required, - a general "van der Waals" term describes short range Pauli repulsion and long range dispersion interactions, which with Coulomb terms are included between all pairs of atoms (no bond or angle exclusions), - no environmental distinctions are made of atoms involving the same element; thus every carbon has the same parameters whether in diamond, graphite, benzene, porphyrin, allyl radical, HMX or TATP. ReaxFF uses the same functional form and parameters for reactive simulations in hydrocarbons, polymers, metal oxides, and metal alloys, allowing mixtures of all these systems into one simulation. We will present an overview of recent progress in ReaxFF developments, including the extension of ReaxFF to nitramine-based (nitromethane, HMX) and peroxide-based (TATP) explosives. To demonstrate the versatility and transferability of ReaxFF, we also present applications to silicone polymer poly
NASA Astrophysics Data System (ADS)
Kikuchi, Y.; de Bock, M. F. M.; Finken, K. H.; Jakubowski, M.; Jaspers, R.; Koslowski, H. R.; Kraemer-Flecken, A.; Lehnen, M.; Liang, Y.; Matsunaga, G.; Reiser, D.; Wolf, R. C.; Zimmermann, O.
2006-08-01
The magnetic field penetration process into a magnetized plasma is of basic interest both for plasma physics and astrophysics. In this context special measurements on the field penetration and field amplification are performed by a Hall probe on the dynamic ergodic divertor (DED) on the TEXTOR tokamak and the data are interpreted by a two-fluid plasma model. It is observed that the growth of the forced magnetic reconnection by the rotating DED field is accompanied by a change of the plasma fluid rotation. The differential rotation frequency between the DED field and the plasma plays an important role in the process of the excitation of tearing modes. The momentum input from the rotating DED field to the plasma is interpreted by both a ponderomotive force at the rational surface and a radial electric field modified by an edge ergodization.
Smith, Micholas Dean; Rao, J Srinivasa; Segelken, Elizabeth; Cruz, Luis
2015-12-28
In this work we examine the dynamics of an intrinsically disordered protein fragment of the amyloid β, the Aβ21-30, under seven commonly used molecular dynamics force fields (OPLS-AA, CHARMM27-CMAP, AMBER99, AMBER99SB, AMBER99SB-ILDN, AMBER03, and GROMOS53A6), and three water models (TIP3P, TIP4P, and SPC/E). We find that the tested force fields and water models have little effect on the measures of radii of gyration and solvent accessible surface area (SASA); however, secondary structure measures and intrapeptide hydrogen-bonding are significantly modified, with AMBER (99, 99SB, 99SB-ILDN, and 03) and CHARMM22/27 force-fields readily increasing helical content and the variety of intrapeptide hydrogen bonds. On the basis of a comparison between the population of helical and β structures found in experiments, our data suggest that force fields that suppress the formation of helical structure might be a better choice to model the Aβ21-30 peptide. PMID:26629886
Smith, Micholas Dean; Rao, J Srinivasa; Segelken, Elizabeth; Cruz, Luis
2015-12-28
In this work we examine the dynamics of an intrinsically disordered protein fragment of the amyloid β, the Aβ21-30, under seven commonly used molecular dynamics force fields (OPLS-AA, CHARMM27-CMAP, AMBER99, AMBER99SB, AMBER99SB-ILDN, AMBER03, and GROMOS53A6), and three water models (TIP3P, TIP4P, and SPC/E). We find that the tested force fields and water models have little effect on the measures of radii of gyration and solvent accessible surface area (SASA); however, secondary structure measures and intrapeptide hydrogen-bonding are significantly modified, with AMBER (99, 99SB, 99SB-ILDN, and 03) and CHARMM22/27 force-fields readily increasing helical content and the variety of intrapeptide hydrogen bonds. On the basis of a comparison between the population of helical and β structures found in experiments, our data suggest that force fields that suppress the formation of helical structure might be a better choice to model the Aβ21-30 peptide.
Effect of Polarimetric Noise on the Estimation of Twist and Magnetic Energy of Force-Free Fields
NASA Astrophysics Data System (ADS)
Tiwari, Sanjiv Kumar; Venkatakrishnan, P.; Gosain, Sanjay; Joshi, Jayant
2009-07-01
The force-free parameter α, also known as helicity parameter or twist parameter, bears the same sign as the magnetic helicity under some restrictive conditions. The single global value of α for a whole active region gives the degree of twist per unit axial length. We investigate the effect of polarimetric noise on the calculation of global α value and magnetic energy of an analytical bipole. The analytical bipole has been generated using the force-free field approximation with a known value of constant α and magnetic energy. The magnetic parameters obtained from the analytical bipole are used to generate Stokes profiles from the Unno-Rachkovsky solutions for polarized radiative transfer equations. Then we add random noise of the order of 10-3 of the continuum intensity (I c ) in these profiles to simulate the real profiles obtained by modern spectropolarimeters such as Hinode (SOT/SP), SVM (USO), ASP, DLSP, POLIS, and SOLIS etc. These noisy profiles are then inverted using a Milne-Eddington inversion code to retrieve the magnetic parameters. Hundred realizations of this process of adding random noise and polarimetric inversion is repeated to study the distribution of error in global α and magnetic energy values. The results show that (1) the sign of α is not influenced by polarimetric noise and very accurate values of global twist can be calculated, and (2) accurate estimation of magnetic energy with uncertainty as low as 0.5% is possible under the force-free condition.
EFFECT OF POLARIMETRIC NOISE ON THE ESTIMATION OF TWIST AND MAGNETIC ENERGY OF FORCE-FREE FIELDS
Tiwari, Sanjiv Kumar; Venkatakrishnan, P.; Gosain, Sanjay; Joshi, Jayant E-mail: pvk@prl.res.in E-mail: jayant@prl.res.in
2009-07-20
The force-free parameter {alpha}, also known as helicity parameter or twist parameter, bears the same sign as the magnetic helicity under some restrictive conditions. The single global value of {alpha} for a whole active region gives the degree of twist per unit axial length. We investigate the effect of polarimetric noise on the calculation of global {alpha} value and magnetic energy of an analytical bipole. The analytical bipole has been generated using the force-free field approximation with a known value of constant {alpha} and magnetic energy. The magnetic parameters obtained from the analytical bipole are used to generate Stokes profiles from the Unno-Rachkovsky solutions for polarized radiative transfer equations. Then we add random noise of the order of 10{sup -3} of the continuum intensity (I {sub c}) in these profiles to simulate the real profiles obtained by modern spectropolarimeters such as Hinode (SOT/SP), SVM (USO), ASP, DLSP, POLIS, and SOLIS etc. These noisy profiles are then inverted using a Milne-Eddington inversion code to retrieve the magnetic parameters. Hundred realizations of this process of adding random noise and polarimetric inversion is repeated to study the distribution of error in global {alpha} and magnetic energy values. The results show that (1) the sign of {alpha} is not influenced by polarimetric noise and very accurate values of global twist can be calculated, and (2) accurate estimation of magnetic energy with uncertainty as low as 0.5% is possible under the force-free condition.
New approaches for molecular conformer force field analysis in combination with ab initio results
NASA Astrophysics Data System (ADS)
Kuramshina, G. M.; Pentin, Yu. A.; Yagola, A. G.
1999-10-01
Ab initio and DFT results on harmonic force constants for trans- and gauche-conformers of CH 3CH 2CH 2Cl, CF 3CH 2CH 2Cl and CCl 3CH 2CH 2Cl are used for formulating constraints in molecular force field models described compounds with hindered internal rotation around the C-C bond.
Many-body effects are essential in a physically motivated CO2 force field.
Yu, Kuang; Schmidt, J R
2012-01-21
We develop a physically motivated many-body force field for CO(2), incorporating explicit three-body interactions parameterized on the basis of two- and three-body symmetry adapted perturbation theory (SAPT) calculations. The potential is parameterized consistently with, and builds upon, our successful SAPT-based two-body CO(2) model ("Schmidt, Yu, and McDaniel" (SYM) model) [K. Yu, J. G. McDaniel, and J. R. Schmidt, J. Phys Chem B 115, 10054 (2011)]. We demonstrate that three-body interactions are essential to achieve an accurate description of bulk properties, and that previous two-body models have therefore necessarily exploited large error cancellations to achieve satisfactory results. The resulting three-body model exhibits excellent second/third virial coefficients and bulk properties over the phase diagram, yielding a nearly empirical parameter-free model. We show that this explicit three-body model can be converted into a computationally efficient, density/temperature-dependent two-body model that reduces almost exactly to our prior SYM model in the high-density limit. PMID:22280763
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
He, Yi; Mozolewska, Magdalena A.; Krupa, Paweł; Sieradzan, Adam K.; Wirecki, Tomasz K.; Liwo, Adam; Kachlishvili, Khatuna; Rackovsky, Shalom; Jagieła, Dawid; Ślusarz, Rafał; Czaplewski, Cezary R.; Ołdziej, Stanisław; Scheraga, Harold A.
2013-01-01
The performance of the physics-based protocol, whose main component is the United Residue (UNRES) physics-based coarse-grained force field, developed in our laboratory for the prediction of protein structure from amino acid sequence, is illustrated. Candidate models are selected, based on probabilities of the conformational families determined by multiplexed replica-exchange simulations, from the 10th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP10). For target T0663, classified as a new fold, which consists of two domains homologous to those of known proteins, UNRES predicted the correct symmetry of packing, in which the domains are rotated with respect to each other by 180° in the experimental structure. By contrast, models obtained by knowledge-based methods, in which each domain is modeled very accurately but not rotated, resulted in incorrect packing. Two UNRES models of this target were featured by the assessors. Correct domain packing was also predicted by UNRES for the homologous target T0644, which has a similar structure to that of T0663, except that the two domains are not rotated. Predictions for two other targets, T0668 and T0684_D2, are among the best ones by global distance test score. These results suggest that our physics-based method has substantial predictive power. In particular, it has the ability to predict domain–domain orientations, which is a significant advance in the state of the art. PMID:23980156
Nano-imaging collagen by atomic force, near-field and nonlinear microscope
NASA Astrophysics Data System (ADS)
Lim, Ken Choong; Tang, Jinkai; Li, Hao; Ng, Boon Ping; Kok, Shaw Wei; Wang, Qijie; Zhang, Ying
2015-03-01
As the most abundant protein in the human body, collagen has a very important role in vast numbers of bio-medical applications. The unique second order nonlinear properties of fibrillar collagen make it a very important index in nonlinear optical imaging based disease diagnosis of the brain, skin, liver, colon, kidney, bone, heart and other organs in the human body. The second-order nonlinear susceptibility of collagen has been explored at the macroscopic level and was explained as a volume-averaged molecular hyperpolarizability. However, details about the origin of optical second harmonic signals from collagen fibrils at the molecular level are still not clear. Such information is necessary for accurate interpolation of bio-information from nonlinear optical imaging techniques. The later has shown great potential in collagen based disease diagnosis methodologies. In this paper, we report our work using an atomic force microscope (AFM), near field (SNOM) and nonlinear laser scanning microscope (NLSM) to study the structure of collagen fibrils and other pro-collagen structures.
Atomistic-scale simulations of energetic materials with ReaxFF reactive force fields
NASA Astrophysics Data System (ADS)
Goddard, W. A., III; Strachan, A.
2005-07-01
Understanding the response of energetic materials to thermal or shock loading at the atomistic level demands a highly accurate description of the reaction dynamics of million atom systems to capture the complex chemical and mechanical behavior involved: nonequilibrium energy/mass transfer, molecule excitation and decomposition under high strain/heat rates, formation of defects, plastic flow, and phase transitions. To enable such simulations, we developed the ReaxFF reactive force fields based on quantum mechanics (QM) calculations of reactants, products, high-energy intermediates and transition states, but using functional forms suitable for large-scale molecular dynamics simulations of chemical reactions under extreme conditions. We will present an overview of recent progress in ReaxFF developments, including the extension of ReaxFF to new nitramine- based (nitromethane, HMX, PETN, TATB) and peroxide-based (TATP) explosives. To demonstrate the versatility and transferability of ReaxFF, we will present applications to solid composite propellants such as Al/Al2O3-metal nanoparticles embedded into solid explosive matrices (RDX, PETN).
Force field parameters for rotation around chi torsion axis in nucleic acids.
Ode, Hirotaka; Matsuo, Yuri; Neya, Saburo; Hoshino, Tyuji
2008-11-30
To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis. The reliability of molecular dynamics (MD) simulation was significantly increased by improving the torsion parameters at C8--N9--C1'--X (X = H1', C2', O4') in A, G and those at C6--N1--C1'--X in C, T, and U. In this work, we constructed small models representing the chemical structure of A, G, C, T, and U, and estimated energy profile for chi-axis rotation by executing numerous quantum mechanical (QM) calculations. The parameters were derived by discrete Fourier transformation of the calculated QM data. A comparison in energy profile between molecular mechanical (MM) calculation and QM one shows that our presently derived parameters well reproduce the energy surface of QM calculation for all the above torsion terms. Furthermore, our parameters show a good performance in MD simulations of some nucleic acids. Hence, the present refinement of parameters will enable us to perform more accurate simulations for various types of nucleic acids.
All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins
2016-01-01
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. PMID:25999804
Akin-Ojo, Omololu; Song, Yang; Wang, Feng
2008-08-14
A new method called adaptive force matching (AFM) has been developed that is capable of producing high quality force fields for condensed phase simulations. This procedure involves the parametrization of force fields to reproduce ab initio forces obtained from condensed phase quantum-mechanics/molecular-mechanics (QM/MM) calculations. During the procedure, the MM part of the QM/MM is iteratively improved so as to approach ab initio quality. In this work, the AFM method has been tested to parametrize force fields for liquid water so that the resulting force fields reproduce forces calculated using the ab initio MP2 and the Kohn-Sham density functional theory with the Becke-Lee-Yang-Parr (BLYP) and Becke three-parameter LYP (B3LYP) exchange correlation functionals. The AFM force fields generated in this work are very simple to evaluate and are supported by most molecular dynamics (MD) codes. At the same time, the quality of the forces predicted by the AFM force fields rivals that of very expensive ab initio calculations and are found to successfully reproduce many experimental properties. The site-site radial distribution functions (RDFs) obtained from MD simulations using the force field generated from the BLYP functional through AFM compare favorably with the previously published RDFs from Car-Parrinello MD simulations with the same functional. Technical aspects of AFM such as the optimal QM cluster size, optimal basis set, and optimal QM method to be used with the AFM procedure are discussed in this paper.
Molecular dynamics simulations data of the twenty encoded amino acids in different force fields.
Vitalini, F; Noé, F; Keller, B G
2016-06-01
We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8].
The Rotational Spectrum and Anharmonic Force Field of Chlorine Dioxide, OClO
NASA Technical Reports Server (NTRS)
Muller, Holger S. P.; Sorensen, G.; Birk, Manfred; Friedl, Randy R.
1997-01-01
The ground state rotational and quartic centrifugal distortion constants, their vibrational changes, and the sextic centrifugal distortion constants were used in a calculation of the quartic force field together with data from infrared studies.
Simulation of lipid bilayer self-assembly using all-atom lipid force fields.
Skjevik, Åge A; Madej, Benjamin D; Dickson, Callum J; Lin, Charles; Teigen, Knut; Walker, Ross C; Gould, Ian R
2016-04-21
In this manuscript we expand significantly on our earlier communication by investigating the bilayer self-assembly of eight different types of phospholipids in unbiased molecular dynamics (MD) simulations using three widely used all-atom lipid force fields. Irrespective of the underlying force field, the lipids are shown to spontaneously form stable lamellar bilayer structures within 1 microsecond, the majority of which display properties in satisfactory agreement with the experimental data. The lipids self-assemble via the same general mechanism, though at formation rates that differ both between lipid types, force fields and even repeats on the same lipid/force field combination. In addition to zwitterionic phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipids, anionic phosphatidylserine (PS) and phosphatidylglycerol (PG) lipids are represented. To our knowledge this is the first time bilayer self-assembly of phospholipids with negatively charged head groups is demonstrated in all-atom MD simulations.
Molecular dynamics simulations data of the twenty encoded amino acids in different force fields.
Vitalini, F; Noé, F; Keller, B G
2016-06-01
We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]. PMID:27054161
Molecular dynamics simulations data of the twenty encoded amino acids in different force fields
Vitalini, F.; Noé, F.; Keller, B.G.
2016-01-01
We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]. PMID:27054161
A new force field including charge directionality for TMAO in aqueous solution
NASA Astrophysics Data System (ADS)
Usui, Kota; Nagata, Yuki; Hunger, Johannes; Bonn, Mischa; Sulpizi, Marialore
2016-08-01
We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (OTMAO) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around OTMAO to mimic the OTMAO lone pairs and we migrate the negative charge on the OTMAO to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasing TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.
Chen, Wei; Shi, Chuanyin; MacKerell, Alexander D; Shen, Jana
2015-06-25
Physics-based force fields are the backbone of molecular dynamics simulations. In recent years, significant progress has been made in the assessment and improvement of commonly used force fields for describing conformational dynamics of folded proteins. However, the accuracy for the unfolded states remains unclear. The latter is however important for detailed studies of protein folding pathways, conformational transitions involving unfolded states, and dynamics of intrinsically disordered proteins. In this work, we compare the three commonly used force fields, AMBER ff99SB-ILDN, CHARMM22/CMAP, and CHARMM36, for modeling the natively unfolded fragment peptides, NTL9(1-22) and NTL9(6-17), using explicit-solvent replica-exchange molecular dynamics simulations. All three simulations show that NTL9(6-17) is completely unstructured, while NTL9(1-22) transiently samples various β-hairpin states, reminiscent of the first β-hairpin in the structure of the intact NTL9 protein. The radius of gyration of the two peptides is force field independent but likely underestimated due to the current deficiency of additive force fields. Compared to the CHARMM force fields, ff99SB-ILDN gives slightly higher β-sheet propensity and more native-like residual structures for NTL9(1-22), which may be attributed to its known β preference. Surprisingly, only two sequence-local pairs of charged residues make appreciable ionic contacts in the simulations of NTL9(1-22), which are sampled slightly more by the CHARMM force fields. Taken together, these data suggest that the current CHARMM and AMBER force fields are globally in agreement in modeling the unfolded states corresponding to β-sheet in the folded structure, while differing in details such as the native-likeness of the residual structures and interactions. PMID:26020564
Chen, Wei; Shi, Chuanyin; MacKerell, Alexander D; Shen, Jana
2015-06-25
Physics-based force fields are the backbone of molecular dynamics simulations. In recent years, significant progress has been made in the assessment and improvement of commonly used force fields for describing conformational dynamics of folded proteins. However, the accuracy for the unfolded states remains unclear. The latter is however important for detailed studies of protein folding pathways, conformational transitions involving unfolded states, and dynamics of intrinsically disordered proteins. In this work, we compare the three commonly used force fields, AMBER ff99SB-ILDN, CHARMM22/CMAP, and CHARMM36, for modeling the natively unfolded fragment peptides, NTL9(1-22) and NTL9(6-17), using explicit-solvent replica-exchange molecular dynamics simulations. All three simulations show that NTL9(6-17) is completely unstructured, while NTL9(1-22) transiently samples various β-hairpin states, reminiscent of the first β-hairpin in the structure of the intact NTL9 protein. The radius of gyration of the two peptides is force field independent but likely underestimated due to the current deficiency of additive force fields. Compared to the CHARMM force fields, ff99SB-ILDN gives slightly higher β-sheet propensity and more native-like residual structures for NTL9(1-22), which may be attributed to its known β preference. Surprisingly, only two sequence-local pairs of charged residues make appreciable ionic contacts in the simulations of NTL9(1-22), which are sampled slightly more by the CHARMM force fields. Taken together, these data suggest that the current CHARMM and AMBER force fields are globally in agreement in modeling the unfolded states corresponding to β-sheet in the folded structure, while differing in details such as the native-likeness of the residual structures and interactions.
An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0.
Malde, Alpeshkumar K; Zuo, Le; Breeze, Matthew; Stroet, Martin; Poger, David; Nair, Pramod C; Oostenbrink, Chris; Mark, Alan E
2011-12-13
The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb ) is a Web-accessible server that can provide topologies and parameters for a wide range of molecules appropriate for use in molecular simulations, computational drug design, and X-ray refinement. The ATB has three primary functions: (1) to act as a repository for molecules that have been parametrized as part of the GROMOS family of force fields, (2) to act as a repository for pre-equilibrated systems for use as starting configurations in molecular dynamics simulations (solvent mixtures, lipid systems pre-equilibrated to adopt a specific phase, etc.), and (3) to generate force field descriptions of novel molecules compatible with the GROMOS family of force fields in a variety of formats (GROMOS, GROMACS, and CNS). Force field descriptions of novel molecules are derived using a multistep process in which results from quantum mechanical (QM) calculations are combined with a knowledge-based approach to ensure compatibility (as far as possible) with a specific parameter set of the GROMOS force field. The ATB has several unique features: (1) It requires that the user stipulate the protonation and tautomeric states of the molecule. (2) The symmetry of the molecule is analyzed to ensure that equivalent atoms are assigned identical parameters. (3) Charge groups are assigned automatically. (4) Where the assignment of a given parameter is ambiguous, a range of possible alternatives is provided. The ATB also provides several validation tools to assist the user to assess the degree to which the topology generated may be appropriate for a given task. In addition to detailing the steps involved in generating a force field topology compatible with a specific GROMOS parameter set (GROMOS 53A6), the challenges involved in the automatic generation of force field parameters for atomic simulations in general are discussed.
Gravitational self-force in nonvacuum spacetimes: An effective field theory derivation
NASA Astrophysics Data System (ADS)
Zimmerman, Peter
2015-09-01
In this paper we investigate the motion of small compact objects in nonvacuum spacetimes using methods from effective field theory in curved spacetime. Although a vacuum formulation is sufficient in many astrophysical contexts, there are applications such as the role of the self-force in enforcing cosmic censorship in the context of the overcharging problem, which necessitate an extension into the nonvacuum regime. The defining feature of the self-force problem in nonvacuum spacetimes is the coupling between gravitational and nongravitational field perturbations. The formulation of the self-force problem for nonvacuum spacetimes was recently provided in simultaneous papers by Zimmerman and Poisson [Gravitational self-force in nonvacuum spacetimes, Phys. Rev. D 90, 084030 (2014)] and Linz, Friedmann, and Wiseman [Combined gravitational and electromagnetic self-force on charged particles in electrovac spacetimes, Phys. Rev. D 90, 084031 (2014)]. Here we distinguish ourselves by working with the effective action rather than the field equations. The formalism utilizes the multi-index notation developed by Zimmerman and Poisson [Gravitational self-force in nonvacuum spacetimes, Phys. Rev. D 90, 084030 (2014) to accommodate the coupling between the different fields. Using dimensional regularization, we arrive at a finite expression for the local self-force expressed in terms of multi-index quantities evaluated in the background spacetime. We then apply the formalism to compute the coupled gravitational self-force in two explicit cases. First, we calculate the self-force on a massive particle possessing scalar charge and moving in a scalarvac spacetime. We then derive an expression for the self-force on an electrically charged, massive particle moving in an electrovac spacetime. In both cases, the force is expressed as a sum of local terms involving tensors defined in the background spacetime and evaluated at the current position of the particle, as well as tail integrals
Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.
2016-01-01
We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370
Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields.
Bergonzo, Christina; Henriksen, Niel M; Roe, Daniel R; Cheatham, Thomas E
2015-09-01
Recent modifications and improvements to standard nucleic acid force fields have attempted to fix problems and issues that have been observed as longer timescale simulations have become routine. Although previous work has shown the ability to fold the UUCG stem-loop structure, until now no group has attempted to quantify the performance of current force fields using highly converged structural populations of the tetraloop conformational ensemble. In this study, we report the use of multiple independent sets of multidimensional replica exchange molecular dynamics (M-REMD) simulations with different initial conditions to generate well-converged conformational ensembles for the tetranucleotides r(GACC) and r(CCCC), as well as the larger UUCG tetraloop motif. By generating what is to our knowledge the most complete RNA structure ensembles reported to date for these systems, we remove the coupling between force field errors and errors due to incomplete sampling, providing a comprehensive comparison between current top-performing MD force fields for RNA. Of the RNA force fields tested in this study, none demonstrate the ability to correctly identify the most thermodynamically stable structure for all three systems. We discuss the deficiencies present in each potential function and suggest areas where improvements can be made. The results imply that although "short" (nsec-μsec timescale) simulations may stay close to their respective experimental structures and may well reproduce experimental observables, inevitably the current force fields will populate alternative incorrect structures that are more stable than those observed via experiment.
Pyzer-Knapp, Edward O; Thompson, Hugh P G; Day, Graeme M
2016-08-01
We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370
Empirical force fields for complex hydrated calcio-silicate layered materials.
Shahsavari, Rouzbeh; Pellenq, Roland J-M; Ulm, Franz-Josef
2011-01-21
The use of empirical force fields is now a standard approach in predicting the properties of hydrated oxides which are omnipresent in both natural and engineering applications. Transferability of force fields to analogous hydrated oxides without rigorous investigations may result in misleading property predictions. Herein, we focus on two common empirical force fields, the simple point charge ClayFF potential and the core-shell potential to study tobermorite minerals, the most prominent family of Calcium-Silicate-Hydrates that are complex hydrated oxides. We benchmark the predictive capabilities of these force fields against first principles results. While the structural information seem to be in close agreement with DFT results, we find that for higher order properties such as elastic constants, the core-shell potential quantitatively improves upon the simple point charge model, and shows a larger degree of transferability to complex materials. In return, to remedy the deficiencies of the simple point charge potential for hydrated calcio-silicates, we suggest using both structural data and elasticity data for potential calibration, a new force field potential, CSH-FF. This re-parameterized version of ClayFF is then applied to simulating an atomistic model of cement (Pellenq et al., PNAS, 2009). We demonstrate that this force field improves the predictive capabilities of ClayFF, being considerably less computational intensive than the core-shell model.
Improved side-chain torsion potentials for the Amber ff99SB protein force field.
Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L; Dror, Ron O; Shaw, David E
2010-06-01
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.
Asymptotic analysis of force-free magnetic fields of cylindrical symmetry
NASA Technical Reports Server (NTRS)
Sturrock, P. A.; Antiochos, S. K.; Roumeliotis, G.
1995-01-01
It is known from computer calculations that if a force-free magnetic-field configuration is stressed progressively by footpoint displacements, the configuration expands and approaches the open configuration with the same surface flux distribution, and, in the process, the energy of the field increases progressively. Analysis of a simple model of force-free fields of cylindrical symmetry leads to simple asymptotic expressions for the extent and energy of such a configuration. The analysis is carried through for both spherical and planar source surfaces. According to this model, the field evolves in a well-behaved manner with no indication of instability or loss of equilibrium.
Force on a heated sphere in a horizontal plane acoustic standing wave field
NASA Technical Reports Server (NTRS)
Leung, E. W.; Wang, T. G.
1985-01-01
The force on a heated sphere in a horizontal plane acoustic standing wave field is the subject of this investigation. The heated sphere produces a thermal gradient in the resonance chamber. The force on the sphere in a direction perpendicular to that of gravity is measured. This force is enhanced in the region near the pressure node, and is weakened in the region near the pressure antinode. Measurements of the force on a heated sphere with sound pressure levels between 148 and 156 dB are presented.
Asaoka, Ryo; Fujino, Yuri; Murata, Hiroshi; Miki, Atsuya; Tanito, Masaki; Mizoue, Shiro; Mori, Kazuhiko; Suzuki, Katsuyoshi; Yamashita, Takehiro; Kashiwagi, Kenji; Shoji, Nobuyuki
2016-01-01
Visual field (VF) data were retrospectively obtained from 491 eyes in 317 patients with open angle glaucoma who had undergone ten VF tests (Humphrey Field Analyzer, 24-2, SITA standard). First, mean of total deviation values (mTD) in the tenth VF was predicted using standard linear regression of the first five VFs (VF1-5) through to using all nine preceding VFs (VF1-9). Then an ‘intraocular pressure (IOP)-integrated VF trend analysis’ was carried out by simply using time multiplied by IOP as the independent term in the linear regression model. Prediction errors (absolute prediction error or root mean squared error: RMSE) for predicting mTD and also point wise TD values of the tenth VF were obtained from both approaches. The mTD absolute prediction errors associated with the IOP-integrated VF trend analysis were significantly smaller than those from the standard trend analysis when VF1-6 through to VF1-8 were used (p < 0.05). The point wise RMSEs from the IOP-integrated trend analysis were significantly smaller than those from the standard trend analysis when VF1-5 through to VF1-9 were used (p < 0.05). This was especially the case when IOP was measured more frequently. Thus a significantly more accurate prediction of VF progression is possible using a simple trend analysis that incorporates IOP measurements. PMID:27562553
2016-01-01
Visual field (VF) data were retrospectively obtained from 491 eyes in 317 patients with open angle glaucoma who had undergone ten VF tests (Humphrey Field Analyzer, 24-2, SITA standard). First, mean of total deviation values (mTD) in the tenth VF was predicted using standard linear regression of the first five VFs (VF1-5) through to using all nine preceding VFs (VF1-9). Then an 'intraocular pressure (IOP)-integrated VF trend analysis' was carried out by simply using time multiplied by IOP as the independent term in the linear regression model. Prediction errors (absolute prediction error or root mean squared error: RMSE) for predicting mTD and also point wise TD values of the tenth VF were obtained from both approaches. The mTD absolute prediction errors associated with the IOP-integrated VF trend analysis were significantly smaller than those from the standard trend analysis when VF1-6 through to VF1-8 were used (p < 0.05). The point wise RMSEs from the IOP-integrated trend analysis were significantly smaller than those from the standard trend analysis when VF1-5 through to VF1-9 were used (p < 0.05). This was especially the case when IOP was measured more frequently. Thus a significantly more accurate prediction of VF progression is possible using a simple trend analysis that incorporates IOP measurements. PMID:27562553
Gong, Yuanzheng; Hu, Danying; Hannaford, Blake; Seibel, Eric J.
2014-01-01
Abstract. Brain tumor margin removal is challenging because diseased tissue is often visually indistinguishable from healthy tissue. Leaving residual tumor leads to decreased survival, and removing normal tissue causes life-long neurological deficits. Thus, a surgical robotics system with a high degree of dexterity, accurate navigation, and highly precise resection is an ideal candidate for image-guided removal of fluorescently labeled brain tumor cells. To image, we developed a scanning fiber endoscope (SFE) which acquires concurrent reflectance and fluorescence wide-field images at a high resolution. This miniature flexible endoscope was affixed to the arm of a RAVEN II surgical robot providing programmable motion with feedback control using stereo-pair surveillance cameras. To verify the accuracy of the three-dimensional (3-D) reconstructed surgical field, a multimodal physical-sized model of debulked brain tumor was used to obtain the 3-D locations of residual tumor for robotic path planning to remove fluorescent cells. Such reconstruction is repeated intraoperatively during margin clean-up so the algorithm efficiency and accuracy are important to the robotically assisted surgery. Experimental results indicate that the time for creating this 3-D surface can be reduced to one-third by using known trajectories of a robot arm, and the error from the reconstructed phantom is within 0.67 mm in average compared to the model design. PMID:26158071
Gong, Yuanzheng; Hu, Danying; Hannaford, Blake; Seibel, Eric J
2014-10-01
Brain tumor margin removal is challenging because diseased tissue is often visually indistinguishable from healthy tissue. Leaving residual tumor leads to decreased survival, and removing normal tissue causes life-long neurological deficits. Thus, a surgical robotics system with a high degree of dexterity, accurate navigation, and highly precise resection is an ideal candidate for image-guided removal of fluorescently labeled brain tumor cells. To image, we developed a scanning fiber endoscope (SFE) which acquires concurrent reflectance and fluorescence wide-field images at a high resolution. This miniature flexible endoscope was affixed to the arm of a RAVEN II surgical robot providing programmable motion with feedback control using stereo-pair surveillance cameras. To verify the accuracy of the three-dimensional (3-D) reconstructed surgical field, a multimodal physical-sized model of debulked brain tumor was used to obtain the 3-D locations of residual tumor for robotic path planning to remove fluorescent cells. Such reconstruction is repeated intraoperatively during margin clean-up so the algorithm efficiency and accuracy are important to the robotically assisted surgery. Experimental results indicate that the time for creating this 3-D surface can be reduced to one-third by using known trajectories of a robot arm, and the error from the reconstructed phantom is within 0.67 mm in average compared to the model design.
Iwakiri, Junichi; Hamada, Michiaki; Asai, Kiyoshi; Kameda, Tomoshi
2016-09-13
RNA-protein interactions play fundamental roles in many biological processes. To understand these interactions, it is necessary to know the three-dimensional structures of RNA-protein complexes. However, determining the tertiary structure of these complexes is often difficult, suggesting that an accurate rigid body docking for RNA-protein complexes is needed. In general, the rigid body docking process is divided into two steps: generating candidate structures from the individual RNA and protein structures and then narrowing down the candidates. In this study, we focus on the former problem to improve the prediction accuracy in RNA-protein docking. Our method is based on the integration of physicochemical information about RNA into ZDOCK, which is known as one of the most successful computer programs for protein-protein docking. Because recent studies showed the current force field for molecular dynamics simulation of protein and nucleic acids is quite accurate, we modeled the physicochemical information about RNA by force fields such as AMBER and CHARMM. A comprehensive benchmark of RNA-protein docking, using three recently developed data sets, reveals the remarkable prediction accuracy of the proposed method compared with existing programs for docking: the highest success rate is 34.7% for the predicted structure of the RNA-protein complex with the best score and 79.2% for 3,600 predicted ones. Three full atomistic force fields for RNA (AMBER94, AMBER99, and CHARMM22) produced almost the same accurate result, which showed current force fields for nucleic acids are quite accurate. In addition, we found that the electrostatic interaction and the representation of shape complementary between protein and RNA plays the important roles for accurate prediction of the native structures of RNA-protein complexes.
Iwakiri, Junichi; Hamada, Michiaki; Asai, Kiyoshi; Kameda, Tomoshi
2016-09-13
RNA-protein interactions play fundamental roles in many biological processes. To understand these interactions, it is necessary to know the three-dimensional structures of RNA-protein complexes. However, determining the tertiary structure of these complexes is often difficult, suggesting that an accurate rigid body docking for RNA-protein complexes is needed. In general, the rigid body docking process is divided into two steps: generating candidate structures from the individual RNA and protein structures and then narrowing down the candidates. In this study, we focus on the former problem to improve the prediction accuracy in RNA-protein docking. Our method is based on the integration of physicochemical information about RNA into ZDOCK, which is known as one of the most successful computer programs for protein-protein docking. Because recent studies showed the current force field for molecular dynamics simulation of protein and nucleic acids is quite accurate, we modeled the physicochemical information about RNA by force fields such as AMBER and CHARMM. A comprehensive benchmark of RNA-protein docking, using three recently developed data sets, reveals the remarkable prediction accuracy of the proposed method compared with existing programs for docking: the highest success rate is 34.7% for the predicted structure of the RNA-protein complex with the best score and 79.2% for 3,600 predicted ones. Three full atomistic force fields for RNA (AMBER94, AMBER99, and CHARMM22) produced almost the same accurate result, which showed current force fields for nucleic acids are quite accurate. In addition, we found that the electrostatic interaction and the representation of shape complementary between protein and RNA plays the important roles for accurate prediction of the native structures of RNA-protein complexes. PMID:27494732
Acoustic radiation force due to arbitrary incident fields on spherical particles in soft tissue
Treweek, Benjamin C. Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.; Hamilton, Mark F.
2015-10-28
Acoustic radiation force is of interest in a wide variety of biomedical applications ranging from tissue characterization (e.g. elastography) to tissue treatment (e.g. high intensity focused ultrasound, kidney stone fragment removal). As tissue mechanical properties are reliable indicators of tissue health, the former is the focus of the present contribution. This is accomplished through an investigation of the acoustic radiation force on a spherical scatterer embedded in tissue. Properties of both the scatterer and the surrounding tissue are important in determining the magnitude and the direction of the force. As these properties vary, the force computation shows changes in magnitude and direction, which may enable more accurate noninvasive determination of tissue properties.
Acoustic radiation force due to arbitrary incident fields on spherical particles in soft tissue
NASA Astrophysics Data System (ADS)
Treweek, Benjamin C.; Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.; Hamilton, Mark F.
2015-10-01
Acoustic radiation force is of interest in a wide variety of biomedical applications ranging from tissue characterization (e.g. elastography) to tissue treatment (e.g. high intensity focused ultrasound, kidney stone fragment removal). As tissue mechanical properties are reliable indicators of tissue health, the former is the focus of the present contribution. This is accomplished through an investigation of the acoustic radiation force on a spherical scatterer embedded in tissue. Properties of both the scatterer and the surrounding tissue are important in determining the magnitude and the direction of the force. As these properties vary, the force computation shows changes in magnitude and direction, which may enable more accurate noninvasive determination of tissue properties.
Fractal growth in the presence of a surface force field
NASA Astrophysics Data System (ADS)
Carlier, F.; Brion, E.; Akulin, V. M.
2012-05-01
We numerically simulate the dynamics of atomic clusters aggregation deposited on a surface interacting with the growing island. We make use of the well-known DLA model but replace the underlying diffusion equation by the Smoluchowski equation which results in a drifted DLA model and anisotropic jump probabilities. The shape of the structures resulting from their aggregation-limited random walk is affected by the presence of a Laplacian potential due to, for instance, the surface stress field. We characterize the morphologies we obtain by their Hausdorff fractal dimension as well as the so-called external fractal dimension. We compare our results to previously published experimental results for antimony and silver clusters deposited onto graphite surface.
NASA Astrophysics Data System (ADS)
Jiménez-Teja, Y.; Benítez, N.; Molino, A.; Fernandes, C. A. C.
2015-10-01
Photometric redshifts, which have become the cornerstone of several of the largest astronomical surveys like PanStarrs, DES, J-PAS and LSST, require precise measurements of galaxy photometry in different bands using a consistent physical aperture. This is not trivial, due to the variation in the shape and width of the point spread function (PSF) introduced by wavelength differences, instrument positions and atmospheric conditions. Current methods to correct for this effect rely on a detailed knowledge of PSF characteristics as a function of the survey coordinates, which can be difficult due to the relative paucity of stars tracking the PSF behaviour. Here we show that it is possible to measure accurate, consistent multicolour photometry without knowing the shape of the PSF. The Chebyshev-Fourier functions (CHEFs) can fit the observed profile of each object and produce high signal-to-noise integrated flux measurements unaffected by the PSF. These total fluxes, which encompass all the galaxy populations, are much more useful for galaxy evolution studies than aperture photometry. We compare the total magnitudes and colours obtained using our software to traditional photometry with SEXTRACTOR, using real data from the COSMOS survey and the Hubble Ultra-Deep Field (HUDF). We also apply the CHEF technique to the recently published eXtreme Deep Field (XDF) and compare the results to those from COLORPRO on the HUDF. We produce a photometric catalogue with 35 732 sources (10 823 with signal-to-noise ratio ≥5), reaching a photometric redshift precision of 2 per cent due to the extraordinary depth and wavelength coverage of the eXtreme Deep Field images.
NASA Astrophysics Data System (ADS)
Skowron, A.; Lee, D. S.; De León, R. R.
2013-08-01
Aviation emissions of NOx result in the formation of tropospheric ozone (warming) and destruction of a small amount of methane (cooling), positive and negative radiative forcing effects. In addition, the reduction of methane results in a small long-term reduction in tropospheric ozone (cooling) and, in addition, a long-term reduction in water vapour in the stratosphere (cooling) from reduced oxidation of methane, both negative radiative forcing impacts. Taking all these radiative effects together, aircraft NOx is still thought to result in a positive (warming) radiative effect under constant emissions assumptions. Previously, comparative modelling studies have focussed on the variability between models, using the same emissions database. In this study, we rather quantify the variability and uncertainty arising from different estimations of present-day aircraft NOx emissions. Six different aircraft NOx emissions inventories were used in the global chemical transport model, MOZART v3. The inventories were normalized to give the same global emission of NOx in order to remove one element of uncertainty. Emissions differed in the normalized cases by 23% at cruise altitudes (283-200 hPa, where the bulk of emission occurs, globally). However, the resultant short-term ozone chemical perturbation varied by 15% between the different inventories. Once all the effects that give rise to positive and negative radiative impacts were accounted for, the variability of net radiative forcing impacts was 94%. Using these radiative effects to formulate a net aviation NOx Global Warming Potential (GWP) for a 100-year time horizon resulted in GWPs ranging from 60 to 4, over an order of magnitude. It is concluded that the detailed placement of emissions at chemically sensitive cruise altitudes strongly affects the assessment of the total radiative impact, introducing a hitherto previously unidentified large fraction of the uncertainty of impacts between different modelling assessments. It
MAGNETIC HELICITY OF SELF-SIMILAR AXISYMMETRIC FORCE-FREE FIELDS
Zhang Mei; Flyer, Natasha; Low, Boon Chye
2012-08-10
In this paper, we continue our theoretical studies addressing the possible consequences of magnetic helicity accumulation in the solar corona. Our previous studies suggest that coronal mass ejections (CMEs) are natural products of coronal evolution as a consequence of magnetic helicity accumulation and that the triggering of CMEs by surface processes such as flux emergence also have their origin in magnetic helicity accumulation. Here, we use the same mathematical approach to study the magnetic helicity of axisymmetric power-law force-free fields but focus on a family whose surface flux distributions are defined by self-similar force-free fields. The semi-analytical solutions of the axisymmetric self-similar force-free fields enable us to discuss the properties of force-free fields possessing a huge amount of accumulated magnetic helicity. Our study suggests that there may be an absolute upper bound on the total magnetic helicity of all bipolar axisymmetric force-free fields. With the increase of accumulated magnetic helicity, the force-free field approaches being fully opened up with Parker-spiral-like structures present around a current-sheet layer as evidence of magnetic helicity in the interplanetary space. It is also found that among the axisymmetric force-free fields having the same boundary flux distribution, the one that is self-similar is the one possessing the maximum amount of total magnetic helicity. This gives a possible physical reason why self-similar fields are often found in astrophysical bodies, where magnetic helicity accumulation is presumably also taking place.
Timing-specific transfer of adapted muscle activity after walking in an elastic force field.
Blanchette, Andreanne; Bouyer, Laurent J
2009-07-01
Human locomotion results from interactions between feedforward (central commands from voluntary and automatic drive) and feedback (peripheral commands from sensory inputs) mechanisms. Recent studies have shown that locomotion can be adapted when an external force is applied to the lower limb. To better understand the neural control of this adaptation, the present study investigated gait modifications resulting from exposure to a position-dependent force field. Ten subjects walked on a treadmill before, during, and after exposure to a force field generated by elastic tubing that pulled the foot forward and up during swing. Lower limb kinematics and electromyographic (EMG) activity were recorded during each walking period. During force field exposure, peak foot velocity was initially increased by 38%. As subjects adapted, peak foot velocity gradually returned to baseline in
Atomistic insight into orthoborate-based ionic liquids: force field development and evaluation.
Wang, Yong-Lei; Shah, Faiz Ullah; Glavatskih, Sergei; Antzutkin, Oleg N; Laaksonen, Aatto
2014-07-24
We have developed an all-atomistic force field for a new class of halogen-free chelated orthoborate-phosphonium ionic liquids. The force field is based on an AMBER framework with determination of force field parameters for phosphorus and boron atoms, as well as refinement of several available parameters. The bond and angle force constants were adjusted to fit vibration frequency data derived from both experimental measurements and ab initio calculations. The force field parameters for several dihedral angles were obtained by fitting torsion energy profiles deduced from ab initio calculations. To validate the proposed force field parameters, atomistic simulations were performed for 12 ionic liquids consisting of tetraalkylphosphonium cations and chelated orthoborate anions. The predicted densities for neat ionic liquids and the [P6,6,6,14][BOB] sample, with a water content of approximately 2.3-2.5 wt %, are in excellent agreement with available experimental data. The potential energy components of 12 ionic liquids were discussed in detail. The radial distribution functions and spatial distribution functions were analyzed and visualized to probe the microscopic ionic structures of these ionic liquids. There are mainly four high-probability regions of chelated orthoborate anions distributed around tetraalkylphosphonium cations in the first solvation shell, and such probability distribution functions are strongly influenced by the size of anions. PMID:25020237
Atomistic insight into orthoborate-based ionic liquids: force field development and evaluation.
Wang, Yong-Lei; Shah, Faiz Ullah; Glavatskih, Sergei; Antzutkin, Oleg N; Laaksonen, Aatto
2014-07-24
We have developed an all-atomistic force field for a new class of halogen-free chelated orthoborate-phosphonium ionic liquids. The force field is based on an AMBER framework with determination of force field parameters for phosphorus and boron atoms, as well as refinement of several available parameters. The bond and angle force constants were adjusted to fit vibration frequency data derived from both experimental measurements and ab initio calculations. The force field parameters for several dihedral angles were obtained by fitting torsion energy profiles deduced from ab initio calculations. To validate the proposed force field parameters, atomistic simulations were performed for 12 ionic liquids consisting of tetraalkylphosphonium cations and chelated orthoborate anions. The predicted densities for neat ionic liquids and the [P6,6,6,14][BOB] sample, with a water content of approximately 2.3-2.5 wt %, are in excellent agreement with available experimental data. The potential energy components of 12 ionic liquids were discussed in detail. The radial distribution functions and spatial distribution functions were analyzed and visualized to probe the microscopic ionic structures of these ionic liquids. There are mainly four high-probability regions of chelated orthoborate anions distributed around tetraalkylphosphonium cations in the first solvation shell, and such probability distribution functions are strongly influenced by the size of anions.
Song, Wei; Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Cai, Wei; Jacobs, Donald J
2013-01-01
We recently developed the Image-Charge Solvation Model (ICSM), which is an explicit/implicit hybrid model to accurately account for long-range electrostatic forces in molecular dynamics simulations [Lin et al., J. Chem. Phys., 131, 154103, 2009]. The ICSM has a productive spherical volume within the simulation cell for which key physical properties of bulk water are reproduced, such as density, radial distribution function, diffusion constants and dielectric properties. Although the reaction field (RF) is essential, it typically accounts for less than 2% of the total electrostatic force on a water molecule. This observation motivates investigating further the role of the RF within the ICSM. In this report we focus on distributions of forces and torques on water molecules as a function of distance from the origin and make extensive tests over a range of model parameters where Coulomb forces are decomposed into direct interactions from waters modeled explicitly and the RF. Molecular torques due to the RF typically account for 20% of the total torque, revealing why the RF plays an important role in the dielectric properties of simulated water. Moreover, it becomes clear that the buffer layer in the ICSM is essential to mitigate artifacts caused by the discontinuous change in dielectric constants at the explicit/implicit interface.
Song, Wei; Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Cai, Wei; Jacobs, Donald J
2013-01-01
We recently developed the Image-Charge Solvation Model (ICSM), which is an explicit/implicit hybrid model to accurately account for long-range electrostatic forces in molecular dynamics simulations [Lin et al., J. Chem. Phys., 131, 154103, 2009]. The ICSM has a productive spherical volume within the simulation cell for which key physical properties of bulk water are reproduced, such as density, radial distribution function, diffusion constants and dielectric properties. Although the reaction field (RF) is essential, it typically accounts for less than 2% of the total electrostatic force on a water molecule. This observation motivates investigating further the role of the RF within the ICSM. In this report we focus on distributions of forces and torques on water molecules as a function of distance from the origin and make extensive tests over a range of model parameters where Coulomb forces are decomposed into direct interactions from waters modeled explicitly and the RF. Molecular torques due to the RF typically account for 20% of the total torque, revealing why the RF plays an important role in the dielectric properties of simulated water. Moreover, it becomes clear that the buffer layer in the ICSM is essential to mitigate artifacts caused by the discontinuous change in dielectric constants at the explicit/implicit interface. PMID:23833681
Ahmed, Mahmoud; Eslamian, Morteza
2015-12-01
Laminar natural convection in differentially heated (β = 0°, where β is the inclination angle), inclined (β = 30° and 60°), and bottom-heated (β = 90°) square enclosures filled with a nanofluid is investigated, using a two-phase lattice Boltzmann simulation approach. The effects of the inclination angle on Nu number and convection heat transfer coefficient are studied. The effects of thermophoresis and Brownian forces which create a relative drift or slip velocity between the particles and the base fluid are included in the simulation. The effect of thermophoresis is considered using an accurate and quantitative formula proposed by the authors. Some of the existing results on natural convection are erroneous due to using wrong thermophoresis models or simply ignoring the effect. Here we show that thermophoresis has a considerable effect on heat transfer augmentation in laminar natural convection. Our non-homogenous modeling approach shows that heat transfer in nanofluids is a function of the inclination angle and Ra number. It also reveals some details of flow behavior which cannot be captured by single-phase models. The minimum heat transfer rate is associated with β = 90° (bottom-heated) and the maximum heat transfer rate occurs in an inclination angle which varies with the Ra number.
Ahmed, Mahmoud; Eslamian, Morteza
2015-12-01
Laminar natural convection in differentially heated (β = 0°, where β is the inclination angle), inclined (β = 30° and 60°), and bottom-heated (β = 90°) square enclosures filled with a nanofluid is investigated, using a two-phase lattice Boltzmann simulation approach. The effects of the inclination angle on Nu number and convection heat transfer coefficient are studied. The effects of thermophoresis and Brownian forces which create a relative drift or slip velocity between the particles and the base fluid are included in the simulation. The effect of thermophoresis is considered using an accurate and quantitative formula proposed by the authors. Some of the existing results on natural convection are erroneous due to using wrong thermophoresis models or simply ignoring the effect. Here we show that thermophoresis has a considerable effect on heat transfer augmentation in laminar natural convection. Our non-homogenous modeling approach shows that heat transfer in nanofluids is a function of the inclination angle and Ra number. It also reveals some details of flow behavior which cannot be captured by single-phase models. The minimum heat transfer rate is associated with β = 90° (bottom-heated) and the maximum heat transfer rate occurs in an inclination angle which varies with the Ra number. PMID:26183389
NASA Astrophysics Data System (ADS)
Miao, Hongchen; Zhou, Xilong; Dong, Shuxiang; Luo, Haosu; Li, Faxin
2014-07-01
Controlling electric polarization (or magnetization) in multiferroic materials with external magnetic fields (or electric fields) is very important for fundamental physics and spintronic devices. Although there has been some progress on magnetic-field-induced polarization reversal in single-phase multiferroics, such behavior has so far never been realized in composites. Here we show that it is possible to reverse ferroelectric polarization using magnetic fields in a bilayer Terfenol-D/PMN-33%PT composite. We realized this by ferroelectric domain imaging using piezoresponse force microscopy (PFM) under applied magnetic field loading. The internal electric field caused by the magnetoelectric (ME) effect in the PMN-PT crystal is considered as the driving force for the 180° polarization switching, and its existence is verified by switching spectroscopy PFM testing under a series of external magnetic fields. A quantitative method is further suggested to estimate the local ME coefficient based on the switching spectroscopy PFM testing results.
Miao, Hongchen; Zhou, Xilong; Dong, Shuxiang; Luo, Haosu; Li, Faxin
2014-08-01
Controlling electric polarization (or magnetization) in multiferroic materials with external magnetic fields (or electric fields) is very important for fundamental physics and spintronic devices. Although there has been some progress on magnetic-field-induced polarization reversal in single-phase multiferroics, such behavior has so far never been realized in composites. Here we show that it is possible to reverse ferroelectric polarization using magnetic fields in a bilayer Terfenol-D/PMN-33%PT composite. We realized this by ferroelectric domain imaging using piezoresponse force microscopy (PFM) under applied magnetic field loading. The internal electric field caused by the magnetoelectric (ME) effect in the PMN-PT crystal is considered as the driving force for the 180° polarization switching, and its existence is verified by switching spectroscopy PFM testing under a series of external magnetic fields. A quantitative method is further suggested to estimate the local ME coefficient based on the switching spectroscopy PFM testing results. PMID:24953042
ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins.
Cerutti, David S; Swope, William C; Rice, Julia E; Case, David A
2014-10-14
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
Zheng, Suqing; Tang, Qing; He, Jian; Du, Shiyu; Xu, Shaofang; Wang, Chaojie; Xu, Yong; Lin, Fu
2016-04-25
Force fields are fundamental to molecular dynamics simulations. However, the incompleteness of force field parameters has been a long-standing problem, especially for metal-related systems. In our previous work, we adopted the Seminario method based on the Hessian matrix to systematically derive the zinc-related force field parameters for AMBER. In this work, in order to further simplify the whole protocol, we have implemented a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools. PMID:26998926
ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
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
ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins.
Cerutti, David S; Swope, William C; Rice, Julia E; Case, David A
2014-10-14
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.
BIOREMEDIATION FIELD EVALUATION: EIELSON AIR FORCE BASE, ALASKA (EPA/540/R-95/533)
This publication, one of a series presenting the findings of the Bioremediation Field Initiatives bioremediation field evaluations, provides a detailed summary of the evaluation conducted at the Eielson Air Force Base (AFB) Superfund site in Fairbanks, Alaska. At this site, the ...
Regulation, Professional Responsibility, and Market Forces in the Health Care Field.
ERIC Educational Resources Information Center
Palmer, Alan K.
1979-01-01
The interrelationship of market forces, government regulation, and self-regulation is discussed and the Federal Trade Commission's (FTC) program involving competition in the health care field is reviewed. Concerns and misconceptions in the medical community about the FTC's involvement in the health care field are addressed. (Author/JMD)
Flute stabilization due to ponderomotive force created by an rf field with a variable gradient
Yasaka, Y.; Itatani, R.
1986-06-30
An rf-stabilization experiment was performed in the axisymmetric single-mirror device HIEI by controlling the radial-gradient scale length of the rf field with the aid of an azimuthally phased antenna array. The flute stability depends sensitively on the scale length of the perpendicular rf electric field, which shows that rf stabilization is caused by the ponderomotive force for ions.
Carroll, Timothy J; de Rugy, Aymar; Howard, Ian S; Ingram, James N; Wolpert, Daniel M
2016-01-01
Humans are able to adapt their motor commands to make accurate movements in novel sensorimotor environments, such as when wielding tools that alter limb dynamics. However, it is unclear to what extent sensorimotor representations, obtained through experience with one limb, are available to the opposite, untrained limb and in which form they are available. Here, we compared crosslimb transfer of force-field compensation after participants adapted to a velocity-dependent curl field, oriented either in the sagittal or the transverse plane. Due to the mirror symmetry of the limbs, the force field had identical effects for both limbs in joint and extrinsic coordinates in the sagittal plane but conflicting joint-based effects in the transverse plane. The degree of force-field compensation exhibited by the opposite arm in probe trials immediately after initial learning was significantly greater after sagittal (26 ± 5%) than transverse plane adaptation (9 ± 4%; P < 0.001), irrespective of whether participants learned initially with the left or the right arm or via abrupt or gradual exposure to the force field. Thus transfer was impaired when the orientation of imposed dynamics conflicted in intrinsic coordinates for the two limbs. The data reveal that neural representations of novel dynamics are only partially available to the opposite limb, since transfer is incomplete even when force-field perturbation is spatially compatible for the two limbs, according to both intrinsic and extrinsic coordinates.
de Rugy, Aymar; Howard, Ian S.; Ingram, James N.; Wolpert, Daniel M.
2015-01-01
Humans are able to adapt their motor commands to make accurate movements in novel sensorimotor environments, such as when wielding tools that alter limb dynamics. However, it is unclear to what extent sensorimotor representations, obtained through experience with one limb, are available to the opposite, untrained limb and in which form they are available. Here, we compared crosslimb transfer of force-field compensation after participants adapted to a velocity-dependent curl field, oriented either in the sagittal or the transverse plane. Due to the mirror symmetry of the limbs, the force field had identical effects for both limbs in joint and extrinsic coordinates in the sagittal plane but conflicting joint-based effects in the transverse plane. The degree of force-field compensation exhibited by the opposite arm in probe trials immediately after initial learning was significantly greater after sagittal (26 ± 5%) than transverse plane adaptation (9 ± 4%; P < 0.001), irrespective of whether participants learned initially with the left or the right arm or via abrupt or gradual exposure to the force field. Thus transfer was impaired when the orientation of imposed dynamics conflicted in intrinsic coordinates for the two limbs. The data reveal that neural representations of novel dynamics are only partially available to the opposite limb, since transfer is incomplete even when force-field perturbation is spatially compatible for the two limbs, according to both intrinsic and extrinsic coordinates. PMID:26581867
NASA Astrophysics Data System (ADS)
Ye, Chang-Qing; Ma, Guang-Tong; Liu, Kun; Wang, Jia-Su
2016-08-01
The superconducting levitation realized by immersing the high-temperature superconductors (HTSs) into nonuniform magnetic field is deemed promising in a wide range of industrial applications such as maglev transportation and kinetic energy storage. Using a well-established electromagnetic model to mathematically describe the HTS, we have developed an efficient scheme that is capable of intelligently and globally optimizing the permanent magnet guideway (PMG) with single or multiple HTSs levitated above for the maglev transportation applications. With maximizing the levitation force as the principal objective, we optimized the dimensions of a Halbach-derived PMG to observe how the field, current and force distribute inside the HTSs when the optimized situation is achieved. Using a pristine PMG as a reference, we have analyzed the critical issues for enhancing the levitation force through comparing the field, current and force distributions between the optimized and pristine PMGs. It was also found that the optimized dimensions of the PMG are highly dependent upon the levitated HTS. Moreover, the guidance force is not always contradictory to the levitation force and may also be enhanced when the levitation force is prescribed to be the principle objective, depending on the configuration of levitation system and lateral displacement.
Computational Investigation of Helical Traveling Wave Tube Transverse RF Field Forces
NASA Technical Reports Server (NTRS)
Kory, Carol L.; Dayton, James A.
1998-01-01
In a previous study using a fully three-dimensional (3D) helical slow-wave circuit cold- test model it was found, contrary to classical helical circuit analyses, that transverse FF electric fields have significant amplitudes compared with the longitudinal component. The RF fields obtained using this helical cold-test model have been scaled to correspond to those of an actual TWT. At the output of the tube, RF field forces reach 61%, 26% and 132% for radial, azimuthal and longitudinal components, respectively, compared to radial space charge forces indicating the importance of considering them in the design of electron beam focusing.
Batista, Marta L S; Pérez-Sánchez, Germán; Gomes, José R B; Coutinho, João A P; Maginn, Edward J
2015-12-10
Glucose is an important carbohydrate, relevant both for its biological functions and as a raw material for industrial processes. As a monomer of cellulose, the most abundant biopolymer, it is an alternative feedstock for fuels and chemicals in the biorefinery framework. Since glucose is often used and processed in aqueous solutions, it is important to understand the structural, volumetric, and dynamic properties of aqueous glucose solutions at varying concentrations. Molecular dynamics (MD) simulations are an effective means for computing the properties of liquid solutions, but the technique relies upon accurate intermolecular potential functions (i.e., "force fields"). Here we evaluate the accuracy of the recently developed GROMOS 56ACARBO glucose force field for its ability to model the density, viscosity, and self-diffusivity of aqueous glucose solutions as a function of concentration. We also compute different structural properties, including hydrogen bonds, radial and spatial distribution functions, and coordination numbers. The results show that the force field accurately models the density and viscosity of dilute solutions up to a glucose mole fraction of 0.1. At higher glucose concentrations, the force field overestimates the experimental density and viscosity. By analyzing the liquid structure, it is found that the glucose molecules tend to associate at higher concentrations, which leads to deviation from the experimental results. This suggests that, while the GROMOS 56ACARBO force field performs well for highly dilute glucose solutions (conditions under which it was developed), it is not appropriate for carrying out simulations of more concentrated glucose solutions. It is possible to obtain much more accurate densities and viscosities at high glucose concentrations by uniformly reducing the partial charges on glucose by 20%, which attenuates the self-association tendencies of glucose. PMID:26572856
Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase
Smith, Dayle MA; Xiong, Yijia; Straatsma, TP; Rosso, Kevin M.; Squier, Thomas C.
2012-05-09
Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexible in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of C{alpha} and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H{sub 2}-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.
Unsteady hydrodynamic forces acting on a robotic hand and its flow field.
Takagi, Hideki; Nakashima, Motomu; Ozaki, Takashi; Matsuuchi, Kazuo
2013-07-26
This study aims to clarify the mechanism of generating unsteady hydrodynamic forces acting on a hand during swimming in order to directly measure the forces, pressure distribution, and flow field around the hand by using a robotic arm and particle image velocimetry (PIV). The robotic arm consisted of the trunk, shoulder, upper arm, forearm, and hand, and it was independently computer controllable in five degrees of freedom. The elbow-joint angle of the robotic arm was fixed at 90°, and the arm was moved in semicircles around the shoulder joint in a plane perpendicular to the water surface. Two-component PIV was used for flow visualization around the hand. The data of the forces and pressure acting on the hand were sampled at 200Hz and stored on a PC. When the maximum resultant force acting on the hand was observed, a pair of counter-rotating vortices appeared on the dorsal surface of the hand. A vortex attached to the hand increased the flow velocity, which led to decreased surface pressure, increasing the hydrodynamic forces. This phenomenon is known as the unsteady mechanism of force generation. We found that the drag force was 72% greater and the lift force was 4.8 times greater than the values estimated under steady flow conditions. Therefore, it is presumable that swimmers receive the benefits of this unsteady hydrodynamic force.
Recent advances toward a general purpose linear-scaling quantum force field.
Giese, Timothy J; Huang, Ming; Chen, Haoyuan; York, Darrin M
2014-09-16
Conspectus There is need in the molecular simulation community to develop new quantum mechanical (QM) methods that can be routinely applied to the simulation of large molecular systems in complex, heterogeneous condensed phase environments. Although conventional methods, such as the hybrid quantum mechanical/molecular mechanical (QM/MM) method, are adequate for many problems, there remain other applications that demand a fully quantum mechanical approach. QM methods are generally required in applications that involve changes in electronic structure, such as when chemical bond formation or cleavage occurs, when molecules respond to one another through polarization or charge transfer, or when matter interacts with electromagnetic fields. A full QM treatment, rather than QM/MM, is necessary when these features present themselves over a wide spatial range that, in some cases, may span the entire system. Specific examples include the study of catalytic events that involve delocalized changes in chemical bonds, charge transfer, or extensive polarization of the macromolecular environment; drug discovery applications, where the wide range of nonstandard residues and protonation states are challenging to model with purely empirical MM force fields; and the interpretation of spectroscopic observables. Unfortunately, the enormous computational cost of conventional QM methods limit their practical application to small systems. Linear-scaling electronic structure methods (LSQMs) make possible the calculation of large systems but are still too computationally intensive to be applied with the degree of configurational sampling often required to make meaningful comparison with experiment. In this work, we present advances in the development of a quantum mechanical force field (QMFF) suitable for application to biological macromolecules and condensed phase simulations. QMFFs leverage the benefits provided by the LSQM and QM/MM approaches to produce a fully QM method that is able to
The rate of separation of magnetic lines of force in a random magnetic field.
NASA Technical Reports Server (NTRS)
Jokipii, J. R.
1973-01-01
The mixing of magnetic lines of force, as represented by their rate of separation, as a function of distance along the magnetic field, is considered with emphasis on neighboring lines of force. This effect is particularly important in understanding the transport of charged particles perpendicular to the average magnetic field. The calculation is carried out in the approximation that the separation changes by an amount small compared with the correlation scale normal to the field, in a distance along the field of a few correlation scales. It is found that the rate of separation is very sensitive to the precise form of the power spectrum. Application to the interplanetary and interstellar magnetic fields is discussed, and it is shown that in some cases field lines, much closer together than the correlation scale, separate at a rate which is effectively as rapid as if they were many correlation lengths apart.
Force Field Effects on a β-Sheet Protein Domain Structure in Thermal Unfolding Simulations.
Wang, Ting; Wade, Rebecca C
2006-01-01
The secondary structure propensities observed in protein simulations depend heavily on the force field parameters used. The existing empirical force fields often have difficulty in balancing the relative stabilities of helical and extended conformations. The resultant secondary structure bias may not be apparent in short simulations at room temperature starting from the native folded states. However, it can manifest itself dramatically at high temperatures and lead to large deviations from experimentally observed secondary structure propensities. Motivated by thermal unfolding simulations of several WW domains, which have a three-stranded β-sheet structure, we chose the FBP28 WW domain as a well-characterized system to investigate several AMBER force fields as well as parametrization of the NPSA (Neutralized, Polarized ionizable side chains with a solvent-accessible Surface Area-dependent term) implicit solvent model. The ff94 force field and two variants with altered parameters for the backbone torsion term were found to convert the native β-sheet structure directly to a single helix at high temperatures, whereas the ff96 force field produced significant non-native β-sheet content at high temperatures. The ff03 force field was able to reproduce the β-sheet-coil transition and experimentally observed unfolding pathways with both an explicit water solvent and the NPSA implicit solvent model at relatively low temperatures. However, the protein domain became predominantly helical after unfolding. Modification of the solvation parameter in the NPSA implicit solvent model was not sufficient to remedy this problem. The results imply that the intrinsic secondary structure bias in a force field cannot easily be solved by modifying a single parameter such as backbone torsion potential or a solvation parameter of a solvent model. Nevertheless, the results show that the AMBER ff03 force field together with an explicit solvent model or the NPSA implicit solvent model is a
Force-field parameterization of the galactic cosmic ray spectrum: Validation for Forbush decreases
NASA Astrophysics Data System (ADS)
Usoskin, I. G.; Kovaltsov, G. A.; Adriani, O.; Barbarino, G. C.; Bazilevskaya, G. A.; Bellotti, R.; Boezio, M.; Bogomolov, E. A.; Bongi, M.; Bonvicini, V.; Bottai, S.; Bruno, A.; Cafagna, F.; Campana, D.; Carbone, R.; Carlson, P.; Casolino, M.; Castellini, G.; De Donato, C.; De Santis, C.; De Simone, N.; Di Felice, V.; Formato, V.; Galper, A. M.; Karelin, A. V.; Koldashov, S. V.; Koldobskiy, S.; Krutkov, S. Y.; Kvashnin, A. N.; Leonov, A.; Malakhov, V.; Marcelli, L.; Martucci, M.; Mayorov, A. G.; Menn, W.; Mergé, M.; Mikhailov, V. V.; Mocchiutti, E.; Monaco, A.; Mori, N.; Munini, R.; Osteria, G.; Palma, F.; Panico, B.; Papini, P.; Pearce, M.; Picozza, P.; Pizzolotto, C.; Ricci, M.; Ricciarini, S. B.; Rossetto, L.; Sarkar, R.; Scotti, V.; Simon, M.; Sparvoli, R.; Spillantini, P.; Stozhkov, Y. I.; Vacchi, A.; Vannuccini, E.; Vasilyev, G. I.; Voronov, S. A.; Yurkin, Y. T.; Zampa, G.; Zampa, N.; Zverev, V. G.
2015-06-01
A useful parametrization of the energy spectrum of galactic cosmic rays (GCR) near Earth is offered by the so-called force-field model which describes the shape of the entire spectrum with a single parameter, the modulation potential. While the usefulness of the force-field approximation has been confirmed for regular periods of solar modulation, it was not tested explicitly for disturbed periods, when GCR are locally modulated by strong interplanetary transients. Here we use direct measurements of protons and α -particles performed by the PAMELA space-borne instrument during December 2006, including a major Forbush decrease, in order to directly test the validity of the force-field parameterization. We conclude that (1) The force-field parametrization works very well in describing the energy spectra of protons and α -particles directly measured by PAMELA outside the Earths atmosphere; (2) The energy spectrum of GCR can be well parameterized by the force-field model also during a strong Forbush decrease; (3) The estimate of the GCR modulation parameter, obtained using data from the world-wide neutron monitor network, is in good agreement with the spectra directly measured by PAMELA during the studied interval. This result is obtained on the basis of a single event analysis, more events need to be analyzed.
Optimization of classical nonpolarizable force fields for OH(-) and H3O(+).
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. PMID:26979693
Development of AMOEBA force field for 1,3-dimethylimidazolium based ionic liquids.
Starovoytov, Oleg N; Torabifard, Hedieh; Cisneros, G Andrés
2014-06-26
The development of AMOEBA (a multipolar polarizable force field) for imidazolium based ionic liquids is presented. Our parametrization method follows the AMOEBA procedure and introduces the use of QM intermolecular total interactions as well as QM energy decomposition analysis (EDA) to fit individual interaction energy components. The distributed multipoles for the cation and anions have been derived using both the Gaussian distributed multipole analysis (GDMA) and Gaussian electrostatic model-distributed multipole (GEM-DM) methods.1 The intermolecular interactions of a 1,3-dimethylimidazolium [dmim(+)] cation with various anions, including fluoride [F(-)], chloride [Cl(-)], nitrate [NO(3)(-)], and tetraflorouborate [BF(4)(-)], were studied using quantum chemistry calculations at the MP2/6-311G(d,p) level of theory. Energy decomposition analysis was performed for each pair using the restricted variational space decomposition approach (RVS) at the HF/6-311G(d,p) level. The new force field was validated by running a series of molecular dynamic (MD) simulations and by analyzing thermodynamic and structural properties of these systems. A number of thermodynamic properties obtained from MD simulations were compared with available experimental data. The ionic liquid structure reproduced using the AMOEBA force field is also compared with the data from neutron diffraction experiment and other MD simulations. Employing GEM-DM force fields resulted in a good agreement on liquid densities ρ, enthalpies of vaporization ΔH(vap), and diffusion coefficients D(±) in comparison with conventional force fields.
Lundborg, Magnus; Lindahl, Erik
2015-01-22
Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.
Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields.
Götz, Andreas W; Bucher, Denis; Lindert, Steffen; McCammon, J Andrew
2014-04-01
The description of aggregation processes with molecular dynamics simulations is a playground for testing biomolecular force fields, including a new generation of force fields that explicitly describe electronic polarization. In this work, we study a system consisting of 50 glycyl-l-alanine (Gly-Ala) dipeptides in solution with 1001 water molecules. Neutron diffraction experiments have shown that at this concentration, Gly-Ala aggregates into large clusters. However, general-purpose force fields in combination with established water models can fail to correctly describe this aggregation process, highlighting important deficiencies in how solute-solute and solute-solvent interactions are parametrized in these force fields. We found that even for the fully polarizable AMOEBA force field, the degree of association is considerably underestimated. Instead, a fixed point-charge approach based on the newly developed IPolQ scheme [Cerutti et al. J. Phys. Chem.2013, 117, 2328] allows for the correct modeling of the dipeptide aggregation in aqueous solution. This result should stimulate interest in novel fitting schemes that aim to improve the description of the solvent polarization effect within both explicitly polarizable and fixed point-charge frameworks.
Optimization of classical nonpolarizable force fields for OH(-) and H3O(+).
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.
Vergadou, Niki; Androulaki, Eleni; Hill, Jörg-Rüdiger; Economou, Ioannis G
2016-03-01
Imidazolium-based ionic liquids (ILs) incorporating the tricyanomethanide ([TCM(-)]) anion are studied using an optimized classical force field. These ILs are very promising candidates for use in a wide range of cutting-edge technologies and, to our knowledge, it is the first time that this IL family is subject to a molecular simulation study with the use of a classical atomistic force field. The [C4mim(+)][TCM(-)] ionic liquid at 298.15 K and at atmospheric pressure was used as the basis for force field optimization which primarily involved the determination of the Lennard-Jones parameters of [TCM(-)] and the implementation of three quantum mechanical schemes for the calculation of the partial charge distribution and the identification of the appropriate scaling factor for the reduction of the total ionic charge. The optimized force field was validated by performing simulations of the 1-alkyl-3-methylimidazolium tricyanomethanide ([Cnmim(+)][TCM(-)], n = 2, 4, 6, and 8) IL family at various temperatures. The results for density, self-diffusivity and viscosity are in very good agreement with the available experimental data for all ILs verifying that the force field reliably reproduces the behaviour of the imidazolium-based [TCM(-)] IL family in a wide temperature range. Furthermore, a detailed analysis of the microscopic structure and the complex dynamic behaviour of the ILs under study was performed. PMID:26878611
A long-lived coronal X-ray arcade. [force-free magnetic field analysis
NASA Technical Reports Server (NTRS)
Mcguire, J. P.; Tandberg-Hanssen, E.; Krall, K. R.; Wu, S. T.; Smith, J. B., Jr.; Speich, D. M.
1977-01-01
A large, long-lived, soft X-ray emitting arch system observed during a Skylab mission is analyzed. The supposition is that these arches owe their stability to the stable coronal magnetic-field configuration. A global constant alpha force-free magnetic field analysis, is used to describe the arches which stayed in the same approximate position for several solar rotations. A marked resemblance is noted between the theoretical magnetic field configuration and the observed X-ray emmitting feature.
Quasi-static evolution of sheared force-free fields and the solar flare problem
NASA Technical Reports Server (NTRS)
Aly, J. J.
1985-01-01
Some new results are given showing the possible evolution of a two-dimensional force-free field in the half-space z greater than 0 toward an open field. This evolution is driven by shearing motions applied to the feet of the field lines on the boundary z = 0. The consequences of these results for a model of the two-ribbon solar flare are discussed.
Mapping the electrostatic force field of single molecules from high-resolution scanning probe images
Hapala, Prokop; Švec, Martin; Stetsovych, Oleksandr; van der Heijden, Nadine J.; Ondráček, Martin; van der Lit, Joost; Mutombo, Pingo; Swart, Ingmar; Jelínek, Pavel
2016-01-01
How electronic charge is distributed over a molecule determines to a large extent its chemical properties. Here, we demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with submolecular resolution. We exploit the fact that distortions typically observed in high-resolution atomic force microscopy images are for a significant part caused by the electrostatic force acting between charges of the tip and the molecule of interest. By finding a geometrical transformation between two high-resolution AFM images acquired with two different tips, the electrostatic force field or potential over individual molecules and self-assemblies thereof can be reconstructed with submolecular resolution. PMID:27230940
Tethyan collision forces and the stress field of the Eurasian Plate
NASA Astrophysics Data System (ADS)
Warners-Ruckstuhl, Karin N.; Govers, Rob; Wortel, Rinus
2013-10-01
Resistive forces along convergent plate boundaries have a major impact on surface deformation, most visibly at collisional plate boundaries. Although quantification of these forces is key to understanding the evolution and present state of mountain belts, they remain highly uncertain due to the complexity of plate boundary structures and rheologies. In previous studies of the Eurasian Plate, we have analysed the balance of plate boundary forces, tractions resulting from lithosphere-mantle coupling, and intraplate variations in topography and density structure. This yielded a range of acceptable force distributions. In this study, we investigate to which extent the observed present-day stress field provides further constraints on the distribution of forces. We address the dynamics of the Eurasian Plate as a whole. This enables us to base our analysis on mechanical equilibrium of a tectonic plate and to evaluate all forces as part of an internally consistent set of forces driving and deforming Eurasia. We incorporate tractions from convective mantle flow modelling in a lithospheric model in which edge and lithospheric body forces are modelled explicitly and compute resulting stresses in a homogeneous elastic thin shell. Intraplate stress observations used are from the World Stress Map project. Eurasia's stress field turns out to be particularly sensitive to the distribution of collision forces on the plate's southern margin and, to a much lesser extent, to lithospheric density structure and tractions from mantle flow. Stress observations require collision forces on the India-Eurasia boundary of 7.0-10.5 TN m-1 and on the Arabia-Eurasia boundary of 1.3-2.7 TN m-1. Implication of mechanical equilibrium of the plate is that forces on the contacts with the African and Australian plates amount to 1.0-2.5 and 0-1.3 TN m-1, respectively. We use our results to assess the validity of the classical view that the mean elevation of an orogenic plateau can be taken as a measure
Zgarbová, Marie; Luque, F Javier; Sponer, Jiří; Cheatham, Thomas E; Otyepka, Michal; Jurečka, Petr
2013-05-14
We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations.
Prueitt, Melvin L.; Mueller, Fred M.; Smith, James L.
1991-01-01
The present invention identifies several configurations of conducting elements capable of storing extremely high magnetic fields for the purpose of energy storage or for other uses, wherein forces experienced by the conducting elements and the magnetic field pollution produced at locations away from the configuration are both significantly reduced over those which are present as a result of the generation of such high fields by currently proposed techniques. It is anticipated that the use of superconducting materials will both permit the attainment of such high fields and further permit such fields to be generated with vastly improved efficiency.
Prueitt, M.L.; Mueller, F.M.; Smith, J.L.
1991-04-09
The present invention identifies several configurations of conducting elements capable of storing extremely high magnetic fields for the purpose of energy storage or for other uses, wherein forces experienced by the conducting elements and the magnetic field pollution produced at locations away from the configuration are both significantly reduced over those which are present as a result of the generation of such high fields by currently proposed techniques. It is anticipated that the use of superconducting materials will both permit the attainment of such high fields and further permit such fields to be generated with vastly improved efficiency. 15 figures.
Debiec, Karl T; Cerutti, David S; Baker, Lewis R; Gronenborn, Angela M; Case, David A; Chong, Lillian T
2016-08-01
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
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
Debiec, Karl T; Cerutti, David S; Baker, Lewis R; Gronenborn, Angela M; Case, David A; Chong, Lillian T
2016-08-01
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.
Experimental studies of protozoan response to intense magnetic fields and forces
NASA Astrophysics Data System (ADS)
Guevorkian, Karine
Intense static magnetic fields of up to 31 Tesla were used as a novel tool to manipulate the swimming mechanics of unicellular organisms. It is shown that homogenous magnetic fields alter the swimming trajectories of the single cell protozoan Paramecium caudatum, by aligning them parallel to the applied field. Immobile neutrally buoyant paramecia also oriented in magnetic fields with similar rates as the motile ones. It was established that the magneto-orientation is mostly due to the magnetic torques acting on rigid structures in the cell body and therefore the response is a non-biological, passive response. From the orientation rate of paramecia in various magnetic field strengths, the average anisotropy of the diamagnetic susceptibility of the cell was estimated. It has also been demonstrated that magnetic forces can be used to create increased, decreased and even inverted simulated gravity environments for the investigation of the gravi-responses of single cells. Since the mechanisms by which Earth's gravity affects cell functioning are still not fully understood, a number of methods to simulate different strength gravity environments, such as centrifugation, have been employed. Exploiting the ability to exert magnetic forces on weakly diamagnetic constituents of the cells, we were able to vary the gravity from -8 g to 10 g, where g is Earth's gravity. Investigations of the swimming response of paramecia in these simulated gravities revealed that they actively regulate their swimming speed to oppose the external force. This result is in agreement with centrifugation experiments, confirming the credibility of the technique. Moreover, the Paramecium's swimming ceased in simulated gravity of 10 g, indicating a maximum possible propulsion force of 0.7 nN. The magnetic force technique to simulate gravity is the only earthbound technique that can create increased and decreased simulated gravities in the same experimental setup. These findings establish a general
Mapping of force fields in a capacitively driven radiofrequency plasma discharge
NASA Astrophysics Data System (ADS)
Dropmann, Michael; Chen, M.; Sabo, H.; Laufer, R.; Herdrich, G.; Matthews, L. S.; Hyde, T. W.
2016-08-01
> In this paper a method is described that allows mapping of the forces acting on dust particles in a GEC reference cell. Monodisperse particles are dropped into the plasma environment and their trajectories are tracked using a high-speed camera system to determine local accelerations and respective forces. Collecting data from a large number of particle drops allows the identification of three-dimensional vector fields for the acting forces. The procedure is described and multiple examples in which the method has been applied are given. These examples include a simple plasma sheath, plasmas perturbed by a horizontal and vertical dipole magnet, an array of multiple magnets mimicking the fields found at a lunar swirl, and the fields inside a glass box used for particle confinement. Further applicability in other plasma environments will be discussed shortly.
NASA Technical Reports Server (NTRS)
Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).
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 Validation Study of the General Amber Force Field Applied to Energetic Molecular Crystals
NASA Astrophysics Data System (ADS)
Bergh, Magnus; Caleman, Carl
2016-01-01
Molecula dynamics is a well-established tool to computationally study molecules. However, to reach predictive capability at the level required for applied research and design, extensive validation of the available force fields is pertinent. Here we present a study of density, isothermal compressibility and coefficients of thermal expansion of four energetic materials (FOX-7, RDX, CL-20 and HMX) based on molecular dynamics simulations with the General Amber Force Field (GAFF), and compare the results to experimental measurements from the literature. Furthermore, we quantify the accuracy of the calculated properties through hydrocode simulation of a typical impact scenario. We find that molecular dynamics simulations with generic and computationally efficient force fields may be used to understand and estimate important physical properties of nitramine-like energetic materials.
Controlling dispersion forces between small particles with artificially created random light fields
Brügger, Georges; Froufe-Pérez, Luis S.; Scheffold, Frank; José Sáenz, Juan
2015-01-01
Appropriate combinations of laser beams can be used to trap and manipulate small particles with optical tweezers as well as to induce significant optical binding forces between particles. These interaction forces are usually strongly anisotropic depending on the interference landscape of the external fields. This is in contrast with the familiar isotropic, translationally invariant, van der Waals and, in general, Casimir–Lifshitz interactions between neutral bodies arising from random electromagnetic waves generated by equilibrium quantum and thermal fluctuations. Here we show, both theoretically and experimentally, that dispersion forces between small colloidal particles can also be induced and controlled using artificially created fluctuating light fields. Using optical tweezers as a gauge, we present experimental evidence for the predicted isotropic attractive interactions between dielectric microspheres induced by laser-generated, random light fields. These light-induced interactions open a path towards the control of translationally invariant interactions with tuneable strength and range in colloidal systems. PMID:26096622
Empirical Corrections to the Amber RNA Force Field with Target Metadynamics.
Gil-Ley, Alejandro; Bottaro, Sandro; Bussi, Giovanni
2016-06-14
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics simulations. We here use experimental data collected from high-resolution X-ray structures to attempt an improvement of the latest version of the AMBER force field. A modified metadynamics algorithm is used to calculate correcting potentials designed to enforce experimental distributions of backbone torsion angles. Replica-exchange simulations of tetranucleotides including these correcting potentials show significantly better agreement with independent solution experiments for the oligonucleotides containing pyrimidine bases. Although the proposed corrections do not seem to be portable to generic RNA systems, the simulations revealed the importance of the α and ζ backbone angles for the modulation of the RNA conformational ensemble. The correction protocol presented here suggests a systematic procedure for force-field refinement.
Magnetic Field, Force, and Inductance Computations for an Axially Symmetric Solenoid
NASA Technical Reports Server (NTRS)
Lane, John E.; Youngquist, Robert C.; Immer, Christopher D.; Simpson, James C.
2001-01-01
The pumping of liquid oxygen (LOX) by magnetic fields (B field), using an array of electromagnets, is a current topic of research and development at Kennedy Space Center, FL. Oxygen is paramagnetic so that LOX, like a ferrofluid, can be forced in the direction of a B field gradient. It is well known that liquid oxygen has a sufficient magnetic susceptibility that a strong magnetic gradient can lift it in the earth's gravitational field. It has been proposed that this phenomenon can be utilized in transporting (i.e., pumping) LOX not only on earth, but on Mars and in the weightlessness of space. In order to design and evaluate such a magnetic pumping system, it is essential to compute the magnetic and force fields, as well as inductance, of various types of electromagnets (solenoids). In this application, it is assumed that the solenoids are air wrapped, and that the current is essentially time independent.
Paramfit: automated optimization of force field parameters for molecular dynamics simulations.
Betz, Robin M; Walker, Ross C
2015-01-15
The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field. PMID:25413259
Paramfit: automated optimization of force field parameters for molecular dynamics simulations.
Betz, Robin M; Walker, Ross C
2015-01-15
The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field.
NASA Astrophysics Data System (ADS)
Stukel, Michael R.; Landry, Michael R.; Ohman, Mark D.; Goericke, Ralf; Samo, Ty; Benitez-Nelson, Claudia R.
2012-03-01
Despite the increasing use of linear inverse modeling techniques to elucidate fluxes in undersampled marine ecosystems, the accuracy with which they estimate food web flows has not been resolved. New Markov Chain Monte Carlo (MCMC) solution methods have also called into question the biases of the commonly used L2 minimum norm (L 2MN) solution technique. Here, we test the abilities of MCMC and L 2MN methods to recover field-measured ecosystem rates that are sequentially excluded from the model input. For data, we use experimental measurements from process cruises of the California Current Ecosystem (CCE-LTER) Program that include rate estimates of phytoplankton and bacterial production, micro- and mesozooplankton grazing, and carbon export from eight study sites varying from rich coastal upwelling to offshore oligotrophic conditions. Both the MCMC and L 2MN methods predicted well-constrained rates of protozoan and mesozooplankton grazing with reasonable accuracy, but the MCMC method overestimated primary production. The MCMC method more accurately predicted the poorly constrained rate of vertical carbon export than the L 2MN method, which consistently overestimated export. Results involving DOC and bacterial production were equivocal. Overall, when primary production is provided as model input, the MCMC method gives a robust depiction of ecosystem processes. Uncertainty in inverse ecosystem models is large and arises primarily from solution under-determinacy. We thus suggest that experimental programs focusing on food web fluxes expand the range of experimental measurements to include the nature and fate of detrital pools, which play large roles in the model.
Pogosyan, Alek; Ashkan, Keyoumars; Cheeran, Binith; FitzGerald, James J.; Green, Alexander L.; Aziz, Tipu; Foltynie, Thomas; Limousin, Patricia; Zrinzo, Ludvic; Brown, Peter
2015-01-01
Local field potential (LFP) recordings from patients with deep brain stimulation electrodes in the basal ganglia have suggested that frequency-specific activities correlate with force or effort, but previous studies have not been able to disambiguate the two. Here, we dissociated effort from actual force generated by contrasting the force generation of different fingers while recording LFP activity from the subthalamic nucleus (STN) in patients with Parkinson's disease who had undergone functional surgery. Patients were studied while on their normal dopaminergic medication. We investigated the relationship between frequency-specific oscillatory activity in the STN and voluntary flexion of either the index or little finger at different effort levels. At each tested effort level (10%, 25%, and 40% of the maximal voluntary contraction force of each individual finger), the index finger generated larger force than the little finger. Movement-related suppression of beta-band power in the STN LFP was significantly modulated by effort, but not by which finger was used, suggesting that the beta suppression in the STN LFP during sustained contraction serves as a proxy for effort. The absolute force scaled with beta power suppression, but with the scaling determined by the maximal voluntary contraction force of the motor effector. Our results argue against the hypothesis that the basal ganglia are directly involved in the parameterization of force during movement and support a role of the STN in the control of motor effort to be attributed to a response. PMID:25878267
Refinement of the application of the GROMOS 54A7 force field to β-peptides.
Lin, Zhixiong; van Gunsteren, Wilfred F
2013-12-15
In this study, a hexa-β-peptide whose conformational equilibrium encompasses two different helical folds, a right-handed 2.7(10/12)-helix and a left-handed 3(14)-helix, is simulated using different GROMOS force-field parameter sets. When applying the recently developed GROMOS 54A7 force field, a significant destabilization effect on the 2.7(10/12)-helix of the peptide is observed, and the agreement with the experimental NOE distance bounds is much worse compared with the ones using previous versions of the GROMOS force field. This led us to investigate the free enthalpy difference between the two helices as a function of a variation of different subsets of force-field parameters. Both long time molecular dynamics simulations and one-step perturbation predictions suggest that the disagreement with the experimental NMR data when using the 54A7 force field is caused by the use for β-peptides of the new backbone φ-/ψ-torsional-angle energy terms introduced in this force field which were based on conformational fitting of backbone φ/ψ angles for a large set of proteins. This means that these parameters of backbone φ- and ψ-torsional-angle terms should not be applied to non-α-peptides such as β-peptides. This modified assignment of torsional-angle energy terms and parameters is denoted as 54A7_β. It corrects the wrong description of the conformational ensemble of the hexa-β-peptide obtained using the previous assignment and yields as good agreement with NMR data for other β-peptides that adopt a single helical or a hairpin fold. PMID:24122968
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.
Kührová, Petra; Best, Robert B; Bottaro, Sandro; Bussi, Giovanni; Šponer, Jiří; Otyepka, Michal; Banáš, Pavel
2016-09-13
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interactions. Although state-of-the-art Molecular Dynamics (MD) force fields correctly describe the native state of these tetraloops as a stable free-energy basin on the microsecond time scale, enhanced sampling techniques reveal that the native state is not the global free energy minimum, suggesting yet unidentified significant imbalances in the force fields. Here, we tested our ability to fold the RNA tetraloops in various force fields and simulation settings. We employed three different enhanced sampling techniques, namely, temperature replica exchange MD (T-REMD), replica exchange with solute tempering (REST2), and well-tempered metadynamics (WT-MetaD). We aimed to separate problems caused by limited sampling from those due to force-field inaccuracies. We found that none of the contemporary force fields is able to correctly describe folding of the 5'-GAGA-3' tetraloop over a range of simulation conditions. We thus aimed to identify which terms of the force field are responsible for this poor description of TL folding. We showed that at least two different imbalances contribute to this behavior, namely, overstabilization of base-phosphate and/or sugar-phosphate interactions and underestimated stability of the hydrogen bonding interaction in base pairing. The first artifact stabilizes the unfolded ensemble, while the second one destabilizes the folded state. The former problem might be partially alleviated by reparametrization of the van der Waals parameters of the phosphate oxygens suggested by Case et al., while in order to overcome the latter effect we suggest local potentials to better capture hydrogen bonding interactions.
Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.
Vanommeslaeghe, K; MacKerell, A D
2012-12-21
Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF's complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/ .
Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing
Vanommeslaeghe, K.; MacKerell, A. D.
2012-01-01
Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF’s complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/. PMID:23146088
NASA Astrophysics Data System (ADS)
Ram, Abhay K.; Dasgupta, Brahmananda; Krishnamurthy, V.; Mitra, Dhrubaditya
2014-07-01
The cosmic magnetic fields in regions of low plasma pressure and large currents, such as in interstellar space and gaseous nebulae, are force-free in the sense that the Lorentz force vanishes. The three-dimensional Arnold-Beltrami-Childress (ABC) field is an example of a force-free, helical magnetic field. In fluid dynamics, ABC flows are steady state solutions of the Euler equation. The ABC magnetic field lines exhibit a complex and varied structure that is a mix of regular and chaotic trajectories in phase space. The characteristic features of field line trajectories are illustrated through the phase space distribution of finite-distance and asymptotic-distance Lyapunov exponents. In regions of chaotic trajectories, an ensemble-averaged variance of the distance between field lines reveals anomalous diffusion—in fact, superdiffusion—of the field lines. The motion of charged particles in the force-free ABC magnetic fields is different from the flow of passive scalars in ABC flows. The particles do not necessarily follow the field lines and display a variety of dynamical behavior depending on their energy, and their initial pitch-angle. There is an overlap, in space, of the regions in which the field lines and the particle orbits are chaotic. The time evolution of an ensemble of particles, in such regions, can be divided into three categories. For short times, the motion of the particles is essentially ballistic; the ensemble-averaged, mean square displacement is approximately proportional to t2, where t is the time of evolution. The intermediate time region is defined by a decay of the velocity autocorrelation function—this being a measure of the time after which the collective dynamics is independent of the initial conditions. For longer times, the particles undergo superdiffusion—the mean square displacement is proportional to tα, where α > 1, and is weakly dependent on the energy of the particles. These super-diffusive characteristics, both of magnetic