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
Thermal bath of Dirac field in non-inertial frames
NASA Astrophysics Data System (ADS)
Zhang, Anwei
2016-07-01
The properties of inertial Dirac thermal bath viewed from the perspective of a uniformly accelerated observer is investigated. Using the single-mode approximation, we obtain the expression of the thermal reduced density matrix, which is constructed by the effective partition function in another way compared with the case of scalar field. We deduce the spectrum of particles and antiparticles seen by Rob and antiRob, respectively. It is found that the fermionic thermal bath will suppress the appearance of Unruh particles.
ERIC Educational Resources Information Center
de Pereira, Alexsandro Pereira; Lima Junior, Paulo; Rodrigues, Renato Felix
2016-01-01
Explaining is one of the most important everyday practices in science education. In this article, we examine how scientific explanations could serve as cultural tools for members of a group of pre-service physics teachers. Specifically, we aim at their use of explanations about forces of inertia in non-inertial frames of reference. A basic…
Non-Maximal Tripartite Entanglement Degradation of Dirac and Scalar Fields in Non-Inertial Frames
NASA Astrophysics Data System (ADS)
Salman, Khan; Niaz, Ali Khan; M. K., Khan
2014-03-01
The π-tangle is used to study the behavior of entanglement of a nonmaximal tripartite state of both Dirac and scalar fields in accelerated frame. For Dirac fields, the degree of degradation with acceleration of both one-tangle of accelerated observer and π-tangle, for the same initial entanglement, is different by just interchanging the values of probability amplitudes. A fraction of both one-tangles and the π-tangle always survives for any choice of acceleration and the degree of initial entanglement. For scalar field, the one-tangle of accelerated observer depends on the choice of values of probability amplitudes and it vanishes in the range of infinite acceleration, whereas for π-tangle this is not always true. The dependence of π-tangle on probability amplitudes varies with acceleration. In the lower range of acceleration, its behavior changes by switching between the values of probability amplitudes and for larger values of acceleration this dependence on probability amplitudes vanishes. Interestingly, unlike bipartite entanglement, the degradation of π-tangle against acceleration in the case of scalar fields is slower than for Dirac fields.
NASA Astrophysics Data System (ADS)
de Pereira, Alexsandro Pereira; Lima Junior, Paulo; Rodrigues, Renato Felix
2016-05-01
Explaining is one of the most important everyday practices in science education. In this article, we examine how scientific explanations could serve as cultural tools for members of a group of pre-service physics teachers. Specifically, we aim at their use of explanations about forces of inertia in non-inertial frames of reference. A basic assumption of our study is that explanatory tools (e.g., typical explanations learned) shape the ways we think and speak about the world. Drawing on the theory of mediated action, analysis illustrates three major claims on scientific explanations: (1) explaining is an act of actively responding to explanations presented by others (and not only to evidence itself); (2) the actual experience of explaining involves the enactment of power and authority; (3) resistance (not acknowledging an explanation as one's own) might be a constitutive part of learning how to explain (hence, teachers could approach scientific explanation in a less dogmatic way). These assertions expand the possibilities of dialogue between studies of scientific explanations and the social sciences. Implications for science teaching and research in science education are presented.
Physics of Non-Inertial Reference Frames
NASA Astrophysics Data System (ADS)
Kamalov, Timur F.
2010-12-01
Physics of non-inertial reference frames is a generalizing of Newton's laws to any reference frames. It is the system of general axioms for classical and quantum mechanics. The first, Kinematics Principle reads: the kinematic state of a body free of forces conserves and equal in absolute value to an invariant of the observer's reference frame. The second, Dynamics Principle extended Newton's second law to non-inertial reference frames and also contains additional variables there are higher derivatives of coordinates. Dynamics Principle reads: a force induces a change in the kinematic state of the body and is proportional to the rate of its change. It is mean that if the kinematic invariant of the reference frame is n-th derivative with respect the time, then the dynamics of a body being affected by the force F is described by the 2n-th differential equation. The third, Statics Principle reads: the sum of all forces acting a body at rest is equal to zero.
Physics of Non-Inertial Reference Frames
Kamalov, Timur F.
2010-12-22
Physics of non-inertial reference frames is a generalizing of Newton's laws to any reference frames. It is the system of general axioms for classical and quantum mechanics. The first, Kinematics Principle reads: the kinematic state of a body free of forces conserves and equal in absolute value to an invariant of the observer's reference frame. The second, Dynamics Principle extended Newton's second law to non-inertial reference frames and also contains additional variables there are higher derivatives of coordinates. Dynamics Principle reads: a force induces a change in the kinematic state of the body and is proportional to the rate of its change. It is mean that if the kinematic invariant of the reference frame is n-th derivative with respect the time, then the dynamics of a body being affected by the force F is described by the 2n-th differential equation. The third, Statics Principle reads: the sum of all forces acting a body at rest is equal to zero.
Non-Inertial Quantization: Truth or Illusion?
NASA Astrophysics Data System (ADS)
Cruz, S. Cruz y.; Mielnik, B.
2016-03-01
The quantum Hamiltonians in non inertial frames, while proper to describe the time evolution, might give a false information about the radiation of physical systems. The formal peculiarities observed for the uniformly rotating and accelerating frames might be caused by an excess of verbal approaches in the present day quantum theories.
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
Quantum mechanics in non-inertial reference frames: Time-dependent rotations and loop prolongations
Klink, W.H.; Wickramasekara, S.
2013-09-15
This is the fourth in a series of papers on developing a formulation of quantum mechanics in non-inertial reference frames. This formulation is grounded in a class of unitary cocycle representations of what we have called the Galilean line group, the generalization of the Galilei group to include transformations amongst non-inertial reference frames. These representations show that in quantum mechanics, just as the case in classical mechanics, the transformations to accelerating reference frames give rise to fictitious forces. In previous work, we have shown that there exist representations of the Galilean line group that uphold the non-relativistic equivalence principle as well as representations that violate the equivalence principle. In these previous studies, the focus was on linear accelerations. In this paper, we undertake an extension of the formulation to include rotational accelerations. We show that the incorporation of rotational accelerations requires a class of loop prolongations of the Galilean line group and their unitary cocycle representations. We recover the centrifugal and Coriolis force effects from these loop representations. Loops are more general than groups in that their multiplication law need not be associative. Hence, our broad theoretical claim is that a Galilean quantum theory that holds in arbitrary non-inertial reference frames requires going beyond groups and group representations, the well-established framework for implementing symmetry transformations in quantum mechanics. -- Highlights: •A formulation of Galilean quantum mechanics in non-inertial reference frames is presented. •The Galilei group is generalized to infinite dimensional Galilean line group. •Loop prolongations of Galilean line group contain central extensions of Galilei group. •Unitary representations of the loops are constructed. •These representations lead to terms in the Hamiltonian corresponding to fictitious forces, including centrifugal and Coriolis
Non-inertial calibration of vibratory gyroscopes
NASA Technical Reports Server (NTRS)
Gutierrez, Roman C. (Inventor); Tang, Tony K. (Inventor)
2003-01-01
The electrostatic elements already present in a vibratory gyroscope are used to simulate the Coriolis forces. An artificial electrostatic rotation signal is added to the closed-loop force rebalance system. Because the Coriolis force is at the same frequency as the artificial electrostatic force, the simulated force may be introduced into the system to perform an inertial test on MEMS vibratory gyroscopes without the use of a rotation table.
Quantum mechanics in non-inertial reference frames: Time-dependent rotations and loop prolongations
NASA Astrophysics Data System (ADS)
Klink, W. H.; Wickramasekara, S.
2013-09-01
This is the fourth in a series of papers on developing a formulation of quantum mechanics in non-inertial reference frames. This formulation is grounded in a class of unitary cocycle representations of what we have called the Galilean line group, the generalization of the Galilei group to include transformations amongst non-inertial reference frames. These representations show that in quantum mechanics, just as the case in classical mechanics, the transformations to accelerating reference frames give rise to fictitious forces. In previous work, we have shown that there exist representations of the Galilean line group that uphold the non-relativistic equivalence principle as well as representations that violate the equivalence principle. In these previous studies, the focus was on linear accelerations. In this paper, we undertake an extension of the formulation to include rotational accelerations. We show that the incorporation of rotational accelerations requires a class of loop prolongations of the Galilean line group and their unitary cocycle representations. We recover the centrifugal and Coriolis force effects from these loop representations. Loops are more general than groups in that their multiplication law need not be associative. Hence, our broad theoretical claim is that a Galilean quantum theory that holds in arbitrary non-inertial reference frames requires going beyond groups and group representations, the well-established framework for implementing symmetry transformations in quantum mechanics.
Lu, Xinyu; Hsu, Jyh-Ping; Xuan, Xiangchun
2015-01-01
Separating particles from a heterogeneous mixture is important and necessary in many engineering and biomedical applications. Electrokinetic flow-based continuous particle separation has thus far been realized primarily by the use of particle dielectrophoresis induced in constricted and/or curved microchannels. We develop in this work a new electrokinetic method that exploits the wall-induced non-inertial lift in a straight uniform microchannel to continuously separate particles by intrinsic properties (e.g., size and surface charge). Such an electrically originated lift force arises from the asymmetric electric field distribution around a particle nearby a planar dielectric wall. We demonstrate this method through separating both a binary and ternary mixture of dispersed polystyrene microspheres by size in a T-shaped microchannel. A semi-analytical model is also developed to simulate and understand the particle separation process. The predicted particle trajectories in the entire microchannel agree reasonably well with the experimental measurements. PMID:25521509
Energy Science and Technology Software Center (ESTSC)
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.
Turbulence modeling in non-inertial frames of reference
NASA Technical Reports Server (NTRS)
Speziale, Charles G.
1988-01-01
The effect of an arbitrary change of frame on the structure of turbulence models is examined from a fundamental theoretical standpoint. It is proven, as a rigorous consequence of the Navier-Stokes equations, that turbulence models must be form invariant under arbitrary translational accelerations of the reference frame and should only be affected by rotations through the intrinsic mean vorticity. A direct application of the invariance property along with the Taylor-Proudman Theorem, material frame-indifference in the limit of two-dimensional turbulence and Rapid Distortion Theory is shown to yield powerful constraints on the allowable form of turbulence models. Most of the commonly used turbulence models are demonstrated to be in serious violation of these constraints and consequently are inconsistent with the Navier-Stokes equations in non-inertial frames. Alternative models with improved non-inertial properties are developed and some simple applications to rotating turbulent flows are considered.
Non-inertial Frames in Special and General Relativity
NASA Astrophysics Data System (ADS)
Lusanna, Luca
A theory of global non-inertial frames in special relativity is developed by taking into account relativistic metrology and by avoiding the coordinate singularities of the rotating disk and of Fermi coordinates. Then this theory is used in general relativity for the treatment of globally hyperbolic, asymptotically Minkowskian space-times solution of Einstein's equations. Also some comments on the problem of dark matter, connecting it to the relativistic metrology used in astrophysics, are made.
Are OPERA neutrinos faster than light because of non-inertial reference frames?
NASA Astrophysics Data System (ADS)
Germanà, C.
2012-02-01
Context. Recent results from the OPERA experiment reported a neutrino beam traveling faster than light. The challenging experiment measured the neutrino time of flight (TOF) over a baseline from the CERN to the Gran Sasso site, concluding that the neutrino beam arrives ~60 ns earlier than a light ray would do. Because the result, if confirmed, has an enormous impact on science, it might be worth double-checking the time definitions with respect to the non-inertial system in which the neutrino travel time was measured. An observer with a clock measuring the proper time τ free of non-inertial effects is the one located at the solar system barycenter (SSB). Aims: Potential problems in the OPERA data analysis connected with the definition of the reference frame and time synchronization are emphasized. We aim to investigate the synchronization of non-inertial clocks on Earth by relating this time to the proper time of an inertial observer at SSB. Methods: The Tempo2 software was used to time-stamp events observed on the geoid with respect to the SSB inertial observer time. Results: Neutrino results from OPERA might carry the fingerprint of non-inertial effects because they are timed by terrestrial clocks. The CERN-Gran Sasso clock synchronization is accomplished by applying corrections that depend on special and general relativistic time dilation effects at the clocks, depending on the position of the clocks in the solar system gravitational well. As a consequence, TOF distributions are centered on values shorter by tens of nanoseconds than expected, integrating over a period from April to December, longer if otherwise. It is worth remarking that the OPERA runs have always been carried out from April/May to November. Conclusions: If the analysis by Tempo2 holds for the OPERA experiment, the excellent measurement by the OPERA collaboration will turn into a proof of the general relativity theory in a weak field approximation. The analysis presented here is falsifiable
Improving an all-atom force field.
Mohanty, Sandipan; Hansmann, U H E
2007-07-01
Experimentally well-characterized proteins that are small enough to be computationally tractable provide useful information for refining existing all-atom force fields. This is used by us for reparametrizing a recently developed all-atom force field. Relying on high statistics parallel tempering simulations of a designed 20 residue beta-sheet peptide, we propose incremental changes that improve the force field's range of applicability. PMID:17677516
A molecular mechanics force field for lignin
Petridis, Loukas; Smith, Jeremy C
2009-02-01
A CHARMM molecular mechanics force field for lignin is derived. Parameterization is based on reproducing quantum mechanical data of model compounds. Partial atomic charges are derived using the RESP electrostatic potential fitting method supplemented by the examination of methoxybenzene:water interactions. Dihedral parameters are optimized by fitting to critical rotational potentials and bonded parameters are obtained by optimizing vibrational frequencies and normal modes. Finally, the force field is validated by performing a molecular dynamics simulation of a crystal of a lignin fragment molecule and comparing simulation-derived structural features with experimental results. Together with the existing force field for polysaccharides, this lignin force field will enable full simulations of lignocellulose.
Polarization effects in molecular mechanical force fields.
Cieplak, Piotr; Dupradeau, François-Yves; Duan, Yong; Wang, Junmei
2009-08-19
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
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
Entanglement dynamics of non-inertial observers in a correlated environment
NASA Astrophysics Data System (ADS)
Ramzan, M.
2013-01-01
Effect of decoherence and correlated noise on the entanglement of X-type state of the Dirac fields in the non-inertial frame is investigated. A two qubit X-state is considered to be shared between the partners where Alice is in inertial frame and Rob in an accelerated frame. The concurrence is used to quantify the entanglement of the X-state system influenced by time correlated amplitude damping, depolarizing and bit flip channels. It is seen that amplitude damping and bit flip channels heavily influence the entanglement of the system as compared to the depolarizing channel. It is found possible to avoid entanglement sudden death (ESD) for all the channels under consideration for μ > 0.75 for any type of initial state. No ESD behaviour is seen for depolarizing channel in the presence of correlated noise for entire range of decoherence parameter p and Rob's acceleration r. It is also seen that the effect of environment is much stronger than that of acceleration of the accelerated partner. Furthermore, it is investigated that correlated noise compensates the loss of entanglement caused by the Unruh effect.
Force Field Development for Lipid Membrane Simulations.
Lyubartsev, Alexander P; Rabinovich, Alexander L
2016-10-01
With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26766518
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.
Three-Dimensional Force Field Spectroscopy
NASA Astrophysics Data System (ADS)
Schwarz, Alexander; Hölscher, Hendrik; Langkat, S. M.; Wiesendanger, R.
2003-12-01
A method is presented that utilizes the frequency modulation technique in ultra-high vacuum to measure the tip-sample force field in all three dimensions with atomic resolution. It is based on a systematic procedure to record frequency shift versus distance curves. After their conversion into the tip-surface potential landscape the complete force field in all three dimensions can be calculated. Experimental results obtained in the non-contact regime on NiO(001) with an iron-coated silicon tip are presented to demonstrate that interatomic vertical and lateral forces can be determined and assigned to specific sites within the surface unit cell.
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.
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
The task of the relativistic oscillator in a non-inertial frame of reference
NASA Astrophysics Data System (ADS)
Perepelkin, E. E.; Sadovnikov, B. I.; Inozemtseva, N. G.
2016-09-01
The relativistic theory is one of the most difficult parts of theoretical physics to understand by high school students and scientists alike. In this paper, the important aspects from this theory are considered. The case of the non-inertial reference frame in which the space–time interval was presented for the Lorentz-like transformations, and the condition by which the transition to the inertial reference frame takes place, is shown.
Harsij, Zeynab Mirza, Behrouz
2014-12-15
A helicity entangled tripartite state is considered in which the degree of entanglement is preserved in non-inertial frames. It is shown that Quantum Entanglement remains observer independent. As another measure of quantum correlation, Quantum Discord has been investigated. It is explicitly shown that acceleration has no effect on the degree of quantum correlation for the bipartite and tripartite helicity entangled states. Geometric Quantum Discord as a Hilbert–Schmidt distance is computed for helicity entangled states. It is shown that living in non-inertial frames does not make any influence on this distance, either. In addition, the analysis has been extended beyond single mode approximation to show that acceleration does not have any impact on the quantum features in the limit beyond the single mode. As an interesting result, while the density matrix depends on the right and left Unruh modes, the Negativity as a measure of Quantum Entanglement remains constant. Also, Quantum Discord does not change beyond single mode approximation. - Highlights: • The helicity entangled states here are observer independent in non-inertial frames. • It is explicitly shown that Quantum Discord for these states is observer independent. • Geometric Quantum Discord is also not affected by acceleration increase. • Extending to beyond single mode does not change the degree of entanglement. • Beyond single mode approximation the degree of Quantum Discord is also preserved.
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
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.
Eddy-current non-inertial displacement sensing for underwater infrasound measurements.
Donskoy, Dimitri M; Cray, Benjamin A
2011-06-01
A non-inertial sensing approach for an Acoustic Vector Sensor (AVS), which utilizes eddy-current displacement sensors and operates well at Ultra-Low Frequencies (ULF), is described here. In the past, most ULF measurements (from mHertz to approximately 10 Hertz) have been conducted using heavy geophones or seismometers that must be installed on the seafloor; these sensors are not suitable for water column measurements. Currently, there are no readily available compact and affordable underwater AVS that operate within this frequency region. Test results have confirmed the validity of the proposed eddy-current AVS design and have demonstrated high acoustic sensitivity. PMID:21682361
Force field dependence of riboswitch dynamics.
Hanke, Christian A; Gohlke, Holger
2015-01-01
Riboswitches are noncoding regulatory elements that control gene expression in response to the presence of metabolites, which bind to the aptamer domain. Metabolite binding appears to occur through a combination of conformational selection and induced fit mechanism. This demands to characterize the structural dynamics of the apo state of aptamer domains. In principle, molecular dynamics (MD) simulations can give insights at the atomistic level into the dynamics of the aptamer domain. However, it is unclear to what extent contemporary force fields can bias such insights. Here, we show that the Amber force field ff99 yields the best agreement with detailed experimental observations on differences in the structural dynamics of wild type and mutant aptamer domains of the guanine-sensing riboswitch (Gsw), including a pronounced influence of Mg2+. In contrast, applying ff99 with parmbsc0 and parmχOL modifications (denoted ff10) results in strongly damped motions and overly stable tertiary loop-loop interactions. These results are based on 58 MD simulations with an aggregate simulation time>11 μs, careful modeling of Mg2+ ions, and thorough statistical testing. Our results suggest that the moderate stabilization of the χ-anti region in ff10 can have an unwanted damping effect on functionally relevant structural dynamics of marginally stable RNA systems. This suggestion is supported by crystal structure analyses of Gsw aptamer domains that reveal χ torsions with high-anti values in the most mobile regions. We expect that future RNA force field development will benefit from considering marginally stable RNA systems and optimization toward good representations of dynamics in addition to structural characteristics. PMID:25726465
Representation-free description of light-pulse atom interferometry including non-inertial effects
NASA Astrophysics Data System (ADS)
Kleinert, Stephan; Kajari, Endre; Roura, Albert; Schleich, Wolfgang P.
2015-12-01
Light-pulse atom interferometers rely on the wave nature of matter and its manipulation with coherent laser pulses. They are used for precise gravimetry and inertial sensing as well as for accurate measurements of fundamental constants. Reaching higher precision requires longer interferometer times which are naturally encountered in microgravity environments such as drop-tower facilities, sounding rockets and dedicated satellite missions aiming at fundamental quantum physics in space. In all those cases, it is necessary to consider arbitrary trajectories and varying orientations of the interferometer set-up in non-inertial frames of reference. Here we provide a versatile representation-free description of atom interferometry entirely based on operator algebra to address this general situation. We show how to analytically determine the phase shift as well as the visibility of interferometers with an arbitrary number of pulses including the effects of local gravitational accelerations, gravity gradients, the rotation of the lasers and non-inertial frames of reference. Our method conveniently unifies previous results and facilitates the investigation of novel interferometer geometries.
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.
Devereux, Mike; Gresh, Nohad; Piquemal, Jean-Philip; Meuwly, Markus
2014-08-01
A supervised, semiautomated approach to force field parameter fitting is described and applied to the SIBFA polarizable force field. The I-NoLLS interactive, nonlinear least squares fitting program is used as an engine for parameter refinement while keeping parameter values within a physical range. Interactive fitting is shown to avoid many of the stability problems that frequently afflict highly correlated, nonlinear fitting problems occurring in force field parametrizations. The method is used to obtain parameters for the H2O, formamide, and imidazole molecular fragments and their complexes with the Mg(2+) cation. Reference data obtained from ab initio calculations using an auc-cc-pVTZ basis set exploit advances in modern computer hardware to provide a more accurate parametrization of SIBFA than has previously been available. PMID:24965869
Transferable force field for alcohols and polyalcohols.
Ferrando, Nicolas; Lachet, Véronique; Teuler, Jean-Marie; Boutin, Anne
2009-04-30
A new force field has been developed for alcohol and polyalcohol molecules. Based on the anisotropic united-atom force field AUA4 developed for hydrocarbons, it only introduces one new anisotropic united atom corresponding to the hydroxyl group OH. In the case of polyalcohols and complex molecules, the calculation of the intramolecular electrostatic energy is revisited. These interactions are calculated between charges belonging to the different local dipoles of the molecule, one dipole being defined as a group of consecutive charges globally neutral. This new method allows avoiding the use of empirical scaling parameters commonly introduced to calculate 1-4 electrostatic interactions. The transferability of the proposed potential is demonstrated through the simulation of a wide variety of alcohol families: primary alcohols (methanol, ethanol, propan-1-ol, hexan-1-ol, octan-1-ol), secondary alcohols (propan-2-ol), tertiary alcohols (2-methylpropan-2-ol), phenol, and diols (1,2-ethanediol, 1,3-propanediol, 1,5-pentanediol). Monte Carlo simulations carried out in the Gibbs ensemble lead to a good agreement between calculated and experimental data for the thermodynamic properties along the liquid/vapor saturation curve, for the critical point coordinates and for the liquid structure at room temperature. Additional simulations were performed on the methanol + n-butane system showing the capability of the proposed potential to reproduce the azeotropic behavior of such mixtures with a good agreement. PMID:19344171
Electromagnetic unification of matter and force fields
NASA Astrophysics Data System (ADS)
John, Sarah
2004-05-01
Special relativity and quantum mechanics are descriptive of electromagnetic propagation in waveguides, with mass analogous to the cutoff frequency of a waveguide mode [S.John, Bull.Am.Phys.Soc. vol.39,no.2,1254 (1994)]. It is further postulated herein that all spin 1/2 matter (necessarily massive) and spin 1 force fields have their origin in the electromagnetic fields E and B. This concept is not new. Majorana, among others have obtained electromagnetic representations of Dirac-like equations valid for the zero-mass case. Here, the spinor representation of the Maxwell equations, as given by Sallhofer, is extended to oscillatory fields with propagation constant m to obtain, in the absence of charge and current densities, the coupled equation (M. hatp + β E)ψ = 0 , where M = diag[ M σ, M^* σ ] , β = offdiag[I,I] , ψ ^ = i ^dag ( σ. B0 ( p), σ. E_0(p)), and M=m+ip, with the energy-mass relation given by E^2 = M M . Further, it is shown that the interaction term of QED is a direct consequence of including the sources and currents of Maxwell equations. Qualitative field patterns for spin 1/2 and spin 1 states, such as the electron, neutrino, magnetic monopole, quarks, photon, and massive gauge bosons are suggested.
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.
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
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…
Motor imagery facilitates force field learning.
Anwar, Muhammad Nabeel; Tomi, Naoki; Ito, Koji
2011-06-13
Humans have the ability to produce an internal reproduction of a specific motor action without any overt motor output. Recent findings show that the processes underlying motor imagery are similar to those active during motor execution and both share common neural substrates. This suggests that the imagery of motor movements might play an important role in acquiring new motor skills. In this study we used haptic robot in conjunction with motor imagery technique to improve learning in a robot-based adaptation task. Two groups of subjects performed reaching movements with or without motor imagery in a velocity-dependent and position-dependent mixed force field. The groups performed movements with motor imagery produced higher after effects and decreased muscle co-contraction with respect to no-motor imagery group. These results showed a positive influence of motor imagery on acquiring new motor skill and suggest that motor learning can be facilitated by mental practice and could be used to increase the rate of adaptation. PMID:21555118
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.
Brief: Field measurements of casing tension forces
Quigley, M.S.; Lewis, D.B.; Boswell, R.S.
1995-02-01
Tension forces acting on individual casing joints were accurately measured during installation of 10,158 ft of 9 5/8-in. {times} 47-lbm/ft casing and 11,960 ft of 11 7/8-in. {times} 71.8-lbm/ft casing. A unique casing load table (CLT) weighed the casing string after the addition of each casing joint. Strain gauges attached inside the pin ends of instrumented casing joints (ICJ`s) directly measured tension force on those joints. A high-speed computer data-acquisition system (DAS) automatically recorded data from all the sensors. Several casing joints were intentionally subjected to extreme deceleration to determine upper limits for dynamic tension forces. Data from these tests clearly show effects of wellbore friction and casing handling conditions. In every case, tension forces in the casing during maximum deceleration were considerably less than expected. In some cases, the highest tension forces occurred when the casing lifted out of the slips. Peak tension forces caused by setting the casing slips were typically no more than 5% greater than tension forces in the casing at rest. This dynamic amplification was far less than the 60% value used in the previous casing design method. Reducing the safety factor for installation loads has permitted use of lighter, less-expensive casing than dictated by older design criteria.
TOPICAL REVIEW: Polarization effects in molecular mechanical force fields
NASA Astrophysics Data System (ADS)
Cieplak, Piotr; Dupradeau, François-Yves; Duan, Yong; Wang, Junmei
2009-08-01
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.
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.
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.
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.
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
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)
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.
Vibrational spectrum and force field of dimethyldimethoxysilane
Tenisheva, T.F.; Lazarev, A.N.
1986-01-01
Experimental data is presented on the spectra of (CH/sub 3/)/sub 2/Si(OCH/sub 3/)/sub 2/ (I), (CH/sub 3/)/sub 2/Si(OCD/sub 3/)/sub 2/ (II), and (CD/sub 3/)/sub 2/Si(OCH/sub 3/)/sub 2/ (III). The results of the determination of the force constants on the basis of the optimization of the solution of the inverse mechanical problem of the theory of molecular vibrations with consideration of all the internal degrees of freedom with the exception of the coordinates corresponding to internal rotations are discussed. Raman spectra of I, II, and III in the liquid phase is shown and the IR spectra of amorphous films of I, II, and III are illustrated.
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
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.
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.
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.
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.
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, 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.
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.
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.
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
Force-Field Compensation in a Manual Tracking Task
Squeri, Valentina; Masia, Lorenzo; Casadio, Maura; Morasso, Pietro; Vergaro, Elena
2010-01-01
This study addresses force/movement control in a dynamic “hybrid” task: the master sub-task is continuous manual tracking of a target moving along an eight-shaped Lissajous figure, with the tracking error as the primary performance index; the slave sub-task is compensation of a disturbing curl viscous field, compatibly with the primary performance index. The two sub-tasks are correlated because the lateral force the subject must exert on the eight-shape must be proportional to the longitudinal movement speed in order to perform a good tracking. The results confirm that visuo-manual tracking is characterized by an intermittent control mechanism, in agreement with previous work; the novel finding is that the overall control patterns are not altered by the presence of a large deviating force field, if compared with the undisturbed condition. It is also found that the control of interaction-forces is achieved by a combination of arm stiffness properties and direct force control, as suggested by the systematic lateral deviation of the trajectories from the nominal path and the comparison between perturbed trials and catch trials. The coordination of the two sub-tasks is quickly learnt after the activation of the deviating force field and is achieved by a combination of force and the stiffness components (about 80% vs. 20%), which is a function of the implicit accuracy of the tracking task. PMID:20567516
Visualization of Force Fields in Protein Structure Prediction
Crawford, Clark; Kreylos, Oliver; Hamann, Bernd; Crivelli, Silvia
2005-04-26
The force fields used in molecular computational biology are not mathematically defined in such a way that their mathematical representation would facilitate the straightforward application of volume visualization techniques. To visualize energy, it is necessary to define a spatial mapping for these fields. Equipped with such a mapping, we can generate volume renderings of the internal energy states in a molecule. We describe our force field, the spatial mapping that we used for energy, and the visualizations that we produced from this mapping. We provide images and animations that offer insight into the computational behavior of the energy optimization algorithms that we employ.
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
Force field dependent solution properties of glycine oligomers
Drake, Justin A.
2015-01-01
Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly3 and Gly10 in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g. end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623
Force field-dependent solution properties of glycine oligomers.
Drake, Justin A; Pettitt, B Montgomery
2015-06-30
Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly(3) and Gly(10) in aqueous solution from all atom, microsecond molecular dynamics (MD) simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly(3) and Gly(10) were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g., end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623
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. PMID:26588554
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.
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
Force-free field model of ball lightning
NASA Astrophysics Data System (ADS)
Tsui, K. H.
2001-03-01
Due to the nature that the force-free magnetic field, whose current carried by the conducting plasma is everywhere parallel to the magnetic field it generates, is the minimum energy configuration under the constraint of magnetic helicity conservation, ball lightning is considered as a self-organized phenomenon with a plasma fireball immersed in a spherical force-free magnetic field. Since this field does not exert force on the plasma, the plasma pressure, by itself, is in equilibrium with the surrounding environment, and the force-free magnetic field can take on any value without affecting the plasma. Due to this second feature, singular solutions of the magnetic field that are otherwise excluded are allowed, which enable a large amount of energy to be stored to sustain the ball lightning. The singularity is truncated only by the physical limit of current density that a plasma can carry. Scaling the customary soccer-size fireball to larger dimensions could account for day and night sightings of luminous objects in the sky.
Toroidal linear force-free magnetic fields with axial symmetry
NASA Astrophysics Data System (ADS)
Vandas, M.; Romashets, E.
2016-01-01
Aims: Interplanetary magnetic flux ropes are often described as linear force-free fields. To account for their curvature, toroidal configurations must be used. The aim is to find an analytic description of a linear force-free magnetic field of the toroidal geometry in which the cross section of flux ropes can be controlled. Methods: The solution is found as a superposition of fields given by linear force-free cylinders tangential to a generating toroid. The cylindrical field is expressed in a series of terms that are not all cylindrically symmetric. Results: We found the general form of a toroidal linear force-free magnetic field. The field is azimuthally symmetric with respect to the torus axis. It depends on a set of coefficients that enables controlling the flux rope shape (cross section) to some extent. By varying the coefficients, flux ropes with circular and elliptic cross sections were constructed. Numerical comparison suggests that the simple analytic formula for calculating the helicity in toroidal flux ropes of the circular cross section can be used for flux ropes with elliptic cross sections if the minor radius in the formula is set to the geometric mean of the semi-axes of the elliptic cross section.
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.
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.
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
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
Transferable force fields for adsorption of small gases in zeolites.
Martin-Calvo, A; Gutiérrez-Sevillano, J J; Parra, J B; Ania, C O; Calero, S
2015-10-01
We provide transferable force fields for oxygen, nitrogen, and carbon monoxide that are able to reproduce experimental adsorption in both pure silica and alumino-substituted zeolites at cryogenic and high temperatures. The force field parameters can be combined with those previously reported for carbon dioxide, methane, and argon, opening the possibility for studying mixtures of interest containing the six components. Using these force field parameters we obtained some adsorption isotherms at cryogenic temperatures that at first sight were in discrepancies with experimental values for certain molecules and structures. We attribute these discrepancies to the sensitiveness of the equipment and to kinetic impedimenta that can lead to erratic results. Additional problems can be found during simulations when extra-framework cations are present in the system as their lack of mobility at low temperatures could lead to kinetic effects that hinder experimental adsorption. PMID:26313242
Water-Silica Force Field for Simulating Nanodevices
Cruz-Chu, Eduardo R.; Aksimentiev, Aleksei; Schulten, Klaus
2008-01-01
Amorphous silica is an inorganic material that is central for many nanotechnology appplications, such as nanoelectronics, microfluidics, and nanopore technology. In order to use molecular dynamics (MD) simulations to study the behavior of biomolecules with silica, we developed a force field for amorphous silica surfaces based on their macroscopic wetting properties that is compatible with the CHARMM force field and TIP3P water model. The contact angle of a water droplet with silica served as a criterion to tune the intermolecular interactions. The resulting force field was used to study the permeation of water through silica nanopores, illustrating the influence of the surface topography and the intermolecular parameters on permeation kinetics. We find that minute modeling of the amorphous surface is critical for MD studies, since the particular arrangement of surface atoms controls sensitively electrostatic interactions between silica and water. PMID:17064100
2012-01-01
Atmospheric humidity strongly influences the interactions between dry granular particles in process containers. To reduce the energy loss in industrial production processes caused by particle agglomeration, a basic understanding of the dependence of particle interactions on humidity is necessary. Hence, in this study, molecular dynamic simulations were carried out to calculate the adhesion between silica surfaces in the presence of adsorbed water. For a realistic description, the choice of force field is crucial. Because of their frequent use and transferability to biochemical systems, the Clay and CWCA force fields were investigated with respect to their ability to describe the water–silica interface in comparison to the more advanced Reax force field, ab initio calculations, and experiments. PMID:23378869
Scattered field generation and optical forces in transformation optics
NASA Astrophysics Data System (ADS)
Novitsky, A. V.
2016-04-01
In this paper we develop an approach for making various scattered electromagnetic fields on the transformation-optics ground. To do so, we use the a special coordinate transformation from the a vacuum virtual space to physical space, which changes the boundary of the scattering device upon transformation. We explore this approach for small scatterers compared with radiation wavelength, which allows us to predict the arbitrarily directed optical forces. Obtaining scattered fields and optical forces can be useful in nano-optics and optical micromanipulation.
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.
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.
Force field development from first principles for materials design
NASA Astrophysics Data System (ADS)
Chan, Maria; Kinaci, Alper; Narayanan, Badri; Sen, Fatih; Gray, Stephen; Davis, Michael; Sankaranaryanan, Subramanian
2015-03-01
The ability to perform accurate calculations efficiently is crucial for computational materials design. In this talk, we will discuss a stream-lined approach to force field development using first principles density functional theory training data and machine learning algorithms. We will also discuss the validation of this approach on precious metal nanoparticles.
An improved generalized AMBER force field (GAFF) for urea.
Ozpinar, Gül Altinbaş; Peukert, Wolfgang; Clark, Timothy
2010-09-01
We describe an improved force field parameter set for the generalized AMBER force field (GAFF) for urea. Quantum chemical computations were used to obtain geometrical and energetic parameters of urea dimers and larger oligomers using AM1 semiempirical MO theory, density functional theory at the B3LYP/6-31G(d,p) level, MP2 and CCSD ab initio calculations with the 6-311++G(d,p), aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets, and with the CBS-QB3 and CBS-APNO complete basis set methods. Seven different urea dimer structures were optimized at the MP2/aug-cc-pVDZ level to obtain accurate interaction energies. Atomic partial charges were calculated at the MP2/aug-cc-pVDZ level with the restrained electrostatic potential (RESP) fitting approach. The interaction energies computed with these new RESP charges in the force field are consistent with those obtained from CCSD and MP2 calculations. The linear dimer structure calculated using the force field with modified geometrical parameters and the new RESP charge set agrees well with available experimental data. PMID:20162312
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. PMID:25714984
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
Generating distributed forcing fields for spatial hydrologic modeling
Technology Transfer Automated Retrieval System (TEKTRAN)
Spatial hydrologic modeling requires the development of distributed forcing fields of weather and precipitation. This is particularly difficult in mountainous regions of the western US, where measurement sites are limited and the landscape is dominated by complex terrain and variations in vegetatio...
The effect of gravitational tidal forces on renormalized quantum fields
NASA Astrophysics Data System (ADS)
Hollowood, Timothy J.; Shore, Graham M.
2012-02-01
The effect of gravitational tidal forces on renormalized quantum fields propagating in curved spacetime is investigated and a generalisation of the optical theorem to curved spacetime is proved. In the case of QED, the interaction of tidal forces with the vacuum polarization cloud of virtual e + e - pairs dressing the renormalized photon has been shown to produce several novel phenomena. In particular, the photon field amplitude can locally increase as well as decrease, corresponding to a negative imaginary part of the refractive index, in apparent violation of unitarity and the optical theorem. Below threshold decays into e + e - pairs may also occur. In this paper, these issues are studied from the point of view of a non-equilibrium initial-value problem, with the field evolution from an initial null surface being calculated for physically distinct initial conditions and for both scalar field theories and QED. It is shown how a generalised version of the optical theorem, valid in curved spacetime, allows a local increase in amplitude while maintaining consistency with unitarity. The picture emerges of the field being dressed and undressed as it propagates through curved spacetime, with the local gravitational tidal forces determining the degree of dressing and hence the amplitude of the renormalized quantum field. These effects are illustrated with many examples, including a description of the undressing of a photon in the vicinity of a black hole singularity.
GLYCAM06: a generalizable biomolecular force field. Carbohydrates.
Kirschner, Karl N; Yongye, Austin B; Tschampel, Sarah M; González-Outeiriño, Jorge; Daniels, Charlisa R; Foley, B Lachele; Woods, Robert J
2008-03-01
A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both alpha- and beta-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies. PMID:17849372
GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates
KIRSCHNER, KARL N.; YONGYE, AUSTIN B.; TSCHAMPEL, SARAH M.; GONZÁLEZ-OUTEIRIÑO, JORGE; DANIELS, CHARLISA R.; FOLEY, B. LACHELE; WOODS, ROBERT J.
2015-01-01
A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both α- and β-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies. PMID:17849372
Radiation from an Accelerated Point Charge and Non-Inertial Observers
ERIC Educational Resources Information Center
Leonov, A. B.
2012-01-01
It is known that observers comoving with a uniformly accelerated point charge detect the electromagnetic field of a charge as a static electric field. We show that one can find a similar family of observers, which detect the field of a charge as a static electric field, in the general case of arbitrary point-charge motion. We find the velocities…
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. PMID:26349916
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.
NASA Astrophysics Data System (ADS)
Brilliantov, N. V.; Seidel, C.
2012-01-01
The response of grafted polyelectrolytes to electrostatic field that favors adsorption is studied theoretically and by means of molecular dynamics (MD). Applying to the free chain end a constant force which counteracts adsorption, we analyze the size of the desorbed part as a function of force and electric field. Simulations with different loads, corresponding to linear, nonlinear and Hertzian springs, applied to the free end have been also performed to explore the generation of mechanical force by electric field. The MD results are in good agreement with the predictions of theory.
Particle energization in a chaotic force-free magnetic field
NASA Astrophysics Data System (ADS)
Li, Xiaocan; Li, Gang; Dasgupta, Brahmananda
2015-04-01
A force-free field (FFF) is believed to be a reasonable description of the solar corona and in general a good approximation for low-beta plasma. The equations describing the magnetic field of FFF is similar to the ABC fluid equations which has been demonstrated to be chaotic. This implies that charged particles will experience chaotic magnetic field in the corona. Here, we study particle energization in a time-dependent FFF using a test particle approach. An inductive electric field is introduced by turbulent motions of plasma parcels. We find efficient particle acceleration with power-law like particle energy spectra. The power-law indices depend on the amplitude of plasma parcel velocity field and the spatial scales of the magnetic field fluctuation. The spectra are similar for different particle species. This model provide a possible mechanism for seed population generation for particle acceleration by, e.g., CME-driven shocks. Generalization of our results to certain non-force-free-field (NFFF) is straightforward as the sum of two or multiple FFFs naturally yield NFFF.
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
Optical field and attractive force at the subwavelength slit.
Shapiro, David; Nies, Daniel; Belai, Oleg; Wurm, Matthias; Nesterov, Vladimir
2016-07-11
In recent works, a novel light-induced attractive force was predicted between two metal plates. This force arises by the interaction of surface plasmons which are excited at the metal when a transverse magnetic mode propagates through a subwavelength slit between two metal bodies. In this paper, the analytical and numerical calculations of this magnetic field are presented for the perfect metal and for gold. The amplitude and the phase transient curves between the known limiting cases of narrow and wide slits compared to the wavelength are found. The curve is shown to oscillate due to the emergence of new waveguide modes. The analytic solution for the perfect metal is in agreement with the computation for gold by means of the finite element method. The simple asymptotic formula for the light-induced attractive force is found in the limit of a narrow slit. PMID:27410865
An assessment of the anharmonic force fields of the halogen cyanides
NASA Astrophysics Data System (ADS)
Lacy, M.
Anharmonic force fields in the ϱ representation (ϱ = Я/ r) have been calculated using the matrix diagonalization technique. A simple model force field and comparison method are used to assess the force fields currently available for these molecules. From this analysis, the potential surfaces defined by the present force fields are estimated to be within 2-5% of the actual molecular potential.
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.
Mapping the force field of a hydrogen-bonded assembly
Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N.R.; Kantorovich, L.; Moriarty, P.
2014-01-01
Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism. PMID:24875276
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.
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
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
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
Tuning the mass of chameleon fields in Casimir force experiments.
Brax, Ph; van de Bruck, C; Davis, A C; Shaw, D J; Iannuzzi, D
2010-06-18
We have calculated the chameleon pressure between two parallel plates in the presence of an intervening medium that affects the mass of the chameleon field. As intuitively expected, the gas in the gap weakens the chameleon interaction mechanism with a screening effect that increases with the plate separation and with the density of the intervening medium. This phenomenon might open up new directions in the search of chameleon particles with future long-range Casimir force experiments. PMID:20867290
Quantum mechanical force field for water with explicit electronic polarization
Han, Jaebeom; Mazack, Michael J. M.; Zhang, Peng; Truhlar, Donald G.; Gao, Jiali
2013-08-07
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{sup 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
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
Current Status of the AMOEBA Polarizable Force Field
Ponder, Jay W.; Wu, Chuanjie; Ren, Pengyu; Pande, Vijay S.; Chodera, John D.; Schnieders, Michael J.; Haque, Imran; Mobley, David L.; Lambrecht, Daniel S.; DiStasio, Robert A.; Head-Gordon, Martin; Clark, Gary N. I.; Johnson, Margaret E.
2010-01-01
Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models towards more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical. PMID:20136072
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.
Design and optimization of force-reduced high field magnets
NASA Astrophysics Data System (ADS)
Rembeczki, Szabolcs
High field magnets have many important applications in different areas of research, in the power industry and also for military purposes. For example, high field magnets are particularly useful in: material sciences, high energy physics, plasma physics (as fusion magnets), high power applications (as energy storage devices), and space applications (in propulsion systems). One of the main issues with high-field magnets is the presence of very large electromagnetic stresses that must be counteracted and therefore require heavy support structures. In superconducting magnets, the problems caused by Lorentz forces are further complicated by the fact that superconductors for high field applications are pressure sensitive. The current carrying capacity is greatly reduced under stress and strain (especially in the case of Nb 3Sn and the new high temperature superconductors) so the reduction of the acting forces is of even greater importance. Different force-reduced magnet concepts have been studied in the past, both numerical and analytical methods have been used to solve this problem. The developed concepts are based on such complex winding geometries that the realization and manufacturing of such coils is extremely difficult and these concepts are mainly of theoretical interest. In the presented research, a novel concept for force-reduced magnets has been developed and analyzed which is easy to realize and therefore is of practical interest. The analysis has been performed with a new methodology, which does not require the time consuming finite element calculations. The developed computer models describe the 3-dimensional winding configuration by sets of filaments (filamentary approximation). This approach is much faster than finite element analysis and therefore allows rapid optimization of concepts. The method has been extensively tested on geometries of force-reduced solenoids where even analytical solutions exist. As a further cross check, the developed computer
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.
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
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
Heinz, Hendrik; Lin, Tzu-Jen; Mishra, Ratan Kishore; Emami, Fateme S
2013-02-12
The complexity of the molecular recognition and assembly of biotic-abiotic interfaces on a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with laboratory instrumentation. We discuss the current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorganic compounds that has been developed and tested over the past decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorganic-organic and inorganic-biomolecular interfaces. The parametrization builds on an in-depth understanding of physical-chemical properties on the atomic scale to assign each parameter, especially atomic charges and van der Waals constants, as well as on the validation of macroscale physical-chemical properties for each compound in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties of up to 2 orders of magnitude using other parametrization protocols and increases the transferability of the parameters by introducing thermodynamic consistency. As a result, a wide range of properties can be computed in quantitative agreement with experiment, including densities, surface energies, solid-water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomolecules, and thermal and mechanical properties. Applications include insight into the assembly of inorganic-organic multiphase materials, the recognition of inorganic facets by biomolecules, growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and
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.
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
Coarse-grained force field; general folding theory
Liwo, Adam; He, Yi; Scheraga, Harold A.
2012-01-01
We review the coarse-grained UNited RESidue (UNRES) force field for the simulations of protein structure and dynamics, which is being developed in our laboratory over the last several years. UNRES is a physics-based force field, the prototype of which is defined as a potential of mean force of polypeptide chains in water, where all the degrees of freedom except the coordinates of α-carbon atoms and side-chain centers have been integrated out. We describe the initial implementation of UNRES to protein-structure prediction formulated as a search for the global minimum of the potential-energy function and its subsequent molecular dynamics and extensions of molecular-dynamics implementation, which enabled us to study protein-folding pathways and thermodynamics, as well as to reformulate the protein-structure prediction problem as a search for the conformational ensemble with the lowest free energy at temperatures below the folding-transition temperature. Applications of UNRES to study biological problems are also described. PMID:21643583
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
Sodium Chloride, NaCl/ϵ: New Force Field.
Fuentes-Azcatl, Raúl; Barbosa, Marcia C
2016-03-10
A new computational model for sodium chloride, the NaCl/ϵ, is proposed. The force field employed for the description of the NaCl is based on a set of radial particle-particle pair potentials involving Lennard-Jones (LJ) and Coulombic forces. The parametrization is obtained by fitting the density of the crystal and the density and the dielectric constant of the mixture of the salt with water at a diluted solution. Our model shows good agreement with the experimental values for the density and for the surface tension of the pure system, and for the density, the viscosity, the diffusion, and the dielectric constant for the mixture with water at various molal concentrations. The NaCl/ϵ together with the water TIP4P/ϵ models provide a good approximation for studying electrolyte solutions. PMID:26890321
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.
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.
Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching
NASA Astrophysics Data System (ADS)
Li, Jicun; Wang, Feng
2015-11-01
Simple non-polarizable potentials were developed for Na+, K+, Cl-, and Br- using the adaptive force matching (AFM) method with ab initio MP2 method as reference. Our MP2-AFM force field predicts the solvation free energies of the four salts formed by the ions with an error of no more than 5%. Other properties such as the ion-water radial distribution functions, first solvation shell water tilt angle distributions, ion diffusion constants, concentration dependent diffusion constant of water, and concentration dependent surface tension of the solutions were calculated with this potential. Very good agreement was achieved for these properties. In particular, the diffusion constants of the ions are within 6% of experimental measurements. The model predicts bromide to be enriched at the interface in the 1.6M KBr solution but predicts the ion to be repelled for the surface at lower concentration.
NASA Astrophysics Data System (ADS)
MacCready, P.; Bryan, F.; Tseng, Y. H.; Whitney, M. M.
2014-12-01
The coastal ocean accounts for about half of the global fish harvest, but is poorly resolved in global climate models (a one-degree grid barely sees the continental shelf). Moreover, coastal ocean circulation is strongly modified by river freshwater sources, often coming from estuarine systems that are completely unresolved in the coarse grid. River freshwater input in CESM is added in a practical but ad hoc way, by imposing a surface salinity sink over a region of the ocean approximating the plume area of a given river. Here we present results from a series of model experiments using a high-resolution (1.5 km) ROMS model of the NE Pacific, including the Columbia River and the inland waters of Puget Sound. The base model does multi-year hindcasts using the best available sources of atmospheric (MM5/WRF), ocean (NCOM), river (USGS), and tidal forcing. It has been heavily validated against observations of all sorts, and performs well, so it is an ideal test bed for downscaling experiments. The model framework also does biogeochemistry, including oxygen, and carbon chemistry is being added to make forecasts of Ocean Acidification.This high-resolution ROMS model is systematically run in downscaling experiments for the year 2005 with combinations of CESM forcing (CAM, POP, and rivers) swapped in. Skill is calculated using observations. It is found that the runs with CESM forcing generally retain much of the skill of the base model. A compact metric of response to freshwater forcing is used, which is the mechanical energy required to destratify a shallow coastal volume. This, along with the average temperature and salinity of the volume, are used to characterize and compare runs, including the original CESM-POP fields. Finally the model is run with projected CESM simulation forcing at the end of 21st century based on a set of RCP scenarios, and the compact metrics are used to quantify differences from 2005.
Nonlinear gravitational self-force: Field outside a small body
NASA Astrophysics Data System (ADS)
Pound, Adam
2012-10-01
A small extended body moving through an external spacetime gαβ creates a metric perturbation hαβ, which forces the body away from geodesic motion in gαβ. The foundations of this effect, called the gravitational self-force, are now well established, but concrete results have mostly been limited to linear order. Accurately modeling the dynamics of compact binaries requires proceeding to nonlinear orders. To that end, I show how to obtain the metric perturbation outside the body at all orders in a class of generalized wave gauges. In a small buffer region surrounding the body, the form of the perturbation can be found analytically as an expansion for small distances r from a representative worldline. Given only a specification of the body’s multipole moments, the field obtained in the buffer region suffices to find the metric everywhere outside the body via a numerical puncture scheme. Following this procedure at first and second order, I calculate the field in the buffer region around an arbitrarily structured compact body at sufficiently high order in r to numerically implement a second-order puncture scheme, including effects of the body’s spin. I also define nth-order (local) generalizations of the Detweiler-Whiting singular and regular fields and show that in a certain sense, the body can be viewed as a skeleton of multipole moments.
Continuum Polarizable Force Field within the Poisson-Boltzmann Framework
Tan, Yu-Hong; Tan, Chunhu; Wang, Junmei; Luo, Ray
2008-01-01
We have developed and tested a complete set of nonbonded parameters for a continuum polarizable force field. Our analysis shows that the new continuum polarizable model is consistent with B3LYP/cc-pVTZ in modeling electronic response upon variation of dielectric environment. Comparison with experiment also shows that the new continuum polarizable model is reasonable, with similar accuracy as B3LYP/cc-pVTZ in reproduction of dipole moments of selected organic molecules in the gas phase. We have further tested the validity to interchange the Amber van der Waals parameters between the explicit and continuum polarizable force fields with a series of dimers. It can be found that the continuum polarizable model agrees well with MP2/cc-pVTZ, with deviations in dimer binding energies less than 0.9 kcal/mol in the aqueous dielectric environment. Finally we have optimized atomic cavity radii with respect to experimental solvation free energies of 177 training molecules. To validate the optimized cavity radii, we have tested these parameters against 176 test molecules. It is found that the optimized PB atomic cavity radii transfer well from the training set to the test set, with an overall root-mean-squared deviation of 1.30 kcal/mol, unsigned average error of 1.07 kacl/mol, and correlation coefficient of 92% for all 353 molecules in both the training and test sets. Given the development documented here, the next natural step is the construction of a full protein/nucleic acid force field within the new continuum polarization framework. PMID:18507452
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.
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.
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
Development of force field parameters for molecular simulation of polylactide
McAliley, James H.; Bruce, David A.
2011-01-01
Polylactide is a biodegradable polymer that is widely used for biomedical applications, and it is a replacement for some petroleum based polymers in applications that range from packaging to carpeting. Efforts to characterize and further enhance polylactide based systems using molecular simulations have to this point been hindered by the lack of accurate atomistic models for the polymer. Thus, we present force field parameters specifically suited for molecular modeling of PLA. The model, which we refer to as PLAFF3, is based on a combination of the OPLS and CHARMM force fields, with modifications to bonded and nonbonded parameters. Dihedral angle parameters were adjusted to reproduce DFT data using newly developed CMAP dihedral cross terms, and the model was further adjusted to reproduce experimentally resolved crystal structure conformations, melt density, volume expansivity, and the glass transition temperature of PLA. We recommend the use of PLAFF3 in modeling PLA in its crystalline or amorphous states and have provided the necessary input files required for the publicly available molecular dynamics code GROMACS. PMID:22180734
Automated conformational energy fitting for force-field development
Guvench, Olgun; MacKerell, Alexander D.
2010-01-01
We present a general conformational-energy fitting procedure based on Monte Carlo simulated annealing (MCSA) for application in the development of molecular mechanics force fields. Starting with a target potential energy surface and an unparameterized molecular mechanics potential energy surface, an optimized set of either dihedral or grid-based correction map (CMAP) parameters is produced that minimizes the root mean squared error (RMSE) between the parameterized and targeted energies. The fitting is done using an MCSA search in parameter space and consistently converges to the same RMSE irrespective of the randomized parameters used to seed the search. Any number of dihedral parameters can be simultaneously parameterized, allowing for fitting to multi-dimensional potential energy scans. Fitting options for dihedral parameters include non-uniform weighting of the target data, constraining multiple optimized parameters to the same value, constraining parameters to be no greater than a user-specified maximum value, including all or only a subset of multiplicities defining the dihedral Fourier series, and optimization of phase angles in addition to force constants. The dihedral parameter fitting algorithm’s performance is characterized through multi-dimensional fitting of cyclohexane, tetrahydropyran, and hexopyranose monosaccharide energetics, with the latter case having a 30-dimensional parameter space. The CMAP fitting is applied in the context of polypeptides, and is used to develop a parameterization that simultaneously captures the φ, ψ energetics of the alanine dipeptide and the alanine tetrapeptide. Because the dihedral energy term is common to many force fields, we have implemented the dihedral-fitting algorithm in the portable Python scripting language and have made it freely available as Supplementary Material. PMID:18458967
Unified Field Theory and Force Formulas of Interactions
NASA Astrophysics Data System (ADS)
Ma, Tian; Wang, Shouhong
2013-04-01
The main objective of this talk is to drive a unified field model coupling four interactions, based on the principle of interaction dynamics (PID) and the principle of representation invariance (PID). Intuitively, PID takes the variation of the action functional under energy-momentum conservation constraint. PRI requires that physical laws be independent of representations of the gauge groups. One important outcome of this unified field model is a natural duality between the interacting fields (g, A, W^a, S^k), corresponding to graviton, photon, intermediate vector bosons W^± and Z and gluons, and the adjoint bosonic fields (φ,, ^aw, ^ks). This duality predicts two Higgs particles of similar mass with one due to weak interaction and the other due to strong interaction. PID and PRI can be applied directly to individual interactions, leading to 1) modified Einstein equations, giving rise to a unified theory for dark matter and dark energy, 2) three levels of strong interaction potentials for quark, nucleon/hadron, and atom respectively, and 3) a weak interaction potential. These potential/force formulas offer a clear mechanism for both quark confinement and asymptotic freedom.
Adaptation and generalization in acceleration dependent force fields
Hwang, Eun Jung; Smith, Maurice A.; Shadmehr, Reza
2005-01-01
Any passive rigid inertial object that we hold in our hand, e.g., a tennis racquet, imposes a field of forces on the arm that depends on limb position, velocity, and acceleration. A fundamental characteristic of this field is that the forces due to acceleration and velocity are linearly separable in the intrinsic coordinates of the limb. In order to learn such dynamics with a collection of basis elements, a control system would generalize correctly and therefore perform optimally if the basis elements that were sensitive to limb velocity were not sensitive to acceleration, and vice versa. However, in the mammalian nervous system proprioceptive sensors like muscle spindles encode a nonlinear combination of all components of limb state, with sensitivity to velocity dominating sensitivity to acceleration. Therefore, limb state in the space of proprioception is not linearly separable despite the fact that this separation is a desirable property of control systems that form models of inertial objects. In building internal models of limb dynamics, does the brain use a representation that is optimal for control of inertial objects, or a representation that is closely tied to how peripheral sensors measure limb state? Here we show that in humans, patterns of generalization of reaching movements in acceleration dependent fields are strongly inconsistent with basis elements that are optimized for control of inertial objects. Unlike a robot controller that models the dynamics of the natural world and represents velocity and acceleration independently, internal models of dynamics that people learn appear to be rooted in the properties of proprioception, nonlinearly responding to the pattern of muscle activation and representing velocity more strongly than acceleration. PMID:16292640
Towards a force field based on density fitting
Piquemal, Jean-Philip; Cisneros, G. Andrés; Reinhardt, Peter; Gresh, Nohad; Darden, Thomas A.
2007-01-01
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. PMID:16542062
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...
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.
The harmonic force field and rz structure of HNCO
NASA Astrophysics Data System (ADS)
Fusina, Luciano; Mills, Ian M.
1981-04-01
The presently available microwave, millimeter wave, and far-infrared data of five isotopic species of isocyanic acid, namely, HNCO, H 15NCO, HN 13CO, HNC 18O, and DNCO, have been used to obtain improved values of the ground-state rotational constants, the five quartic distortion constants, and some higher-order distortion constants in the IrS reduced Hamiltonian of Watson. The appropriate planarity relation among the quartic centrifugal distortion constants has been imposed in the fitting procedure. The general harmonic force field of isocyanic acid has been determined using all existing data, and assuming a trans bent equilibrium geometry of the molecule with an NCO angle of 170°. Finally an rz structure has been obtained using the Az, Bz, and Cz rotational constants of five isotopic species. The bending of the NCO chain is found to be 8° in the trans configuration.
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).
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.
Force field development and simulations of senior dialkyl sulfoxides.
Chaban, Vitaly V
2016-04-21
Thermodynamics, structure, and dynamics of diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) were investigated using ab initio calculations and non-polarizable potential based molecular dynamics (MD) simulations. The additive pairwise force field (FF) for EMSO and DESO was proposed for the first time, preserving explicit compatibility with their most known homologue, DMSO. The simulations reveal similar structures and thermodynamic properties of DMSO, DESO and EMSO. However, the transport properties are significantly different: DESO and DMSO are less mobile and an order of magnitude more viscous. Furthermore, dipole reorientation in DESO and EMSO occurs ca. 2-4 times slower than in DMSO at room temperature. This observation favors applications of higher sulfoxides as cryoprotectants and provides a microscopic interpretation of the earlier experimental data. PMID:27031577
Development of the CHARMM Force Field for Lipids
Pastor, R.W.; MacKerell, A.D.
2011-01-01
The development of the CHARMM additive all-atom lipid force field (FF) is traced from the early 1990’s to the most recent version (C36) published in 2010. Though simulations with early versions yielded useful results, they failed to reproduce two important quantities: a zero surface tension at the experimental bilayer surface area, and the signature splitting of the deuterium order parameters in the glycerol and upper chain carbons. Systematic optimization of parameters based on high level quantum mechanical data and free energy simulations have resolved these issues, and bilayers with a wide range of lipids can be simulated in tensionless ensembles using C36. Issues associated with other all-atom lipid FFs, success and limitations in the C36 FF and ongoing developments are also discussed. PMID:21760975
NASA Astrophysics Data System (ADS)
Guiral, A.; Alonso, A.; Giménez, J. G.
2015-10-01
Vehicle-track interaction in the mid- and high-frequency range has become an important issue for rolling-stock manufacturers, railway operators and administrations. Previous modelling approaches have been focused on the development of flexible wheelset-track systems based on the assumption that the unsprung masses are decoupled from the high-frequency dynamic behaviour of carbody and bogies. In this respect, the available flexible wheelset models account for gyroscopic and inertial effects due to the main rotation but are, in general, developed from the viewpoint of inertial spaces and consequently restricted to the study of tangent layouts. The aim of this paper is to present the formulation of a flexible rotating wheelset derived within the framework of a non-inertial vehicle moving reference frame. This brings a double advantage; on the one hand, the formulation is not restricted to tangent tracks, but is also suitable for the study of transition curves and curve negotiation. On the other hand, the use of a vehicle moving reference frame allows the introduction of the hypothesis of small displacement for the degrees of freedom of the wheelset. This hypothesis is not applied to the pitch angle, as it is associated with the main axis of rotation. In addition, unlike previous flexible wheelset models that only consider the rotation around the main axis, all the degrees of freedom will be considered when developing the dynamic equations of motion. Results for the proposed model will be presented and the influence of the inertial and gyroscopic terms not taken into account in previous derived formulations will be evaluated.
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.
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
The Space Structure, Force Fields and Quantum Mechanics
NASA Astrophysics Data System (ADS)
Krasnoholovets, Volodymyr; Chung, Ding-Yu
2006-06-01
It is proposed that the cosmic digital code consists of 1 and 0 for an attachment space and a detachment space, respectively. The attachment space attaches to an object, while the detachment space detaches from the object. The cosmic digital code relates to the reduction of > 4D space-time into 4D space-time and the derivation of the space structure. Through the detachment space, > 4D space-time is sliced into infinitely many 4D slices surrounding the 4D core attachment space. The space structurally is a partition space, or a lattice space. The lattice space consists of repetitive units of alternative attachment space and detachment space and provides for a coherent wave function and gauge force fields, while the partition space consists of separated continuous phases of attachment space and detachment space providing the space structure for the collapse of wave function and the permanent detachment or attachment of gauge bosons. Thus, the wave function and gauge bosons become pure physical fields. The mechanism for the emergence of the space structure is varying dimension numbers, ensuring the metric for the slicing of > 4D space-time.
Critical Casimir forces in the presence of random surface fields
NASA Astrophysics Data System (ADS)
Maciołek, A.; Vasilyev, O.; Dotsenko, V.; Dietrich, S.
2015-03-01
We study critical Casimir forces (CCFs) fC for films of thickness L which in the three-dimensional bulk belong to the Ising universality class and which are exposed to random surface fields (RSFs) on both surfaces. We consider the case in which, in the absence of RSFs, the surfaces of the film belong to the surface universality class of the so-called ordinary transition. We carry out a finite-size scaling analysis and show that for weak disorder, CCFs still exhibit scaling, acquiring a random field scaling variable w that is zero for pure systems. We confirm these analytic predictions by Monte Carlo (MC) simulations. Moreover, our MC data show that fC varies as fC(w →0 ) -fC(w =0 ) ˜w2 . Asymptotically, for large L , w scales as w ˜L-0.26→0 , indicating that this type of disorder is an irrelevant perturbation of the ordinary surface universality class. However, for thin films such that w ≃1 , we find that the presence of RSFs with vanishing mean value increases significantly the strength of CCFs, as compared to systems without them, and it shifts the extremum of the scaling function of fC toward lower temperatures. But fC remains attractive.
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
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
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
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. PMID:25339714
Automation of AMOEBA polarizable force field parameterization for small molecules
Wu, Johnny C.; Chattree, Gaurav
2012-01-01
A protocol to generate parameters for the AMOEBA polarizable force field for small organic molecules has been established, and polarizable atomic typing utility, Poltype, which fully automates this process, has been implemented. For validation, we have compared with quantum mechanical calculations of molecular dipole moments, optimized geometry, electrostatic potential, and conformational energy for a variety of neutral and charged organic molecules, as well as dimer interaction energies of a set of amino acid side chain model compounds. Furthermore, parameters obtained in gas phase are substantiated in liquid-phase simulations. The hydration free energy (HFE) of neutral and charged molecules have been calculated and compared with experimental values. The RMS error for the HFE of neutral molecules is less than 1 kcal/mol. Meanwhile, the relative error in the predicted HFE of salts (cations and anions) is less than 3% with a correlation coefficient of 0.95. Overall, the performance of Poltype is satisfactory and provides a convenient utility for applications such as drug discovery. Further improvement can be achieved by the systematic study of various organic compounds, particularly ionic molecules, and refinement and expansion of the parameter database. PMID:22505837
Searching the Force Field Electrostatic Multipole Parameter Space.
Jakobsen, Sofie; Jensen, Frank
2016-04-12
We show by tensor decomposition analyses that the molecular electrostatic potential for amino acid peptide models has an effective rank less than twice the number of atoms. This rank indicates the number of parameters that can be derived from the electrostatic potential in a statistically significant way. Using this as a guideline, we investigate different strategies for deriving a reduced set of atomic charges, dipoles, and quadrupoles capable of reproducing the reference electrostatic potential with a low error. A full combinatorial search of selected parameter subspaces for N-methylacetamide and a cysteine peptide model indicates that there are many different parameter sets capable of providing errors close to that of the global minimum. Among the different reduced multipole parameter sets that have low errors, there is consensus that atoms involved in π-bonding require higher order multipole moments. The possible correlation between multipole parameters is investigated by exhaustive searches of combinations of up to four parameters distributed in all possible ways on all possible atomic sites. These analyses show that there is no advantage in considering combinations of multipoles compared to a simple approach where the importance of each multipole moment is evaluated sequentially. When combined with possible weighting factors related to the computational efficiency of each type of multipole moment, this may provide a systematic strategy for determining a computational efficient representation of the electrostatic component in force field calculations. PMID:26925529
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
The FoldX web server: an online force field
Schymkowitz, Joost; Borg, Jesper; Stricher, Francois; Nys, Robby; Rousseau, Frederic; Serrano, Luis
2005-01-01
FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at . The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed. PMID:15980494
Force field independent metal parameters using a nonbonded dummy model.
Duarte, Fernanda; Bauer, Paul; Barrozo, Alexandre; Amrein, Beat Anton; Purg, Miha; Aqvist, Johan; Kamerlin, Shina Caroline Lynn
2014-04-24
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 Mn(2+), Zn(2+), Mg(2+), and Ca(2+), as well as providing new parameters for Ni(2+), Co(2+), and Fe(2+). In all the cases, we are able to reproduce both M(2+)-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
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
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.
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)
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.
A turbulent nonisothermal jet in an Archimedean force field
NASA Astrophysics Data System (ADS)
Elemasov, V. E.; Glebov, G. A.; Kozlov, A. P.
An integral method for calculating a vertical nonisothermal jet is presented which allows for the effects of Archimedean forces and nonisothermality. The method can be extended to the calculation of axisymmetric and plane jets in a slipstream and also to the case of jets issuing into a medium of a different concentration. It is shown that the consideration of Archimedean forces and nonisothermality results in a better agreement between calculations and experimental data.
Dirac Field, Gravity, Inertial Effects, and Computer Algebra
NASA Astrophysics Data System (ADS)
Vulcanov, Dumitru N.; Cotăescu, Ion I.
The article presents some new results obtained for the non-relativistic approximation of the Dirac equation in a non-inertial reference frame — rotated and accelerated — and in Schwarzschild gravitational field. These results are obtained with new routines of algebraic programming in REDUCE + EXCALC language for the Dirac equation in a non-inertial reference frame and after three successive Foldy-Wouthuysen transformations.
Quantum field theory of the Casimir force for graphene
NASA Astrophysics Data System (ADS)
Klimchitskaya, G. L.
2016-01-01
We present theoretical description of the Casimir interaction in graphene systems which is based on the Lifshitz theory of dispersion forces and the formalism of the polarization tensor in (2+1)-dimensional space-time. The representation for the polarization tensor of graphene allowing the analytic continuation to the whole plane of complex frequencies is given. This representation is used to obtain simple asymptotic expressions for the reflection coefficients at all Matsubara frequencies and to investigate the origin of large thermal effect in the Casimir force for graphene. The developed theory is shown to be in a good agreement with the experimental data on measuring the gradient of the Casimir force between a Au-coated sphere and a graphene-coated substrate. The possibility to observe the thermal effect for graphene due to a minor modification of the already existing experimental setup is demonstrated.
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.
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.
Communication: Multiple atomistic force fields in a single enhanced sampling simulation
NASA Astrophysics Data System (ADS)
Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H.
2015-07-01
The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.
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.
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. PMID:27070322
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
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. PMID:27230942
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.
Generation of mechanical force by grafted polyelectrolytes in an electric field
NASA Astrophysics Data System (ADS)
Brilliantov, N. V.; Budkov, Yu. A.; Seidel, C.
2016-03-01
We study theoretically and by means of molecular dynamics (MD) simulations the generation of mechanical force by grafted polyelectrolytes in an external electric field, which favors its adsorption on the grafting plane. The force arises in deformable bodies linked to the free end of the chain. Varying the field, one controls the length of the nonadsorbed part of the chain and hence the deformation of the target body, i.e., the arising force too. We consider target bodies with a linear force-deformation relation and with a Hertzian one. While the first relation models a coiled Gaussian chain, the second one describes the force response of a squeezed colloidal particle. The theoretical dependences of generated force and compression of the target body on an applied field agree very well with the results of MD simulations. The analyzed phenomenon may play an important role in future nanomachinery, e.g., it may be used to design nanovices to fix nanosized objects.
Superdiffusion to normal diffusion: particle motion in three-dimensional force-free magnetic fields
NASA Astrophysics Data System (ADS)
Holguin, F.; Ram, A. K.; Krishnamurthy, V.; Dasgupta, B.
2015-11-01
Magnetic fields in regions of low plasma pressure and large currents, such as in interstellar space and gaseous nebulae, are force-free as the Lorentz force vanishes. The Arnold-Beltrami-Childress (ABC) field is an example of a three-dimensional, force-free, helical magnetic field. The field lines form complex and varied structures in space that are a mix of regular and chaotic lines of force. Charged particles moving in the region of chaotic field lines exhibit anomalous superdiffusion. The sine field, or the Archontis field, is a special case of ABC field with the cosine terms left out. The lines of force of a sine field are completely chaotic in space. However, the diffusion of particles in the sine field is normal. The time evolution of an ensemble of particles can be divided into three domains. For short times, the motion is essentially ballistic. For intermediate times, the motion is characterized by a decay of the velocity autocorrelation function. For longer times, the particles undergo diffusion. We present results on the diffusion of field lines, and of particles, in the ABC and sine fields. In particular, the transition from superdiffusion to normal diffusion is discussed.
Mapping the electrostatic force field of single molecules from high-resolution scanning probe images
NASA Astrophysics Data System (ADS)
Hapala, Prokop; Švec, Martin; Stetsovych, Oleksandr; van der Heijden, Nadine J.; Ondráček, Martin; van der Lit, Joost; Mutombo, Pingo; Swart, Ingmar; Jelínek, Pavel
2016-05-01
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.
Catch trials in force field learning influence adaptation and consolidation of human motor memory
Stockinger, Christian; Focke, Anne; Stein, Thorsten
2014-01-01
Force field studies are a common tool to investigate motor adaptation and consolidation. Thereby, subjects usually adapt their reaching movements to force field perturbations induced by a robotic device. In this context, so-called catch trials, in which the disturbing forces are randomly turned off, are commonly used to detect after-effects of motor adaptation. However, catch trials also produce sudden large motor errors that might influence the motor adaptation and the consolidation process. Yet, the detailed influence of catch trials is far from clear. Thus, the aim of this study was to investigate the influence of catch trials on motor adaptation and consolidation in force field experiments. Therefore, 105 subjects adapted their reaching movements to robot-generated force fields. The test groups adapted their reaching movements to a force field A followed by learning a second interfering force field B before retest of A (ABA). The control groups were not exposed to force field B (AA). To examine the influence of diverse catch trial ratios, subjects received catch trials during force field adaptation with a probability of either 0, 10, 20, 30, or 40%, depending on the group. First, the results on motor adaptation revealed significant differences between the diverse catch trial ratio groups. With increasing amount of catch trials, the subjects' motor performance decreased and subjects' ability to accurately predict the force field—and therefore internal model formation—was impaired. Second, our results revealed that adapting with catch trials can influence the following consolidation process as indicated by a partial reduction to interference. Here, the optimal catch trial ratio was 30%. However, detection of consolidation seems to be biased by the applied measure of performance. PMID:24795598
Rauscher, Sarah; Gapsys, Vytautas; Gajda, Michal J; Zweckstetter, Markus; de Groot, Bert L; Grubmüller, Helmut
2015-11-10
Intrinsically disordered proteins (IDPs) are notoriously challenging to study both experimentally and computationally. The structure of IDPs cannot be described by a single conformation but must instead be described as an ensemble of interconverting conformations. Atomistic simulations are increasingly used to obtain such IDP conformational ensembles. Here, we have compared the IDP ensembles generated by eight all-atom empirical force fields against primary small-angle X-ray scattering (SAXS) and NMR data. Ensembles obtained with different force fields exhibit marked differences in chain dimensions, hydrogen bonding, and secondary structure content. These differences are unexpectedly large: changing the force field is found to have a stronger effect on secondary structure content than changing the entire peptide sequence. The CHARMM 22* ensemble performs best in this force field comparison: it has the lowest error in chemical shifts and J-couplings and agrees well with the SAXS data. A high population of left-handed α-helix is present in the CHARMM 36 ensemble, which is inconsistent with measured scalar couplings. To eliminate inadequate sampling as a reason for differences between force fields, extensive simulations were carried out (0.964 ms in total); the remaining small sampling uncertainty is shown to be much smaller than the observed differences. Our findings highlight how IDPs, with their rugged energy landscapes, are highly sensitive test systems that are capable of revealing force field deficiencies and, therefore, contributing to force field development. PMID:26574339
Comparison of three empirical force fields for phonon calculations in CdSe quantum dots
NASA Astrophysics Data System (ADS)
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.
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. PMID:26537332
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.
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.
Parameters for the AMBER force field for the molecular mechanics modeling of the cobalt corrinoids
NASA Astrophysics Data System (ADS)
Marques, H. M.; Ngoma, B.; Egan, T. J.; Brown, K. L.
2001-04-01
Additional parameters for the AMBER force field have been developed for the molecular mechanics modeling of the cobalt corrinoids. Parameter development was based on a statistical analysis of the reported structures of these compounds. The resulting force field reproduces bond lengths, bond angles, and torsional angles within 0.01 Å, 0.8°, and 4.0° of the mean crystallographic values, respectively. Parameters for the Co-C bond length and the Co-C-C bond angle for modeling the alkylcobalamins were developed by modeling six alkylcobalamins. The validity of the force field was tested by comparing the results obtained with known experimental features of the structures of the cobalt corrinoids as well as with the results from their modeling using a parameter set for the MM2 force field that has been previously developed and extensively tested. The AMBER force field reproduces the structures of the cobalt corrinoids as well as the MM2 force field, although it tends to underestimate the corrin fold angle, the angle between mean planes through the corrin atoms in the northern and southern half of the molecules, respectively. The force field was applied to a study of the structures of 5'-deoxy-5'-(3-isoadenosyl)cobalamin, 2',5'-dideoxy-5'-adenosylcobalamin and 2',3',5'-trideoxy-5'-adenosylcobalamin. This expansion of the standard AMBER force field provides a force field that can be used for modeling the structures of the B 12-dependent proteins, the structures of some of which are now beginning to emerge. This was verified in a preliminary modeling of the coenzyme B 12 binding site of methylmalonyl coenzyme A mutase.
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.
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.
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
Tailoring the Optical Dipole Force for Molecules by Field-Induced Alignment
NASA Astrophysics Data System (ADS)
Purcell, S. M.; Barker, P. F.
2009-10-01
We report on the ability to tailor the optical dipole force for molecules by tuning their effective polarizability with strong field alignment using polarized fields. We have measured a difference of 20% in the dipole force on cold CS2 molecules when changing from linear to near-circular polarization using peak field intensities of 5.7×1011Wcm-2. A variation in the focal length with laser polarization of a molecular-optical lens formed by a single focused laser beam was also measured. This provides a new way of modifying this force for many molecules.
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
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
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.
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.
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. PMID:23039579
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
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...
Magnetic field dependence of magnetic domains in Co doped Mn2Sb using magnetic force microscopy
NASA Astrophysics Data System (ADS)
Singh, Vikram; Saha, Pampi; Kushwaha, Pallavi; Thamizhavel, A.; Rawat, Rajeev
2016-05-01
Magnetic domains in the ferrimagnetic state of Co doped Mn2Sb single crystal has been visualized using Magnetic Force Microscopy. It shows fractal like domain structure. With the application of magnetic field, single domain state is achieved around 2000 Oe. The MFM images collected during field increasing and decreasing cycles show different morphology for same field value.
NASA Astrophysics Data System (ADS)
Sujak, Peter
2014-03-01
This work derives the relation between the Planck constant and currently valid Einstein's gravitational constant h / c = κ = 8 πG /c4 = 2 . 13 - 2 . 21 ×10-42 . The relation between the Planck constant and Newton's gravitational, between the Planck constant and 1 Coulomb and 1 Henry is deduced. This work establishes that the Planck constant represents the density of momentum of the void space in the Universe, and momentum of a photon p = h / λ represents the compression of this density, and that the momentum of the photon p = h /λo inevitably equals internal momentum of created proton by ppi = h /λo =mp c . In this work, we state that through generating mass particles, by compressing the density of momentum of the vacuum into a photon and bring this photon to stop, we concurrently generate a gravitational field of these particles. The value of momentum of the gravitational field on the surface of the proton is equal in size, but reversely oriented to the value of the internal momentum of the proton in explicit direction as ppi / π = h /λo =mp c / π . This work proves that gravitational force has its opposite force in the internal momentum of atomic particles of matter. This work maintains that the essence of the composition of all mass matter, as well as force fields in its vicinity, are created in full by the compression of the momentum of the void space in the universe.
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
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
2006-08-25
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. PMID:17026312
NASA Astrophysics Data System (ADS)
Akin-Ojo, Omololu; Song, Yang; Wang, Feng
2008-08-01
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]. 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.
Theoretical study on the HIV-1 integrase-5CITEP complex based on polarized force fields
NASA Astrophysics Data System (ADS)
Wei, Caiyi; Mei, Ye; Zhang, Dawei
2010-07-01
Molecular dynamics studies of 5CITEP binding with HIV-1 integrase (IN) are presented using both polarized and nonpolarized force fields. When nonpolarized force field is used, the ligand drifts away from the original binding site. However, this depressing behavior can be curbed by introducing electronic polarization effect into the force field that stabilizes the protein structure and keeps the ligand in the binding pocket. Moreover, simulation under polarized force field gives a binding energy of -4.85 kcal/mol which is in excellent agreement with the experimental Δ G of -4.38 kcal/mol. The results demonstrate the importance of intra-protein electronic polarization in stabilizing the binding complex of IN-5CITEP and accurately predicting the binding energy.
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.
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
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
Chen, Wei; Shi, Chuanyin; MacKerell, Alexander D.; Shen, Jana
2015-01-01
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 NT9 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
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.
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
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
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
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.
Influence of mechanical force field on the electromechanical stability of dielectric elastomers
NASA Astrophysics Data System (ADS)
Liu, Yanju; Liu, Liwu; Leng, Jinsong
2009-12-01
Arbitrary free energy functions, as is proposed by Zhao and Suo, can be applied to analyze the electromechanical stability of the dielectric elastomer. To study the electromechanical stability of mechanical force field placed on dielectric elastomer, variable free energy functions are applied to analyze the mechanical performance of dielectric elastomer. The relation among critical nominal electric field, critical real electric field, nominal stress and mechanical force field is derived, which agrees well with the experimental results. Such a result is capable of understanding better the stability conditions of dielectric elastomers and furthermore guiding the design and manufacture of sensors and actuators based on dielectric elastomers.
Influence of mechanical force field on the electromechanical stability of dielectric elastomers
NASA Astrophysics Data System (ADS)
Liu, Yanju; Liu, Liwu; Leng, Jinsong
2010-03-01
Arbitrary free energy functions, as is proposed by Zhao and Suo, can be applied to analyze the electromechanical stability of the dielectric elastomer. To study the electromechanical stability of mechanical force field placed on dielectric elastomer, variable free energy functions are applied to analyze the mechanical performance of dielectric elastomer. The relation among critical nominal electric field, critical real electric field, nominal stress and mechanical force field is derived, which agrees well with the experimental results. Such a result is capable of understanding better the stability conditions of dielectric elastomers and furthermore guiding the design and manufacture of sensors and actuators based on dielectric elastomers.
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.
Submolecular features of epitaxially grown PTCDA on Cu(111) analyzed by force field spectroscopy.
Braun, D-A; Weiner, D; Such, B; Fuchs, H; Schirmeisen, A
2009-07-01
Submolecular features of epitaxially grown 3,4,9,10-perylenetetra-carboxylic-dianhydride (PTCDA) on Cu(111) are resolved in non-contact atomic force microscopy topography scans in ultrahigh vacuum. While molecules in the first layer above the Cu substrate are depicted as featureless ovals, the second layer molecules show an intramolecular structure with a height corrugation of up to 40 pm. Force field spectroscopy experiments with submolecular resolution show that the tip-molecule forces differ significantly on the first and second layer molecules. Possible contributions to these force differences from mechanical deformations of the molecules as well as the internal charge density distribution are discussed. PMID:19509447
Ab initio calculation and anharmonic force field of hypochlorous acid, HOCl
NASA Astrophysics Data System (ADS)
Halonen, L.; Ha, T.-K.
1988-03-01
Ab initio calculations on HOCl have been performed at the third-order Møller-Plesset perturbation theory level to determine the equilibrium structure and the anharmonic force field. An empirical anharmonic force field based on the ab initio results is obtained using available experimental vibration-rotation data. Four of the six harmonic and six of the ten cubic force constants have been determined experimentally, the remaining values being fixed at the ab initio values. A good fit to the experimental vibration-rotation data of four isotopic species is obtained.
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.
Mie scattering and optical forces from evanescent fields: a complex-angle approach.
Bekshaev, Aleksandr Y; Bliokh, Konstantin Y; Nori, Franco
2013-03-25
Mie theory is one of the main tools describing scattering of propagating electromagnetic waves by spherical particles. Evanescent optical fields are also scattered by particles and exert radiation forces which can be used for optical near-field manipulations. We show that the Mie theory can be naturally adopted for the scattering of evanescent waves via rotation of its standard solutions by a complex angle. This offers a simple and powerful tool for calculations of the scattered fields and radiation forces. Comparison with other, more cumbersome, approaches shows perfect agreement, thereby validating our theory. As examples of its application, we calculate angular distributions of the scattered far-field irradiance and radiation forces acting on dielectric and conducting particles immersed in an evanescent field. PMID:23546090
reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.
Müller, Julian; Hartke, Bernd
2016-08-01
Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach. PMID:27415976
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
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
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
NASA Astrophysics Data System (ADS)
Esquivel-Sirvent, Raul
Thermally induced electromagnetic fields give rise to the Casimir force and the near field heat transfer between two bodies separated by a gap. These phenomena are described by Rytova's theory of fluctuating electromagnetic fields and both the Casimir force and the near field heat transfer depend on the local dielectric function of the bodies. In this work we present a theoretical calculation on the modulation of fluctuation-induced interactions in the presence of an external magnetic field. The system consists of two parallel plates separated by a gap d. Each plate is isotropic and has a local dielectric function. Applying an external magnetic field parallel to the plates, in the so called Voigt configuration, the plates become anisotropic. In particular, we consider plates of InSb. For the Casimir force the two plates are kept at the same temperature and the external field reduces the magnitude of the force. Similarly if the two plates are kept at different temperature the near field radiative heat transfer is modulated by the magnitude of the external magnetic field. The results are extended to semiconducting quantum wells. In both cases, the excitation of magnetoplasmons provides an explanation for the observed effect.
Relativistic mean field model based on realistic nuclear forces
Hirose, S.; Serra, M.; Ring, P.; Otsuka, T.; Akaishi, Y.
2007-02-15
In order to predict properties of asymmetric nuclear matter, we construct a relativistic mean field (RMF) model consisting of one-meson exchange (OME) terms and point coupling (PC) terms. In order to determine the density dependent parameters of this model, we use properties of isospin symmetric nuclear matter in combination with the information on nucleon-nucleon scattering data, which are given in the form of the density dependent G-matrix derived from Brueckner calculations based on the Tamagaki potential. We show that the medium- and long-range components of this G-matrix can be described reasonably well by our effective OME interaction. In order to take into account the short-range part of the nucleon-nucleon interaction, which cannot be described well in this manner, a point coupling term is added. Its analytical form is taken from a model based on chiral perturbation theory. It contains only one additional parameter, which does not depend on the density. It is, together with the parameters of the OME potentials adjusted to the equation of state of symmetric nuclear matter. We apply this model for the investigation of asymmetric nuclear matter and find that the results for the symmetry energy as well as for the equation of state of pure neutron matter are in good agreement with either experimental data or with presently adopted theoretical predictions. In order to test the model at higher density, we use its equation of state for an investigation of properties of neutron stars.
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
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
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
Lupyan, Dmitry; Abramov, Yuriy A; Sherman, Woody
2012-11-01
The Cambridge Structural Database (CSD) offers an excellent data source to study small molecule conformations and molecular interactions. We have analyzed 130 small molecules from the CSD containing an intramolecular sulfur-oxygen distance less than the sum of their van der Waals (vdW) radii. Close S···O distances are observed in several important medicinal chemistry motifs (e.g. a carbonyl oxygen connected by a carbon or nitrogen linker to a sulfur) and are not treated well with existing parameters in the MMFFs or OPLS_2005 force fields, resulting in suboptimal geometries and energetics. In this work, we develop modified parameters for the OPLS_2005 force field to better treat this specific interaction in order to generate conformations close to those found in the CSD structures. We use a combination of refitting a force field torsional parameter, adding a specific atom pair vdW term, and attenuating the electrostatic interactions to obtain an improvement in the accuracy of geometry minimizations and conformational searches for these molecules. Specifically, in a conformational search 58 % of the cases produced a conformation less than 0.25 Å from the CSD crystal conformation with the modified OPLS force field parameters developed in this work. In contrast, 25 and 37 % produced a conformation less than 0.25 Å with the MMFFs and OPLS_2005 force fields, respectively. As an application of the new parameters, we generated conformations for the tyrosine kinase inhibitor axitinib (trade name Inlyta) that could be correctly repacked into three observed polymorphic structures, which was not possible with conformations generated using MMFFs or OPLS_2005. The improved parameters can be mapped directly onto physical characteristics of the systems that are treated inadequately with the molecular mechanics force fields used in this study and potentially other force fields as well. PMID:23053737
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
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.
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.
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 ...
Forcing a Global, Offline Land Surface Modeling System with Observation-Based Fields
NASA Technical Reports Server (NTRS)
Rodell, Matthew; Houser, Paul R.; Jambor, U.; Gottschalck, J.; Radakovich, J.; Arsenault, K.; Meng, C.-J.; Mitchell, K. E.
2002-01-01
The Global Land Data Assimilation System (GLDAS) drives multiple uncoupled land surface models in order to produce optimal output fields of surface states in near-real time, globally, at 1/4 degree spatial resolution. These fields are then made available for coupled atmospheric model initialization and further research. One of the unique aspects of GLDAS is its ability to ingest both modeled and observation-derived forcing for running global scale land surface models. This paper compares results of runs forced by modeled and observed precipitation and shortwave radiation fields. Differences are examined and the impact of the observations on model skill is assessed.
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.
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
NASA Astrophysics Data System (ADS)
Sheng, Wenbin; Ma, Chunxue; Gu, Wanli
2011-06-01
Based on the steady flow in a tube, a mathematical model has been established for the consideration of centrifuging force field by combining the equations of continuity, conservation of momentum and general energy. Effects of centrifugal field on the filling and solidification are modeled by two accessional terms: centrifugal force and Chorios force. In addition, the transfer of heat by convection is considered to achieve a coupling calculation of velocity field and temperature field. The solution of pressure item is avoided by introducing the stream function ψ(x,y) and the eddy function ξ(x,y). Corresponding difference formats for the simultaneous equations of centrifugal filling, the accessional terms and the solidifying latent heat have been established by the finite difference technique. Furthermore, the centrifugal filling and solidification processes in a horizontal tube are summarized to interpret the mechanism by which internal defects are formed in centrifugal castings.
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. PMID:23764175
HE, YI; XIAO, YI; LIWO, ADAM; SCHERAGA, HAROLD A.
2009-01-01
We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal α-helical and a minimal β-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with α or α + β structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. PMID:19242966
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.
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.
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. PMID:24901255
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
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. PMID:25343332
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
NASA Technical Reports Server (NTRS)
Gregg, Watson; Casey, Nancy
2010-01-01
Ocean biogeochemistry models are typically forced by atmospheric and oceanic data derived from reanalysis products. For the NASA Ocean Biogeochemistry Model (NOBM) such reanalysis forcing fields include: surface wind stress, sea surface temperature, ice distributions, shortwave radiation, surface wind speeds and surface atmospheric pressure. Additionally, proper computation of ocean irradiance requires reanalysis products of relative humidity and precipitable water (in addition to aerosol and cloud information which is derived from satellite data). The question posed here is, does the choice of reanalysis products make a difference in the representation of ocean biology and biogeochemistry? NOBM was forced by NCEP and MERRA reanalysis products for the period 2002-2009. We find that in 2009 global distributions and abundances of biological variables (total chlorophyll and nutrients) and carbon (dissolved inorganic and organic carbon and surface pCO2) were similar between the two different forcing fields. Global statistical comparisons with satellite and in situ data also showed negligible differences.
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.
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
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.
Wang, Gou-Jen; Hsu, Wen-Haw; Chang, Yau-Zin; Yang, Hsiharng
2004-03-01
In this article, we propose a versatile CD-like multi-channel electrophoresis-based biomedical separation system that is driven by the interactive forces between the centrifugal force and the electric field force. The centrifugal force control of this system is realized through the velocity control of a DC servo motor, while the electric field is governed through the concentric conducting circuits, which are suitably designed and fabricated by sputtering on metal mask method, and can be adjusted to provide multi-stage voltages. Experimental results demonstrate that the electro-osmotic flow (EOF) effect can be effectively reduced when the electric field force and centrifugal force are in the opposite direction. Benefits from this are that the electrophoresis separation time can be prolonged and the length of the microfluidic channels can be shortened; therefore, more effective separation efficiency can be obtained. Moreover, other advantages, such as lower joule-heat generation, low-chemistry reaction, and no variation on the ion concentration during processes, make this biomedical separation system more useful. PMID:15307444
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
Controlling dispersion forces between small particles with artificially created random light fields
NASA Astrophysics Data System (ADS)
Brügger, Georges; Froufe-Pérez, Luis S.; Scheffold, Frank; José Sáenz, Juan
2015-06-01
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.
Magnetic field sensor based on the Ampere's force using dual-polarization DBR fiber laser
NASA Astrophysics Data System (ADS)
Yao, Shuang; Zhang, Yang; Guan, Baiou
2015-08-01
A novel magnetic field sensor using distributed Bragg reflector (DBR) fiber laser by Ampere's force effect is proposed and experimentally demonstrated. The key sensing element, that is the dual-polarization DBR fiber laser, is fixed on the middle part of two copper plates which carry the current. Ampere's force is applied onto the coppers due to an external magnetic field generated by a DC solenoid. Thus, the lateral force from the coppers is converted to a corresponding beat frequency signal shift produced by the DBR laser. The electric current sensing is also realized by the same configuration and same principle simultaneously in an intuitive manner. Good agreement between the theory calculation and the experimental results is obtained, which shows a good linearity. This sensor's sensitivity to the magnetic field and to the electric current finally reaches ~258.92 kHz/mT and ~1.08727 MHz/A, respectively.
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. PMID:26493154
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).
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
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.
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.
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.
Yin, Jian; Fenley, Andrew T.; Henriksen, Niel M.; Gilson, Michael K.
2015-01-01
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 non-optimal 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. PMID:26181208
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
Higher-order nonlocal effects of a relativistic ponderomotive force in high-intensity laser fields.
Iwata, Natsumi; Kishimoto, Yasuaki
2014-01-24
We have developed a new formula for a relativistic ponderomotive force of transversely localized laser fields based on the noncanonical Lie perturbation method by finding proper coordinates and gauges in the variational principle. The formula involves new terms represented by second and third spatial derivatives of the field amplitude, so that the ponderomotive force depends not only on the local field gradient, but also on the curvature and its variation. The formula is then applicable to a regime in which the conventional formula is hardly applied such that nonlocal and/or global extent of the field profile becomes important. The result can provide a theoretical basis for describing nonlinear laser-plasma interaction including such nonlocal effects, which is examined via particle-in-cell simulation of laser propagation in a plasma with a super Gaussian transverse field profile. PMID:24484146
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.
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
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
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
Ram, Abhay K.; Dasgupta, Brahmananda; Krishnamurthy, V.; Mitra, Dhrubaditya
2014-07-15
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 t{sup 2}, 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 t{sup α}, where α > 1, and is weakly dependent on the energy of the particles. These super-diffusive characteristics
Soules, T F; Gilmer, G H; Matthews, M J; Stolken, J S; Feit, M D
2010-10-21
We compare force fields (FF's) that have been used in molecular dynamic (MD) simulations of silica in order to assess their applicability for use in simulating IR-laser damage mitigation. Although pairwise FF?s obtained by fitting quantum mechanical calculations such as the BKS and CHIK potentials have been shown to reproduce many of the properties of silica including the stability of silica polymorphs and the densification of the liquid, we show that melting temperatures and fictive temperatures are much too high. Softer empirical force fields give liquid and glass properties at experimental temperatures but may not predict all properties important to laser mitigation experiments.
Explicit polarization: a quantum mechanical framework for developing next generation force fields.
Gao, Jiali; Truhlar, Donald G; Wang, Yingjie; Mazack, Michael J M; Löffler, Patrick; Provorse, Makenzie R; Rehak, Pavel
2014-09-16
Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples
Transferability of coarse-grained force field for nCB liquid crystal systems.
Zhang, Jianguo; Guo, Hongxia
2014-05-01
In this paper, the transferability of the coarse-grained (CG) force field originally developed for the liquid crystal (LC) molecule 5CB ( Zhang et al. J. Phys. Chem. B 2012 , 116 , 2075 - 2089 ) was investigated by its homologues 6CB and 8CB molecules. Note that, to construct the 5CB CG force field, we combined the structure-based and thermodynamic quantities-based methods and at the same time attempted to use several fragment molecular systems to derive the CG nonbonded interaction parameters. The resultant 5CB CG force field exhibits a good transferability to some extent. For example, not only the experimental densities, the local packing of atom groups, and the antiparallel arrangements of nearest neighboring molecules, but also the unique LC mesophases as well as the nematic-isotropic phase transition temperatures of 6CB and 8CB were reproduced. Meanwhile, the limitations of this 5CB CG force field were also observed, such as the phase transition from nematic to smectic was postponed to the lower temperature and the resulting smectic phase structure is single-layer-like instead of partially interdigitated bilayer-like as observed in underlying atomistic model. Apparently, more attention should be paid when applying a CG force field to the state point which is quite different from which the force field is explicitly parametrized for. The origin of the above limitations can be potentially traced back to the inherent simplifications and some approximations often adopted in the creation process of CG force field, for example, choosing symmetric CG potentials which do not explicitly include electrostatic interactions and are parametrized by reproducing the target properties of the specific nematic 5CB phase at 300 K and 1 atm, as well as using soft nonbonded potential and excluding torsion barriers. Moreover, although by construction this CG force field could inevitably incorporate both thermodynamic and local structural information on the nematic 5CB phase, the
Zhu, X. S.; Wang, H. N.; Du, Z. L.; Fan, Y. L.
2013-05-10
We undertake an attempt to reconstruct the Sun's non-force-free magnetic field. The solar corona is often considered to be magnetohydrostatic. We solve the full MHD equations with a semi-realistic atmosphere model to attain this stationary state. Our method is tested with a Sun-like model which simulates the emergence of a magnetic flux rope passing from below the photosphere into the corona. Detailed diagnostics shows that our method can model the forced field more successfully than the optimization and potential method, but it still needs to be applied to real data.
Explicit Polarization: A Quantum Mechanical Framework for Developing Next Generation Force Fields
2015-01-01
Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems (“fragments”) to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative
Improved Force Field Parameters Lead to a Better Description of RNA Structure.
Bergonzo, Christina; Cheatham, Thomas E
2015-09-01
We compare the performance of two different RNA force fields in four water models in simulating the conformational ensembles r(GACC) and r(CCCC). With the increased sampling facilitated by multidimensional replica exchange molecular dynamics (M-REMD), populations are compared to NMR data to evaluate force field reliability. The combination of AMBER ff12 with vdW(bb) modifications and the OPC water model produces results in quantitative agreement with the NMR ensemble that have eluded us to date. PMID:26575892
Examination of forced unsteady separated flow fields on a rotating wind turbine blade
Huyer, S. )
1993-04-01
The wind turbine industry faces many problems regarding the construction of efficient and predictable wind turbine machines. Steady state, two-dimensional wind tunnel data are generally used to predict aerodynamic loads on wind turbine blades. Preliminary experimental evidence indicates that some of the underlying fluid dynamic phenomena could be attributed to dynamic stall, or more specifically to generation of forced unsteady separated flow fields. A collaborative research effort between the University of Colorado and the National Renewable Energy Laboratory was conducted to systematically categorize the local and global effects of three- dimensional forced unsteady flow fields.
NASA Astrophysics Data System (ADS)
Endo, Y.; Fukushima, M.; Arai, K.; Yanagi, K.; Shimada, Y.; Yamaguchi, M.
2014-05-01
This paper describes the measurement of microscopic radio frequency (RF) field distribution with a magnetic force microscope (MFM) tip exploring the beat signal from a coplanar waveguide (CPW) with a signal line as fine as 5 μm and a ground line of 50 μm. To produce a beating field in close proximity to the CPW, two RF currents with slightly different frequencies are supplied, where one is the signal current with a fixed frequency of 1.1 GHz and the other is the reference. The reference is adjusted to produce a beat with a frequency near the cantilever mechanical resonance frequency. Thus, the mechanical resonance of the cantilever excited by the beat field includes information about the 1.1 GHz field distribution from the CPW signal current. Detection of a beating field with a MFM tip can provide very high resolutions of the RF field distribution in the proximity of RF circuit component.
Unified boundary conditions and Casimir forces for fields with arbitrary spin
NASA Astrophysics Data System (ADS)
Bennett, Robert; Stokes, Adam
The electromagnetic Casimir effect is well-known and has been extensively studied for the last half-century. This attractive force between parallel plates arises from the imposition of boundary conditions upon the fluctuating spin-1 photon field, so a natural further question is wether fields of different spin can cause similar forces when confined in the same way. However, so far it has not been clear what the appropriate boundary conditions for physically-confined spinor fields may be. Here we present work that generalises the physically well-motivated electromagnetic boundary conditions to fields of arbitrary spin, thus arriving at physically reasonable boundary conditions and Casimir forces for a selection of interesting fields. For example, the so-called `bag model' boundary conditions from nuclear physics emerge from our generalised boundary condition as a special case, as do the linearised gravity boundary conditions suggested in a remarkable recent proposal concerning possible measurement of gravitonic Casimir forces. Supported by the UK Engineering and Physical Sciences Research Council (EPSRC).
NASA Technical Reports Server (NTRS)
Parker, E. N.
1986-01-01
The surfaces of discontinuity (SDs) identified by Parker (1986) in the torsion of a force-free magnetic field in an infinitely conducting fluid contained betweeen two fixed boundary planes are characterized analytically. It is shown that field discontinuities (current sheets) occur whenever an SD terminates within the fluid or intersects with another SD, that intersections occur in most cases, and that the resulting current sheets are responsible for most field dissipation in highly conducting fluids. The astrophysical implications of these findings and a number of unresolved problems are discussed.
Thalmann, J. K.; Tiwari, S. K.; Wiegelmann, T.
2013-05-20
Photospheric magnetic vector maps from two different instruments are used to model the nonlinear force-free coronal magnetic field above an active region. We use vector maps inferred from polarization measurements of the Solar Dynamics Observatory/Helioseismic and Magnetic Imager (HMI) and the Solar Optical Telescope's Spectropolarimeter (SP) on board Hinode. Besides basing our model calculations on HMI data, we use both SP data of original resolution and scaled down to the resolution of HMI. This allows us to compare the model results based on data from different instruments and to investigate how a binning of high-resolution data affects the model outcome. The resulting three-dimensional magnetic fields are compared in terms of magnetic energy content and magnetic topology. We find stronger magnetic fields in the SP data, translating into a higher total magnetic energy of the SP models. The net Lorentz forces of the HMI and SP lower boundaries verify their force-free compatibility. We find substantial differences in the absolute estimates of the magnetic field energy but similar relative estimates, e.g., the fraction of excess energy and of the flux shared by distinct areas. The location and extension of neighboring connectivity domains differ and the SP model fields tend to be higher and more vertical. Hence, conclusions about the magnetic connectivity based on force-free field models are to be drawn with caution. We find that the deviations of the model solution when based on the lower-resolution SP data are small compared to the differences of the solutions based on data from different instruments.
A nonlinear eigenvalue problem for self-similar spherical force-free magnetic fields
NASA Astrophysics Data System (ADS)
Lerche, I.; Low, B. C.
2014-10-01
An axisymmetric force-free magnetic field B(r, θ) in spherical coordinates is defined by a function r sin θ B φ = Q ( A ) relating its azimuthal component to its poloidal flux-function A. The power law r sin θ B φ = a A | A | 1/ n, n a positive constant, admits separable fields with A = An/(θ)rn, posing a nonlinear boundary-value problem for the constant parameter a as an eigenvalue and An(θ) as its eigenfunction [B. C. Low and Y. Q Lou, Astrophys. J. 352, 343 (1990)]. A complete analysis is presented of the eigenvalue spectrum for a given n, providing a unified understanding of the eigenfunctions and the physical relationship between the field's degree of multi-polarity and rate of radial decay via the parameter n. These force-free fields, self-similar on spheres of constant r, have basic astrophysical applications. As explicit solutions they have, over the years, served as standard benchmarks for testing 3D numerical codes developed to compute general force-free fields in the solar corona. The study presented includes a set of illustrative multipolar field solutions to address the magnetohydrodynamics (MHD) issues underlying the observation that the solar corona has a statistical preference for negative and positive magnetic helicities in its northern and southern hemispheres, respectively; a hemispherical effect, unchanging as the Sun's global field reverses polarity in successive eleven-year cycles. Generalizing these force-free fields to the separable form B = H/(θ ,φ)rn+2 promises field solutions of even richer topological varieties but allowing for φ-dependence greatly complicates the governing equations that have remained intractable. The axisymmetric results obtained are discussed in relation to this generalization and the Parker Magnetostatic Theorem. The axisymmetric solutions are mathematically related to a family of 3D time-dependent ideal MHD solutions for a polytropic fluid of index γ = 4/3 as discussed in the Appendix.
Changes in tibiofemoral contact forces during running in response to in-field gait retraining.
Willy, Richard W; Meardon, Stacey A; Schmidt, André; Blaylock, Nathan R; Hadding, Scott A; Willson, John D
2016-09-01
We evaluated the efficacy of an in-field gait retraining programme using mobile biofeedback to reduce cumulative and peak tibiofemoral loads during running. Thirty runners were randomised to either a retraining group or control group. Retrainers were asked to increase their step rate by 7.5% over preferred in response to real-time feedback provided by a wrist mounted running computer for 8 routine in-field runs. An inverse dynamics driven musculoskeletal model estimated total and medial tibiofemoral joint compartment contact forces. Peak and impulse per step total tibiofemoral contact forces were immediately reduced by 7.6% and 10.6%, respectively (P < 0.001). Similarly, medial tibiofemoral compartment peak and impulse per step tibiofemoral contact forces were reduced by 8.2% and 10.6%, respectively (P < 0.001). Interestingly, no changes were found in knee adduction moment measures. Post gait retraining, reductions in medial tibiofemoral compartment peak and impulse per step tibiofemoral contact force were still present (P < 0.01). At the 1-month post-retraining follow-up, these reductions remained (P < 0.05). With these per stance reductions in tibiofemoral contact forces in mind, cumulative tibiofemoral contact forces did not change due to the estimated increase in number of steps to run 1 km. PMID:26679058
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; 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; 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
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
Direct Measurement of Optical Force Induced by Near-Field Plasmonic Cavity Using Dynamic Mode AFM
NASA Astrophysics Data System (ADS)
Guan, Dongshi; Hang, Zhi Hong; Marcet, Zsolt; Liu, Hui; Kravchenko, I. I.; Chan, C. T.; Chan, H. B.; Tong, Penger
2015-11-01
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.
NASA Technical Reports Server (NTRS)
Sturrock, P. A.; Antiochos, S. K.; Klinchuk, J. A.; Roumeliotis, G.
1994-01-01
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 the energy of the field increases progressively. For configurations of translationalsymmetry, it has been found empirically that the energy tends asymptotically to a certain functional form. It is here shown that analysis of a simple model of the asymptotic form of force-free fields of translational symmetry leads to and therefore justifies this functional form. According to this model, the field evolves in a well-behaved manner with no indication of instability or loss of equilibrium.
Scalar field self-force effects on orbits about a Schwarzschild black hole
Diaz-Rivera, Luz Maria; Whiting, Bernard F.; Detweiler, Steven; Messaritaki, Eirini
2004-12-15
For a particle of mass {mu} and scalar charge q, we compute the effects of the scalar field self-force upon circular orbits, upon slightly eccentric orbits and upon the innermost stable circular orbit (ISCO) of a Schwarzschild black hole of mass m. For circular orbits the self-force is outward and causes the angular frequency at a given radius to decrease. For slightly eccentric orbits the self-force decreases the rate of the precession of the orbit. The effect of the self-force moves the radius of the innermost stable circular orbit inward by 0.122 701xq{sup 2}/{mu}, and it increases the angular frequency of the ISCO by the fraction 0.029 165 7xq{sup 2}/{mu}m.
Force field inside the void in complex plasmas under microgravity conditions
Kretschmer, M.; Khrapak, S.A.; Zhdanov, S.K.; Thomas, H.M.; Morfill, G.E.; Fortov, V.E.; Lipaev, A.M.; Molotkov, V.I.; Ivanov, A.I.; Turin, M.V.
2005-05-01
Observations of complex plasmas under microgravity conditions onboard the International Space Station performed with the Plasma-Kristall experiment-Nefedov facility are reported. A weak instability of the boundary between the central void (region free of microparticles) and the microparticle cloud is observed at low gas pressures. The instability leads to periodic injections of a relatively small number of particles into the void region (by analogy this effect is called the 'trampoline effect'). The trajectories of injected particles are analyzed providing information on the force field inside the void. The experimental results are compared with theory which assumes that the most important forces inside the void are the electric and the ion drag forces. Good agreement is found clearly indicating that under conditions investigated the void formation is caused by the ion drag force.
The effect of dissipation on the torque and force experienced by nanoparticles in an AC field
NASA Astrophysics Data System (ADS)
Claro, F.; Fuchs, R.; Robles, P.; Rojas, R.
2015-09-01
We discuss the force and torque acting on spherical particles in an ensemble in the presence of a uniform AC electric field. We show that for a torque causing particle rotation to appear the particle must be absorptive. Our proof includes all electromagnetic excitations, which in the case of two or more particles gives rise to one or more resonances in the spectrum of force and torque depending on interparticle distance. Several peaks are found in the force and torque between two spheres at small interparticle distances, which coalesce to just one as the separation grows beyond three particle radii. We also show that in the presence of dissipation the force on each particle is nonconservative and may not be derived from the classical interaction potential energy as has been done in the past.
Lipid Bilayers: The Effect of Force Field on Ordering and Dynamics.
Poger, David; Mark, Alan E
2012-11-13
The sensitivity of the structure and dynamics of a fully hydrated pure bilayer of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in molecular dynamics simulations to changes in force-field and simulation parameters has been assessed. Three related force fields (the Gromos 54A7 force field, a Gromos 53A6-derived parameter set and a variant of the Berger parameters) in combination with either particle-mesh Ewald (PME) or a reaction field (RF) were compared. Structural properties such as the area per lipid, carbon-deuterium order parameters, electron density profile and bilayer thicknesses, are reproduced by all the parameter sets within the uncertainty of the available experimental data. However, there are clear differences in the ordering of the glycerol backbone and choline headgroup, and the orientation of the headgroup dipole. In some cases, the degree of ordering was reminiscent of a liquid-ordered phase. It is also shown that, although the lateral diffusion of the lipids in the plane of the bilayer is often used to validate lipid force fields, because of the uncertainty in the experimental measurements and the fact that the lateral diffusion is dependent on the choice of the simulation conditions, it should not be employed as a measure of quality. Finally, the simulations show that the effect of small changes in force-field parameters on the structure and dynamics of a bilayer is more significant than the treatment of the long-range electrostatic interactions using RF or PME. Overall, the Gromos 54A7 best reproduced the range of experimental data examined. PMID:26605633
Teodorescu, C.; Young, W. C.; Swan, G. W. S.; Ellis, R. F.; Hassam, A. B.; Romero-Talamas, C. A.
2010-08-20
Interferometric density measurements in plasmas rotating in shaped, open magnetic fields demonstrate strong confinement of plasma parallel to the magnetic field, with density drops of more than a factor of 10. Taken together with spectroscopic measurements of supersonic ExB rotation of sonic Mach 2, these measurements are in agreement with ideal MHD theory which predicts large parallel pressure drops balanced by centrifugal forces in supersonically rotating plasmas.
Spinmotive force due to motion of magnetic bubble arrays driven by magnetic field gradient
Yamane, Yuta; Hemmatiyan, Shayan; Ieda, Jun'ichi; Maekawa, Sadamichi; Sinova, Jairo
2014-01-01
Interaction between local magnetization and conduction electrons is responsible for a variety of phenomena in magnetic materials. It has been recently shown that spin current and associated electric voltage can be induced by magnetization that depends on both time and space. This effect, called spinmotive force, provides for a powerful tool for exploring the dynamics and the nature of magnetic textures, as well as a new source for electromotive force. Here we theoretically demonstrate the generation of electric voltages in magnetic bubble array systems subjected to a magnetic field gradient. It is shown by deriving expressions for the electric voltages that the present system offers a direct measure of phenomenological parameter β that describes non-adiabaticity in the current induced magnetization dynamics. This spinmotive force opens a door for new types of spintronic devices that exploit the field-gradient. PMID:25365971
LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.
Kratz, Eric G; Walker, Alice R; Lagardère, Louis; Lipparini, Filippo; Piquemal, Jean-Philip; Andrés Cisneros, G
2016-04-30
We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc. PMID:26781073
The spectroscopic constants and anharmonic force field of AgSH: An ab initio study.
Zhao, Yanliang; Wang, Meishan; Yang, Chuanlu; Ma, Xiaoguang; Zhu, Ziliang
2016-07-01
The equilibrium structure, spectroscopy constants, and anharmonic force field of silver hydrosulfide (AgSH) have been calculated at B3P86, B3PW91 and MP2 methods employing two basis sets, TZP and QZP, respectively. The calculated geometries, ground state rotational constants, harmonic vibrational wave numbers, and quartic and sextic centrifugal distortion constants are compared with the available experimental and theoretical data. The equilibrium rotational constants, fundamental frequencies, anharmonic constants, and vibration-rotation interaction constants, Coriolis coupling constants, cubic and quartic force constants are predicted. The calculated results show that the MP2/TZP results are in good agreement with experiment observation and are also an advisable choice to study the anharmonic force field of AgSH. PMID:27085293
The spectroscopic constants and anharmonic force field of AgSH: An ab initio study
NASA Astrophysics Data System (ADS)
Zhao, Yanliang; Wang, Meishan; Yang, Chuanlu; Ma, Xiaoguang; Zhu, Ziliang
2016-07-01
The equilibrium structure, spectroscopy constants, and anharmonic force field of silver hydrosulfide (AgSH) have been calculated at B3P86, B3PW91 and MP2 methods employing two basis sets, TZP and QZP, respectively. The calculated geometries, ground state rotational constants, harmonic vibrational wave numbers, and quartic and sextic centrifugal distortion constants are compared with the available experimental and theoretical data. The equilibrium rotational constants, fundamental frequencies, anharmonic constants, and vibration-rotation interaction constants, Coriolis coupling constants, cubic and quartic force constants are predicted. The calculated results show that the MP2/TZP results are in good agreement with experiment observation and are also an advisable choice to study the anharmonic force field of AgSH.
Active control of sound fields in elastic cylinders by multi-control forces
NASA Technical Reports Server (NTRS)
Jones, J. D.; Fuller, C. R.
1987-01-01
An unstiffened cylindrical model was used to study the control of sound transmission into aircraft cabins by the use of multi-control forces applied directly to the cylinder wall. External acoustic monopoles were located on each side of the cylinder to approximate the propeller noise source. This allowed the study of a dual control system utilizing multi-control forces in conjunction with synchrophasing of the twin acoustic monopole sources. For acoustic resonant conditions within the cavity, a spatially averaged noise reduction of approximately 30 dB was achieved using the active control system for both in-phase and out-of-phase monopoles; however, effective reduction of the sound field was dependent upon judiciously positioning the control forces for optimal control of the sound field.
Mean first-passage time for an overdamped particle in a disordered force field
NASA Astrophysics Data System (ADS)
Denisov, S. I.; Horsthemke, Werner
2000-09-01
We derive a rigorous expression for the mean first-passage time of an overdamped particle subject to a constant bias in a force field with quenched disorder. Depending on the statistics of the disorder, the disorder-averaged mean first-passage time can undergo a transition from an infinite value for small bias to a finite value for large bias. This corresponds to a depinning transition of the particle. We obtain exact values for the depinning threshold for Gaussian disorder and also for a class of piecewise constant random forces, which we call generalized kangaroo disorder. For Gaussian disorder, we investigate how the correlations of the random force field affect the average motion of the particle. For kangaroo disorder, we apply the general results for the depinning transition to two specific examples, viz., dichotomous disorder and random fractal disorder.
Henriques, João; Cragnell, Carolina; Skepö, Marie
2015-07-14
An increasing number of studies using molecular dynamics (MD) simulations of unfolded and intrinsically disordered proteins (IDPs) suggest that current force fields sample conformations that are overly collapsed. Here, we study the applicability of several state-of-the-art MD force fields, of the AMBER and GROMOS variety, for the simulation of Histatin 5, a short (24 residues) cationic salivary IDP with antimicrobial and antifungal properties. The quality of the simulations is assessed in three complementary analyses: (i) protein shape and size comparison with recent experimental small-angle X-ray scattering data; (ii) secondary structure prediction; (iii) energy landscape exploration and conformational class analysis. Our results show that, indeed, standard force fields sample conformations that are too compact, being systematically unable to reproduce experimental evidence such as the scattering function, the shape of the protein as compared with the Kratky plot, and intrapeptide distances obtained through the pair distance distribution function, p(r). The consistency of this deviation suggests that the problem is not mainly due to protein-protein or water-water interactions, whose parametrization varies the most between force fields and water models. In fact, as originally proposed in [ Best et al. J. Chem. Theory Comput. 2014, 10, 5113 - 5124.], balanced protein-water interactions may be the key to solving this problem. Our simulations using this approach produce results in very good agreement with experiment. PMID:26575776
2013-01-01
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. PMID:24634618
Solvation structure and dynamics of Ni2+(aq) from a polarizable force field
NASA Astrophysics Data System (ADS)
Mareš, Jiří; Vaara, Juha
2014-10-01
An aqueous solution of Ni2+ has often been used as a prototypic transition-metal system for experimental and theoretical studies in nuclear and electron-spin magnetic resonance (NMR and ESR). Molecular dynamics (MD) simulation of Ni2+(aq) has been a part of many of these studies. As a transition metal complex, its MD simulation is particularly difficult using common force fields. In this work, we parameterize the Ni2+ ion for a simulation of the aqueous solution within the modern polarizable force field AMOEBA. We show that a successful parameterization is possible for this specific case when releasing the physical interpretation of the electrostatic and polarization parameters of the force field. In doing so, particularly the Thole damping parameter and also the ion charge and polarizability were used as fitting parameters. The resulting parameterizations give in a MD simulation good structural and dynamical properties of the [Ni(H2O)6 ] 2 + complex, along with the expected excellent performance of AMOEBA for the water solvent. The presented parameterization is appropriate for high-accuracy simulations of both structural and dynamic properties of Ni2+(aq). This work documents possible approaches of parameterization of a transition metal within the AMOEBA force field.
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.
Harder, Edward; Damm, Wolfgang; Maple, Jon; Wu, Chuanjie; Reboul, Mark; Xiang, Jin Yu; Wang, Lingle; Lupyan, Dmitry; Dahlgren, Markus K; Knight, Jennifer L; Kaus, Joseph W; Cerutti, David S; Krilov, Goran; Jorgensen, William L; Abel, Robert; Friesner, Richard A
2016-01-12
The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addition of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native structure of proteins. To adequately cover medicinal chemical space, OPLS3 employs over an order of magnitude more reference data and associated parameter types relative to other commonly used small molecule force fields (e.g., MMFF and OPLS_2005). As a consequence, OPLS3 achieves a high level of accuracy across performance benchmarks that assess small molecule conformational propensities and solvation. The newly fitted peptide dihedrals lead to significant improvements in the representation of secondary structure elements in simulated peptides and native structure stability over a number of proteins. Together, the improvements made to both the small molecule and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field. PMID:26584231
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.
Molecular dynamics simulations of a new branched antimicrobial peptide: A comparison of force fields
NASA Astrophysics Data System (ADS)
Li, Jianguo; Lakshminarayanan, Rajamani; Bai, Yang; Liu, Shouping; Zhou, Lei; Pervushin, Konstantin; Verma, Chandra; Beuerman, Roger W.
2012-12-01
Branched antimicrobial peptides are promising as a new class of antibiotics displaying high activity and low toxicity and appear to work through a unique mechanism of action. We explore the structural dynamics of a covalently branched 18 amino acid peptide (referred to as B2088) in aqueous and membrane mimicking environments through molecular dynamics (MD) simulations. Towards this, we carry out conventional MD simulations and supplement these with replica exchange simulations. The simulations are carried out using four different force fields that are commonly employed for simulating biomolecular systems. These force fields are GROMOS53a6, CHARMM27 with cMAP, CHARMM27 without cMAP and AMBER99sb. The force fields are benchmarked against experimental data available from circular dichroism and nuclear magnetic resonance spectroscopies, and show that CHARMM27 without cMAP correction is the most successful in reproducing the structural dynamics of B2088 both in water and in the presence of micelles. Although the four force fields predict different structures of B2088, they all show that B2088 stabilizes against the head group of the lipid through hydrogen bonding of its Lys and Arg side chains. This leads us to hypothesize that B2088 is unlikely to penetrate into the hydrophobic region of the membrane owing to the high free energy costs of transfer from water, and possibly acts by carpeting and thus disrupting the membrane.
Sibaev, M; Crittenden, D L
2016-06-01
In this paper, we outline a general, scalable, and black-box approach for calculating high-order strongly coupled force fields in rectilinear normal mode coordinates, based upon constructing low order expansions in curvilinear coordinates with naturally limited mode-mode coupling, and then transforming between coordinate sets analytically. The optimal balance between accuracy and efficiency is achieved by transforming from 3 mode representation quartic force fields in curvilinear normal mode coordinates to 4 mode representation sextic force fields in rectilinear normal modes. Using this reduced mode-representation strategy introduces an error of only 1 cm(-1) in fundamental frequencies, on average, across a sizable test set of molecules. We demonstrate that if it is feasible to generate an initial semi-quartic force field in curvilinear normal mode coordinates from ab initio data, then the subsequent coordinate transformation procedure will be relatively fast with modest memory demands. This procedure facilitates solving the nuclear vibrational problem, as all required integrals can be evaluated analytically. Our coordinate transformation code is implemented within the extensible PyPES library program package, at http://sourceforge.net/projects/pypes-lib-ext/. PMID:27276945
Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field.
Robertson, Michael J; Tirado-Rives, Julian; Jorgensen, William L
2015-07-14
The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1, and χ2 potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields. PMID:26190950
Toward a Broadly Applicable Force Field for d(6)-Piano Stool Complexes.
Schmid, Maurus H; Ward, Thomas R; Meuwly, Markus
2013-05-14
Three-legged piano stool complexes are prototypical organometallic complexes relevant to a wide range of chemically relevant questions. Force field parametrization of transition-metal complexes is difficult and underdeveloped, and metal-specific force fields and software are required. Here we report our efforts to derive parameters for the conventional CHARMM and the Valbond-CHARMM force fields for d(6)-piano stool complexes. In Valbond-CHARMM, the usual angular term is replaced with hybrid orbital strength functions. These functions describe the energy not only of distorted bond angles around the minimum but also at very large distortions. Structure optimizations led to a good agreement between the calculated force field and the X-ray structures. They were comparable to RMSDs obtained between X-ray and DFT structures. In addition, and contrary to treating the systems with DFT, molecular dynamics simulations on the multiple nanosecond time scale are possible and allow to compute meaningful structural and energetic observables. Explicit solvent simulations of the complexes in methanol and water allow to determine the solvent distribution around the complexes. The parametrization presented here will be a useful starting point for dynamics investigations of catalysts in structurally more demanding environments. PMID:26583724
Lee, Myung Won; Meuwly, Markus
2013-12-14
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. PMID:24170171
Empirical anharmonic force field and equilibrium structure of hypochlorous acid, HOCl
NASA Astrophysics Data System (ADS)
Escribano, R. M.; Di Lonardo, G.; Fusina, L.
1996-09-01
The cubic and quartic force fields of HOCl are investigated on the basis of the most recent experimental data on vibration-rotation interaction constants and anharmonicity constants. Some discrepancies with respect to previously reported ab initio results are found and discussed. The geometrical parameters of this molecule are also evaluated from recent data on the equilibrium values of the moments of inertia.
An Energy Conservative Ray-Tracing Method With a Time Interpolation of the Force Field
Yao, Jin
2015-02-10
A new algorithm that constructs a continuous force field interpolated in time is proposed for resolving existing difficulties in numerical methods for ray-tracing. This new method has improved accuracy, but with the same degree of algebraic complexity compared to Kaisers method.
Gravitomagnetic Field of the Universe and Coriolis Force on the Rotating Earth
ERIC Educational Resources Information Center
Veto, B.
2011-01-01
The Machian effect of distant masses of the universe in the frame of reference of the rotating Earth is demonstrated using the gravitomagnetic approach of general relativity. This effect appears in the form of a gravitomagnetic Lorentz force acting on moving bodies on the Earth. The gravitomagnetic field of the universe--deduced from a simple…
ERIC Educational Resources Information Center
Mason, Elisa
1999-01-01
Describes the evolution of refugee and forced migration studies, identifies factors that render it a challenging field to research, and highlights a variety of Internet-based and other electronic resources that can be used to locate monographs, periodicals, grey literature, and current information. Provides a bibliography of reference materials in…
Self-force of a scalar field for circular orbits about a Schwarzschild black hole
NASA Astrophysics Data System (ADS)
Detweiler, Steven; Messaritaki, Eirini; Whiting, Bernard F.
2003-05-01
The foundations are laid for the numerical computation of the actual worldline for a particle orbiting a black hole and emitting gravitational waves. The essential practicalities of this computation are illustrated here for a scalar particle of infinitesimal size and small but finite scalar charge. This particle deviates from a geodesic because it interacts with its own retarded field ψret. A recently introduced Green’s function GS precisely determines the singular part ψS of the retarded field. This part exerts no force on the particle. The remainder of the field ψR=ψret-ψS is a vacuum solution of the field equation and is entirely responsible for the self-force. A particular, locally inertial coordinate system is used to determine an expansion of ψS in the vicinity of the particle. For a particle in a circular orbit in the Schwarzschild geometry, the mode-sum decomposition of the difference between ψret and the dominant terms in the expansion of ψS provide a mode-sum decomposition of an approximation for ψR from which the self-force is obtained. When more terms are included in the expansion, the approximation for ψR is increasingly differentiable, and the mode sum for the self-force converges more rapidly.
NASA Technical Reports Server (NTRS)
Tadesse, T.; Wiegelmann, T.; Gosain, S.; MacNeice, P.; Pevtsov, A. A.
2014-01-01
Context. The magnetic field permeating the solar atmosphere is generally thought to provide the energy for much of the activity seen in the solar corona, such as flares, coronal mass ejections (CMEs), etc. To overcome the unavailability of coronal magnetic field measurements, photospheric magnetic field vector data can be used to reconstruct the coronal field. Currently, there are several modelling techniques being used to calculate three-dimensional field lines into the solar atmosphere. Aims. For the first time, synoptic maps of a photospheric-vector magnetic field synthesized from the vector spectromagnetograph (VSM) on Synoptic Optical Long-term Investigations of the Sun (SOLIS) are used to model the coronal magnetic field and estimate free magnetic energy in the global scale. The free energy (i.e., the energy in excess of the potential field energy) is one of the main indicators used in space weather forecasts to predict the eruptivity of active regions. Methods. We solve the nonlinear force-free field equations using an optimization principle in spherical geometry. The resulting threedimensional magnetic fields are used to estimate the magnetic free energy content E(sub free) = E(sub nlfff) - E(sub pot), which is the difference of the magnetic energies between the nonpotential field and the potential field in the global solar corona. For comparison, we overlay the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the atmospheric imaging assembly (AIA) on board the Solar Dynamics Observatory (SDO). Results. For a single Carrington rotation 2121, we find that the global nonlinear force-free field (NLFFF) magnetic energy density is 10.3% higher than the potential one. Most of this free energy is located in active regions.
Guo, Y.; Ding, M. D.; Liu, Y.; Sun, X. D.; DeRosa, M. L.; Wiegelmann, T.
2012-11-20
We test a nonlinear force-free field (NLFFF) optimization code in spherical geometry using an analytical solution from Low and Lou. Several tests are run, ranging from idealized cases where exact vector field data are provided on all boundaries, to cases where noisy vector data are provided on only the lower boundary (approximating the solar problem). Analytical tests also show that the NLFFF code in the spherical geometry performs better than that in the Cartesian one when the field of view of the bottom boundary is large, say, 20 Degree-Sign Multiplication-Sign 20 Degree-Sign . Additionally, we apply the NLFFF model to an active region observed by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory (SDO) both before and after an M8.7 flare. For each observation time, we initialize the models using potential field source surface (PFSS) extrapolations based on either a synoptic chart or a flux-dispersal model, and compare the resulting NLFFF models. The results show that NLFFF extrapolations using the flux-dispersal model as the boundary condition have slightly lower, therefore better, force-free, and divergence-free metrics, and contain larger free magnetic energy. By comparing the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the Atmospheric Imaging Assembly on board SDO, we find that the NLFFF performs better than the PFSS not only for the core field of the flare productive region, but also for large EUV loops higher than 50 Mm.
Reactive Force Field Study of Li/C Systems for Electrical Energy Storage.
Raju, Muralikrishna; Ganesh, P; Kent, Paul R C; van Duin, Adri C T
2015-05-12
Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length, time-scales, and Li-ion concentrations. In this paper, we describe the development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon-based materials using atomistic simulations. We develop force field parameters for Li-C systems using van der Waals-corrected density functional theory (DFT). Grand canonical Monte Carlo simulations of Li intercalation in perfect graphite with this new force field not only give a voltage profile in good agreement with known experimental and DFT results but also capture the in-plane Li ordering and interlayer separations for stage I and II compounds. In defective graphite, the ratio of Li/C (i.e., the capacitance increases and voltage shifts) both in proportion to the concentration of vacancy defects and metallic lithium is observed to explain the lithium plating seen in recent experiments. We also demonstrate the robustness of the force field by simulating model carbon nanostructures (i.e., both 0D and 1D structures) that can be potentially used as battery electrode materials. Whereas a 0D defective onion-like carbon facilitates fast charging/discharging rates by surface Li adsorption, a 1D defect-free carbon nanorod requires a critical density of Li for intercalation to occur at the edges. Our force field approach opens the opportunity for studying energetics and kinetics of perfect and defective Li/C structures containing thousands of atoms as a function of intercalation. This is a key step toward modeling of realistic carbon materials for energy applications. PMID:26574418
An improved DNA force field for ssDNA interactions with gold nanoparticles
Jiang, Xiankai; Huai, Ping; Fan, Chunhai; Song, Bo E-mail: bosong@sinap.ac.cn; Gao, Jun; Huynh, Tien; Zhou, Ruhong E-mail: bosong@sinap.ac.cn
2014-06-21
The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones “protecting” hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the “protection” by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.
A reactive force field study of Li/C systems for electrical energy storage
Raju, Muralikrishna; Ganesh, P.; Kent, Paul R. C.; van Duin, Adri C.T.
2015-04-02
Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length, time-scales, and Li-ion concentrations. In this paper, we describe the development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon-based materials using atomistic simulations. We develop force field parameters for Li–C systems using van der Waals-corrected density functional theory (DFT). Grand canonical Monte Carlo simulations of Li intercalation in perfect graphitemore » with this new force field not only give a voltage profile in good agreement with known experimental and DFT results but also capture the in-plane Li ordering and interlayer separations for stage I and II compounds. In defective graphite, the ratio of Li/C (i.e., the capacitance increases and voltage shifts) both in proportion to the concentration of vacancy defects and metallic lithium is observed to explain the lithium plating seen in recent experiments. We also demonstrate the robustness of the force field by simulating model carbon nanostructures (i.e., both 0D and 1D structures) that can be potentially used as battery electrode materials. Whereas a 0D defective onion-like carbon facilitates fast charging/discharging rates by surface Li adsorption, a 1D defect-free carbon nanorod requires a critical density of Li for intercalation to occur at the edges. Our force field approach opens the opportunity for studying energetics and kinetics of perfect and defective Li/C structures containing thousands of atoms as a function of intercalation. As a result, this is a key step toward modeling of realistic carbon materials for energy applications.« less
A reactive force field study of Li/C systems for electrical energy storage
Raju, Muralikrishna; Ganesh, P.; Kent, Paul R. C.; van Duin, Adri C.T.
2015-04-02
Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length, time-scales, and Li-ion concentrations. In this paper, we describe the development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon-based materials using atomistic simulations. We develop force field parameters for Li–C systems using van der Waals-corrected density functional theory (DFT). Grand canonical Monte Carlo simulations of Li intercalation in perfect graphite with this new force field not only give a voltage profile in good agreement with known experimental and DFT results but also capture the in-plane Li ordering and interlayer separations for stage I and II compounds. In defective graphite, the ratio of Li/C (i.e., the capacitance increases and voltage shifts) both in proportion to the concentration of vacancy defects and metallic lithium is observed to explain the lithium plating seen in recent experiments. We also demonstrate the robustness of the force field by simulating model carbon nanostructures (i.e., both 0D and 1D structures) that can be potentially used as battery electrode materials. Whereas a 0D defective onion-like carbon facilitates fast charging/discharging rates by surface Li adsorption, a 1D defect-free carbon nanorod requires a critical density of Li for intercalation to occur at the edges. Our force field approach opens the opportunity for studying energetics and kinetics of perfect and defective Li/C structures containing thousands of atoms as a function of intercalation. As a result, this is a key step toward modeling of realistic carbon materials for energy applications.
Lay, Wesley K; Miller, Mark S; Elcock, Adrian H
2016-04-12
GLYCAM06 and CHARMM36 are successful force fields for modeling carbohydrates. To correct recently identified deficiencies with both force fields, we adjusted intersolute nonbonded parameters to reproduce the experimental osmotic coefficient of glucose at 1 M. The modified parameters improve behavior of glucose and sucrose up to 4 M and improve modeling of a dextran 55-mer. While the modified parameters may not be applicable to all carbohydrates, they highlight the use of osmotic simulations to optimize force fields. PMID:26967542
NASA Astrophysics Data System (ADS)
Ben-Abdallah, Philippe
2006-10-01
The dynamic structure and the formation of clusters in nanoparticle colloidal solutions (nanofluids) confined between two parallel walls and submitted to the action of an external force field is studied by extensive Brownian-dynamics simulations. The self-correlation of individual particles and the time correlation between distinct particles are analyzed by calculating the density-density time correlation (van Hove) function. It is shown that the self-diffusion is reduced by the external force field while the lifetime of collective modes of nanoparticles (i.e., natural phonons) is significantly enhanced by this force. We demonstrate that this result is related to disorder-order transitions in the nanoparticle spatial distribution under perturbation. Interestingly, we highlight that the interaction forces mediated by the walls act like repulsive interparticle forces. They tend to increase the structural disorder and to lower the lifetime of collective modes. Our results suggest that the heat transport properties of nanofluids could be actively controlled in nanometer-size systems.
The thermal near-field: Coherence, spectroscopy, heat-transfer, and optical forces
NASA Astrophysics Data System (ADS)
Jones, Andrew C.; O'Callahan, Brian T.; Yang, Honghua U.; Raschke, Markus B.
2013-12-01
One of the most universal physical processes shared by all matter at finite temperature is the emission of thermal radiation. The experimental characterization and theoretical description of far-field black-body radiation was a cornerstone in the development of modern physics with the groundbreaking contributions from Gustav Kirchhoff and Max Planck. With its origin in thermally driven fluctuations of the charge carriers, thermal radiation reflects the resonant and non-resonant dielectric properties of media, which is the basis for far-field thermal emission spectroscopy. However, associated with the underlying fluctuating optical source polarization are fundamentally distinct spectral, spatial, resonant, and coherence properties of the evanescent thermal near-field. These properties have been recently predicted theoretically and characterized experimentally for systems with thermally excited molecular, surface plasmon polariton (SPP), and surface phonon polariton (SPhP) resonances. We review, starting with the early historical developments, the emergence of theoretical models, and the description of the thermal near-field based on the fluctuation-dissipation theory and in terms of the electromagnetic local density of states (EM-LDOS). We discuss the optical and spectroscopic characterization of distance dependence, magnitude, spectral distribution, and coherence of evanescent thermal fields. Scattering scanning near-field microscopy proved instrumental as an enabling technique for the investigations of several of these fundamental thermal near-field properties. We then discuss the role of thermal fields in nano-scale heat transfer and optical forces, and the correlation to the van der Waals, Casimir, and Casimir-Polder forces. We conclude with an outlook on the possibility of intrinsic and extrinsic resonant manipulation of optical forces, control of nano-scale radiative heat transfer with optical antennas and metamaterials, and the use of thermal infrared near-field
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
Can an isotropic plasma pressure distribution be in force balance with the T96 model field?
NASA Astrophysics Data System (ADS)
Zaharia, Sorin; Cheng, C. Z.
2003-11-01
In this paper we investigate how close the gradient force of an isotropic pressure distribution P can be in force balance with the magnetic (Lorentz) force in the T96 empirical model. The study leads to the conclusion that no isotropic pressure can be found in exact force balance with the magnetic field of the quiet time T96 model. The conclusion is derived from several analyses: (1) computing the loop integral of J × B from the model along a closed contour in the equatorial plane (the integral should vanish if J × B = ∇P); (2) obtaining one-dimensional profiles for P on the Sun-Earth axis by integrating ∇P = J × B and comparing them with observations; and (3) decomposing J × B into gradient-free and curl-free terms (the former term would be zero in an exact equilibrium) and subsequently computing the two terms by solving a Poisson-like equation with constraints. Possible physical reasons for our finding that no P exists such that J × B = ∇P include small mass flows as well as nonisotropic (and possibly even nongyrotropic) terms in the magnetospheric pressure tensor. While the lack of exact force balance with isotropic P will probably be not too serious for many situations, for some physical applications, such as the computation of Birkeland currents using the Vasyliunas relation, care must be exercised if one uses the model field in conjunction with isotropic pressure. Finally, we discuss possible ways of computing magnetospheric configurations in exact force balance with isotropic P by using empirical model fields as a starting point.
Field-driven crossover from attractive-to-repulsive Casimir-like force in smectic films.
de Oliveira, I N; Lyra, M L
2004-11-01
External fields have a profound effect on the fluctuations of strongly correlated fluids, such as a liquid crystal. Within a harmonic functional integral approach, we compute the fluctuation-induced force between the surfaces of a smectic liquid-crystal film under the presence of an ordering field. In particular, we show that for asymmetrically anchored films, the thermal Casimir interaction energy can be collapsed into a universal form crossing over from a repulsive to an attractive interaction as the film thickness is increased. We discuss the possible relevance of this field effect in nematic-smectic wetting transitions. PMID:15600581
Study of the leakage field of magnetic force microscopy thin-film tips using electron holography
Frost, B.G.; van Hulst, N.F.; Lunedei, E.; Matteucci, G.
1996-03-01
Electron holography is applied for the study of the leakage field of thin-film ferromagnetic tips used as probes in magnetic force microscopy. We used commercially available pyramidal tips covered on one face with a thin NiCo film, which were then placed in a high external magnetic field directed along the pyramid axis. Good agreement between simulated and experimental electron phase difference maps allows to measure the local flux from the ferromagnetic tips and therefore to evaluate the perturbation induced by the microprobe stray field on the sample area. {copyright} {ital 1996 American Institute of Physics.}
Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids.
Tessier, Matthew B; Demarco, Mari L; Yongye, Austin B; Woods, Robert J
2008-01-01
GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials.In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein-lipid complexes and proteins in biologically relevant membrane-like environments. PMID:22247593
Molecular Dynamics Simulation of Tri-n-Butyl-Phophate Liquid: A Force Field Comparative Study
Cui, Shengting; de Almeida, Valmor F; Hay, Benjamin; Ye, Xianggui; Khomami, Bamin
2012-01-01
Molecular dynamics (MD) simulations were conducted to compare the performance of four force fields in predicting thermophysical properties of tri-n-butyl-phosphate (TBP) in the liquid phase. The intramolecular force parameters used were from the Assisted Model Building with Energy Refinement (AMBER) force field model. The van der Waals parameters were based on either the AMBER or the Optimized Potential for Liquid Simulation (OPLS) force fields. The atomic partial charges were either assigned by performing quantum chemistry calculations or utilized previously published data, and were scaled to approximate the average experimental value of the electric dipole moment. Canonical ensemble computations based on the aforementioned parameters were performed near the atmospheric pressure and temperature to obtain the electric dipole moment, mass density, and self-diffusion coefficient. In addition, the microscopic structure of the liquid was characterized via pair correlation functions between selected atoms. It has been demonstrated that the electric dipole moment can be approximated within 1% of the average experimental value by virtue of scaled atomic partial charges. The liquid mass density can be predicted within 0.5-1% of its experimentally determined value when using the corresponding charge scaling. However, in all cases the predicted self- diffusion coefficient is significantly smaller than a commonly quoted experimental measurement; this result is qualified by the fact that the uncertainty of the experimental value was not available.
The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation
Spasic, Aleksandar; Serafini, John; Mathews, David H.
2012-01-01
The ability of the Amber ff99 force field to predict relative free energies of RNA helix formation was investigated. The test systems were three hexaloop RNA hairpins with identical loops and varying stems. The potential of mean force of stretching the hairpins from the native state to an extended conformation was calculated with umbrella sampling. Because the hairpins have identical loop sequence, the differences in free energy changes are only from the stem composition. The Amber ff99 force field was able to correctly predict the order of stabilities of the hairpins, although the magnitude of the free energy change is larger than that determined by optical melting experiments. The two measurements cannot be compared directly because the unfolded state in the optical melting experiments is a random coil, while the end state in the umbrella sampling simulations was an elongated chain. The calculations can be compared to reference data by using a thermodynamic cycle. By applying the thermodynamic cycle to the transitions between the hairpins using simulations and nearest neighbor data, agreement was found to be within the sampling error of simulations, thus demonstrating that ff99 force field is able to accurately predict relative free energies of RNA helix formation. PMID:23112748
Optical forces on a Rayleigh dielectric particle in a patterned near-field landscape
NASA Astrophysics Data System (ADS)
Zelenina, Anna; Quidant, Romain; Petrov, Dmitri; Badenes, Goncal
2005-07-01
The trapping of micro-objects by optical radiation forces, so-called optical tweezers, has become widely used in physical, chemical and biological experiments where accurate and non-invasive manipulation is required. Recent advances in beam shaping render it possible for instance to rotate or to dynamically manipulate independently several elements. Today, one of the remaining challenges of conventional optical tweezers is the direct manipulation of systems with sizes belonging to the sub-wavelength or Rayleigh regime. Indeed, the diffraction limit prevents in that case from achieving a commensurable trapping volume and thus does not allow for minimizing the fluctuations in position of the trapped object due to its strong Brownian motion. In order to overcome this limitation, it has been proposed to use evanescent fields instead of the usual propagating fields. Recent advances in optics of noble metal nano-structures have recently provided new configurations to achieve nano-optical tweezers. Especially, tightly localized modes resulting from the coupling between resonant noble metal nanostructures may offer the gradient forces able to trap and manipulate Rayleigh objects. In this work, we calculate the radiation forces exerted on a nanometric dielectric sphere when exposed to a patterned optical near-field landscape at an interface decorated with resonant gold nanostructures. By comparing their magnitude with other forces that affect the movement of the particle, we discuss the practical ability of our configuration for multiple parallel optical manipulation.
On some properties of force-free magnetic fields in infinite regions of space
NASA Technical Reports Server (NTRS)
Aly, J. J.
1984-01-01
Techniques for solving boundary value problems (BVP) for a force free magnetic field (FFF) in infinite space are presented. A priori inequalities are defined which must be satisfied by the force-free equations. It is shown that upper bounds may be calculated for the magnetic energy of the region provided the value of the magnetic normal component at the boundary of the region can be shown to decay sufficiently fast at infinity. The results are employed to prove a nonexistence theorem for the BVP for the FFF in the spatial region. The implications of the theory for modeling the origins of solar flares are discussed.
Effects of external force fields on peptide self-assembly and biomimetic silica synthesis
NASA Astrophysics Data System (ADS)
Yu, Jun; Wang, Qinrong; Zhang, Xin
2014-08-01
This study investigated the influence of physical parameters on the dynamic self-assembly of short peptide amphiphiles (A6K and V6K) and the peptide-mediated silica morphologies by applying external force fields (electric and flow fields). Diverse self-assembled structures (nanofibers, nanorods, or lamellar stacks) can be obtained depending on field intensities and molecular architectures. Although the trend in the structural transitions observed from the electrostatic stimulation differed from that obtained in flow field, the common features indicate that the formed structures exhibit a higher extent of end-to-end merging or lateral association. These self-assembled peptide-based nanostructures then were used as organic templates to tailor silica deposition. It was found that the application of flow fields can stably produce fibril morphology. However, in the case of electric fields, different silica structures were obtained by using different systems. The silica morphologies directed by V6K peptide were transformed from fibrils to plate-like structures, and A6K peptide produced fibril silica materials. The difference may be attributed to different biomimetic conditions, including external forces, solubility of hydrophobic blocks, and intensity of peptide-silicate interactions. This understanding of the mechanism by which external fields affect the self-assembled amphiphilic peptide nanostructures and the silicification process allows us to manipulate the role of short amphiphilic peptides in silica formation in vitro.
NASA Astrophysics Data System (ADS)
Jenke, Martin Günter; Santschi, Christian; Hoffmann, Patrik
2008-02-01
Accurate simultaneous measurements on the topography and electrostatic force field of 500nm pitch interdigitated electrodes embedded in a thin SiO2 layer in a plane perpendicular to the orientation of the electrodes are shown for the first time. A static force distance curve (FDC) based method has been developed, which allows a lateral and vertical resolution of 25 and 2nm, respectively. The measured force field distribution remains stable as result of the well controlled fabrication procedure of Pt cantilever tips that allows thousands of FDC measurements. A numerical model is established as well which demonstrates good agreement with the experimental results.
Zhu, Tao; Zhou, Liming; Liu, Min; Zhang, Jingdong; Shi, Leilei
2015-01-01
The traditional electrical field sensing can be realized by utilizing electro-optic materials or liquid crystals, and has limitations of easy breakdown, free assembly and difficult measurement of low-frequency. Here, we propose a new method to realize safe measurement of spatial dynamic electric field by using a micro fiber interferometer integrated with gold nanofilm. The energy of the electric charge received through antenna forms the intrinsic electric field with two micro electrodes, one of which is the 120 nm gold film vibration beam micromachined by femtosecond lasers and integrated with the micro fiber. The change of the intrinsic electric field force due to the spatial electric field will cause the vibration of the film beam. By demodulating the output signal of the micro fiber interferometer, the electric field can be measured. We demonstrate the detectable frequency ranges from tens of Hz to tens of KHz, and the minimum electric field intensity is ~200 V/m at 1 KHz. Our electric field measurement technology combining optical fiber interference with gold nanostructures shows the advantages of security, high sensitivity, compact size, and multiplexed multi-point and remote detection. PMID:26507680
Zhu, Tao; Zhou, Liming; Liu, Min; Zhang, Jingdong; Shi, Leilei
2015-01-01
The traditional electrical field sensing can be realized by utilizing electro-optic materials or liquid crystals, and has limitations of easy breakdown, free assembly and difficult measurement of low-frequency. Here, we propose a new method to realize safe measurement of spatial dynamic electric field by using a micro fiber interferometer integrated with gold nanofilm. The energy of the electric charge received through antenna forms the intrinsic electric field with two micro electrodes, one of which is the 120 nm gold film vibration beam micromachined by femtosecond lasers and integrated with the micro fiber. The change of the intrinsic electric field force due to the spatial electric field will cause the vibration of the film beam. By demodulating the output signal of the micro fiber interferometer, the electric field can be measured. We demonstrate the detectable frequency ranges from tens of Hz to tens of KHz, and the minimum electric field intensity is ~200 V/m at 1 KHz. Our electric field measurement technology combining optical fiber interference with gold nanostructures shows the advantages of security, high sensitivity, compact size, and multiplexed multi-point and remote detection. PMID:26507680
NASA Astrophysics Data System (ADS)
Zhu, Tao; Zhou, Liming; Liu, Min; Zhang, Jingdong; Shi, Leilei
2015-10-01
The traditional electrical field sensing can be realized by utilizing electro-optic materials or liquid crystals, and has limitations of easy breakdown, free assembly and difficult measurement of low-frequency. Here, we propose a new method to realize safe measurement of spatial dynamic electric field by using a micro fiber interferometer integrated with gold nanofilm. The energy of the electric charge received through antenna forms the intrinsic electric field with two micro electrodes, one of which is the 120 nm gold film vibration beam micromachined by femtosecond lasers and integrated with the micro fiber. The change of the intrinsic electric field force due to the spatial electric field will cause the vibration of the film beam. By demodulating the output signal of the micro fiber interferometer, the electric field can be measured. We demonstrate the detectable frequency ranges from tens of Hz to tens of KHz, and the minimum electric field intensity is ~200 V/m at 1 KHz. Our electric field measurement technology combining optical fiber interference with gold nanostructures shows the advantages of security, high sensitivity, compact size, and multiplexed multi-point and remote detection.
A NEW CODE FOR NONLINEAR FORCE-FREE FIELD EXTRAPOLATION OF THE GLOBAL CORONA
Jiang Chaowei; Feng Xueshang; Xiang Changqing
2012-08-10
Reliable measurements of the solar magnetic field are still restricted to the photosphere, and our present knowledge of the three-dimensional coronal magnetic field is largely based on extrapolations from photospheric magnetograms using physical models, e.g., the nonlinear force-free field (NLFFF) model that is usually adopted. Most of the currently available NLFFF codes have been developed with computational volume such as a Cartesian box or a spherical wedge, while a global full-sphere extrapolation is still under development. A high-performance global extrapolation code is in particular urgently needed considering that the Solar Dynamics Observatory can provide a full-disk magnetogram with resolution up to 4096 Multiplication-Sign 4096. In this work, we present a new parallelized code for global NLFFF extrapolation with the photosphere magnetogram as input. The method is based on the magnetohydrodynamics relaxation approach, the CESE-MHD numerical scheme, and a Yin-Yang spherical grid that is used to overcome the polar problems of the standard spherical grid. The code is validated by two full-sphere force-free solutions from Low and Lou's semi-analytic force-free field model. The code shows high accuracy and fast convergence, and can be ready for future practical application if combined with an adaptive mesh refinement technique.
Effects of auroral-particle anisotropies and mirror forces on high-latitude electric fields
NASA Technical Reports Server (NTRS)
Chiu, Y. T.; Schulz, M.; Cornwall, J. M.
1981-01-01
It is noted that, for most of the mechanisms for the strong electric fields that characterize the narrow regions in which there is acceleration and precipitation of ring current and/or plasma-sheet plasma, certain effects must be taken into account in simulations of auroral electric fields. The effects are those of auroral particle anisotropy, of mirror forces due to the inhomogeneous geomagnetic field, of auroral electron backscatter by the atmosphere, and of electron trapping by the combination of magnetic mirroring and electrostatic forces. What is more, the effects of the very strong perpendicular electric field must also be taken into account in a kinetic description of the Poisson equation in order to achieve a unified theory of the auroral electrostatic structure. Progress in these areas during the past few years is reviewed. It is shown that particle anisotropies and mirror forces can account for some basic electrostatic features of the quiet arc, while additional effects may be occurring in strong events in which the parallel potential drop is more than about 10 kV.
Fano resonance of the ultrasensitve optical force excited by Gaussian evanescent field
NASA Astrophysics Data System (ADS)
Yang, Yang; Li, Jiafang; Li, Zhi-Yuan
2015-07-01
In this paper, we study the angle-dependent Fano-like optical force spectra of plasmonic Ag nanoparticles, which exhibit extraordinary transformation from Lorentzian resonance to Fano resonance when excited by a Gaussian evanescent wave. We systematically analyze the behavior of this asymmetric scattering induced optical force under different conditions and find that this Fano interference-induced force is ultrasensitive to the excitation wavelength, incident angle and particle size, as well as the core-shell configuration, which could be useful for wavelength- and angle-dependent size-selective optical manipulation. The origin of this Fano resonance is further identified as the interference between the two adjacent-order multipolar plasmonic modes excited in the Ag particle under the excitation of an inhomogeneously distributed evanescent field.
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.
A method to study precision grip control in viscoelastic force fields using a robotic gripper.
Lambercy, Olivier; Metzger, Jean-Claude; Santello, Marco; Gassert, Roger
2015-01-01
Instrumented objects and multipurpose haptic displays have commonly been used to investigate sensorimotor control of grasping and manipulation. A major limitation of these devices, however, is the extent to which the experimenter can vary the interaction dynamics to fully probe sensorimotor control mechanisms. We propose a novel method to study precision grip control using a grounded robotic gripper with two moving, mechanically coupled finger pads instrumented with force sensors. The device is capable of stably rendering virtual mechanical properties with a wide dynamic range of achievable impedances. Eight viscoelastic force fields with different combinations of stiffness and damping parameters were implemented, and tested on eight healthy subjects performing 30 consecutive repetitions of a grasp, hold, and release task with time and position constraints. Rates of thumb and finger force were found to be highly correlated (r>0.9) during grasping, revealing that, despite the mechanical coupling of the two finger pads, subjects performed grasping movements in a physiological fashion. Subjects quickly adapted to the virtual dynamics (within seven trials), but, depending on the presented force field condition, used different control strategies to correctly perform the task. The proof of principle presented in this paper underscores the potential of such a one-degree-of-freedom robotic gripper to study neural control of grasping, and to provide novel insights on sensorimotor control mechanisms. PMID:25014953
Relating GRACE terrestrial water storage variations to global fields of atmospheric forcing
NASA Astrophysics Data System (ADS)
Humphrey, Vincent; Gudmundsson, Lukas; Isabelle Seneviratne, Sonia
2015-04-01
Synoptic, seasonal and inter-annual fluctuations in atmospheric dynamics all influence terrestrial water storage, with impacts on ecosystems functions, human activities and land-climate interactions. Here we explore to which degree atmospheric variables can explain GRACE estimates of terrestrial water storage on different time scales. Since 2012, the most recent GRACE gravity field solutions (Release 05) can be used to monitor global changes in terrestrial water storage with an unprecedented level of accuracy over more than a decade. In addition, the release of associated gridded and post-processed products facilitates comparisons with other global datasets such as land surface model outputs or satellite observations. We investigate how decadal trends, inter-annual fluctuations as well as monthly anomalies of the seasonal cycle of terrestrial water storage can be related to fields of atmospheric forcing, including e.g. precipitation and temperature as estimated in global reanalysis products using statistical techniques. In the majority of the locations with high signal to noise ratio, both short and long-term fluctuations of total terrestrial water storage can be reconstructed to a large degree based on available atmospheric forcing. However, in some locations atmospheric forcing alone is not sufficient to explain the total change in water storage, suggesting strong influence of other processes. Within that framework, the question of an amplification or attenuation of atmospheric forcing through land-surface feedbacks and changes in long term water storage is discussed, also with respect to uncertainties and potential systematic biases in the results.
Unsteady hydrodynamic forces acting on a hand and its flow field during sculling motion.
Takagi, Hideki; Shimada, Shohei; Miwa, Takahiro; Kudo, Shigetada; Sanders, Ross; Matsuuchi, Kazuo
2014-12-01
The goal of this research is to clarify the mechanism by which unsteady forces are generated during sculling by a skilled swimmer and thereby to contribute to improving propulsive techniques. We used particle image velocimetry (PIV) to acquire data on the kinematics of the hand during sculling, such as fluid forces and flow field. By investigating the correlations between these data, we expected to find a new propulsion mechanism. The experiment was performed in a flow-controlled water channel. The participant executed sculling motions to remain at a fixed position despite constant water flow. PIV was used to visualize the flow-field cross-section in the plane of hand motion. Moreover, the fluid forces acting on the hand were estimated from pressure distribution measurements performed on the hand and simultaneous three-dimensional motion analysis. By executing the sculling motion, a skilled swimmer produces large unsteady fluid forces when the leading-edge vortex occurs on the dorsal side of the hand and wake capture occurs on the palm side. By using a new approach, we observed interesting unsteady fluid phenomena similar to those of flying insects. The study indicates that it is essential for swimmers to fully exploit vortices. A better understanding of these phenomena might lead to an improvement in sculling techniques. PMID:25310026
Dagdeviren, Omur E; Schwendemann, Todd C; Mönig, Harry; Altman, Eric I
2012-01-01
Summary Noncontact atomic force microscopy (NC-AFM) is being increasingly used to measure the interaction force between an atomically sharp probe tip and surfaces of interest, as a function of the three spatial dimensions, with picometer and piconewton accuracy. Since the results of such measurements may be affected by piezo nonlinearities, thermal and electronic drift, tip asymmetries, and elastic deformation of the tip apex, these effects need to be considered during image interpretation. In this paper, we analyze their impact on the acquired data, compare different methods to record atomic-resolution surface force fields, and determine the approaches that suffer the least from the associated artifacts. The related discussion underscores the idea that since force fields recorded by using NC-AFM always reflect the properties of both the sample and the probe tip, efforts to reduce unwanted effects of the tip on recorded data are indispensable for the extraction of detailed information about the atomic-scale properties of the surface. PMID:23019560
NASA Astrophysics Data System (ADS)
Agboola, Babatunde Omogbolahan
Continuum thermodynamic constitutive phase field models are developed to simulate the rate dependent, thermomechanical response and precipitate formation in shape memory alloys (SMAs). The two models are based on the application of the balance of configurational forces, a scalar order parameter (a phase field) and atomic concentration to extend standard continuum thermodynamics approach. Constitutive field equations that capture the kinetics of solid-solid martensitic phase transition in SMA and the diffusion mediated precipitate formation in an elastic solid are developed. The coupled set of thermodynamically consistent field equations results from balance of configuration forces, balance of linear momentum, balance of energy and balance of atomic species mass. The field equations capture the kinetics of phase transition, deformation and elastic wave, heat transfer and atomic diffusion respectively. The first model is thermomechanical and is used to simulate the macroscopic response of SMA such as pseudoelasticity; transformation induced pseudo-creep, stress relaxation as well as the effect of cooling rate on mechanical and thermally induced phase transformation of SMA. The second model couples diffusion with elasticity to simulate growth and coarsening of precipitate and experimentally observed concentration depletion near the precipitates Results of the simulations of the macroscopic SMA response are in very good agreement with experimental observation. Simulations suggest that rate dependent and complex thermomechanical response of SMA are due to the interaction of an inherent time scale ( as well as length scale) of phase transformation, introduced through the balance of configurational forces, with other time scales. This work contributes to improved SMA modeling, scientific understanding and design. In particular, for aerospace application under stringent requirement and severe environmental conditions. Contribution of fundamental use of balance of
A nonlinear eigenvalue problem for self-similar spherical force-free magnetic fields
Lerche, I.; Low, B. C.
2014-10-15
An axisymmetric force-free magnetic field B(r, θ) in spherical coordinates is defined by a function r sin θB{sub φ}=Q(A) relating its azimuthal component to its poloidal flux-function A. The power law r sin θB{sub φ}=aA|A|{sup 1/n}, n a positive constant, admits separable fields with A=(A{sub n}(θ))/(r{sup n}) , posing a nonlinear boundary-value problem for the constant parameter a as an eigenvalue and A{sub n}(θ) as its eigenfunction [B. C. Low and Y. Q Lou, Astrophys. J. 352, 343 (1990)]. A complete analysis is presented of the eigenvalue spectrum for a given n, providing a unified understanding of the eigenfunctions and the physical relationship between the field's degree of multi-polarity and rate of radial decay via the parameter n. These force-free fields, self-similar on spheres of constant r, have basic astrophysical applications. As explicit solutions they have, over the years, served as standard benchmarks for testing 3D numerical codes developed to compute general force-free fields in the solar corona. The study presented includes a set of illustrative multipolar field solutions to address the magnetohydrodynamics (MHD) issues underlying the observation that the solar corona has a statistical preference for negative and positive magnetic helicities in its northern and southern hemispheres, respectively; a hemispherical effect, unchanging as the Sun's global field reverses polarity in successive eleven-year cycles. Generalizing these force-free fields to the separable form B=(H(θ,φ))/(r{sup n+2}) promises field solutions of even richer topological varieties but allowing for φ-dependence greatly complicates the governing equations that have remained intractable. The axisymmetric results obtained are discussed in relation to this generalization and the Parker Magnetostatic Theorem. The axisymmetric solutions are mathematically related to a family of 3D time-dependent ideal MHD solutions for a polytropic fluid of index γ = 4/3 as
An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins
Herges, T.; Wenzel, W.
2004-01-01
We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688
A test of improved force field parameters for urea: molecular-dynamics simulations of urea crystals.
Özpınar, Gül Altınbaş; Beierlein, Frank R; Peukert, Wolfgang; Zahn, Dirk; Clark, Timothy
2012-08-01
Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from the MD data. The cohesive energies computed from simulations of cubic and rectangular prismatic urea crystals in vacuo at 300 K agreed very well with the experimental sublimation enthalpies reported at 298 K. We also found very good agreement between the melting points as observed experimentally and from simulations. Annealing the crystals just below the melting point leads to reconstruction to form crystal faces that are consistent with experimental observations. The simulations reveal a melting mechanism that involves surface (corner/edge) melting well below the melting point, and rotational disordering of the urea molecules in the corner/edge regions of the crystal, which then facilitates the translational motion of these molecules. PMID:22281810
Geng, Hao; Jiang, Fan; Wu, Yun-Dong
2016-05-19
Cyclic peptides (CPs) are promising candidates for drugs, chemical biology tools, and self-assembling nanomaterials. However, the development of reliable and accurate computational methods for their structure prediction has been challenging. Here, 20 all-trans CPs of 5-12 residues selected from Cambridge Structure Database have been simulated using replica-exchange molecular dynamics with four different force fields. Our recently developed residue-specific force fields RSFF1 and RSFF2 can correctly identify the crystal-like conformations of more than half CPs as the most populated conformation. The RSFF2 performs the best, which consistently predicts the crystal structures of 17 out of 20 CPs with rmsd < 1.1 Å. We also compared the backbone (ϕ, ψ) sampling of residues in CPs with those in short linear peptides and in globular proteins. In general, unlike linear peptides, CPs have local conformational free energies and entropies quite similar to globular proteins. PMID:27128113
Surface Tension of Organic Liquids Using the OPLS/AA Force Field.
Zubillaga, Rafael A; Labastida, Ariana; Cruz, Bibiana; Martínez, Juan Carlos; Sánchez, Enrique; Alejandre, José
2013-03-12
Molecular dynamics simulations are performed to obtain the surface tension of 61 organic liquids using the OPLS/AA (all-atom optimized potential for liquid simulations). The force field parameters are the same as those recently used (Caleman et al. J. Chem. Theory Comput.2012, 8, 61) to determine several thermodynamic properties of 146 organic liquids. The correct evaluation of surface tension using slab simulations of liquids requires one to properly take into account the long-range interactions (Trukhymchuk and Alejandre J. Chem. Phys.1999, 111, 8510). In addition, the liquid density from slab simulations has to be the same as that obtained in liquid simulations at constant temperature and pressure. The new results of surface tensions from this work improve those reported by Caleman et al. The OPLS/AA force field gives good surface tensions compared with experimental data for most of the systems studied in this work, although it was developed to simulate liquids. PMID:26587622
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.
General AMBER Force Field Parameters for Diphenyl Diselenides and Diphenyl Ditellurides.
Torsello, Mauro; Pimenta, Antonio C; Wolters, Lando P; Moreira, Irina S; Orian, Laura; Polimeno, Antonino
2016-06-30
The General AMBER Force Field (GAFF) has been extended to describe a series of selenium and tellurium diphenyl dichalcogenides. These compounds, besides being eco-friendly catalysts for numerous oxidations in organic chemistry, display peroxidase activity, i.e., can reduce hydrogen peroxide and harmful organic hydroperoxides to water/alcohols and as such are very promising antioxidant drugs. The novel GAFF parameters are tested in MD simulations in different solvents and the (77)Se NMR chemical shift of diphenyl diselenide is computed using structures extracted from MD snapshots and found in nice agreement with the measured value in CDCl3. The whole computational protocol is described in detail and integrated with in-house code to allow easy derivation of the force field parameters for analogous compounds as well as for Se/Te organocompounds in general. PMID:27267296
Effects of neutrals on internal forces and thermal conduction of a plasma in a magnetic field
NASA Astrophysics Data System (ADS)
Hirano, K.
1984-08-01
Using the Chapman-Enskog approximation the Boltzmann equation was solved to obtain friction and thermal forces appearing between ions and their parent atoms remaining in a plasma. The heat fluxes due to thermal conduction through ions and atoms were also evaluated. Charge transfer and the elastic scattering assuming the Sutherland potential were adopted as the basic collision process between ions and atoms. It was demonstrated that thermal force on neutrals always pushes them toward higher temperature region across a strong magnetic field but colder place along the field lines if the temperature is higher than 25 eV. A very small amount of neutrals, e.g., 1 ppm to the ion density, is found to be enough for neutrals transfering even much larger heat flux than the one by ion thermal conduction loss at a fusion temperature.
Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF
2014-01-01
We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted. PMID:25574157
NASA Astrophysics Data System (ADS)
Liu, Dongzi; Mo, Kangxin; Ding, Xidong; Zhao, Liangbing; Lin, Guocong; Zhang, Yueli; Chen, Dihu
2015-09-01
A bimodal magnetic force microscopy (MFM) that uses an external magnetic field for the detection and imaging of magnetic thin films is developed. By applying the external modulation magnetic field, the vibration of a cantilever probe is excited by its magnetic tip at its higher eigenmode. Using magnetic nanoparticle samples, the capacity of the technique which allows single-pass imaging of topography and magnetic forces is demonstrated. For the detection of magnetic properties of thin film materials, its signal-to-noise ratio and sensitivity are demonstrated to be superior to conventional MFM in lift mode. The secondary resonance MFM technique provides a promising tool for the characterization of nanoscale magnetic properties of various materials, especially of magnetic thin films with weak magnetism.
Thermodynamic and Transport Properties of H2O + NaCl from Polarizable Force Fields.
Jiang, Hao; Mester, Zoltan; Moultos, Othonas A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z
2015-08-11
Molecular dynamics and Monte Carlo simulations were performed to obtain thermodynamic and transport properties of the binary H2O + NaCl system using the polarizable force fields of Kiss and Baranyai ( J. Chem. Phys. 2013 , 138 , 204507 and 2014 , 141 , 114501 ). In particular, liquid densities, electrolyte and crystal chemical potentials of NaCl, salt solubilities, mean ionic activity coefficients, vapor pressures, vapor-liquid interfacial tensions, and viscosities were obtained as functions of temperature, pressure, and salt concentration. We compared the performance of the polarizable force fields against fixed-point-charge (nonpolarizable) models. Most of the properties of interest are better represented by the polarizable models, which also remain physically realistic at elevated temperatures. PMID:26574461
A study of the force-field equation for the propagation of galactic cosmic rays
NASA Technical Reports Server (NTRS)
Gleeson, L. J.; Urch, I. H.
1973-01-01
A new development is given of the solution of the equation of the force-field approximation for the propagation of galactic cosmic rays in the interplanetary region. It leads to simpler methods for determining the force-field parameters. A method is given for determining the separable diffusion coefficient from observations of galactic electron spectrum and near-earth electron spectra; it is shown that this diffusion coefficient is not unique but may have a periodic-like dependence upon rigidity; and the method is used to obtain diffusion coefficients for 1965 and 1968. Approximate formulae relating small changes in intensity and diffusion coefficient are developed and some applications of these noted; in one it is shown that the form of, and changes in, diffusion coefficient deduced previously for a neutron monitor event during June-September 1969 are unnecessarily constrained and therefore probably not correct.
2015-01-01
A polarizable empirical force field based on the classical Drude oscillator is presented for the hexopyranose form of selected monosaccharides. Parameter optimization targeted quantum mechanical (QM) dipole moments, solute–water interaction energies, vibrational frequencies, and conformational energies. Validation of the model was based on experimental data on crystals, densities of aqueous-sugar solutions, diffusion constants of glucose, and rotational preferences of the exocylic hydroxymethyl of d-glucose and d-galactose in aqueous solution as well as additional QM data. Notably, the final model involves a single electrostatic model for all sixteen diastereomers of the monosaccharides, indicating the transferability of the polarizable model. The presented parameters are anticipated to lay the foundation for a comprehensive polarizable force field for saccharides that will be compatible with the polarizable Drude parameters for lipids and proteins, allowing for simulations of glycolipids and glycoproteins. PMID:24564643
Antila, Hanne S; Salonen, Emppu
2015-04-15
The Thole induced point dipole model is combined with three different point charge fitting methods, Merz-Kollman (MK), charges from electrostatic potentials using a grid (CHELPG), and restrained electrostatic potential (RESP), and two multipole algorithms, distributed multipole analysis (DMA) and Gaussian multipole model (GMM), which can be used to describe the electrostatic potential (ESP) around molecules in molecular mechanics force fields. This is done to study how the different methods perform when intramolecular polarizability contributions are self-consistently removed from the fitting done in the force field parametrization. It is demonstrated that the polarizable versions of the partial charge models provide a good compromise between accuracy and computational efficiency in describing the ESP of small organic molecules undergoing conformational changes. For the point charge models, the inclusion of polarizability reduced the the average root mean square error of ESP over the test set by 4-10%. PMID:25753482
Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof
2015-12-31
A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities.
NASA Astrophysics Data System (ADS)
Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof
2015-12-01
A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities.
Multifactorial global search algorithm in the problem of optimizing a reactive force field
NASA Astrophysics Data System (ADS)
Stepanova, M. M.; Shefov, K. S.; Slavyanov, S. Yu.
2016-04-01
We present a new multifactorial global search algorithm ( MGSA) and check the operability of the algorithm on the Michalewicz and Rastrigin functions. We discuss the choice of an objective function and additional search criteria in the context of the problem of reactive force field ( ReaxFF) optimization and study the ranking of the ReaxFF parameters together with their impact on the objective function.
A force field for 3,3,3-fluoro-1-propenes, including HFO-1234yf.
Raabe, Gabriele; Maginn, Edward J
2010-08-12
The European Union (EU) legislation 2006/40/EC bans from January 2011 the cooperative marketing of new car types that use refrigerants in their heating, ventilation, and air conditioning (HVAC) systems with global warming potentials (GWP) higher than 150. Thus, the phase-out of the presently used tetrafluoroethane refrigerant R134a necessitates the adoption of alternative refrigerants. Fluoropropenes such as 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf) are currently regarded as promising low GWP refrigerants, but the lack of experimental data on their thermophysical properties hampers independent studies on their performance in HVAC systems or in other technical applications. In principle, molecular modeling can be used to predict the relevant properties of refrigerants, but adequate intermolecular potential functions ("force fields") are lacking for fluoropropenes. Thus, we developed a transferable force field for fluoropropenes composed of CF(3)-, -CF=, -CH=, CF(2)=, and CH(2)= groups and applied the force field to study 3,3,3 trifluoro-1-propene (HFO-1243zf), 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), and hexafluoro-1-propene (HFO-1216). We performed Gibbs ensemble simulations on these three fluoropropenes to compute the vapor pressure, saturated densities, and heats of vaporization. In addition, molecular dynamics simulations were conducted to provide predictions for the density, thermal expansivity, isobaric heat capacity, and transport properties of liquid HFO-1234yf in the temperature range from 263.15 to 310 K and pressures up to 2 MPa. Agreement between simulation results and experimental data and/or correlations (when available) was good, thereby validating the predictive ability of the force field. PMID:20684636
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
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 Water Model for the Coarse-Grained MARTINI Force Field
Sengupta, Durba; Marrink, Siewert J.
2010-01-01
Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models. PMID:20548957
Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field.
Li, Hui; Ngo, Van; Da Silva, Mauricio Chagas; Salahub, Dennis R; Callahan, Karen; Roux, Benoît; Noskov, Sergei Yu
2015-07-23
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(+), Ca(2+), 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 Ca(2+) 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.
2010-01-01
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 non-polarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Towards 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 non-polarizable 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
Vanommeslaeghe, K; Raman, E Prabhu; MacKerell, A D
2012-12-21
Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biological systems. In these simulations, 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 partial atomic charges is required. In the present article, algorithms for the assignment of parameters and charges for the CHARMM General Force Field (CGenFF) are presented. These algorithms rely on the existing parameters and charges that were determined as part of the parametrization of the force field. Bonded parameters are assigned based on the similarity between the atom types that define said parameters, while charges are determined using an extended bond-charge increment scheme. Charge increments were optimized to reproduce the charges on model compounds that were part of the parametrization of the force field. A "penalty score" is returned for every bonded parameter and charge, allowing the user to quickly and conveniently assess the quality of the force field representation of different parts of the compound of interest. Case studies are presented to clarify the functioning of the algorithms and the significance of their output data. PMID:23145473
NASA Astrophysics Data System (ADS)
Matsuzaki, Hiroshi; Kumagai, Yuji; Kawashima, Kazuhiko
Recently, high acceleration and high frequency near-field vertical ground motions were recorded at several sites. The extreme vertical ground motions can induce high frequency varying axial force which develop even tensile force in reinforced concrete bridge columns. Cyclic loading experiments of RC columns were conducted to clarify the seismic performance of RC bridge columns under near-field vertical ground motions. It is shown that core concrete is crushed extensively due to varying axial force after longitudinal bars buckle.
A new force field for molecular dynamics studies of Li + and Na +-nafion
NASA Astrophysics Data System (ADS)
Soolo, Endel; Liivat, Anti; Kasemägi, Heiki; Tamm, Tarmo; Brandell, Daniel; Aabloo, Alvo
2008-03-01
Nafion is widely known as one of the most popular membrane materials for low temperature fuel cell applications. However, the particular exchange membrane material properties make it also valuable for other applications. One of the electroactive polymer (EAP) subclasses, ionic polymer metal composites (IPMC) commonly exploits Nafion as the ion exchange polymer membrane. The ion conducting properties of Nafion are extremely important for IPMCs. Although, ion conductivity depends strongly on the structural properties of the polymer matrix, there has been very little insight at the atomistic level. Molecular dynamics simulations are one of the possibilities to study the ion conduction mechanism at atomistic level. So far, the simulation results have been rather contradictory and very much dependent from the force fields and polymer matrix setup used. In the present work, new force field parameters for Li + and Na + - nafion based on DFT calculations are presented. The developed potentials and the force field were tested by molecular dynamics simulations. It can be concluded that Li + and Na + ions are coordinated to different Nafion side-chain terminal group (SO 3 -) oxygens and to very few water molecules. One cation is coordinated to three different side-chains. Oxygens of SO 3 groups and cations form complicated multi-header systems. In the equilibrium state, no cations dissociated from side chains were found.
Bradshaw, Richard T; Essex, Jonathan W
2016-08-01
Hydration free energy (HFE) calculations are often used to assess the performance of biomolecular force fields and the quality of assigned parameters. The AMOEBA polarizable force field moves beyond traditional pairwise additive models of electrostatics and may be expected to improve upon predictions of thermodynamic quantities such as HFEs over and above fixed-point-charge models. The recent SAMPL4 challenge evaluated the AMOEBA polarizable force field in this regard but showed substantially worse results than those using the fixed-point-charge GAFF model. Starting with a set of automatically generated AMOEBA parameters for the SAMPL4 data set, we evaluate the cumulative effects of a series of incremental improvements in parametrization protocol, including both solute and solvent model changes. Ultimately, the optimized AMOEBA parameters give a set of results that are not statistically significantly different from those of GAFF in terms of signed and unsigned error metrics. This allows us to propose a number of guidelines for new molecule parameter derivation with AMOEBA, which we expect to have benefits for a range of biomolecular simulation applications such as protein-ligand binding studies. PMID:27341007
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. PMID:26850737
A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation
Gu, Junfeng; Bai, Fang; Li, Honglin; Wang, Xicheng
2012-01-01
Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the Cα root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled. PMID:23203075
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. PMID:27153317
Mera-Adasme, Raúl; Sadeghian, Keyarash; Sundholm, Dage; Ochsenfeld, Christian
2014-11-20
Classical force-field parameters of the metal site of metalloproteins usually comprise only the partial charges of the involved atoms, as well as the bond-stretching and bending parameters of the metal-ligand interactions. Although for certain metal ligands such as histidine residues, the torsional motions at the metal site play an important role for the dynamics of the protein, no such terms have been considered to be crucial in the parametrization of the force fields, and they have therefore been omitted in the parametrization. In this work, we have optimized AMBER-compatible force-field parameters for the reduced state of the metal site of copper, zinc superoxide dismutase (SOD1) and assessed the effect of including torsional parameters for the histidine-metal interactions in molecular dynamics simulations. On the basis of the obtained results, we recommend that torsion parameters of the metal site are included when processes at the metal site are investigated or when free-energy calculations are performed. As the torsion parameters mainly affect the structure of the metal site, other kinds of structural studies can be performed without considering the torsional parameters of the metal site. PMID:25410708
Development of a force field for zeolitic imidazolate framework-8 with structural flexibility.
Hu, Zhongqiao; Zhang, Liling; Jiang, Jianwen
2012-06-28
A force field is developed for zeolitic imidazolate framework-8 (ZIF-8) with structural flexibility by combining quantum chemical calculations and classical Amber force field. The predicted crystalline properties of ZIF-8 (lattice constants, bond lengths, angles, dihedrals, and x-ray diffraction patterns) agree well with experimental results. A structural transition from crystalline to amorphous as found in experiment is observed. The mechanical properties of ZIF-8 are also described fairly well by the force field, particularly the Young's modulus predicted matches perfectly with measured value. Furthermore, the heat capacity of ZIF-8 as a typical thermophysical property is predicted and close to experimental data available for other metal-organic frameworks. It is revealed the structural flexibility of ZIF-8 exerts a significant effect on gas diffusion. In rigid ZIF-8, no diffusive behavior is observed for CH(4) within the simulation time scale of current study. With the structural flexibility, however, the predicted diffusivities of CH(4) and CO(2) are close to reported data in the literature. The density distributions and free energy profiles of CH(4) and CO(2) in the pore of ZIF-8 are estimated to analyze the mechanism of gas diffusion. PMID:22755595
All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model
Savelyev, Alexey; MacKerell, Alexander D.
2014-01-01
Presented is a first generation atomistic force field for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting QM data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude force field yields stable DNA duplexes on the 100 ns time scale and satisfactorily reproduces (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII sub-states of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive force field, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978
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
Dielectrophoretic forces and potentials induced on pairs of cells in an electric field.
Foster, K R; Sowers, A E
1995-01-01
A combined numerical/experimental study is reported of the membrane potentials and dielectrophoretically induced forces between cells, membrane pressures, and velocity of attraction of cells under the influence of an electric field. This study was designed to explore electrical and mechanical effects produced by a field on cells in close proximity or undergoing electrically induced fusion. Laplace's equation for pairs of membrane-covered spheres in close proximity was solved numerically by the boundary element method, and the electrically induced forces on the cells and between cells were obtained by evaluating the Maxwell stress tensor. The velocity of approach of erythrocyte ghosts or fused ghosts in a 60-Hz field of 6 V/mm was measured experimentally, and the data were interpreted by using Batchelor's theory for hydrodynamic interaction of hard spheres. The numerical results show clearly the origin of the dielectrophoretic pressures and forces in fused and unfused cells and the effects of a nearby cell on the induced membrane potentials. The experimental results agree well with predictions based on the simple electrical model of the cell. The analysis shows the strong effect of hydrodynamic interactions between the cells in determining their velocity of approach. PMID:8519978
The Design of a Next Generation Force Field: The X-POL Potential
Xie, Wangshen; Gao, Jiali
2008-01-01
An electronic structure-based polarization method, called the X-POL potential, has been described for the purpose of constructing an empirical force field for modeling polypeptides. In the X-POL potential, the internal, bonded interactions are fully represented by an electronic structure theory augmented with some empirical torsional terms. Non-bonded interactions are modeled by an iterative, combined quantum mechanical and molecular mechanical method, in which the molecular mechanical partial charges are derived from the molecular wave functions of the individual fragments. In this paper, the feasibility of such an electronic structure force field is illustrated by small model compounds. A method has been developed for separating a polypeptide chain into peptide units and its parameterization procedure in the X-POL potential is documented and tested on glycine dipeptide. We envision that the next generation of force fields for biomolecular polymer simulations will be developed based on electronic structure theory, which can adequately define and treat many-body polarization and charge delocalization effects. PMID:18985172
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
Simplified TiO2 force fields for studies of its interaction with biomolecules
NASA Astrophysics Data System (ADS)
Luan, Binquan; Huynh, Tien; Zhou, Ruhong
2015-06-01
Engineered TiO2 nanoparticles have been routinely applied in nanotechnology, as well as in cosmetics and food industries. Despite active experimental studies intended to clarify TiO2's biological effects, including potential toxicity, the relation between experimentally inferred nanotoxicity and industry standards for safely applying nanoparticles remains somewhat ambiguous with justified concerns. Supplemental to experiments, molecular dynamics simulations have proven to be efficacious in investigating the molecular mechanism of a biological process occurring at nanoscale. In this article, to facilitate the nanotoxicity and nanomedicine research related to this important metal oxide, we provide a simplified force field, based on the original Matsui-Akaogi force field but compatible to the Lennard-Jones potentials normally used in modeling biomolecules, for simulating TiO2 nanoparticles interacting with biomolecules. The force field parameters were tested in simulating the bulk structure of TiO2, TiO2 nanoparticle-water interaction, as well as the adsorption of proteins on the TiO2 nanoparticle. We demonstrate that these simulation results are consistent with experimental data/observations. We expect that simulations will help to better understand the interaction between TiO2 and molecules.
Cost-Effective Force Field Tailored for Solid-Phase Simulations of OLED Materials.
Moral, M; Son, W-J; Sancho-García, J C; Olivier, Y; Muccioli, L
2015-07-14
A united atom force field is empirically derived by minimizing the difference between experimental and simulated crystal cells and melting temperatures for eight compounds representative of organic electronic materials used in OLEDs and other devices: biphenyl, carbazole, fluorene, 9,9'-(1,3-phenylene)bis(9H-carbazole)-1,3-bis(N-carbazolyl)benzene (mCP), 4,4'-bis(N-carbazolyl)-1,1'-biphenyl (pCBP), phenazine, phenylcarbazole, and triphenylamine. The force field is verified against dispersion-corrected DFT calculations and shown to also successfully reproduce the crystal structure for two larger compounds employed as hosts in phosphorescent and thermally activated delayed fluorescence OLEDs: N,N'-di(1-naphthyl)-N,N'-diphenyl-(1,1'-biphenyl)-4,4'-diamine (NPD), and 1,3,5-tri(1-phenyl-1H-benzo[d]imidazol-2-yl)phenyl (TPBI). The good performances of the force field coupled to the large computational savings granted by the united atom approximation make it an ideal choice for the simulation of the morphology of emissive layers for OLED materials in crystalline or glassy phases. PMID:26575772
Polarizable Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical Drude Oscillator
He, Xibing; Lopes, Pedro E. M.; MacKerell, Alexander D.
2014-01-01
A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an emphasis on the transferability of the developed parameters among molecules of different sizes in this series and on the condensed-phase properties validated against experimental data. The importance of the explicit treatment of electronic polarizability in empirical force fields is demonstrated in the cases of this series of molecules with vicinal hydroxyl groups that can form cooperative intra- and intermolecular hydrogen bonds. Compared to the CHARMM additive force field, improved treatment of the electrostatic interactions avoids overestimation of the gas-phase dipole moments, results in significant improvement in the treatment of the conformational energies, and leads to the correct balance of intra- and intermolecular hydrogen bonding of glycerol as evidenced by calculated heat of vaporization being in excellent agreement with experiment. Computed condensed phase data, including crystal lattice parameters and volumes and densities of aqueous solutions are in better agreement with experimental data as compared to the corresponding additive model. Such improvements are anticipated to significantly improve the treatment of polymers in general, including biological macromolecules. PMID:23703219
NASA Astrophysics Data System (ADS)
Leuty, Gary; Berry, Rajiv; Muratore, Christopher; Varshney, Vikas; Turner, Heath
Transition metal dichalcogenides (TMDs) such as molybdenum disulfide (MoS2) have garnered significant interest in recent years. With a layered structure similar to graphene, TMDs also have an intrinsic band gap. This band gap makes them an attractive alternative to graphene in many applications. MoS2 in particular has received attention due to the placement and tenability of its band gap, via functionalization, mechanical manipulation or physisorption. The latter of these is of interest in biosensor devices. Such applications are dependent on understanding physisorption on the MoS2 surface at the molecular level. This can be difficult experimentally but is possible via computer simulation techniques such as molecular dynamics (MD) simulations. MD simulations, however, require a force field accurate to the process modeled. Such a force field must correctly describe non-bonded interactions between substrate layers and between the surface and adsorbates. The force fields we are aware of have focused on intra-layer covalent bonding for structural and vibrational analysis. This work seeks to develop, through DFT and MD simulations with experimental characterization of surface adsorption, a more accurate parameterization for non-bonded interactions for MoS2.
Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.
Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele
2015-10-01
It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754
Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
Dijkstra, Maurits J. J.; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele
2015-01-01
It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754
What Do Effective Field Theories Tell Us About the Nuclear Force?
NASA Astrophysics Data System (ADS)
Friar, J. L.
2003-10-01
Potentials are the tools that traditional nuclear physics uses to calculate bound states and reaction rates. First-generation potentials (developed more than a decade ago) used many different mechanisms to motivate shapes and strengths, while their fits to nucleon-nucleon scattering data were indifferent. Second-generation potentials, whose fits to data range from good to excellent, were constructed within the past decade using the same motivations. Accurate third-generation potentials are now being developed using the language and techniques of chiral perturbation theory, which is an effective field theory based on the symmetries of QCD. The philosophy of such effective field theories has made a large impact on the way I view nuclear potentials. Power counting, for example, uses the scales of strongly interacting systems to provide a systematic and concise organizational scheme that subsumes both two-nucleon and three-nucleon potentials. Although this new development has led to a rapid advance in our understanding of nuclear forces (especially in isospin violation), much of this work mirrors traditional approaches. Many of the techniques usually associated with field theory (such as regularization and renormalization, for example) also have direct analogues in more traditional approaches to constructing potentials. Examples of nuclear-force mechanisms and their associated scales will be discussed throughout the talk, together with my appreciation of how well we understand the nuclear force.
Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins.
Ye, Wei; Ji, Dingjue; Wang, Wei; Luo, Ray; Chen, Hai-Feng
2015-05-26
Over 40% of eukaryotic proteomic sequences have been predicted to be intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) and confirmed to be associated with many diseases. However, widely used force fields cannot well reproduce the conformers of IDPs. Previously the ff99IDPs force field was released to simulate IDPs with CMAP energy corrections for the eight disorder-promoting residues. In order to further confirm the performance of ff99IDPs, three representative IDP systems (arginine-rich HIV-1 Rev, aspartic proteinase inhibitor IA3, and α-synuclein) were used to test and evaluate the simulation results. The results show that for free disordered proteins, the chemical shifts from the ff99IDPs simulations are in quantitative agreement with those from reported NMR measurements and better than those from ff99SBildn. Thus, ff99IDPs can sample more clusters of disordered conformers than ff99SBildn. For structural proteins, both ff99IDPs and ff99SBildn can well reproduce the conformations. In general, ff99IDPs can successfully be used to simulate the conformations of IDPs and IDRs in both bound and free states. However, relative errors could still be found at the boundaries of ordered residues scattered in long disorder-promoting sequences. Therefore, polarizable force fields might be one of the possible ways to further improve the performance on IDPs. PMID:25919886
Empirical Corrections to the Amber RNA Force Field with Target Metadynamics
2016-01-01
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. PMID:27153317
GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates.
Pol-Fachin, Laercio; Rusu, Victor H; Verli, Hugo; Lins, Roberto D
2012-11-13
An improved parameter set for explicit-solvent simulations of carbohydrates (referred to as GROMOS 53A6GLYC) is presented, allowing proper description of the most stable conformation of all 16 possible aldohexopyranose-based monosaccharides. This set includes refinement of torsional potential parameters associated with the determination of hexopyranose rings conformation by fitting to their corresponding quantum-mechanical profiles. Other parameters, as the rules for third and excluded neighbors, are taken directly from the GROMOS 53A6 force field. Comparisons of the herein presented parameter set to our previous version (GROMOS 45A4), the GLYCAM06 force field, and available NMR data are presented in terms of ring puckering free energies, conformational distribution of the hydroxymethyl group, and glycosidic linkage geometries for 16 selected monosaccharides and eight disaccharides. The proposed parameter modifications have shown a significant improvement for the above-mentioned quantities over the two tested force fields, while retaining full compatibility with the GROMOS 53A6 and 54A7 parameter sets for other classes of biomolecules. PMID:26605624
2016-01-01
Classical molecular mechanics force fields typically model interatomic electrostatic interactions with point charges or multipole expansions, which can fail for atoms in close contact due to the lack of a description of penetration effects between their electron clouds. These short-range penetration effects can be significant and are essential for accurate modeling of intermolecular interactions. In this work we report parametrization of an empirical charge–charge function previously reported (PiquemalJ.-P.; J. Phys. Chem. A2003, 107, 1035326313624) to correct for the missing penetration term in standard molecular mechanics force fields. For this purpose, we have developed a database (S101×7) of 101 unique molecular dimers, each at 7 different intermolecular distances. Electrostatic, induction/polarization, repulsion, and dispersion energies, as well as the total interaction energy for each complex in the database are calculated using the SAPT2+ method (ParkerT. M.; J. Chem. Phys.2014, 140, 09410624606352). This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element. Given the simplicity and effectiveness of the model, we expect the electrostatic penetration correction will become a standard component of future molecular mechanics force fields. PMID:26413036
Exploring Adsorption of Water and Ions on Carbon Surfaces using a Polarizable Force Field
Schyman, Patric; Jorgensen, William L.
2013-01-01
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 (C6H6) and coronene (C24H12) well; however, for acenes larger than circumcoronene (C54H18) and especially for C60, 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. PMID:23440601
Screening in nanowires and nanocontacts: field emission, adhesion force, and contact resistance
Zhang, Xiaoguang; Pantelides, Sokrates T.
2009-01-01
The explanations of several nanoscale phenomena such as the field enhancement factor in field emission, the large decay length of the adhesion force between a metallic tip and a surface, and the contact resistance in a nanowire break junction have been elusive. Here we develop an analytical theory of Thomas-Fermi screening in nanoscale structures. We demonstrate that nanoscale dimensions give rise to an effective screening length that depends on geometry and physical boundary conditions. The above phenomena are shown to be manifestations of the effective screening length.
Mean-field Ohm's law and coaxial helicity injection in force-free plasmas
Weening, R. H.
2011-12-15
A theoretical analysis of steady-state coaxial helicity injection (CHI) in force-free plasmas is presented using a parallel mean-field Ohm's law that includes resistivity {eta} and hyper-resistivity {Lambda} terms. Using Boozer coordinates, a partial differential equation is derived for the time evolution of the mean-field poloidal magnetic flux, or magnetic Hamiltonian function, from the parallel mean-field Ohm's law. A general expression is obtained from the mean-field theory for the efficiency of CHI current drive in force-free plasmas. Inductances of internal energy, magnetic helicity, and poloidal magnetic flux are used to characterize axisymmetric plasma equilibria that have a model current profile. Using the model current profile, a method is suggested to determine the level of magnetohydrodynamic activity at the magnetic axis and the consequent deviation from the completely relaxed Taylor state. The mean-field Ohm's law model suggests that steady-state CHI can be viewed most simply as a boundary layer problem.
Study on Two Methods for Nonlinear Force-Free Extrapolation Based on Semi-Analytical Field
NASA Astrophysics Data System (ADS)
Liu, S.; Zhang, H. Q.; Su, J. T.; Song, M. T.
2011-03-01
In this paper, two semi-analytical solutions of force-free fields (Low and Lou, Astrophys. J. 352, 343, 1990) have been used to test two nonlinear force-free extrapolation methods. One is the boundary integral equation (BIE) method developed by Yan and Sakurai ( Solar Phys. 195, 89, 2000), and the other is the approximate vertical integration (AVI) method developed by Song et al. ( Astrophys. J. 649, 1084, 2006). Some improvements have been made to the AVI method to avoid the singular points in the process of calculation. It is found that the correlation coefficients between the first semi-analytical field and extrapolated field using the BIE method, and also that obtained by the improved AVI method, are greater than 90% below a height 10 of the 64×64 lower boundary. For the second semi-analytical field, these correlation coefficients are greater than 80% below the same relative height. Although differences between the semi-analytical solutions and the extrapolated fields exist for both the BIE and AVI methods, these two methods can give reliable results for heights of about 15% of the extent of the lower boundary.
Papadichev, V.A.
1995-12-31
Various types of undulators with or without axial magnetic field are used in FELs. Supplementary beam focusing can be applied by wedging, inclining or profiling pole faces of plan undulators or superposing external focusing magnetic fields in addition to undulator own focusing. Space-charge forces influence significantly particle motion in high-current, low-energy electron beams. Finally, one can use simultaneously two or more different undulators for some specific purpose: more efficient and selective higher harmonics generation, changing polarization types and direction, gain enhancement in double-period undulator etc. All these cases can be treated by solving the generalized equations of transverse orbital motion in a linear approximation, which is widely used for orbit calculation, gives sufficient accuracy for practical purposes and allows to consider many variants and optimize the chosen one. The undulator field is described as a field of two plane undulators with mutually orthogonal fields and an arbitrary axial (phase) shift between them. Various values of the phase shift correspond to right- or left-handed helical undulators, plane undulator of different polarization etc. The general formulae are reduced to forms that allow easier examination of particular cases: planar or helical undulator combined with axial magnetic field or without it, gyroresonance, limiting beam current, polarization etc.
GENERATION OF SEED MAGNETIC FIELD AROUND FIRST STARS: EFFECTS OF RADIATION FORCE
Ando, Masashi; Doi, Kentaro; Susa, Hajime E-mail: mn921009@center.konan-u.ac.j
2010-06-20
We investigate seed magnetic field generation in the early universe by the radiation force of first stars. In a previous study with the steady assumption, large amplitudes ({approx}10{sup -15} G for first stars, {approx}10{sup -11} G for QSOs) are predicted. In this study, we formulate this issue in an unsteady framework. Then, we consider a specific model of magnetic field generation around a very massive first star. Consequently, we (1) find that the steady assumption is not valid in realistic situations and (2) obtain a much smaller magnetic field strength than that predicted by Langer et al. In addition, we find that the momentum transfer process during photoionization is more important than Thomson scattering. The resultant magnetic flux density around the first star is {approx_lt}10{sup -19} G. This seed magnetic field will not affect subsequent star formation in the neighborhood of first stars.
Generation of Seed Magnetic Field Around First Stars: Effects of Radiation Force
NASA Astrophysics Data System (ADS)
Ando, Masashi; Doi, Kentaro; Susa, Hajime
2010-06-01
We investigate seed magnetic field generation in the early universe by the radiation force of first stars. In a previous study with the steady assumption, large amplitudes (~10-15 G for first stars, ~10-11 G for QSOs) are predicted. In this study, we formulate this issue in an unsteady framework. Then, we consider a specific model of magnetic field generation around a very massive first star. Consequently, we (1) find that the steady assumption is not valid in realistic situations and (2) obtain a much smaller magnetic field strength than that predicted by Langer et al. In addition, we find that the momentum transfer process during photoionization is more important than Thomson scattering. The resultant magnetic flux density around the first star is lsim10-19 G. This seed magnetic field will not affect subsequent star formation in the neighborhood of first stars.
NASA Astrophysics Data System (ADS)
Zareie Rajani, H. R.; Phillion, A. B.
2015-08-01
Formation of hot cracks is strongly affected by the transient force field acting on the semisolid weld-base metal interface. This paper presents a model that numerically simulates such a transient force field as a function of welding parameters. The model consists of two modules: (1) By means of a granular model of solidification, the microstructure of the semisolid area within the weld is reconstructed in three dimensions; (2) Since the transient force field is developed through the mechanical interaction between the semisolid weld and its base metal, the mechanical response of the base metal to the solidification of the weld is then simulated through finite element analysis. The results show that changing welding parameters and welding constraints varies the transient force field. Based on the obtained force fields, a qualitative study is also conducted to predict the susceptibility of various welds to hot cracking.
Aerodynamic forces and flow fields of a two-dimensional hovering wing
NASA Astrophysics Data System (ADS)
Lua, K. B.; Lim, T. T.; Yeo, K. S.
2008-12-01
This paper reports the results of an experimental investigation on a two-dimensional (2-D) wing undergoing symmetric simple harmonic flapping motion. The purpose of this investigation is to study how flapping frequency (or Reynolds number) and angular amplitude affect aerodynamic force generation and the associated flow field during flapping for Reynolds number ( Re) ranging from 663 to 2652, and angular amplitudes ( α A) of 30°, 45° and 60°. Our results support the findings of earlier studies that fluid inertia and leading edge vortices play dominant roles in the generation of aerodynamic forces. More importantly, time-resolved force coefficients during flapping are found to be more sensitive to changes in α A than in Re. In fact, a subtle change in α A may lead to considerable changes in the lift and drag coefficients, and there appears to be an optimal mean lift coefficient left( {overline {C_{{text{l}}} } } right) around α A = 45°, at least for the range of flow parameters considered here. This optimal condition coincides with the development a reverse Karman Vortex street in the wake, which has a higher jet stream than a vortex dipole at α A = 30° and a neutral wake structure at α A = 60°. Although Re has less effect on temporal force coefficients and the associated wake structures, increasing Re tends to equalize mean lift coefficients (and also mean drag coefficients) during downstroke and upstroke, thus suggesting an increasing symmetry in the mean force generation between these strokes. Although the current study deals with a 2-D hovering motion only, the unique force characteristics observed here, particularly their strong dependence on α A, may also occur in a three-dimensional hovering motion, and flying insects may well have taken advantage of these characteristics to help them to stay aloft and maneuver.
Torque-consistent 3D force balance and optimization of non-resonant fields in tokamaks
NASA Astrophysics Data System (ADS)
Park, Jong-Kyu
2015-11-01
A non-axisymmetric magnetic perturbation in tokamaks breaks the toroidal symmetry and produces toroidal torque, which is well known as neoclassical toroidal viscosity (NTV) effects. Although NTV torque is second order, it is the first-order change in the pressure anisotropy that drives currents associated with local torques and thereby modifies the field penetration in force balance. The force operator becomes non-Hermitian, but can be directly solved using parallel, toroidal, and radial force balance, leading to a modified Euler-Lagrange equation. The general perturbed equilibrium code (GPEC), which has been successfully developed to solve the modified Euler-Lagrange equation, gives the torque-consistent 3D force balance as well as self-consistent NTV torque. The self-shielding of the torque becomes apparent in the solutions in high β, which was implied in recent MARS-K applications. Furthermore, the full response matrix including the torque in GPEC provides a new and systematic way of optimizing torque and non-resonant fields. Recently the optimization of 3D fields for torque has been actively studied using the stellarator optimizing tools, but the efficiency and accuracy can be greatly improved by directly incorporating the torque response matrix. There are salient features uncovered by response with the torque, as the response can become invisible in amplitudes but only significant in toroidal phase shift. A perturbation in backward helicity is an example, in which NTV can be induced substantially but quietly without measurable response in amplitudes. A number of other GPEC applications will also be discussed, including the multi-mode responses in high- β tokamak plasmas and the new non-axisymmetric control coil (NCC) design in NSTX-U. This work was supported by DOE Contract DE-AC02-09CH11466.
A Bidirectional Brain-Machine Interface Algorithm That Approximates Arbitrary Force-Fields
Semprini, Marianna; Mussa-Ivaldi, Ferdinando A.; Panzeri, Stefano
2014-01-01
We examine bidirectional brain-machine interfaces that control external devices in a closed loop by decoding motor cortical activity to command the device and by encoding the state of the device by delivering electrical stimuli to sensory areas. Although it is possible to design this artificial sensory-motor interaction while maintaining two independent channels of communication, here we propose a rule that closes the loop between flows of sensory and motor information in a way that approximates a desired dynamical policy expressed as a field of forces acting upon the controlled external device. We previously developed a first implementation of this approach based on linear decoding of neural activity recorded from the motor cortex into a set of forces (a force field) applied to a point mass, and on encoding of position of the point mass into patterns of electrical stimuli delivered to somatosensory areas. However, this previous algorithm had the limitation that it only worked in situations when the position-to-force map to be implemented is invertible. Here we overcome this limitation by developing a new non-linear form of the bidirectional interface that can approximate a virtually unlimited family of continuous fields. The new algorithm bases both the encoding of position information and the decoding of motor cortical activity on an explicit map between spike trains and the state space of the device computed with Multi-Dimensional-Scaling. We present a detailed computational analysis of the performance of the interface and a validation of its robustness by using synthetic neural responses in a simulated sensory-motor loop. PMID:24626393
A Dust-Penetrated Classification Scheme for Bars as Inferred from their Gravitational Force Fields
NASA Astrophysics Data System (ADS)
Buta, R.; Block, D. L.
2001-05-01
The division of galaxies into barred (SB) and normal (S) spirals is a fundamental aspect of the Hubble galaxy classification system. This tuning fork view was revised by de Vaucouleurs, whose classification volume recognized apparent bar strength (SA, SAB, SB) as a continuous property of galaxies called the ``family.'' However, the SA, SAB, and SB families are purely visual judgments that can have little bearing on the actual bar strength in a given galaxy. Until recently, published bar judgments were based exclusively on blue light images, where internal extinction or star formation can completely mask a bar. Near-infrared camera arrays, which principally trace the old stellar population in both normal and barred galaxies, now facilitate a quantification of bar strength in terms of gravitational potentials and force fields. In this paper, we show that the maximum value of the ratio of the tangential force to the mean axisymmetric radial force is a quantitative measure of the strength of a bar that can be straightforwardly derived for many galaxies. We show that a wide range of true bar strengths characterizes the category SB, while category SAB corresponds to a narrower range of bar strengths. Based on the force ratio, we define seven classes of bar strength and incorporate these classes into a dust-penetrated classification system for spiral galaxies. This work was supported by NSF grant AST 9617154 and the Anglo-American Chairman's Fund, Mrs. M. Keeton, CEO.
Modeling of Gamma-ray Pulsar Light Curves Using the Force-free Magnetic Field
NASA Astrophysics Data System (ADS)
Bai, Xue-Ning; Spitkovsky, Anatoly
2010-06-01
Gamma-ray emission from pulsars has long been modeled using a vacuum dipole field. This approximation ignores changes in the field structure caused by the magnetospheric plasma and strong plasma currents. We present the first results of gamma-ray pulsar light-curve modeling using the more realistic field taken from three-dimensional force-free (FF) magnetospheric simulations. Having the geometry of the field, we apply several prescriptions for the location of the emission zone, comparing the light curves to observations. We find that when the emission region is chosen according to the conventional slot-gap (or two-pole caustic) prescription, the model fails to produce double-peak pulse profiles, mainly because the size of the polar cap in the FF magnetosphere is larger than the vacuum field polar cap. This suppresses caustic formation in the inner magnetosphere. The conventional outer-gap model is capable of producing only one peak under general conditions because a large fraction of open field lines does not cross the null charge surface. We propose a novel "separatrix layer" model, where the high-energy emission originates from a thin layer on the open field lines just inside of the separatrix that bounds the open flux tube. The emission from this layer generates two strong caustics on the sky map due to the effect we term "Sky Map Stagnation" (SMS). It is related to the fact that the FF field asymptotically approaches the field of a rotating split monopole, and the photons emitted on such field lines in the outer magnetosphere arrive to the observer in phase. The double-peak light curve is a natural consequence of SMS. We show that most features of the currently available gamma-ray pulsar light curves can be reasonably well reproduced and explained with the separatrix layer model using the FF field. Association of the emission region with the current sheet will guide more detailed future studies of the magnetospheric acceleration physics.
NASA Astrophysics Data System (ADS)
Dias, F. L.; Assumpcao, M.
2014-12-01
The knowledge of stress field is fundamental not only to understand driving forces and plate deformation but also in the study of intraplate seismicity. In Brazil, the stress field has been determined mainly using focal mechanisms and a breakout data and in-situ measurements. However, the stress field still is poorly known in Brazil. We show a recent compilation of focal mechanism determined in Brazil (Fig 1). The focal mechanisms of some recent earthquakes (magnitude lower than 5 mb) were studied using waveform modeling. We stacked the record of several teleseismic stations (> 30°) with a good signal/noise ratio and we grouped then according to distance and azimuth. With the focal mechanisms available in literature and those obtained in this work, we were able to identify some patterns: the central region shows compressional pattern (E-W SHmax), which is predicted by regional theoretical models ( Coblentz & Richardson, 1996 and the TD0 model of Lithgow & Bertelloni, 2004). This compression is mainly due to the interaction of tectonic plate forces. Meanwhile in the Amazon region, we find an indication of SHMax oriented in the SE-NW direction, probably caused by the Caribbean plate interaction (Meijer, 1995) and Amazon Fan, we have flexural stresses caused by sedimentary load with is in agreement with local theoretical models (Watts et al., 2009) . In northern coastal region, the compression rotates following the coastline, which indicates an important local component related to spreading effects at the continental/oceanic transition (Assumpção, 1998). We determine the focal mechanism of several events in Brazil using different techniques according to the available data. The major difficulty is to determine focal mechanism of low magnitudes events (< 5.0 mb) using distant or few seismograph stations. We find examples of stress perturbations induced by local effects (e.g. flexure and continental spreading). The results of this work should be useful for future
Yoo, Jejoong; Wilson, James; Aksimentiev, Aleksei
2016-10-01
Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA-DNA interactions. In the simulations performed using the two standard models, Ca(2+) ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2 and CaCl2 solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca(2+) ions in the simulations of Ca(2+) -mediated DNA-DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca(2+) to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca(2+) model, we introduce a custom model of a hydrated Ca(2+) ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca(2+) can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752-763, 2016. PMID:27144470
Xu, Dong; Zhang, Yang
2012-01-01
Ab initio protein folding is one of the major unsolved problems in computational biology due to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1–20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) experiment, QUARK server outperformed the second and third best servers by 18% and 47% based on the cumulative Z-score of global distance test-total (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field. PMID:22411565
Thermal field fluctuations in a magnetic tip / implications for magnetic resonance force microscopy
NASA Astrophysics Data System (ADS)
Hannay, J. D.; Chantrell, R. W.; Rugar, D.
2000-05-01
Thermally excited magnetic fluctuations are fundamental to the behavior of small ferromagnetic particles and have practical consequences for the proposed detection of individual spins by magnetic resonance force microscopy (MRFM). In particular, fluctuating fields from a nearby magnetic tip can increase the relaxation rate of spins in a sample if there is significant spectral density of field fluctuation at the Larmor frequency of the target spin. As an initial step toward understanding this issue, magnetic field fluctuations have been simulated which emanate from a magnetic tip with dimensions 60 nm×60 nm×2 μm. It was found that the fluctuations in a cobalt magnetic tip were too strong for MRFM experiments aimed at detecting individual electron spins. However, the results obtained for a PrFeB tip fell within the tolerance required.
Active control of structurally-coupled sound fields in elastic cylinders by vibrational force inputs
NASA Technical Reports Server (NTRS)
Jones, J. D.; Fuller, C. R.
1990-01-01
Active control of structurally-coupled sound fields in elastic cylinders is analytically and experimentally studied. The primary (noise) field in the cylinder model is generated by the coupled dynamic response of the shell under loading by a single exterior acoustic source. Control of the interior sound field is achieved by applying vibrational force inputs directly to the shell wall. Action of the point controllers serve to increase the input impedance of select structural modes of the shell which are well-coupled to the interior acoustic cavity, thus substantially reducing sound transmission into the cavity. Spatially-averaged noise reductions in excess of 30 dB are demonstrated for acoustic resonant conditions within the cavity. Twin controller configurations are presented which demonstrate the ability to independently control orthogonal modes of the interior acoustic space. Benefits and drawbacks of this new methodology for noise control are discussed and clearly demonstrated.
The fast multipole method and point dipole moment polarizable force fields
NASA Astrophysics Data System (ADS)
Coles, Jonathan P.; Masella, Michel
2015-01-01
We present an implementation of the fast multipole method for computing Coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected O(N) scaling of that approach by performing single energy point calculations on hexamer protein subunits of the mature HIV-1 capsid. We also show the long time energy conservation in molecular dynamics at the nanosecond scale by performing simulations of a protein complex embedded in a coarse-grained solvent using a standard integrator and a multiple time step integrator. Our tests show the applicability of fast multipole method combined with state-of-the-art chemical models in molecular dynamical systems.
Estimating unsteady aerodynamic forces on a cascade in a three-dimensional turbulence field
NASA Technical Reports Server (NTRS)
Norman, T.; Johnson, W.
1985-01-01
An analytical method has been developed to estimate the unsteady aerodynamic forces caused by flow field turbulence on a wind tunnel turning vane cascade system (vane set). This method approximates dynamic lift and drag by linearly perturbing the appropriate steady state force equations, assuming that the dynamic loads are due only to free stream turbulence and that this turbulence is homogeneous, isotropic, and Gaussian. Correlation and unsteady aerodynamic effects are also incorporated into the analytical model. Using these assumptions, equations relating dynamic lift and drag to flow turbulence, mean velocity, and vane set geometry are derived. From these equations, estimates for the power spectra and rms (root mean squared value, delta) loading of both lift and drag can be determined.
Centrifugal Force Based Magnetic Micro-Pump Driven by Rotating Magnetic Fields
NASA Astrophysics Data System (ADS)
Kim, S. H.; Hashi, S.; Ishiyama, K.
2011-01-01
This paper presents a centrifugal force based magnetic micro-pump for the pumping of blood. Most blood pumps are driven by an electrical motor with wired control. To develop a wireless and battery-free blood pump, the proposed pump is controlled by external rotating magnetic fields with a synchronized impeller. Synchronization occurs because the rotor is divided into multi-stage impeller parts and NdFeB permanent magnet. Finally, liquid is discharged by the centrifugal force of multi-stage impeller. The proposed pump length is 30 mm long and19 mm in diameter which much smaller than currently pumps; however, its pumping ability satisfies the requirement for a blood pump. The maximum pressure is 120 mmHg and the maximum flow rate is 5000ml/min at 100 Hz. The advantage of the proposed pump is that the general mechanical problems of a normal blood pump are eliminated by the proposed driving mechanism.
The fast multipole method and point dipole moment polarizable force fields.
Coles, Jonathan P; Masella, Michel
2015-01-14
We present an implementation of the fast multipole method for computing Coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected O(N) scaling of that approach by performing single energy point calculations on hexamer protein subunits of the mature HIV-1 capsid. We also show the long time energy conservation in molecular dynamics at the nanosecond scale by performing simulations of a protein complex embedded in a coarse-grained solvent using a standard integrator and a multiple time step integrator. Our tests show the applicability of fast multipole method combined with state-of-the-art chemical models in molecular dynamical systems. PMID:25591340
Novel System for Bite-Force Sensing and Monitoring Based on Magnetic Near Field Communication
Lantada, Andres Diaz; Bris, Carlos González; Morgado, Pilar Lafont; Maudes, Jesús Sanz
2012-01-01
Intraoral devices for bite-force sensing have several applications in odontology and maxillofacial surgery, as bite-force measurements provide additional information to help understand the characteristics of bruxism disorders and can also be of help for the evaluation of post-surgical evolution and for comparison of alternative treatments. A new system for measuring human bite forces is proposed in this work. This system has future applications for the monitoring of bruxism events and as a complement for its conventional diagnosis. Bruxism is a pathology consisting of grinding or tight clenching of the upper and lower teeth, which leads to several problems such as lesions to the teeth, headaches, orofacial pain and important disorders of the temporomandibular joint. The prototype uses a magnetic field communication scheme similar to low-frequency radio frequency identification (RFID) technology (NFC). The reader generates a low-frequency magnetic field that is used as the information carrier and powers the sensor. The system is notable because it uses an intra-mouth passive sensor and an external interrogator, which remotely records and processes information regarding a patient's dental activity. This permits a quantitative assessment of bite-force, without requiring intra-mouth batteries, and can provide supplementary information to polysomnographic recordings, current most adequate early diagnostic method, so as to initiate corrective actions before irreversible dental wear appears. In addition to describing the system's operational principles and the manufacture of personalized prototypes, this report will also demonstrate the feasibility of the system and results from the first in vitro and in vivo trials. PMID:23112669
Wang, Hao; Yang, Weitao
2016-06-14
We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities. PMID:27305996
Non-linear force-free field modeling: model techniques, boundary conditions, hares, and hounds
NASA Astrophysics Data System (ADS)
Schrijver, C. J.; De Rosa, M. L.; Metcalf, T.
2005-05-01
Understanding the conditions under which solar magnetic fields can destabilize to erupt in flares and coronal mass ejections requires a quantitative understanding of the coronal magnetic field and of the currents that it carries. The increased availability of vector magnetograms, together with EUV and X-ray coronal images, should provide adequate constraints to model the coronal field, and thus to visualize its 3D geometry and to measure the available free energy and helicity. Non-linear force-free fields (NLFFF) are likely a useful model to use when extrapolating the solar surface field upward into the coronal volume. It may even be possible to use the observed trajectories of coronal loops, evident in EUV images of the corona, as a further constraint. We present initial results of a team effort to understand the intricacies of NLFFF modeling: we discuss and evaluate comparisons of NLFFF models computed with different models and applications of boundary conditions, and look ahead to full coronal field modeling for the upcoming Solar-B and SDO missions.
Perspectives on the simulation of protein-surface interactions using empirical force field methods.
Latour, Robert A
2014-12-01
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
Application of a force field algorithm for creating strongly correlated multiscale sphere packings
NASA Astrophysics Data System (ADS)
Zauner, Thomas
2016-05-01
This work presents a protocol driven force field algorithm, used to create multiscale correlated dense sphere packings. It was developed as part of a tool chain for the reconstruction of realistic multiscale porous rock samples. It overcomes limitations of Monte-Carlo or deposition based approaches, that are quite common in this field and were used previously. The new algorithm can create large, low porosity sphere packings with radius distributions covering two decades. Highly correlated structures that model pore clogging and sedimentation can be generated. To achieve this, an adequate force field and proper termination strategies are necessary. By changing the algorithm parameters in a controlled way during the simulation, a complex protocol driven process can be established. The implementation of the algorithm targets large parallel computer platforms to perform simulations with more than 10 million spheres. This article includes an application of the algorithm used to generate a highly polydisperse sphere packing with roughly 106 spheres and radii from 1 to 100 μm. The continuum description of this packing is discretized at resolutions from 0.25 to 1 μm and investigated using geometric and statistical characterizations and results from Lattice-Boltzmann flow simulations. These resolution dependent results affirm that reliable, predictive calculations for multiscale porous microstructures depend on the availability of large realistic continuum models. To obtain such models the algorithm presented herein can be used as a starting point.
Application of a force field algorithm for creating strongly correlated multiscale sphere packings
NASA Astrophysics Data System (ADS)
Zauner, Thomas
2016-05-01
This work presents a protocol driven force field algorithm, used to create multiscale correlated dense sphere packings. It was developed as part of a tool chain for the reconstruction of realistic multiscale porous rock samples. It overcomes limitations of Monte-Carlo or deposition based approaches, that are quite common in this field and were used previously. The new algorithm can create large, low porosity sphere packings with radius distributions covering two decades. Highly correlated structures that model pore clogging and sedimentation can be generated. To achieve this, an adequate force field and proper termination strategies are necessary. By changing the algorithm parameters in a controlled way during the simulation, a complex protocol driven process can be established. The implementation of the algorithm targets large parallel computer platforms to perform simulations with more than 10 million spheres. This article includes an application of the algorithm used to generate a highly polydisperse sphere packing with roughly 106 spheres and radii from 1 to 100 μm. The continuum description of this packing is discretized at resolutions from 0.25 to 1 μm and investigated using geometric and statistical characterizations and results from Lattice-Boltzmann flow simulations. These resolution dependent results affirm that reliable, predictive calculations for multiscale porous microstructures depend on the availability of large realistic continuum models. To obtain such models the algorithm presented herein can be used as a starting point.
Tien, Homer; Beckett, Andrew; Garraway, Naisan; Talbot, Max; Pannell, Dylan; Alabbasi, Thamer
2015-06-01
Medical support to deployed field forces is increasingly becoming a shared responsibility among allied nations. National military medical planners face several key challenges, including fiscal restraints, raised expectations of standards of care in the field and a shortage of appropriately trained specialists. Even so, medical services are now in high demand, and the availability of medical support may become the limiting factor that determines how and where combat units can deploy. The influence of medical factors on operational decisions is therefore leading to an increasing requirement for multinational medical solutions. Nations must agree on the common standards that govern the care of the wounded. These standards will always need to take into account increased public expectations regarding the quality of care. The purpose of this article is to both review North Atlantic Treaty Organization (NATO) policies that govern multinational medical missions and to discuss how recent scientific advances in prehospital battlefield care, damage control resuscitation and damage control surgery may inform how countries within NATO choose to organize and deploy their field forces in the future. PMID:26100784
Tien, Col Homer; Beckett, Maj Andrew; Garraway, LCol Naisan; Talbot, LCol Max; Pannell, Capt Dylan; Alabbasi, Thamer
2015-01-01
Medical support to deployed field forces is increasingly becoming a shared responsibility among allied nations. National military medical planners face several key challenges, including fiscal restraints, raised expectations of standards of care in the field and a shortage of appropriately trained specialists. Even so, medical services are now in high demand, and the availability of medical support may become the limiting factor that determines how and where combat units can deploy. The influence of medical factors on operational decisions is therefore leading to an increasing requirement for multinational medical solutions. Nations must agree on the common standards that govern the care of the wounded. These standards will always need to take into account increased public expectations regarding the quality of care. The purpose of this article is to both review North Atlantic Treaty Organization (NATO) policies that govern multinational medical missions and to discuss how recent scientific advances in prehospital battlefield care, damage control resuscitation and damage control surgery may inform how countries within NATO choose to organize and deploy their field forces in the future. PMID:26100784
A method for embedding circular force-free flux ropes in potential magnetic fields
Titov, V. S.; Török, T.; Mikic, Z.; Linker, J. A.
2014-08-01
We propose a method for constructing approximate force-free equilibria in pre-eruptive configurations in which a thin force-free flux rope is embedded into a locally bipolar-type potential magnetic field. The flux rope is assumed to have a circular-arc axis, a circular cross-section, and electric current that is either concentrated in a thin layer at the boundary of the rope or smoothly distributed across it with a maximum of the current density at the center. The entire solution is described in terms of the magnetic vector potential in order to facilitate the implementation of the method in numerical magnetohydrodynamic (MHD) codes that evolve the vector potential rather than the magnetic field itself. The parameters of the flux rope can be chosen so that its subsequent MHD relaxation under photospheric line-tied boundary conditions leads to nearly exact numerical equilibria. To show the capabilities of our method, we apply it to several cases with different ambient magnetic fields and internal flux-rope structures. These examples demonstrate that the proposed method is a useful tool for initializing data-driven simulations of solar eruptions.
Interfacial force field characterization of a constrained vapor bubble thermosyphon using IAI
NASA Technical Reports Server (NTRS)
Dasgupta, Sunando; Plawsky, Joel L.; Wayner, Peter C., Jr.
1994-01-01
The isothermal profiles of the extended meniscus in a quartz cuvette were measured in a gravitational field using IAI (image analyzing interferometer) which is based on computer enhanced video microscopy of the naturally occurring interference fringes. The experimental results for heptane and pentane menisci were analyzed using the extended Young-Laplace Equation. These isothermal results characterized the interfacial force field in-situ at the start of the heat transfer experiments by quantifying the dispersion constant for the specific liquid-solid system. The experimentally obtained values of the disjoining pressures and the dispersion constants are compared to the subsequent non-isothermal experiments because one of the major variables in the heat sink capability of the CVBT is the dispersion constant. In all previous studies of micro heat pipes the value of the dispersion constant has been 'guesstimated'. The major advantages of the current glass cell is the ability to view the extended meniscus at all times. Experimentally, we find that the extended Young-Laplace Equation is an excellent model for for the force field at the solid-liquid vapor interfaces.
Inoue, S.; Magara, T.; Choe, G. S.; Kim, K. S.; Pandey, V. S.; Shiota, D.; Kusano, K.
2014-01-01
We develop a nonlinear force-free field (NLFFF) extrapolation code based on the magnetohydrodynamic (MHD) relaxation method. We extend the classical MHD relaxation method in two important ways. First, we introduce an algorithm initially proposed by Dedner et al. to effectively clean the numerical errors associated with ∇ · B . Second, the multigrid type method is implemented in our NLFFF to perform direct analysis of the high-resolution magnetogram data. As a result of these two implementations, we successfully extrapolated the high resolution force-free field introduced by Low and Lou with better accuracy in a drastically shorter time. We also applied our extrapolation method to the MHD solution obtained from the flux-emergence simulation by Magara. We found that NLFFF extrapolation may be less effective for reproducing areas higher than a half-domain, where some magnetic loops are found in a state of continuous upward expansion. However, an inverse S-shaped structure consisting of the sheared and twisted loops formed in the lower region can be captured well through our NLFFF extrapolation method. We further discuss how well these sheared and twisted fields are reconstructed by estimating the magnetic topology and twist quantitatively.
Giulianotti, Richard; Robertson, Roland
2012-06-01
This paper provides a sociological model of the key transnational political and economic forces that are shaping the 'global football field'. The model draws upon, and significantly extends, the theory of the 'global field' developed previously by Robertson. The model features four quadrants, each of which contains a dominant operating principle, an 'elemental reference point', and an 'elemental theme'. The quadrants contain, first, neo-liberalism, associated with the individual and elite football clubs; second, neo-mercantilism, associated with nation-states and national football systems; third, international relations, associated with international governing bodies; and fourth, global civil society, associated with diverse institutions that pursue human development and/or social justice. We examine some of the interactions and tensions between the major institutional and ideological forces across the four quadrants. We conclude by examining how the weakest quadrant, featuring global civil society, may gain greater prominence within football. In broad terms, we argue that our four-fold model may be utilized to map and to examine other substantive research fields with reference to globalization. PMID:22670645
NASA Astrophysics Data System (ADS)
He, Han; Wang, Huaning; Yan, Yihua
2011-01-01
The Hinode satellite can obtain high-quality photospheric vector magnetograms of solar active regions and the simultaneous coronal loop images in soft X-ray and extreme ultraviolet (EUV) bands. In this paper, we continue the work of He and Wang (2008) and apply the newly developed upward boundary integration computational scheme for the nonlinear force-free field (NLFFF) extrapolation of the coronal magnetic field to the photospheric vector magnetograms acquired by the Spectro-Polarimeter of the Solar Optical Telescope aboard Hinode. Three time series vector magnetograms of the same solar active region, NOAA 10930, are selected for the NLFFF extrapolations, which were observed within the time interval of 26 h during 10-11 December 2006 when the active region crossed the central area of the Sun's disk. Parallel computation of the NLFFF extrapolation code was realized through OpenMP multithreaded, shared memory parallelism and Fortran 95 programming language for the extrapolation calculations. The comparison between the extrapolated field lines and the coronal loop images obtained by the X-Ray Telescope and the EUV Imaging Spectrometer of Hinode shows that, in the central area of the active region, the field line configurations generally agree with the coronal images, and the orientations of the field lines basically coincide with the coronal loop observations for all three successive magnetograms. This result supports the NLFFF model being used for tracing the time series evolution of the 3-D coronal magnetic structures as the responses of the quasi-equilibrium solar atmosphere to the vector magnetic field changes in the photosphere.
NASA Astrophysics Data System (ADS)
Saito, Hitoshi; Ito, Ryoichi; Egawa, Genta; Li, Zhenghua; Yoshimura, Satoru
2011-04-01
Direction detectable static magnetic field imaging, which directly distinguishes the up and down direction of static perpendicular magnetic field from a sample surface and the polarity of magnetic charges on the surface, was demonstrated for CoCrPt-SiO2 perpendicular magnetic recording media based on a frequency-modulated magnetic force microscopy (FM-MFM), which uses a frequency modulation of the cantilever oscillation induced by an alternating force from the tip-sample magnetic interaction. In this study, to generate the alternating force, we used a NiFe soft magnetic tip driven by the ac magnetic field of a soft ferrite core and imaged the direction and the amplitude of the static magnetic field from the recorded bits. This method enables measurement of the static magnetic field near a sample surface, which is masked by short range forces of the surface. The present method will be effective in analyzing the microscopic magnetic domain structure of hard magnetic samples.
Full-disk nonlinear force-free field extrapolation of SDO/HMI and SOLIS/VSM magnetograms
NASA Astrophysics Data System (ADS)
Tadesse, T.; Wiegelmann, T.; Inhester, B.; MacNeice, P.; Pevtsov, A.; Sun, X.
2013-02-01
Context. The magnetic field configuration is essential for understanding solar explosive phenomena, such as flares and coronal mass ejections. To overcome the unavailability of coronal magnetic field measurements, photospheric magnetic field vector data can be used to reconstruct the coronal field. Two complications of this approach are that the measured photospheric magnetic field is not force-free and that one has to apply a preprocessing routine to achieve boundary conditions suitable for the force-free modeling. Furthermore the nonlinear force-free extrapolation code should take uncertainties into account in the photospheric field data. They occur due to noise, incomplete inversions, or azimuth ambiguity-removing techniques. Aims: Extrapolation codes in Cartesian geometry for modeling the magnetic field in the corona do not take the curvature of the Sun's surface into account and can only be applied to relatively small areas, e.g., a single active region. Here we apply a method for nonlinear force-free coronal magnetic field modeling and preprocessing of photospheric vector magnetograms in spherical geometry using the optimization procedure to full disk vector magnetograms. We compare the analysis of the photospheric magnetic field and subsequent force-free modeling based on full-disk vector maps from Helioseismic and Magnetic Imager (HMI) onboard the solar dynamics observatory (SDO) and Vector Spectromagnetograph (VSM) of the Synoptic Optical Long-term Investigations of the Sun (SOLIS). Methods: We used HMI and VSM photospheric magnetic field measurements to model the force-free coronal field above multiple solar active regions, assuming magnetic forces to dominate. We solved the nonlinear force-free field equations by minimizing a functional in spherical coordinates over a full disk and excluding the poles. After searching for the optimum modeling parameters for the particular data sets, we compared the resulting nonlinear force-free model fields. We compared
Predicting the thermodynamic properties of gold nanoparticles using different force fields
NASA Astrophysics Data System (ADS)
Park, Yongjin
The objective of this research was to learn how to predict the thermodynamic properties of gold nanoparticles using computational tools. The lowest energy structures of gold nanoparticles of various sizes were determined and thermodynamic properties such as the free energy (F), internal energy (U), entropy (S), and specific heat (Cv) of the gold nanoparticles were investigated using a fully-atomistic Monte Carlo simulation method that utilizes a modified Wang-Landau algorithm. Eight well-known force fields for metallic systems were employed to model gold nanoparticles: the Lennard-Jones potential (LJ), the Lennard-Jones potential with Heinz's parameterization (LJH), the Gupta potential, the Sutton-Chen potential (SC), the Sutton-Chen potential with Pawluk's parameterization for small clusters (SCP), the Quantum Sutton-Chen potential (Q-SC), the Embedded Atom Method (EAM) by Cai and Ye, and the empirical potential for gold proposed by Olivier and coworkers (POT). Subsequently, we explored the accuracy of each force field in the description of the thermodynamic behavior of gold nanoparticles. The thermodynamic properties of gold nanoparticles were computed from the Density of States which was obtained as a result of the Monte Carlo simulation. Afterwards, the melting point of gold nanoparticles was determined from the behavior of the calculated thermodynamic properties and was compared with theory, experimental observations and other simulation results. The force fields employed predicted melting points of gold nanoparticles over a wide range of temperatures. A thorough comparison with the available experimental observations showed that the Quantum Sutton-Chen potential (Q-SC) correctly described the melting behavior of gold nanoparticles with sizes smaller than 1.3 nanometers.
Exploring solvent effects upon the Menshutkin reaction using a polarizable force field.
Acevedo, Orlando; Jorgensen, William L
2010-07-01
The energetics of the Menshutkin reaction between triethylamine and ethyl iodide have been computed using B3LYP and MP2 with the LANL2DZ, LANL2DZd, SVP, MIDI!, 6-311G(d,p), and aug-cc-PVTZ basis sets. Small- and large-core energy-consistent relativistic pseudopotentials were employed. Solvent effect corrections were computed from QM/MM Monte Carlo simulations utilizing free-energy perturbation theory, PDDG/PM3, and both a nonpolarizable OPLS and polarizable OPLS-AAP force field. The B3LYP/MIDI! theory level provided the best DeltaG(++) values with a mean absolute error (MAE) of 4.9 kcal/mol from experiment in cyclohexane, CCl(4), THF, DMSO, acetonitrile, water, and methanol. However, the relative rates in cyclohexane, and to a certain extent CCl(4), were determined to be greatly underestimated when using the nonpolarizable OPLS force field. An overall reduction in the MAE to 3.1 kcal/mol using B3LYP/MIDI!/OPLS-AAP demonstrated the need for a fully polarizable force field when computing solvent effects for highly dipolar transition structures in low-dielectric media. The MAEs obtained with PDDG/PM3/OPLS and OPLS-AAP of 5.3 and 3.8 kcal/mol, respectively, provided comparable results to B3LYP at a fraction of the computational resources. The large rate accelerations observed in the reaction were correlated to an increased stabilization of the emerging charge separation at the transition state via favorable solute-solvent interactions. PMID:20527873
Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.
2009-01-01
An additive all-atom empirical force field for aldopentofuranoses, methyl-aldopentofuranosides (Me-aldopentofuranosides) and fructofuranose carbohydrates, compatible with existing CHARMM carbohydrate parameters, is presented. Building on existing parameters transferred from cyclic ethers and hexopyranoses, parameters were further developed using target data for complete furanose carbohydrates as well as O-methyl tetrahydrofuran. The bond and angle equilibrium parameters were adjusted to reproduce target geometries from a survey of furanose crystal structures, and dihedral parameters were fit to over 1700 quantum mechanical (QM) MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. The conformational energies were for a variety of complete furanose monosaccharides, and included two-dimensional ring pucker energy surfaces. Bonded parameter optimization led to the correct description of the ring pucker for a large set of furanose compounds, while furanose-water interaction energies and distances reproduced QM HF/6-31G(d) results for a number of furanose monosaccharides, thereby validating the nonbonded parameters. Crystal lattice unit cell parameters and volumes, aqueous-phase densities, and aqueous NMR ring pucker and exocyclic data were used to validate the parameters in condensed-phase environments. Conformational sampling analysis of the ring pucker and exocyclic group showed excellent agreement with experimental NMR data, demonstrating that the conformational energetics in aqueous solution are accurately described by the optimized force field. Overall, the parameters reproduce available experimental data well and are anticipated to be of utility in future computational studies of carbohydrates, including in the context of proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields. PMID:19694450
Schnieders, Michael J.; Baltrusaitis, Jonas; Shi, Yue; Chattree, Gaurav; Zheng, Lianqing; Yang, Wei; Ren, Pengyu
2012-01-01
An important unsolved problem in materials science is prediction of the thermodynamic stability of organic crystals and their solubility from first principles. Solubility can be defined as the saturating concentration of a molecule within a liquid solvent, where the physical picture is of solvated molecules in equilibrium with their solid phase. Despite the importance of solubility in determining the oral bioavailability of pharmaceuticals, prediction tools are currently limited to quantitative structure–property relationships that are fit to experimental solubility measurements. For the first time, we describe a consistent procedure for the prediction of the structure, thermodynamic stability and solubility of organic crystals from molecular dynamics simulations using the polarizable multipole AMOEBA force field. Our approach is based on a thermodynamic cycle that decomposes standard state solubility into the sum of solid-vapor sublimation and vapor-liquid solvation free energies ΔGsolubilityo=ΔGsubo+ΔGsolvo, which are computed via the orthogonal space random walk (OSRW) sampling strategy. Application to the n-alkylamides series from aeetamide through octanamide was selected due to the dependence of their solubility on both amide hydrogen bonding and the hydrophobic effect, which are each fundamental to protein structure and solubility. On average, the calculated absolute standard state solubility free energies are accurate to within 1.1 kcal/mol. The experimental trend of decreasing solubility as a function of n-alkylamide chain length is recapitulated by the increasing stability of the crystalline state and to a lesser degree by decreasing favorability of solvation (i.e. the hydrophobic effect). Our results suggest that coupling the polarizable AMOEBA force field with an orthogonal space based free energy algorithm, as implemented in the program Force Field X, is a consistent procedure for predicting the structure, thermodynamic stability and solubility of
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
The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins
Shi, Yue; Xia, Zhen; Zhang, Jiajing; Best, Robert; Wu, Chuanjie; Ponder, Jay W.; Ren, Pengyu
2013-01-01
Development of the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes permanent electrostatic multipole moments through the quadrupole at each atom, and explicitly treats polarization effects in various chemical and physical environments. The atomic multipole electrostatic parameters for each amino acid residue type are derived from high-level gas phase quantum mechanical calculations via a consistent and extensible protocol. Molecular polarizability is modeled via a Thole-style damped interactive induction model based upon distributed atomic polarizabilities. Inter- and intramolecular polarization is treated in a consistent fashion via the Thole model. The intramolecular polarization model ensures transferability of electrostatic parameters among different conformations, as demonstrated by the agreement between QM and AMOEBA electrostatic potentials, and dipole moments of dipeptides. The backbone and side chain torsional parameters were determined by comparing to gas-phase QM (RI-TRIM MP2/CBS) conformational energies of dipeptides and to statistical distributions from the Protein Data Bank. Molecular dynamics simulations are reported for short peptides in explicit water to examine their conformational properties in solution. Overall the calculated conformational free energies and J-coupling constants are consistent with PDB statistics and experimental NMR results, respectively. In addition, the experimental crystal structures of a number of proteins are well maintained during molecular dynamics (MD) simulation. While further calculations are necessary to fully validate the force field, initial results suggest the AMOEBA polarizable multipole force field is able to describe the structure and energetics of peptides and proteins, in both gas-phase and solution environments. PMID:24163642
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
Magneto-frictional Modeling of Coronal Nonlinear Force-free Fields. II. Application to Observations
NASA Astrophysics Data System (ADS)
Guo, Y.; Xia, C.; Keppens, R.
2016-09-01
A magneto-frictional module has been implemented and tested in the Message Passing Interface Adaptive Mesh Refinement Versatile Advection Code (MPI-AMRVAC) in the first paper of this series. Here, we apply the magneto-frictional method to observations to demonstrate its applicability in both Cartesian and spherical coordinates, and in uniform and block-adaptive octree grids. We first reconstruct a nonlinear force-free field (NLFFF) on a uniform grid of 1803 cells in Cartesian coordinates, with boundary conditions provided by the vector magnetic field observed by the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO) at 06:00 UT on 2010 November 11 in active region NOAA 11123. The reconstructed NLFFF successfully reproduces the sheared and twisted field lines and magnetic null points. Next, we adopt a three-level block-adaptive grid to model the same active region with a higher spatial resolution on the bottom boundary and a coarser treatment of regions higher up. The force-free and divergence-free metrics obtained are comparable to the run with a uniform grid, and the reconstructed field topology is also very similar. Finally, a group of active regions, including NOAA 11401, 11402, 11405, and 11407, observed at 03:00 UT on 2012 January 23 by SDO/HMI is modeled with a five-level block-adaptive grid in spherical coordinates, where we reach a local resolution of 0\\buildrel{\\circ}\\over{.} 06 pixel‑1 in an area of 790 Mm × 604 Mm. Local high spatial resolution and a large field of view in NLFFF modeling can be achieved simultaneously in parallel and block-adaptive magneto-frictional relaxations.
Ab initio prediction of protein structure with both all-atom and simplified force fields
NASA Astrophysics Data System (ADS)
Scheraga, Harold
2004-03-01
Using only a physics-based ab initio method, and both all-atom (ECEPP/3) and simplified united-residue (UNRES) force fields, global optimization of both potential functions with Monte Carlo-plus-Minimization (MCM) and Conformational Space Annealing (CSA), respectively, provides predicted structures of proteins without use of knowledge-based information. The all-atom approach has been applied to the 46-residue protein A, and the UNRES approach has been applied to larger CASP targets. The predicted structures will be described.
Ab initio based force field and molecular dynamics simulations of crystalline TATB.
Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E
2004-04-15
An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608
The force field for imidazolium-based ionic liquids: Novel anions with polar residues
NASA Astrophysics Data System (ADS)
Fileti, Eudes Eterno; Chaban, Vitaly V.
2015-07-01
Many molecules can be converted into ions via relatively simple procedures. These ions can be combined into ionic liquids (ILs). We develop a new force field (FF) for the seven selected AAILs comprising 1-ethyl-3-methylimidazolium cation and amino acid anions with polar residues. All anions were obtained via deprotonation of carboxyl group in analogy with acetate anion. We account for peculiar interactions between the anion and the cation by fitting electrostatic potential for an ion pair, in contrast to isolated ions. Furthermore, we account for hydrogen bonds obtained via electronic structure consideration. The developed model fosters computational investigation of ionic liquids.
Stability of an ellipsoidal stellar cluster in the tidal force field of the Galaxy
NASA Astrophysics Data System (ADS)
Kozhanov, T. S.
1992-02-01
Attention is given to the dynamical characteristics of an ellipsoidal stellar cluster which rotates on an elliptical orbit relative to the center of the Galaxy in the field of its tidal forces. Regions of stability and instability of the cluster as a function of its form are defined on the basis of a numerical solution of the equations of the motion of stars inside the cluster. It is shown that, if the flattening of the cluster along the Y-axis, which coincides with the rotation direction, is larger than along the X-axis, which is directed toward the center of the Galaxy), the cluster is unstable.
Fields and forces in flywheel energy storage with high-temperature superconducting bearings
Turner, L.R.
1997-03-01
The development of low-loss bearings employing high-temperature superconductors has brought closer the advent of practical flywheel energy storage systems. These systems require magnetic fields and forces for levitation, stabilization, and energy transfer. This paper describes the status of experiments on flywheel energy storage at Argonne National Laboratory and computations in support of that project, in particular computations for the permanent-magnet rotor of the motor-generator that transfers energy to and from the flywheel, for other energy-transfer systems under consideration, and for the levitation and stability subsystems.
Fields and forces in flywheel energy storage with high-temperature superconducting bearings
Turner, L.R.
1996-05-01
The development of low-loss bearings employing high-temperature superconductors has brought closer the advent of practical flywheel energy storage systems. These systems require magnetic fields and forces for levitation, stabilization, and energy transfer. This paper describes the status of experiments on flywheel energy storage at Argonne National Laboratory and computations in support of that project, in particular computations for the permanent-magnet rotor of the motor-generator that transfers energy to and from the flywheel, for other energy-transfer systems under consideration, and for the levitation and stabilization subsystem.
Koch, Markus; Lunde, Lars-Kristian; Ernst, Michael; Knardahl, Stein; Veiersted, Kaj Bo
2016-03-01
This study aimed to test the validity and reliability of pressure-measurement insoles (medilogic® insoles) when measuring vertical ground reaction forces in field situations. Various weights were applied to and removed from the insoles in static mechanical tests. The force values measured simultaneously by the insoles and force plates were compared for 15 subjects simulating work activities. Reliability testing during the static mechanical tests yielded an average interclass correlation coefficient of 0.998. Static loads led to a creeping pattern of the output force signal. An individual load response could be observed for each insole. The average root mean square error between the insoles and force plates ranged from 6.6% to 17.7% in standing, walking, lifting and catching trials and was 142.3% in kneeling trials. The results show that the use of insoles may be an acceptable method for measuring vertical ground reaction forces in field studies, except for kneeling positions. PMID:26674403
Emmrich, Matthias; Schneiderbauer, Maximilian; Huber, Ferdinand; Weymouth, Alfred J; Okabayashi, Norio; Giessibl, Franz J
2015-04-10
We study the physics of atomic manipulation of CO on a Cu(111) surface by combined scanning tunneling microscopy and atomic force microscopy at liquid helium temperatures. In atomic manipulation, an adsorbed atom or molecule is arranged on the surface using the interaction of the adsorbate with substrate and tip. While previous experiments are consistent with a linear superposition model of tip and substrate forces, we find that the force threshold depends on the force field of the tip. Here, we use carbon monoxide front atom identification (COFI) to characterize the tip's force field. Tips that show COFI profiles with an attractive center can manipulate CO in any direction while tips with a repulsive center can only manipulate in certain directions. The force thresholds are independent of bias voltage in a range from 1 to 10 mV and independent of temperature in a range of 4.5 to 7.5 K. PMID:25910137
Trapping and micromanipulation using ultrasonic fields and dual ultrasonic/magnetic forces
NASA Astrophysics Data System (ADS)
Hill, Martyn; Glynne-Jones, Peter; Harris, Nicholas R.; Boltryk, Rosemary J.; Stanley, Christopher; Bond, Damian
2010-08-01
Ultrasonic fields can be used to trap and manipulate micron-scale particles and second-phase fluids, utilising energy densities that do not impair cell viability. The technology can be seen as complementary to optical trapping as the size of the potential wells generated can be relatively large, making ultrasound suitable for the formation and manipulation of cell agglomerates, but less suitable for the manipulation of individual cells. This paper discusses physical phenomena associated with ultrasonic manipulation, including radiation forces, cavitation, and acoustic streaming. The technology is well suited to integration within "Lab on a Chip" devices and can involve excitation by plane, focussed, flexural, or surface acoustic waves. Example applications of resonators are discussed including particle filtration and concentration, cell washing, and biosensor enhancement. A recently developed device that uses both ultrasonic and magnetic forces to enhance the detection of tuberculosis bacteria using magnetic beads is discussed in detail. This approach uses ultrasonic levitation forces to overcome some of the issues associated with purely magnetic trapping. The technology has been implemented in a device in which the main fluidic components are disposable to allow for low production costs and improved control of biohazards.
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
Three-dimensional flow fields and forces on revolving flat plates
NASA Astrophysics Data System (ADS)
Percin, Mustafa; van Oudheusden, Bas W.
2014-11-01
The evolution of three-dimensional flow structures of revolving low-aspect-ratio plates in the Reynolds number range of 10,000 to 20,000 was studied, combining Tomographic Particle Image Velocimetry with force measurements. Two motion kinematics were considered: (1) a revolving surge motion where the wing accelerates to a terminal velocity with a constant acceleration at a fixed angle of attack and then remains to revolve at a constant rate; (2) a revolving pitch motion which is initiated by a constant acceleration from rest to a terminal velocity at zero angle of attack, followed by a pitch-up motion at a constant pitch rate and revolution at a constant rate. In the experiments, the terminal velocity, acceleration, angle of attack and pitch rate were varied to study their effect on the resultant flow fields and forces. In general, a vortex system that consists of a leading edge vortex, a tip vortex and a trailing edge vortex is observed. The vortex system bursts into substructures as the motion progresses, which does not lead to a decrease in the forces. The evolution of spanwise flow and the effects of centrifugal acceleration and spanwise pressure gradient are discussed. This research is supported by the Dutch Technology Foundation STW, Project Number 11023.
History force effects on contrast agent microbubbles in an ultrasound field
NASA Astrophysics Data System (ADS)
Garbin, Valeria; Dollet, Benjamin; van Wijngaarden, Leen; de Jong, Nico; Lohse, Detlef; Versluis, Michel
2008-11-01
We study experimentally the radial and translational dynamics of an ultrasound contrast agent microbubble pair pulsating in an ultrasound field. The two bubbles attract each other through the so-called secondary Bjerknes force; quantifying these bubble-bubble interactions is therefore crucial for optimized medical imaging protocols. Using optical tweezers, we trap and control the distance between two microbubbles (BR-14, Bracco Research S.A., Geneva). We position the bubble pair away from the sample chamber wall, to prevent wall effects and quantify purely the acoustic bubble-bubble interaction and the dissipation due to viscosity in the fluid. The ultra-high speed Brandaris camera recorded the bubble dynamics at 15 million frames per second; from the optical measurements we track the instantaneous bubble radii and positions. We write a force balance for each bubble, assuming a no-slip boundary condition since the bubble interface is coated with a lipid monolayer to prevent dissolution. By comparison with the experimental results, we find that history effects are crucial to correctly account for the viscous forces.
Field evidence of the viscous sublayer in a tidally forced developing boundary layer
NASA Astrophysics Data System (ADS)
Wengrove, M. E.; Foster, D. L.
2014-07-01
Field observations of boundary layer development within a tidally forced estuary revealed evidence of an observable viscous sublayer. Evidence is provided by several independent measures of the flow field, including hydrodynamic smoothness, an immobile bed, and characteristic velocity, constant stress, and higher-order moment structures. This investigation reports what may be the second comprehensive observation of the viscous sublayer in a marine environment, and what could be the first observation of a momentum balance that includes the viscous sublayer within a shallow estuarine environment. Hydrodynamic observations were made in a straight channel within the Great Bay Estuary of New Hampshire over a flat sandy mud with low water depth of 1.5 m at the sampling location. Beyond quantifying the role of the benthic boundary layer in nutrient dynamics, these observations are useful to provide insight into very near boundary stress estimates leading to incipient motion in estuarine and coastal environments.
Gravitational forces in the Randall-Sundrum model with a scalar stabilizing field
NASA Astrophysics Data System (ADS)
Arnowitt, R.; Dent, J.
2007-03-01
We consider the problem of gravitational forces between point particles on the branes in a five-dimensional (5D) Randall-Sundrum model with two branes (at y1 and y2) and S1/Z2 symmetry of the fifth dimension. The matter on the branes is viewed as a perturbation on the vacuum metric and treated to linear order. In a previous work [R. Arnowitt and J. Dent, Phys. Rev. D 71, 124024 (2005).PRVDAQ0556-282110.1103/PhysRevD.71.124024] it was seen that the trace of the transverse part of the 4D metric on the TeV brane, fT(y2), contributed a Newtonian potential enhanced by e2βy2≅1032 and thus produced gross disagreement with the experiment. In this work we include a scalar stabilizing field ϕ and solve the coupled Einstein and scalar equations to leading order for the case where ϕ02/M53 is small and the vacuum field ϕ0(y) is a decreasing function of y. fT then grows a mass factor e-μr where, however, μ is suppressed from its natural value, O(MPl), by an exponential factor e-(1+λb)βy2, λb>0. Thus agreement with the experiment depends on the interplay between the enhancing and decaying exponentials. Current data eliminates a significant part of the parameter space, and the Randall-Sundrum model will be sensitive to any improvements on the tests of the Newtonian force law at smaller distances. An example of coupling of the ϕ field to the Higgs field is examined and found to generally produce very small effects.
Liikala, T.L.; Evans, J.C.
1995-01-01
Source area ST58 is the site of the old Quartermaster service station at Eielson Air Force Base, Alaska. The source area is one of several Source Evaluation Report sites being investigated by Pacific Northwest Laboratory for the US Air Force as candidates for no further remedial action, interim removal action, or a remedial investigation/feasibility study under a Federal Facilities Agreement. The purpose of this work was to characterize source area ST58 and excavate the most contaminated soils for use in composting treatability studies. A field investigation was conducted to determine the nature and extent of soil contamination. The field investigation entailed a records search; grid node location, surface geophysical, and soil gas surveys; and test pit soil sampling. Soil excavation followed based on the results of the field investigation. The site was backfilled with clean soil. Results from this work indicate close spatial correlation between screening instruments, used during the field investigation and soil excavation, and laboratory analyses. Gasoline was identified as the main subsurface contaminant based on the soil gas surveys and test pit soil sampling. A center of contamination was located near the northcentral portion of the source area, and a center was located in the northwestern comer. The contamination typically occurred near or below a former soil horizon probably as a result of surface spills and leaks from discontinuities and/or breaks in the underground piping. Piping locations were delineated during the surface geophysical surveys and corresponded very well to unscaled drawings of the site. The high subsurface concentrations of gasoline detected in the northwestern comer of the source area probably reflect ground-water contamination and/or possibly floating product.
Optical Characterization of Lorentz Force Based CMOS-MEMS Magnetic Field Sensor
Dennis, John Ojur; Ahmad, Farooq; Khir, M. Haris Bin Md; Hamid, Nor Hisham Bin
2015-01-01
Magnetic field sensors are becoming an essential part of everyday life due to the improvements in their sensitivities and resolutions, while at the same time they have become compact, smaller in size and economical. In the work presented herein a Lorentz force based CMOS-MEMS magnetic field sensor is designed, fabricated and optically characterized. The sensor is fabricated by using CMOS thin layers and dry post micromachining is used to release the device structure and finally the sensor chip is packaged in DIP. The sensor consists of a shuttle which is designed to resonate in the lateral direction (first mode of resonance). In the presence of an external magnetic field, the Lorentz force actuates the shuttle in the lateral direction and the amplitude of resonance is measured using an optical method. The differential change in the amplitude of the resonating shuttle shows the strength of the external magnetic field. The resonance frequency of the shuttle is determined to be 8164 Hz experimentally and from the resonance curve, the quality factor and damping ratio are obtained. In an open environment, the quality factor and damping ratio are found to be 51.34 and 0.00973 respectively. The sensitivity of the sensor is determined in static mode to be 0.034 µm/mT when a current of 10 mA passes through the shuttle, while it is found to be higher at resonance with a value of 1.35 µm/mT at 8 mA current. Finally, the resolution of the sensor is found to be 370.37 µT. PMID:26225972
Optical Characterization of Lorentz Force Based CMOS-MEMS Magnetic Field Sensor.
Dennis, John Ojur; Ahmad, Farooq; Khir, M Haris Bin Md; Bin Hamid, Nor Hisham
2015-01-01
Magnetic field sensors are becoming an essential part of everyday life due to the improvements in their sensitivities and resolutions, while at the same time they have become compact, smaller in size and economical. In the work presented herein a Lorentz force based CMOS-MEMS magnetic field sensor is designed, fabricated and optically characterized. The sensor is fabricated by using CMOS thin layers and dry post micromachining is used to release the device structure and finally the sensor chip is packaged in DIP. The sensor consists of a shuttle which is designed to resonate in the lateral direction (first mode of resonance). In the presence of an external magnetic field, the Lorentz force actuates the shuttle in the lateral direction and the amplitude of resonance is measured using an optical method. The differential change in the amplitude of the resonating shuttle shows the strength of the external magnetic field. The resonance frequency of the shuttle is determined to be 8164 Hz experimentally and from the resonance curve, the quality factor and damping ratio are obtained. In an open environment, the quality factor and damping ratio are found to be 51.34 and 0.00973 respectively. The sensitivity of the sensor is determined in static mode to be 0.034 µm/mT when a current of 10 mA passes through the shuttle, while it is found to be higher at resonance with a value of 1.35 µm/mT at 8 mA current. Finally, the resolution of the sensor is found to be 370.37 µT. PMID:26225972
A Dust-penetrated Classification Scheme for Bars as Inferred from Their Gravitational Force Fields
NASA Astrophysics Data System (ADS)
Buta, R.; Block, D. L.
2001-03-01
The division of galaxies into ``barred'' (SB) and ``normal'' (S) spirals is a fundamental aspect of the Hubble galaxy classification system. This ``tuning fork'' view was revised by de Vaucouleurs, whose classification volume recognized apparent ``bar strength'' (SA, SAB, SB) as a continuous property of galaxies called the ``family.'' However, the SA, SAB, and SB families are purely visual judgments that can have little bearing on the actual bar strength in a given galaxy. Until very recently, published bar judgments were based exclusively on blue light images, where internal extinction or star formation can either mask a bar completely or give the false impression of a bar in a nonbarred galaxy. Near-infrared camera arrays, which principally trace the old stellar population in both normal and barred galaxies, now facilitate a quantification of bar strength in terms of their gravitational potentials and force fields. In this paper, we show that the maximum value, Qb, of the ratio of the tangential force to the mean axisymmetric radial force in a barred disk galaxy is a quantitative measure of the strength of a bar. Qb does not measure bar ellipticity or bar shape but rather depends on the actual forcing due to the bar embedded in its disk. We show that a wide range of true bar strengths characterizes the category ``SB,'' while the de Vaucouleurs category ``SAB'' corresponds to a narrower range of bar strengths. We present Qb values for 36 galaxies, and we incorporate our bar classes into a dust-penetrated classification system for spiral galaxies.
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
Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent.
Arnarez, Clément; Uusitalo, Jaakko J; Masman, Marcelo F; Ingólfsson, Helgi I; de Jong, Djurre H; Melo, Manuel N; Periole, Xavier; de Vries, Alex H; Marrink, Siewert J
2015-01-13
Coarse-grained (CG) models allow simulation of larger systems for longer times by decreasing the number of degrees of freedom compared with all-atom models. Here we introduce an implicit-solvent version of the popular CG Martini model, nicknamed "Dry" Martini. To account for the omitted solvent degrees of freedom, the nonbonded interaction matrix underlying the Martini force field was reparametrized. The Dry Martini force field reproduces relatively well a variety of lipid membrane properties such as area per lipid, bilayer thickness, bending modulus, and coexistence of liquid-ordered and disordered domains. Furthermore, we show that the new model can be applied to study membrane fusion and tether formation, with results similar to those of the standard Martini model. Membrane proteins can also be included, but less quantitative results are obtained. The absence of water in Dry Martini leads to a significant speedup for large systems, opening the way to the study of complex multicomponent membranes containing millions of lipids. PMID:26574224
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.
Nonlinear Force-free Magnetic Field Fitting to Coronal Loops with and without Stereoscopy
NASA Astrophysics Data System (ADS)
Aschwanden, Markus J.
2013-02-01
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 μ2 = 2.°7 ± 1.°3 between the model field lines and observed loops, and an accuracy of ≈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.
Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.
Maciejewski, Arkadiusz; Pasenkiewicz-Gierula, Marta; Cramariuc, Oana; Vattulainen, Ilpo; Rog, Tomasz
2014-05-01
We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM). PMID:24745688
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, Jordan R.
2016-06-23
Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less
eReaxFF: A Pseudoclassical Treatment of Explicit Electrons within Reactive Force Field Simulations.
Islam, Md Mahbubul; Kolesov, Grigory; Verstraelen, Toon; Kaxiras, Efthimios; van Duin, Adri C T
2016-08-01
We present a computational tool, eReaxFF, for simulating explicit electrons within the framework of the standard ReaxFF reactive force field method. We treat electrons explicitly in a pseudoclassical manner that enables simulation several orders of magnitude faster than quantum chemistry (QC) methods, while retaining the ReaxFF transferability. We delineate here the fundamental concepts of the eReaxFF method and the integration of the Atom-condensed Kohn-Sham DFT approximated to second order (ACKS2) charge calculation scheme into the eReaxFF. We trained our force field to capture electron affinities (EA) of various species. As a proof-of-principle, we performed a set of molecular dynamics (MD) simulations with an explicit electron model for representative hydrocarbon radicals. We establish a good qualitative agreement of EAs of various species with experimental data, and MD simulations with eReaxFF agree well with the corresponding Ehrenfest dynamics simulations. The standard ReaxFF parameters available in the literature are transferrable to the eReaxFF method. The computationally economic eReaxFF method will be a useful tool for studying large-scale chemical and physical systems with explicit electrons as an alternative to computationally demanding QC methods. PMID:27399177
Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning
2016-01-01
Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme. PMID:27057643
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
Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.
Cole, Daniel J; Vilseck, Jonah Z; Tirado-Rives, Julian; Payne, Mike C; Jorgensen, William L
2016-05-10
Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme. PMID:27057643
Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
a Beccara, Silvio; Škrbić, Tatjana; Covino, Roberto; Micheletti, Cristian; Faccioli, Pietro
2013-01-01
We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native -sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting. PMID:23555232
Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field.
Boulanger, Eliot; Thiel, Walter
2014-04-01
The polarization of the environment can influence the results from hybrid quantum mechanical/molecular mechanical (QM/MM) simulations of enzymatic reactions. In this article, we address several technical aspects in the development of polarizable QM/MM embedding using the Drude Oscillator (DO) force field. We propose a stable and converging update of the DO polarization state for geometry optimizations and a suitable treatment of the QM/MM-DO boundary when the QM and MM regions are separated by cutting through a covalent bond. We assess the performance of our approach by computing binding energies and geometries of three selected complexes relevant to biomolecular modeling, namely the water trimer, the N-methylacetamide dimer, and the cationic bis(benzene)sodium sandwich complex. Using a recently published MM-DO force field for proteins, we evaluate the effect of MM polarization on the QM/MM energy profiles of the enzymatic reactions catalyzed by chorismate mutase and by p-hydroxybenzoate hydroxylase. We find that inclusion of MM polarization affects the computed barriers by about 10%. PMID:26580386
Matching of additive and polarizable force fields for multiscale condensed phase simulations
Baker, Christopher M.; Best, Robert B.
2013-01-01
Inclusion of electronic polarization effects is one of the key aspects in which the accuracy of current biomolecular force fields may be improved. The principal drawback of such approaches is the computational cost, which typically ranges from 3 – 10 times that of the equivalent additive model, and may be greater for more sophisticated treatments of polarization or other many-body effects. Here, we present a multiscale approach which may be used to enhance the sampling in simulations with polarizable models, by using the additive model as a tool to explore configuration space. We use a method based on information theory to determine the charges for an additive model that has optimal overlap with the polarizable one, and we demonstrate the feasibility of enhancing sampling via a hybrid replica exchange scheme for several model systems. An additional advantage is that, in the process, we obtain a systematic method for deriving charges for an additive model that will be the natural complement to its polarizable parent. The additive charges are found by an effective coarse-graining of the polarizable force field, rather than by ad hoc procedures. PMID:23997691
Development of an Empirical Force Field for Silica. Application to the Quartz-Water Interface
Lopes, Pedro E. M.; Murashov, Vladimir; Tazi, Mouhsine; Demchuk, Eugene; MacKerell, Alexander D.
2008-01-01
Interactions of pulverized crystalline silica with biological systems, including the lungs, cause cell damage, inflammation, and apoptosis. To allow computational atomistic modeling of these pathogenic processes, including interactions between silica surfaces and biological molecules, new parameters for quartz, compatible with the CHARMM empirical force field were developed. Parameters were optimized to reproduce the experimental geometry of α-quartz, ab initio vibrational spectra and interactions between model compounds and water. The newly developed force field was used to study interactions of water with two singular surfaces of α-quartz, (011) and (100). Properties monitored and analyzed include the variation of the density of water molecules in the plane perpendicular to the surface, disruption of the water H-bond network upon adsorption, and space-time correlations of water oxygen atoms in terms of Van Hove self correlation functions. The Vibrational Density of States (VDOS) spectra of water in confined compartments were also computed and compared with experimental neutron-scattering results. Both the attenuation and shifting to higher frequencies of the hindered translational peaks upon confinement are clearly reproduced by the model. However, an upshift of librational peaks under the conditions of model confinement still remains underrepresented at the current empirical level. PMID:16471886
A hierarchical Bayesian framework for force field selection in molecular dynamics simulations.
Wu, S; Angelikopoulos, P; Papadimitriou, C; Moser, R; Koumoutsakos, P
2016-02-13
We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure. PMID:26712642
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
CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol
Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.
2009-01-01
Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute-water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde and glycerol. C-C-C-C, C-C-C-O, C-C-OH and O-C-C-O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed condensed-phase data, including crystal lattice parameters and densities, NMR proton-proton couplings, densities and diffusion coefficients of aqueous solutions, to experimental data validated the optimized parameters. Parameter development for these compounds proved particularly challenging because of the flexibility of the acyclic sugars and polyalcohols as well as the intramolecular hydrogen bonding between vicinal hydroxyls for all of the compounds. The newly optimized additive CHARMM force field parameters are anticipated to be of utility for atomic level of detail simulations of acyclic polyalcohols, acyclic carbohydrates and inositol in solution. PMID:20160980
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
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
O'Dell, Dakota; Adam, Ian S.; DiPaolo, Brian; Sabharwal, Manit; Shi, Ce; Hart, Robert; Earhart, Christopher; Erickson, David
2015-01-01
Nanoparticles are quickly becoming commonplace in many commercial and industrial products, ranging from cosmetics to pharmaceuticals to medical diagnostics. Predicting the stability of the engineered nanoparticles within these products a priori remains an important and difficult challenge. Here we describe our techniques for measuring the mechanical interactions between nanoparticles and surfaces using near-field light scattering. Particle-surface interfacial forces are measured by optically “pushing” a particle against a reference surface and observing its motion using scattered near-field light. Unlike atomic force microscopy, this technique is not limited by thermal noise, but instead takes advantage of it. The integrated waveguide and microfluidic architecture allow for high-throughput measurements of about 1000 particles per hour. We characterize the reproducibility of and experimental uncertainty in the measurements made using the NanoTweezer surface instrument. We report surface interaction studies on gold nanoparticles with 50 nm diameters, smaller than previously reported in the literature using similar techniques. PMID:26855473
Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development.
Verstraelen, Toon; Vandenbrande, Steven; Heidar-Zadeh, Farnaz; Vanduyfhuys, Louis; Van Speybroeck, Veronique; Waroquier, Michel; Ayers, Paul W
2016-08-01
Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using the distributed nature of the electron cloud and atomic multipoles. In this work, an electrostatic force field is defined through a concise approximation of the electron density, for which the Coulomb interaction is trivially evaluated. This approximate "pro-density" is expanded in a minimal basis of atom-centered s-type Slater density functions, whose parameters are optimized by minimizing the Kullback-Leibler divergence of the pro-density from a reference electron density, e.g., obtained from an electronic structure calculation. The proposed method, Minimal Basis Iterative Stockholder (MBIS), is a variant of the Hirshfeld AIM method, but it can also be used as a density-fitting technique. An iterative algorithm to refine the pro-density is easily implemented with a linear-scaling computational cost, enabling applications to supramolecular systems. The benefits of the MBIS method are demonstrated with systematic applications to molecular databases and extended models of condensed phases. A comparison to 14 other AIM methods shows its effectiveness when modeling electrostatic interactions. MBIS is also suitable for rescaling atomic polarizabilities in the Tkatchenko-Scheffler scheme for dispersion interactions. PMID:27385073
Anharmonic force field, vibrational energies, and barrier to inversion of SiH{sub 3}{sup -}
Aarset, Kirsten; Csaszar, Attila G.; Sibert, Edwin L. III; Allen, Wesley D.; Schaefer, Henry F. III; Klopper, Wim; Theoretical Chemistry Group, Debye Institute, Utrecht University, Padualaan 14, NL-3584 CH Utrecht, The Netherlands ; Noga, Jozef
2000-03-01
The full quartic force field of the ground electronic state of the silyl anion (SiH{sub 3}{sup -}) has been determined at the CCSD(T)-R12 level employing a [Si/H]=[16s11p6d5f/7s5p4d] basis set. The vibrational energy levels, using the quartic force field as a representation of the potential energy hypersurface around equilibrium, have been determined by vibrational perturbation theory carried out to second, fourth, and sixth order. The undetected vibrational fundamental for the umbrella mode, {nu}{sub 2}, is predicted to be 844 cm-1. High-quality ab initio quantum chemical methods, including higher-order coupled cluster (CC) and many-body perturbation (MP) theory with basis sets ranging from [Si/H] [5s4p2d/3s2p] to [8s7p6d5f4g3h/7s6p5d4f3g] have been employed to obtain the best possible value for the inversion barrier of the silyl anion. The rarely quantified effects of one- and two-particle relativistic terms, core correlation, and the diagonal Born-Oppenheimer correction (DBOC) have been included in the determination of the barrier for this model system. The final electronic (vibrationless) extrapolated barrier height of this study is 8351{+-}100 cm{sup -1}. (c) 2000 American Institute of Physics.
Directly resolving particles in an electric field: local charge, force, torque, and applications
NASA Astrophysics Data System (ADS)
Liu, Qianlong
2011-11-01
Prosperetti's seminal Physalis method for fluid flows with suspended particles is extended to electric fields to directly resolve finite-sized particles and to investigate accurately the mutual fluid-particle, particle-particle, and particle-boundary interactions. The method can be used for uncharged/charged dielectrics, uncharged/charged conductors, conductors with specified voltage, and general weak and strong discontinuous interface conditions. These interface conditions can be in terms of field variable, its gradients, and surface integration which has not been addesed by other numerical methods. In addition, for the first time, we rigorously derive the force and torque on the finite-sized particles resulting from the interactions between harmonics. The method, for the first time, directly resolves the particles with accurate local charge distribution, force, and torque on the particles, making many applications in engineering, mechanics, physics, chemistry, and biology possible, such as heterogeneous materials, microfluidics, electrophotography, electric double layer capacitors, and microstructures of nanodispersions. The efficiency of the method is demonstrated with up to one hundred thousand 3D particles, which suggests that the method can be used for many important engineering applications of broad interest. This research is supported by the Department of Energy under funding for an EFRC (the HeteroFoaM Center), grant no. DE-SC0001061.
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. PMID:26331258
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
NASA Astrophysics Data System (ADS)
G, Ravi; Goyal, Vidhi
2012-10-01
Experimental investigations on the role of applied external magnetic field and return current closure in the force balance mechanism of a plasma torch are reported. The plasma torch is of low power and has wall, gas and magnetic stabilization mechanisms incorporated in it. Gas flow is divided into two parts: axial-central and peripheral-shroud, applied magnetic field is axial and return current is co-axial. Results indicate that application of large external magnetic field gives rise to not only J x B force but also, coupled with gas flow, to a new drag-cum-centrifugal force that acts on the plasma arc root and column. The magnetic field also plays a role in the return current closure dynamics and thus in the overall force balance mechanism. This in turn affects the electro-thermal efficiency of the plasma torch. Detailed experimental results, analytical calculations and physical model representing the processes will be presented and discussed.
NASA Technical Reports Server (NTRS)
Parker, E. N.
1986-01-01
Consideration is given to the static force-free equilibrium of a magnetic field in which all of the lines of force connect without knotting between parallel planes. The field is formed by continuous deformation from an initial uniform field, and is conventiently described in terms of the scalar function psi, which is the stream function for the incompressible wrapping and interweaving of the lines of force. Local compression and expansion of the lines of force is described in terms of the scalar function Phi. Equilibrium in the field requires satisfaction of two independent equations which cannot be accomplished without the full freedom of both psi and Phi. It is shown that discontinuities in the torsional characteristics of the lines occur when psi is predetermined by an arbitrary pattern. Discontinuities in the winding pattern of the lines can lead to discontinuities in the associated current sheets.
Harley, Linda R; Prilutsky, Boris I
2013-01-01
This study examined the effects of force-field direction (extrinsic vs. intrinsic) on transfer of learning during bimanual reaching. Subjects performed bimanual reaching tasks in two force-fields: (1) intrinsic and (2) extrinsic. Motor adaptation of each arm was determined by measuring the deviation of the hand trajectory from a straight line. It was found that rate of motor adaptation of the dominant arm was the same in the two tasks. For the nondominant arm, the rate of motor adaptation was greater during reaching in the intrinsic force-field than in the extrinsic force-field. It is concluded that the load-related sensory feedback from the dominant arm interfered with motor adaptation of the nondominant arm. PMID:24111328
Barone, Vincenzo; Cacelli, Ivo; De Mitri, Nicola; Licari, Daniele; Monti, Susanna; Prampolini, Giacomo
2013-03-21
The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case. PMID:23389748
On an analogy to the Steklov case for a balanced gyrostat in a Newtonian gravitational force field
NASA Astrophysics Data System (ADS)
Zlochevskii, S. I.
1982-12-01
New particular solutions are obtained for the equations of motion of a gyrostat about a fixed center of mass in a Newtonian gravitational force field. Arkhangel'skii's (1977) modification of Steklov's (1899) method is the basis of the investigation.